- C - Static variable in class loci.formats.in.CellSensReader
-
- c - Variable in class loci.formats.in.LeicaSCNReader.Dimension
-
- c - Variable in class loci.formats.in.MicromanagerReader.Index
-
- c - Variable in class loci.formats.in.OperettaReader.Plane
-
- c - Variable in class loci.formats.tools.AmiraParameters
-
- C01_MAGIC_BYTES - Static variable in class loci.formats.in.CellomicsReader
-
- C_AXIS - Static variable in class loci.formats.AxisGuesser
-
Axis type for channels.
- C_KEY - Static variable in class loci.formats.in.LiFlimReader
-
- C_PREFIXES - Static variable in class loci.formats.AxisGuesser
-
Prefixes indicating channel dimension.
- C_STRING - Static variable in class loci.formats.in.SDTInfo
-
- Cache - Class in loci.formats.cache
-
Cache provides a means of managing subsets of large collections of image
planes in memory.
- Cache(ICacheStrategy, ICacheSource, boolean) - Constructor for class loci.formats.cache.Cache
-
Constructs an object cache with the given cache strategy and source.
- cache - Variable in class loci.formats.cache.Cache
-
Master array containing cached objects.
- cache - Variable in class loci.formats.cache.CacheUpdater
-
- cache - Variable in class loci.formats.gui.CacheComponent
-
The cache that this component controls.
- cache - Variable in class loci.formats.gui.CacheIndicator
-
- cache - Variable in class loci.plugins.util.BFVirtualStack
-
- CacheComponent - Class in loci.formats.gui
-
GUI component for managing a cache.
- CacheComponent(Cache, String[]) - Constructor for class loci.formats.gui.CacheComponent
-
Creates a cache GUI component.
- CacheComponent(Cache, String[], String) - Constructor for class loci.formats.gui.CacheComponent
-
Creates a cache GUI component with the ability to change between the
various source types (mainly for debugging purposes).
- CacheConsole - Class in loci.formats.tools
-
CacheConsole provides an interactive interpreter for
testing the Bio-Formats caching implementation.
- CacheConsole() - Constructor for class loci.formats.tools.CacheConsole
-
- cachedTileBuffer - Variable in class loci.formats.in.MIASReader
-
Cached tile buffer to avoid re-allocations when reading tiles.
- cachedTileBuffer - Variable in class loci.formats.tiff.TiffParser
-
Cached tile buffer to avoid re-allocations when reading tiles.
- CacheEvent - Class in loci.formats.cache
-
A event indicating a cache update.
- CacheEvent(Object, int) - Constructor for class loci.formats.cache.CacheEvent
-
Constructs a cache event.
- CacheEvent(Object, int, int) - Constructor for class loci.formats.cache.CacheEvent
-
Constructs a cache event.
- CacheException - Exception in loci.formats.cache
-
CacheException is the exception thrown when something
goes wrong performing a cache operation.
- CacheException() - Constructor for exception loci.formats.cache.CacheException
-
- CacheException(String) - Constructor for exception loci.formats.cache.CacheException
-
- CacheException(String, Throwable) - Constructor for exception loci.formats.cache.CacheException
-
- CacheException(Throwable) - Constructor for exception loci.formats.cache.CacheException
-
- CacheIndicator - Class in loci.formats.gui
-
Indicator GUI component showing which planes are currently in the cache
for a given dimensional axis at a particular dimensional position.
- CacheIndicator(Cache, int) - Constructor for class loci.formats.gui.CacheIndicator
-
Creates a new cache indicator for the given cache.
- CacheIndicator(Cache, int, Component, int, int) - Constructor for class loci.formats.gui.CacheIndicator
-
Creates a new cache indicator.
- CacheListener - Interface in loci.formats.cache
-
A listener for cache updates.
- CacheReporter - Interface in loci.formats.cache
-
Interface for components capable of reporting cache updates.
- CacheSource - Class in loci.formats.cache
-
Superclass of cache sources that retrieve image planes
from a data source (e.g., a file) using Bio-Formats.
- CacheSource(IFormatReader) - Constructor for class loci.formats.cache.CacheSource
-
Constructs a cache source from the given Bio-Formats reader.
- CacheSource(String) - Constructor for class loci.formats.cache.CacheSource
-
Constructs a cache source that draws from the given file.
- CacheStrategy - Class in loci.formats.cache
-
Superclass of cache strategies.
- CacheStrategy(int[]) - Constructor for class loci.formats.cache.CacheStrategy
-
Constructs a cache strategy.
- cacheUpdated(CacheEvent) - Method in interface loci.formats.cache.CacheListener
-
Called when cache is updated.
- cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheComponent
-
Updates GUI to match latest cache state.
- cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheIndicator
-
- CacheUpdater - Class in loci.formats.cache
-
Thread responsible for updating the cache
(loading and dropping planes) in the background.
- CacheUpdater(Cache) - Constructor for class loci.formats.cache.CacheUpdater
-
- calcPhotons - Variable in class loci.formats.in.SDTInfo
-
No of photons.
- calculateDimensions() - Method in class loci.formats.in.ZeissCZIReader
-
- calculateDimensions(int, boolean) - Method in class loci.formats.in.ZeissCZIReader
-
- CALIBRATION - Static variable in class loci.formats.in.OpenlabReader
-
- calibrationTable - Variable in class loci.plugins.util.BFVirtualStack
-
- calibrationUnit - Variable in class loci.formats.in.TiffReader
-
- Calibrator - Class in loci.plugins.in
-
Logic for calibrating images.
- Calibrator(ImportProcess) - Constructor for class loci.plugins.in.Calibrator
-
- callLegacyReader() - Method in class loci.formats.DelegateReader
-
- CAMERA_GAIN - Static variable in class loci.formats.in.CellSensReader
-
- CAMERA_GAMMA - Static variable in class loci.formats.in.CellSensReader
-
- CAMERA_OFFSET - Static variable in class loci.formats.in.CellSensReader
-
- CAMERA_SERIAL_SETTING - Static variable in class loci.formats.in.FluoviewReader
-
- cameraIDs - Variable in class loci.formats.in.FlexReader
-
- cameraMode - Variable in class loci.formats.in.MicromanagerReader.Position
-
- cameraModel - Variable in class loci.formats.in.ND2Handler
-
- cameraName - Variable in class loci.formats.in.SimplePCITiffReader
-
- cameraName - Variable in class loci.formats.in.SISReader
-
- cameraRef - Variable in class loci.formats.in.MicromanagerReader.Position
-
- cameraRefs - Variable in class loci.formats.in.FlexReader
-
- cameraType - Variable in class loci.formats.in.SimplePCITiffReader
-
- CAN_GROUP - Static variable in class loci.formats.FormatTools
-
- CAN_GROUP - Static variable in interface loci.formats.IFormatReader
-
- canAdjustDimensions - Variable in class loci.formats.in.ND2Handler
-
- cancel - Variable in class loci.plugins.in.ImportProcess
-
Whether the process has been canceled.
- cancel() - Method in class loci.plugins.in.ImportProcess
-
Cancels the import process.
- canceled - Variable in class loci.plugins.LociImporter
-
Flag indicating whether last operation was canceled.
- canceled - Variable in class loci.plugins.Slicer
-
Flag indicating whether last operation was canceled.
- canceled - Variable in class loci.plugins.Updater
-
Flag indicating whether last operation was canceled.
- canChangePattern() - Method in class loci.formats.FileStitcher
-
- canCloseReader - Variable in class loci.formats.gui.ImageViewer
-
- canDoQT() - Method in class loci.formats.gui.LegacyQTTools
-
Whether QuickTime is available to this JVM.
- canDoStacks() - Method in class loci.formats.FormatWriter
-
- canDoStacks() - Method in interface loci.formats.IFormatWriter
-
Reports whether the writer can save multiple images to a single file.
- canDoStacks() - Method in class loci.formats.ImageWriter
-
- canDoStacks() - Method in class loci.formats.out.APNGWriter
-
- canDoStacks() - Method in class loci.formats.out.AVIWriter
-
- canDoStacks() - Method in class loci.formats.out.CellH5Writer
-
- canDoStacks() - Method in class loci.formats.out.ICSWriter
-
- canDoStacks() - Method in class loci.formats.out.JavaWriter
-
- canDoStacks() - Method in class loci.formats.out.JPEG2000Writer
-
Overridden to indicate that stacks are not supported.
- canDoStacks() - Method in class loci.formats.out.LegacyQTWriter
-
- canDoStacks() - Method in class loci.formats.out.OMEXMLWriter
-
- canDoStacks() - Method in class loci.formats.out.QTWriter
-
- canDoStacks() - Method in class loci.formats.out.TiffWriter
-
- canDoStacks() - Method in class loci.formats.out.V3DrawWriter
-
- canDoStacks() - Method in class loci.formats.out.WlzWriter
-
- canDoStacks() - Method in class loci.formats.WriterWrapper
-
- canDoUpgradeCheck() - Method in class loci.formats.UpgradeChecker
-
Return whether or not we are ever allowed to perform an upgrade check.
- canImport(JComponent, DataFlavor[]) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
-
- canLookForND - Variable in class loci.formats.in.MetamorphReader
-
- canMerge() - Method in class loci.formats.ChannelMerger
-
Determines whether the channels in the file can be merged.
- CANNOT_GROUP - Static variable in class loci.formats.FormatTools
-
- CANNOT_GROUP - Static variable in interface loci.formats.IFormatReader
-
- CANON_TAG - Static variable in class loci.formats.in.DNGReader
-
- CanonRawReader - Class in loci.formats.in
-
CanonRawReader is the file format reader for Canon RAW files.
- CanonRawReader() - Constructor for class loci.formats.in.CanonRawReader
-
Constructs a new Canon RAW reader.
- canParse - Variable in class loci.formats.in.LeicaHandler
-
- canReadAttachments() - Method in class loci.formats.in.ZeissCZIReader
-
- canUseBankDataDirectly(WritableRaster, int, Class<? extends DataBuffer>) - Static method in class loci.formats.gui.AWTImageTools
-
Whether we can return the data buffer's bank data
without performing any copy or conversion operations.
- canUsePrevious - Variable in class loci.formats.in.NativeQTReader
-
Flag indicating whether we can safely use prevPixels.
- CANVAS_COLOR_1 - Static variable in class loci.formats.in.CellSensReader
-
- CANVAS_COLOR_2 - Static variable in class loci.formats.in.CellSensReader
-
- CAPTURE_EDITOR_DATA - Static variable in class loci.formats.in.NikonReader
-
- cast(Class<?>) - Method in class loci.formats.ClassList
-
Cast the given class to something that extends the base class.
- category - Variable in class loci.formats.in.BaseZeissReader.Tag
-
- category - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
-
- category - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
-
- cBegin - Variable in class loci.plugins.in.ImporterOptions
-
- CCD_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
-
- cChoice - Variable in class loci.formats.gui.DataConverter
-
- cChoice - Variable in class loci.plugins.in.SwapDialog
-
- cdata - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- cdata - Variable in class loci.formats.in.ZeissTIFFHandler
-
- CELL_LENGTH - Static variable in class loci.formats.tiff.IFD
-
- CELL_WIDTH - Static variable in class loci.formats.tiff.IFD
-
- CellH5Constants() - Constructor for class loci.formats.in.CellH5Reader.CellH5Constants
-
- CellH5Coordinate(String, String, String) - Constructor for class loci.formats.in.CellH5Reader.CellH5Coordinate
-
- CellH5PathsToImageData - Variable in class loci.formats.in.CellH5Reader
-
- CellH5PositionList - Variable in class loci.formats.in.CellH5Reader
-
- CellH5Reader - Class in loci.formats.in
-
Reader for CellH5 (HDF) files.
- CellH5Reader() - Constructor for class loci.formats.in.CellH5Reader
-
Constructs a new CellH5 HDF reader.
- CellH5Reader.CellH5Constants - Class in loci.formats.in
-
- CellH5Reader.CellH5Coordinate - Class in loci.formats.in
-
- CellH5Writer - Class in loci.formats.out
-
CellH5Writer is the file format writer for CellH5 format.
- CellH5Writer() - Constructor for class loci.formats.out.CellH5Writer
-
- CellH5Writer(String, String[]) - Constructor for class loci.formats.out.CellH5Writer
-
- cellObjectNames - Variable in class loci.formats.in.CellH5Reader
-
- cellomicsPattern - Variable in class loci.formats.in.CellomicsReader
-
- CellomicsReader - Class in loci.formats.in
-
Reader for Cellomics C01 files.
- CellomicsReader() - Constructor for class loci.formats.in.CellomicsReader
-
Constructs a new Cellomics reader.
- CellSensReader - Class in loci.formats.in
-
CellSensReader is the file format reader for cellSens .vsi files.
- CellSensReader() - Constructor for class loci.formats.in.CellSensReader
-
Constructs a new cellSens reader.
- CellSensReader.Pyramid - Class in loci.formats.in
-
- CellSensReader.TileCoordinate - Class in loci.formats.in
-
- CellSensWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats CellSens .vsi support.
- CellSensWidgets() - Constructor for class loci.plugins.config.CellSensWidgets
-
- CellVoyagerReader - Class in loci.formats.in
-
- CellVoyagerReader() - Constructor for class loci.formats.in.CellVoyagerReader
-
- CellVoyagerReader.AreaInfo - Class in loci.formats.in
-
- CellVoyagerReader.ChannelInfo - Class in loci.formats.in
-
- CellVoyagerReader.FieldInfo - Class in loci.formats.in
-
- CellVoyagerReader.WellInfo - Class in loci.formats.in
-
- CellWorxReader - Class in loci.formats.in
-
CellWorxReader is the file format reader for CellWorx .pnl files.
- CellWorxReader() - Constructor for class loci.formats.in.CellWorxReader
-
Constructs a new CellWorx reader.
- cEnd - Variable in class loci.plugins.in.ImporterOptions
-
- CENTERED_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
-
- centerPixelValue - Variable in class loci.formats.in.DicomReader
-
- centerX - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
-
- centerY - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
-
- certain - Variable in class loci.formats.AxisGuesser
-
Whether the guesser is confident that all axis types are correct.
- certain - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
-
Certainty flag, for dealing with unspecified NumPlanes.
- cf - Variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Custom filter instance
- CFA_PATTERN - Static variable in class loci.formats.tiff.IFD
-
- cfaPattern - Variable in class loci.formats.in.DNGReader
-
- cfaPattern - Variable in class loci.formats.in.NikonReader
-
- cfdHF - Variable in class loci.formats.in.SDTInfo
-
- cfdLH - Variable in class loci.formats.in.SDTInfo
-
- cfdLL - Variable in class loci.formats.in.SDTInfo
-
- cfdZC - Variable in class loci.formats.in.SDTInfo
-
- CFG_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
-
- CFG_SUFFIX - Static variable in class loci.formats.in.PrairieReader
-
- cfgFile - Variable in class loci.formats.in.PrairieReader
-
The associated XML files.
- CHAINED_LAYERS - Static variable in class loci.formats.in.CellSensReader
-
- chan - Variable in class loci.formats.in.SDTInfo
-
Routing channel number.
- CHANDESC - Static variable in class loci.formats.in.LeicaReader
-
- changedUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
-
- changeOutputFile(String) - Method in class loci.formats.FormatWriter
-
- changeOutputFile(String) - Method in interface loci.formats.IFormatWriter
-
Switch the output file for the current dataset.
- changeOutputFile(String) - Method in class loci.formats.ImageWriter
-
- changeOutputFile(String) - Method in class loci.formats.WriterWrapper
-
- chanMax - Variable in class loci.formats.MinMaxCalculator
-
Max values for each channel.
- chanMin - Variable in class loci.formats.MinMaxCalculator
-
Min values for each channel.
- CHANNEL - Static variable in class loci.formats.FormatTools
-
Identifies the Channel dimensional type,
representing a generic channel dimension.
- channel - Variable in class loci.formats.in.ColumbusReader.Plane
-
- Channel() - Constructor for class loci.formats.in.LeicaHandler.Channel
-
- channel - Variable in class loci.formats.in.LeicaHandler.Detector
-
- channel - Variable in class loci.formats.in.LeicaHandler.MultiBand
-
- Channel() - Constructor for class loci.formats.in.OIRReader.Channel
-
- channel - Variable in class loci.formats.in.PrairieMetadata.PFile
-
channel of this <File>.
- channel - Variable in class loci.formats.in.SPCReader
-
- Channel() - Constructor for class loci.formats.in.ZeissCZIReader.Channel
-
- Channel(int) - Constructor for class loci.formats.in.ZeissTIFFReader.Channel
-
- CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
-
- CHANNEL_AMPLIFIER_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
-
- CHANNEL_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
-
- CHANNEL_COUNT_TAG - Static variable in class loci.formats.in.FlowSightReader
-
- CHANNEL_DESCS_TAG - Static variable in class loci.formats.in.FlowSightReader
-
- CHANNEL_DETECTOR_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
-
- CHANNEL_DIM - Static variable in class loci.formats.in.CellSensReader
-
- CHANNEL_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
-
- CHANNEL_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
-
- CHANNEL_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
-
- CHANNEL_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- CHANNEL_NAME - Static variable in class loci.formats.FormatTools
-
- CHANNEL_NAME - Static variable in class loci.formats.in.CellSensReader
-
- CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
-
- CHANNEL_NAMES_TAG - Static variable in class loci.formats.in.FlowSightReader
-
- CHANNEL_NUM - Static variable in class loci.formats.FormatTools
-
- CHANNEL_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
-
- CHANNEL_PINHOLE_DIAMETER - Static variable in class loci.formats.in.ZeissLSMReader
-
- CHANNEL_PRIORITIES - Static variable in class loci.formats.in.LIFReader
-
- CHANNEL_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- CHANNEL_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
-
- CHANNEL_TRANSPARENCY_VALUE - Static variable in class loci.formats.in.CellSensReader
-
- CHANNEL_VISIBLE - Static variable in class loci.formats.in.CellSensReader
-
- channelColor - Variable in class loci.formats.in.ColumbusReader.Plane
-
- channelColor - Variable in class loci.formats.in.LeicaReader
-
- channelColor - Variable in class loci.formats.in.ZeissLSMReader
-
- channelColors - Variable in class loci.formats.in.BaseZeissReader
-
- channelColors - Variable in class loci.formats.in.ImprovisionTiffReader
-
- channelColors - Variable in class loci.formats.in.NativeND2Reader
-
- ChannelData() - Constructor for class loci.formats.in.FV1000Reader.ChannelData
-
- channelDescs - Variable in class loci.formats.in.FlowSightReader
-
- ChannelFiller - Class in loci.formats
-
For indexed color data representing true color, factors out
the indices, replacing them with the color table values directly.
- ChannelFiller() - Constructor for class loci.formats.ChannelFiller
-
Constructs a ChannelFiller around a new image reader.
- ChannelFiller(IFormatReader) - Constructor for class loci.formats.ChannelFiller
-
Constructs a ChannelFiller with a given reader.
- channelFiller - Variable in class loci.plugins.in.ImportProcess
-
- channelId - Variable in class loci.formats.in.OIRReader.Detector
-
- channelIndices - Variable in class loci.formats.in.BaseZeissReader
-
- ChannelInfo() - Constructor for class loci.formats.in.CellVoyagerReader.ChannelInfo
-
- channelInfos - Variable in class loci.formats.in.CellVoyagerReader
-
- channelLengths - Variable in class loci.formats.in.ICSReader
-
The length of each channel axis.
- channelMax - Variable in class loci.formats.in.ImarisHDFReader
-
- ChannelMerger - Class in loci.formats
-
Logic to automatically merge channels in a file.
- ChannelMerger() - Constructor for class loci.formats.ChannelMerger
-
Constructs a ChannelMerger around a new image reader.
- ChannelMerger(IFormatReader) - Constructor for class loci.formats.ChannelMerger
-
Constructs a ChannelMerger with the given reader.
- channelMin - Variable in class loci.formats.in.ImarisHDFReader
-
- channelName - Variable in class loci.formats.in.BaseZeissReader
-
- channelName - Variable in class loci.formats.in.ColumbusReader.Plane
-
- channelName - Variable in class loci.formats.in.ImarisHDFReader
-
- channelName - Variable in class loci.formats.in.MetamorphHandler
-
- channelName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
-
- channelName - Variable in class loci.formats.in.OperettaReader.Plane
-
- channelName - Variable in class loci.formats.in.PrairieMetadata.PFile
-
channelName attribute of this <File>.
- channelName - Variable in class loci.formats.in.SISReader
-
- channelName - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
-
- channelNames - Variable in class loci.formats.in.BDReader
-
- channelNames - Variable in class loci.formats.in.CellSensReader.Pyramid
-
- channelNames - Variable in class loci.formats.in.FlexReader
-
- channelNames - Variable in class loci.formats.in.FlowSightReader
-
- channelNames - Variable in class loci.formats.in.FluoviewReader
-
- channelNames - Variable in class loci.formats.in.InCellReader
-
- channelNames - Variable in class loci.formats.in.LeicaReader
-
- channelNames - Variable in class loci.formats.in.LIFReader
-
- channelNames - Variable in class loci.formats.in.MetamorphHandler
-
- channelNames - Variable in class loci.formats.in.ND2Handler
-
- channelNames - Variable in class loci.formats.in.ScanrReader
-
- channelNames - Variable in class loci.formats.in.SlidebookTiffReader
-
- channelNames - Variable in class loci.formats.in.VolocityReader.Stack
-
- channelNames - Variable in class loci.formats.in.ZeissLSMReader
-
- channelNumber - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
-
- channelNumber - Variable in class loci.plugins.util.RecordedImageProcessor
-
- channelOrder - Variable in class loci.formats.in.PhotoshopTiffReader
-
- channels - Variable in class loci.formats.codec.CodecOptions
-
Number of channels.
- channels - Variable in class loci.formats.in.FV1000Reader
-
- channels - Variable in class loci.formats.in.LeicaHandler
-
- channels - Variable in class loci.formats.in.LiFlimReader
-
- channels - Variable in class loci.formats.in.MicromanagerReader.Position
-
- channels - Variable in class loci.formats.in.OIRReader
-
- channels - Variable in class loci.formats.in.PrairieReader
-
List of active channels.
- channels - Variable in class loci.formats.in.SDTInfo
-
- channels - Variable in class loci.formats.in.SDTReader
-
Number of spectral channels.
- channels - Variable in class loci.formats.in.TextReader
-
List of channel labels.
- channels - Variable in class loci.formats.in.ZeissCZIReader
-
- channels - Variable in class loci.formats.in.ZeissTIFFReader
-
- ChannelSeparator - Class in loci.formats
-
Logic to automatically separate the channels in a file.
- ChannelSeparator() - Constructor for class loci.formats.ChannelSeparator
-
Constructs a ChannelSeparator around a new image reader.
- ChannelSeparator(IFormatReader) - Constructor for class loci.formats.ChannelSeparator
-
Constructs a ChannelSeparator with the given reader.
- channelSeparator - Variable in class loci.plugins.in.ImportProcess
-
- channelsPerTimepoint - Variable in class loci.formats.in.InCellReader
-
- channelTypes - Variable in class loci.formats.in.ICSReader
-
The type of each channel axis.
- channelWavelengths - Variable in class loci.formats.in.CellSensReader.Pyramid
-
- CHAR - Static variable in class loci.formats.in.CellSensReader
-
- CHAR - Static variable in class loci.formats.in.GatanReader
-
- characters(char[], int, int) - Method in class loci.formats.in.AFIReader.AFIHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.FEITiffReader.FEIHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.FlexReader.FlexHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.ImaconReader.ImaconHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.InCellReader.InCellHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.IvisionReader.IvisionHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.ScanrReader.ScanrHandler
-
- characters(char[], int, int) - Method in class loci.formats.in.ZeissTIFFHandler
-
- characters(char[], int, int) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
-
- charData - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- CHARS - Static variable in class loci.formats.tools.AsciiImage
-
- Charset(int, String) - Constructor for enum loci.formats.in.BaseZeissReader.Charset
-
- charset - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- CHECK - Static variable in class loci.formats.in.ZeissLMSReader
-
- checkBufferSize(IFormatReader, int) - Static method in class loci.formats.FormatTools
-
- checkBufferSize(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools
-
Checks that the given buffer size is large enough to hold a w * h
image as returned by the given reader.
- checkClass(String) - Static method in class loci.plugins.util.LibraryChecker
-
Checks whether the given class is available.
- checkClassDependency(Class<? extends Object>) - Method in class loci.formats.services.WlzServiceImpl
-
- checkCommentImageJ(String) - Method in class loci.formats.in.TiffReader
-
- checkCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
-
- checkElement(Element, String) - Method in class loci.formats.in.PrairieMetadata
-
Checks that the given element has the specified name.
- checkHeader() - Method in class loci.formats.tiff.TiffParser
-
Checks the TIFF header.
- checkImageJ() - Static method in class loci.plugins.util.LibraryChecker
-
Checks whether ImageJ is new enough for the Bio-Formats plugins.
- checkImageJ(String, String) - Static method in class loci.plugins.util.LibraryChecker
-
Returns true the current ImageJ version is greater than or equal to the
specified version.
- checkImageJ(String, String, String) - Static method in class loci.plugins.util.LibraryChecker
-
Returns true the current ImageJ version is greater than or equal to the
specified version.
- checkJava() - Static method in class loci.plugins.util.LibraryChecker
-
Checks for a new enough version of the Java Runtime Environment.
- checkKey(String, String) - Method in class loci.formats.in.MetamorphHandler
-
Check if the value needs to be saved.
- checkKey(String, String) - Method in class loci.plugins.in.ImporterOptions
-
Tests whether the given boolean key is set in the specified options.
- checkLatest(String, String) - Static method in class loci.plugins.config.InstallWizard
-
- checkLibrary(LibraryChecker.Library, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
-
Checks for a required library.
- checkLibrary(String, String, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
-
Checks whether the given class is available; if not,
adds the specified JAR file name to the hash set
(presumably to report it missing to the user).
- checkMissing(HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
-
Reports missing libraries in the given hash set to the user.
- checkObsoleteOptions() - Method in class loci.plugins.in.ImporterOptions
-
Handles obsolete macro keys, for backward compatibility.
- checkPALM(String) - Method in class loci.formats.in.ZeissCZIReader
-
- checkParams(int, byte[], int, int, int, int) - Method in class loci.formats.FormatWriter
-
Ensure that the arguments that are being passed to saveBytes(...) are
valid.
- checkParams - Variable in class loci.formats.out.TiffWriter
-
Whether or not to check the parameters passed to saveBytes.
- checkPerformed - Static variable in class loci.plugins.in.UpgradeDialog
-
Whether an upgrade check has already been performed this session.
- checkPlaneNumber(IFormatReader, int) - Static method in class loci.formats.FormatTools
-
Checks that the given plane number is valid for the given reader.
- checkPlaneParameters(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Convenience method for checking that the plane number, tile size and
buffer sizes are all valid for the given reader.
- checkPoints(int) - Method in enum loci.formats.in.BaseZeissReader.FeatureType
-
- checkQTLibrary() - Method in class loci.formats.gui.LegacyQTTools
-
Checks whether QTJava is available, throwing an exception if not.
- checkSuffix(String, String) - Static method in class loci.formats.FormatHandler
-
Performs suffix matching for the given filename.
- checkSuffix(String, String[]) - Static method in class loci.formats.FormatHandler
-
Performs suffix matching for the given filename.
- checkTileSize(IFormatReader, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Checks that the given tile size is valid for the given reader.
- checkTime(long, int, long, long) - Method in class loci.formats.in.TextReader
-
- checkUnit(String, String...) - Method in class loci.formats.in.ICSReader
-
Verifies that a unit matches the expected value.
- CHIP_SIZE_X - Static variable in class loci.formats.in.FluoviewReader
-
- CHIP_SIZE_Y - Static variable in class loci.formats.in.FluoviewReader
-
- chksum - Variable in class loci.formats.in.SDTInfo
-
- CHUNK_SIZE - Static variable in class loci.formats.UpgradeChecker
-
Number of bytes to read from the CI server at a time.
- ChunkMapEntry() - Constructor for class loci.formats.in.NativeND2Reader.ChunkMapEntry
-
- chunkSizes - Variable in class loci.formats.in.NativeQTReader
-
Number of bytes in each plane.
- CI_SERVER - Static variable in class loci.formats.UpgradeChecker
-
Location of the OME continuous integration server.
- cIndex - Variable in class loci.formats.in.BaseZeissReader
-
- cIndex - Variable in class loci.plugins.util.DataBrowser
-
- CIRCLE - Static variable in class loci.formats.in.FV1000Reader
-
- CIRCLE - Static variable in class loci.formats.in.ZeissLSMReader
-
- CIRCLE_3POINT - Static variable in class loci.formats.in.ZeissLSMReader
-
- cLabel - Variable in class loci.formats.gui.DataConverter
-
- CLASS_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions
-
- CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- CLASS_VIEW_5D - Static variable in class loci.plugins.in.ImporterOptions
-
- classes - Variable in class loci.formats.ClassList
-
List of classes.
- classes - Variable in class loci.formats.in.CellH5Reader
-
- ClassList<T> - Class in loci.formats
-
ClassList is a list of classes for use with
ImageReader or
ImageWriter, parsed from a configuration file such as readers.txt
or writers.txt.
- ClassList(Class<T>) - Constructor for class loci.formats.ClassList
-
Constructs a list of classes, initially empty.
- ClassList(String, Class<T>) - Constructor for class loci.formats.ClassList
-
Constructs a list of classes from the given configuration file.
- ClassList(String, Class<T>, Class<?>) - Constructor for class loci.formats.ClassList
-
Constructs a list of classes from the given configuration file.
- classList - Variable in class loci.formats.FileStitcher
-
- cleanup() - Method in class loci.formats.Memoizer
-
- clear() - Method in class loci.formats.codec.ByteVector
-
- clearSeries() - Method in class loci.plugins.in.ImporterOptions
-
- clearXML() - Method in class loci.formats.in.ZeissCZIReader.Metadata
-
- cLengths - Variable in class loci.plugins.util.DataBrowser
-
- CLIPPING - Static variable in class loci.formats.in.CellSensReader
-
- CLIPPING_MAGIC_STRING - Static variable in class loci.formats.in.VolocityClippingReader
-
- CLIPPING_STATE - Static variable in class loci.formats.in.CellSensReader
-
- clippingData - Variable in class loci.formats.in.VolocityReader.Stack
-
- CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
-
- clone() - Method in class loci.formats.CoreMetadata
-
- clone(IFormatReader, int) - Method in class loci.formats.CoreMetadata
-
- clone() - Method in class loci.formats.SwappableMetadata
-
- clone(IFormatReader, int) - Method in class loci.formats.SwappableMetadata
-
- close(boolean) - Method in class loci.formats.ChannelSeparator
-
- close() - Method in class loci.formats.codec.JPEGTileDecoder
-
- close(boolean) - Method in class loci.formats.DelegateReader
-
- close() - Method in class loci.formats.FileStitcher
-
- close(boolean) - Method in class loci.formats.FileStitcher
-
- close(boolean) - Method in class loci.formats.FormatReader
-
- close() - Method in class loci.formats.FormatReader
-
- close() - Method in class loci.formats.FormatWriter
-
- close() - Method in class loci.formats.gui.PreviewPane
-
Closes the underlying image reader.
- close(boolean) - Method in interface loci.formats.IFormatReader
-
Closes the currently open file.
- close(boolean) - Method in class loci.formats.ImageReader
-
- close() - Method in class loci.formats.ImageReader
-
- close() - Method in class loci.formats.ImageWriter
-
- close(boolean) - Method in class loci.formats.in.AFIReader
-
- close(boolean) - Method in class loci.formats.in.AIMReader
-
- close(boolean) - Method in class loci.formats.in.AliconaReader
-
- close(boolean) - Method in class loci.formats.in.AmiraReader
-
- close(boolean) - Method in class loci.formats.in.AnalyzeReader
-
- close(boolean) - Method in class loci.formats.in.APLReader
-
- close(boolean) - Method in class loci.formats.in.APNGReader
-
- close(boolean) - Method in class loci.formats.in.AVIReader
-
- close(boolean) - Method in class loci.formats.in.BaseZeissReader
-
- close(boolean) - Method in class loci.formats.in.BDReader
-
- close(boolean) - Method in class loci.formats.in.BioRadReader
-
- close(boolean) - Method in class loci.formats.in.BioRadSCNReader
-
- close(boolean) - Method in class loci.formats.in.BMPReader
-
- close(boolean) - Method in class loci.formats.in.BrukerReader
-
- close(boolean) - Method in class loci.formats.in.BurleighReader
-
- close(boolean) - Method in class loci.formats.in.CanonRawReader
-
- close(boolean) - Method in class loci.formats.in.CellH5Reader
-
- close(boolean) - Method in class loci.formats.in.CellomicsReader
-
- close(boolean) - Method in class loci.formats.in.CellSensReader
-
- close(boolean) - Method in class loci.formats.in.CellWorxReader
-
- close(boolean) - Method in class loci.formats.in.ColumbusReader
-
- close(boolean) - Method in class loci.formats.in.DeltavisionReader
-
- close(boolean) - Method in class loci.formats.in.DicomReader
-
- close(boolean) - Method in class loci.formats.in.DNGReader
-
- close(boolean) - Method in class loci.formats.in.EPSReader
-
- close(boolean) - Method in class loci.formats.in.FakeReader
-
- close(boolean) - Method in class loci.formats.in.FEIReader
-
- close(boolean) - Method in class loci.formats.in.FEITiffReader
-
- close(boolean) - Method in class loci.formats.in.FilePatternReader
-
- close() - Method in class loci.formats.in.FilePatternReader
-
- close(boolean) - Method in class loci.formats.in.FitsReader
-
- close(boolean) - Method in class loci.formats.in.FlexReader
-
- close(boolean) - Method in class loci.formats.in.FlowSightReader
-
- close(boolean) - Method in class loci.formats.in.FluoviewReader
-
- close(boolean) - Method in class loci.formats.in.FujiReader
-
- close(boolean) - Method in class loci.formats.in.FV1000Reader
-
- close(boolean) - Method in class loci.formats.in.GatanDM2Reader
-
- close(boolean) - Method in class loci.formats.in.GatanReader
-
- close(boolean) - Method in class loci.formats.in.GIFReader
-
- close(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
-
- close(boolean) - Method in class loci.formats.in.HitachiReader
-
- close(boolean) - Method in class loci.formats.in.HRDGDFReader
-
- close(boolean) - Method in class loci.formats.in.ICSReader
-
- close(boolean) - Method in class loci.formats.in.IM3Reader
-
- close(boolean) - Method in class loci.formats.in.ImaconReader
-
- close(boolean) - Method in class loci.formats.in.ImageIOReader
-
- close(boolean) - Method in class loci.formats.in.ImagicReader
-
- close(boolean) - Method in class loci.formats.in.ImarisHDFReader
-
- close(boolean) - Method in class loci.formats.in.ImarisReader
-
- close(boolean) - Method in class loci.formats.in.IMODReader
-
- close(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
-
- close(boolean) - Method in class loci.formats.in.ImspectorReader
-
- close(boolean) - Method in class loci.formats.in.InCell3000Reader
-
- close(boolean) - Method in class loci.formats.in.InCellReader
-
- close(boolean) - Method in class loci.formats.in.InveonReader
-
- close(boolean) - Method in class loci.formats.in.IPLabReader
-
- close(boolean) - Method in class loci.formats.in.IPWReader
-
- close(boolean) - Method in class loci.formats.in.IvisionReader
-
- close(boolean) - Method in class loci.formats.in.JEOLReader
-
- close(boolean) - Method in class loci.formats.in.JPEG2000Reader
-
- close(boolean) - Method in class loci.formats.in.JPEGReader
-
- close(boolean) - Method in class loci.formats.in.JPXReader
-
- close(boolean) - Method in class loci.formats.in.KhorosReader
-
- close(boolean) - Method in class loci.formats.in.KodakReader
-
- close(boolean) - Method in class loci.formats.in.L2DReader
-
- close(boolean) - Method in class loci.formats.in.LegacyQTReader
-
- close(boolean) - Method in class loci.formats.in.LeicaReader
-
- close(boolean) - Method in class loci.formats.in.LeicaSCNReader
-
- close(boolean) - Method in class loci.formats.in.LiFlimReader
-
- close(boolean) - Method in class loci.formats.in.LIFReader
-
- close(boolean) - Method in class loci.formats.in.LIMReader
-
- close(boolean) - Method in class loci.formats.in.MetamorphReader
-
- close(boolean) - Method in class loci.formats.in.MetamorphTiffReader
-
- close(boolean) - Method in class loci.formats.in.MIASReader
-
- close(boolean) - Method in class loci.formats.in.MicromanagerReader
-
- close(boolean) - Method in class loci.formats.in.MINCReader
-
- close(boolean) - Method in class loci.formats.in.MinimalTiffReader
-
- close(boolean) - Method in class loci.formats.in.MNGReader
-
- close(boolean) - Method in class loci.formats.in.MolecularImagingReader
-
- close(boolean) - Method in class loci.formats.in.MRCReader
-
- close(boolean) - Method in class loci.formats.in.MRWReader
-
- close(boolean) - Method in class loci.formats.in.NAFReader
-
- close(boolean) - Method in class loci.formats.in.NativeND2Reader
-
- close(boolean) - Method in class loci.formats.in.NativeQTReader
-
- close(boolean) - Method in class loci.formats.in.NDPIReader
-
- close(boolean) - Method in class loci.formats.in.NDPISReader
-
- close(boolean) - Method in class loci.formats.in.NiftiReader
-
- close(boolean) - Method in class loci.formats.in.NikonElementsTiffReader
-
- close(boolean) - Method in class loci.formats.in.NikonReader
-
- close(boolean) - Method in class loci.formats.in.NikonTiffReader
-
- close(boolean) - Method in class loci.formats.in.NRRDReader
-
- close(boolean) - Method in class loci.formats.in.OBFReader
-
- close(boolean) - Method in class loci.formats.in.OIRReader
-
- close(boolean) - Method in class loci.formats.in.OMETiffReader
-
- close(boolean) - Method in class loci.formats.in.OMEXMLReader
-
- close(boolean) - Method in class loci.formats.in.OpenlabRawReader
-
- close(boolean) - Method in class loci.formats.in.OpenlabReader
-
- close(boolean) - Method in class loci.formats.in.OperettaReader
-
- close(boolean) - Method in class loci.formats.in.PCIReader
-
- close(boolean) - Method in class loci.formats.in.PCORAWReader
-
- close(boolean) - Method in class loci.formats.in.PCXReader
-
- close(boolean) - Method in class loci.formats.in.PDSReader
-
- close(boolean) - Method in class loci.formats.in.PerkinElmerReader
-
- close(boolean) - Method in class loci.formats.in.PGMReader
-
- close(boolean) - Method in class loci.formats.in.PhotoshopTiffReader
-
- close(boolean) - Method in class loci.formats.in.PictReader
-
- close(boolean) - Method in class loci.formats.in.PQBinReader
-
- close(boolean) - Method in class loci.formats.in.PrairieReader
-
- close(boolean) - Method in class loci.formats.in.PSDReader
-
- close(boolean) - Method in class loci.formats.in.QuesantReader
-
- close(boolean) - Method in class loci.formats.in.RHKReader
-
- close(boolean) - Method in class loci.formats.in.SBIGReader
-
- close(boolean) - Method in class loci.formats.in.ScanrReader
-
- close(boolean) - Method in class loci.formats.in.ScreenReader
-
- close(boolean) - Method in class loci.formats.in.SDTReader
-
- close(boolean) - Method in class loci.formats.in.SIFReader
-
- close(boolean) - Method in class loci.formats.in.SimplePCITiffReader
-
- close(boolean) - Method in class loci.formats.in.SISReader
-
- close(boolean) - Method in class loci.formats.in.SlidebookReader
-
- close(boolean) - Method in class loci.formats.in.SlidebookTiffReader
-
- close(boolean) - Method in class loci.formats.in.SPCReader
-
- close(boolean) - Method in class loci.formats.in.SPEReader
-
- close(boolean) - Method in class loci.formats.in.SpiderReader
-
- close(boolean) - Method in class loci.formats.in.SVSReader
-
- close(boolean) - Method in class loci.formats.in.TargaReader
-
- close(boolean) - Method in class loci.formats.in.TCSReader
-
- close(boolean) - Method in class loci.formats.in.TextReader
-
- close(boolean) - Method in class loci.formats.in.TiffReader
-
- close(boolean) - Method in class loci.formats.in.TileJPEGReader
-
- close(boolean) - Method in class loci.formats.in.TillVisionReader
-
- close(boolean) - Method in class loci.formats.in.TopometrixReader
-
- close(boolean) - Method in class loci.formats.in.TrestleReader
-
- close(boolean) - Method in class loci.formats.in.UBMReader
-
- close(boolean) - Method in class loci.formats.in.UnisokuReader
-
- close(boolean) - Method in class loci.formats.in.VarianFDFReader
-
- close(boolean) - Method in class loci.formats.in.VeecoReader
-
- close(boolean) - Method in class loci.formats.in.VisitechReader
-
- close(boolean) - Method in class loci.formats.in.VolocityClippingReader
-
- close(boolean) - Method in class loci.formats.in.VolocityReader
-
- close(boolean) - Method in class loci.formats.in.WlzReader
-
- close(boolean) - Method in class loci.formats.in.ZeissCZIReader
-
- close() - Method in class loci.formats.in.ZeissCZIReader.Segment
-
- close(boolean) - Method in class loci.formats.in.ZeissLMSReader
-
- close(boolean) - Method in class loci.formats.in.ZeissLSMReader
-
- close(boolean) - Method in class loci.formats.in.ZeissTIFFReader
-
- close(boolean) - Method in class loci.formats.in.ZeissZVIReader
-
- close(boolean) - Method in class loci.formats.in.ZipReader
-
- close() - Method in class loci.formats.Memoizer
-
- close(boolean) - Method in class loci.formats.Memoizer
-
- close() - Method in interface loci.formats.Memoizer.Deser
-
- close() - Method in class loci.formats.Memoizer.KryoDeser
-
- close(boolean) - Method in class loci.formats.MinMaxCalculator
-
- close() - Method in class loci.formats.out.APNGWriter
-
- close() - Method in class loci.formats.out.AVIWriter
-
- close() - Method in class loci.formats.out.CellH5Writer
-
- close() - Method in class loci.formats.out.ICSWriter
-
- close() - Method in class loci.formats.out.JavaWriter
-
- close() - Method in class loci.formats.out.LegacyQTWriter
-
- close() - Method in class loci.formats.out.OMETiffWriter
-
- close() - Method in class loci.formats.out.OMEXMLWriter
-
- close() - Method in class loci.formats.out.QTWriter
-
- close() - Method in class loci.formats.out.TiffWriter
-
- close() - Method in class loci.formats.out.V3DrawWriter
-
- close() - Method in class loci.formats.out.WlzWriter
-
- close(boolean) - Method in class loci.formats.ReaderWrapper
-
- close() - Method in class loci.formats.ReaderWrapper
-
- close() - Method in interface loci.formats.services.EXIFService
-
- close() - Method in class loci.formats.services.EXIFServiceImpl
-
- close() - Method in interface loci.formats.services.JHDFService
-
Closes and resets the service.
- close() - Method in class loci.formats.services.JHDFServiceImpl
-
- close() - Method in interface loci.formats.services.JPEGTurboService
-
- close() - Method in class loci.formats.services.JPEGTurboServiceImpl
-
- close() - Method in interface loci.formats.services.MDBService
-
Close the currently initialized file.
- close() - Method in class loci.formats.services.MDBServiceImpl
-
- close() - Method in interface loci.formats.services.MetakitService
-
- close() - Method in class loci.formats.services.MetakitServiceImpl
-
- close() - Method in interface loci.formats.services.NetCDFService
-
Closes and resets the service.
- close() - Method in class loci.formats.services.NetCDFServiceImpl
-
- close() - Method in interface loci.formats.services.POIService
-
Close the current POI file system.
- close() - Method in class loci.formats.services.POIServiceImpl
-
- close() - Method in interface loci.formats.services.WlzService
-
Closes the file.
- close() - Method in class loci.formats.services.WlzServiceImpl
-
- close() - Method in class loci.formats.tiff.OnDemandLongArray
-
- close() - Method in class loci.formats.tiff.TiffSaver
-
Closes the output stream if not null.
- close() - Method in class loci.formats.WriterWrapper
-
- close() - Method in class loci.plugins.config.TextAreaWriter
-
Closing a TextAreaWriter does nothing.
- close() - Method in class loci.plugins.macro.LociFunctions
-
- close() - Method in class loci.plugins.util.VirtualImagePlus
-
- close() - Method in class loci.plugins.util.VirtualReader
-
- close() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Free the native structures associated with this compressor instance.
- close() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Free the native structures associated with this decompressor instance.
- CLOSED_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
-
- CLOSED_BEZIER - Static variable in class loci.formats.in.ZeissLSMReader
-
- CLOSED_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
-
- closeFileOnly() - Method in class loci.plugins.macro.LociFunctions
-
- cm - Variable in class loci.formats.FormatWriter
-
Default color model.
- cNames - Variable in class loci.formats.in.ImprovisionTiffReader
-
- co2Percent - Variable in class loci.formats.in.ZeissCZIReader
-
- COARSE_FRAME_IFD - Static variable in class loci.formats.in.CellSensReader
-
- COARSE_PYRAMID_LEVEL - Static variable in class loci.formats.in.CellSensReader
-
- code - Variable in enum loci.formats.codec.CompressionType
-
Code for the compression.
- code - Variable in enum loci.formats.codec.JPEG2000BoxType
-
Code for the box type.
- code - Variable in enum loci.formats.codec.JPEG2000SegmentMarker
-
Code for the segment marker.
- code - Variable in class loci.formats.in.FV1000Reader
-
- code - Variable in enum loci.formats.tiff.IFDType
-
Code for the IFD type in the actual TIFF file.
- code - Variable in enum loci.formats.tiff.PhotoInterp
-
Code for the IFD type in the actual TIFF file.
- code - Variable in enum loci.formats.tiff.TiffCompression
-
Code for the TIFF compression in the actual TIFF file.
- codeBlockSize - Variable in class loci.formats.codec.JPEG2000CodecOptions
-
The maximum code-block size to use per tile-component as it would be
provided to:
J2KImageWriteParam.setCodeBlockSize(int[])
(WRITE).
- Codec - Interface in loci.formats.codec
-
This class is an interface for any kind of compression or decompression.
- codec - Variable in class loci.formats.codec.WrappedCodec
-
- codec - Variable in class loci.formats.gui.DataConverter
-
- codec - Variable in class loci.formats.in.NativeND2Reader
-
Codec to use when decompressing pixel data.
- codec - Variable in class loci.formats.in.NativeQTReader
-
Video codec used by this movie.
- codec - Variable in class loci.formats.out.LegacyQTWriter
-
The codec to use.
- codec - Variable in class loci.formats.out.QTWriter
-
The codec to use.
- codec - Variable in enum loci.formats.tiff.TiffCompression
-
TIFF compression codec.
- CODEC_ANIMATION - Static variable in class loci.formats.out.QTWriter
-
Value indicating Animation codec.
- CODEC_CINEPAK - Static variable in class loci.formats.out.QTWriter
-
Value indicating Cinepak codec.
- CODEC_H_263 - Static variable in class loci.formats.out.QTWriter
-
Value indicating H.263 codec.
- CODEC_MOTION_JPEG_B - Static variable in class loci.formats.out.QTWriter
-
Value indicating Motion JPEG-B codec.
- CODEC_MPEG_4 - Static variable in class loci.formats.out.QTWriter
-
Value indicating MPEG-4 codec.
- CODEC_RAW - Static variable in class loci.formats.out.QTWriter
-
Value indicating Raw codec.
- CODEC_SORENSON - Static variable in class loci.formats.out.QTWriter
-
Value indicating Sorenson codec.
- CODEC_SORENSON_3 - Static variable in class loci.formats.out.QTWriter
-
Value indicating Sorenson 3 codec.
- codecName - Variable in enum loci.formats.tiff.TiffCompression
-
Name of the TIFF compression codec.
- CodecOptions - Class in loci.formats.codec
-
Options for compressing and decompressing data.
- CodecOptions() - Constructor for class loci.formats.codec.CodecOptions
-
Construct a new CodecOptions.
- CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.CodecOptions
-
Construct a new CodecOptions using the given CodecOptions.
- codecOptions - Variable in class loci.formats.tiff.TiffParser
-
Codec options to be used when decoding compressed pixel data.
- codestreamOffset - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Offset to first contiguous codestream.
- codestreamPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Pixel type as specified in the JPEG 2000 codestream..
- codestreamSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Number of channels the image as specified in the JPEG 2000 codestream.
- codestreamSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Width of the image as specified in the JPEG 2000 codestream.
- codestreamSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Height of the image as specified in the JPEG 2000 codestream.
- col - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
-
- col - Variable in class loci.formats.in.ColumbusReader.Plane
-
- col - Variable in class loci.formats.in.OperettaReader.Plane
-
- col - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- colCount - Variable in class loci.formats.in.BaseZeissReader
-
- collection - Variable in class loci.formats.in.LeicaHandler
-
- collection - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- COLLECTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
-
- colName - Variable in class loci.formats.in.InCellReader
-
- color - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
-
- color - Variable in class loci.formats.in.LeicaHandler.ROI
-
- color - Variable in class loci.formats.in.LIFReader.ROI
-
- color - Variable in class loci.formats.in.OIRReader.Channel
-
- color - Variable in class loci.formats.in.ZeissCZIReader.Channel
-
- color16 - Variable in class loci.formats.in.IvisionReader
-
- COLOR_BAR - Static variable in class loci.formats.in.FV1000Reader
-
- COLOR_MAP - Static variable in class loci.formats.in.CanonRawReader
-
- COLOR_MAP - Static variable in class loci.formats.in.DNGReader
-
- COLOR_MAP - Static variable in class loci.formats.in.NikonReader
-
- COLOR_MAP - Static variable in class loci.formats.tiff.IFD
-
- COLOR_MAP_1 - Static variable in class loci.formats.in.MRWReader
-
- COLOR_MAP_2 - Static variable in class loci.formats.in.MRWReader
-
- COLOR_MODE - Static variable in class loci.formats.in.NikonReader
-
- COLOR_MODE_COLORIZED - Static variable in class loci.plugins.in.ImporterOptions
-
- COLOR_MODE_COMPOSITE - Static variable in class loci.plugins.in.ImporterOptions
-
- COLOR_MODE_CUSTOM - Static variable in class loci.plugins.in.ImporterOptions
-
- COLOR_MODE_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
-
- COLOR_MODE_GRAYSCALE - Static variable in class loci.plugins.in.ImporterOptions
-
- COLOR_SPACE - Static variable in class loci.formats.in.CellSensReader
-
- COLOR_SPACE - Static variable in class loci.formats.tiff.IFD
-
- ColorDialog - Class in loci.plugins.in
-
Bio-Formats Importer custom color chooser dialog box.
- ColorDialog(ImportProcess) - Constructor for class loci.plugins.in.ColorDialog
-
- colorize - Variable in class loci.plugins.util.BFVirtualStack
-
- Colorizer - Class in loci.plugins.in
-
Logic for colorizing images.
- Colorizer(ImportProcess) - Constructor for class loci.plugins.in.Colorizer
-
- colorMap - Variable in class loci.formats.in.TargaReader
-
- colorModeChoice - Variable in class loci.plugins.in.MainDialog
-
- colorModel - Variable in class loci.formats.codec.CodecOptions
-
Color model to use when constructing an image (WRITE).
- COLORS - Variable in class loci.formats.in.CellH5Reader
-
- colors - Variable in class loci.formats.in.ImarisHDFReader
-
- colors - Variable in class loci.formats.in.IMODReader
-
- colors - Variable in class loci.formats.in.NativeND2Reader
-
- colors - Variable in class loci.formats.in.ND2Handler
-
- COLORSPACE - Static variable in class loci.formats.in.CellSensReader
-
- colorTables - Variable in class loci.formats.in.GIFReader
-
- cols - Variable in class loci.formats.in.CellSensReader
-
- colT - Variable in class loci.formats.in.SDTInfo
-
- ColumbusReader - Class in loci.formats.in
-
ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
- ColumbusReader() - Constructor for class loci.formats.in.ColumbusReader
-
Constructs a new Columbus reader.
- ColumbusReader.MeasurementHandler - Class in loci.formats.in
-
- ColumbusReader.Plane - Class in loci.formats.in
-
- column - Variable in class loci.formats.in.FlexReader.FlexFile
-
- column - Variable in class loci.formats.in.OMEXMLReader.BinData
-
- column - Variable in class loci.formats.tools.AmiraParameters
-
- COLUMNS - Static variable in class loci.formats.gui.DataConverter
-
- COLUMNS - Static variable in class loci.formats.in.DicomReader
-
- ComboFileFilter - Class in loci.formats.gui
-
A file filter that recognizes files from a union of other filters.
- ComboFileFilter(FileFilter[], String) - Constructor for class loci.formats.gui.ComboFileFilter
-
Constructs a new filter from a list of other filters.
- comment - Variable in class loci.formats.in.FluoviewReader
-
- comment - Variable in class loci.formats.in.MicromanagerReader.Position
-
- comment - Variable in class loci.formats.in.QuesantReader
-
- COMMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
-
- COMMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
-
- comments - Variable in class loci.formats.in.JPEG2000MetadataParser
-
List of comments stored in the file.
- comments - Variable in class loci.formats.in.SVSReader
-
- comp - Variable in class loci.formats.gui.CacheIndicator
-
- COMPANION_KEY - Static variable in class loci.formats.out.OMETiffWriter
-
- COMPANION_SUFFIXES - Static variable in class loci.formats.in.TiffReader
-
- companionFile - Variable in class loci.formats.in.TiffReader
-
- companionFiles - Variable in class loci.formats.in.DicomReader
-
- compare(Object, Object) - Method in class loci.formats.cache.CacheStrategy
-
Default comparator orders dimensional positions based on distance from the
current position, taking into account axis priorities and planar ordering.
- compare(String, String) - Method in class loci.formats.in.MetamorphTiffReader.NumericComparator
-
- compareTo(Object) - Method in class loci.formats.gui.ComboFileFilter
-
Compares two FileFilter objects alphanumerically.
- compareTo(Object) - Method in class loci.formats.gui.ExtensionFileFilter
-
Compares two FileFilter objects alphanumerically.
- compareTo(Object) - Method in class loci.formats.gui.FormatFileFilter
-
Compares two FileFilter objects alphanumerically.
- compareTo(Object) - Method in class loci.formats.gui.NoExtensionFileFilter
-
Compares two FileFilter objects alphanumerically.
- compareTo(Object) - Method in class loci.formats.tiff.TiffIFDEntry
-
- compareTo(TiffRational) - Method in class loci.formats.tiff.TiffRational
-
Compares this object with the specified object for order.
- compareTo(Object) - Method in class loci.plugins.config.FormatEntry
-
- compareTo(Object) - Method in class loci.plugins.config.LibraryEntry
-
- compareTo(ThumbLoader.SeriesInfo) - Method in class loci.plugins.in.ThumbLoader.SeriesInfo
-
- compareTokens(String[], int, String[], int) - Method in class loci.formats.in.ICSReader
-
- COMPLEX - Static variable in class loci.formats.in.CellSensReader
-
- COMPLEX - Static variable in class loci.formats.in.ZeissCZIReader
-
- COMPLEX_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
-
- COMPONENT_HEIGHT - Static variable in class loci.formats.gui.CacheIndicator
-
- COMPONENT_WIDTH - Static variable in class loci.formats.gui.CacheIndicator
-
- COMPONENTS_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
-
- compress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec
-
2D data block encoding default implementation.
- compress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec
-
Compresses a block of data.
- compress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec
-
Compresses a block of data.
- compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
-
- compress(byte[], CodecOptions) - Method in class loci.formats.codec.NikonCodec
-
- compress(byte[], CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
-
- compress(byte[], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
-
- compress(byte[][], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
-
- compress(byte[]) - Method in class loci.formats.out.OMEXMLWriter
-
Compress the given byte array using the current codec.
- compress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
-
Encodes a strip of data.
- compress(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image associated with this compressor
instance and output a JPEG image to the given destination buffer.
- compress(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image associated with this compressor
instance and return a buffer containing a JPEG image.
- compress(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image stored in srcImage
and output a JPEG image to the given destination buffer.
- compress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image stored in srcImage
and return a buffer containing a JPEG image.
- compress(byte[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
- compress(int[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
- compressBuffer(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
-
Compresses the buffer.
- compressed - Variable in class loci.formats.in.NAFReader
-
- compressed - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
-
- compressed - Variable in class loci.formats.in.PSDReader
-
- compressed - Variable in class loci.formats.in.SBIGReader
-
- compressed - Variable in class loci.formats.in.TargaReader
-
- COMPRESSED_BITS_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
-
- compressedSize - Variable in class loci.formats.in.AmiraReader.HxRLE
-
- compressedSize - Variable in class loci.formats.in.AmiraReader.HxZip
-
- compressedSize - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
-
- compression - Variable in enum loci.formats.codec.CompressionType
-
The compression used.
- compression - Variable in class loci.formats.FormatWriter
-
Current compression type.
- compression - Variable in class loci.formats.in.AmiraReader
-
- compression - Variable in class loci.formats.in.APNGReader
-
- compression - Variable in class loci.formats.in.BMPReader
-
Compression type
- compression - Variable in class loci.formats.in.LiFlimReader
-
- compression - Variable in class loci.formats.in.OBFReader.Stack
-
- compression - Variable in class loci.formats.in.OMEXMLReader
-
- compression - Variable in class loci.formats.in.PhotoshopTiffReader
-
- compression - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
-
- COMPRESSION - Static variable in class loci.formats.tiff.IFD
-
- COMPRESSION_GZIP - Static variable in class loci.formats.in.LiFlimReader
-
- COMPRESSION_J2K - Static variable in class loci.formats.out.TiffWriter
-
- COMPRESSION_J2K_LOSSY - Static variable in class loci.formats.out.TiffWriter
-
- COMPRESSION_JPEG - Static variable in class loci.formats.out.TiffWriter
-
- COMPRESSION_KEY - Static variable in class loci.formats.in.LiFlimReader
-
- COMPRESSION_LZW - Static variable in class loci.formats.out.TiffWriter
-
- COMPRESSION_NONE - Static variable in class loci.formats.in.LiFlimReader
-
- COMPRESSION_SUFFIXES - Static variable in class loci.formats.FormatHandler
-
Suffixes for supported compression types.
- COMPRESSION_UNCOMPRESSED - Static variable in class loci.formats.out.TiffWriter
-
- CompressionType - Enum in loci.formats.codec
-
An enumeration of compression types.
- CompressionType(int, String) - Constructor for enum loci.formats.codec.CompressionType
-
Default constructor.
- compressionType - Variable in class loci.formats.in.CellSensReader
-
- compressionTypes - Variable in class loci.formats.FormatWriter
-
Available compression types.
- compressionTypes - Variable in class loci.formats.ImageWriter
-
Compression types for all file format writers.
- computeAxisLengths() - Method in class loci.formats.FileStitcher
-
Computes axis length arrays, and total axis lengths.
- computeIndices(int) - Method in class loci.formats.FileStitcher
-
Gets the file index, and image index into that file,
corresponding to the given global image index.
- computeNameAndLocation() - Method in class loci.plugins.in.ImportProcess
-
Initializes the idName and idLoc derived values.
- computePhysicalSize(int, String, String) - Method in class loci.formats.in.VarianFDFReader
-
Return the physical size of a pixel, in microns, along an arbitrary axis
based on the supplied physical and pixel lengths of the axis.
- computeSeriesLabels(IFormatReader) - Method in class loci.plugins.in.ImportProcess
-
- computeSizeT(int) - Method in class loci.formats.in.PrairieReader
-
Scans the parsed metadata to determine the number of actual time points
versus the number of actual stage positions.
- computeVariableTimeInterval(IMetadata, int) - Method in class loci.plugins.in.Calibrator
-
- concatenate(List<ImagePlus>) - Method in class loci.plugins.in.Concatenator
-
Concatenates the list of images as appropriate.
- concatenate(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
-
- concatenateBox - Variable in class loci.plugins.in.MainDialog
-
- concatenateTokens(String[], int, int) - Method in class loci.formats.in.ICSReader
-
- Concatenator - Class in loci.plugins.in
-
Logic for concatenating multiple images together.
- Concatenator() - Constructor for class loci.plugins.in.Concatenator
-
- config - Variable in class loci.formats.in.PrairieMetadata
-
Key/value pairs from CFG and/or ENV files.
- ConfigWindow - Class in loci.plugins.config
-
A window for managing configuration of the Bio-Formats plugins.
- ConfigWindow() - Constructor for class loci.plugins.config.ConfigWindow
-
- constructDialog() - Method in class loci.plugins.in.ColorDialog
-
- constructDialog() - Method in class loci.plugins.in.CropDialog
-
- constructDialog() - Method in class loci.plugins.in.FilePatternDialog
-
- constructDialog() - Method in class loci.plugins.in.IdDialog
-
- constructDialog() - Method in class loci.plugins.in.ImporterDialog
-
- constructDialog() - Method in class loci.plugins.in.LocationDialog
-
- constructDialog() - Method in class loci.plugins.in.MainDialog
-
- constructDialog() - Method in class loci.plugins.in.MemoryDialog
-
- constructDialog() - Method in class loci.plugins.in.RangeDialog
-
- constructDialog() - Method in class loci.plugins.in.SeriesDialog
-
- constructDialog() - Method in class loci.plugins.in.SwapDialog
-
- constructDialog() - Method in class loci.plugins.in.UpgradeDialog
-
- constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image with the given DataBuffer.
- constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image with the given DataBuffer.
- constructImageTitle(IFormatReader, String, String, boolean) - Method in class loci.plugins.in.ImagePlusReader
-
- constructLoader() - Static method in class loci.formats.gui.LegacyQTTools
-
- constructSliceLabel(int, IFormatReader, IMetadata, int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
-
- CONTAINER_TYPES - Static variable in class loci.formats.in.NativeQTReader
-
List of identifiers for each container atom.
- ContainerRecord(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.ContainerRecord
-
- contentFileType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
-
- contentGUID - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
-
- Context() - Constructor for enum loci.formats.in.BaseZeissReader.Context
-
- context - Variable in class loci.formats.in.BaseZeissReader.Tag
-
- CONTRAST - Static variable in class loci.formats.in.CellSensReader
-
- CONTRAST - Static variable in class loci.formats.tiff.IFD
-
- CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
-
- CONTRAST_TARGET - Static variable in class loci.formats.in.CellSensReader
-
- convert(String, String) - Static method in class loci.formats.FormatTools
-
Convenience method for converting the specified input file to the
specified output file.
- convert(IFormatReader, IFormatWriter, String) - Static method in class loci.formats.FormatTools
-
Convenience method for writing all of the images and metadata obtained
from the specified IFormatReader into the specified IFormatWriter.
- convert - Variable in class loci.formats.gui.DataConverter
-
- convertMetadata(MetadataRetrieve, MetadataStore) - Static method in class loci.formats.meta.MetadataConverter
-
Deprecated.
Copies information from a metadata retrieval object
(source) into a metadata store (destination).
- convertMetadata(String, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
-
Converts information from an OME-XML string (source)
into a metadata store (destination).
- convertMetadata(MetadataRetrieve, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
-
Copies information from a metadata retrieval object
(source) into a metadata store (destination).
- convertMetadata(String, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- convertMetadata(MetadataRetrieve, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- convertPixelType(int) - Method in class loci.formats.in.CellSensReader
-
- convertPixelType(int) - Method in class loci.formats.in.JPEG2000MetadataParser
-
- convertPixelType(int) - Method in class loci.formats.in.TillVisionReader
-
- convertPixelType(int) - Method in class loci.formats.in.ZeissCZIReader
-
- convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.ZeissCZIReader
-
- convertRenderedImage(RenderedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Converts a java.awt.image.RenderedImage into a
java.awt.image.BufferedImage.
- convertTo8Bit(short[][]) - Method in class loci.plugins.util.ImageProcessorReader
-
- convertToByte(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
-
- convertToFloat() - Method in class loci.plugins.util.RecordedImageProcessor
-
- convertToRGB() - Method in class loci.plugins.util.RecordedImageProcessor
-
- convertToShort(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
-
- convertUnits(String) - Method in class loci.formats.in.GatanReader
-
- convertUnits(int) - Method in class loci.formats.in.IMODReader
-
- convolve(float[], int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- convolve3x3(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
-
- COOKIE - Static variable in class loci.formats.in.IM3Reader
-
First 4 bytes of file is "1985"
- COOLING_ON - Static variable in class loci.formats.in.CellSensReader
-
- coordinate - Variable in class loci.formats.in.CellSensReader.TileCoordinate
-
- Coordinate(int, int, int) - Constructor for class loci.formats.in.ZeissCZIReader.Coordinate
-
- coordinates - Variable in class loci.formats.in.BaseZeissReader
-
- copyBits(ImageProcessor, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- copyOptions(CodecOptions, CodecOptions) - Static method in class loci.formats.codec.WrappedCodec
-
- copyPixels(int, int, int, int, int, int, byte[], byte[], boolean) - Method in class loci.formats.in.NativeND2Reader
-
- COPYRIGHT - Static variable in class loci.formats.tiff.IFD
-
- copyScaled(BufferedImage, BufferedImage, Object) - Static method in class loci.formats.gui.AWTImageTools
-
Copies the source image into the target, applying scaling.
- core - Variable in class loci.formats.DimensionSwapper
-
Core metadata associated with this dimension swapper.
- core - Variable in class loci.formats.FileStitcher
-
Core metadata.
- core - Variable in class loci.formats.FormatReader
-
Core metadata values.
- core - Variable in class loci.formats.in.LeicaHandler
-
- core - Variable in class loci.formats.in.ND2Handler
-
- core - Variable in class loci.formats.in.VolocityReader.Stack
-
- coreIndex - Variable in class loci.formats.FileStitcher
-
The number of the current series.
- coreIndex - Variable in class loci.formats.FormatReader
-
The number of the current series.
- coreIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- coreIndexToSeries(int) - Method in class loci.formats.FileStitcher
-
- coreIndexToSeries(int) - Method in class loci.formats.FormatReader
-
- coreIndexToSeries(int) - Method in interface loci.formats.IFormatReader
-
Returns the series corresponding to the specified core index.
- coreIndexToSeries(int) - Method in class loci.formats.ImageReader
-
- coreIndexToSeries(int) - Method in class loci.formats.in.FilePatternReader
-
- coreIndexToSeries(int) - Method in class loci.formats.ReaderWrapper
-
- CoreMetadata - Class in loci.formats
-
Encompasses core metadata values.
- CoreMetadata() - Constructor for class loci.formats.CoreMetadata
-
- CoreMetadata(IFormatReader, int) - Constructor for class loci.formats.CoreMetadata
-
- CoreMetadata(CoreMetadata) - Constructor for class loci.formats.CoreMetadata
-
- coreMetaData - Static variable in class loci.formats.in.SPEReader
-
- correction - Variable in class loci.formats.in.ND2Handler
-
- correction - Variable in class loci.formats.in.NikonTiffReader
-
- correction - Variable in class loci.formats.in.ZeissLSMReader.Recording
-
- correctionCollar - Variable in class loci.formats.in.ZeissCZIReader
-
- corrections - Variable in class loci.formats.in.LIFReader
-
- correctUnits(Double, String) - Method in class loci.formats.in.ColumbusReader
-
- cortime - Variable in class loci.formats.in.SDTInfo
-
Correlation time [ms].
- count - Variable in class loci.formats.in.LeicaHandler
-
- count() - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- count - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
-
- COUNTER_CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
-
- countImages() - Method in class loci.formats.in.BaseZeissReader
-
- countImages() - Method in class loci.formats.in.ZeissTIFFReader
-
- countImages() - Method in class loci.formats.in.ZeissZVIReader
-
- crc(byte[]) - Method in class loci.formats.out.APNGWriter
-
- crc(byte[], int, int) - Method in class loci.formats.out.APNGWriter
-
- createAngle(Double, Unit<Angle>) - Static method in class loci.formats.FormatTools
-
- createAngle(Integer, Unit<Angle>) - Static method in class loci.formats.FormatTools
-
- createAngle(T, Unit<Angle>) - Static method in class loci.formats.FormatTools
-
- createBaseReader() - Method in class loci.plugins.in.ImportProcess
-
Initializes an
IFormatReader
according to the current configuration.
- createChannelPriorities() - Static method in class loci.formats.in.LIFReader
-
- createCodec(boolean) - Method in class loci.formats.in.NativeND2Reader
-
- createColorModel() - Method in class loci.plugins.util.ImageProcessorReader
-
- createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.Index16ColorModel
-
- createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.SignedColorModel
-
- createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- created - Variable in class loci.formats.out.QTWriter
-
Time the file was created.
- createElectricPotential(Double, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
-
- createElectricPotential(Integer, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
-
- createElectricPotential(T, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
-
- createFileInfo() - Method in class loci.plugins.in.ImagePlusReader
-
- createFrequency(Double, Unit<Frequency>) - Static method in class loci.formats.FormatTools
-
- createFrequency(Integer, Unit<Frequency>) - Static method in class loci.formats.FormatTools
-
- createFrequency(T, Unit<Frequency>) - Static method in class loci.formats.FormatTools
-
- createGroup(String) - Method in interface loci.formats.services.JHDFService
-
Writes an array as sub-slice into an existing HDF5 dataset
- createGroup(String) - Method in class loci.formats.services.JHDFServiceImpl
-
- createImage(String, List<ImageProcessor>) - Static method in class loci.plugins.in.ImagePlusReader
-
Creates an ImagePlus from the given image processors.
- createImage(String, ImageStack, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
-
Creates an ImagePlus from the given image stack.
- createImage() - Method in class loci.plugins.util.RecordedImageProcessor
-
- createIndexMap(int) - Method in class loci.formats.in.FakeReader
-
Creates a mapping between indices and color values.
- createInputStream() - Method in class loci.formats.out.TiffWriter
-
- createKeys() - Static method in class loci.formats.in.ZeissLSMReader
-
- createLength(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
- createLength(Integer, Unit<Length>) - Static method in class loci.formats.FormatTools
-
- createLength(T, Unit<Length>) - Static method in class loci.formats.FormatTools
-
- createLSID(String, int...) - Static method in class loci.formats.MetadataTools
-
Constructs an LSID, given the object type and indices.
- createMetadata(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
-
- createModulo(OMEXMLMetadata, Modulo, StructuredAnnotations, Image, int, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Create a ModuloAlong* annotation corresponding to the given
Modulo.
- createOMEXMLMetadata() - Static method in class loci.formats.MetadataTools
-
Creates an OME-XML metadata object using reflection, to avoid
direct dependencies on the optional
loci.formats.ome package.
- createOMEXMLMetadata() - Method in interface loci.formats.services.OMEXMLService
-
Creates an OME-XML metadata object using reflection, to avoid
direct dependencies on the optional
loci.formats.ome package.
- createOMEXMLMetadata(String) - Method in interface loci.formats.services.OMEXMLService
-
Creates an OME-XML metadata object using reflection, to avoid
direct dependencies on the optional
loci.formats.ome package,
wrapping a DOM representation of the given OME-XML string.
- createOMEXMLMetadata(String, String) - Method in interface loci.formats.services.OMEXMLService
-
Creates an OME-XML metadata object using reflection, to avoid
direct dependencies on the optional
loci.formats.ome package,
wrapping a DOM representation of the given OME-XML string.
- createOMEXMLMetadata() - Method in class loci.formats.services.OMEXMLServiceImpl
-
- createOMEXMLMetadata(String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- createOMEXMLMetadata(String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- createOMEXMLRoot(String) - Method in interface loci.formats.services.OMEXMLService
-
Constructs an OME root node.
- createOMEXMLRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- createOutputStream() - Method in class loci.formats.FormatWriter
-
- createPlane(String, CoreMetadata, int) - Method in class loci.formats.tools.MakeTestOmeTiff
-
- createPower(Double, Unit<Power>) - Static method in class loci.formats.FormatTools
-
- createPower(Integer, Unit<Power>) - Static method in class loci.formats.FormatTools
-
- createPower(T, Unit<Power>) - Static method in class loci.formats.FormatTools
-
- createPressure(Double, Unit<Pressure>) - Static method in class loci.formats.FormatTools
-
- createPressure(Integer, Unit<Pressure>) - Static method in class loci.formats.FormatTools
-
- createPressure(T, Unit<Pressure>) - Static method in class loci.formats.FormatTools
-
- createProcessor(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- createRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Constructs an OME root node.
- createStack(List<ImageProcessor>, List<String>, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
-
Creates an image stack from the given image processors.
- createSwatch(Color) - Method in class loci.plugins.in.ColorDialog
-
- createTemperature(Double, Unit<Temperature>) - Static method in class loci.formats.FormatTools
-
- createTemperature(Integer, Unit<Temperature>) - Static method in class loci.formats.FormatTools
-
- createTemperature(T, Unit<Temperature>) - Static method in class loci.formats.FormatTools
-
- createTiffSaver() - Method in class loci.formats.out.TiffWriter
-
- createTime(Double, Unit<Time>) - Static method in class loci.formats.FormatTools
-
- createTime(Integer, Unit<Time>) - Static method in class loci.formats.FormatTools
-
- createTime(T, Unit<Time>) - Static method in class loci.formats.FormatTools
-
- createVirtualStack(ImportProcess, int, List<LUT>) - Method in class loci.plugins.in.ImagePlusReader
-
- createWriter(String, CoreMetadata, String) - Method in class loci.formats.tools.MakeTestOmeTiff
-
- CREATION_TIME - Static variable in class loci.formats.in.CellSensReader
-
- creationDate - Variable in class loci.formats.in.FV1000Reader
-
- creationDate - Variable in class loci.formats.in.ImaconReader
-
- creationDate - Variable in class loci.formats.in.InCellReader
-
- creationDate - Variable in class loci.formats.in.IvisionReader
-
- creationDate - Variable in class loci.formats.in.LeicaSCNReader.Image
-
- creationDate - Variable in class loci.formats.in.PCIReader
-
- CREATOR - Static variable in class loci.formats.FormatTools
-
Value to use when setting creator/software fields in exported files.
- CREATOR_TAG - Static variable in class loci.formats.in.ImaconReader
-
- crop() - Method in class loci.plugins.util.RecordedImageProcessor
-
- cropBox - Variable in class loci.plugins.in.MainDialog
-
- CropDialog - Class in loci.plugins.in
-
Bio-Formats Importer crop options dialog box.
- CropDialog(ImportProcess) - Constructor for class loci.plugins.in.CropDialog
-
Creates a crop options dialog for the Bio-Formats Importer.
- cropRegion - Variable in class loci.plugins.in.ImporterOptions
-
- crossChan - Variable in class loci.formats.in.SDTInfo
-
Cross FCS routing channel number
when chan = crossChan and mod == crossMod - Auto FCS
otherwise - Cross FCS.
- CrosshairStrategy - Class in loci.formats.cache
-
A crosshair strategy caches planes extending from the the current
dimensional position along each individual axis, but not combinations of
axes.
- CrosshairStrategy(int[]) - Constructor for class loci.formats.cache.CrosshairStrategy
-
Constructs a crosshair strategy.
- crossMod - Variable in class loci.formats.in.SDTInfo
-
Cross FCS module number.
- crossMtResol - Variable in class loci.formats.in.SDTInfo
-
Macro time clock of cross FCS module in 0.1 ns units.
- CS - Static variable in class loci.formats.in.DicomReader
-
- CS_2C - Static variable in class loci.formats.gui.TwoChannelColorSpace
-
- cScroll - Variable in class loci.plugins.util.DataBrowser
-
- cSlider - Variable in class loci.formats.gui.ImageViewer
-
- cSliders - Variable in class loci.plugins.util.DataBrowser
-
- cStep - Variable in class loci.plugins.in.ImporterOptions
-
- CSV_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
-
- curCycle - Variable in class loci.formats.in.SDTInfo
-
Current cycle (accumulation cycle in FLOW mode) -
(if multi-cycle measurement).
- curPage - Variable in class loci.formats.in.SDTInfo
-
Current measured page.
- current - Variable in class loci.formats.ImageReader
-
Current form index.
- current - Variable in class loci.formats.ImageWriter
-
Current form index.
- current_layer - Variable in class loci.formats.in.ZeissTIFFHandler
-
- current_scaling - Variable in class loci.formats.in.ZeissTIFFHandler
-
- current_shape - Variable in class loci.formats.in.ZeissTIFFHandler
-
- current_tag - Variable in class loci.formats.in.ZeissTIFFHandler
-
- current_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
-
- currentBlock - Variable in class loci.formats.in.APNGReader.PNGInputStream
-
- currentBlock - Variable in class loci.formats.in.PQBinReader
-
Block of time bins currently stored for faster loading.
- currentBlock - Variable in class loci.formats.in.SDTReader
-
Block of time bins currently stored for faster loading.
- currentCol - Variable in class loci.formats.in.InCellReader.InCellHandler
-
- currentElement - Variable in class loci.formats.in.AFIReader.AFIHandler
-
- currentElement - Variable in class loci.formats.in.IvisionReader.IvisionHandler
-
- currentField - Variable in class loci.formats.in.InCellReader.InCellHandler
-
- currentFile - Variable in class loci.formats.services.JHDFServiceImpl
-
- currentFile - Variable in class loci.formats.services.NetCDFServiceImpl
-
- currentFragment - Variable in class loci.formats.out.OMEXMLWriter
-
- currentFrame - Variable in class loci.formats.in.SPCReader
-
- currentIcsId - Variable in class loci.formats.in.ICSReader
-
Current filename.
- currentId - Variable in class loci.formats.FormatHandler
-
Name of current file.
- currentId - Variable in class loci.formats.ImageReader
-
Name of current file.
- currentId - Variable in class loci.formats.ImageWriter
-
Name of current file.
- currentIdsId - Variable in class loci.formats.in.ICSReader
-
- currentImage - Variable in class loci.formats.in.InCellReader.InCellHandler
-
- currentImage - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- currentImageFile - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
-
- currentInflatedFrame - Variable in class loci.formats.in.OBFReader
-
- currentLine - Variable in class loci.formats.in.SPCReader
-
- currentName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- currentName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- currentNo - Variable in class loci.formats.in.AmiraReader.HxRLE
-
- currentNo - Variable in class loci.formats.in.AmiraReader.HxZip
-
- currentPixel - Variable in class loci.formats.in.SPCReader
-
- currentPlane - Variable in class loci.formats.in.InCellReader.InCellHandler
-
- currentPos - Variable in class loci.formats.cache.Cache
-
Current dimensional position.
- currentProcessor - Variable in class loci.plugins.util.BFVirtualStack
-
- currentQName - Variable in class loci.formats.in.InCellReader.InCellHandler
-
- currentQName - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
-
- currentRow - Variable in class loci.formats.in.InCellReader.InCellHandler
-
- currentSlice - Variable in class loci.plugins.util.BFVirtualStack
-
- currentThumbnail - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
-
- currentValue - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- currentValue - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- currentValue - Variable in class loci.formats.in.ScanrReader.ScanrHandler
-
- curStep - Variable in class loci.formats.in.SDTInfo
-
Current step (if multi-step measurement).
- curve - Variable in class loci.formats.codec.NikonCodecOptions
-
- CURVE - Static variable in class loci.formats.in.NikonReader
-
- curve - Variable in class loci.formats.in.NikonReader
-
- CUSTOM_BITS - Static variable in class loci.formats.in.SimplePCITiffReader
-
- CUSTOM_GRAYSCALE - Static variable in class loci.formats.in.CellSensReader
-
- CUSTOM_RENDERED - Static variable in class loci.formats.tiff.IFD
-
- customColors - Variable in class loci.plugins.in.ImporterOptions
-
- customFilter(ShortBuffer, Rectangle, Rectangle, int, int, TJTransform) - Method in interface org.libjpegturbo.turbojpeg.TJCustomFilter
-
A callback function that can be used to modify the DCT coefficients after
they are losslessly transformed but before they are transcoded to a new
JPEG file.
- cutIn - Variable in class loci.formats.in.LeicaHandler.MultiBand
-
- cutInPopulated - Variable in class loci.formats.in.LeicaReader
-
- cutIns - Variable in class loci.formats.in.LIFReader
-
- cutOut - Variable in class loci.formats.in.LeicaHandler.MultiBand
-
- cutOutPopulated - Variable in class loci.formats.in.LeicaReader
-
- cutOuts - Variable in class loci.formats.in.LIFReader
-
- cycle - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
cycle of this <Sequence>.
- cycleMax - Variable in class loci.formats.in.PrairieMetadata
-
Maximum cycle value.
- cycleMin - Variable in class loci.formats.in.PrairieMetadata
-
Minimum cycle value.
- cycles - Variable in class loci.formats.in.SDTInfo
-
Cycles (accumulation cycles in FLOW mode).
- CYTELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
-
- CZI_MAGIC_STRING - Static variable in class loci.formats.in.ZeissCZIReader
-
- F_KEY - Static variable in class loci.formats.in.LiFlimReader
-
- F_NUMBER - Static variable in class loci.formats.tiff.IFD
-
- factor - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
-
- factors - Variable in class loci.formats.in.FlexReader.FlexFile
-
- factors - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- factory - Variable in class loci.formats.FormatReader
-
- FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.CellSensReader
-
- FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.CellSensReader
-
- failOnMissingETS() - Method in class loci.formats.in.CellSensReader
-
- FAKE_EXT - Static variable in class loci.formats.ResourceNamer
-
- fakeBigTiff - Variable in class loci.formats.tiff.TiffParser
-
Whether or not 64-bit offsets are used for non-BigTIFF files.
- FakeImage - Class in loci.formats.tools
-
Generates fake image structures.
- FakeImage(Location) - Constructor for class loci.formats.tools.FakeImage
-
- FakeReader - Class in loci.formats.in
-
FakeReader is the file format reader for faking input data.
- FakeReader() - Constructor for class loci.formats.in.FakeReader
-
Constructs a new fake reader.
- fakeSeries - Variable in class loci.formats.in.FakeReader
-
List of used files if the fake is a SPW structure
- falseColor - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not we can ignore the color map (if present).
- FAN_SPEED - Static variable in class loci.formats.in.CellSensReader
-
- fb - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- fcc - Variable in class loci.formats.in.AVIReader
-
- FCS_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
-
For .sdt files created in FIFO mode
(setup, data blocks = Decay, FCS, FIDA, FILDA & MCS curves
for each used routing channel).
- fcsDecayCalc - Variable in class loci.formats.in.SDTInfo
-
Bit 0 = 1 - decay curve calculated.
- fcsPoints - Variable in class loci.formats.in.SDTInfo
-
No of FCS values.
- fcsType - Variable in class loci.formats.in.SDTInfo
-
0 - linear FCS with log binning (100 bins/log)
when bit 15 = 1 (0x8000) - Multi-Tau FCS
where bits 14-0 = ktau parameter.
- fctlCount - Variable in class loci.formats.in.APNGReader.PNGInputStream
-
- FD - Static variable in class loci.formats.in.DicomReader
-
- fdatValid - Variable in class loci.formats.in.APNGReader.PNGInputStream
-
- FEATURE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- FeatureType(int, int) - Constructor for enum loci.formats.in.BaseZeissReader.FeatureType
-
- FEI_MAGIC_STRING - Static variable in class loci.formats.in.FEIReader
-
- FEIHandler() - Constructor for class loci.formats.in.FEITiffReader.FEIHandler
-
- FEIReader - Class in loci.formats.in
-
FEIReader is the file format reader for FEI and Philips .img files.
- FEIReader() - Constructor for class loci.formats.in.FEIReader
-
Constructs a new FEI reader.
- FEITiffReader - Class in loci.formats.in
-
FEITiffReader is the file format reader for TIFF files produced by various
FEI software.
- FEITiffReader() - Constructor for class loci.formats.in.FEITiffReader
-
- FEITiffReader.FEIHandler - Class in loci.formats.in
-
- fetchRow(MdbTableDef) - Method in class loci.formats.services.MDBServiceImpl
-
Fetches the next row from the table, ignoring potential parsing exceptions.
- fidaPoints - Variable in class loci.formats.in.SDTInfo
-
No of FIDA values.
- fidaTime - Variable in class loci.formats.in.SDTInfo
-
Interval time [ms] for FIDA histogram.
- field - Variable in class loci.formats.in.ColumbusReader.Plane
-
- field - Variable in class loci.formats.in.FlexReader.FlexFile
-
- field - Variable in class loci.formats.in.OperettaReader.Plane
-
- FIELD - Static variable in class loci.formats.ResourceNamer
-
- FIELD_AUX_FLAGS - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_BAND_INDEX - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_BANDS - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_CLASS_ID - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_DATA - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_DATA_SET - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_EXPOSURE - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_FILE_VERSION - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_FILTER_PAIR - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_FIXED_FILTER - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_HOMOGENEOUS - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_INDEX - Static variable in class loci.formats.in.ND2Handler
-
- FIELD_MAGNITUDES - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_MANUFACTURER - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_MILLIMETERS_PER_PIXEL - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_NAME - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_NUANCE_FLAGS - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_OBJECTIVE - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_PART_NUMBER - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_PROTOCOL - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_PROXY_PARENT_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_SAMPLE_ID - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_SHAPE - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_SOURCE_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_SPECTRA - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_SPECTRAL_BASIS_INFO - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_SPECTRAL_LIBRARY - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_SPECTRUM - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_THUMBNAIL - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_TIMESTAMP - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_TYPE - Static variable in class loci.formats.in.CellSensReader
-
- FIELD_TYPE_ID - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_USER_COMMENTS - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_VALUES - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_WAVELENGTH - Static variable in class loci.formats.in.IM3Reader
-
- FIELD_WAVELENGTHS - Static variable in class loci.formats.in.IM3Reader
-
- fieldCol - Variable in class loci.formats.in.MetamorphTiffReader.Well
-
- fieldCols - Variable in class loci.formats.in.BDReader
-
- fieldColumnCount - Variable in class loci.formats.in.MetamorphTiffReader
-
- fieldColumns - Variable in class loci.formats.in.ScanrReader
-
- fieldCount - Variable in class loci.formats.in.CellWorxReader
-
- fieldCount - Variable in class loci.formats.in.FlexReader
-
- fieldCount - Variable in class loci.formats.in.InCellReader
-
- fieldIndex - Variable in class loci.formats.in.FluoviewReader
-
- fieldIndex - Variable in class loci.formats.in.NativeND2Reader
-
- FieldInfo() - Constructor for class loci.formats.in.CellVoyagerReader.FieldInfo
-
- fieldMap - Variable in class loci.formats.in.CellWorxReader
-
- fieldOffsets - Variable in class loci.formats.in.FluoviewReader
-
- fieldPositionX - Variable in class loci.formats.in.ScanrReader
-
- fieldPositionY - Variable in class loci.formats.in.ScanrReader
-
- fieldPosX - Variable in class loci.formats.in.LIFReader
-
- fieldPosY - Variable in class loci.formats.in.LIFReader
-
- fieldRow - Variable in class loci.formats.in.MetamorphTiffReader.Well
-
- fieldRowCount - Variable in class loci.formats.in.MetamorphTiffReader
-
- fieldRows - Variable in class loci.formats.in.BDReader
-
- fieldRows - Variable in class loci.formats.in.ScanrReader
-
- fields - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
-
- fifoTyp - Variable in class loci.formats.in.SDTInfo
-
- fildaPoints - Variable in class loci.formats.in.SDTInfo
-
No of FILDA values.
- fildaTime - Variable in class loci.formats.in.SDTInfo
-
Interval time [ms] for FILDA histogram.
- file - Variable in class loci.formats.in.ColumbusReader.Plane
-
- file - Variable in class loci.formats.in.FlexReader.FlexFile
-
- file - Variable in class loci.formats.tools.EditTiffG
-
- FILE_LENGTH - Static variable in class loci.formats.in.CanonRawReader
-
- FILE_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
-
- FILE_SOURCE - Static variable in class loci.formats.tiff.IFD
-
- fileBox - Variable in class loci.formats.tools.EditTiffG
-
- fileGroupOption(String) - Method in class loci.formats.FormatReader
-
- fileGroupOption(String) - Method in interface loci.formats.IFormatReader
-
Returns an int indicating that we cannot, must, or might group the files
in a given dataset.
- fileGroupOption(String) - Method in class loci.formats.ImageReader
-
- fileGroupOption(String) - Method in class loci.formats.in.AFIReader
-
- fileGroupOption(String) - Method in class loci.formats.in.AnalyzeReader
-
- fileGroupOption(String) - Method in class loci.formats.in.APLReader
-
- fileGroupOption(String) - Method in class loci.formats.in.BDReader
-
- fileGroupOption(String) - Method in class loci.formats.in.BioRadReader
-
- fileGroupOption(String) - Method in class loci.formats.in.BrukerReader
-
- fileGroupOption(String) - Method in class loci.formats.in.CellomicsReader
-
- fileGroupOption(String) - Method in class loci.formats.in.CellSensReader
-
- fileGroupOption(String) - Method in class loci.formats.in.CellVoyagerReader
-
- fileGroupOption(String) - Method in class loci.formats.in.ColumbusReader
-
- fileGroupOption(String) - Method in class loci.formats.in.DicomReader
-
- fileGroupOption(String) - Method in class loci.formats.in.FlexReader
-
- fileGroupOption(String) - Method in class loci.formats.in.FujiReader
-
- fileGroupOption(String) - Method in class loci.formats.in.FV1000Reader
-
- fileGroupOption(String) - Method in class loci.formats.in.HitachiReader
-
- fileGroupOption(String) - Method in class loci.formats.in.ICSReader
-
- fileGroupOption(String) - Method in class loci.formats.in.ImagicReader
-
- fileGroupOption(String) - Method in class loci.formats.in.InCellReader
-
- fileGroupOption(String) - Method in class loci.formats.in.L2DReader
-
- fileGroupOption(String) - Method in class loci.formats.in.LeicaReader
-
- fileGroupOption(String) - Method in class loci.formats.in.MetamorphReader
-
- fileGroupOption(String) - Method in class loci.formats.in.MIASReader
-
- fileGroupOption(String) - Method in class loci.formats.in.MicromanagerReader
-
- fileGroupOption(String) - Method in class loci.formats.in.NDPIReader
-
- fileGroupOption(String) - Method in class loci.formats.in.NDPISReader
-
- fileGroupOption(String) - Method in class loci.formats.in.NiftiReader
-
- fileGroupOption(String) - Method in class loci.formats.in.NRRDReader
-
- fileGroupOption(String) - Method in class loci.formats.in.OMETiffReader
-
- fileGroupOption(String) - Method in class loci.formats.in.OperettaReader
-
- fileGroupOption(String) - Method in class loci.formats.in.PerkinElmerReader
-
- fileGroupOption(String) - Method in class loci.formats.in.PrairieReader
-
- fileGroupOption(String) - Method in class loci.formats.in.ScanrReader
-
- fileGroupOption(String) - Method in class loci.formats.in.ScreenReader
-
- fileGroupOption(String) - Method in class loci.formats.in.SPCReader
-
- fileGroupOption(String) - Method in class loci.formats.in.SVSReader
-
- fileGroupOption(String) - Method in class loci.formats.in.TCSReader
-
- fileGroupOption(String) - Method in class loci.formats.in.TillVisionReader
-
- fileGroupOption(String) - Method in class loci.formats.in.TrestleReader
-
- fileGroupOption(String) - Method in class loci.formats.in.VisitechReader
-
- fileGroupOption(String) - Method in class loci.formats.in.ZeissLSMReader
-
- fileGroupOption(String) - Method in class loci.formats.in.ZeissTIFFReader
-
- fileGroupOption(String) - Method in class loci.formats.ReaderWrapper
-
- fileGroupOption(String, String[]) - Method in class loci.plugins.macro.LociFunctions
-
- fileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
-
- FileHeader() - Constructor for class loci.formats.in.ZeissCZIReader.FileHeader
-
- fileIndex - Variable in class loci.formats.in.ColumbusReader.Plane
-
- FileInfo - Class in loci.formats
-
Encompasses basic metadata about a file.
- FileInfo() - Constructor for class loci.formats.FileInfo
-
- FILEINFO_STRING - Static variable in class loci.formats.in.KodakReader
-
- fileLength - Variable in class loci.formats.in.LeicaReader
-
Length of each file name.
- fileList - Variable in class loci.formats.in.DicomReader
-
- fileMap - Variable in class loci.formats.in.CellSensReader
-
- filename - Variable in class loci.formats.FileInfo
-
Absolute path to this file.
- filename - Variable in class loci.formats.gui.ImageViewer
-
- filename - Variable in class loci.formats.in.InCellReader.Image
-
- filename - Variable in class loci.formats.in.MIASReader.AnalysisFile
-
- filename - Variable in class loci.formats.in.OperettaReader.Plane
-
- filename - Variable in class loci.formats.in.PrairieMetadata.PFile
-
filename attribute of this <File>.
- filename - Variable in class loci.formats.in.ZeissCZIReader.Segment
-
- filename - Variable in class loci.formats.in.ZeissTIFFReader.Plane
-
- filename - Variable in class loci.formats.tiff.TiffSaver
-
Output filename.
- fileNameMap - Variable in class loci.formats.in.MicromanagerReader.Position
-
- filenames - Variable in class loci.formats.in.FV1000Reader
-
- filePart - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
-
- filePart - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
-
- filePart - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
-
- filePath - Variable in class loci.formats.services.POIServiceImpl
-
- FilePattern - Class in loci.formats
-
Represents a collection of files meant to be part of the same
data series.
- FilePattern(Location) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object using the given file as a template.
- FilePattern(String, String) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object using the given
filename and directory path as a template.
- FilePattern(String) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object for files with the given pattern string.
- FilePatternBlock - Class in loci.formats
-
FilePatternBlock represents a single block in a
FilePattern.
- FilePatternBlock(String) - Constructor for class loci.formats.FilePatternBlock
-
Builds a FilePatternBlock from a block string.
- FilePatternDialog - Class in loci.plugins.in
-
Bio-Formats Importer file pattern dialog box.
- FilePatternDialog(ImportProcess) - Constructor for class loci.plugins.in.FilePatternDialog
-
Creates a file pattern dialog for the Bio-Formats Importer.
- FilePatternReader - Class in loci.formats.in
-
- FilePatternReader() - Constructor for class loci.formats.in.FilePatternReader
-
Constructs a new pattern reader.
- filePosition - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
-
- filePosition - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
-
- fileReader - Variable in class loci.formats.gui.ImageViewer
-
Reader for files on disk.
- files - Variable in class loci.formats.FilePattern
-
File listing for this file pattern.
- files - Variable in class loci.formats.FileStitcher.ExternalSeries
-
- files - Variable in class loci.formats.in.CellomicsReader
-
- files - Variable in class loci.formats.in.HamamatsuVMSReader
-
- files - Variable in class loci.formats.in.ImprovisionTiffReader
-
- files - Variable in class loci.formats.in.LeicaReader
-
Array of image file names.
- files - Variable in class loci.formats.in.MetamorphTiffReader
-
- files - Variable in class loci.formats.in.PerkinElmerReader
-
List of files to open.
- files - Variable in class loci.formats.in.PrairieMetadata.Frame
-
<File> elements beneath this <Frame>, keyed on each
file's channel.
- files - Variable in class loci.formats.in.SlidebookTiffReader
-
- files - Variable in class loci.formats.in.TrestleReader
-
- files - Variable in class loci.formats.in.VarianFDFReader
-
- files - Variable in class loci.formats.in.VisitechReader
-
Files in this dataset.
- files - Variable in class loci.formats.in.ZeissZVIReader
-
- files - Variable in class loci.formats.services.POIServiceImpl
-
- fileSave - Variable in class loci.formats.gui.ImageViewer
-
- fileSizes - Variable in class loci.formats.services.POIServiceImpl
-
- FileStitcher - Class in loci.formats
-
Logic to stitch together files with similar names.
- FileStitcher() - Constructor for class loci.formats.FileStitcher
-
Constructs a FileStitcher around a new image reader.
- FileStitcher(boolean) - Constructor for class loci.formats.FileStitcher
-
Constructs a FileStitcher around a new image reader.
- FileStitcher(IFormatReader) - Constructor for class loci.formats.FileStitcher
-
Constructs a FileStitcher with the given reader.
- FileStitcher(IFormatReader, boolean) - Constructor for class loci.formats.FileStitcher
-
Constructs a FileStitcher with the given reader.
- fileStitcher - Variable in class loci.plugins.in.ImportProcess
-
- FileStitcher.ExternalSeries - Class in loci.formats
-
- fileSystem - Variable in class loci.formats.services.POIServiceImpl
-
- fileView - Variable in class loci.formats.gui.ImageViewer
-
- fileWriter - Variable in class loci.formats.gui.ImageViewer
-
Writer for files on disk.
- fill() - Method in class loci.plugins.util.RecordedImageProcessor
-
- fill(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
-
- FILL_ORDER - Static variable in class loci.formats.tiff.IFD
-
- fillAcquisitionDate(MetadataStore, String, int) - Method in class loci.formats.in.FakeReader
-
- fillAnnotations(MetadataStore, int) - Method in class loci.formats.in.FakeReader
-
- fillColour - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- filled - Variable in class loci.formats.ChannelFiller
-
Whether to fill in the indices.
- fillExposureTime(MetadataStore) - Method in class loci.formats.in.FakeReader
-
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.Attachment
-
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
-
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.Directory
-
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.FileHeader
-
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
-
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.Segment
-
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
-
- fillInIFD(IFD) - Method in class loci.formats.tiff.TiffParser
-
Fill in IFD entries that are stored at an arbitrary offset.
- fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
-
- fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
-
- fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
-
- fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
-
- fillMetadataPass4(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
-
- fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
-
- fillMetadataPass6(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass7(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Store basic dimensions in model
- fillOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- fillPhysicalSizes(MetadataStore) - Method in class loci.formats.in.FakeReader
-
- fillPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
-
- fillRegions(MetadataStore, int) - Method in class loci.formats.in.FakeReader
-
- FillStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.FillStyle
-
- fillStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- filter - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
-
- filter - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
-
- filter(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- FilterGroup() - Constructor for class loci.formats.in.FlexReader.FilterGroup
-
- filterMap - Variable in class loci.formats.in.FlexReader
-
- filterMetadata - Variable in class loci.formats.FormatReader
-
Whether or not to filter out invalid metadata.
- FilterMetadata - Class in loci.formats.meta
-
- FilterMetadata(MetadataStore, boolean) - Constructor for class loci.formats.meta.FilterMetadata
-
- filterModels - Variable in class loci.formats.in.LIFReader
-
- filterModels - Variable in class loci.formats.in.NikonTiffReader
-
- filterRefPopulated - Variable in class loci.formats.in.LeicaReader
-
- filterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- FILTERSET - Static variable in class loci.formats.in.LeicaReader
-
- filterSet - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
-
- filterSet - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
-
- filterSetMap - Variable in class loci.formats.in.FlexReader
-
- filterSetRef - Variable in class loci.formats.in.ZeissCZIReader.Channel
-
- filterSets - Variable in class loci.formats.in.FlexReader
-
- filts - Variable in class loci.formats.gui.ComboFileFilter
-
List of filters to be combined.
- finalize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
- finalize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
- find(String[]) - Method in class loci.formats.in.PrairieReader
-
Finds the first file with one of the given suffixes.
- find(String, String) - Static method in class loci.plugins.Updater
-
- findChildWithID(Node, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Return the child node with specified value for the "ID" attribute.
- findEdges() - Method in class loci.plugins.util.RecordedImageProcessor
-
- findFiles(Location) - Method in class loci.formats.in.FlexReader
-
Search for files that correspond to the given file.
- findFiles(Location, String[]) - Method in class loci.formats.in.FlexReader
-
- findImages(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
-
- findKeyValue(String[], String[][]) - Method in class loci.formats.in.ICSReader
-
- findKeyValueForCategory(String[], String[][]) - Method in class loci.formats.in.ICSReader
-
- findKeyValueOther(String[], String[][]) - Method in class loci.formats.in.ICSReader
-
- findLEIFile(String) - Method in class loci.formats.in.LeicaReader
-
Find the .lei file that belongs to the same dataset as the given file.
- findLogFiles() - Method in class loci.formats.in.DeltavisionReader
-
Find the log files.
- findLogFiles() - Method in class loci.formats.in.FakeReader
-
- findMetadataFiles() - Method in class loci.formats.in.PrairieReader
-
- findNextBlock() - Method in class loci.formats.in.OpenlabReader
-
- findNextOffset(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
-
- findNextOffset(RandomAccessInputStream, byte[]) - Method in class loci.formats.in.TillVisionReader
-
- findOffset() - Method in class loci.formats.in.ImspectorReader
-
Find the offset to the next block of pixel data.
- findOffset(boolean) - Method in class loci.formats.in.ImspectorReader
-
- findOIFFile(String) - Method in class loci.formats.in.FV1000Reader
-
- findPattern(String) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPattern(Location) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPattern(File) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPattern(String, String) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given filename and directory.
- findPattern(String, String, String[]) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given filename, directory and
list of candidate filenames.
- findPattern(String, String, String[], int[]) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given filename, directory and
list of candidate filenames.
- findPattern(String[]) - Static method in class loci.formats.FilePattern
-
Generate a pattern from a list of file names.
- findPattern(String, String[], int, int, String) - Static method in class loci.formats.FilePattern
-
- findPattern(String) - Method in class loci.formats.FileStitcher
-
- findPatterns(String) - Method in class loci.formats.FileStitcher
-
Finds the file pattern for the given ID, based on the state of the file
stitcher.
- findPixelOffsets() - Method in class loci.formats.in.JPXReader
-
- findPixelsOffset(int) - Method in class loci.formats.in.VisitechReader
-
- findRootNode(Node) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Return the absolute root node for the specified child node.
- findSeriesPatterns(String) - Static method in class loci.formats.FilePattern
-
- findSeriesPatterns(String, String, String[]) - Static method in class loci.formats.FilePattern
-
- findString(String) - Method in class loci.formats.in.KodakReader
-
- findTIFFs() - Method in class loci.formats.in.MetamorphTiffReader
-
- findXML(String) - Static method in class loci.formats.in.ColumbusReader
-
- finish(ImportProcess) - Method in class loci.plugins.in.Importer
-
- finishTime - Variable in class loci.formats.in.PerkinElmerReader
-
- finishTiming() - Method in class loci.plugins.in.ImagePlusReader
-
- FIRMWARE_VERSION - Static variable in class loci.formats.in.NikonReader
-
- firstAvailable(int...) - Method in class loci.plugins.in.SwapDialog
-
- firstDataStream - Variable in class loci.formats.tools.AmiraParameters
-
- firstFile - Variable in class loci.formats.in.PrairieMetadata.Frame
-
The first actual <File> element for this <Frame>.
- firstFrame - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
The first actual <Frame> element for this <Sequence>.
- firstIFD - Variable in class loci.formats.tiff.TiffParser
-
Cached first IFD in the current file.
- firstIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
-
- firstSequence - Variable in class loci.formats.in.PrairieMetadata
-
The first actual <Sequence> element.
- firstSeriesChannels - Variable in class loci.formats.in.MetamorphReader
-
- firstStamp - Variable in class loci.formats.in.LeicaHandler
-
- firstTimeLoop - Variable in class loci.formats.in.ND2Handler
-
- firstWellPlanes() - Method in class loci.formats.in.FlexReader
-
Returns the number of planes in the first well that has data.
- fis - Variable in class loci.formats.Memoizer.KryoDeser
-
- FitsReader - Class in loci.formats.in
-
FitsReader is the file format reader for
Flexible Image Transport System (FITS) images.
- FitsReader() - Constructor for class loci.formats.in.FitsReader
-
Constructs a new FitsReader.
- fixed - Variable in class loci.formats.FilePatternBlock
-
Whether or not this is a fixed-width block.
- FL - Static variable in class loci.formats.in.DicomReader
-
- FLAG_ACCURATEDCT - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Use the most accurate DCT/IDCT algorithm available in the underlying
codec.
- FLAG_BOTTOMUP - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
The uncompressed source/destination image is stored in bottom-up (Windows,
OpenGL) order, not top-down (X11) order.
- FLAG_FASTDCT - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Use the fastest DCT/IDCT algorithm available in the underlying codec.
- FLAG_FASTUPSAMPLE - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
When decompressing, use the fastest chrominance upsampling algorithm
available in the underlying codec.
- FLAG_FORCEMMX - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Turn off CPU auto-detection and force TurboJPEG to use MMX code
(if the underlying codec supports it.)
- FLAG_FORCESSE - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Turn off CPU auto-detection and force TurboJPEG to use SSE code
(if the underlying codec supports it.)
- FLAG_FORCESSE2 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Turn off CPU auto-detection and force TurboJPEG to use SSE2 code
(if the underlying codec supports it.)
- FLAG_FORCESSE3 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Turn off CPU auto-detection and force TurboJPEG to use SSE3 code
(if the underlying codec supports it.)
- flags - Variable in class loci.formats.in.BaseZeissReader.Layer
-
- flags - Variable in class loci.formats.in.SDTInfo
-
Scan clocks bits 2-0 (frame, line, pixel), rates_read - bit 15.
- FLASH - Static variable in class loci.formats.tiff.IFD
-
- FLASH_COMPENSATION - Static variable in class loci.formats.in.NikonReader
-
- FLASH_ENERGY - Static variable in class loci.formats.tiff.IFD
-
- FLASH_MODE - Static variable in class loci.formats.in.NikonReader
-
- FLASH_PIX_VERSION - Static variable in class loci.formats.tiff.IFD
-
- FLASH_SETTING - Static variable in class loci.formats.in.NikonReader
-
- FLASH_USED - Static variable in class loci.formats.in.NikonReader
-
- flattenedResolutions - Variable in class loci.formats.FormatReader
-
Whether or not resolutions are flattened.
- flattenHashtables() - Method in class loci.formats.FormatReader
-
- flbckX - Variable in class loci.formats.in.SDTInfo
-
- flbckY - Variable in class loci.formats.in.SDTInfo
-
- FLEX - Static variable in class loci.formats.in.FlexReader
-
Custom IFD entry for Flex XML.
- flex - Variable in class loci.formats.in.FlexReader.MeaHandler
-
- FLEX_SUFFIX - Static variable in class loci.formats.in.FlexReader
-
- FlexFile() - Constructor for class loci.formats.in.FlexReader.FlexFile
-
- flexFiles - Variable in class loci.formats.in.FlexReader
-
- FlexHandler(List<String>, List<String>, MetadataStore, boolean, int, int) - Constructor for class loci.formats.in.FlexReader.FlexHandler
-
- FlexReader - Class in loci.formats.in
-
FlexReader is a file format reader for Evotec Flex files.
- FlexReader() - Constructor for class loci.formats.in.FlexReader
-
Constructs a new Flex reader.
- FlexReader.FilterGroup - Class in loci.formats.in
-
Stores a grouping of filters.
- FlexReader.FlexFile - Class in loci.formats.in
-
- FlexReader.FlexHandler - Class in loci.formats.in
-
SAX handler for parsing XML.
- FlexReader.MeaHandler - Class in loci.formats.in
-
SAX handler for parsing XML from .mea files.
- FlexReader.ResHandler - Class in loci.formats.in
-
SAX handler for parsing XML from .res files.
- FlexWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats Flex support.
- FlexWidgets() - Constructor for class loci.plugins.config.FlexWidgets
-
- FLIM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the fluorescence-lifetime domain.
- flip - Variable in class loci.formats.in.NativeQTReader
-
- flipHorizontal() - Method in class loci.plugins.util.RecordedImageProcessor
-
- flipVertical() - Method in class loci.plugins.util.RecordedImageProcessor
-
- FLOAT - Static variable in class loci.formats.FormatTools
-
Identifies the FLOAT data type used to store pixel values.
- FLOAT - Static variable in class loci.formats.in.CellSensReader
-
- FLOAT - Static variable in class loci.formats.in.GatanReader
-
- FLOAT - Static variable in class loci.formats.in.SPEReader
-
- FloatIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.FloatIM3Record
-
- floatValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as a float.
- FLOW_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
-
For .sdt files created automatically in Continuous Flow mode measurement
(no setup, only data).
- FlowSightReader - Class in loci.formats.in
-
- FlowSightReader() - Constructor for class loci.formats.in.FlowSightReader
-
- fluor - Variable in class loci.formats.in.ZeissCZIReader.Channel
-
- FLUOVIEW_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
-
String identifying a Fluoview file.
- FluoviewReader - Class in loci.formats.in
-
FluoviewReader is the file format reader for
Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.
- FluoviewReader() - Constructor for class loci.formats.in.FluoviewReader
-
Constructs a new Fluoview TIFF reader.
- flush() - Method in class loci.plugins.config.TextAreaWriter
-
Flushing a TextAreaWriter does nothing .
- fmt - Variable in class loci.formats.in.GelReader
-
- fmt - Variable in class loci.formats.in.OpenlabReader
-
- FOCAL_LENGTH - Static variable in class loci.formats.tiff.IFD
-
- FOCAL_LENGTH_35MM_FILM - Static variable in class loci.formats.tiff.IFD
-
- FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
-
- FOCAL_PLANE_X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
-
- FOCAL_PLANE_Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
-
- FOCUS_IMAGE - Static variable in class loci.formats.in.CellSensReader
-
- FOCUS_MODE - Static variable in class loci.formats.in.NikonReader
-
- focusGained(FocusEvent) - Method in class loci.plugins.in.MainDialog
-
Handles information pane updates when component focus changes.
- focusLost(FocusEvent) - Method in class loci.plugins.in.MainDialog
-
- font - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
-
- fontName - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- fontName - Variable in class loci.formats.in.LeicaHandler.ROI
-
- fontName - Variable in class loci.formats.in.LIFReader.ROI
-
- fontSize - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- fontSize - Variable in class loci.formats.in.GatanReader.ROIShape
-
- fontSize - Variable in class loci.formats.in.LeicaHandler.ROI
-
- fontSize - Variable in class loci.formats.in.LIFReader.ROI
-
- fontWeight - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- FOOTER_SIZE - Static variable in class loci.formats.in.SIFReader
-
- footerPointer - Variable in class loci.formats.out.APNGWriter
-
- force - Variable in class loci.formats.gui.DataConverter
-
- forceType - Variable in class loci.formats.gui.DataConverter
-
- forkFile - Variable in class loci.formats.in.NativeQTReader
-
- format - Variable in class loci.formats.FormatHandler
-
Name of this file format.
- formatCompression(IFD) - Method in class loci.formats.out.TiffWriter
-
Sets the compression code for the specified IFD.
- FormatEntry - Class in loci.plugins.config
-
A list entry for the configuration window's Formats tab.
- FormatEntry(PrintWriter, Object) - Constructor for class loci.plugins.config.FormatEntry
-
- FormatException - Exception in loci.formats
-
FormatException is the exception thrown when something
goes wrong performing a file format operation.
- FormatException() - Constructor for exception loci.formats.FormatException
-
- FormatException(String) - Constructor for exception loci.formats.FormatException
-
- FormatException(String, Throwable) - Constructor for exception loci.formats.FormatException
-
- FormatException(Throwable) - Constructor for exception loci.formats.FormatException
-
- FormatFileFilter - Class in loci.formats.gui
-
A file filter for a biological file format, for use with a JFileChooser.
- FormatFileFilter(IFormatReader) - Constructor for class loci.formats.gui.FormatFileFilter
-
Constructs a new filter that accepts files of the given reader's type.
- FormatFileFilter(IFormatReader, boolean) - Constructor for class loci.formats.gui.FormatFileFilter
-
Constructs a new filter that accepts files of the given reader's type,
allowing the reader to open files only if the allowOpen flag is set.
- FormatHandler - Class in loci.formats
-
Abstract superclass of all biological file format readers and writers.
- FormatHandler(String, String) - Constructor for class loci.formats.FormatHandler
-
Constructs a format handler with the given name and default suffix.
- FormatHandler(String, String[]) - Constructor for class loci.formats.FormatHandler
-
Constructs a format handler with the given name and default suffixes.
- formatInfo - Variable in class loci.plugins.config.ConfigWindow
-
- formatLabel - Variable in class loci.formats.gui.PreviewPane
-
Labels containing thumbnail and dimensional information.
- formatName - Variable in class loci.plugins.config.FormatEntry
-
- FormatReader - Class in loci.formats
-
Abstract superclass of all biological file format readers.
- FormatReader(String, String) - Constructor for class loci.formats.FormatReader
-
Constructs a format reader with the given name and default suffix.
- FormatReader(String, String[]) - Constructor for class loci.formats.FormatReader
-
Constructs a format reader with the given name and default suffixes.
- FORMATS - Static variable in class loci.formats.in.GelReader
-
- formatsList - Variable in class loci.plugins.config.ConfigWindow
-
- formatsListModel - Variable in class loci.plugins.config.ConfigWindow
-
- formatTag(int) - Method in class loci.formats.in.DicomReader
-
- formatText - Variable in class loci.formats.gui.PreviewPane
-
- formatTip - Variable in class loci.formats.gui.PreviewPane
-
- FormatTools - Class in loci.formats
-
A utility class for format reader and writer implementations.
- FormatTools() - Constructor for class loci.formats.FormatTools
-
- FormatWriter - Class in loci.formats
-
Abstract superclass of all biological file format writers.
- FormatWriter(String, String) - Constructor for class loci.formats.FormatWriter
-
Constructs a format writer with the given name and default suffix.
- FormatWriter(String, String[]) - Constructor for class loci.formats.FormatWriter
-
Constructs a format writer with the given name and default suffixes.
- FORWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
-
- fos - Variable in class loci.formats.Memoizer.KryoDeser
-
- found - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
-
- foundChannelTag - Variable in class loci.formats.in.CellSensReader
-
- foundPlateLayout - Variable in class loci.formats.in.ScanrReader.ScanrHandler
-
- foundPositions - Variable in class loci.formats.in.ScanrReader
-
- fp - Variable in class loci.formats.AxisGuesser
-
File pattern identifying dimensional axis blocks.
- fp - Variable in class loci.plugins.in.FilePatternDialog
-
- fps - Variable in class loci.formats.FormatWriter
-
Frame rate to use when writing in frames per second, if applicable.
- fps - Variable in class loci.formats.gui.DataConverter
-
- fps - Variable in class loci.formats.gui.ImageViewer
-
- fpsSpin - Variable in class loci.plugins.util.DataBrowser
-
- Frame() - Constructor for class loci.formats.in.OBFReader.Frame
-
- Frame(PrairieMetadata.Sequence, Element) - Constructor for class loci.formats.in.PrairieMetadata.Frame
-
Creates a new frame by parsing the given <Frame> element.
- frame - Variable in class loci.formats.in.PrairieMetadata.PFile
-
The <Frame> containing this <File>.
- FRAME_OFFSET - Static variable in class loci.formats.out.AVIWriter
-
- FRAME_OFFSET_2 - Static variable in class loci.formats.out.AVIWriter
-
- FRAME_ORIGIN - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_SCALE - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_SIZE - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_TRANSFER - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_TYPE - Static variable in class loci.formats.in.CellSensReader
-
- frameClockList - Variable in class loci.formats.in.SPCReader
-
- frameCoordinates - Variable in class loci.formats.in.APNGReader
-
- frameIndex(PrairieMetadata.Sequence, int, int, int) - Method in class loci.formats.in.PrairieReader
-
Gets the frame index associated with the given (Z, T) position of the
specified series.
- frames - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
<Frame> elements beneath this <Sequence>, keyed on each
frame's index.
- framesAreTime - Variable in class loci.formats.in.PrairieReader
-
Whether a series uses Frames as time points rather than focal
planes (i.e., sizeZ and sizeT values inverted).
- frameValues - Variable in class loci.formats.in.PrairieMetadata.Frame
-
Table of key/value pairs for this <Frame>.
- FREE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
-
- FREE_LINE - Static variable in class loci.formats.in.FV1000Reader
-
- FREE_OFFSETS - Static variable in class loci.formats.tiff.IFD
-
- FREE_SHAPE - Static variable in class loci.formats.in.FV1000Reader
-
- frequencies - Variable in class loci.formats.in.LiFlimReader
-
- FREQUENCY - Static variable in class loci.formats.FormatTools
-
Identifies the Frequency dimensional type,
representing a dimension consisting of frequencies.
- fromCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
-
- fromRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
-
- FujiReader - Class in loci.formats.in
-
FujiReader is the file format reader for Fuji LAS 3000 datasets.
- FujiReader() - Constructor for class loci.formats.in.FujiReader
-
Constructs a new Fuji reader.
- fullImage - Variable in class loci.formats.in.MRWReader
-
- FV1000_MAGIC_STRING_1 - Static variable in class loci.formats.in.FV1000Reader
-
- FV1000_MAGIC_STRING_2 - Static variable in class loci.formats.in.FV1000Reader
-
- FV1000_SUFFIXES - Static variable in class loci.formats.in.FV1000Reader
-
- FV1000Reader - Class in loci.formats.in
-
FV1000Reader is the file format reader for Fluoview FV 1000 OIB and
Fluoview FV 1000 OIF files.
- FV1000Reader() - Constructor for class loci.formats.in.FV1000Reader
-
Constructs a new FV1000 reader.
- FV1000Reader.ChannelData - Class in loci.formats.in
-
- FV1000Reader.PlaneData - Class in loci.formats.in
-
- gain - Variable in class loci.formats.in.BDReader
-
- gain - Variable in class loci.formats.in.BioRadReader
-
- gain - Variable in class loci.formats.in.BioRadSCNReader
-
- gain - Variable in class loci.formats.in.CellSensReader.Pyramid
-
- gain - Variable in class loci.formats.in.FV1000Reader.ChannelData
-
- gain - Variable in class loci.formats.in.ImarisHDFReader
-
- gain - Variable in class loci.formats.in.InCellReader
-
- gain - Variable in class loci.formats.in.IvisionReader
-
- gain - Variable in class loci.formats.in.LeicaHandler.Channel
-
- gain - Variable in class loci.formats.in.MetamorphHandler
-
- gain - Variable in class loci.formats.in.MetamorphReader
-
- gain - Variable in class loci.formats.in.MicromanagerReader.Position
-
- gain - Variable in class loci.formats.in.ND2Handler
-
- gain - Variable in class loci.formats.in.NikonTiffReader
-
- gain - Variable in class loci.formats.in.OIRReader.Detector
-
- gain - Variable in class loci.formats.in.OpenlabReader
-
- gain - Variable in class loci.formats.in.ZeissCZIReader.Channel
-
- gain - Variable in class loci.formats.in.ZeissCZIReader
-
- gain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
-
- GAIN_CONTROL - Static variable in class loci.formats.tiff.IFD
-
- GAIN_UNIT - Static variable in class loci.formats.in.CellSensReader
-
- gains - Variable in class loci.formats.in.FluoviewReader
-
- gains - Variable in class loci.formats.in.LIFReader
-
- gains - Variable in class loci.formats.in.ZeissCZIReader
-
- gamma - Variable in class loci.formats.in.GatanReader
-
- gamma(double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
-
- GatanDM2Reader - Class in loci.formats.in
-
GatanDM2Reader is the file format reader for Gatan .dm2 files.
- GatanDM2Reader() - Constructor for class loci.formats.in.GatanDM2Reader
-
Constructs a new Gatan .dm2 reader.
- GatanReader - Class in loci.formats.in
-
GatanReader is the file format reader for Gatan files.
- GatanReader() - Constructor for class loci.formats.in.GatanReader
-
Constructs a new Gatan reader.
- GatanReader.ROIShape - Class in loci.formats.in
-
- gct - Variable in class loci.formats.in.GIFReader
-
Global color table.
- GEL_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the gel and blot imaging domain.
- GelReader - Class in loci.formats.in
-
GelReader is the file format reader for
Molecular Dynamics GEL TIFF files.
- GelReader() - Constructor for class loci.formats.in.GelReader
-
Constructs a new GEL reader.
- generateScreen(int, int, int, int, int) - Method in class loci.formats.tools.FakeImage
-
Creates a fake SPW file/directory structure.
- get(int) - Method in class loci.formats.codec.ByteVector
-
- get(int) - Static method in enum loci.formats.codec.CompressionType
-
Retrieves the compression by reverse lookup of its "code".
- get(int) - Static method in enum loci.formats.codec.JPEG2000BoxType
-
Retrieves the box type by reverse lookup of its "code".
- get(int) - Static method in enum loci.formats.codec.JPEG2000SegmentMarker
-
Retrieves the segment marker by reverse lookup of its "code".
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.Charset
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.DrawStyle
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.FeatureType
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.FillStyle
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndPositions
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndStyle
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.PointStyle
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.TextAlignment
-
- get(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name.
- get(String, String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name.
- get(Object) - Method in interface loci.formats.in.PrairieMetadata.Value
-
- get(int) - Method in interface loci.formats.in.PrairieMetadata.Value
-
- get(Object) - Method in class loci.formats.in.PrairieMetadata.ValueItem
-
- get(int) - Method in class loci.formats.in.PrairieMetadata.ValueItem
-
- get(int) - Method in class loci.formats.in.PrairieMetadata.ValueTable
-
- get(int) - Static method in enum loci.formats.tiff.IFDType
-
Retrieves a IFD type by reverse lookup of its "code".
- get(int) - Method in class loci.formats.tiff.OnDemandLongArray
-
- get(int) - Static method in enum loci.formats.tiff.PhotoInterp
-
Retrieves a photometric interpretation by reverse lookup of its "code".
- get(int) - Static method in enum loci.formats.tiff.TiffCompression
-
Retrieves a TIFF compression instance by code.
- get(List<T>, int, T) - Method in class loci.plugins.in.ImporterOptions
-
- get(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- get(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- get16BitLookupTable() - Method in class loci.formats.ChannelFiller
-
- get16BitLookupTable() - Method in class loci.formats.DelegateReader
-
- get16BitLookupTable() - Method in class loci.formats.FileStitcher
-
- get16BitLookupTable() - Method in class loci.formats.FormatReader
-
- get16BitLookupTable() - Method in interface loci.formats.IFormatReader
-
Gets the 16-bit color lookup table associated with
the most recently opened image.
- get16BitLookupTable() - Method in class loci.formats.ImageReader
-
- get16BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
-
- get16BitLookupTable() - Method in class loci.formats.in.DicomReader
-
- get16BitLookupTable() - Method in class loci.formats.in.FakeReader
-
- get16BitLookupTable() - Method in class loci.formats.in.FilePatternReader
-
- get16BitLookupTable() - Method in class loci.formats.in.FV1000Reader
-
- get16BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
-
- get16BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
-
- get16BitLookupTable() - Method in class loci.formats.in.InCellReader
-
- get16BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
-
- get16BitLookupTable() - Method in class loci.formats.in.JPXReader
-
- get16BitLookupTable() - Method in class loci.formats.in.LeicaReader
-
- get16BitLookupTable() - Method in class loci.formats.in.LIFReader
-
- get16BitLookupTable() - Method in class loci.formats.in.MIASReader
-
- get16BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
-
- get16BitLookupTable() - Method in class loci.formats.in.NativeND2Reader
-
- get16BitLookupTable() - Method in class loci.formats.in.OIRReader
-
- get16BitLookupTable() - Method in class loci.formats.in.OMETiffReader
-
- get16BitLookupTable() - Method in class loci.formats.in.PDSReader
-
- get16BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
-
- get16BitLookupTable() - Method in class loci.formats.in.ScreenReader
-
- get16BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
-
- get16BitLookupTable() - Method in class loci.formats.in.TCSReader
-
- get16BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
-
- get16BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
-
- get16BitLookupTable() - Method in class loci.formats.in.ZipReader
-
- get16BitLookupTable() - Method in class loci.formats.ReaderWrapper
-
- get8BitLookupTable() - Method in class loci.formats.ChannelFiller
-
- get8BitLookupTable() - Method in class loci.formats.DelegateReader
-
- get8BitLookupTable() - Method in class loci.formats.FileStitcher
-
- get8BitLookupTable() - Method in class loci.formats.FormatReader
-
- get8BitLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Converts an IndexColorModel to a 2D byte array.
- get8BitLookupTable() - Method in interface loci.formats.IFormatReader
-
Gets the 8-bit color lookup table associated with
the most recently opened image.
- get8BitLookupTable() - Method in class loci.formats.ImageReader
-
- get8BitLookupTable() - Method in class loci.formats.in.AmiraReader
-
- get8BitLookupTable() - Method in class loci.formats.in.APNGReader
-
- get8BitLookupTable() - Method in class loci.formats.in.AVIReader
-
- get8BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
-
- get8BitLookupTable() - Method in class loci.formats.in.BioRadReader
-
- get8BitLookupTable() - Method in class loci.formats.in.BMPReader
-
- get8BitLookupTable() - Method in class loci.formats.in.CellH5Reader
-
- get8BitLookupTable() - Method in class loci.formats.in.DicomReader
-
- get8BitLookupTable() - Method in class loci.formats.in.FakeReader
-
- get8BitLookupTable() - Method in class loci.formats.in.FilePatternReader
-
- get8BitLookupTable() - Method in class loci.formats.in.GIFReader
-
- get8BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
-
- get8BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
-
- get8BitLookupTable() - Method in class loci.formats.in.InCellReader
-
- get8BitLookupTable() - Method in class loci.formats.in.IPWReader
-
- get8BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
-
- get8BitLookupTable() - Method in class loci.formats.in.JPXReader
-
- get8BitLookupTable() - Method in class loci.formats.in.KhorosReader
-
- get8BitLookupTable() - Method in class loci.formats.in.LeicaReader
-
- get8BitLookupTable() - Method in class loci.formats.in.LIFReader
-
- get8BitLookupTable() - Method in class loci.formats.in.MIASReader
-
- get8BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
-
- get8BitLookupTable() - Method in class loci.formats.in.NativeND2Reader
-
- get8BitLookupTable() - Method in class loci.formats.in.OIRReader
-
- get8BitLookupTable() - Method in class loci.formats.in.OMETiffReader
-
- get8BitLookupTable() - Method in class loci.formats.in.OpenlabReader
-
- get8BitLookupTable() - Method in class loci.formats.in.PCXReader
-
- get8BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
-
- get8BitLookupTable() - Method in class loci.formats.in.PictReader
-
- get8BitLookupTable() - Method in class loci.formats.in.PSDReader
-
- get8BitLookupTable() - Method in class loci.formats.in.ScreenReader
-
- get8BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
-
- get8BitLookupTable() - Method in class loci.formats.in.TargaReader
-
- get8BitLookupTable() - Method in class loci.formats.in.TCSReader
-
- get8BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
-
- get8BitLookupTable() - Method in class loci.formats.in.ZeissLMSReader
-
- get8BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
-
- get8BitLookupTable() - Method in class loci.formats.in.ZipReader
-
- get8BitLookupTable() - Method in class loci.formats.ReaderWrapper
-
- getAbsoluteTime() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the absoluteTime associated with this Frame.
- getAcquisitionMode(String) - Method in class loci.formats.FormatReader
-
Retrieves an AcquisitionMode enumeration
value for the given String.
- getActiveChannels() - Method in class loci.formats.in.PrairieMetadata
-
Gets the list of active channel indices, in sorted order.
- getAdjustedIndex(int) - Method in class loci.formats.FileStitcher
-
Gets the local reader index for use with the given image plane.
- getAdjustedOrder() - Method in class loci.formats.AxisGuesser
-
Gets the adjusted dimension order.
- getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
-
- getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
-
- getAdvancedSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Returns an array of FileInfo objects representing the files needed to
open the current series.
- getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
-
- getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
-
- getAdvancedUsedFiles(boolean) - Method in class loci.formats.FileStitcher
-
- getAdvancedUsedFiles(boolean) - Method in class loci.formats.FormatReader
-
- getAdvancedUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Returns an array of FileInfo objects representing the files needed
to open this dataset.
- getAdvancedUsedFiles(boolean) - Method in class loci.formats.ImageReader
-
- getAdvancedUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
-
- getAllChildren(Integer) - Method in class loci.formats.in.VolocityReader
-
- getAllFiles(String) - Method in class loci.formats.FilePattern
-
- getAlpha(int) - Method in class loci.formats.gui.Index16ColorModel
-
- getAlpha(int) - Method in class loci.formats.gui.SignedColorModel
-
- getAlpha(Object) - Method in class loci.formats.gui.SignedColorModel
-
- getAlpha(int) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getAlpha(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getAlphas() - Method in class loci.formats.gui.Index16ColorModel
-
Return the array of alpha color components.
- getArcType(String) - Method in class loci.formats.FormatReader
-
Retrieves an ArcType enumeration
value for the given String.
- getArray(String, int[], int[]) - Method in interface loci.formats.services.NetCDFService
-
Retrieves an HDF path's values.
- getArray(String, int[], int[]) - Method in class loci.formats.services.NetCDFServiceImpl
-
- getAttributeList() - Method in interface loci.formats.services.NetCDFService
-
Retrieves an exhaustive list of the HDF paths for all attributes in the
HDF document.
- getAttributeList() - Method in class loci.formats.services.NetCDFServiceImpl
-
- getAttributeValue(String) - Method in interface loci.formats.services.NetCDFService
-
Retrieves an attribute's value.
- getAttributeValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
- getAutoscaleInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getAutoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getAutoThreshold(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getAvailableMemory() - Method in class loci.plugins.in.MemoryDialog
-
- getAxisCount(int) - Method in class loci.formats.AxisGuesser
-
Gets the number of axes in the pattern of the given type.
- getAxisCountC() - Method in class loci.formats.AxisGuesser
-
Gets the number of C axes in the pattern.
- getAxisCountS() - Method in class loci.formats.AxisGuesser
-
Gets the number of S axes in the pattern.
- getAxisCountT() - Method in class loci.formats.AxisGuesser
-
Gets the number of T axes in the pattern.
- getAxisCountZ() - Method in class loci.formats.AxisGuesser
-
Gets the number of Z axes in the pattern.
- getAxisGuesser() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getAxisGuesser() - Method in class loci.formats.FileStitcher
-
Gets the axis guesser object used to guess
which dimensional axes are which.
- getAxisType(String) - Static method in class loci.formats.AxisGuesser
-
Convert the given label to an axis type.
- getAxisTypes() - Method in class loci.formats.AxisGuesser
-
Gets the guessed axis type for each dimensional block.
- getAxisTypes() - Method in class loci.formats.FileStitcher
-
Gets the axis type for each dimensional block.
- getBackgroundValue() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getBaseReader() - Method in class loci.plugins.in.ImportProcess
-
- getBestIndex(Color) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getBinaryOnlyOMEXML(String, String, String) - Method in class loci.formats.out.OMETiffWriter
-
- getBinning(String) - Method in class loci.formats.FormatReader
-
Retrieves an Binning enumeration
value for the given String.
- getBinning() - Method in class loci.formats.in.MetamorphHandler
-
- getBinnings() - Method in class loci.formats.in.ND2Handler
-
- getBitDepth() - Method in class loci.formats.in.PrairieMetadata
-
Gets the bitDepth recorded in the configuration.
- getBits(int) - Method in class loci.formats.codec.BitBuffer
-
Deprecated.
Returns an int value representing the value of the bits read from
the byte array, from the current position.
- getBitsPerPixel() - Method in class loci.formats.FileStitcher
-
- getBitsPerPixel() - Method in class loci.formats.FormatReader
-
- getBitsPerPixel() - Method in interface loci.formats.IFormatReader
-
Gets the number of valid bits per pixel.
- getBitsPerPixel() - Method in class loci.formats.ImageReader
-
- getBitsPerPixel() - Method in class loci.formats.in.FilePatternReader
-
- getBitsPerPixel(int) - Method in class loci.formats.in.OBFReader
-
- getBitsPerPixel() - Method in class loci.formats.ReaderWrapper
-
- getBitsPerSample() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given
TIFF IFD.
- getBlankThumbBytes() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getBlock(int) - Method in class loci.formats.FilePattern
-
Gets the specified file pattern block (e.g., <0-9>).
- getBlock() - Method in class loci.formats.FilePatternBlock
-
Gets the block string.
- getBlock(int, String) - Method in class loci.formats.in.ScanrReader
-
- getBlocks() - Method in class loci.formats.FilePattern
-
Gets all file pattern blocks.
- getBlue(int) - Method in class loci.formats.gui.Index16ColorModel
-
- getBlue(int) - Method in class loci.formats.gui.SignedColorModel
-
- getBlue(Object) - Method in class loci.formats.gui.SignedColorModel
-
- getBlue(int) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getBlue(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getBlueOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
For the given pixel format, returns the number of bytes that the blue
component is offset from the start of the pixel.
- getBlues() - Method in class loci.formats.gui.Index16ColorModel
-
Return the array of blue color components.
- getBoolean(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a Boolean.
- getBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a Boolean.
- getBooleanOption(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the boolean option with the given key.
- getBooleanValue(String) - Method in class loci.plugins.Slicer
-
Gets the value of the given macro key as a boolean.
- getBounds(BigInteger[], boolean) - Static method in class loci.formats.FilePattern
-
Gets a string containing start, end and step values
for a sorted list of numbers.
- getBufferedImage() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getBuildDate(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getByte(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Byte entries into the SPE header table
- getByte(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a Byte value from the SPE header
- getByteBuffer() - Method in class loci.formats.codec.BitBuffer
-
Deprecated.
Return the backing byte array.
- getBytes(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned bytes, one per channel.
- getBytes(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned bytes, one per channel.
- getBytes(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned bytes, one per channel.
- getBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Get the bytes from an image, merging the channels as necessary.
- getBytesPerElement() - Method in enum loci.formats.tiff.IFDType
-
Retrieves the number of bytes per element.
- getBytesPerPixel(int) - Static method in class loci.formats.FormatTools
-
Retrieves how many bytes per pixel the current plane or section has.
- getBytesPerPixel(String) - Static method in class loci.formats.FormatTools
-
Retrieves the number of bytes per pixel in the current plane.
- getBytesPerPixel(int) - Method in class loci.formats.in.LegacyND2Reader
-
- getBytesPerSample() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's bytes per sample (derived from tag BitsPerSample)
from this IFD.
- getC() - Method in class loci.formats.gui.ImageViewer
-
Gets the C value of the currently displayed image.
- getCache() - Method in class loci.formats.gui.CacheComponent
-
- getCache() - Method in class loci.plugins.util.BFVirtualStack
-
- getCacheListeners() - Method in class loci.formats.cache.Cache
-
- getCacheListeners() - Method in interface loci.formats.cache.CacheReporter
-
Gets a list of all registered status update listeners.
- getCacheListeners() - Method in class loci.formats.cache.CacheStrategy
-
- getCalibrationTable() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getCameraModel() - Method in class loci.formats.in.ND2Handler
-
- getCategory() - Method in class loci.formats.in.BaseZeissReader.Tag
-
- getCBegin(int) - Method in class loci.plugins.in.ImporterOptions
-
- getCBegin(int) - Method in class loci.plugins.in.ImportProcess
-
- getCCount(int) - Method in class loci.plugins.in.ImportProcess
-
- getCEnd(int) - Method in class loci.plugins.in.ImporterOptions
-
- getCEnd(int) - Method in class loci.plugins.in.ImportProcess
-
- getChannel(String) - Method in class loci.formats.in.CellomicsReader
-
- getChannel() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the channel associated with this File.
- getChannel(int) - Method in class loci.formats.in.ZeissTIFFReader
-
- getChannelColor(int) - Method in class loci.formats.in.LIFReader
-
- getChannelColorFromFile(String) - Method in class loci.formats.in.MIASReader
-
Get the color associated with the given file's channel.
- getChannelColors() - Method in class loci.formats.in.ND2Handler
-
- getChannelCount() - Method in class loci.formats.in.SDTReader
-
Gets the number of spectral channels.
- getChannelDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
-
- getChannelDimCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getChannelDimLength(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getChannelDimType(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getChannelFiller() - Method in class loci.plugins.in.ImportProcess
-
- getChannelGlobalMaximum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves a specified channel's global maximum.
- getChannelGlobalMinimum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves a specified channel's global minimum.
- getChannelIndex(Element) - Method in class loci.formats.in.LIFReader
-
- getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.CellH5Reader
-
- getChannelKnownMaximum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves the specified channel's maximum based on the images that
have been read.
- getChannelKnownMinimum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves the specified channel's minimum based on the images that have
been read.
- getChannelLabel(int) - Method in class loci.formats.in.TextReader
-
Gets the label for the given channel.
- getChannelName(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getChannelName() - Method in class loci.formats.in.MetamorphHandler
-
- getChannelName() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the channelName associated with this File.
- getChannelNames() - Method in class loci.formats.in.MetamorphHandler
-
- getChannelNames() - Method in class loci.formats.in.ND2Handler
-
- getChannels(int) - Method in class loci.formats.in.LegacyND2Reader
-
- getChannelSeparator() - Method in class loci.plugins.in.ImportProcess
-
- getChar(int) - Method in class loci.formats.tools.AsciiImage
-
- getCheckboxes(GenericDialog) - Static method in class loci.plugins.util.WindowTools
-
- getChild(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
-
- getChild(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
-
- getChild() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getChildIndex(Integer, String) - Method in class loci.formats.in.VolocityReader
-
- getChildNodes(Element) - Method in class loci.formats.in.OBFReader
-
- getChildren(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
-
- getChildText(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
-
- getChildText(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
-
- getChoices(GenericDialog) - Static method in class loci.plugins.util.WindowTools
-
- getClass(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a class.
- getClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a class.
- getClasses() - Method in class loci.formats.ClassList
-
Gets the list of classes as an array.
- getCode() - Method in enum loci.formats.codec.CompressionType
-
Implemented as specified by the CodedEnum I/F.
- getCode() - Method in enum loci.formats.codec.JPEG2000BoxType
-
Implemented as specified by the CodedEnum I/F.
- getCode() - Method in enum loci.formats.codec.JPEG2000SegmentMarker
-
Implemented as specified by the CodedEnum I/F.
- getCode() - Method in enum loci.formats.tiff.IFDType
-
- getCode() - Method in enum loci.formats.tiff.PhotoInterp
-
- getCode() - Method in enum loci.formats.tiff.TiffCompression
-
- getCodecName(int) - Method in class loci.formats.in.AVIReader
-
- getCodecName() - Method in enum loci.formats.tiff.TiffCompression
-
Retrieves the name of the TIFF compression codec.
- getCodecOptions() - Method in class loci.formats.tiff.TiffParser
-
Retrieves the current set of codec options being used to decompress pixel
data.
- getCodestreamOffset() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Retrieves the offset to the first contiguous codestream.
- getCodestreamPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the pixel type as specified in the header.
- getCodestreamSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the number of channels the image has as specified in the header.
- getCodestreamSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the width of the image as specified in the header.
- getCodestreamSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the height of the image as specified in the header.
- getColorMap(IFD) - Method in class loci.formats.tiff.TiffParser
-
Retrieve the color map associated with the given IFD.
- getColorMode() - Method in class loci.plugins.in.ImporterOptions
-
- getColorModeInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getColorModel() - Method in class loci.formats.FormatWriter
-
- getColorModel() - Method in interface loci.formats.IFormatWriter
-
Gets the color model.
- getColorModel() - Method in class loci.formats.ImageWriter
-
- getColorModel() - Method in class loci.formats.WriterWrapper
-
- getColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getColorModes() - Method in class loci.plugins.in.ImporterOptions
-
- getColorValue(TextField) - Method in class loci.plugins.in.ColorDialog
-
- getColumn() - Method in class loci.formats.in.OMEXMLReader.BinData
-
- getColumn(String) - Method in class loci.formats.in.ScreenReader
-
- getColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getColumNames(int) - Method in interface loci.formats.services.MetakitService
-
- getColumNames(int) - Method in class loci.formats.services.MetakitServiceImpl
-
- getColumnNames(String) - Method in interface loci.formats.services.MetakitService
-
- getColumnNames(String) - Method in class loci.formats.services.MetakitServiceImpl
-
- getColumnTypes(int) - Method in interface loci.formats.services.MetakitService
-
- getColumnTypes(String) - Method in interface loci.formats.services.MetakitService
-
- getColumnTypes(int) - Method in class loci.formats.services.MetakitServiceImpl
-
- getColumnTypes(String) - Method in class loci.formats.services.MetakitServiceImpl
-
- getComment(int, int) - Method in class loci.formats.in.MetamorphReader
-
- getComment() - Method in class loci.formats.tiff.IFD
-
Convenience method for obtaining the ImageDescription from this IFD.
- getComment() - Method in class loci.formats.tiff.TiffParser
-
Convenience method for obtaining a stream's first ImageDescription.
- getComments() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Retrieves the list of comments stored in the file.
- getCompanion() - Method in class loci.formats.out.OMETiffWriter
-
- getComponent(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getCompressedSize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Returns the size of the image (in bytes) generated by the most recent
compress/encode operation.
- getCompression() - Method in enum loci.formats.codec.CompressionType
-
Returns the compression.
- getCompression(String) - Method in class loci.formats.FormatReader
-
Retrieves an Compression enumeration
value for the given String.
- getCompression() - Method in class loci.formats.FormatWriter
-
- getCompression() - Method in interface loci.formats.IFormatWriter
-
Gets the current compression type.
- getCompression() - Method in class loci.formats.ImageWriter
-
- getCompression(int) - Method in class loci.formats.in.OBFReader
-
- getCompression() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's compression type (TIFF tag Compression) from
this IFD.
- getCompression() - Method in class loci.formats.WriterWrapper
-
- getCompressionCodecOptions(IFD) - Method in enum loci.formats.tiff.TiffCompression
-
Creates a set of codec options for compression.
- getCompressionCodecOptions(IFD, CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
-
Creates a set of codec options for compression.
- getCompressionMap() - Static method in enum loci.formats.tiff.TiffCompression
-
- getCompressionTypes() - Method in class loci.formats.FormatWriter
-
- getCompressionTypes() - Method in interface loci.formats.IFormatWriter
-
Gets the available compression types.
- getCompressionTypes() - Method in class loci.formats.ImageWriter
-
- getCompressionTypes() - Method in class loci.formats.WriterWrapper
-
- getConcatenateInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getConfig(String) - Method in class loci.formats.in.PrairieMetadata
-
Gets the value of the given configuration key.
- getConfig() - Method in class loci.formats.in.PrairieMetadata
-
Gets the map of configuration key/value pairs.
- getConstraintsForCell(int, int, Container, int) - Static method in class loci.plugins.config.SpringUtilities
-
- getContrastMethod(String) - Method in class loci.formats.FormatReader
-
Retrieves an ContrastMethod enumeration
value for the given String.
- getCoreIndex() - Method in class loci.formats.FileStitcher
-
- getCoreIndex() - Method in class loci.formats.FormatReader
-
- getCoreIndex() - Method in interface loci.formats.IFormatReader
-
Return the index into CoreMetadata of the current resolution/series.
- getCoreIndex() - Method in class loci.formats.ImageReader
-
- getCoreIndex() - Method in class loci.formats.in.FilePatternReader
-
- getCoreIndex() - Method in class loci.formats.ReaderWrapper
-
- getCoreMetadataList() - Method in class loci.formats.DimensionSwapper
-
- getCoreMetadataList() - Method in class loci.formats.FileStitcher
-
- getCoreMetadataList() - Method in class loci.formats.FormatReader
-
- getCoreMetadataList() - Method in interface loci.formats.IFormatReader
-
Obtains the core metadata values for the current file.
- getCoreMetadataList() - Method in class loci.formats.ImageReader
-
- getCoreMetadataList() - Method in class loci.formats.in.FilePatternReader
-
- getCoreMetadataList() - Method in class loci.formats.in.LeicaHandler
-
- getCoreMetadataList() - Method in class loci.formats.in.ND2Handler
-
- getCoreMetadataList() - Method in class loci.formats.ReaderWrapper
-
- getCorrection(String) - Method in class loci.formats.FormatReader
-
Retrieves an Correction enumeration
value for the given String.
- getCorrection() - Method in class loci.formats.in.ND2Handler
-
- getCount() - Method in class loci.formats.FilePattern
-
Gets the number of elements for each pattern block.
- getCreationDate() - Method in interface loci.formats.services.EXIFService
-
- getCreationDate() - Method in class loci.formats.services.EXIFServiceImpl
-
- getCropInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getCropRegion(int) - Method in class loci.plugins.in.ImporterOptions
-
- getCropRegion(int) - Method in class loci.plugins.in.ImportProcess
-
- getCStep(int) - Method in class loci.plugins.in.ImporterOptions
-
- getCStep(int) - Method in class loci.plugins.in.ImportProcess
-
- getCurrentColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getCurrentFile() - Method in class loci.formats.FormatReader
-
- getCurrentFile() - Method in interface loci.formats.IFormatReader
-
Returns the current file.
- getCurrentFile() - Method in class loci.formats.ImageReader
-
- getCurrentFile() - Method in class loci.formats.ReaderWrapper
-
- getCurrentFile() - Method in class loci.plugins.in.ImportProcess
-
- getCurrentFile(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getCurrentPos() - Method in class loci.formats.cache.Cache
-
Gets the current dimensional position.
- getCustomColor(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- getCustomColorKey(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- getCutIn(Double) - Static method in class loci.formats.FormatTools
-
- getCutOut(Double) - Static method in class loci.formats.FormatTools
-
- getCycle() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the cycle associated with this Sequence.
- getCycleCount() - Method in class loci.formats.in.PrairieMetadata
-
Gets the number of recorded cycles.
- getCycleMax() - Method in class loci.formats.in.PrairieMetadata
-
Gets the maximum cycle value.
- getCycleMin() - Method in class loci.formats.in.PrairieMetadata
-
Gets the minimum cycle value.
- getCZTag(IFD) - Method in class loci.formats.in.ZeissLSMReader
-
- getData() - Method in class loci.formats.gui.SignedByteBuffer
-
- getData(int) - Method in class loci.formats.gui.SignedByteBuffer
-
- getData() - Method in class loci.formats.gui.SignedShortBuffer
-
- getData(int) - Method in class loci.formats.gui.SignedShortBuffer
-
- getData() - Method in class loci.formats.gui.UnsignedIntBuffer
-
- getData(int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- getDataElements(int, Object) - Method in class loci.formats.gui.Index16ColorModel
-
- getDataElements(int, Object) - Method in class loci.formats.gui.SignedColorModel
-
- getDataElements(int, Object) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getDatasetStructureDescription() - Method in class loci.formats.FormatReader
-
- getDatasetStructureDescription() - Method in interface loci.formats.IFormatReader
-
Returns a short description of the dataset structure.
- getDatasetStructureDescription() - Method in class loci.formats.ImageReader
-
- getDatasetStructureDescription() - Method in class loci.formats.in.FilePatternReader
-
- getDatasetStructureDescription() - Method in class loci.formats.ReaderWrapper
-
- getDate() - Method in class loci.formats.in.MetamorphHandler
-
- getDate() - Method in class loci.formats.in.ND2Handler
-
- getDate() - Method in class loci.formats.in.PrairieMetadata
-
Gets the date of the acquisition.
- getDatestamp() - Method in class loci.formats.in.SVSReader
-
- getDecompressedStream(String) - Method in class loci.formats.in.CellomicsReader
-
- getDefault() - Method in class loci.plugins.prefs.BooleanOption
-
Gets the default value of the option.
- getDefault() - Method in class loci.plugins.prefs.DoubleOption
-
Gets the default value of the option.
- getDefault() - Method in class loci.plugins.prefs.StringOption
-
Gets the default value of the option.
- getDefaultColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getDefaultConfiguration() - Static method in class loci.formats.gui.AWTImageTools
-
Gets the default graphics configuration for the environment.
- getDefaultCustomColor(int) - Method in class loci.plugins.in.ImporterOptions
-
- getDefaultOptions() - Static method in class loci.formats.codec.CodecOptions
-
Return CodecOptions with reasonable default values.
- getDefaultOptions() - Static method in class loci.formats.codec.JPEG2000CodecOptions
-
Return JPEG2000CodecOptions with reasonable default values.
- getDefaultOptions(CodecOptions) - Static method in class loci.formats.codec.JPEG2000CodecOptions
-
Return JPEG2000CodecOptions using the given CodecOptions as the default.
- getDefaultReaderClasses() - Static method in class loci.formats.ImageReader
-
- getDefaultValue(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the default value of the string option with the given key.
- getDefaultWriterClasses() - Static method in class loci.formats.ImageWriter
-
- getDenom() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns denominator
- getDenominator() - Method in class loci.formats.tiff.TiffRational
-
Gets this number's denominator.
- getDescription() - Method in class loci.formats.gui.ComboFileFilter
-
Returns the filter's description.
- getDescription() - Method in class loci.formats.gui.ExtensionFileFilter
-
Gets the filter's description.
- getDescription() - Method in class loci.formats.gui.FormatFileFilter
-
Gets the filter's description.
- getDescription() - Method in class loci.formats.gui.NoExtensionFileFilter
-
Gets the filter's description.
- getDeser() - Method in class loci.formats.Memoizer
-
Returns a configured Kryo instance.
- getDetectorType(String) - Method in class loci.formats.FormatReader
-
Retrieves an DetectorType enumeration
value for the given String.
- getDeviceSubtype(String) - Method in class loci.formats.in.CellSensReader
-
- getDimension(String) - Method in class loci.formats.in.ZeissTIFFHandler.Scaling
-
Get a dimension by its index.
- getDimension(String) - Method in interface loci.formats.services.NetCDFService
-
Retrieves the length of a dimension.
- getDimension(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
- getDimensionDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
-
- getDimensionOrder() - Method in class loci.formats.ChannelMerger
-
- getDimensionOrder() - Method in class loci.formats.ChannelSeparator
-
- getDimensionOrder() - Method in class loci.formats.DimensionSwapper
-
- getDimensionOrder() - Method in class loci.formats.FileStitcher
-
- getDimensionOrder() - Method in class loci.formats.FormatReader
-
- getDimensionOrder(String) - Method in class loci.formats.FormatReader
-
Retrieves an DimensionOrder enumeration
value for the given String.
- getDimensionOrder() - Method in interface loci.formats.IFormatReader
-
Gets a five-character string representing the
dimension order in which planes will be returned.
- getDimensionOrder() - Method in class loci.formats.ImageReader
-
- getDimensionOrder() - Method in class loci.formats.in.FilePatternReader
-
- getDimensionOrder() - Method in class loci.formats.ReaderWrapper
-
- getDimensionOrder(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getDimensionSwapper() - Method in class loci.plugins.in.ImportProcess
-
- getDirectory(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
- getDocument() - Method in class loci.formats.gui.XMLWindow
-
Gets the XML document currently being displayed within the window.
- getDocumentBytes(String) - Method in interface loci.formats.services.POIService
-
Retrieve all of the raw bytes that correspond to the given file name.
- getDocumentBytes(String, int) - Method in interface loci.formats.services.POIService
-
Retrieve at most 'length' bytes that correspond to the given file name.
- getDocumentBytes(String) - Method in class loci.formats.services.POIServiceImpl
-
- getDocumentBytes(String, int) - Method in class loci.formats.services.POIServiceImpl
-
- getDocumentList() - Method in interface loci.formats.services.POIService
-
Retrieve a list of all files in the current POI file system.
- getDocumentList() - Method in class loci.formats.services.POIServiceImpl
-
- getDocumentStream(String) - Method in interface loci.formats.services.POIService
-
Retrieve a RandomAccessInputStream corresponding to the given file name.
- getDocumentStream(String) - Method in class loci.formats.services.POIServiceImpl
-
- getDomains() - Method in class loci.formats.FormatReader
-
- getDomains() - Method in interface loci.formats.IFormatReader
-
Returns the list of domains represented by the current file.
- getDomains() - Method in class loci.formats.ImageReader
-
- getDomains() - Method in class loci.formats.in.CellomicsReader
-
- getDomains() - Method in class loci.formats.in.FilePatternReader
-
- getDomains() - Method in class loci.formats.in.ICSReader
-
- getDomains() - Method in class loci.formats.in.MetamorphTiffReader
-
- getDomains() - Method in class loci.formats.in.NiftiReader
-
- getDomains() - Method in class loci.formats.in.OMETiffReader
-
- getDomains() - Method in class loci.formats.in.OMEXMLReader
-
- getDomains() - Method in class loci.formats.ReaderWrapper
-
- getDouble(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a Double.
- getDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a Double.
- getDoubles(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of doubles, one per channel.
- getDoubles(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of doubles, one per channel.
- getDoubles(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of doubles, one per channel.
- getDoubleValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
-
- getDT(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getDX(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getDY(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getDZ(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getEffectiveSeries(int) - Method in class loci.formats.in.ZeissLSMReader
-
- getEffectiveSizeC() - Method in class loci.formats.FormatReader
-
- getEffectiveSizeC() - Method in interface loci.formats.IFormatReader
-
Gets the effective size of the C dimension, guaranteeing that
getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount()
regardless of the result of isRGB().
- getEffectiveSizeC() - Method in class loci.formats.ImageReader
-
- getEffectiveSizeC() - Method in class loci.formats.in.FilePatternReader
-
- getEffectiveSizeC() - Method in class loci.formats.ReaderWrapper
-
- getEffectiveSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getElem(int) - Method in class loci.formats.gui.SignedByteBuffer
-
- getElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
-
- getElem(int, int) - Method in class loci.formats.gui.SignedShortBuffer
-
- getElem(int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- getElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- getElemDouble(int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- getElemDouble(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- getElements() - Method in class loci.formats.FilePattern
-
Gets individual elements for each pattern block.
- getElements() - Method in class loci.formats.FilePatternBlock
-
Gets all block elements.
- getElementSize(String) - Method in interface loci.formats.services.JHDFService
-
Retrieves the Element Size of a dataset in Byte.
- getElementSize(String) - Method in class loci.formats.services.JHDFServiceImpl
-
- getElemFloat(int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- getElemFloat(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- getEmission() - Method in class loci.formats.in.SVSReader
-
- getEmissionWavelength(Double) - Static method in class loci.formats.FormatTools
-
- getEmissionWavelengths() - Method in class loci.formats.in.ND2Handler
-
- getEndX() - Method in class loci.formats.in.SPEReader.SpeROI
-
- getEndY() - Method in class loci.formats.in.SPEReader.SpeROI
-
- getEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
-
Return all entries as an array
- getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record
-
Get the boolean value at the given index
- getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
-
Get the floating-point value at the given index
- getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.IntIM3Record
-
Get the integer value at the given index
- getEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as an enumerated type.
- getErrorMessage() - Method in class loci.formats.FilePattern
-
Gets the file pattern error message, if any.
- getExcitation() - Method in class loci.formats.in.SVSReader
-
- getExcitationWavelength(Double) - Static method in class loci.formats.FormatTools
-
- getExcitationWavelengths() - Method in class loci.formats.in.ND2Handler
-
- getExifIFDs() - Method in class loci.formats.tiff.TiffParser
-
Returns EXIF IFDs.
- getExifTagName(int) - Static method in class loci.formats.in.BaseTiffReader
-
- getExperimenterName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getExperimentType(String) - Method in class loci.formats.FormatReader
-
Retrieves an ExperimentType enumeration
value for the given String.
- getExposures() - Method in class loci.formats.in.MetamorphHandler
-
- getExposureTime() - Method in class loci.formats.in.SVSReader
-
- getExposureTimes() - Method in class loci.formats.in.ND2Handler
-
- getExtension() - Method in class loci.formats.gui.ExtensionFileFilter
-
Gets the filter's first valid extension.
- getExtensionFunctions() - Method in class loci.plugins.macro.MacroFunctions
-
- getExtensions() - Method in class loci.formats.gui.ExtensionFileFilter
-
Gets the filter's valid extensions.
- getExternalSeries() - Method in class loci.formats.FileStitcher
-
- getExternalSeries(int) - Method in class loci.formats.FileStitcher
-
- getExtraSeries(String) - Method in class loci.formats.in.ZeissLSMReader
-
- getf(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getf(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getField(String) - Method in class loci.formats.in.CellomicsReader
-
- getField(String) - Method in class loci.formats.in.FlexReader
-
- getField(int) - Method in class loci.formats.in.FluoviewReader
-
- getField(String) - Method in class loci.formats.in.MetamorphTiffReader
-
- getFieldFromSeries(int) - Method in class loci.formats.in.InCellReader
-
- getFieldIndex() - Method in class loci.formats.in.ND2Handler
-
- getFieldName(int) - Static method in class loci.formats.tiff.IFD
-
This method uses reflection to scan the values of this class's
static fields, returning the first matching field's name.
- getFilamentType(String) - Method in class loci.formats.FormatReader
-
Retrieves an FilamentType enumeration
value for the given String.
- getFile(int, int) - Method in class loci.formats.in.CellWorxReader
-
Retrieve the .pnl file corresponding to the given series.
- getFile(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a file object.
- getFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a file object.
- getFile(String) - Method in class loci.formats.in.FV1000Reader
-
- getFile(int) - Method in class loci.formats.in.MicromanagerReader.Position
-
- getFile(String, int, int, int, int, int) - Method in class loci.formats.in.MicromanagerReader.Position
-
- getFile(int) - Method in class loci.formats.in.PerkinElmerReader
-
- getFile(int) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the File with the given channel.
- getFile(int, int, int) - Method in class loci.formats.in.PrairieMetadata
-
Gets the Frame at the given (cycle, index,
channel).
- getFile(int, int) - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the Frame at the given (cycle, index,
channel).
- getFile(Integer, Location) - Method in class loci.formats.in.VolocityReader
-
- getFile() - Method in interface loci.formats.services.JHDFService
-
Retrieves the current initialized file path.
- getFile() - Method in class loci.formats.services.JHDFServiceImpl
-
- getFile() - Method in interface loci.formats.services.NetCDFService
-
Retrieves the current initialized file path.
- getFile() - Method in class loci.formats.services.NetCDFServiceImpl
-
- getFileHandle(String) - Method in class loci.formats.in.FlexReader
-
- getFileIndex(int) - Method in class loci.formats.in.PerkinElmerReader
-
- getFilename(int, int, IFormatReader, String) - Static method in class loci.formats.FormatTools
-
- getFilename(int, int, IFormatReader, String, boolean) - Static method in class loci.formats.FormatTools
-
- getFilename(int, int, MetadataRetrieve, String, boolean) - Static method in class loci.formats.FormatTools
-
- getFilename(int, int) - Method in class loci.formats.in.BDReader
-
- getFilename() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the filename associated with this File.
- getFilenames(String, IFormatReader) - Static method in class loci.formats.FormatTools
-
- getFilePattern() - Method in class loci.formats.AxisGuesser
-
Gets the file pattern.
- getFilePattern() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getFilePattern() - Method in class loci.formats.FileStitcher
-
Gets the file pattern object used to build the list of files.
- getFiles() - Method in class loci.formats.FilePattern
-
Gets a listing of all files matching this file pattern.
- getFiles() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getFileSize(String) - Method in interface loci.formats.services.POIService
-
Retrieve the total number of bytes in the given file.
- getFileSize(String) - Method in class loci.formats.services.POIServiceImpl
-
- getFileStitcher() - Method in class loci.plugins.in.ImportProcess
-
- getFileVersion(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
-
- getFillRule(String) - Method in class loci.formats.FormatReader
-
Retrieves an FillRule enumeration
value for the given String.
- getFilter(String) - Method in class loci.formats.in.FV1000Reader.ChannelData
-
- getFilters() - Method in class loci.formats.gui.ComboFileFilter
-
Gets the list of file filters forming this filter combination.
- getFilterType(String) - Method in class loci.formats.FormatReader
-
Retrieves an FilterType enumeration
value for the given String.
- getFirst() - Method in class loci.formats.FilePattern
-
Gets the START element for all blocks.
- getFirst() - Method in class loci.formats.FilePatternBlock
-
Gets the first element in a range block.
- getFirstChannel(String) - Method in class loci.formats.in.SlidebookTiffReader
-
- getFirstChild(Element, String) - Method in class loci.formats.in.OIRReader
-
- getFirstChild(Element, String) - Method in class loci.formats.in.PrairieMetadata
-
Gets the first child element with the given name.
- getFirstComment(int) - Method in class loci.formats.in.MetamorphReader
-
Returns the TIFF comment from the first IFD of the first STK file in the
given series.
- getFirstFile() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the first File of the Sequence.
- getFirstFrame() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the first Frame of the Sequence.
- getFirstIFD() - Method in class loci.formats.tiff.TiffParser
-
Gets the first IFD within the TIFF file, or null
if the input source is not a valid TIFF file.
- getFirstIFDEntry(int) - Method in class loci.formats.tiff.TiffParser
-
Retrieve a given entry from the first IFD in the stream.
- getFirstNode(Element, String) - Method in class loci.formats.in.ZeissCZIReader
-
- getFirstNodeValue(Element, String) - Method in class loci.formats.in.ZeissCZIReader
-
- getFirstOffset() - Method in class loci.formats.tiff.TiffParser
-
Gets offset to the first IFD, or -1 if stream is not TIFF.
- getFirstSequence() - Method in class loci.formats.in.PrairieMetadata
-
Gets the first Sequence.
- getFirstTimeInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getFixedHeader() - Method in class loci.formats.services.JPEGTurboServiceImpl
-
- getFlexFiles() - Method in class loci.formats.in.FlexReader.MeaHandler
-
- getFloat(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a Float.
- getFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a Float.
- getFloatArray() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getFloats(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of floats, one per channel.
- getFloats(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of floats, one per channel.
- getFloats(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of floats, one per channel.
- getFloatValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
-
- getFontFamily(String) - Method in class loci.formats.FormatReader
-
Retrieves an FontFamily enumeration
value for the given String.
- getFontMetrics() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getFontSize(Integer) - Static method in class loci.formats.FormatTools
-
- getFontStyle(String) - Method in class loci.formats.FormatReader
-
Retrieves an FontStyle enumeration
value for the given String.
- getForceThumbnailsInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getFormat() - Method in class loci.formats.FormatHandler
-
- getFormat() - Method in interface loci.formats.IFormatHandler
-
Gets the name of this file format.
- getFormat(String) - Method in class loci.formats.ImageReader
-
Gets a string describing the file format for the given file.
- getFormat() - Method in class loci.formats.ImageReader
-
- getFormat(String) - Method in class loci.formats.ImageWriter
-
Gets a string describing the file format for the given file.
- getFormat() - Method in class loci.formats.ImageWriter
-
- getFormat() - Method in class loci.formats.ReaderWrapper
-
- getFormat() - Method in class loci.formats.WriterWrapper
-
- getFormat(String, String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getFrame(int, int) - Method in class loci.formats.in.PrairieMetadata
-
Gets the Frame at the given (cycle and index).
- getFrame() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the <Frame> containing this <File>.
- getFrame(int) - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the Frame with the given index.
- getFramesPerSecond() - Method in class loci.formats.FormatWriter
-
- getFramesPerSecond() - Method in interface loci.formats.IFormatWriter
-
Gets the frames per second to use when writing.
- getFramesPerSecond() - Method in class loci.formats.ImageWriter
-
- getFramesPerSecond() - Method in class loci.formats.WriterWrapper
-
- getGain() - Method in class loci.formats.in.MetamorphHandler
-
- getGain(int) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the cth gain for this Frame.
- getGains() - Method in class loci.formats.in.ND2Handler
-
- getGlobalMeta(String) - Method in class loci.formats.FormatReader
-
Gets a value from the global metadata table.
- getGlobalMetadata() - Method in class loci.formats.FormatReader
-
- getGlobalMetadata() - Method in interface loci.formats.IFormatReader
-
Obtains the hashtable containing the metadata field/value pairs from
the current file.
- getGlobalMetadata() - Method in class loci.formats.ImageReader
-
- getGlobalMetadata() - Method in class loci.formats.in.FilePatternReader
-
- getGlobalMetadata() - Method in class loci.formats.in.LeicaHandler
-
- getGlobalMetadata() - Method in class loci.formats.ReaderWrapper
-
- getGrandchildren(Element, String) - Method in class loci.formats.in.ZeissCZIReader
-
- getGrandchildren(Element, String, String) - Method in class loci.formats.in.ZeissCZIReader
-
- getGreen(int) - Method in class loci.formats.gui.Index16ColorModel
-
- getGreen(int) - Method in class loci.formats.gui.SignedColorModel
-
- getGreen(Object) - Method in class loci.formats.gui.SignedColorModel
-
- getGreen(int) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getGreen(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getGreenOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
For the given pixel format, returns the number of bytes that the green
component is offset from the start of the pixel.
- getGreens() - Method in class loci.formats.gui.Index16ColorModel
-
Return the array of green color components.
- getGroup(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
Retrieves a group based on its fully qualified path.
- getGroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getGroupX() - Method in class loci.formats.in.SPEReader.SpeROI
-
- getGroupY() - Method in class loci.formats.in.SPEReader.SpeROI
-
- getHeader() - Method in class loci.formats.in.SPEReader.SpeHeader
-
- getHeaderInfo(int, String) - Method in class loci.formats.in.DicomReader
-
- getHeaderPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the pixel type as specified in the header.
- getHeaderSize() - Method in class loci.formats.in.SPEReader.SpeHeader
-
- getHeaderSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the number of channels the image has as specified in the header.
- getHeaderSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the width of the image as specified in the header.
- getHeaderSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the height of the image as specified in the header.
- getHeight() - Method in class loci.formats.codec.JPEGTileDecoder
-
- getHeight(int) - Method in class loci.formats.in.LegacyND2Reader
-
- getHeight() - Method in interface loci.formats.services.LuraWaveService
-
Wraps lwfDecoder.getHeight()
- getHeight() - Method in class loci.formats.services.LuraWaveServiceImpl
-
- getHeight(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
-
- getHeight() - Method in class loci.plugins.util.BFVirtualStack
-
- getHeight() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getHeight() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the height of the JPEG image associated with this decompressor
instance.
- getHistogram() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getHistogramMax() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getHistogramMin() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getHistogramSize() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getId(String) - Method in class loci.formats.tools.MakeTestOmeTiff
-
- getId() - Method in class loci.plugins.in.ImporterOptions
-
- getIdInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getIdLocation() - Method in class loci.plugins.in.ImportProcess
-
- getIdName() - Method in class loci.plugins.in.ImportProcess
-
- getIFD(long) - Method in class loci.formats.tiff.TiffParser
-
Gets the IFD stored at the given offset.
- getIFDIndex(int, int) - Method in class loci.formats.in.NDPIReader
-
- getIFDIndex(int) - Method in class loci.formats.in.SVSReader
-
- getIFDIntArray(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry values in int format
from this IFD, performing some error checking.
- getIFDIntValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value in int format from this IFD,
or -1 if the given directory does not exist.
- getIFDIntValue(int, int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value in int format from this IFD,
performing some error checking.
- getIFDLongArray(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry values in long format
from this IFD, performing some error checking.
- getIFDLongValue(int, long) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value in long format from this IFD,
performing some error checking.
- getIFDOffsets() - Method in class loci.formats.tiff.TiffParser
-
Gets the offsets to every IFD in the file.
- getIFDRationalValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value in rational format from this IFD,
performing some error checking.
- getIFDs() - Method in class loci.formats.in.MinimalTiffReader
-
Gets the list of IFDs associated with the current TIFF's image planes.
- getIFDs() - Method in class loci.formats.tiff.TiffParser
-
Returns all IFDs in the file.
- getIFDShortArray(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry values in short format
from this IFD, performing some error checking.
- getIFDStringValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value as a string from this IFD,
performing some error checking.
- getIFDTagName(int) - Static method in class loci.formats.tiff.IFD
-
Gets the name of the IFD tag encoded by the given number.
- getIFDTextValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value as a string (regardless of type).
- getIFDValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value from this IFD.
- getIFDValue(int, Class) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value from this IFD,
performing some error checking.
- getIFDValue(TiffIFDEntry) - Method in class loci.formats.tiff.TiffParser
-
Retrieve the value corresponding to the given TiffIFDEntry.
- getIlluminationType(String) - Method in class loci.formats.FormatReader
-
Retrieves an IlluminationType enumeration
value for the given String.
- getImage() - Method in class loci.formats.gui.ImageViewer
-
Gets the currently displayed image.
- getImage(byte[], int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getImageCount() - Method in class loci.formats.ChannelMerger
-
- getImageCount() - Method in class loci.formats.ChannelSeparator
-
- getImageCount() - Method in class loci.formats.FileStitcher
-
- getImageCount() - Method in class loci.formats.FormatReader
-
- getImageCount() - Method in interface loci.formats.IFormatReader
-
Determines the number of image planes in the current file.
- getImageCount() - Method in class loci.formats.ImageReader
-
- getImageCount() - Method in class loci.formats.in.FilePatternReader
-
- getImageCount() - Method in class loci.formats.ReaderWrapper
-
- getImageCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getImageCreationDate() - Method in class loci.formats.in.BaseTiffReader
-
Retrieves the image creation date.
- getImageCreationDate(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getImageData(int, int, int) - Method in class loci.formats.in.CellH5Reader
-
- getImageData(int, int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader
-
Retrieve an array corresponding to the specified image tile.
- getImageDescription(Element) - Method in class loci.formats.in.LIFReader
-
- getImageIndex() - Method in class loci.formats.gui.ImageViewer
-
Gets the index of the currently displayed image.
- getImageIndex(int) - Method in class loci.formats.in.FluoviewReader
-
- getImageIndex(String) - Method in class loci.formats.in.PCIReader
-
Get the image index from the image file name.
- getImageLength() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
- getImageName() - Method in class loci.formats.in.MetamorphHandler
-
- getImageNumber(String, int) - Method in class loci.formats.in.ZeissZVIReader
-
- getImageReader() - Method in class loci.plugins.in.ImportProcess
-
- getImageSequence(int) - Method in class loci.formats.in.DeltavisionReader
-
Get the image sequence string.
- getImagesPerFile() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getImagesPerFile(String, IFormatReader) - Static method in class loci.formats.FormatTools
-
- getImageWidth() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
- getImagingDevice() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the imaging device associated with this Frame.
- getImmersion(String) - Method in class loci.formats.FormatReader
-
Retrieves an Immersion enumeration
value for the given String.
- getImmersion() - Method in class loci.formats.in.ND2Handler
-
- getImmersion() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Extracts the immersion from the objective lens string.
- getIndex() - Method in class loci.formats.cache.CacheEvent
-
Gets the index relevant to the cache update, if any.
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelMerger
-
- getIndex(int, int, int) - Method in class loci.formats.ChannelMerger
-
- getIndex(int, int, int) - Method in class loci.formats.ChannelSeparator
-
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
-
- getIndex(int, int, int) - Method in class loci.formats.DimensionSwapper
-
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
-
- getIndex(int, int, int) - Method in class loci.formats.FileStitcher
-
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.FileStitcher
-
- getIndex(int, int, int) - Method in class loci.formats.FormatReader
-
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.FormatReader
-
- getIndex(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the rasterized index corresponding
to the given Z, C and T coordinates (real sizes).
- getIndex(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the rasterized index corresponding to the given Z, C, T,
ModuloZ, ModuloC and ModuloT coordinates (effective sizes).
- getIndex(String, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the rasterized index corresponding
to the given Z, C and T coordinates (real sizes).
- getIndex(String, int, int, int, int, int, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the rasterized index corresponding to the given Z, C, T,
ModuloZ, ModuloC, ModuloT coordinates (effective sizes).
- getIndex(int, int, int) - Method in interface loci.formats.IFormatReader
-
Gets the rasterized index corresponding
to the given Z, C and T coordinates (real sizes).
- getIndex(int, int, int, int, int, int) - Method in interface loci.formats.IFormatReader
-
Gets the rasterized index corresponding to the given Z, C, T,
moduloZ, moduloC and moduloT coordinates (effective sizes).
- getIndex(int, int, int) - Method in class loci.formats.ImageReader
-
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.ImageReader
-
- getIndex() - Method in class loci.formats.in.BaseZeissReader.Tag
-
- getIndex(int, int, int) - Method in class loci.formats.in.FilePatternReader
-
- getIndex() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the index associated with this Frame.
- getIndex(int, int, int) - Method in class loci.formats.ReaderWrapper
-
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
-
- getIndex(Double, Double, Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getIndexCount() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the number of recorded indices at this Sequence.
- getIndexMax() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the maximum index value.
- getIndexMin() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the minimum index value.
- getInfo() - Method in class loci.formats.in.SDTReader
-
Gets object containing SDT header information.
- getInfo() - Method in class loci.plugins.prefs.Option
-
Gets documentation about the option.
- getInfo(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the documentation for the option with the given key.
- getIniFile(String) - Method in class loci.formats.in.FV1000Reader
-
- getInputOrder() - Method in class loci.formats.DimensionSwapper
-
- getInputOrder(int) - Method in class loci.plugins.in.ImporterOptions
-
- getInputStream(String) - Method in interface loci.formats.services.POIService
-
Retrieve an InputStream corresponding to the given file name.
- getInputStream(String) - Method in class loci.formats.services.POIServiceImpl
-
- getInstance(int) - Static method in class loci.formats.gui.TwoChannelColorSpace
-
- getInt(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Integer entries into the SPE header table
- getInt(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve an Integer value from the SPE header
- getIntArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Integer Array entries into the SPE header table
- getIntArray() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getInteger(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as an Integer.
- getInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as an Integer.
- getInterpolate() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getInterpolatedPixel(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getInts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of signed integers, one per channel.
- getInts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of signed integers, one per channel.
- getInts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of signed integers, one per channel.
- getIntValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
-
- getJPEGBuf() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the JPEG image buffer associated with this decompressor instance.
- getJPEGSize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the size of the JPEG image (in bytes) associated with this
decompressor instance.
- getKey() - Method in class loci.formats.in.BaseZeissReader.Tag
-
- getKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag
-
Return the string corresponding to the given ID.
- getKey(int) - Method in class loci.formats.in.MetamorphReader
-
- getKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation
-
- getKey() - Method in class loci.plugins.prefs.Option
-
Gets the option's key name.
- getKeyID() - Method in class loci.formats.in.BaseZeissReader.Tag
-
- getLabel() - Method in class loci.plugins.prefs.Option
-
Gets label describing the option.
- getLabel(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the label for the option with the given key.
- getLabels() - Method in class loci.plugins.config.CellSensWidgets
-
- getLabels() - Method in class loci.plugins.config.FlexWidgets
-
- getLabels() - Method in interface loci.plugins.config.IFormatWidgets
-
- getLabels() - Method in class loci.plugins.config.LIFWidgets
-
- getLabels() - Method in class loci.plugins.config.ND2Widgets
-
- getLabels() - Method in class loci.plugins.config.PictWidgets
-
- getLabels() - Method in class loci.plugins.config.QTWidgets
-
- getLabels() - Method in class loci.plugins.config.SDTWidgets
-
- getLabels() - Method in class loci.plugins.config.TiffDelegateWidgets
-
- getLabels() - Method in class loci.plugins.config.ZeissCZIWidgets
-
- getLaserMedium(String) - Method in class loci.formats.FormatReader
-
Retrieves an LaserMedium enumeration
value for the given String.
- getLaserPower() - Method in class loci.formats.in.PrairieMetadata
-
Gets the first laserPower recorded in the configuration.
- getLaserType(String) - Method in class loci.formats.FormatReader
-
Retrieves an LaserType enumeration
value for the given String.
- getLast() - Method in class loci.formats.FilePattern
-
Gets the STOP element for all blocks.
- getLast() - Method in class loci.formats.FilePatternBlock
-
Gets the last element in a range block.
- getLatestVersion() - Method in interface loci.formats.services.OMEXMLService
-
Retrieves the latest supported version of the OME-XML schema.
- getLatestVersion() - Method in class loci.formats.services.OMEXMLServiceImpl
-
- getLength(RandomAccessInputStream, int) - Method in class loci.formats.in.DicomReader
-
- getLength(long) - Method in class loci.formats.in.OBFReader
-
- getLengths() - Method in class loci.formats.cache.CacheStrategy
-
- getLengths() - Method in interface loci.formats.cache.ICacheStrategy
-
Gets the lengths of all the axes.
- getLengths(IFormatReader) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for constructing lengths array, used by main.
- getLensNA() - Method in class loci.formats.in.MetamorphHandler
-
- getLensRI() - Method in class loci.formats.in.MetamorphHandler
-
- getLetter() - Method in class loci.formats.ResourceNamer
-
Returns a String representing a single letter (in the case
where the class instance has been initialized with a resource count lower
than 26) or a concatenation of two letters (if resource count is higher
than 26).
- getLicenseCode() - Method in interface loci.formats.services.LuraWaveService
-
Retrieves the current license code as a string.
- getLicenseCode() - Method in class loci.formats.services.LuraWaveServiceImpl
-
- getLine(double, double, double, double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getLinesPerFrame() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the lines per frame for this Frame.
- getLoadList(int[]) - Method in class loci.formats.cache.CacheStrategy
-
- getLoadList(int[]) - Method in interface loci.formats.cache.ICacheStrategy
-
Gets the indices of the objects to cache,
surrounding the object at the given position.
- getLocation() - Method in class loci.plugins.in.ImporterOptions
-
- getLocationFromResourceName(Location, String, int, String) - Method in class loci.formats.ResourceNamer
-
Creates a new Location instance using the provided parent path and
child node name.
- getLocationInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getLocations() - Method in class loci.plugins.in.ImporterOptions
-
- getLong(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a Long.
- getLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as a Long.
- getLong(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Long enteries into the SPE header table
- getLong(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a Long value from the SPE header
- getLongArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Long Array entries into the SPE header table
- getLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Convers an Index16ColorModel to a 2D short array.
- getLookupTable(Map) - Method in class loci.formats.in.AmiraReader
-
- getLookupTable() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the color lookup table stored in the file, or null if a lookup
table is not present.
- getLookupTableComponentCount() - Method in class loci.formats.ChannelFiller
-
Gets the number of color components in the lookup table.
- getLSMFileFromSeries(int) - Method in class loci.formats.in.ZeissLSMReader
-
- getLutNames() - Method in class loci.formats.in.LeicaHandler
-
- getLutUpdateMode() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getMagnification(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getMagnification() - Method in class loci.formats.in.ND2Handler
-
- getMagnification() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Extracts the magnification from the objective lens string.
- getMagnification() - Method in class loci.formats.in.SVSReader
-
- getMagnitudes() - Method in class loci.formats.in.IM3Reader.Spectrum
-
- getMap() - Method in class loci.formats.tools.AmiraParameters
-
- getMarker(String) - Method in class loci.formats.FormatReader
-
Retrieves an Marker enumeration
value for the given String.
- getMask() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getMaskArray() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getMax() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getMaxFieldCount(Integer) - Static method in class loci.formats.FormatTools
-
- getMaximumSize() - Method in class loci.formats.gui.CacheIndicator
-
- getMaximumSize() - Method in class loci.formats.gui.DataConverter.RowPanel
-
- getMaxThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getMCUHeight(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns the MCU block height for the given level of chrominance
subsampling.
- getMCUWidth(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns the MCU block width for the given level of chrominance
subsampling.
- getMDBFile(String) - Method in class loci.formats.in.ZeissLSMReader
-
- getMeasurementID() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- getMeasurementID() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getMeasurementName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- getMeasurementTime() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getMedium(String) - Method in class loci.formats.FormatReader
-
Retrieves an Medium enumeration
value for the given String.
- getMember(String) - Method in interface loci.formats.services.JHDFService
-
Retrieves the all members of a group.
- getMember(String) - Method in class loci.formats.services.JHDFServiceImpl
-
- getMemoFile(String) - Method in class loci.formats.Memoizer
-
Constructs a
File object from
id string.
- getMemoryUsage() - Method in class loci.plugins.in.ImportProcess
-
Gets a projection of required memory in bytes.
- getMessage() - Method in enum loci.plugins.in.ImportStep
-
- getMetadata() - Method in class loci.formats.in.ND2Handler
-
- getMetadataLevel() - Method in class loci.formats.in.DefaultMetadataOptions
-
- getMetadataLevel() - Method in class loci.formats.in.DynamicMetadataOptions
-
- getMetadataLevel() - Method in interface loci.formats.in.MetadataOptions
-
Get the configured metadata level.
- getMetadataOptions() - Method in class loci.formats.DelegateReader
-
- getMetadataOptions() - Method in class loci.formats.FormatHandler
-
- getMetadataOptions() - Method in class loci.formats.ImageReader
-
- getMetadataOptions() - Method in class loci.formats.ImageWriter
-
- getMetadataOptions() - Method in interface loci.formats.IMetadataConfigurable
-
- getMetadataOptions() - Method in class loci.formats.ReaderWrapper
-
- getMetadataOptions() - Method in class loci.formats.WriterWrapper
-
- getMetadataRetrieve() - Method in class loci.formats.FormatWriter
-
- getMetadataRetrieve() - Method in interface loci.formats.IFormatWriter
-
Retrieves the current metadata retrieval object for this writer.
- getMetadataRetrieve() - Method in class loci.formats.ImageWriter
-
- getMetadataRetrieve() - Method in class loci.formats.WriterWrapper
-
- getMetadataRoot(String) - Method in class loci.formats.in.LIFReader
-
- getMetadataStore() - Method in class loci.formats.FileStitcher
-
- getMetadataStore() - Method in class loci.formats.FormatReader
-
- getMetadataStore() - Method in interface loci.formats.IFormatReader
-
Retrieves the current metadata store for this reader.
- getMetadataStore() - Method in class loci.formats.ImageReader
-
- getMetadataStore() - Method in class loci.formats.in.FilePatternReader
-
- getMetadataStore() - Method in class loci.formats.Memoizer
-
- getMetadataStore() - Method in class loci.formats.ReaderWrapper
-
- getMetadataStoreForConversion() - Method in class loci.formats.in.OMETiffReader
-
- getMetadataStoreForDisplay() - Method in class loci.formats.in.OMETiffReader
-
- getMetadataStoreRoot() - Method in class loci.formats.FileStitcher
-
- getMetadataStoreRoot() - Method in class loci.formats.FormatReader
-
- getMetadataStoreRoot() - Method in interface loci.formats.IFormatReader
-
Retrieves the current metadata store's root object.
- getMetadataStoreRoot() - Method in class loci.formats.ImageReader
-
- getMetadataStoreRoot() - Method in class loci.formats.in.FilePatternReader
-
- getMetadataStoreRoot() - Method in class loci.formats.ReaderWrapper
-
- getMetadataString(String) - Method in class loci.plugins.in.ImporterMetadata
-
Returns a string with each key/value pair on its own line.
- getMetadataType() - Method in enum loci.formats.tiff.PhotoInterp
-
Retrieves the metadata type of the photometric interpretation.
- getMetadataValue(String) - Method in class loci.formats.FormatReader
-
- getMetadataValue(String) - Method in interface loci.formats.IFormatReader
-
Obtains the specified metadata field's value for the current file.
- getMetadataValue(String) - Method in class loci.formats.ImageReader
-
- getMetadataValue(String) - Method in class loci.formats.in.FilePatternReader
-
- getMetadataValue(String) - Method in class loci.formats.ReaderWrapper
-
- getMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getMethodStack() - Method in class loci.plugins.util.BFVirtualStack
-
- getMethodStack() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getMicrobeamManipulationType(String) - Method in class loci.formats.FormatReader
-
Retrieves an MicrobeamManipulationType
enumeration value for the given String.
- getMicronsPerPixelX() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the microns per pixel along X for this Frame.
- getMicronsPerPixelY() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the microns per pixel along Y for this Frame.
- getMicroscopeType(String) - Method in class loci.formats.FormatReader
-
Retrieves an MicroscopeType enumeration
value for the given String.
- getMin() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getMinimumSize() - Method in class loci.formats.gui.CacheIndicator
-
- getMinMaxCalculator() - Method in class loci.plugins.in.ImportProcess
-
- getMinMaxStore() - Method in class loci.formats.MinMaxCalculator
-
Retrieves the current active min-max store for the calculator.
- getMinThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getModalities() - Method in class loci.formats.in.ND2Handler
-
- getModality(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getModuloAlong(OMEXMLMetadata, String, int) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Create a
Modulo corresponding to the given ModuloAlong* tag.
- getModuloAlongC(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
-
Retrieve the ModuloAlongC annotation in the given Image in the given
OME-XML metadata object.
- getModuloAlongC(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- getModuloAlongT(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
-
Retrieve the ModuloAlongT annotation in the given Image in the given
OME-XML metadata object.
- getModuloAlongT(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- getModuloAlongZ(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
-
Retrieve the ModuloAlongZ annotation in the given Image in the given
OME-XML metadata object.
- getModuloAlongZ(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- getModuloC() - Method in class loci.formats.FormatReader
-
- getModuloC() - Method in interface loci.formats.IFormatReader
-
- getModuloC() - Method in class loci.formats.ImageReader
-
- getModuloC() - Method in class loci.formats.in.FilePatternReader
-
- getModuloC() - Method in class loci.formats.ReaderWrapper
-
- getModuloT() - Method in class loci.formats.FormatReader
-
- getModuloT() - Method in interface loci.formats.IFormatReader
-
- getModuloT() - Method in class loci.formats.ImageReader
-
- getModuloT() - Method in class loci.formats.in.FilePatternReader
-
- getModuloT() - Method in class loci.formats.ReaderWrapper
-
- getModuloZ() - Method in class loci.formats.FormatReader
-
- getModuloZ() - Method in interface loci.formats.IFormatReader
-
- getModuloZ() - Method in class loci.formats.ImageReader
-
- getModuloZ() - Method in class loci.formats.in.FilePatternReader
-
- getModuloZ() - Method in class loci.formats.ReaderWrapper
-
- getMontage(int) - Method in class loci.formats.in.FluoviewReader
-
- getMustGroupInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getNA(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getName() - Method in enum loci.formats.codec.JPEG2000BoxType
-
Returns the name of the box type.
- getName() - Method in enum loci.formats.codec.JPEG2000SegmentMarker
-
Returns the name of the segment marker.
- getName(int) - Method in class loci.formats.gui.TwoChannelColorSpace
-
- getName() - Method in enum loci.formats.in.BaseZeissReader.Charset
-
- getName() - Method in class loci.formats.in.IM3Reader.Spectrum
-
- getName(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
- getName() - Method in enum loci.formats.tiff.PhotoInterp
-
Retrieves the given name of the photometric interpretation.
- getNamingConvention(String) - Method in class loci.formats.FormatReader
-
Retrieves an NamingConvention enumeration
value for the given String.
- getNativeDataType() - Method in class loci.formats.ChannelFiller
-
- getNativeDataType() - Method in class loci.formats.ChannelMerger
-
- getNativeDataType() - Method in class loci.formats.ChannelSeparator
-
- getNativeDataType() - Method in class loci.formats.FormatHandler
-
- getNativeDataType() - Method in interface loci.formats.IFormatHandler
-
- getNativeDataType() - Method in class loci.formats.ImageReader
-
- getNativeDataType() - Method in class loci.formats.ImageWriter
-
- getNativeDataType() - Method in class loci.formats.in.BIFormatReader
-
- getNativeDataType() - Method in class loci.formats.in.FilePatternReader
-
- getNativeDataType() - Method in class loci.formats.in.TextReader
-
- getNativeDataType() - Method in class loci.formats.MinMaxCalculator
-
- getNativeDataType() - Method in class loci.formats.out.ImageIOWriter
-
- getNativeDataType() - Method in class loci.formats.out.LegacyQTWriter
-
- getNativeDataType() - Method in class loci.formats.ReaderWrapper
-
- getNativeDataType() - Method in class loci.formats.TileStitcher
-
- getNativeDataType() - Method in class loci.formats.WriterWrapper
-
- getNativeDataType() - Method in class loci.plugins.util.ImageProcessorReader
-
- getNChannels() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getNextLine(List<String>) - Method in class loci.formats.in.TextReader
-
- getNextOffset(long) - Method in class loci.formats.tiff.TiffParser
-
Read a file offset.
- getNextTag(RandomAccessInputStream) - Method in class loci.formats.in.DicomReader
-
- getNextTag(RandomAccessInputStream, boolean) - Method in class loci.formats.in.DicomReader
-
- getNextTag(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
-
- getNodes(Element, String) - Method in class loci.formats.in.LIFReader
-
- getNonThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser
-
Returns non-thumbnail IFDs.
- getNoWlzMsg() - Method in interface loci.formats.services.WlzService
-
Gets the text string for when Woolz has not been found.
- getNoWlzMsg() - Method in class loci.formats.services.WlzServiceImpl
-
- getNum() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns numerator
- getNumber(String) - Method in class loci.formats.NumberFilter
-
Gets numbers filling the asterisk positions.
- getNumBytes(int) - Method in class loci.formats.in.GatanReader
-
- getNumComponents() - Method in class loci.formats.gui.TwoChannelColorSpace
-
- getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record
-
Get the # of boolean values in this record
- getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
-
Get the # of floating-point values in this record
- getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.IntIM3Record
-
Get the # of integer values in this record
- getNumerator() - Method in class loci.formats.tiff.TiffRational
-
Gets this number's numerator.
- getNumericalAperture() - Method in class loci.formats.in.ND2Handler
-
- getNumericFields(GenericDialog) - Method in class loci.plugins.in.ColorDialog
-
- getNumericFields(GenericDialog) - Static method in class loci.plugins.util.WindowTools
-
- getNumSeries() - Method in class loci.formats.in.LegacyND2Reader
-
- getObject(int) - Method in class loci.formats.cache.ByteArraySource
-
- getObject(int[]) - Method in class loci.formats.cache.Cache
-
Gets the cached object at the given dimensional position.
- getObject(int) - Method in class loci.formats.cache.CacheSource
-
- getObject(int) - Method in interface loci.formats.cache.ICacheSource
-
Get the object corresponding to the given index.
- getObject(int) - Method in class loci.formats.gui.BufferedImageSource
-
- getObject(int) - Method in class loci.plugins.util.ImageProcessorSource
-
- getObjectCount() - Method in class loci.formats.cache.CacheSource
-
- getObjectCount() - Method in interface loci.formats.cache.ICacheSource
-
Get the total number of objects that this source can retrieve.
- getObjectCount() - Method in class loci.formats.gui.BufferedImageSource
-
- getObjectCount() - Method in class loci.plugins.util.ImageProcessorSource
-
- getObjectiveLens() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the objective lens string for this Frame.
- getObjectiveLensNA() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the numerical aperture of the lens for this Frame.
- getObjectiveManufacturer() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Extracts the objective manufacturer from the objective lens string.
- getObjectiveModel() - Method in class loci.formats.in.ND2Handler
-
- getObjectiveName(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getOffset(int) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the cth offset for this Frame.
- getOMEMetadata(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
-
Returns a
OMEXMLMetadata object with the same
contents as the given MetadataRetrieve, converting it if necessary.
- getOMEMetadata(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- getOMEMetadata() - Method in class loci.plugins.in.ImportProcess
-
- getOMEXML(String) - Method in class loci.formats.out.OMETiffWriter
-
- getOMEXML(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
-
Extracts an OME-XML metadata string from the given metadata object,
by converting to an OME-XML metadata object if necessary.
- getOMEXML(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- getOMEXML() - Method in class loci.plugins.in.ImportProcess
-
- getOmeXmlMetadata() - Method in class loci.formats.in.FakeReader
-
- getOmeXmlService() - Method in class loci.formats.in.FakeReader
-
- getOMEXMLVersion(Object) - Method in interface loci.formats.services.OMEXMLService
-
Gets the schema version for the given OME-XML metadata or root object
(e.g., "2007-06" or "2003-FC").
- getOMEXMLVersion(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- getOnDemandStripOffsets() - Method in class loci.formats.tiff.IFD
-
- getOpenAllSeriesInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getOpticalZoom() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the optical zoom associated with this Frame.
- getOptimalTileHeight() - Method in class loci.formats.DelegateReader
-
- getOptimalTileHeight() - Method in class loci.formats.FormatReader
-
- getOptimalTileHeight() - Method in interface loci.formats.IFormatReader
-
Returns the optimal sub-image height for use with openBytes.
- getOptimalTileHeight() - Method in class loci.formats.ImageReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.AFIReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.AmiraReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.APLReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.BaseZeissReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.BDReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.BioRadReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.CellH5Reader
-
- getOptimalTileHeight() - Method in class loci.formats.in.CellSensReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.EPSReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.FilePatternReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.FlexReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.FV1000Reader
-
- getOptimalTileHeight() - Method in class loci.formats.in.HamamatsuVMSReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.ImageIOReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.ImarisHDFReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.InCellReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.IPWReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.L2DReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.LeicaReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.LeicaSCNReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.LIFReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.MIASReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.MicromanagerReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.MinimalTiffReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.ND2Reader
-
- getOptimalTileHeight() - Method in class loci.formats.in.NDPIReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.NDPISReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.NRRDReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.OMETiffReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.OpenlabReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.PCIReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.PerkinElmerReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.PrairieReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.PyramidTiffReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.ScanrReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.SVSReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.TrestleReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.VisitechReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.ZeissCZIReader
-
- getOptimalTileHeight() - Method in class loci.formats.in.ZeissLSMReader
-
- getOptimalTileHeight() - Method in class loci.formats.ReaderWrapper
-
- getOptimalTileWidth() - Method in class loci.formats.DelegateReader
-
- getOptimalTileWidth() - Method in class loci.formats.FormatReader
-
- getOptimalTileWidth() - Method in interface loci.formats.IFormatReader
-
Returns the optimal sub-image width for use with openBytes.
- getOptimalTileWidth() - Method in class loci.formats.ImageReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.AFIReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.APLReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.BDReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.CellSensReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.EPSReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.FilePatternReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.FlexReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.FV1000Reader
-
- getOptimalTileWidth() - Method in class loci.formats.in.HamamatsuVMSReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.ImarisHDFReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.InCellReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.IPWReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.L2DReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.LeicaReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.LeicaSCNReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.MIASReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.MicromanagerReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.MinimalTiffReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.NDPIReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.NDPISReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.OMETiffReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.PCIReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.PerkinElmerReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.PrairieReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.PyramidTiffReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.ScanrReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.SVSReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.TrestleReader
-
- getOptimalTileWidth() - Method in class loci.formats.in.ZeissCZIReader
-
- getOptimalTileWidth() - Method in class loci.formats.ReaderWrapper
-
- getOptimalWidth() - Method in class loci.formats.in.ZeissLSMReader
-
- getOption(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the option with the given key.
- getOptions() - Method in class loci.formats.ClassList
-
Gets the list of options as a map.
- getOptions(CodecOptions) - Static method in class loci.formats.codec.WrappedCodec
-
- getOptions() - Method in class loci.plugins.in.ImportProcess
-
- getOrder() - Method in class loci.formats.cache.CacheStrategy
-
- getOrder() - Method in interface loci.formats.cache.ICacheStrategy
-
Retrieves the order in which objects should be loaded along each axis.
- getOrgX() - Method in interface loci.formats.services.WlzService
-
Gets column origin.
- getOrgX() - Method in class loci.formats.services.WlzServiceImpl
-
- getOrgY() - Method in interface loci.formats.services.WlzService
-
Gets line origin.
- getOrgY() - Method in class loci.formats.services.WlzServiceImpl
-
- getOrgZ() - Method in interface loci.formats.services.WlzService
-
Gets plane origin.
- getOrgZ() - Method in class loci.formats.services.WlzServiceImpl
-
- getOriginalIndex(int) - Method in class loci.formats.ChannelMerger
-
Returns the image number in the original dataset that corresponds to the
given image number.
- getOriginalIndex(int) - Method in class loci.formats.ChannelSeparator
-
Returns the image number in the original dataset that corresponds to the
given image number.
- getOriginalMetadata(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
-
Parse any OriginalMetadata annotations from the given OME-XML metadata
object and store them in a Hashtable.
- getOriginalMetadata(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- getOriginalMetadata() - Method in class loci.plugins.in.ImportProcess
-
- getOriginalOrder() - Method in class loci.formats.AxisGuesser
-
Gets the original dimension order.
- getOriginalOrder() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getParent(int) - Method in class loci.formats.in.LeicaSCNReader
-
- getPath(PrairieMetadata.PFile) - Method in class loci.formats.in.PrairieReader
-
- getPath() - Method in class loci.plugins.util.BFVirtualStack
-
- getPattern() - Method in class loci.formats.FilePattern
-
Gets the file pattern string.
- getPhotometricInterpretation() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's photometric interpretation (TIFF tag
PhotometricInterpretation) from this IFD.
- getPhysicalSize(Double, String) - Static method in class loci.formats.FormatTools
-
- getPhysicalSizes() - Method in class loci.formats.in.SVSReader
-
- getPhysicalSizeX(Double) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in X into a length in
microns
- getPhysicalSizeX(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in X into a length of the
given unit.
- getPhysicalSizeX(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in X into a length of the
given unit.
- getPhysicalSizeY(Double) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Y into a length in
microns
- getPhysicalSizeY(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Y into a length of the
given unit.
- getPhysicalSizeY(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Y into a length of the
given unit.
- getPhysicalSizeZ(Double) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Z into a length in
microns.
- getPhysicalSizeZ(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Z into a length of the
given unit.
- getPhysicalSizeZ(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Z into a length of the
given unit.
- getPictDimensions(byte[]) - Method in class loci.formats.gui.LegacyQTTools
-
Gets width and height for the given PICT bytes.
- getPinholeSize() - Method in class loci.formats.in.ND2Handler
-
- getPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getPixelBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Return a 2D array of bytes representing the image.
- getPixelBytes(WritableRaster, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Return a 2D array of bytes representing the image.
- getPixelBytes(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Return a 2D array of bytes representing the image.
- getPixelBytes(WritableRaster, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Return a 2D array of bytes representing the image.
- getPixelCount() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getPixelInterpolated(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getPixels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the image's pixel data as arrays of primitives, one per channel.
- getPixels(BufferedImage, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the image's pixel data as arrays of primitives, one per channel.
- getPixels(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the raster's pixel data as arrays of primitives, one per channel.
- getPixels(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the raster's pixel data as arrays of primitives, one per channel.
- getPixels() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getPixelsCopy() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getPixelSize(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns the pixel size (in bytes) of the given pixel format.
- getPixelSizeX() - Method in class loci.formats.in.MetamorphHandler
-
- getPixelSizeX() - Method in class loci.formats.in.ND2Handler
-
- getPixelSizeY() - Method in class loci.formats.in.MetamorphHandler
-
- getPixelSizeY() - Method in class loci.formats.in.ND2Handler
-
- getPixelSizeZ() - Method in class loci.formats.in.ND2Handler
-
- getPixelsPerLine() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the pixels per line for this Frame.
- getPixelsPhysicalSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getPixelsPhysicalSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getPixelsPhysicalSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getPixelsTimeIncrement(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getPixelString(int) - Method in class loci.formats.in.DeltavisionReader
-
Get a descriptive string representing the pixel type.
- getPixelType() - Method in class loci.formats.FileStitcher
-
- getPixelType() - Method in class loci.formats.FormatReader
-
- getPixelType(String) - Method in class loci.formats.FormatReader
-
Retrieves an PixelType enumeration
value for the given String.
- getPixelType(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the pixel type of the given image.
- getPixelType() - Method in interface loci.formats.IFormatReader
-
Gets the pixel type.
- getPixelType() - Method in class loci.formats.ImageReader
-
- getPixelType(int) - Method in class loci.formats.in.DeltavisionReader
-
Get the OME pixel type from the pixel type stored in the file.
- getPixelType() - Method in class loci.formats.in.FilePatternReader
-
- getPixelType(int) - Method in class loci.formats.in.OBFReader
-
- getPixelType() - Method in class loci.formats.ReaderWrapper
-
- getPixelType() - Method in interface loci.formats.services.WlzService
-
Gets the image pixel type.
- getPixelType() - Method in class loci.formats.services.WlzServiceImpl
-
- getPixelType() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's pixel type based on the BitsPerSample tag.
- getPixelType(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getPixelTypeFromString(String) - Method in class loci.formats.in.LiFlimReader
-
- getPixelTypes() - Method in class loci.formats.FormatWriter
-
- getPixelTypes(String) - Method in class loci.formats.FormatWriter
-
- getPixelTypes() - Method in interface loci.formats.IFormatWriter
-
Gets the supported pixel types.
- getPixelTypes(String) - Method in interface loci.formats.IFormatWriter
-
Gets the supported pixel types for the given codec.
- getPixelTypes() - Method in class loci.formats.ImageWriter
-
- getPixelTypes(String) - Method in class loci.formats.ImageWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.APNGWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.AVIWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.CellH5Writer
-
- getPixelTypes(String) - Method in class loci.formats.out.EPSWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.ICSWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.ImageIOWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.JavaWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.JPEG2000Writer
-
Overridden to return the formats supported by the writer.
- getPixelTypes(String) - Method in class loci.formats.out.JPEGWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.OMEXMLWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.QTWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.TiffWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.V3DrawWriter
-
- getPixelTypes(String) - Method in class loci.formats.out.WlzWriter
-
- getPixelTypes() - Method in class loci.formats.WriterWrapper
-
- getPixelTypes(String) - Method in class loci.formats.WriterWrapper
-
- getPixelTypeString(int) - Static method in class loci.formats.FormatTools
-
Takes a pixel type value and gets a corresponding string representation.
- getPixelValue(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getPlanarConfiguration() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's planar configuration (TIFF tag PlanarConfiguration)
from this IFD.
- getPlane(int, int) - Method in class loci.formats.in.FV1000Reader
-
- getPlane(int[]) - Method in class loci.formats.in.OpenlabReader
-
- getPlaneByteOffset(int, int, int) - Method in class loci.formats.in.DeltavisionReader
-
Given any specific Z, W, and T of a plane, determine the absolute
byte offset of the plane in the file.
- getPlaneCount() - Method in class loci.formats.FormatWriter
-
Retrieve the total number of planes in the current series.
- getPlaneCount(int) - Method in class loci.formats.FormatWriter
-
Retrieve the total number of planes in given series.
- getPlaneCount() - Method in class loci.formats.out.CellH5Writer
-
- getPlaneCount() - Method in class loci.formats.out.TiffWriter
-
- getPlaneCount(int) - Method in class loci.formats.out.TiffWriter
-
- getPlaneIndex(IFormatReader, int) - Static method in class loci.plugins.macro.LociFunctions
-
Finds the Plane index corresponding to the given image plane number.
- getPlaneMaximum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves the maximum pixel value for the specified plane.
- getPlaneMinimum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves the minimum pixel value for the specified plane.
- getPlanePositionX(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
-
- getPlanePositionY(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
-
- getPlanePositionZ(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
-
- getPlanes() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getPlaneSize(IFormatReader) - Static method in class loci.formats.FormatTools
-
Returns the size in bytes of a single plane.
- getPlaneSize(IFormatReader, int, int) - Static method in class loci.formats.FormatTools
-
Returns the size in bytes of a w * h tile.
- getPlanesToLoad(int) - Method in class loci.plugins.in.ImagePlusReader
-
- getPlaneTimingDeltaT(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
-
- getPlaneTimingExposureTime(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
-
- getPlateColumns() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- getPlateColumns() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getPlateDescription() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getPlateIdentifier() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getPlateName(String) - Method in class loci.formats.in.CellomicsReader
-
- getPlateName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- getPlateName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getPlateRows() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- getPlateRows() - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- getPlateType() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- getPoints() - Method in enum loci.formats.in.BaseZeissReader.FeatureType
-
- getPoints(int) - Method in class loci.formats.in.FakeReader
-
- getPos(int) - Method in class loci.formats.in.FluoviewReader
-
- getPosition(int) - Method in class loci.formats.in.ZeissLSMReader
-
- getPositionFromFile(String) - Method in class loci.formats.in.MIASReader
-
Returns an array of length 5 that contains the well, time point,
Z and channel indices corresponding to the given analysis file.
- getPositionNames() - Method in class loci.formats.in.ND2Handler
-
- getPositionX() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the X stage position associated with this Frame.
- getPositionY() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the Y stage position associated with this Frame.
- getPositionZ() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the Z stage position associated with this Frame.
- getPossible(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the possible values for the string option with the given key.
- getPossible() - Method in class loci.plugins.prefs.StringOption
-
Gets the list of possible values.
- getPossibleDomains(String) - Method in class loci.formats.FormatReader
-
- getPossibleDomains(String) - Method in interface loci.formats.IFormatReader
-
Returns a list of scientific domains in which this format is used.
- getPossibleDomains(String) - Method in class loci.formats.ImageReader
-
- getPossibleDomains(String) - Method in class loci.formats.in.FilePatternReader
-
- getPossibleDomains(String) - Method in class loci.formats.ReaderWrapper
-
- getPossiblePositions() - Method in class loci.formats.cache.CacheStrategy
-
Gets positions to consider for possible inclusion in the cache,
assuming a current position at the origin (0).
- getPossiblePositions() - Method in class loci.formats.cache.CrosshairStrategy
-
- getPossiblePositions() - Method in class loci.formats.cache.RectangleStrategy
-
- getPowers() - Method in class loci.formats.in.ND2Handler
-
- getPref(String, Class<? extends IFormatReader>, boolean) - Static method in class loci.plugins.util.LociPrefs
-
- getPreferredSize() - Method in class loci.formats.gui.CacheIndicator
-
- getPreferredSize() - Method in class loci.formats.gui.PreviewPane
-
- getPrefix() - Method in class loci.formats.FilePattern
-
Gets the pattern's substring that comes before any block sections.
- getPrefix(int) - Method in class loci.formats.FilePattern
-
Gets the pattern's substring between block i-1 (or the beginning
of the pattern, if i is 0) and block i.
- getPrefix(String) - Method in class loci.formats.in.ZeissTIFFReader
-
- getPrefixes() - Method in class loci.formats.FilePattern
-
Gets all block prefixes.
- getPrefixMetadataName(String) - Method in class loci.formats.in.MicromanagerReader
-
- getPreviewNameIndex(String) - Method in class loci.formats.in.FV1000Reader
-
- getPriorities() - Method in class loci.formats.cache.CacheStrategy
-
- getPriorities() - Method in interface loci.formats.cache.ICacheStrategy
-
Retrieves the priority for caching each axis.
- getProcessor(int) - Method in class loci.plugins.util.BFVirtualStack
-
- getPulse(String) - Method in class loci.formats.FormatReader
-
Retrieves an Pulse enumeration
value for the given String.
- getQTVersion() - Method in class loci.formats.gui.LegacyQTTools
-
Gets the QuickTime for Java version number.
- getQuietInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getRange() - Method in class loci.formats.cache.CacheStrategy
-
- getRange() - Method in interface loci.formats.cache.ICacheStrategy
-
Retrieves the number of objects to cache along each axis.
- getRasterLength(int[]) - Static method in class loci.formats.FormatTools
-
Computes the number of raster values for a positional array
with the given lengths.
- getReader(int) - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getReader() - Method in class loci.formats.FileStitcher
-
Gets the wrapped reader prototype.
- getReader(int) - Method in class loci.formats.FileStitcher
-
Gets the reader appropriate for use with the given image plane.
- getReader(int, int) - Method in class loci.formats.FileStitcher
-
Gets the reader that should be used with the given series and image plane.
- getReader(IFormatReader, Class<? extends IFormatReader>) - Static method in class loci.formats.FormatTools
-
Recursively look for the first underlying reader that is an
instance of the given class.
- getReader() - Method in class loci.formats.gui.FormatFileFilter
-
Returns the filter's reader.
- getReader(String) - Method in class loci.formats.ImageReader
-
Gets the reader used to open the given file.
- getReader() - Method in class loci.formats.ImageReader
-
Gets the reader used to open the current file.
- getReader(Class<? extends IFormatReader>) - Method in class loci.formats.ImageReader
-
Gets the file format reader instance matching the given class.
- getReader(String, boolean) - Method in class loci.formats.in.CellWorxReader
-
- getReader() - Method in class loci.formats.ReaderWrapper
-
Gets the wrapped reader.
- getReader() - Method in class loci.formats.services.JAIIIOServiceImpl
-
Set up the JPEG-2000 image reader.
- getReader() - Method in class loci.plugins.in.ImportProcess
-
- getReader() - Method in class loci.plugins.util.BFVirtualStack
-
- getReaders() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getReaders() - Method in class loci.formats.ImageReader
-
Gets all constituent file format readers.
- getReadOutRate() - Method in class loci.formats.in.MetamorphHandler
-
- getRealSTKFile(Location) - Method in class loci.formats.in.MetamorphReader
-
Check that the given STK file exists.
- getRecordedProcessor() - Method in class loci.plugins.util.BFVirtualStack
-
- getRed(int) - Method in class loci.formats.gui.Index16ColorModel
-
- getRed(int) - Method in class loci.formats.gui.SignedColorModel
-
- getRed(Object) - Method in class loci.formats.gui.SignedColorModel
-
- getRed(int) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getRed(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- getRedOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
For the given pixel format, returns the number of bytes that the red
component is offset from the start of the pixel.
- getReds() - Method in class loci.formats.gui.Index16ColorModel
-
Return the array of red color components.
- getRefractiveIndex() - Method in class loci.formats.in.ND2Handler
-
- getRelativeTime() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the relativeTime associated with this Frame.
- getReorderedIndex(IFormatReader, String, int) - Static method in class loci.formats.FormatTools
-
Converts index from the given dimension order to the reader's native one.
- getReorderedIndex(String, String, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Converts index from one dimension order to another.
- getRequiredDirectories(String[]) - Method in class loci.formats.FileStitcher
-
- getRequiredDirectories(String[]) - Method in class loci.formats.FormatReader
-
- getRequiredDirectories(String[]) - Method in interface loci.formats.IFormatReader
-
Returns the number of parent directories that are important when
processing the given list of files.
- getRequiredDirectories(String[]) - Method in class loci.formats.ImageReader
-
- getRequiredDirectories(String[]) - Method in class loci.formats.in.BrukerReader
-
- getRequiredDirectories(String[]) - Method in class loci.formats.in.CellVoyagerReader
-
- getRequiredDirectories(String[]) - Method in class loci.formats.in.ColumbusReader
-
- getRequiredDirectories(String[]) - Method in class loci.formats.in.DicomReader
-
- getRequiredDirectories(String[]) - Method in class loci.formats.in.MIASReader
-
- getRequiredDirectories(String[]) - Method in class loci.formats.in.OperettaReader
-
- getRequiredDirectories(String[]) - Method in class loci.formats.ReaderWrapper
-
- getResolution() - Method in class loci.formats.FormatReader
-
- getResolution() - Method in interface loci.formats.IFormatReader
-
Get the current resolution level.
- getResolution() - Method in class loci.formats.ImageReader
-
- getResolution() - Method in class loci.formats.in.FilePatternReader
-
- getResolution() - Method in class loci.formats.ReaderWrapper
-
- getResolutionCount() - Method in class loci.formats.FormatReader
-
- getResolutionCount() - Method in interface loci.formats.IFormatReader
-
Return the number of resolutions for the current series.
- getResolutionCount() - Method in class loci.formats.ImageReader
-
- getResolutionCount() - Method in class loci.formats.in.FilePatternReader
-
- getResolutionCount() - Method in class loci.formats.ReaderWrapper
-
- getResolutionLevels() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the number of resolution levels the file JPEG 2000 data has.
- getResolutionMultiplier() - Method in class loci.formats.tiff.IFD
-
Retrieve the value by which to multiply the X and Y resolution so that
the resolutions are in microns per pixel.
- getResolutionUnitFromComment(IFD) - Method in class loci.formats.in.BaseTiffReader
-
Extracts the resolution unit symbol from the comment field
- getRestartMarkers() - Method in interface loci.formats.services.JPEGTurboService
-
- getRestartMarkers() - Method in class loci.formats.services.JPEGTurboServiceImpl
-
- getRevision(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getRGBChannelCount() - Method in class loci.formats.FormatReader
-
- getRGBChannelCount() - Method in interface loci.formats.IFormatReader
-
Gets the number of channels returned with each call to openBytes.
- getRGBChannelCount() - Method in class loci.formats.ImageReader
-
- getRGBChannelCount() - Method in class loci.formats.in.FilePatternReader
-
- getRGBChannelCount() - Method in class loci.formats.ReaderWrapper
-
- getRGBChannelCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getRoi() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getROIs() - Method in class loci.formats.in.ND2Handler
-
- getROIs() - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table
- getROIsMode() - Method in class loci.plugins.in.ImporterOptions
-
- getROIsModeInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getROIsModes() - Method in class loci.plugins.in.ImporterOptions
-
- getRotationTransform(double) - Method in class loci.formats.FormatReader
-
Construct an AffineTransform corresponding to
the given angle.
- getRow() - Method in class loci.formats.in.OMEXMLReader.BinData
-
- getRow(String) - Method in class loci.formats.in.ScreenReader
-
- getRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getRowAndColumn(int) - Method in class loci.formats.in.ScreenReader
-
- getRowCount(int) - Method in interface loci.formats.services.MetakitService
-
- getRowCount(String) - Method in interface loci.formats.services.MetakitService
-
- getRowCount(int) - Method in class loci.formats.services.MetakitServiceImpl
-
- getRowCount(String) - Method in class loci.formats.services.MetakitServiceImpl
-
- getRowData(String[], double[]) - Method in class loci.formats.in.TextReader
-
Parses numerical row data from the given tokens.
- getRowData(int, String) - Method in interface loci.formats.services.MetakitService
-
- getRowData(int, int) - Method in interface loci.formats.services.MetakitService
-
- getRowData(int, String) - Method in class loci.formats.services.MetakitServiceImpl
-
- getRowData(int, int) - Method in class loci.formats.services.MetakitServiceImpl
-
- getRowsPerStrip() - Method in class loci.formats.tiff.IFD
-
Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip)
from this IFD.
- getSample(BitBuffer, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
-
Deprecated.
- getSample(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
-
- getSamples(IFD, byte[]) - Method in class loci.formats.tiff.TiffParser
-
- getSamples(IFD, byte[], int, int, long, long) - Method in class loci.formats.tiff.TiffParser
-
- getSamples(IFD, byte[], int, int, long, long, int, int) - Method in class loci.formats.tiff.TiffParser
-
- getSamplesPerPixel() - Method in class loci.formats.FormatWriter
-
Retrieve the number of samples per pixel for the current series.
- getSamplesPerPixel(int) - Method in class loci.formats.FormatWriter
-
Retrieve the number of samples per pixel for given series.
- getSamplesPerPixel() - Method in class loci.formats.tiff.IFD
-
Retrieves the number of samples per pixel for the image (TIFF tag
SamplesPerPixel) from this IFD.
- getScaled(int) - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns the scaled value of dimension.
- getScaledHeight(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the height of the largest scaled down image that the TurboJPEG
decompressor can generate without exceeding the desired image width and
height.
- getScaledWidth(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the width of the largest scaled down image that the TurboJPEG
decompressor can generate without exceeding the desired image width and
height.
- getScalingFactors() - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns a list of fractional scaling factors that the JPEG decompressor in
this implementation of TurboJPEG supports.
- getScanline(int) - Method in class loci.formats.codec.JPEGTileDecoder
-
- getScanlinePad() - Method in class loci.formats.in.NativeND2Reader
-
- getScanNames() - Method in class loci.formats.in.L2DReader
-
Return a list of scan names.
- getScreenName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- getSequence() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the <Sequence> containing this <Frame>.
- getSequence(int) - Method in class loci.formats.in.PrairieMetadata
-
Gets the Sequence at the given cycle.
- getSequences() - Method in class loci.formats.in.PrairieMetadata
-
Gets all Sequences, ordered by cycle.
- getSeries() - Method in class loci.formats.FileStitcher
-
- getSeries() - Method in class loci.formats.FormatReader
-
- getSeries() - Method in class loci.formats.FormatWriter
-
- getSeries() - Method in interface loci.formats.IFormatReader
-
Gets the currently active series.
- getSeries() - Method in interface loci.formats.IFormatWriter
-
Returns the current series.
- getSeries() - Method in class loci.formats.ImageReader
-
- getSeries() - Method in class loci.formats.ImageWriter
-
- getSeries() - Method in class loci.formats.in.FilePatternReader
-
- getSeries() - Method in class loci.formats.ReaderWrapper
-
- getSeries() - Method in class loci.formats.WriterWrapper
-
- getSeries(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getSeriesCount() - Method in class loci.formats.FileStitcher
-
- getSeriesCount() - Method in class loci.formats.FormatReader
-
- getSeriesCount() - Method in interface loci.formats.IFormatReader
-
Gets the number of series in this file.
- getSeriesCount() - Method in class loci.formats.ImageReader
-
- getSeriesCount() - Method in class loci.formats.in.FilePatternReader
-
- getSeriesCount() - Method in class loci.formats.in.ND2Handler
-
- getSeriesCount() - Method in class loci.formats.ReaderWrapper
-
- getSeriesCount() - Method in class loci.formats.TileStitcher
-
- getSeriesCount() - Method in class loci.plugins.in.ImportProcess
-
- getSeriesCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getSeriesHashtable(int) - Method in class loci.formats.in.LeicaHandler
-
- getSeriesIndex(int, int, int) - Method in class loci.formats.in.MetamorphTiffReader
-
- getSeriesIndex(int, int) - Method in class loci.formats.in.ScreenReader
-
- getSeriesLabel(int) - Method in class loci.plugins.in.ImportProcess
-
- getSeriesMeta(String) - Method in class loci.formats.FormatReader
-
Gets an entry from the metadata table for the current series.
- getSeriesMetadata() - Method in class loci.formats.FileStitcher
-
- getSeriesMetadata() - Method in class loci.formats.FormatReader
-
- getSeriesMetadata() - Method in interface loci.formats.IFormatReader
-
Obtains the hashtable containing metadata field/value pairs from the
current series in the current file.
- getSeriesMetadata() - Method in class loci.formats.ImageReader
-
- getSeriesMetadata() - Method in class loci.formats.in.FilePatternReader
-
- getSeriesMetadata() - Method in class loci.formats.ReaderWrapper
-
- getSeriesMetadataValue(String) - Method in class loci.formats.FormatReader
-
- getSeriesMetadataValue(String) - Method in interface loci.formats.IFormatReader
-
Obtains the specified metadata field's value for the current series
in the current file.
- getSeriesMetadataValue(String) - Method in class loci.formats.ImageReader
-
- getSeriesMetadataValue(String) - Method in class loci.formats.in.FilePatternReader
-
- getSeriesMetadataValue(String) - Method in class loci.formats.ReaderWrapper
-
- getSeriesMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getSeriesName(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.DelegateReader
-
- getSeriesUsedFiles() - Method in class loci.formats.FileStitcher
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
-
- getSeriesUsedFiles() - Method in class loci.formats.FormatReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
-
- getSeriesUsedFiles() - Method in interface loci.formats.IFormatReader
-
Returns an array of filenames needed to open the current series.
- getSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Returns an array of filenames needed to open the current series.
- getSeriesUsedFiles() - Method in class loci.formats.ImageReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AFIReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AnalyzeReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.APLReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BDReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BioRadReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BrukerReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellomicsReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellSensReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellVoyagerReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellWorxReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ColumbusReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DeltavisionReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DicomReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FakeReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FlexReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FujiReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FV1000Reader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HitachiReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ICSReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImagicReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.InCellReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JEOLReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JPEGReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.L2DReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LeicaReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetamorphReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MIASReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicromanagerReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NativeQTReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NDPISReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NiftiReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NRRDReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OMETiffReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PCORAWReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PDSReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PerkinElmerReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PrairieReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ScanrReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ScreenReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SlidebookTiffReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SPCReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TCSReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TiffReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TillVisionReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TrestleReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VarianFDFReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VisitechReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VolocityReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissCZIReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissLSMReader
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissTIFFReader
-
- getSeriesUsedFiles() - Method in class loci.formats.ReaderWrapper
-
- getSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
-
- getService() - Method in class loci.formats.Memoizer
-
- getShape(String) - Method in interface loci.formats.services.JHDFService
-
Retrieves the shape of a dataset.
- getShape(String) - Method in class loci.formats.services.JHDFServiceImpl
-
- getShort(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Short entries into the SPE header table
- getShort(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a Short value from the SPE header
- getShortArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Short Array entries into the SPE header table
- getShorts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned shorts, one per channel.
- getShorts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned shorts, one per channel.
- getShorts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned shorts, one per channel.
- getShowMetadataInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getShowOMEXMLInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getShowROIsInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getSize(Image) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the width and height of the given AWT image,
waiting for it to finish loading if necessary.
- getSize() - Method in class loci.plugins.util.BFVirtualStack
-
- getSizeC() - Method in class loci.formats.ChannelFiller
-
- getSizeC() - Method in class loci.formats.DimensionSwapper
-
- getSizeC() - Method in class loci.formats.FileStitcher
-
- getSizeC() - Method in class loci.formats.FormatReader
-
- getSizeC() - Method in interface loci.formats.IFormatReader
-
Gets the size of the C dimension.
- getSizeC() - Method in class loci.formats.ImageReader
-
- getSizeC() - Method in class loci.formats.in.FilePatternReader
-
- getSizeC() - Method in class loci.formats.ReaderWrapper
-
- getSizeC() - Method in interface loci.formats.services.WlzService
-
Gets number of channels.
- getSizeC() - Method in class loci.formats.services.WlzServiceImpl
-
- getSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getSizeT() - Method in class loci.formats.DimensionSwapper
-
- getSizeT() - Method in class loci.formats.FileStitcher
-
- getSizeT() - Method in class loci.formats.FormatReader
-
- getSizeT() - Method in interface loci.formats.IFormatReader
-
Gets the size of the T dimension.
- getSizeT() - Method in class loci.formats.ImageReader
-
- getSizeT() - Method in class loci.formats.in.FilePatternReader
-
- getSizeT() - Method in class loci.formats.ReaderWrapper
-
- getSizeT() - Method in interface loci.formats.services.WlzService
-
Gets number of time samples.
- getSizeT() - Method in class loci.formats.services.WlzServiceImpl
-
- getSizeT(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getSizeX() - Method in class loci.formats.DimensionSwapper
-
- getSizeX() - Method in class loci.formats.FileStitcher
-
- getSizeX() - Method in class loci.formats.FormatReader
-
- getSizeX() - Method in interface loci.formats.IFormatReader
-
Gets the size of the X dimension.
- getSizeX() - Method in class loci.formats.ImageReader
-
- getSizeX() - Method in class loci.formats.in.FilePatternReader
-
- getSizeX() - Method in class loci.formats.ReaderWrapper
-
- getSizeX() - Method in interface loci.formats.services.WlzService
-
Gets width in pixels/voxels.
- getSizeX() - Method in class loci.formats.services.WlzServiceImpl
-
- getSizeX() - Method in class loci.formats.TileStitcher
-
- getSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getSizeY() - Method in class loci.formats.DimensionSwapper
-
- getSizeY() - Method in class loci.formats.FileStitcher
-
- getSizeY() - Method in class loci.formats.FormatReader
-
- getSizeY() - Method in interface loci.formats.IFormatReader
-
Gets the size of the Y dimension.
- getSizeY() - Method in class loci.formats.ImageReader
-
- getSizeY() - Method in class loci.formats.in.FilePatternReader
-
- getSizeY() - Method in class loci.formats.ReaderWrapper
-
- getSizeY() - Method in interface loci.formats.services.WlzService
-
Gets height in pixels/voxels.
- getSizeY() - Method in class loci.formats.services.WlzServiceImpl
-
- getSizeY() - Method in class loci.formats.TileStitcher
-
- getSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getSizeZ() - Method in class loci.formats.DimensionSwapper
-
- getSizeZ() - Method in class loci.formats.FileStitcher
-
- getSizeZ() - Method in class loci.formats.FormatReader
-
- getSizeZ() - Method in interface loci.formats.IFormatReader
-
Gets the size of the Z dimension.
- getSizeZ() - Method in class loci.formats.ImageReader
-
- getSizeZ() - Method in class loci.formats.in.FilePatternReader
-
- getSizeZ() - Method in class loci.formats.ReaderWrapper
-
- getSizeZ() - Method in interface loci.formats.services.WlzService
-
Gets depth (number of x-y planes) in voxels.
- getSizeZ() - Method in class loci.formats.services.WlzServiceImpl
-
- getSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getslice(int) - Method in class loci.formats.in.ZeissTIFFReader
-
- getSliceLabelBaseIndex() - Static method in class loci.plugins.util.LociPrefs
-
- getSliceLabelPattern() - Static method in class loci.plugins.util.LociPrefs
-
- getSnapshotPixels() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getSource() - Method in class loci.formats.cache.Cache
-
Gets the cache's caching source.
- getSource() - Method in class loci.formats.cache.CacheEvent
-
Gets the source of the cache update.
- getSpecifyRangesInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getSpectra() - Method in class loci.formats.in.IM3Reader
-
If a Nuance file is a spectral library set (.csl) file,
there is a spectral library inside that contains a profile
of spectral bin magnitudes for each of several measured
fluorophores (or auto fluorescence).
- getSpeeds() - Method in class loci.formats.in.ND2Handler
-
- getSplitChannelsInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getSplitFocalPlanesInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getSplitTimepointsInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getSPWIndexes(int) - Method in class loci.formats.in.ScreenReader
-
- getStackFormat() - Method in class loci.plugins.in.ImporterOptions
-
- getStackFormatInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getStackFormats() - Method in class loci.plugins.in.ImporterOptions
-
- getStackOrder() - Method in class loci.plugins.in.ImporterOptions
-
- getStackOrder() - Method in class loci.plugins.in.ImportProcess
-
- getStackOrderInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getStackOrders() - Method in class loci.plugins.in.ImporterOptions
-
- getStackSize() - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to determined the stack size of the SPE file.
- getStackType(String) - Method in class loci.formats.in.CellSensReader
-
- getStageLabel() - Method in class loci.formats.in.MetamorphHandler
-
- getStagePosition(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
Formats the input value for the stage position into a length of the given
unit.
- getStagePosition(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the stage position into a length of the given
unit.
- getStagePositionX() - Method in class loci.formats.in.MetamorphHandler
-
- getStagePositionY() - Method in class loci.formats.in.MetamorphHandler
-
- getStart(Hashtable<String, Object>) - Method in class loci.formats.in.MINCReader
-
- getStartX() - Method in class loci.formats.in.SPEReader.SpeROI
-
- getStartY() - Method in class loci.formats.in.SPEReader.SpeROI
-
- getStatistics(int, int, double, double) - Method in class loci.plugins.util.VirtualImagePlus
-
- getStep() - Method in class loci.formats.FilePattern
-
Gets the STEP element for all blocks.
- getStep() - Method in class loci.formats.FilePatternBlock
-
Gets the difference between consecutive elements in a range block.
- getStep(int) - Static method in enum loci.plugins.in.ImportStep
-
- getStep() - Method in enum loci.plugins.in.ImportStep
-
- getStepSize(Hashtable<String, Object>) - Method in class loci.formats.in.MINCReader
-
- getStitchTilesInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getStrategy() - Method in class loci.formats.cache.Cache
-
Gets the cache's caching strategy.
- getStream(int) - Method in class loci.formats.in.VolocityReader
-
- getStream() - Method in class loci.formats.in.ZeissCZIReader.Segment
-
- getStream() - Method in class loci.formats.tiff.OnDemandLongArray
-
- getStream() - Method in class loci.formats.tiff.TiffParser
-
Gets the stream from which TIFF data is being parsed.
- getStream() - Method in class loci.formats.tiff.TiffSaver
-
Gets the stream from which TIFF data is being saved.
- getStreams() - Method in class loci.formats.tools.AmiraParameters
-
- getString(int) - Method in class loci.formats.in.LeicaReader
-
- getString(boolean) - Method in class loci.formats.in.LeicaReader
-
- getString(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for String entries into the SPE header table
- getString(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a String value from the SPE header
- getString(Integer) - Method in class loci.formats.in.VolocityReader
-
- getStringOption(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the string option with the given key.
- getStringValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
-
- getStringWidth(String) - Method in class loci.plugins.util.RecordedImageProcessor
-
- getStripByteCounts() - Method in class loci.formats.tiff.IFD
-
Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from
this IFD.
- getStripOffsets() - Method in class loci.formats.tiff.IFD
-
Retrieves the strip offsets for the image (TIFF tag StripOffsets) from
this IFD.
- getSubimage(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Returns a subimage of the specified image.
- getSubimage(byte[], byte[], int, int, int, int, int, int, int, int, boolean) - Static method in class loci.formats.ImageTools
-
- getSubsamp() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the level of chrominance subsampling used in the JPEG image
associated with this decompressor instance.
- getSuffix() - Method in class loci.formats.FilePattern
-
Gets the pattern's substring that comes after all block sections.
- getSuffixes() - Method in class loci.formats.FormatHandler
-
- getSuffixes() - Method in interface loci.formats.IFormatHandler
-
Gets the default file suffixes for this file format.
- getSuffixes() - Method in class loci.formats.ImageReader
-
- getSuffixes() - Method in class loci.formats.ImageWriter
-
- getSuffixes() - Method in class loci.formats.ReaderWrapper
-
- getSuffixes() - Method in class loci.formats.WriterWrapper
-
- getSupPixelTypes() - Method in interface loci.formats.services.WlzService
-
Gets supported pixel types.
- getSupPixelTypes() - Method in class loci.formats.services.WlzServiceImpl
-
- getSupportedMetadataLevels() - Method in class loci.formats.DelegateReader
-
- getSupportedMetadataLevels() - Method in class loci.formats.FormatHandler
-
- getSupportedMetadataLevels() - Method in class loci.formats.ImageReader
-
- getSupportedMetadataLevels() - Method in class loci.formats.ImageWriter
-
- getSupportedMetadataLevels() - Method in interface loci.formats.IMetadataConfigurable
-
- getSupportedMetadataLevels() - Method in class loci.formats.ReaderWrapper
-
- getSupportedMetadataLevels() - Method in class loci.formats.WriterWrapper
-
- getSwapDimensionsInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getT() - Method in class loci.formats.gui.ImageViewer
-
Gets the T value of the currently displayed image.
- getTableCount() - Method in interface loci.formats.services.MetakitService
-
- getTableCount() - Method in class loci.formats.services.MetakitServiceImpl
-
- getTableData(String) - Method in interface loci.formats.services.MetakitService
-
- getTableData(int) - Method in interface loci.formats.services.MetakitService
-
- getTableData(String) - Method in class loci.formats.services.MetakitServiceImpl
-
- getTableData(int) - Method in class loci.formats.services.MetakitServiceImpl
-
- getTableNames() - Method in interface loci.formats.services.MetakitService
-
- getTableNames() - Method in class loci.formats.services.MetakitServiceImpl
-
- getTag() - Method in class loci.formats.tiff.TiffIFDEntry
-
Retrieves the entry's Tag value.
- getTagName(int) - Method in class loci.formats.in.CellSensReader
-
- getTags() - Method in interface loci.formats.services.EXIFService
-
- getTags() - Method in class loci.formats.services.EXIFServiceImpl
-
- getTBegin(int) - Method in class loci.plugins.in.ImporterOptions
-
- getTBegin(int) - Method in class loci.plugins.in.ImportProcess
-
- getTCount(int) - Method in class loci.plugins.in.ImportProcess
-
- getTemperature() - Method in class loci.formats.in.MetamorphHandler
-
- getTemperatures() - Method in class loci.formats.in.ND2Handler
-
- getTEnd(int) - Method in class loci.plugins.in.ImporterOptions
-
- getTEnd(int) - Method in class loci.plugins.in.ImportProcess
-
- getTFrames(int) - Method in class loci.formats.in.LegacyND2Reader
-
- getThumbnailIFDs() - Method in class loci.formats.in.MinimalTiffReader
-
Gets the list of IFDs associated with the current TIFF's thumbnails.
- getThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser
-
Returns thumbnail IFDs.
- getThumbSizeX() - Method in class loci.formats.FileStitcher
-
- getThumbSizeX() - Method in class loci.formats.FormatReader
-
- getThumbSizeX() - Method in interface loci.formats.IFormatReader
-
Get the size of the X dimension for the thumbnail.
- getThumbSizeX() - Method in class loci.formats.ImageReader
-
- getThumbSizeX() - Method in class loci.formats.in.FilePatternReader
-
- getThumbSizeX() - Method in class loci.formats.in.LeicaSCNReader
-
- getThumbSizeX() - Method in class loci.formats.in.MinimalTiffReader
-
- getThumbSizeX() - Method in class loci.formats.ReaderWrapper
-
- getThumbSizeY() - Method in class loci.formats.FileStitcher
-
- getThumbSizeY() - Method in class loci.formats.FormatReader
-
- getThumbSizeY() - Method in interface loci.formats.IFormatReader
-
Get the size of the Y dimension for the thumbnail.
- getThumbSizeY() - Method in class loci.formats.ImageReader
-
- getThumbSizeY() - Method in class loci.formats.in.FilePatternReader
-
- getThumbSizeY() - Method in class loci.formats.in.LeicaSCNReader
-
- getThumbSizeY() - Method in class loci.formats.in.MinimalTiffReader
-
- getThumbSizeY() - Method in class loci.formats.ReaderWrapper
-
- getTiffFiles(String, char, int, int, int) - Method in class loci.formats.in.CellWorxReader
-
- getTIFFList() - Method in class loci.formats.in.LeicaReader
-
- getTiffs() - Method in class loci.formats.in.BDReader
-
- getTile(int, int, int, int, Region) - Method in class loci.formats.in.MIASReader
-
- getTile(byte[], Region, Region) - Method in class loci.formats.out.TiffWriter
-
- getTile(byte[], int, int, int, int) - Method in interface loci.formats.services.JPEGTurboService
-
- getTile(int, int) - Method in interface loci.formats.services.JPEGTurboService
-
- getTile(byte[], int, int, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
-
- getTile(int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
-
- getTile(IFD, byte[], int, int) - Method in class loci.formats.tiff.TiffParser
-
- getTileFilename(int, int, int, String) - Static method in class loci.formats.FormatTools
-
- getTileIndex(int) - Method in class loci.formats.in.LIFReader
-
- getTileLength() - Method in class loci.formats.tiff.IFD
-
Returns the length of an image tile.
- getTileSize() - Method in class loci.formats.in.CellSensReader
-
- getTileSizeX() - Method in class loci.formats.FormatWriter
-
- getTileSizeX() - Method in interface loci.formats.IFormatWriter
-
Retrieves the current tile width
Defaults to full image width if not supported
- getTileSizeX() - Method in class loci.formats.ImageWriter
-
- getTileSizeX() - Method in class loci.formats.out.TiffWriter
-
- getTileSizeX() - Method in class loci.formats.WriterWrapper
-
- getTileSizeY() - Method in class loci.formats.FormatWriter
-
- getTileSizeY() - Method in interface loci.formats.IFormatWriter
-
Retrieves the current tile height
Defaults to full image height if not supported
- getTileSizeY() - Method in class loci.formats.ImageWriter
-
- getTileSizeY() - Method in class loci.formats.out.TiffWriter
-
- getTileSizeY() - Method in class loci.formats.WriterWrapper
-
- getTilesPerColumn() - Method in class loci.formats.tiff.IFD
-
Returns the number of image tiles per column.
- getTilesPerRow() - Method in class loci.formats.tiff.IFD
-
Returns the number of image tiles per row.
- getTileWidth() - Method in class loci.formats.tiff.IFD
-
Returns the width of an image tile.
- getTime(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the time into a length of the
given unit.
- getTimeBinCount() - Method in class loci.formats.in.SDTReader
-
Gets the number of bins in the lifetime histogram.
- getTimepoint(int) - Method in class loci.formats.in.ZeissTIFFReader
-
- getTimepoints() - Method in class loci.formats.in.ND2Handler
-
- getTimestamp(String) - Method in class loci.formats.in.BDReader
-
- getTimestamp(String) - Method in class loci.formats.in.SlidebookTiffReader
-
- getTimestampIndex(String) - Method in class loci.formats.in.PCIReader
-
- getTimestamps() - Method in class loci.formats.in.MetamorphHandler
-
- getTotalOffset(int, int, int) - Method in class loci.formats.in.DeltavisionReader
-
Given any specific Z, W, and T of a plane, determine the totalOffset from
the start of the extended header.
- getTransformedSizes() - Method in class org.libjpegturbo.turbojpeg.TJTransformer
-
Returns an array containing the sizes of the transformed JPEG images from
the most recent call to
transform().
- getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class loci.formats.gui.XMLCellRenderer
-
- getTStep(int) - Method in class loci.plugins.in.ImporterOptions
-
- getTStep(int) - Method in class loci.plugins.in.ImportProcess
-
- getType() - Method in class loci.formats.cache.CacheEvent
-
Gets the type of cache update.
- getType() - Method in class loci.formats.gui.TwoChannelColorSpace
-
- getType() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the type associated with this Sequence.
- getType() - Method in class loci.formats.tiff.TiffIFDEntry
-
Retrieves the entry's Type value.
- getUnderlyingReaders() - Method in class loci.formats.FileStitcher
-
- getUnderlyingReaders() - Method in class loci.formats.FormatReader
-
- getUnderlyingReaders() - Method in interface loci.formats.IFormatReader
-
Retrieves all underlying readers.
- getUnderlyingReaders() - Method in class loci.formats.ImageReader
-
- getUnderlyingReaders() - Method in class loci.formats.in.FilePatternReader
-
- getUnderlyingReaders() - Method in class loci.formats.ReaderWrapper
-
- getUngroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getUniverse() - Method in class loci.formats.gui.LegacyQTTools
-
Gets QuickTime for Java reflected universe.
- getUpgradeCheckInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getUsedFile(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getUsedFileCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getUsedFiles() - Method in class loci.formats.FileStitcher
-
- getUsedFiles(boolean) - Method in class loci.formats.FileStitcher
-
- getUsedFiles() - Method in class loci.formats.FormatReader
-
- getUsedFiles(boolean) - Method in class loci.formats.FormatReader
-
- getUsedFiles() - Method in interface loci.formats.IFormatReader
-
Returns an array of filenames needed to open this dataset.
- getUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Returns an array of filenames needed to open this dataset.
- getUsedFiles() - Method in class loci.formats.ImageReader
-
- getUsedFiles(boolean) - Method in class loci.formats.ImageReader
-
- getUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
-
- getUsedFiles(boolean) - Method in class loci.formats.in.InveonReader
-
- getUsedFiles(boolean) - Method in class loci.formats.in.MetamorphTiffReader
-
- getUsedFiles(boolean) - Method in class loci.formats.in.UnisokuReader
-
- getUsedFiles() - Method in class loci.formats.ReaderWrapper
-
- getUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
-
- getUUID(String) - Method in class loci.formats.in.ImprovisionTiffReader
-
- getUUID(String) - Method in class loci.formats.out.OMETiffWriter
-
Gets the UUID corresponding to the given filename.
- getValue() - Method in enum loci.formats.in.BaseZeissReader.Charset
-
- getValue() - Method in enum loci.formats.in.BaseZeissReader.DrawStyle
-
- getValue() - Method in enum loci.formats.in.BaseZeissReader.FeatureType
-
- getValue() - Method in enum loci.formats.in.BaseZeissReader.FillStyle
-
- getValue() - Method in enum loci.formats.in.BaseZeissReader.LineEndPositions
-
- getValue() - Method in enum loci.formats.in.BaseZeissReader.LineEndStyle
-
- getValue() - Method in enum loci.formats.in.BaseZeissReader.PointStyle
-
- getValue() - Method in class loci.formats.in.BaseZeissReader.Tag
-
- getValue() - Method in enum loci.formats.in.BaseZeissReader.TextAlignment
-
- getValue(IRandomAccess) - Method in class loci.formats.in.IM3Reader.StringIM3Record
-
Return the string value for this record
- getValue(String) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the value of the given key, beneath this
Frame, inferring the value from the parent <Sequence>
or grandparent <PVScan> section as needed.
- getValue(String) - Method in class loci.formats.in.PrairieMetadata
-
Gets the value of the given key, at the top-level
<PVScan> element.
- getValue(String) - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the value of the given key, beneath this
Sequence, inferring the value from the parent <PVScan>
section as needed.
- getValue() - Method in class loci.plugins.prefs.BooleanOption
-
Gets the current value of the option.
- getValue() - Method in class loci.plugins.prefs.DoubleOption
-
Gets the current value of the option.
- getValue(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the value of the string option with the given key.
- getValue() - Method in class loci.plugins.prefs.StringOption
-
Gets the current value of the option.
- getValueCount() - Method in class loci.formats.tiff.TiffIFDEntry
-
Retrieves the entry's ValueCount value.
- getValueForKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation
-
Return just the value (i.e.
- getValueOffset() - Method in class loci.formats.tiff.TiffIFDEntry
-
Retrieves the entry's ValueOffset value.
- getValues() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the table of Frame key/value pairs.
- getValues() - Method in class loci.formats.in.PrairieMetadata
-
Gets the table of PVScan key/value pairs.
- getValues() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the table of Frame key/value pairs.
- getVariableAttributes(String) - Method in interface loci.formats.services.NetCDFService
-
Retrieves all of a variable's attributes.
- getVariableAttributes(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
- getVariableList() - Method in interface loci.formats.services.NetCDFService
-
Retrieves an exhaustive list of the HDF paths for all variables in the
HDF document.
- getVariableList() - Method in class loci.formats.services.NetCDFServiceImpl
-
- getVariableValue(String) - Method in interface loci.formats.services.NetCDFService
-
Retrieves a variable's value.
- getVariableValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
- getVersionNumber(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- getVirtualInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getVirtualReader() - Method in class loci.plugins.in.ImportProcess
-
- getVoltage() - Method in class loci.formats.in.ND2Handler
-
- getVolumeName(int) - Method in class loci.formats.in.CellSensReader
-
- getVoxSzX() - Method in interface loci.formats.services.WlzService
-
Gets voxel width.
- getVoxSzX() - Method in class loci.formats.services.WlzServiceImpl
-
- getVoxSzY() - Method in interface loci.formats.services.WlzService
-
Gets voxel height.
- getVoxSzY() - Method in class loci.formats.services.WlzServiceImpl
-
- getVoxSzZ() - Method in interface loci.formats.services.WlzService
-
Gets voxel depth.
- getVoxSzZ() - Method in class loci.formats.services.WlzServiceImpl
-
- getWaitTime() - Method in class loci.formats.in.PrairieMetadata
-
Gets the waitTime recorded in the configuration.
- getWavelength(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the wavelength into a length of the
given unit.
- getWavelength(Double) - Static method in class loci.formats.FormatTools
-
- getWavelength(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
-
- getWavelengthMax() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the wavelengthMax associated with this File.
- getWavelengthMin() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the wavelengthMin associated with this File.
- getWavelengths() - Method in class loci.formats.in.IM3Reader.Spectrum
-
- getWavelengths() - Method in class loci.formats.in.MetamorphHandler
-
- getWell(int) - Method in class loci.formats.in.CellWorxReader
-
Retrieve the well index corresponding to the given series.
- getWell(String) - Method in class loci.formats.in.FlexReader
-
Returns a two-element array containing the well row and well column
corresponding to the given file.
- getWell(int) - Method in class loci.formats.in.MetamorphTiffReader
-
- getWellColumn(String) - Method in class loci.formats.in.CellomicsReader
-
- getWellColumn(int) - Method in class loci.formats.in.CellWorxReader
-
Retrieve the well column corresponding to the given series.
- getWellColumn(String) - Method in class loci.formats.in.MetamorphTiffReader
-
- getWellCoords(String) - Method in class loci.formats.in.MetamorphReader
-
- getWellFromSeries(int) - Method in class loci.formats.in.InCellReader
-
- getWellName(String) - Method in class loci.formats.in.CellomicsReader
-
- getWellRow(String) - Method in class loci.formats.in.CellomicsReader
-
- getWellRow(int) - Method in class loci.formats.in.CellWorxReader
-
Retrieve the well row corresponding to the given series.
- getWellRow(String) - Method in class loci.formats.in.MetamorphTiffReader
-
- getWidgets() - Method in class loci.plugins.config.CellSensWidgets
-
- getWidgets() - Method in class loci.plugins.config.FlexWidgets
-
- getWidgets() - Method in interface loci.plugins.config.IFormatWidgets
-
- getWidgets() - Method in class loci.plugins.config.LIFWidgets
-
- getWidgets() - Method in class loci.plugins.config.ND2Widgets
-
- getWidgets() - Method in class loci.plugins.config.PictWidgets
-
- getWidgets() - Method in class loci.plugins.config.QTWidgets
-
- getWidgets() - Method in class loci.plugins.config.SDTWidgets
-
- getWidgets() - Method in class loci.plugins.config.TiffDelegateWidgets
-
- getWidgets() - Method in class loci.plugins.config.ZeissCZIWidgets
-
- getWidth() - Method in class loci.formats.codec.JPEGTileDecoder
-
- getWidth(int) - Method in class loci.formats.in.LegacyND2Reader
-
- getWidth() - Method in interface loci.formats.services.LuraWaveService
-
Wraps lwfDecoder.getWidth()
- getWidth() - Method in class loci.formats.services.LuraWaveServiceImpl
-
- getWidth(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
-
- getWidth() - Method in class loci.plugins.util.BFVirtualStack
-
- getWidth() - Method in class loci.plugins.util.RecordedImageProcessor
-
- getWidth() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the width of the JPEG image associated with this decompressor
instance.
- getWindowlessInfo() - Method in class loci.plugins.in.ImporterOptions
-
- getWlzOrgLabelName() - Method in interface loci.formats.services.WlzService
-
Gets the text string used for the Woolz origin label.
- getWlzOrgLabelName() - Method in class loci.formats.services.WlzServiceImpl
-
- getWrapped() - Method in class loci.formats.codec.BitBuffer
-
Deprecated.
- getWrapped() - Method in class loci.formats.codec.BitWriter
-
Deprecated.
- getWrapped() - Method in class loci.formats.codec.ByteVector
-
- getWrapped() - Method in class loci.formats.codec.JPEGTileDecoder
-
- getWriter(String) - Method in class loci.formats.ImageWriter
-
Gets the writer used to save the given file.
- getWriter() - Method in class loci.formats.ImageWriter
-
Gets the writer used to save the current file.
- getWriter(Class<? extends IFormatWriter>) - Method in class loci.formats.ImageWriter
-
Gets the file format writer instance matching the given class.
- getWriter() - Method in class loci.formats.WriterWrapper
-
Gets the wrapped writer.
- getWriters() - Method in class loci.formats.ImageWriter
-
Gets all constituent file format writers.
- getX(int) - Method in class loci.formats.in.FakeReader
-
- getX(double[]) - Method in class loci.formats.in.TextReader
-
- getXFields() - Method in class loci.formats.in.ND2Handler
-
- getXML() - Method in class loci.formats.tools.EditTiffG
-
- getXPositions() - Method in class loci.formats.in.ND2Handler
-
- getXResolution() - Method in class loci.formats.tiff.IFD
-
Retrieve the X resolution (TIFF tag XResolution) from this IFD.
- getY(int) - Method in class loci.formats.in.FakeReader
-
- getY(double[]) - Method in class loci.formats.in.TextReader
-
- getYPositions() - Method in class loci.formats.in.ND2Handler
-
- getYResolution() - Method in class loci.formats.tiff.IFD
-
Retrieve the Y resolution (TIFF tag YResolution) from this IFD.
- getZ() - Method in class loci.formats.gui.ImageViewer
-
Gets the Z value of the currently displayed image.
- getZBegin(int) - Method in class loci.plugins.in.ImporterOptions
-
- getZBegin(int) - Method in class loci.plugins.in.ImportProcess
-
- getZCount(int) - Method in class loci.plugins.in.ImportProcess
-
- getZCTCoords(int) - Method in class loci.formats.ChannelMerger
-
- getZCTCoords(int) - Method in class loci.formats.ChannelSeparator
-
- getZCTCoords(int) - Method in class loci.formats.DimensionSwapper
-
- getZCTCoords(int) - Method in class loci.formats.FileStitcher
-
- getZCTCoords(int) - Method in class loci.formats.FormatReader
-
- getZCTCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools
-
Gets the Z, C and T coordinates corresponding
to the given rasterized index value (real sizes).
- getZCTCoords(String, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the Z, C and T coordinates corresponding to the given rasterized
index value (real sizes).
- getZCTCoords(String, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the Z, C and T coordinates corresponding to the given
rasterized index value.
- getZCTCoords(int) - Method in interface loci.formats.IFormatReader
-
Gets the Z, C and T coordinates (real sizes) corresponding to the
given rasterized index value.
- getZCTCoords(int) - Method in class loci.formats.ImageReader
-
- getZCTCoords(int) - Method in class loci.formats.in.FilePatternReader
-
- getZCTCoords(int) - Method in class loci.formats.ReaderWrapper
-
- getZCTCoords(Double, Double[], Double[], Double[]) - Method in class loci.plugins.macro.LociFunctions
-
- getZCTModuloCoords(int) - Method in class loci.formats.ChannelMerger
-
- getZCTModuloCoords(int) - Method in class loci.formats.ChannelSeparator
-
- getZCTModuloCoords(int) - Method in class loci.formats.DimensionSwapper
-
- getZCTModuloCoords(int) - Method in class loci.formats.FileStitcher
-
- getZCTModuloCoords(int) - Method in class loci.formats.FormatReader
-
- getZCTModuloCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools
-
Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates
corresponding to the given rasterized index value (effective
sizes).
- getZCTModuloCoords(int) - Method in interface loci.formats.IFormatReader
-
Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates
(effective sizes) corresponding to the given rasterized index
value.
- getZCTModuloCoords(int) - Method in class loci.formats.ImageReader
-
- getZCTModuloCoords(int) - Method in class loci.formats.ReaderWrapper
-
- getZEnd(int) - Method in class loci.plugins.in.ImporterOptions
-
- getZEnd(int) - Method in class loci.plugins.in.ImportProcess
-
- getZeroOffset(ImagePlus) - Static method in class loci.plugins.in.Colorizer
-
- getZoom() - Method in class loci.formats.in.MetamorphHandler
-
- getZPositions() - Method in class loci.formats.in.MetamorphHandler
-
- getZPositions() - Method in class loci.formats.in.ND2Handler
-
- getZSections() - Method in class loci.formats.in.ND2Handler
-
- getZSlices(int) - Method in class loci.formats.in.LegacyND2Reader
-
- getZStep(int) - Method in class loci.plugins.in.ImporterOptions
-
- getZStep(int) - Method in class loci.plugins.in.ImportProcess
-
- GIF_MAGIC_STRING - Static variable in class loci.formats.in.GIFReader
-
- GIFReader - Class in loci.formats.in
-
GIFReader is the file format reader for Graphics Interchange Format
(GIF) files.
- GIFReader() - Constructor for class loci.formats.in.GIFReader
-
Constructs a new GIF reader.
- global - Variable in class loci.formats.in.BMPReader
-
Offset to image data.
- globalMetadata - Variable in class loci.formats.in.LeicaHandler
-
- gradient(int, int, int) - Method in class loci.formats.tools.MakeTestOmeTiff
-
- GRADIENT_LUT - Static variable in class loci.formats.in.CellSensReader
-
- GRAPHICS - Static variable in class loci.formats.in.GIFReader
-
- GRAPHICS_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the graphics domain.
- GRAY16 - Static variable in class loci.formats.in.ZeissCZIReader
-
- GRAY32 - Static variable in class loci.formats.in.ZeissCZIReader
-
- GRAY8 - Static variable in class loci.formats.in.ZeissCZIReader
-
Pixel type constants.
- GRAY_ALPHA - Static variable in class loci.formats.in.APNGReader
-
- GRAY_DOUBLE - Static variable in class loci.formats.in.ZeissCZIReader
-
- GRAY_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
-
- GRAY_RESPONSE_CURVE - Static variable in class loci.formats.tiff.IFD
-
- GRAY_RESPONSE_UNIT - Static variable in class loci.formats.tiff.IFD
-
- GRAYSCALE - Static variable in class loci.formats.in.APNGReader
-
Color types.
- GREEN_GAIN - Static variable in class loci.formats.in.CellSensReader
-
- GREEN_OFFSET - Static variable in class loci.formats.in.CellSensReader
-
- GREEN_TO_RED_MIN - Static variable in class loci.plugins.in.Colorizer
-
- greenGain - Variable in class loci.formats.in.CellSensReader.Pyramid
-
- greenOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
-
- greenOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
- greenShort - Variable in class loci.formats.gui.Index16ColorModel
-
Lookup tables.
- GREYSCALE_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
-
- GRID - Static variable in class loci.formats.in.FV1000Reader
-
- GRIDSIZE_OFFSET - Static variable in class loci.formats.in.MRCReader
-
- group - Variable in class loci.formats.FileStitcher
-
- group - Variable in class loci.formats.FormatReader
-
Whether or not to group multi-file formats.
- GROUP - Static variable in class loci.formats.in.GatanReader
-
Tag types.
- groupFiles(String[], MetadataStore) - Method in class loci.formats.in.FlexReader
-
- groupFiles() - Method in class loci.formats.in.TCSReader
-
- groupFilesBox - Variable in class loci.plugins.in.MainDialog
-
- groupX - Variable in class loci.formats.in.SPEReader.SpeROI
-
- groupY - Variable in class loci.formats.in.SPEReader.SpeROI
-
- GUITools - Class in loci.formats.gui
-
A utility class for working with graphical user interfaces.
- GUITools() - Constructor for class loci.formats.gui.GUITools
-
- gz - Variable in class loci.formats.in.LiFlimReader
-
Stream to use for reading gzip-compressed pixel data.
- gzip - Variable in class loci.formats.in.ICSReader
-
Whether or not the pixels are GZIP-compressed.
- gzip - Variable in class loci.formats.in.LiFlimReader
-
True if gzip compression was used to deflate the pixels.
- gzipStream - Variable in class loci.formats.in.ICSReader
-
- gzPos - Variable in class loci.formats.in.LiFlimReader
-
Image number indicating position in gzip stream.
- gzSeries - Variable in class loci.formats.in.LiFlimReader
-
Series number indicating position in gzip stream.
- i(String) - Method in class loci.formats.in.PrairieMetadata
-
Converts the given string to an
Integer, or null if incompatible.
- I2IReader - Class in loci.formats.in
-
I2IReader is the file format reader for I2I files.
- I2IReader() - Constructor for class loci.formats.in.I2IReader
-
Constructs a new I2I reader.
- ICacheSource - Interface in loci.formats.cache
-
Interface for cache sources.
- ICacheStrategy - Interface in loci.formats.cache
-
Interface for cache strategies.
- ICC_ENABLED - Static variable in class loci.formats.in.CellSensReader
-
- icon - Variable in class loci.formats.gui.ImageViewer
-
- icon - Variable in class loci.formats.gui.PreviewPane
-
- ICON_IMAGE_SEQUENCE - Static variable in class loci.formats.in.DicomReader
-
- iconLabel - Variable in class loci.formats.gui.ImageViewer
-
- iconLabel - Variable in class loci.formats.gui.PreviewPane
-
Labels containing thumbnail and dimensional information.
- iconText - Variable in class loci.formats.gui.PreviewPane
-
- iconTip - Variable in class loci.formats.gui.PreviewPane
-
- ICSReader - Class in loci.formats.in
-
ICSReader is the file format reader for ICS (Image Cytometry Standard)
files.
- ICSReader() - Constructor for class loci.formats.in.ICSReader
-
Constructs a new ICSReader.
- ICSWriter - Class in loci.formats.out
-
ICSWriter is the file format writer for ICS files.
- ICSWriter() - Constructor for class loci.formats.out.ICSWriter
-
- id - Variable in class loci.formats.gui.CacheComponent
-
File name that the cache is working with (debugging only).
- id - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- id - Variable in class loci.formats.in.FlexReader.FilterGroup
-
- id - Variable in class loci.formats.in.LeicaHandler.Laser
-
- id - Variable in class loci.formats.in.LeicaReader.Detector
-
- id - Variable in class loci.formats.in.OIRReader.Channel
-
- id - Variable in class loci.formats.in.OIRReader.Detector
-
- id - Variable in class loci.formats.in.OIRReader.Laser
-
- id - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
-
File containing this plane.
- id - Variable in class loci.formats.in.ZeissCZIReader.Segment
-
- id - Variable in class loci.formats.in.ZeissTIFFReader.Channel
-
- id - Variable in class loci.formats.in.ZeissTIFFReader.Slice
-
- id - Variable in class loci.formats.in.ZeissTIFFReader.Timepoint
-
- id - Variable in class loci.plugins.util.BFVirtualStack
-
- idatCount - Variable in class loci.formats.in.APNGReader
-
- IdDialog - Class in loci.plugins.in
-
Bio-Formats Importer id chooser dialog box.
- IdDialog(ImportProcess) - Constructor for class loci.plugins.in.IdDialog
-
Creates an id chooser dialog for the Bio-Formats Importer.
- idLoc - Variable in class loci.plugins.in.ImportProcess
-
- idName - Variable in class loci.plugins.in.ImportProcess
-
- idx1Pos - Variable in class loci.formats.out.AVIWriter
-
- ifd - Variable in class loci.formats.in.LeicaSCNReader.Dimension
-
- ifd - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
-
IFD number of this plane.
- IFD - Class in loci.formats.tiff
-
Data structure for working with TIFF Image File Directories (IFDs).
- IFD() - Constructor for class loci.formats.tiff.IFD
-
- IFD(IFD) - Constructor for class loci.formats.tiff.IFD
-
- ifdCounts - Variable in class loci.formats.out.OMETiffWriter
-
- IFDList - Class in loci.formats.tiff
-
Data structure for working with a list of TIFF
IFDs.
- IFDList() - Constructor for class loci.formats.tiff.IFDList
-
- ifdList - Variable in class loci.formats.tiff.TiffParser
-
Cached list of IFDs in the current file.
- IFDMap - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- ifdmap - Variable in class loci.formats.in.SVSReader
-
- ifdOffsets - Variable in class loci.formats.in.FlowSightReader
-
- ifds - Variable in class loci.formats.in.APLReader
-
- ifds - Variable in class loci.formats.in.CellSensReader
-
- ifds - Variable in class loci.formats.in.EPSReader
-
- ifds - Variable in class loci.formats.in.FlexReader.FlexFile
-
- ifds - Variable in class loci.formats.in.FV1000Reader
-
- ifds - Variable in class loci.formats.in.LeicaReader
-
- ifds - Variable in class loci.formats.in.MinimalTiffReader
-
List of IFDs for the current TIFF.
- ifdsList - Variable in class loci.formats.in.ZeissLSMReader
-
- IFDType - Enum in loci.formats.tiff
-
An enumeration of IFD types.
- IFDType(int, int) - Constructor for enum loci.formats.tiff.IFDType
-
Default constructor.
- IFormatHandler - Interface in loci.formats
-
Interface for all biological file format readers and writers.
- IFormatReader - Interface in loci.formats
-
Interface for all biological file format readers.
- IFormatWidgets - Interface in loci.plugins.config
-
Interface for defining custom widgets for a specific file format reader.
- IFormatWriter - Interface in loci.formats
-
Interface for all biological file format writers.
- ignore - Variable in class loci.plugins.util.SearchableWindow.SearchBox
-
- ignoreCase - Variable in class loci.plugins.util.SearchableWindow.SearchBox
-
- ih - Variable in class loci.formats.in.GIFReader
-
Current image rectangle.
- IJStatusEchoer - Class in loci.plugins.util
-
Echoes status messages to the ImageJ status bar.
- IJStatusEchoer() - Constructor for class loci.plugins.util.IJStatusEchoer
-
- IllegalBlockException - Exception in loci.formats
-
- IllegalBlockException() - Constructor for exception loci.formats.IllegalBlockException
-
- IllegalBlockException(String) - Constructor for exception loci.formats.IllegalBlockException
-
- IllegalBlockException(String, Throwable) - Constructor for exception loci.formats.IllegalBlockException
-
- IllegalBlockException(Throwable) - Constructor for exception loci.formats.IllegalBlockException
-
- ILLUM_CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
-
- ILLUM_CHANNEL_ATTENUATION - Static variable in class loci.formats.in.ZeissLSMReader
-
- ILLUM_CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
-
- ILLUM_CHANNEL_WAVELENGTH - Static variable in class loci.formats.in.ZeissLSMReader
-
- ILLUMINATION - Static variable in class loci.formats.FormatTools
-
Identifies the Illumination dimensional type,
representing a dimension consisting of illuminations.
- illumination - Variable in class loci.formats.in.ZeissCZIReader.Channel
-
- IlluminationChannel() - Constructor for class loci.formats.in.ZeissLSMReader.IlluminationChannel
-
- illuminationLabels - Variable in class loci.formats.in.ZeissCZIReader
-
- illuminations - Variable in class loci.formats.in.FV1000Reader
-
- illuminations - Variable in class loci.formats.in.ZeissCZIReader
-
- illuminations - Variable in class loci.formats.in.ZeissLSMReader
-
- illumNA - Variable in class loci.formats.in.LeicaSCNReader.Image
-
- illumSource - Variable in class loci.formats.in.LeicaSCNReader.Image
-
- IM3Reader - Class in loci.formats.in
-
- IM3Reader() - Constructor for class loci.formats.in.IM3Reader
-
Construct an uninitialized reader of .im3 files.
- IM3Reader.BooleanIM3Record - Class in loci.formats.in
-
A record containing boolean values
- IM3Reader.ContainerRecord - Class in loci.formats.in
-
- IM3Reader.FloatIM3Record - Class in loci.formats.in
-
- IM3Reader.IM3Record - Class in loci.formats.in
-
- IM3Reader.IntIM3Record - Class in loci.formats.in
-
- IM3Reader.Spectrum - Class in loci.formats.in
-
- IM3Reader.StringIM3Record - Class in loci.formats.in
-
- IM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IM3Record
-
- ImaconHandler() - Constructor for class loci.formats.in.ImaconReader.ImaconHandler
-
- ImaconReader - Class in loci.formats.in
-
ImaconReader is the file format reader for Imacon .fff (TIFF) files.
- ImaconReader() - Constructor for class loci.formats.in.ImaconReader
-
Constructs a new Imacon reader.
- ImaconReader.ImaconHandler - Class in loci.formats.in
-
- IMAGE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- Image() - Constructor for class loci.formats.in.InCellReader.Image
-
- image - Variable in class loci.formats.in.LegacyQTReader
-
Image containing current frame.
- Image(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Image
-
- image - Variable in class loci.formats.in.VeecoReader
-
- IMAGE_BOUNDARY - Static variable in class loci.formats.in.CellSensReader
-
- IMAGE_COLLECTION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- IMAGE_DESCRIPTION - Static variable in class loci.formats.tiff.IFD
-
- IMAGE_FRAME_VOLUME - Static variable in class loci.formats.in.CellSensReader
-
- IMAGE_LENGTH - Static variable in class loci.formats.tiff.IFD
-
- IMAGE_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- IMAGE_PRO_TAG_1 - Static variable in class loci.formats.in.SEQReader
-
An array of shorts (length 12) with identical values in all of our
samples; assuming this is some sort of format identifier.
- IMAGE_PRO_TAG_2 - Static variable in class loci.formats.in.SEQReader
-
Frame rate.
- IMAGE_PRO_TAG_3 - Static variable in class loci.formats.in.SEQReader
-
- IMAGE_SEPARATOR - Static variable in class loci.formats.in.GIFReader
-
- IMAGE_SOURCE_DATA - Static variable in class loci.formats.in.PhotoshopTiffReader
-
- IMAGE_TYPE_1 - Static variable in class loci.formats.in.OpenlabReader
-
Tag types.
- IMAGE_TYPE_2 - Static variable in class loci.formats.in.OpenlabReader
-
- IMAGE_TYPES - Static variable in class loci.formats.in.DeltavisionReader
-
- IMAGE_WIDTH - Static variable in class loci.formats.tiff.IFD
-
- ImageCollection(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.ImageCollection
-
- imageCount - Variable in class loci.formats.CoreMetadata
-
Total number of images.
- imageCount - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
-
- imageCreationDate - Variable in class loci.formats.in.MetamorphReader
-
The TIFF's creation date
- imageDepth - Variable in class loci.formats.in.FV1000Reader
-
- imageDescription - Variable in class loci.formats.in.BaseZeissReader
-
- imageDescription - Variable in class loci.formats.in.FEITiffReader
-
- imageDescriptions - Variable in class loci.formats.in.SlidebookReader
-
- imageDimensions - Variable in class loci.formats.services.JPEGTurboServiceImpl
-
- imageFile - Variable in class loci.formats.in.PCORAWReader
-
- imageFiles - Variable in class loci.formats.in.BaseZeissReader
-
- imageFiles - Variable in class loci.formats.in.InCellReader
-
- imageFiles - Variable in class loci.formats.in.IPWReader
-
List of embedded image file names (one per image plane).
- imageFiles - Variable in class loci.formats.in.PCIReader
-
- imageFolder - Variable in class loci.formats.in.CellVoyagerReader
-
- imageHeight - Variable in class loci.formats.in.InCellReader
-
- imageHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
-
- imageIFD(int) - Method in class loci.formats.in.LeicaSCNReader
-
- ImageIOReader - Class in loci.formats.in
-
ImageIOReader is the superclass for file format readers
that use the javax.imageio package.
- ImageIOReader(String, String) - Constructor for class loci.formats.in.ImageIOReader
-
Constructs a new ImageIOReader.
- ImageIOReader(String, String[]) - Constructor for class loci.formats.in.ImageIOReader
-
Constructs a new ImageIOReader.
- ImageIOWriter - Class in loci.formats.out
-
ImageIOWriter is the superclass for file format writers that use the
javax.imageio library.
- ImageIOWriter(String, String, String) - Constructor for class loci.formats.out.ImageIOWriter
-
Constructs an ImageIO-based writer with the given name, default suffix
and output type (e.g., png, jpeg).
- ImageIOWriter(String, String[], String) - Constructor for class loci.formats.out.ImageIOWriter
-
Constructs an ImageIO-based writer with the given name, default suffixes
and output type (e.g., png, jpeg).
- IMAGEJ_MSG - Static variable in class loci.plugins.util.LibraryChecker
-
Message to be displayed if ImageJ is too old for Bio-Formats plugins.
- IMAGEJ_TAG - Static variable in class loci.formats.in.TiffReader
-
- IMAGEJ_VERSION - Static variable in class loci.plugins.util.LibraryChecker
-
Minimum version of ImageJ necessary for Bio-Formats plugins.
- imageLocations - Variable in class loci.formats.out.OMETiffWriter
-
- imageMap - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- imageName - Variable in class loci.formats.in.BioRadSCNReader
-
- imageName - Variable in class loci.formats.in.FEITiffReader
-
- imageName - Variable in class loci.formats.in.ImaconReader
-
- imageName - Variable in class loci.formats.in.MetamorphHandler
-
- imageName - Variable in class loci.formats.in.MetamorphReader
-
The TIFF's name
- imageName - Variable in class loci.formats.in.SISReader
-
- imageName - Variable in class loci.formats.in.ZeissCZIReader
-
- imageNames - Variable in class loci.formats.in.LIFReader
-
- imageNames - Variable in class loci.formats.in.TillVisionReader
-
- imageNames - Variable in class loci.formats.in.ZeissLSMReader
-
- imageNumber - Variable in class loci.formats.in.APNGReader.PNGInputStream
-
- imageNumEnd - Variable in class loci.formats.in.LeicaSCNReader.Image
-
- imageNumStart - Variable in class loci.formats.in.LeicaSCNReader.Image
-
- imageOffset - Variable in class loci.formats.in.IvisionReader
-
- ImagePlusReader - Class in loci.plugins.in
-
A high-level reader for ImagePlus objects.
- ImagePlusReader() - Constructor for class loci.plugins.in.ImagePlusReader
-
Constructs an ImagePlusReader with the default options.
- ImagePlusReader(ImportProcess) - Constructor for class loci.plugins.in.ImagePlusReader
-
Constructs an ImagePlusReader with the
given complete import preparation process.
- ImageProcessorReader - Class in loci.plugins.util
-
A low-level reader for ImageProcessor objects.
- ImageProcessorReader() - Constructor for class loci.plugins.util.ImageProcessorReader
-
Constructs an ImageProcessorReader around a new image reader.
- ImageProcessorReader(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorReader
-
Constructs an ImageProcessorReader with the given reader.
- ImageProcessorSource - Class in loci.plugins.util
-
Retrieves ImageJ image processors from an image reader.
- ImageProcessorSource(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorSource
-
- ImageReader - Class in loci.formats
-
ImageReader is the master file format reader for all supported formats.
- ImageReader() - Constructor for class loci.formats.ImageReader
-
Constructs a new ImageReader with the default
list of reader classes from readers.txt.
- ImageReader(ClassList<IFormatReader>) - Constructor for class loci.formats.ImageReader
-
Constructs a new ImageReader from the given list of reader classes.
- imageReader - Variable in class loci.plugins.in.ImportProcess
-
- imageROIs - Variable in class loci.formats.in.LIFReader
-
- imageRX - Variable in class loci.formats.in.SDTInfo
-
- imageRY - Variable in class loci.formats.in.SDTInfo
-
- images - Variable in class loci.formats.gui.ImageViewer
-
- images - Variable in class loci.formats.in.GIFReader
-
- IMAGES - Static variable in class loci.formats.in.LeicaReader
-
- images - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
-
- imagesPerFile - Variable in class loci.formats.FileStitcher.ExternalSeries
-
- imagesPerFile - Variable in class loci.formats.in.DicomReader
-
- imageThumbnail - Variable in class loci.formats.in.LeicaSCNReader.Image
-
- ImageTools - Class in loci.formats
-
A utility class with convenience methods for manipulating images
in primitive array form.
- ImageTools() - Constructor for class loci.formats.ImageTools
-
- imageType - Variable in class loci.formats.in.DicomReader
-
- ImageViewer - Class in loci.formats.gui
-
ImageViewer is a simple viewer/converter
for the Bio-Formats image formats.
- ImageViewer() - Constructor for class loci.formats.gui.ImageViewer
-
Constructs an image viewer.
- ImageViewer(boolean) - Constructor for class loci.formats.gui.ImageViewer
-
Constructs an image viewer.
- imageWidth - Variable in class loci.formats.in.InCellReader
-
- imageWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
-
- ImageWriter - Class in loci.formats
-
ImageWriter is the master file format writer for all supported formats.
- ImageWriter() - Constructor for class loci.formats.ImageWriter
-
Constructs a new ImageWriter with the default
list of writer classes from writers.txt.
- ImageWriter(ClassList<IFormatWriter>) - Constructor for class loci.formats.ImageWriter
-
Constructs a new ImageWriter from the given list of writer classes.
- imageX - Variable in class loci.formats.in.SDTInfo
-
4 subsequent fields valid only for Camera mode
or FIFO_IMAGE mode.
- imageY - Variable in class loci.formats.in.SDTInfo
-
- ImagicReader - Class in loci.formats.in
-
ImagicReader is the file format reader for IMAGIC files.
- ImagicReader() - Constructor for class loci.formats.in.ImagicReader
-
Constructs a new IMAGIC reader.
- IMARIS_MAGIC_BYTES - Static variable in class loci.formats.in.ImarisReader
-
Magic number; present in all files.
- ImarisHDFReader - Class in loci.formats.in
-
Reader for Bitplane Imaris 5.5 (HDF) files.
- ImarisHDFReader() - Constructor for class loci.formats.in.ImarisHDFReader
-
Constructs a new Imaris HDF reader.
- ImarisReader - Class in loci.formats.in
-
ImarisReader is the file format reader for Bitplane Imaris files.
- ImarisReader() - Constructor for class loci.formats.in.ImarisReader
-
Constructs a new Imaris reader.
- ImarisTiffReader - Class in loci.formats.in
-
ImarisTiffReader is the file format reader for
Bitplane Imaris 3 files (TIFF variant).
- ImarisTiffReader() - Constructor for class loci.formats.in.ImarisTiffReader
-
Constructs a new Imaris TIFF reader.
- IMetadata - Interface in loci.formats.meta
-
- IMetadataConfigurable - Interface in loci.formats
-
- img - Variable in class loci.formats.in.ImageIOReader
-
- img - Variable in class loci.formats.tools.AsciiImage
-
- IMinMaxStore - Interface in loci.formats.meta
-
Interface for consumers of minima and maxima pixel intensities across a
given wavelength.
- immersion - Variable in class loci.formats.in.ND2Handler
-
- immersion - Variable in class loci.formats.in.NikonTiffReader
-
- immersion - Variable in class loci.formats.in.OIRReader.Objective
-
- immersion - Variable in class loci.formats.in.SimplePCITiffReader
-
- immersion - Variable in class loci.formats.in.ZeissLSMReader.Recording
-
- immersions - Variable in class loci.formats.in.LIFReader
-
- IMODReader - Class in loci.formats.in
-
Reader for IMOD binary files.
- IMODReader() - Constructor for class loci.formats.in.IMODReader
-
Constructs a new IMOD reader.
- IMODSTAMP_OFFSET - Static variable in class loci.formats.in.MRCReader
-
- imp - Variable in class loci.plugins.out.Exporter
-
Current stack.
- imp - Variable in class loci.plugins.Slicer
-
Current image stack.
- IMPLICIT_VR - Static variable in class loci.formats.in.DicomReader
-
- importData(JComponent, Transferable) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
-
- Importer - Class in loci.plugins.in
-
Core logic for the Bio-Formats Importer ImageJ plugin.
- Importer(LociImporter) - Constructor for class loci.plugins.in.Importer
-
- ImporterDialog - Class in loci.plugins.in
-
Abstract superclass of importer dialogs.
- ImporterDialog(ImportProcess) - Constructor for class loci.plugins.in.ImporterDialog
-
- ImporterMetadata - Class in loci.plugins.in
-
Helper class for storing original metadata key/value pairs.
- ImporterMetadata(IFormatReader, ImportProcess, boolean) - Constructor for class loci.plugins.in.ImporterMetadata
-
- ImporterOptions - Class in loci.plugins.in
-
Helper class for managing Bio-Formats Importer options.
- ImporterOptions() - Constructor for class loci.plugins.in.ImporterOptions
-
- ImporterPrompter - Class in loci.plugins.in
-
Helper class for presenting the user with dialog boxes
for configuring importer options.
- ImporterPrompter(ImportProcess) - Constructor for class loci.plugins.in.ImporterPrompter
-
- ImportProcess - Class in loci.plugins.in
-
Manages the import preparation process.
- ImportProcess() - Constructor for class loci.plugins.in.ImportProcess
-
- ImportProcess(ImporterOptions) - Constructor for class loci.plugins.in.ImportProcess
-
- ImportStep - Enum in loci.plugins.in
-
An enumeration of the steps in the import preparation process.
- ImportStep(int, String) - Constructor for enum loci.plugins.in.ImportStep
-
- IMPROVISION_MAGIC_STRING - Static variable in class loci.formats.in.ImprovisionTiffReader
-
- ImprovisionTiffReader - Class in loci.formats.in
-
ImprovisionTiffReader is the file format reader for
Improvision TIFF files.
- ImprovisionTiffReader() - Constructor for class loci.formats.in.ImprovisionTiffReader
-
- ImspectorReader - Class in loci.formats.in
-
ImspectorReader is the file format reader for Imspector .msr files.
- ImspectorReader() - Constructor for class loci.formats.in.ImspectorReader
-
Constructs a new Imspector reader.
- in - Variable in class loci.formats.FormatReader
-
Current file.
- in - Variable in class loci.formats.gui.ImageViewer
-
- in - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Stream that we're parsing metadata from.
- in - Variable in class loci.formats.in.ZeissTIFFReader.Plane
-
- in - Variable in class loci.formats.out.TiffWriter
-
Input stream to use when overwriting data.
- in - Variable in class loci.formats.services.JPEGTurboServiceImpl
-
- in - Variable in class loci.formats.tiff.TiffParser
-
Input source from which to parse TIFF data.
- in - Variable in class loci.formats.tools.AmiraParameters
-
- inCache - Variable in class loci.formats.cache.Cache
-
Whether each position is currently supposed to be cached.
- InCell3000Reader - Class in loci.formats.in
-
InCell3000Reader is the file format reader for InCell 3000.
- InCell3000Reader() - Constructor for class loci.formats.in.InCell3000Reader
-
Constructs a new InCell 3000 reader.
- INCELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
-
- InCellHandler(MetadataStore) - Constructor for class loci.formats.in.InCellReader.InCellHandler
-
- InCellReader - Class in loci.formats.in
-
InCellReader is the file format reader for InCell 1000/2000 datasets.
- InCellReader() - Constructor for class loci.formats.in.InCellReader
-
Constructs a new InCell 1000/2000 reader.
- InCellReader.Image - Class in loci.formats.in
-
- InCellReader.InCellHandler - Class in loci.formats.in
-
SAX handler for parsing XML.
- InCellReader.MinimalInCellHandler - Class in loci.formats.in
-
- INCLUDE_ATTACHMENTS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
-
- INCLUDE_ATTACHMENTS_KEY - Static variable in class loci.formats.in.ZeissCZIReader
-
- includeC - Variable in class loci.formats.gui.DataConverter
-
- includeCZIAttachments() - Static method in class loci.plugins.util.LociPrefs
-
- includeT - Variable in class loci.formats.gui.DataConverter
-
- includeZ - Variable in class loci.formats.gui.DataConverter
-
- incr - Variable in class loci.formats.in.SDTInfo
-
- index - Variable in class loci.formats.cache.CacheEvent
-
Relevant index to the event, if any.
- index - Variable in class loci.formats.in.BaseZeissReader.Tag
-
- index - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
-
- index - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
-
- index - Variable in class loci.formats.in.LeicaHandler.Laser
-
- index - Variable in class loci.formats.in.LeicaReader.Detector
-
- Index(int[]) - Constructor for class loci.formats.in.MicromanagerReader.Index
-
- index - Variable in class loci.formats.in.PrairieMetadata.Frame
-
index of this <Frame>.
- index - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
-
- index - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
-
- index - Variable in class loci.plugins.util.SearchableWindow
-
- Index16ColorModel - Class in loci.formats.gui
-
ColorModel that handles 16 bits per channel lookup tables.
- Index16ColorModel(int, int, short[][], boolean) - Constructor for class loci.formats.gui.Index16ColorModel
-
- indexed - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not the images are stored as indexed color.
- INDEXED - Static variable in class loci.formats.in.APNGReader
-
- indexedAsRGB - Variable in class loci.formats.FormatReader
-
Whether or not MetadataStore sets C = 3 for indexed color images.
- indexedToRGB(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Converts an indexed color BufferedImage to an RGB BufferedImage.
- indexedToRGB(byte[][], byte[]) - Static method in class loci.formats.ImageTools
-
Converts a LUT and an array of indices into an array of RGB tuples.
- indexedToRGB(short[][], byte[], boolean) - Static method in class loci.formats.ImageTools
-
Converts a LUT and an array of indices into an array of RGB tuples.
- indexIntoPlanes - Variable in class loci.formats.in.ZeissCZIReader
-
- indexMax - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
Maximum index value.
- indexMin - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
Minimum index value.
- indexToValue - Variable in class loci.formats.in.FakeReader
-
For indexed color, mapping from indices to values and vice versa.
- inDimensionProperties - Variable in class loci.formats.in.CellSensReader
-
- INDIVIDUAL_JARS - Static variable in class loci.formats.UpgradeChecker
-
Names of the individual JARs.
- infFile - Variable in class loci.formats.in.FujiReader
-
- infFiles - Variable in class loci.formats.in.TillVisionReader
-
- inflater - Variable in class loci.formats.in.OBFReader
-
- info - Variable in class loci.formats.in.GatanReader
-
- info - Variable in class loci.formats.in.OMETiffReader
-
Mapping from series and plane numbers to files and IFD entries.
- info - Variable in class loci.formats.in.SDTInfo
-
- info - Variable in class loci.formats.in.SDTReader
-
Object containing SDT header information.
- info - Variable in class loci.plugins.prefs.Option
-
Documentation about the option, in HTML.
- INFO_DEFAULT - Static variable in class loci.plugins.in.MainDialog
-
Initial message to display in help text box.
- INFO_TABLE - Static variable in class loci.formats.in.LiFlimReader
-
- infoLength - Variable in class loci.formats.in.SDTInfo
-
Length of the info part.
- infoOffs - Variable in class loci.formats.in.SDTInfo
-
Offset of the info part which contains general text
information (Title, date, time, contents etc.).
- infoPane - Variable in class loci.plugins.in.MainDialog
-
- infoTable - Variable in class loci.plugins.in.MainDialog
-
- ini - Variable in class loci.formats.in.LiFlimReader
-
Parsed configuration data.
- INI_DEFAULT - Static variable in class loci.plugins.prefs.Option
-
INI key indicating option's default value.
- INI_INFO - Static variable in class loci.plugins.prefs.Option
-
INI key indicating option's info.
- INI_KEY - Static variable in class loci.plugins.prefs.Option
-
INI key indicating option's key.
- INI_LABEL - Static variable in class loci.plugins.prefs.Option
-
INI key indicating option's label.
- INI_POSSIBLE - Static variable in class loci.plugins.prefs.StringOption
-
INI key indicating option's possible values.
- INI_SAVE - Static variable in class loci.plugins.prefs.Option
-
INI key indicating whether option should be saved to prefs file.
- INI_TYPE - Static variable in class loci.plugins.prefs.OptionsList
-
INI key indicating option's type.
- iniFile - Variable in class loci.formats.in.FakeReader
-
Properties companion file which can be associated with this fake file
- init() - Method in class loci.formats.services.NetCDFServiceImpl
-
- init() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
- init() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
- init() - Method in class org.libjpegturbo.turbojpeg.TJTransformer
-
- initAlternateMetadata() - Method in class loci.formats.in.FluoviewReader
-
- initAlternateMetadataStore() - Method in class loci.formats.in.FluoviewReader
-
- initClass() - Method in class loci.formats.gui.LegacyQTTools
-
Initializes the class.
- initCoreMetadata(int, int) - Method in class loci.formats.in.LeicaSCNReader
-
- initCoreMetadata() - Method in class loci.formats.in.LiFlimReader
-
- initDecompressor() - Method in class loci.formats.in.AmiraReader.HxZip
-
- initExtraMetadata() - Method in class loci.formats.in.DeltavisionReader
-
- initFile(String) - Method in class loci.formats.FileStitcher
-
Initializes the given file or file pattern.
- initFile(String) - Method in class loci.formats.FormatReader
-
Initializes the given file (parsing header information, etc.).
- initFile(String) - Method in class loci.formats.in.AFIReader
-
- initFile(String) - Method in class loci.formats.in.AIMReader
-
- initFile(String) - Method in class loci.formats.in.AliconaReader
-
- initFile(String) - Method in class loci.formats.in.AmiraReader
-
- initFile(String) - Method in class loci.formats.in.AnalyzeReader
-
- initFile(String) - Method in class loci.formats.in.APLReader
-
- initFile(String) - Method in class loci.formats.in.APNGReader
-
- initFile(String) - Method in class loci.formats.in.ARFReader
-
- initFile(String) - Method in class loci.formats.in.AVIReader
-
- initFile(String) - Method in class loci.formats.in.BaseTiffReader
-
- initFile(String) - Method in class loci.formats.in.BDReader
-
- initFile(String) - Method in class loci.formats.in.BioRadGelReader
-
- initFile(String) - Method in class loci.formats.in.BioRadReader
-
- initFile(String) - Method in class loci.formats.in.BioRadSCNReader
-
- initFile(String) - Method in class loci.formats.in.BMPReader
-
- initFile(String) - Method in class loci.formats.in.BrukerReader
-
- initFile(String) - Method in class loci.formats.in.BurleighReader
-
- initFile(String) - Method in class loci.formats.in.CanonRawReader
-
- initFile(String) - Method in class loci.formats.in.CellH5Reader
-
- initFile(String) - Method in class loci.formats.in.CellomicsReader
-
- initFile(String) - Method in class loci.formats.in.CellSensReader
-
- initFile(String) - Method in class loci.formats.in.CellVoyagerReader
-
- initFile(String) - Method in class loci.formats.in.CellWorxReader
-
- initFile(String) - Method in class loci.formats.in.ColumbusReader
-
- initFile(String) - Method in class loci.formats.in.DeltavisionReader
-
- initFile(String) - Method in class loci.formats.in.DicomReader
-
- initFile(String) - Method in class loci.formats.in.DNGReader
-
- initFile(String) - Method in class loci.formats.in.Ecat7Reader
-
- initFile(String) - Method in class loci.formats.in.EPSReader
-
- initFile(String) - Method in class loci.formats.in.FakeReader
-
- initFile(String) - Method in class loci.formats.in.FEIReader
-
- initFile(String) - Method in class loci.formats.in.FilePatternReader
-
- initFile(String) - Method in class loci.formats.in.FitsReader
-
- initFile(String) - Method in class loci.formats.in.FlexReader
-
- initFile(String) - Method in class loci.formats.in.FlowSightReader
-
- initFile(String) - Method in class loci.formats.in.FujiReader
-
- initFile(String) - Method in class loci.formats.in.FV1000Reader
-
- initFile(String) - Method in class loci.formats.in.GatanDM2Reader
-
- initFile(String) - Method in class loci.formats.in.GatanReader
-
- initFile(String) - Method in class loci.formats.in.GIFReader
-
- initFile(String) - Method in class loci.formats.in.HamamatsuVMSReader
-
- initFile(String) - Method in class loci.formats.in.HISReader
-
- initFile(String) - Method in class loci.formats.in.HitachiReader
-
- initFile(String) - Method in class loci.formats.in.HRDGDFReader
-
- initFile(String) - Method in class loci.formats.in.I2IReader
-
- initFile(String) - Method in class loci.formats.in.ICSReader
-
- initFile(String) - Method in class loci.formats.in.IM3Reader
-
- initFile(String) - Method in class loci.formats.in.ImageIOReader
-
- initFile(String) - Method in class loci.formats.in.ImagicReader
-
- initFile(String) - Method in class loci.formats.in.ImarisHDFReader
-
- initFile(String) - Method in class loci.formats.in.ImarisReader
-
- initFile(String) - Method in class loci.formats.in.ImarisTiffReader
-
- initFile(String) - Method in class loci.formats.in.IMODReader
-
- initFile(String) - Method in class loci.formats.in.ImspectorReader
-
- initFile(String) - Method in class loci.formats.in.InCell3000Reader
-
- initFile(String) - Method in class loci.formats.in.InCellReader
-
- initFile(String) - Method in class loci.formats.in.INRReader
-
- initFile(String) - Method in class loci.formats.in.InveonReader
-
- initFile(String) - Method in class loci.formats.in.IPLabReader
-
- initFile(String) - Method in class loci.formats.in.IPWReader
-
- initFile(String) - Method in class loci.formats.in.IvisionReader
-
- initFile(String) - Method in class loci.formats.in.JEOLReader
-
- initFile(String) - Method in class loci.formats.in.JPEG2000Reader
-
- initFile(String) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
-
- initFile(String) - Method in class loci.formats.in.JPXReader
-
- initFile(String) - Method in class loci.formats.in.KhorosReader
-
- initFile(String) - Method in class loci.formats.in.KodakReader
-
- initFile(String) - Method in class loci.formats.in.L2DReader
-
- initFile(String) - Method in class loci.formats.in.LegacyND2Reader
-
- initFile(String) - Method in class loci.formats.in.LegacyQTReader
-
- initFile(String) - Method in class loci.formats.in.LeicaReader
-
- initFile(String) - Method in class loci.formats.in.LiFlimReader
-
- initFile(String) - Method in class loci.formats.in.LIFReader
-
- initFile(String) - Method in class loci.formats.in.LIMReader
-
- initFile(String) - Method in class loci.formats.in.MetamorphReader
-
- initFile(String) - Method in class loci.formats.in.MetamorphTiffReader
-
- initFile(String) - Method in class loci.formats.in.MIASReader
-
- initFile(String) - Method in class loci.formats.in.MicromanagerReader
-
- initFile(String) - Method in class loci.formats.in.MINCReader
-
- initFile(String) - Method in class loci.formats.in.MinimalTiffReader
-
- initFile(String) - Method in class loci.formats.in.MNGReader
-
- initFile(String) - Method in class loci.formats.in.MolecularImagingReader
-
- initFile(String) - Method in class loci.formats.in.MRCReader
-
- initFile(String) - Method in class loci.formats.in.MRWReader
-
- initFile(String) - Method in class loci.formats.in.NAFReader
-
- initFile(String) - Method in class loci.formats.in.NativeND2Reader
-
- initFile(String) - Method in class loci.formats.in.NativeQTReader
-
- initFile(String) - Method in class loci.formats.in.NDPIReader
-
- initFile(String) - Method in class loci.formats.in.NDPISReader
-
- initFile(String) - Method in class loci.formats.in.NiftiReader
-
- initFile(String) - Method in class loci.formats.in.NikonReader
-
- initFile(String) - Method in class loci.formats.in.NRRDReader
-
- initFile(String) - Method in class loci.formats.in.OBFReader
-
- initFile(String) - Method in class loci.formats.in.OIRReader
-
- initFile(String) - Method in class loci.formats.in.OMETiffReader
-
- initFile(String) - Method in class loci.formats.in.OMEXMLReader
-
- initFile(String) - Method in class loci.formats.in.OpenlabRawReader
-
- initFile(String) - Method in class loci.formats.in.OpenlabReader
-
- initFile(String) - Method in class loci.formats.in.OperettaReader
-
- initFile(String) - Method in class loci.formats.in.OxfordInstrumentsReader
-
- initFile(String) - Method in class loci.formats.in.PCIReader
-
- initFile(String) - Method in class loci.formats.in.PCORAWReader
-
- initFile(String) - Method in class loci.formats.in.PCXReader
-
- initFile(String) - Method in class loci.formats.in.PDSReader
-
- initFile(String) - Method in class loci.formats.in.PerkinElmerReader
-
- initFile(String) - Method in class loci.formats.in.PGMReader
-
- initFile(String) - Method in class loci.formats.in.PhotoshopTiffReader
-
- initFile(String) - Method in class loci.formats.in.PictReader
-
- initFile(String) - Method in class loci.formats.in.PovrayReader
-
- initFile(String) - Method in class loci.formats.in.PQBinReader
-
- initFile(String) - Method in class loci.formats.in.PrairieReader
-
- initFile(String) - Method in class loci.formats.in.PSDReader
-
- initFile(String) - Method in class loci.formats.in.QuesantReader
-
- initFile(String) - Method in class loci.formats.in.RHKReader
-
- initFile(String) - Method in class loci.formats.in.SBIGReader
-
- initFile(String) - Method in class loci.formats.in.ScanrReader
-
- initFile(String) - Method in class loci.formats.in.ScreenReader
-
- initFile(String) - Method in class loci.formats.in.SDTReader
-
- initFile(String) - Method in class loci.formats.in.SeikoReader
-
- initFile(String) - Method in class loci.formats.in.SIFReader
-
- initFile(String) - Method in class loci.formats.in.SlidebookReader
-
- initFile(String) - Method in class loci.formats.in.SMCameraReader
-
- initFile(String) - Method in class loci.formats.in.SPCReader
-
- initFile(String) - Method in class loci.formats.in.SPEReader
-
- initFile(String) - Method in class loci.formats.in.SpiderReader
-
- initFile(String) - Method in class loci.formats.in.TargaReader
-
- initFile(String) - Method in class loci.formats.in.TCSReader
-
- initFile(String) - Method in class loci.formats.in.TextReader
-
- initFile(String) - Method in class loci.formats.in.TiffJAIReader
-
- initFile(String) - Method in class loci.formats.in.TileJPEGReader
-
- initFile(String) - Method in class loci.formats.in.TillVisionReader
-
- initFile(String) - Method in class loci.formats.in.TopometrixReader
-
- initFile(String) - Method in class loci.formats.in.TrestleReader
-
- initFile(String) - Method in class loci.formats.in.UBMReader
-
- initFile(String) - Method in class loci.formats.in.UnisokuReader
-
- initFile(String) - Method in class loci.formats.in.VarianFDFReader
-
- initFile(String) - Method in class loci.formats.in.VeecoReader
-
- initFile(String) - Method in class loci.formats.in.VGSAMReader
-
- initFile(String) - Method in class loci.formats.in.VisitechReader
-
- initFile(String) - Method in class loci.formats.in.VolocityClippingReader
-
- initFile(String) - Method in class loci.formats.in.VolocityReader
-
- initFile(String) - Method in class loci.formats.in.WATOPReader
-
- initFile(String) - Method in class loci.formats.in.WlzReader
-
- initFile(String) - Method in class loci.formats.in.ZeissCZIReader
-
- initFile(String) - Method in class loci.formats.in.ZeissLMSReader
-
- initFile(String) - Method in class loci.formats.in.ZeissLSMReader
-
- initFile(String) - Method in class loci.formats.in.ZeissTIFFReader
-
- initFile(String) - Method in class loci.formats.in.ZeissZVIReader
-
- initFile(String) - Method in class loci.formats.in.ZipReader
-
- initFileMain(String) - Method in class loci.formats.in.BaseZeissReader
-
- initFlexFile(String) - Method in class loci.formats.in.FlexReader
-
- initialize(String, int) - Method in class loci.formats.codec.JPEGTileDecoder
-
- initialize(RandomAccessInputStream, int) - Method in class loci.formats.codec.JPEGTileDecoder
-
- initialize(RandomAccessInputStream, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder
-
- initialize() - Method in class loci.formats.codec.JPEGXRCodec
-
Initializes the JPEG-XR dependency service.
- initialize(String) - Method in interface loci.formats.services.EXIFService
-
- initialize(String) - Method in class loci.formats.services.EXIFServiceImpl
-
- initialize(RandomAccessInputStream, int, int) - Method in interface loci.formats.services.JPEGTurboService
-
- initialize(RandomAccessInputStream, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
-
- initialize(InputStream) - Method in interface loci.formats.services.LuraWaveService
-
Wraps lwfDecoder.lwfDecoder(InputStream, String, String).
- initialize(InputStream) - Method in class loci.formats.services.LuraWaveServiceImpl
-
- initialize(String) - Method in interface loci.formats.services.MDBService
-
Prepare the given .mdb file for reading.
- initialize(String) - Method in class loci.formats.services.MDBServiceImpl
-
- initialize(String) - Method in interface loci.formats.services.MetakitService
-
- initialize(RandomAccessInputStream) - Method in interface loci.formats.services.MetakitService
-
- initialize(String) - Method in class loci.formats.services.MetakitServiceImpl
-
- initialize(RandomAccessInputStream) - Method in class loci.formats.services.MetakitServiceImpl
-
- initialize(String) - Method in interface loci.formats.services.POIService
-
Construct a new POI filesystem around the given file.
- initialize(RandomAccessInputStream) - Method in interface loci.formats.services.POIService
-
Construct a new POI filesystem around the given stream.
- initialize(String) - Method in class loci.formats.services.POIServiceImpl
-
- initialize(RandomAccessInputStream) - Method in class loci.formats.services.POIServiceImpl
-
- initializeColors() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.COLORS notification.
- initializeCrop() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.CROP notification.
- initialized - Variable in class loci.formats.FormatWriter
-
Whether each plane in each series of the current file has been
prepped for writing.
- initialized - Variable in class loci.formats.gui.LegacyQTTools
-
Flag indicating this class has been initialized.
- initializedFile - Variable in class loci.formats.in.HamamatsuVMSReader
-
- initializeDimOrder() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.DIM_ORDER notification.
- initializedPlane - Variable in class loci.formats.in.HamamatsuVMSReader
-
- initializedPlane - Variable in class loci.formats.in.NDPIReader
-
- initializedSeries - Variable in class loci.formats.in.HamamatsuVMSReader
-
- initializedSeries - Variable in class loci.formats.in.NDPIReader
-
- initializeFile() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.FILE notification.
- initializeHelper - Variable in class loci.formats.in.NRRDReader
-
- initializeJHDFService(String) - Method in class loci.formats.in.CellH5Reader
-
- initializeMetadata() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.METADATA notification.
- initializeRange() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.RANGE notification.
- initializeReader() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.READER notification.
- initializeSeries() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.SERIES notification.
- initializeStack() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.STACK notification.
- initImage() - Method in class loci.formats.in.ImageIOReader
-
- initIntArray(String, long[], long) - Method in interface loci.formats.services.JHDFService
-
Creates an HDF5 dataset in path consisting of integers specified
by bytes per pixel bpp.
- initIntArray(String, long[], long) - Method in class loci.formats.services.JHDFServiceImpl
-
- initLicense() - Method in class loci.formats.services.LuraWaveServiceImpl
-
- initLicenseCode() - Static method in class loci.plugins.util.LuraWave
-
Reads LuraWave license code from ImageJ preferences, if available.
- initMeaFile(String) - Method in class loci.formats.in.FlexReader
-
Initialize the dataset from a .mea file.
- initMetadata() - Method in class loci.formats.in.BaseTiffReader
-
Populates the metadata hashtable and metadata store.
- initMetadata() - Method in class loci.formats.in.GelReader
-
- initMetadata(String) - Method in class loci.formats.in.LIFReader
-
Parses a string of XML and puts the values in a Hashtable.
- initMetadata(int) - Method in class loci.formats.in.ZeissLSMReader
-
- initMetadataStore() - Method in class loci.formats.in.BaseTiffReader
-
- initMetadataStore() - Method in class loci.formats.in.FEITiffReader
-
- initMetadataStore() - Method in class loci.formats.in.FluoviewReader
-
- initMetadataStore() - Method in class loci.formats.in.ImaconReader
-
- initMetadataStore() - Method in class loci.formats.in.ImprovisionTiffReader
-
- initMetadataStore() - Method in class loci.formats.in.JPKReader
-
- initMetadataStore() - Method in class loci.formats.in.LeicaSCNReader
-
- initMetadataStore() - Method in class loci.formats.in.LEOReader
-
- initMetadataStore() - Method in class loci.formats.in.NDPIReader
-
- initMetadataStore() - Method in class loci.formats.in.NikonElementsTiffReader
-
- initMetadataStore() - Method in class loci.formats.in.NikonTiffReader
-
- initMetadataStore() - Method in class loci.formats.in.PyramidTiffReader
-
- initMetadataStore() - Method in class loci.formats.in.SimplePCITiffReader
-
- initMetadataStore() - Method in class loci.formats.in.SISReader
-
- initMetadataStore() - Method in class loci.formats.in.SlidebookTiffReader
-
- initMetadataStore() - Method in class loci.formats.in.SVSReader
-
- initMetadataStore() - Method in class loci.formats.in.TiffReader
-
- initMetadataStore() - Method in class loci.formats.in.TrestleReader
-
- initMinMax() - Method in class loci.formats.MinMaxCalculator
-
Ensures internal min/max variables are initialized properly.
- initOMEMetadata() - Method in class loci.formats.in.LiFlimReader
-
- initOriginalMetadata() - Method in class loci.formats.in.LiFlimReader
-
- initPixels() - Method in class loci.formats.in.DeltavisionReader
-
- initPlaneReader() - Method in class loci.formats.in.AmiraReader
-
- initPOIService() - Method in class loci.formats.in.FV1000Reader
-
- initPOIService() - Method in class loci.formats.in.IPWReader
-
- initPOIService() - Method in class loci.formats.in.PCIReader
-
- initPOIService() - Method in class loci.formats.in.ZeissZVIReader
-
- initReader(int, int) - Method in class loci.formats.FileStitcher
-
- initResFile(String) - Method in class loci.formats.in.FlexReader
-
Initialize the dataset from a .res file.
- initStack(long, int) - Method in class loci.formats.in.OBFReader
-
- initStandardMetadata() - Method in class loci.formats.in.BaseTiffReader
-
Parses standard metadata.
- initStandardMetadata() - Method in class loci.formats.in.DNGReader
-
- initStandardMetadata() - Method in class loci.formats.in.FEITiffReader
-
- initStandardMetadata() - Method in class loci.formats.in.FluoviewReader
-
- initStandardMetadata() - Method in class loci.formats.in.ImaconReader
-
- initStandardMetadata() - Method in class loci.formats.in.ImprovisionTiffReader
-
- initStandardMetadata() - Method in class loci.formats.in.JPKReader
-
- initStandardMetadata() - Method in class loci.formats.in.LeicaSCNReader
-
- initStandardMetadata() - Method in class loci.formats.in.LEOReader
-
- initStandardMetadata() - Method in class loci.formats.in.MetamorphReader
-
- initStandardMetadata() - Method in class loci.formats.in.NDPIReader
-
- initStandardMetadata() - Method in class loci.formats.in.NikonElementsTiffReader
-
- initStandardMetadata() - Method in class loci.formats.in.NikonReader
-
- initStandardMetadata() - Method in class loci.formats.in.NikonTiffReader
-
- initStandardMetadata() - Method in class loci.formats.in.PyramidTiffReader
-
- initStandardMetadata() - Method in class loci.formats.in.SEQReader
-
- initStandardMetadata() - Method in class loci.formats.in.SimplePCITiffReader
-
- initStandardMetadata() - Method in class loci.formats.in.SISReader
-
- initStandardMetadata() - Method in class loci.formats.in.SlidebookTiffReader
-
- initStandardMetadata() - Method in class loci.formats.in.SVSReader
-
- initStandardMetadata() - Method in class loci.formats.in.TiffReader
-
- initStandardMetadata() - Method in class loci.formats.in.TrestleReader
-
- initTiffParser() - Method in class loci.formats.in.MinimalTiffReader
-
Reinitialize the underlying TiffParser.
- initVars(String) - Method in class loci.formats.in.BaseZeissReader
-
- initVars(String) - Method in class loci.formats.in.ZeissTIFFReader
-
- initVars(String) - Method in class loci.formats.in.ZeissZVIReader
-
- INK_NAMES - Static variable in class loci.formats.tiff.IFD
-
- INK_SET - Static variable in class loci.formats.tiff.IFD
-
- inPixels - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
-
- input - Variable in class loci.formats.gui.DataConverter
-
- input - Variable in class loci.formats.Memoizer.KryoDeser
-
- inputOrder - Variable in class loci.formats.SwappableMetadata
-
Order in which dimensions are stored.
- inputOrder - Variable in class loci.plugins.in.ImporterOptions
-
- INR_MAGIC - Static variable in class loci.formats.in.INRReader
-
- INRReader - Class in loci.formats.in
-
INRReader is the file format reader for INR files.
- INRReader() - Constructor for class loci.formats.in.INRReader
-
Constructs a new INR reader.
- inSequence - Variable in class loci.formats.in.DicomReader
-
- insert(ImageProcessor, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- insertUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
-
- insertWarningComment(String) - Method in class loci.formats.out.OMETiffWriter
-
- install(String, String) - Method in class loci.formats.UpgradeChecker
-
Download and install a JAR file from the given URL.
- install(String) - Static method in class loci.plugins.Updater
-
Install the tools bundle which can be retrieved from the specified path.
- installButton - Variable in class loci.plugins.config.ConfigWindow
-
- installIndividualJars(String, String) - Method in class loci.formats.UpgradeChecker
-
Download and install all of the individual JAR files into the given
directory.
- InstallWizard - Class in loci.plugins.config
-
A wizard for walking users through installation of third party
libraries and plugins used by the Bio-Formats plugins.
- InstallWizard() - Constructor for class loci.plugins.config.InstallWizard
-
- instrumentModel - Variable in class loci.formats.in.NDPIReader
-
- INT - Static variable in class loci.formats.in.CellSensReader
-
- INT - Static variable in class loci.formats.in.GatanReader
-
- INT16 - Static variable in class loci.formats.FormatTools
-
Identifies the INT16 data type used to store pixel values.
- INT16 - Static variable in class loci.formats.in.SPEReader
-
- INT32 - Static variable in class loci.formats.FormatTools
-
Identifies the INT32 data type used to store pixel values.
- INT32 - Static variable in class loci.formats.in.SPEReader
-
- INT8 - Static variable in class loci.formats.FormatTools
-
Identifies the INT8 data type used to store pixel values.
- INT_2 - Static variable in class loci.formats.in.CellSensReader
-
- INT_3 - Static variable in class loci.formats.in.CellSensReader
-
- INT_4 - Static variable in class loci.formats.in.CellSensReader
-
- INT_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
-
- INT_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
-
- INT_ARRAY_4 - Static variable in class loci.formats.in.CellSensReader
-
- INT_ARRAY_5 - Static variable in class loci.formats.in.CellSensReader
-
- INT_INTERVAL - Static variable in class loci.formats.in.CellSensReader
-
- INT_RECT - Static variable in class loci.formats.in.CellSensReader
-
- intenScaling - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Intensity scaling factor.
- intensity - Variable in class loci.formats.in.LeicaHandler.Laser
-
- intensity - Variable in class loci.formats.in.SDTReader
-
Whether to combine lifetime bins into single intensity image planes.
- interlace - Variable in class loci.formats.in.APNGReader
-
- interlace - Variable in class loci.formats.in.GIFReader
-
Interlace flag.
- interlaced - Variable in class loci.formats.codec.MJPBCodecOptions
-
Indicates whether or not channels are interlaced.
- interlaced - Variable in class loci.formats.in.NativeQTReader
-
Set to true if the scanlines in a plane are interlaced (mjpb only).
- interleaved - Variable in class loci.formats.codec.CodecOptions
-
Indicates whether or not channels are interleaved.
- interleaved - Variable in class loci.formats.CoreMetadata
-
True if channels are stored RGBRGBRGB...; false if channels are stored
RRR...GGG...BBB...
- interleaved - Variable in class loci.formats.FormatWriter
-
Whether the channels in an RGB image are interleaved.
- internalOffsets - Variable in class loci.formats.in.AmiraReader.HxRLE
-
- internalStamps - Variable in class loci.formats.in.MetamorphReader
-
- interpolate(short[], byte[], int[], int, int, boolean) - Static method in class loci.formats.ImageTools
-
- intFormat(int, int) - Static method in class loci.formats.in.MetamorphReader
-
Formats an integer value with leading 0s if needed.
- intFormatMax(int, int) - Static method in class loci.formats.in.MetamorphReader
-
Formats an integer with leading 0 using maximum sequence number.
- IntIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IntIM3Record
-
- intValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as an int.
- INVALID_LICENSE_MSG - Static variable in class loci.formats.services.LuraWaveServiceImpl
-
Message to display if an invalid LuraWave license code is given.
- INVALID_PIXELS - Static variable in class loci.formats.in.FEIReader
-
- invalidAndMark(int) - Method in class loci.formats.in.SPCReader
-
- invalidAndMarkInit(int) - Method in class loci.formats.in.SPCReader
-
- InveonReader - Class in loci.formats.in
-
InveonReader is the file format reader for Inveon files.
- InveonReader() - Constructor for class loci.formats.in.InveonReader
-
Constructs a new Inveon reader.
- invert() - Method in class loci.plugins.util.RecordedImageProcessor
-
- inverted - Variable in class loci.formats.in.DicomReader
-
- invertLut() - Method in class loci.plugins.util.RecordedImageProcessor
-
- invertX - Variable in class loci.formats.in.RHKReader
-
- invertY - Variable in class loci.formats.in.BMPReader
-
- invertY - Variable in class loci.formats.in.ICSReader
-
Whether or not the image is inverted along the Y axis.
- invertY - Variable in class loci.formats.in.RHKReader
-
- invokeMethod(String, String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
-
- IPLabReader - Class in loci.formats.in
-
IPLabReader is the file format reader for IPLab (.IPL) files.
- IPLabReader() - Constructor for class loci.formats.in.IPLabReader
-
Constructs a new IPLab reader.
- IPW_MAGIC_BYTES - Static variable in class loci.formats.in.IPWReader
-
- IPWReader - Class in loci.formats.in
-
IPWReader is the file format reader for Image-Pro Workspace (IPW) files.
- IPWReader() - Constructor for class loci.formats.in.IPWReader
-
Constructs a new IPW reader.
- ir - Variable in class loci.plugins.in.ThumbLoader
-
- iris - Variable in class loci.formats.in.ZeissLSMReader.Recording
-
- IS - Static variable in class loci.formats.in.DicomReader
-
- IS_GLITCHED - Static variable in class loci.plugins.prefs.OptionsDialog
-
Flag indicating whether to invoke workaround for AWT refresh bug.
- IS_LITTLE - Static variable in class loci.formats.in.ImarisReader
-
Specifies endianness.
- IS_TRANSMISSION - Static variable in class loci.formats.in.CellSensReader
-
- isAutoscale() - Method in class loci.plugins.in.ImporterOptions
-
- isBigTiff - Variable in class loci.formats.out.TiffWriter
-
Whether or not the output file is a BigTIFF file.
- isBigTiff() - Method in class loci.formats.tiff.IFD
-
Gets whether this is a BigTIFF IFD.
- isBigTiff() - Method in class loci.formats.tiff.TiffParser
-
Returns whether or not the current TIFF file contains BigTIFF data.
- isBigTiff() - Method in class loci.formats.tiff.TiffSaver
-
Returns whether or not we are writing BigTIFF data.
- isBitOnByteBoundary() - Method in class loci.formats.codec.BitBuffer
-
Deprecated.
Checks if the current position is on a byte boundary, that is the next
bit in the byte array is the first bit in a byte.
- isCellsensFailOnMissing() - Static method in class loci.plugins.util.LociPrefs
-
- isCertain() - Method in class loci.formats.AxisGuesser
-
Gets whether the guesser is confident that all axes are correct.
- isColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
-
- isColorModeColorized() - Method in class loci.plugins.in.ImporterOptions
-
- isColorModeComposite() - Method in class loci.plugins.in.ImporterOptions
-
- isColorModeCustom() - Method in class loci.plugins.in.ImporterOptions
-
- isColorModeDefault() - Method in class loci.plugins.in.ImporterOptions
-
- isColorModeGrayscale() - Method in class loci.plugins.in.ImporterOptions
-
- isCompatibleRaster(Raster) - Method in class loci.formats.gui.Index16ColorModel
-
- isCompatibleRaster(Raster) - Method in class loci.formats.gui.SignedColorModel
-
- isCompatibleRaster(Raster) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- isCompressed - Variable in class loci.formats.in.LIMReader
-
- isConcatenate() - Method in class loci.plugins.in.ImporterOptions
-
- isContainer(String) - Method in class loci.formats.in.NativeQTReader
-
Checks if the given String is a container atom type.
- isCS_sRGB() - Method in class loci.formats.gui.TwoChannelColorSpace
-
- isDeflate - Variable in class loci.formats.in.DicomReader
-
- isDimensions(String) - Method in class loci.formats.in.ND2Handler
-
Returns whether or not the specified key is denotes dimensions.
- isEnabled - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
-
- isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
-
Determine whether or not two OMEXMLMetadata objects are equal.
- isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- isFalseColor() - Method in class loci.formats.FileStitcher
-
- isFalseColor() - Method in class loci.formats.FormatReader
-
- isFalseColor() - Method in interface loci.formats.IFormatReader
-
- isFalseColor() - Method in class loci.formats.ImageReader
-
- isFalseColor() - Method in class loci.formats.in.FilePatternReader
-
- isFalseColor() - Method in class loci.formats.ReaderWrapper
-
- isFiji() - Static method in class loci.plugins.Updater
-
Returns true if the current ImageJ instance is actually a Fiji instance.
- isFilled() - Method in class loci.formats.ChannelFiller
-
Returns true if the indices are being factored out.
- isFirstTime() - Method in class loci.plugins.in.ImporterOptions
-
- isFixed() - Method in class loci.formats.FilePatternBlock
-
Whether or not this is a fixed-width block.
- isFLIM - Variable in class loci.formats.in.ImspectorReader
-
Whether or not this file contains FLIM data.
- isFloatingPoint(IFormatReader) - Static method in class loci.formats.FormatTools
-
Determines whether the given reader represents any floating point data.
- isFloatingPoint(int) - Static method in class loci.formats.FormatTools
-
Determines whether the given pixel type is floating point or integer.
- isForceThumbnails() - Method in class loci.plugins.in.ImporterOptions
-
- isFullPlane(int, int, int, int) - Method in class loci.formats.FormatWriter
-
Returns true if the given rectangle coordinates correspond to a full
image in the given series.
- isGreaterThanEpsilon(double) - Method in class loci.formats.in.SlidebookReader
-
Returns true if the given double is greater than epsilon (defined here as
0.000001), i.e.
- isGroupFiles() - Method in class loci.formats.FileStitcher
-
- isGroupFiles() - Method in class loci.formats.FormatReader
-
- isGroupFiles() - Method in interface loci.formats.IFormatReader
-
Returns true if we should group files in multi-file formats.
- isGroupFiles() - Method in class loci.formats.ImageReader
-
- isGroupFiles() - Method in class loci.formats.in.FilePatternReader
-
- isGroupFiles() - Method in class loci.formats.ReaderWrapper
-
- isGroupFiles() - Method in class loci.plugins.in.ImporterOptions
-
- isGroupFiles(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isHCS - Variable in class loci.formats.in.MetamorphReader
-
- isHTTP() - Method in class loci.plugins.in.ImporterOptions
-
- isInCache(int[]) - Method in class loci.formats.cache.Cache
-
Returns true if the object at the given dimensional position is
in the cache.
- isInCache(int) - Method in class loci.formats.cache.Cache
-
Returns true if the object at the given index is in the cache.
- isIndexed() - Method in class loci.formats.ChannelFiller
-
- isIndexed() - Method in class loci.formats.ChannelMerger
-
- isIndexed() - Method in class loci.formats.FileStitcher
-
- isIndexed() - Method in class loci.formats.FormatReader
-
- isIndexed() - Method in interface loci.formats.IFormatReader
-
Gets whether the image planes are indexed color.
- isIndexed() - Method in class loci.formats.ImageReader
-
- isIndexed() - Method in class loci.formats.in.FilePatternReader
-
- isIndexed() - Method in class loci.formats.ReaderWrapper
-
- isIndexed(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isIntensity() - Method in class loci.formats.in.SDTReader
-
Gets whether the reader is combining each lifetime
histogram into a summed intensity image plane.
- isInterleaved() - Method in class loci.formats.ChannelMerger
-
- isInterleaved() - Method in class loci.formats.FileStitcher
-
- isInterleaved(int) - Method in class loci.formats.FileStitcher
-
- isInterleaved() - Method in class loci.formats.FormatReader
-
- isInterleaved(int) - Method in class loci.formats.FormatReader
-
- isInterleaved() - Method in class loci.formats.FormatWriter
-
- isInterleaved() - Method in interface loci.formats.IFormatReader
-
Gets whether or not the channels are interleaved.
- isInterleaved(int) - Method in interface loci.formats.IFormatReader
-
Gets whether or not the given sub-channel is interleaved.
- isInterleaved() - Method in interface loci.formats.IFormatWriter
-
Gets whether or not the channels in an image are interleaved.
- isInterleaved() - Method in class loci.formats.ImageReader
-
- isInterleaved(int) - Method in class loci.formats.ImageReader
-
- isInterleaved() - Method in class loci.formats.ImageWriter
-
- isInterleaved() - Method in class loci.formats.in.FilePatternReader
-
- isInterleaved(int) - Method in class loci.formats.in.FilePatternReader
-
- isInterleaved(int) - Method in class loci.formats.in.ICSReader
-
- isInterleaved(int) - Method in class loci.formats.in.SDTReader
-
- isInterleaved() - Method in class loci.formats.ReaderWrapper
-
- isInterleaved(int) - Method in class loci.formats.ReaderWrapper
-
- isInterleaved() - Method in class loci.formats.WriterWrapper
-
- isInterleaved(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isInterleavedSubC(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isInvertedLut() - Method in class loci.plugins.util.RecordedImageProcessor
-
- isInvertX() - Method in class loci.formats.in.PrairieMetadata
-
Gets whether the stage position X coordinates are inverted (i.e.,
left-to-right).
- isInvertY() - Method in class loci.formats.in.PrairieMetadata
-
Gets whether the stage position Y coordinates are inverted (i.e.,
bottom-to-top).
- isJNG - Variable in class loci.formats.in.MNGReader
-
- isJP2K - Variable in class loci.formats.in.DicomReader
-
- isJPEG - Variable in class loci.formats.in.BaseZeissReader
-
- isJPEG - Variable in class loci.formats.in.DicomReader
-
- isJPEG - Variable in class loci.formats.in.NativeND2Reader
-
Whether or not the pixel data is compressed using JPEG 2000.
- isJVM64Bit() - Method in class loci.formats.gui.LegacyQTTools
-
Whether this JVM is 64-bit.
- isLegacy() - Method in class loci.formats.DelegateReader
-
Gets whether to use the legacy reader by default.
- isLeicaLIFPhysicalSizeBackwardsCompatible() - Static method in class loci.plugins.util.LociPrefs
-
- isLicenseCodeException(FormatException) - Static method in class loci.plugins.util.LuraWave
-
Returns true if the given exception was cause
by a missing or invalid LuraWave license code.
- isLittleEndian() - Method in class loci.formats.FileStitcher
-
- isLittleEndian() - Method in class loci.formats.FormatReader
-
- isLittleEndian() - Method in interface loci.formats.IFormatReader
-
Gets whether the data is in little-endian format.
- isLittleEndian() - Method in class loci.formats.ImageReader
-
- isLittleEndian() - Method in class loci.formats.in.FilePatternReader
-
- isLittleEndian() - Method in class loci.formats.ReaderWrapper
-
- isLittleEndian() - Method in class loci.formats.tiff.IFD
-
Gets whether the TIFF information in this IFD is little-endian.
- isLittleEndian() - Method in class loci.formats.tiff.TiffSaver
-
Returns whether or not we are writing little-endian data.
- isLittleEndian(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isLoadedFromMemo() - Method in class loci.formats.Memoizer
-
- isLocal() - Method in class loci.plugins.in.ImporterOptions
-
- isLossless - Variable in class loci.formats.in.NativeND2Reader
-
Whether or not the pixel data is losslessly compressed.
- isLossless - Variable in class loci.formats.in.ND2Handler
-
- isLossless() - Method in class loci.formats.in.ND2Handler
-
- isMetadataComplete() - Method in class loci.formats.FormatReader
-
- isMetadataComplete() - Method in interface loci.formats.IFormatReader
-
Returns true if this format's metadata is completely parsed.
- isMetadataComplete() - Method in class loci.formats.ImageReader
-
- isMetadataComplete() - Method in class loci.formats.in.FilePatternReader
-
- isMetadataComplete() - Method in class loci.formats.ReaderWrapper
-
- isMetadataComplete(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isMetadataFiltered() - Method in class loci.formats.FormatReader
-
- isMetadataFiltered() - Method in interface loci.formats.IFormatReader
-
Returns true if ugly metadata (entries with unprintable characters,
and extremely large entries) are discarded from the metadata table.
- isMetadataFiltered() - Method in class loci.formats.ImageReader
-
- isMetadataFiltered() - Method in class loci.formats.in.FilePatternReader
-
- isMetadataFiltered() - Method in class loci.formats.ReaderWrapper
-
- isMetadataFiltered(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isMINC2 - Variable in class loci.formats.in.MINCReader
-
- isMinimumMetadata() - Method in class loci.formats.in.PrairieReader
-
Gets whether to populate only the minimum required metadata.
- isMinMaxPopulated() - Method in class loci.formats.MinMaxCalculator
-
Returns true if the values returned by
getChannelGlobalMinimum/Maximum can be trusted.
- isModulo - Variable in class loci.formats.tools.MakeTestOmeTiff
-
- isND2Nikon() - Static method in class loci.plugins.util.LociPrefs
-
- isNormalized() - Method in class loci.formats.FormatReader
-
- isNormalized() - Method in interface loci.formats.IFormatReader
-
Returns true if we should normalize float data.
- isNormalized() - Method in class loci.formats.ImageReader
-
- isNormalized() - Method in class loci.formats.in.FilePatternReader
-
- isNormalized() - Method in class loci.formats.ReaderWrapper
-
- isNormalized(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
-
- isNumeric() - Method in class loci.formats.FilePatternBlock
-
Whether or not this is a numeric block.
- ISO - Static variable in class loci.formats.in.NikonReader
-
- ISO_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
-
- ISO_SPEED_RATINGS - Static variable in class loci.formats.tiff.IFD
-
- isOIB - Variable in class loci.formats.in.FV1000Reader
-
Flag indicating this is an OIB dataset.
- isOMERO() - Method in class loci.plugins.in.ImporterOptions
-
- isOMEXMLMetadata(Object) - Method in interface loci.formats.services.OMEXMLService
-
Checks whether the given object is an OME-XML metadata object.
- isOMEXMLMetadata(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- isOMEXMLRoot(Object) - Method in interface loci.formats.services.OMEXMLService
-
Checks whether the given object is an OME-XML root object.
- isOMEXMLRoot(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- isOne() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns true or false, depending on whether this instance is equal to
1/1.
- isOrderCertain() - Method in class loci.formats.FileStitcher
-
- isOrderCertain() - Method in class loci.formats.FormatReader
-
- isOrderCertain() - Method in interface loci.formats.IFormatReader
-
Gets whether the dimension order and sizes are known, or merely guesses.
- isOrderCertain() - Method in class loci.formats.ImageReader
-
- isOrderCertain() - Method in class loci.formats.in.FilePatternReader
-
- isOrderCertain() - Method in class loci.formats.ReaderWrapper
-
- isOrderCertain(String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isOriginalMetadataPopulated() - Method in class loci.formats.FormatReader
-
- isOriginalMetadataPopulated() - Method in interface loci.formats.IFormatReader
-
Returns true if we should save proprietary metadata
in the MetadataStore.
- isOriginalMetadataPopulated() - Method in class loci.formats.ImageReader
-
- isOriginalMetadataPopulated() - Method in class loci.formats.in.FilePatternReader
-
- isOriginalMetadataPopulated() - Method in class loci.formats.ReaderWrapper
-
- isOriginalMetadataPopulated(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
-
- isPictQTJava() - Static method in class loci.plugins.util.LociPrefs
-
- isPositiveValue(Double) - Static method in class loci.formats.FormatTools
-
- isPossible(String, String) - Method in class loci.plugins.prefs.OptionsList
-
Gets whether the specified value is a possible one
for the string option with the given key.
- isPreviewName(String) - Method in class loci.formats.in.FV1000Reader
-
- isPseudoColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
-
- isQTExpired() - Method in class loci.formats.gui.LegacyQTTools
-
Whether QuickTime for Java has expired.
- isQTQTJava() - Static method in class loci.plugins.util.LociPrefs
-
- isQuiet() - Method in class loci.plugins.in.ImporterOptions
-
- isRawCodestream - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Whether or not the codestream is raw and not JP2 boxed.
- isRawCodestream() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Whether or not the codestream is raw and not JP2 boxed.
- isReaderEnabled(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
-
- isReaderEnabled(Class<? extends IFormatReader>) - Static method in class loci.plugins.util.LociPrefs
-
- isReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
-
- isReaderWindowless(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
-
- isRegex - Variable in class loci.formats.FilePattern
-
Whether or not this FilePattern represents a regular expression.
- isRegex() - Method in class loci.formats.FilePattern
-
Returns whether or not this pattern is a regular expression.
- isRGB() - Method in class loci.formats.ChannelFiller
-
- isRGB() - Method in class loci.formats.ChannelMerger
-
- isRGB() - Method in class loci.formats.ChannelSeparator
-
- isRGB() - Method in class loci.formats.FileStitcher
-
- isRGB() - Method in class loci.formats.FormatReader
-
- isRGB() - Method in interface loci.formats.IFormatReader
-
- isRGB() - Method in class loci.formats.ImageReader
-
- isRGB() - Method in class loci.formats.in.FilePatternReader
-
- isRGB() - Method in class loci.formats.ReaderWrapper
-
- isRGB() - Method in interface loci.formats.services.WlzService
-
Gets boolean for whether image is colour or not.
- isRGB() - Method in class loci.formats.services.WlzServiceImpl
-
- isRLE - Variable in class loci.formats.in.DicomReader
-
- isSaved() - Method in class loci.plugins.prefs.Option
-
Gets whether option should be saved to ImageJ preferences file.
- isSaved(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets whether the option with the given key
is saved to the ImageJ preferences file.
- isSavedToMemo() - Method in class loci.formats.Memoizer
-
- isSDTIntensity() - Static method in class loci.plugins.util.LociPrefs
-
- isSeriesOn(int) - Method in class loci.plugins.in.ImporterOptions
-
- isSet(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the value of the boolean option with the given key.
- isSetByDefault(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the default value of the boolean option with the given key.
- isShowMetadata() - Method in class loci.plugins.in.ImporterOptions
-
- isShowOMEXML() - Method in class loci.plugins.in.ImporterOptions
-
- isSigned(int) - Static method in class loci.formats.FormatTools
-
Determines whether the given pixel type is signed or unsigned.
- isSingleFile(String) - Method in class loci.formats.FormatReader
-
- isSingleFile(String) - Method in interface loci.formats.IFormatReader
-
Returns true if this is a single-file format.
- isSingleFile(String) - Method in class loci.formats.ImageReader
-
- isSingleFile(String) - Method in class loci.formats.in.AFIReader
-
- isSingleFile(String) - Method in class loci.formats.in.AnalyzeReader
-
- isSingleFile(String) - Method in class loci.formats.in.APLReader
-
- isSingleFile(String) - Method in class loci.formats.in.BDReader
-
- isSingleFile(String) - Method in class loci.formats.in.BioRadReader
-
- isSingleFile(String) - Method in class loci.formats.in.BrukerReader
-
- isSingleFile(String) - Method in class loci.formats.in.CellSensReader
-
- isSingleFile(String) - Method in class loci.formats.in.CellVoyagerReader
-
- isSingleFile(String) - Method in class loci.formats.in.ColumbusReader
-
- isSingleFile(String) - Method in class loci.formats.in.DeltavisionReader
-
- isSingleFile(String) - Method in class loci.formats.in.FakeReader
-
- isSingleFile(String) - Method in class loci.formats.in.FilePatternReader
-
- isSingleFile(String) - Method in class loci.formats.in.FlexReader
-
- isSingleFile(String) - Method in class loci.formats.in.FujiReader
-
- isSingleFile(String) - Method in class loci.formats.in.FV1000Reader
-
- isSingleFile(String) - Method in class loci.formats.in.HitachiReader
-
- isSingleFile(String) - Method in class loci.formats.in.ICSReader
-
- isSingleFile(String) - Method in class loci.formats.in.ImagicReader
-
- isSingleFile(String) - Method in class loci.formats.in.InCellReader
-
- isSingleFile(String) - Method in class loci.formats.in.L2DReader
-
- isSingleFile(String) - Method in class loci.formats.in.LeicaReader
-
- isSingleFile(String) - Method in class loci.formats.in.MetamorphReader
-
- isSingleFile(String) - Method in class loci.formats.in.MIASReader
-
- isSingleFile(String) - Method in class loci.formats.in.MicromanagerReader
-
- isSingleFile(String) - Method in class loci.formats.in.NDPISReader
-
- isSingleFile(String) - Method in class loci.formats.in.NiftiReader
-
- isSingleFile(String) - Method in class loci.formats.in.NRRDReader
-
- isSingleFile(String) - Method in class loci.formats.in.OMETiffReader
-
- isSingleFile(String) - Method in class loci.formats.in.OperettaReader
-
- isSingleFile(String) - Method in class loci.formats.in.PerkinElmerReader
-
- isSingleFile(String) - Method in class loci.formats.in.PrairieReader
-
- isSingleFile(String) - Method in class loci.formats.in.ScanrReader
-
- isSingleFile(String) - Method in class loci.formats.in.ScreenReader
-
- isSingleFile(String) - Method in class loci.formats.in.SPCReader
-
- isSingleFile(String) - Method in class loci.formats.in.TCSReader
-
- isSingleFile(String) - Method in class loci.formats.in.TillVisionReader
-
- isSingleFile(String) - Method in class loci.formats.in.VisitechReader
-
- isSingleFile(String) - Method in class loci.formats.in.ZeissLSMReader
-
- isSingleFile(String) - Method in class loci.formats.in.ZeissTIFFReader
-
- isSingleFile(String) - Method in class loci.formats.ReaderWrapper
-
- isSpecifyRanges() - Method in class loci.plugins.in.ImporterOptions
-
- isSpectralMode() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
- isSplitChannels() - Method in class loci.plugins.in.ImporterOptions
-
- isSplitFocalPlanes() - Method in class loci.plugins.in.ImporterOptions
-
- isSplitTimepoints() - Method in class loci.plugins.in.ImporterOptions
-
- isSpool - Variable in class loci.formats.in.SlidebookReader
-
- isSPWStructure(String) - Method in class loci.formats.in.FakeReader
-
- isSupportedType(int) - Method in class loci.formats.FormatWriter
-
- isSupportedType(int) - Method in interface loci.formats.IFormatWriter
-
Checks if the given pixel type is supported.
- isSupportedType(int) - Method in class loci.formats.ImageWriter
-
- isSupportedType(int) - Method in class loci.formats.WriterWrapper
-
- isSwapDimensions() - Method in class loci.plugins.in.ImporterOptions
-
- isTable() - Method in interface loci.formats.in.PrairieMetadata.Value
-
- isTable() - Method in class loci.formats.in.PrairieMetadata.ValueItem
-
- isTable() - Method in class loci.formats.in.PrairieMetadata.ValueTable
-
- isThisType(String, boolean) - Method in class loci.formats.DelegateReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.DelegateReader
-
- isThisType(String) - Method in class loci.formats.FormatHandler
-
Checks if a file matches the type of this format handler.
- isThisType(String, boolean) - Method in class loci.formats.FormatReader
-
Checks if a file matches the type of this format reader.
- isThisType(byte[]) - Method in class loci.formats.FormatReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.FormatReader
-
- isThisType(String) - Method in class loci.formats.FormatReader
-
- isThisType(String) - Method in interface loci.formats.IFormatHandler
-
Checks if the given string is a valid filename for this file format.
- isThisType(String, boolean) - Method in interface loci.formats.IFormatReader
-
Checks if the given file is a valid instance of this file format.
- isThisType(byte[]) - Method in interface loci.formats.IFormatReader
-
Checks if the given block is a valid header for this file format.
- isThisType(RandomAccessInputStream) - Method in interface loci.formats.IFormatReader
-
Checks if the given stream is a valid stream for this file format.
- isThisType(String, boolean) - Method in class loci.formats.ImageReader
-
- isThisType(byte[]) - Method in class loci.formats.ImageReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.ImageReader
-
- isThisType(String) - Method in class loci.formats.ImageReader
-
- isThisType(String) - Method in class loci.formats.ImageWriter
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AFIReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AliconaReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AmiraReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.AnalyzeReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AnalyzeReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.APLReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.APNGReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ARFReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AVIReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.BDReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BDReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadGelReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.BioRadReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadSCNReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BMPReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.BrukerReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BrukerReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BurleighReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CanonRawReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.CellH5Reader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellH5Reader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellomicsReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.CellVoyagerReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.CellWorxReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.ColumbusReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ColumbusReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.DeltavisionReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DeltavisionReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.DicomReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DicomReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DNGReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.Ecat7Reader
-
- isThisType(String, boolean) - Method in class loci.formats.in.FakeReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEIReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEITiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FlowSightReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FluoviewReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.FujiReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FujiReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.FV1000Reader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FV1000Reader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanDM2Reader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GelReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GIFReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HISReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.HitachiReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HitachiReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HRDGDFReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.I2IReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IM3Reader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImaconReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.ImagicReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisHDFReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IMODReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImprovisionTiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImspectorReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCell3000Reader
-
- isThisType(String, boolean) - Method in class loci.formats.in.InCellReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCellReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.INRReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.InveonReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InveonReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPLabReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPWReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IvisionReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.JEOLReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JEOLReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEG2000Reader
-
- isThisType(String, boolean) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.JPKReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPXReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KhorosReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KodakReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.L2DReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.L2DReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.LegacyND2Reader
-
- isThisType(String, boolean) - Method in class loci.formats.in.LeicaReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LeicaReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.LeicaSCNReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LEOReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LIFReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.MetamorphReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphTiffReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.MIASReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MIASReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.MicromanagerReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MicromanagerReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MinimalTiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MNGReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MolecularImagingReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRCReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRWReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NativeND2Reader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NativeQTReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.NDPIReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NDPISReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.NiftiReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NiftiReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonElementsTiffReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.NikonReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonTiffReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.NRRDReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NRRDReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.OMETiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMETiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMEXMLReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.OMEXMLReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabRawReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.OperettaReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OperettaReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OxfordInstrumentsReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCIReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.PCORAWReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCORAWReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCXReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.PDSReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PDSReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.PerkinElmerReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PGMReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PhotoshopTiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PQBinReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.PrairieReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PrairieReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PSDReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PyramidTiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SBIGReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.ScanrReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ScanrReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.ScreenReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ScreenReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SEQReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SIFReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SimplePCITiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SISReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookTiffReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SMCameraReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.SPCReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SPEReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SpiderReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.SVSReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.TCSReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TCSReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TextReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.TillVisionReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TopometrixReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.TrestleReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TrestleReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.UnisokuReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.UnisokuReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VarianFDFReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VGSAMReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.VisitechReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityClippingReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.VolocityReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.WATOPReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.WlzReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLMSReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLSMReader
-
- isThisType(String, boolean) - Method in class loci.formats.in.ZeissTIFFReader
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
-
- isThisType(String, boolean) - Method in class loci.formats.ReaderWrapper
-
- isThisType(byte[]) - Method in class loci.formats.ReaderWrapper
-
- isThisType(RandomAccessInputStream) - Method in class loci.formats.ReaderWrapper
-
- isThisType(String) - Method in class loci.formats.ReaderWrapper
-
- isThisType(String) - Method in class loci.formats.WriterWrapper
-
- isThisType(String, String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isThisTypeFast(String, String[]) - Method in class loci.plugins.macro.LociFunctions
-
- isThumbnailSeries() - Method in class loci.formats.FileStitcher
-
- isThumbnailSeries() - Method in class loci.formats.FormatReader
-
- isThumbnailSeries() - Method in interface loci.formats.IFormatReader
-
Gets whether the current series is a lower resolution copy of a different
series.
- isThumbnailSeries() - Method in class loci.formats.ImageReader
-
- isThumbnailSeries() - Method in class loci.formats.in.FilePatternReader
-
- isThumbnailSeries() - Method in class loci.formats.ReaderWrapper
-
- isTiff - Variable in class loci.formats.in.EPSReader
-
- isTiff - Variable in class loci.formats.in.InCellReader.Image
-
- isTiff - Variable in class loci.formats.in.PerkinElmerReader
-
Flag indicating that the image data is in TIFF format.
- isTiffImageIO() - Static method in class loci.plugins.util.LociPrefs
-
- isTiled() - Method in class loci.formats.tiff.IFD
-
- isTimeSeries() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets whether this Sequence should be considered a time series.
- isUngroupFiles() - Method in class loci.plugins.in.ImporterOptions
-
- isUsedFile(String) - Method in class loci.formats.FormatReader
-
Returns true if the given file name is in the used files list.
- isUsingPatternIds() - Method in class loci.formats.FileStitcher
-
Gets whether the reader is using file patterns for IDs.
- isValid() - Method in class loci.formats.FilePattern
-
Returns whether or not the file pattern is valid.
- isValidate() - Method in class loci.formats.in.DefaultMetadataOptions
-
- isValidate() - Method in class loci.formats.in.DynamicMetadataOptions
-
- isValidate() - Method in interface loci.formats.in.MetadataOptions
-
Checks whether file validation has been set.
- isValidHeader() - Method in class loci.formats.tiff.TiffParser
-
Tests this stream to see if it represents a TIFF file.
- isValidPlateName(String) - Method in class loci.formats.in.ScreenReader
-
- isValidRange(int, int, int) - Static method in class loci.formats.tools.FakeImage
-
- isValidWellName(String) - Method in class loci.formats.in.ScreenReader
-
- isVersionChecking() - Method in class loci.formats.Memoizer
-
Returns whether or not version checking is done based upon major/minor
version numbers.
- isViewBrowser() - Method in class loci.plugins.in.ImporterOptions
-
- isViewHyperstack() - Method in class loci.plugins.in.ImporterOptions
-
- isViewImage5D() - Method in class loci.plugins.in.ImporterOptions
-
- isViewNone() - Method in class loci.plugins.in.ImporterOptions
-
- isViewStandard() - Method in class loci.plugins.in.ImporterOptions
-
- isViewView5D() - Method in class loci.plugins.in.ImporterOptions
-
- isVirtual() - Method in class loci.plugins.in.ImporterOptions
-
- isWhitelistedKey(String) - Method in class loci.formats.ClassList
-
Returns whether a given key is a whitelisted option.
- isWindowless() - Method in class loci.plugins.in.ImporterOptions
-
- isWindowless() - Method in class loci.plugins.in.ImportProcess
-
- isWindowless(IFormatReader) - Static method in class loci.plugins.util.LociPrefs
-
Gets whether windowless mode should be used when
opening this reader's currently initialized dataset.
- isZlib - Variable in class loci.formats.in.BaseZeissReader
-
- italic - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- ITEM - Static variable in class loci.formats.in.DicomReader
-
- ITEM_DELIMINATION - Static variable in class loci.formats.in.DicomReader
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.CellSensWidgets
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ConfigWindow
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.LIFWidgets
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ND2Widgets
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.PictWidgets
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.QTWidgets
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.SDTWidgets
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.TiffDelegateWidgets
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ZeissCZIWidgets
-
- itemStateChanged(ItemEvent) - Method in class loci.plugins.in.MainDialog
-
Handles toggling of mutually exclusive options.
- itemStateChanged(ItemEvent) - Method in class loci.plugins.in.SwapDialog
-
- iterateIn(RandomAccessInputStream, Long) - Method in class loci.formats.in.NativeND2Reader
-
Function for iterating through ND2 metaAttributes
- IvisionHandler() - Constructor for class loci.formats.in.IvisionReader.IvisionHandler
-
- IvisionReader - Class in loci.formats.in
-
IvisionReader is the file format reader for IVision (.IPM) files.
- IvisionReader() - Constructor for class loci.formats.in.IvisionReader
-
Constructs a new Ivision reader.
- IvisionReader.IvisionHandler - Class in loci.formats.in
-
- iw - Variable in class loci.formats.in.GIFReader
-
Current image rectangle.
- ix - Variable in class loci.formats.in.GIFReader
-
Current image rectangle.
- iy - Variable in class loci.formats.in.GIFReader
-
Current image rectangle.
- L2DReader - Class in loci.formats.in
-
L2DReader is the file format reader for Li-Cor L2D datasets.
- L2DReader() - Constructor for class loci.formats.in.L2DReader
-
Construct a new L2D reader.
- label - Variable in class loci.plugins.prefs.Option
-
Label describing the option, for use with ImageJ dialogs.
- LABEL_X - Static variable in class loci.formats.in.TextReader
-
- LABEL_Y - Static variable in class loci.formats.in.TextReader
-
- labels - Variable in class loci.formats.in.FakeReader
-
- labels - Variable in class loci.formats.in.ICSReader
-
Dimensional reordering for lifetime data
- labels - Variable in class loci.formats.Modulo
-
- labels - Variable in class loci.plugins.config.CellSensWidgets
-
- labels - Variable in class loci.plugins.config.FlexWidgets
-
- labels - Variable in class loci.plugins.config.FormatEntry
-
- labels - Variable in class loci.plugins.config.LIFWidgets
-
- labels - Variable in class loci.plugins.config.ND2Widgets
-
- labels - Variable in class loci.plugins.config.PictWidgets
-
- labels - Variable in class loci.plugins.config.QTWidgets
-
- labels - Variable in class loci.plugins.config.SDTWidgets
-
- labels - Variable in class loci.plugins.config.TiffDelegateWidgets
-
- labels - Variable in class loci.plugins.config.ZeissCZIWidgets
-
- LAMBDA - Static variable in class loci.formats.in.CellSensReader
-
- LAMBDA_INCREMENT - Static variable in class loci.formats.in.CellSensReader
-
- LAMBDA_START - Static variable in class loci.formats.in.CellSensReader
-
- LAMBDA_VALUE - Static variable in class loci.formats.in.CellSensReader
-
- Laser() - Constructor for class loci.formats.in.LeicaHandler.Laser
-
- Laser() - Constructor for class loci.formats.in.OIRReader.Laser
-
- Laser() - Constructor for class loci.formats.in.ZeissLSMReader.Laser
-
- LASER_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
-
- LASER_NAME - Static variable in class loci.formats.in.ZeissLSMReader
-
- LASER_POWER - Static variable in class loci.formats.in.ZeissLSMReader
-
- LASER_SCAN_CONFOCAL - Static variable in class loci.formats.in.LegacyND2Reader
-
- laserActive - Variable in class loci.formats.in.LIFReader
-
- laserCount - Variable in class loci.formats.in.LeicaHandler
-
- laserFrap - Variable in class loci.formats.in.LIFReader
-
- laserIDs - Variable in class loci.formats.in.NikonTiffReader
-
- laserIndex - Variable in class loci.formats.in.OIRReader.Channel
-
- laserIntensity - Variable in class loci.formats.in.LIFReader
-
- lasers - Variable in class loci.formats.in.LeicaHandler
-
- lasers - Variable in class loci.formats.in.OIRReader
-
- laserWavelength - Variable in class loci.formats.in.LIFReader
-
- lastChannel - Variable in class loci.formats.in.BioRadReader
-
- lastChannel - Variable in class loci.formats.in.CellH5Reader
-
- lastChannel - Variable in class loci.formats.in.FV1000Reader
-
- lastChannel - Variable in class loci.formats.in.ImarisHDFReader
-
- lastChannel - Variable in class loci.formats.in.LIFReader
-
- lastChannel - Variable in class loci.formats.in.NativeND2Reader
-
- lastChannel - Variable in class loci.formats.in.OIRReader
-
- lastCodeOffset - Variable in class loci.formats.in.AmiraReader.HxRLE
-
- lastDispose - Variable in class loci.formats.in.GIFReader
-
- lastFile - Variable in class loci.formats.in.CellWorxReader
-
- lastFile - Variable in class loci.formats.in.ImprovisionTiffReader
-
- lastFile - Variable in class loci.formats.in.SlidebookTiffReader
-
- lastId - Variable in class loci.formats.gui.PreviewPane
-
Last ID loaded.
- lastIFD - Variable in class loci.formats.in.LeicaSCNReader.Pixels
-
- lastImage - Variable in class loci.formats.ChannelSeparator
-
Last image opened.
- lastImage - Variable in class loci.formats.in.APNGReader
-
- lastImage - Variable in class loci.formats.in.AVIReader
-
- lastImageHeight - Variable in class loci.formats.ChannelSeparator
-
Height of last image opened.
- lastImageIndex - Variable in class loci.formats.ChannelSeparator
-
Index of last image opened.
- lastImageIndex - Variable in class loci.formats.in.APNGReader
-
- lastImageNo - Variable in class loci.formats.in.AVIReader
-
- lastImageRow - Variable in class loci.formats.in.APNGReader
-
- lastImageSeries - Variable in class loci.formats.ChannelSeparator
-
Series of last image opened.
- lastImageWidth - Variable in class loci.formats.ChannelSeparator
-
Width of last image opened.
- lastImageX - Variable in class loci.formats.ChannelSeparator
-
X index of last image opened.
- lastImageY - Variable in class loci.formats.ChannelSeparator
-
Y index of last image opened.
- lastIndex - Variable in class loci.formats.in.DNGReader
-
- lastIndex - Variable in class loci.formats.in.NikonReader
-
- lastPlane - Variable in class loci.formats.in.BaseZeissReader
-
- lastPlane - Variable in class loci.formats.in.DNGReader
-
- lastPlane - Variable in class loci.formats.in.JPXReader
-
- lastPlane - Variable in class loci.formats.in.LeicaReader
-
- lastPlane - Variable in class loci.formats.in.MinimalTiffReader
-
- lastPlane - Variable in class loci.formats.in.NikonReader
-
- lastPlane - Variable in class loci.formats.in.OMETiffReader
-
- lastPlane - Variable in class loci.formats.in.OpenlabReader
-
- lastPlane - Variable in class loci.formats.in.TCSReader
-
- lastPlane - Variable in class loci.formats.out.ICSWriter
-
- lastPlane - Variable in class loci.formats.out.V3DrawWriter
-
- lastReader - Variable in class loci.formats.in.CellWorxReader
-
- lastSeries - Variable in class loci.formats.in.BrukerReader
-
- lastSeries - Variable in class loci.formats.in.JPEG2000Reader
-
- lastSeries - Variable in class loci.formats.in.JPXReader
-
- lastSeriesPlane - Variable in class loci.formats.in.JPEG2000Reader
-
- lastSeriesPlane - Variable in class loci.formats.in.JPXReader
-
- LATEST_VERSION - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
Latest OME-XML version namespace.
- Layer() - Constructor for class loci.formats.in.BaseZeissReader.Layer
-
- layer_count - Variable in class loci.formats.in.ZeissTIFFHandler
-
- LAYER_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- LAYER_SELECTION - Static variable in class loci.formats.in.CellSensReader
-
- LAYER_SELECTION_INDEX - Static variable in class loci.formats.in.CellSensReader
-
- LAYER_XY_FIXED - Static variable in class loci.formats.in.CellSensReader
-
- layerNames - Variable in class loci.formats.in.PhotoshopTiffReader
-
- layerOffset - Variable in class loci.formats.in.PhotoshopTiffReader
-
- layers - Variable in class loci.formats.in.BaseZeissReader
-
- layers - Variable in class loci.formats.in.ZeissTIFFHandler
-
- LAYOUT_KEYS - Static variable in class loci.formats.in.ICSReader
-
- LAYOUT_TABLE - Static variable in class loci.formats.in.LiFlimReader
-
- lblockNo - Variable in class loci.formats.in.SDTInfo
-
Long blockNo - see remarks below.
- legacy - Variable in class loci.formats.in.PictReader
-
- legacy - Variable in class loci.formats.out.QTWriter
-
Legacy QuickTime writer.
- LegacyND2Reader - Class in loci.formats.in
-
LegacyND2Reader is a file format reader for Nikon ND2 files that uses
the Nikon ND2 SDK - it is only usable on Windows machines.
- LegacyND2Reader() - Constructor for class loci.formats.in.LegacyND2Reader
-
- LegacyQTReader - Class in loci.formats.in
-
LegacyQTReader is a file format reader for QuickTime movie files.
- LegacyQTReader() - Constructor for class loci.formats.in.LegacyQTReader
-
Constructs a new QT reader.
- LegacyQTTools - Class in loci.formats.gui
-
Utility class for working with QuickTime for Java.
- LegacyQTTools() - Constructor for class loci.formats.gui.LegacyQTTools
-
- LegacyQTWriter - Class in loci.formats.out
-
LegacyQTWriter is a file format writer for QuickTime movies.
- LegacyQTWriter() - Constructor for class loci.formats.out.LegacyQTWriter
-
- legacyReader - Variable in class loci.formats.DelegateReader
-
Legacy reader.
- legacyReaderInitialized - Variable in class loci.formats.DelegateReader
-
Flag indicating that the legacy reader was successfully initialized.
- LEI_SUFFIX - Static variable in class loci.formats.in.LeicaReader
-
- LEICA_MAGIC_TAG - Static variable in class loci.formats.in.LeicaReader
-
All Leica TIFFs have this tag.
- LeicaHandler - Class in loci.formats.in
-
SAX handler for parsing XML in Leica LIF and Leica TCS files.
- LeicaHandler(MetadataStore, MetadataLevel) - Constructor for class loci.formats.in.LeicaHandler
-
- LeicaHandler.Channel - Class in loci.formats.in
-
- LeicaHandler.Detector - Class in loci.formats.in
-
- LeicaHandler.Laser - Class in loci.formats.in
-
- LeicaHandler.MultiBand - Class in loci.formats.in
-
- LeicaHandler.ROI - Class in loci.formats.in
-
- LeicaReader - Class in loci.formats.in
-
LeicaReader is the file format reader for Leica files.
- LeicaReader() - Constructor for class loci.formats.in.LeicaReader
-
Constructs a new Leica reader.
- LeicaReader.Detector - Class in loci.formats.in
-
- LeicaSCNHandler() - Constructor for class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- LeicaSCNReader - Class in loci.formats.in
-
LeicaSCNReader is the file format reader for Leica SCN TIFF files.
- LeicaSCNReader() - Constructor for class loci.formats.in.LeicaSCNReader
-
Constructs a new LeicaSCN reader.
- LeicaSCNReader.Dimension - Class in loci.formats.in
-
- LeicaSCNReader.Image - Class in loci.formats.in
-
- LeicaSCNReader.ImageCollection - Class in loci.formats.in
-
- LeicaSCNReader.LeicaSCNHandler - Class in loci.formats.in
-
SAX handler for parsing XML in Leica SCN files.
- LeicaSCNReader.Pixels - Class in loci.formats.in
-
- leiFilename - Variable in class loci.formats.in.LeicaReader
-
Name of current LEI file
- len - Variable in class loci.plugins.util.BFVirtualStack
-
- lenC - Variable in class loci.formats.FileStitcher
-
Component lengths for each axis type.
- length() - Method in class loci.formats.cache.CacheStrategy
-
Shortcut for computing total number of positions.
- length - Variable in class loci.formats.in.APNGReader.PNGBlock
-
- length - Variable in class loci.formats.in.IM3Reader.IM3Record
-
- length - Variable in class loci.formats.in.NativeND2Reader.ChunkMapEntry
-
- length - Variable in class loci.formats.in.OBFReader.Stack
-
- length - Variable in class loci.formats.in.OIRReader.PixelBlock
-
- length() - Method in class loci.formats.Modulo
-
- lengths - Variable in class loci.formats.cache.CacheStrategy
-
Length of each dimensional axis.
- lengths - Variable in class loci.formats.gui.CacheComponent
-
Length of each dimensional axis, obtained from cache strategy.
- lengths - Variable in class loci.formats.in.AVIReader
-
Number of bytes in each plane.
- lengths - Variable in class loci.formats.in.DeltavisionReader
-
- lengths - Variable in class loci.formats.in.MNGReader.SeriesInfo
-
- LENS - Static variable in class loci.formats.in.NikonReader
-
- lens - Variable in class loci.formats.in.PSDReader
-
- LENS_TYPE - Static variable in class loci.formats.in.NikonReader
-
- lensNA - Variable in class loci.formats.in.FluoviewReader
-
- lensNA - Variable in class loci.formats.in.FV1000Reader
-
- lensNA - Variable in class loci.formats.in.IvisionReader
-
- lensNA - Variable in class loci.formats.in.LIFReader
-
- lensNA - Variable in class loci.formats.in.MetamorphHandler
-
- lensNA - Variable in class loci.formats.in.NikonTiffReader
-
- lensNA - Variable in class loci.formats.in.OperettaReader.Plane
-
- lensNA - Variable in class loci.formats.in.ZeissLSMReader.Recording
-
- lensRI - Variable in class loci.formats.in.MetamorphHandler
-
- lenT - Variable in class loci.formats.FileStitcher
-
Component lengths for each axis type.
- lenZ - Variable in class loci.formats.FileStitcher
-
Component lengths for each axis type.
- LEO_TAG - Static variable in class loci.formats.in.LEOReader
-
- LEOReader - Class in loci.formats.in
-
LEOReader is the file format reader for LEO EM files.
- LEOReader() - Constructor for class loci.formats.in.LEOReader
-
Constructs a new LEO reader.
- letter - Variable in class loci.formats.ResourceNamer
-
- level - Variable in class loci.formats.in.BioRadReader.Note
-
- level - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- level - Variable in class loci.formats.in.LeicaHandler
-
- libClass - Variable in class loci.plugins.config.LibraryEntry
-
- Library() - Constructor for enum loci.plugins.util.LibraryChecker.Library
-
- LibraryChecker - Class in loci.plugins.util
-
Utility methods for verifying that classes
are present and versions are correct.
- LibraryChecker() - Constructor for class loci.plugins.util.LibraryChecker
-
- LibraryChecker.Library - Enum in loci.plugins.util
-
List of possible libraries for which to check.
- LibraryEntry - Class in loci.plugins.config
-
A list entry for the configuration window's Libraries tab.
- LibraryEntry(PrintWriter, HashMap<String, String>) - Constructor for class loci.plugins.config.LibraryEntry
-
- LibraryEntry(PrintWriter, String, String, String, String, String, String, String) - Constructor for class loci.plugins.config.LibraryEntry
-
- libraryFound - Static variable in class loci.formats.in.LegacyND2Reader
-
- libraryLoaded - Static variable in class loci.formats.services.JPEGTurboServiceImpl
-
- libsList - Variable in class loci.plugins.config.ConfigWindow
-
- libsListModel - Variable in class loci.plugins.config.ConfigWindow
-
- license - Variable in class loci.formats.services.LuraWaveServiceImpl
-
License code.
- license - Variable in class loci.plugins.config.ConfigWindow
-
- license - Variable in class loci.plugins.config.LibraryEntry
-
- LICENSE_PROPERTY - Static variable in class loci.formats.services.LuraWaveServiceImpl
-
System property to check for the LuraWave license code.
- licenseBox - Variable in class loci.plugins.config.FlexWidgets
-
- LICOR_MAGIC_STRING - Static variable in class loci.formats.in.L2DReader
-
- LIF_MAGIC_BYTE - Static variable in class loci.formats.in.LIFReader
-
- LIF_MEMORY_BYTE - Static variable in class loci.formats.in.LIFReader
-
- LIFETIME - Static variable in class loci.formats.FormatTools
-
Identifies the Lifetime dimensional type,
representing a dimension consisting of a lifetime histogram.
- lifetime - Variable in class loci.formats.in.ICSReader
-
Whether or not the channels represent lifetime histogram bins.
- LIFF_MAGIC_BYTES - Static variable in class loci.formats.in.OpenlabReader
-
- LiFlimReader - Class in loci.formats.in
-
LiFlimReader is the file format reader for LI-FLIM files.
- LiFlimReader() - Constructor for class loci.formats.in.LiFlimReader
-
Constructs a new LI-FLIM reader.
- LiFlimReader.ROI - Class in loci.formats.in
-
- LIFReader - Class in loci.formats.in
-
LIFReader is the file format reader for Leica LIF files.
- LIFReader() - Constructor for class loci.formats.in.LIFReader
-
Constructs a new Leica LIF reader.
- LIFReader.ROI - Class in loci.formats.in
-
- LIFWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats Leica LIF support.
- LIFWidgets() - Constructor for class loci.plugins.config.LIFWidgets
-
- LIGHT_SOURCE - Static variable in class loci.formats.tiff.IFD
-
- LIGHT_TYPE - Static variable in class loci.formats.in.NikonReader
-
- lightSourceCombinationIDs - Variable in class loci.formats.in.FlexReader
-
- lightSourceCombinationRefs - Variable in class loci.formats.in.FlexReader
-
- lightSourceID - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- lightSourceIDs - Variable in class loci.formats.in.FlexReader
-
- limitHeight(JComponent) - Method in class loci.formats.gui.DataConverter
-
- LIMReader - Class in loci.formats.in
-
LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
- LIMReader() - Constructor for class loci.formats.in.LIMReader
-
Constructs a new LIM reader.
- LINE - Static variable in class loci.formats.in.FV1000Reader
-
- line - Variable in class loci.formats.in.FV1000Reader
-
- LINE - Static variable in class loci.formats.in.GatanReader
-
Shape types
- LINE - Static variable in class loci.formats.in.LeicaHandler.ROI
-
- LINE - Static variable in class loci.formats.in.LIFReader.ROI
-
- LINE - Static variable in class loci.formats.in.ZeissLSMReader
-
- line - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
-
- LINE_LENGTH - Static variable in class loci.formats.in.FitsReader
-
- LINEAR - Static variable in class loci.formats.in.GelReader
-
- linediv - Variable in class loci.formats.in.SDTInfo
-
Line predivider = 2 ** (linediv).
- LineEndPositions(int) - Constructor for enum loci.formats.in.BaseZeissReader.LineEndPositions
-
- lineEndPositions - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- lineEndSize - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- LineEndStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.LineEndStyle
-
- lineEndStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- lineMode - Variable in class loci.formats.in.SPCReader
-
- lines - Variable in class loci.formats.in.FakeReader
-
- lineTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- lineWidth - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- linewidth - Variable in class loci.formats.in.LeicaHandler.ROI
-
- linewidth - Variable in class loci.formats.in.LIFReader.ROI
-
- linkedInstruments - Variable in class loci.formats.in.LeicaHandler
-
- listeners - Variable in class loci.formats.cache.Cache
-
List of cache event listeners.
- listeners - Variable in class loci.formats.cache.CacheStrategy
-
List of cache event listeners.
- listeners - Variable in class loci.plugins.in.ImagePlusReader
-
- listeners - Variable in class loci.plugins.in.ImportProcess
-
- listFakeSeries(String) - Method in class loci.formats.in.FakeReader
-
Traverses a fake file folder structure indicated by traversedDirectory
- listString - Variable in class loci.formats.in.AVIReader
-
- LITTLE - Static variable in class loci.formats.tiff.TiffConstants
-
- LITTLE_ENDIAN - Static variable in class loci.formats.in.BioRadReader
-
Always little endian.
- LITTLE_ENDIAN - Static variable in class loci.formats.in.DeltavisionReader
-
- LITTLE_ENDIAN - Static variable in class loci.formats.in.OBFReader
-
- LITTLE_ENDIAN - Static variable in class loci.formats.in.TextReader
-
- LITTLE_ENDIAN - Static variable in class loci.formats.tiff.IFD
-
- littleEndian - Variable in class loci.formats.codec.CodecOptions
-
Indicates endianness of pixel data.
- littleEndian - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not each pixel's bytes are in little endian order.
- littleEndian - Variable in class loci.formats.out.APNGWriter
-
- littleEndian - Variable in class loci.formats.tools.AmiraParameters
-
- LIVE_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
-
- LM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the light microscopy domain.
- LO - Static variable in class loci.formats.in.DicomReader
-
- load(String, File, boolean) - Static method in class loci.formats.Memoizer
-
- load() - Static method in class org.libjpegturbo.turbojpeg.TJLoader
-
- loadedFromMemo - Variable in class loci.formats.Memoizer
-
- LOADER - Static variable in class loci.formats.gui.LegacyQTTools
-
This custom class loader searches additional paths for the QTJava.zip
library.
- loader - Variable in class loci.formats.gui.PreviewPane
-
Thumbnail loading thread.
- loader - Variable in class loci.plugins.in.ThumbLoader
-
- loaderAlive - Variable in class loci.formats.gui.PreviewPane
-
Flag indicating whether loader thread should keep running.
- loadId - Variable in class loci.formats.gui.PreviewPane
-
Current ID to load.
- loadImage(Image) - Static method in class loci.formats.gui.AWTImageTools
-
Ensures the given AWT image is fully loaded.
- loadManifest() - Static method in class loci.formats.FormatTools
-
- loadMemo() - Method in class loci.formats.Memoizer
-
Load a memo file if possible, returning a null if not.
- loadOption() - Method in class loci.plugins.prefs.BooleanOption
-
- loadOption() - Method in class loci.plugins.prefs.DoubleOption
-
- loadOption() - Method in class loci.plugins.prefs.Option
-
Loads the option's value from the ImageJ preferences file.
- loadOption() - Method in class loci.plugins.prefs.StringOption
-
- loadOptions() - Method in class loci.plugins.prefs.OptionsList
-
Loads option values from the ImageJ preferences file.
- loadProperties() - Static method in class loci.formats.FormatTools
-
- loadReader() - Method in interface loci.formats.Memoizer.Deser
-
- loadReader() - Method in class loci.formats.Memoizer.KryoDeser
-
- loadReader() - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- loadReleaseVersion() - Method in interface loci.formats.Memoizer.Deser
-
- loadReleaseVersion() - Method in class loci.formats.Memoizer.KryoDeser
-
- loadReleaseVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- loadRevision() - Method in interface loci.formats.Memoizer.Deser
-
- loadRevision() - Method in class loci.formats.Memoizer.KryoDeser
-
- loadRevision() - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- loadStart(File) - Method in interface loci.formats.Memoizer.Deser
-
- loadStart(File) - Method in class loci.formats.Memoizer.KryoDeser
-
- loadStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- loadStop() - Method in interface loci.formats.Memoizer.Deser
-
- loadStop() - Method in class loci.formats.Memoizer.KryoDeser
-
- loadStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- loadStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
-
- loadThumb(BufferedImageReader, int, Panel, boolean) - Static method in class loci.plugins.in.ThumbLoader
-
- loadVersion() - Method in interface loci.formats.Memoizer.Deser
-
- loadVersion() - Method in class loci.formats.Memoizer.KryoDeser
-
- loadVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- locateExperimentFile(String) - Method in class loci.formats.in.BDReader
-
- locateFirstValidFile() - Method in class loci.formats.in.MetamorphReader
-
Locates the first valid file in the STK arrays.
- location - Variable in class loci.formats.in.DicomReader
-
- LOCATION_HTTP - Static variable in class loci.plugins.in.ImporterOptions
-
- LOCATION_LOCAL - Static variable in class loci.plugins.in.ImporterOptions
-
- LOCATION_OMERO - Static variable in class loci.plugins.in.ImporterOptions
-
- LocationDialog - Class in loci.plugins.in
-
Bio-Formats Importer location chooser dialog box.
- LocationDialog(ImportProcess) - Constructor for class loci.plugins.in.LocationDialog
-
Creates a location chooser dialog for the Bio-Formats Importer.
- locator - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
-
- loci.formats - package loci.formats
-
Bio-Formats: a library for reading and writing popular microscopy file
formats.
- loci.formats.cache - package loci.formats.cache
-
Package containing Bio-Formats caching logic, for managing
subsets of large collections of image planes in memory.
- loci.formats.codec - package loci.formats.codec
-
- loci.formats.gui - package loci.formats.gui
-
Package containing Bio-Formats graphical user interface code.
- loci.formats.in - package loci.formats.in
-
Package containing Bio-Formats file format readers.
- loci.formats.meta - package loci.formats.meta
-
Package containing core Bio-Formats metadata interfaces for the OME data model.
- loci.formats.ome - package loci.formats.ome
-
Package containing Bio-Formats OME-related logic for
OME-XML metadata, and database import, upload and download.
- loci.formats.out - package loci.formats.out
-
Package containing Bio-Formats file format writers.
- loci.formats.services - package loci.formats.services
-
- loci.formats.tiff - package loci.formats.tiff
-
Package containing Bio-Formats TIFF code of general utility.
- loci.formats.tools - package loci.formats.tools
-
Package containing utility methods corresponding
to the Bio-Formats command line tools.
- loci.plugins - package loci.plugins
-
Bio-Formats Plugins: a collection of plugins for ImageJ, including the
Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions,
Data Browser and Stack Slicer.
- loci.plugins.config - package loci.plugins.config
-
Bio-Formats Plugins Configuration plugin for ImageJ.
- loci.plugins.in - package loci.plugins.in
-
Bio-Formats Importer plugin for ImageJ.
- loci.plugins.macro - package loci.plugins.macro
-
Bio-Formats Macro Extensions plugin for ImageJ.
- loci.plugins.out - package loci.plugins.out
-
Bio-Formats Exporter plugin for ImageJ.
- loci.plugins.prefs - package loci.plugins.prefs
-
Classes for managing Bio-Formats plugins preferences.
- loci.plugins.shortcut - package loci.plugins.shortcut
-
Bio-Formats Plugins Shortcut Window plugin for ImageJ.
- loci.plugins.util - package loci.plugins.util
-
Utility classes and methods for the Bio-Formats plugins for ImageJ.
- LociConfig - Class in loci.plugins.config
-
An ImageJ plugin for displaying the Bio-Formats plugins configuration dialog.
- LociConfig() - Constructor for class loci.plugins.config.LociConfig
-
- LociExporter - Class in loci.plugins
-
ImageJ plugin for writing files using the OME Bio-Formats package.
- LociExporter() - Constructor for class loci.plugins.LociExporter
-
- LociFunctions - Class in loci.plugins.macro
-
This class provides macro extensions in ImageJ for Bio-Formats.
- LociFunctions() - Constructor for class loci.plugins.macro.LociFunctions
-
- LociImporter - Class in loci.plugins
-
ImageJ plugin for reading files using the OME Bio-Formats package.
- LociImporter() - Constructor for class loci.plugins.LociImporter
-
- LociInstaller - Class in loci.plugins.config
-
An ImageJ plugin for installing and upgrading libraries
related to the Bio-Formats plugins.
- LociInstaller() - Constructor for class loci.plugins.config.LociInstaller
-
- LociPrefs - Class in loci.plugins.util
-
Utility methods for ImageJ preferences for Bio-Formats plugins.
- LociPrefs() - Constructor for class loci.plugins.util.LociPrefs
-
- log - Variable in class loci.plugins.config.ConfigWindow
-
- log() - Method in class loci.plugins.util.RecordedImageProcessor
-
- logFile - Variable in class loci.formats.in.DeltavisionReader
-
- logFiles - Variable in class loci.formats.in.CellWorxReader
-
- LOGGER - Static variable in class loci.formats.cache.CacheUpdater
-
- LOGGER - Static variable in class loci.formats.ClassList
-
- LOGGER - Static variable in class loci.formats.codec.BaseCodec
-
- LOGGER - Static variable in class loci.formats.FileStitcher
-
- LOGGER - Static variable in class loci.formats.FormatHandler
-
- LOGGER - Static variable in class loci.formats.FormatTools
-
- LOGGER - Static variable in class loci.formats.gui.AWTImageTools
-
- LOGGER - Static variable in class loci.formats.gui.CacheComponent
-
- LOGGER - Static variable in class loci.formats.gui.DataConverter
-
- LOGGER - Static variable in class loci.formats.gui.ImageViewer
-
- LOGGER - Static variable in class loci.formats.gui.LegacyQTTools
-
- LOGGER - Static variable in class loci.formats.gui.PreviewPane
-
- LOGGER - Static variable in class loci.formats.ImageReader
-
- LOGGER - Static variable in class loci.formats.ImageWriter
-
- LOGGER - Static variable in class loci.formats.in.BaseTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.DNGReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.IM3Reader
-
Logger for outputting summary diagnostics.
- LOGGER - Static variable in class loci.formats.in.ImarisTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.JPEG2000MetadataParser
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.JPEG2000Reader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.JPXReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.LeicaHandler
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.LeicaReader
-
- LOGGER - Static variable in class loci.formats.in.LeicaSCNReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.MetamorphReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.MinimalTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.ND2Handler
-
- LOGGER - Static variable in class loci.formats.in.NikonReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.PyramidTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.SVSReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.TiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.TrestleReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.ZeissTIFFHandler
-
- LOGGER - Static variable in class loci.formats.Memoizer
-
Default Logger for the memoizer class
- LOGGER - Static variable in class loci.formats.MetadataTools
-
- logger - Variable in class loci.formats.services.JPEGTurboServiceImpl
-
- LOGGER - Static variable in class loci.formats.services.JPEGXRServiceImpl
-
- LOGGER - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.tiff.IFD
-
- LOGGER - Static variable in enum loci.formats.tiff.TiffCompression
-
- LOGGER - Static variable in class loci.formats.tiff.TiffParser
-
- LOGGER - Static variable in class loci.formats.tiff.TiffSaver
-
- LOGGER - Static variable in class loci.formats.TileStitcher
-
- LOGGER - Static variable in class loci.formats.tools.EditTiffG
-
- LOGGER - Static variable in class loci.formats.tools.FakeImage
-
- LOGGER - Static variable in class loci.formats.UpgradeChecker
-
- LONG - Static variable in class loci.formats.in.CellSensReader
-
- LONG_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader
-
- longValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as a long.
- lookup - Static variable in enum loci.formats.codec.CompressionType
-
Map used to retrieve the compression type corresponding to the code.
- lookup - Static variable in enum loci.formats.codec.JPEG2000BoxType
-
Map used to retrieve the box type corresponding to the code.
- lookup - Static variable in enum loci.formats.codec.JPEG2000SegmentMarker
-
Map used to retrieve the segment marker corresponding to the code.
- lookup - Static variable in enum loci.formats.in.BaseZeissReader.Charset
-
- lookup - Static variable in enum loci.formats.in.BaseZeissReader.DrawStyle
-
- lookup - Static variable in enum loci.formats.in.BaseZeissReader.FeatureType
-
- lookup - Static variable in enum loci.formats.in.BaseZeissReader.FillStyle
-
- lookup - Static variable in enum loci.formats.in.BaseZeissReader.LineEndPositions
-
- lookup - Static variable in enum loci.formats.in.BaseZeissReader.LineEndStyle
-
- lookup - Static variable in enum loci.formats.in.BaseZeissReader.PointStyle
-
- lookup - Static variable in enum loci.formats.in.BaseZeissReader.TextAlignment
-
- lookup - Variable in class loci.formats.in.PictReader
-
Color lookup table for palette color images.
- lookup - Static variable in enum loci.formats.tiff.IFDType
-
- lookup - Static variable in enum loci.formats.tiff.PhotoInterp
-
- lookup - Static variable in enum loci.formats.tiff.TiffCompression
-
Reverse lookup of code to TIFF compression enumerate value.
- lookupDimension(int, int, int) - Method in class loci.formats.in.LeicaSCNReader.Pixels
-
- lookupFile(int, int, int) - Method in class loci.formats.in.FlexReader
-
- lookupFile(int) - Method in class loci.formats.in.FlexReader
-
- lookupFile(int) - Method in class loci.formats.in.PerkinElmerReader
-
- lookupPlane(int, int, int, int, int) - Method in class loci.formats.in.ColumbusReader
-
- lossless - Variable in class loci.formats.codec.CodecOptions
-
Used with codecs allowing lossy and lossless compression.
- LOSSLESS_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
-
- LOSSLESS_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
-
- LosslessJPEGCodec - Class in loci.formats.codec
-
Decompresses lossless JPEG images.
- LosslessJPEGCodec() - Constructor for class loci.formats.codec.LosslessJPEGCodec
-
- LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
-
- LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
-
- lossyCompression - Variable in class loci.formats.in.NikonReader
-
- LOW_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
-
- lPad - Variable in class loci.formats.gui.CacheIndicator
-
- lsmFilenames - Variable in class loci.formats.in.ZeissLSMReader
-
- LT - Static variable in class loci.formats.in.DicomReader
-
- LUMA_BLUE - Static variable in enum loci.formats.tiff.PhotoInterp
-
- LUMA_GREEN - Static variable in enum loci.formats.tiff.PhotoInterp
-
- LUMA_RED - Static variable in enum loci.formats.tiff.PhotoInterp
-
Default luminance values for YCbCr data.
- LuraWave - Class in loci.plugins.util
-
Utility methods for dealing with proprietary LuraWave licensing.
- LuraWave() - Constructor for class loci.plugins.util.LuraWave
-
- LuraWaveCodec - Class in loci.formats.codec
-
This class provides LuraWave decompression, using LuraWave's Java decoding
library.
- LuraWaveCodec() - Constructor for class loci.formats.codec.LuraWaveCodec
-
- LuraWaveService - Interface in loci.formats.services
-
- LuraWaveServiceImpl - Class in loci.formats.services
-
- LuraWaveServiceImpl() - Constructor for class loci.formats.services.LuraWaveServiceImpl
-
Default constructor.
- lut - Variable in class loci.formats.in.AmiraReader
-
- lut - Variable in class loci.formats.in.APNGReader
-
- lut - Variable in class loci.formats.in.AVIReader
-
- lut - Variable in class loci.formats.in.BioRadReader
-
- lut - Variable in class loci.formats.in.DicomReader
-
- lut - Variable in class loci.formats.in.FV1000Reader
-
- lut - Variable in class loci.formats.in.IvisionReader
-
- lut - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Color lookup table stored in the file.
- lut - Variable in class loci.formats.in.JPEG2000Reader
-
The color lookup table associated with this file.
- lut - Variable in class loci.formats.in.JPXReader
-
The color lookup table associated with this file.
- lut - Variable in class loci.formats.in.KhorosReader
-
Global lookup table.
- lut - Variable in class loci.formats.in.OIRReader.Channel
-
- lut - Variable in class loci.formats.in.PCXReader
-
- lut - Variable in class loci.formats.in.PSDReader
-
Lookup table.
- lut - Variable in class loci.formats.in.ZeissLMSReader
-
- lut - Variable in class loci.formats.in.ZeissLSMReader
-
- lut16 - Variable in class loci.formats.in.FakeReader
-
16-bit lookup table, if indexed color, one per channel.
- lut8 - Variable in class loci.formats.in.FakeReader
-
8-bit lookup table, if indexed color, one per channel.
- LUT_LENGTH - Static variable in class loci.formats.in.BioRadReader
-
- LUT_SIZE - Static variable in class loci.formats.in.NAFReader
-
- LUTDESC - Static variable in class loci.formats.in.LeicaReader
-
- lutIndex - Variable in class loci.formats.in.PDSReader
-
- lutLength - Variable in class loci.formats.ChannelFiller
-
Number of LUT components.
- lutNames - Variable in class loci.formats.in.FV1000Reader
-
- lutNames - Variable in class loci.formats.in.LeicaHandler
-
- lutNames - Variable in class loci.formats.in.LIFReader
-
- luts - Variable in class loci.formats.in.OpenlabReader
-
- luts - Variable in class loci.plugins.util.VirtualImagePlus
-
- LZOCodec - Class in loci.formats.codec
-
This class implements LZO decompression.
- LZOCodec() - Constructor for class loci.formats.codec.LZOCodec
-
- LZW - Static variable in class loci.formats.in.ZeissCZIReader
-
- LZWCodec - Class in loci.formats.codec
-
This is an optimized LZW codec for use with TIFF files.
- LZWCodec() - Constructor for class loci.formats.codec.LZWCodec
-
- MAC_16_BIT_COLOR - Static variable in class loci.formats.in.OpenlabReader
-
- MAC_16_COLORS - Static variable in class loci.formats.in.OpenlabReader
-
- MAC_16_GREYS - Static variable in class loci.formats.in.OpenlabReader
-
- MAC_1_BIT - Static variable in class loci.formats.in.OpenlabReader
-
Image types.
- MAC_24_BIT_COLOR - Static variable in class loci.formats.in.OpenlabReader
-
- MAC_256_COLORS - Static variable in class loci.formats.in.OpenlabReader
-
- MAC_256_GREYS - Static variable in class loci.formats.in.OpenlabReader
-
- MAC_4_GREYS - Static variable in class loci.formats.in.OpenlabReader
-
- MAC_OS_X - Static variable in class loci.formats.gui.LegacyQTTools
-
- MACRO_IMAGE - Static variable in class loci.formats.in.CellSensReader
-
- macroFile - Variable in class loci.formats.in.HamamatsuVMSReader
-
- MacroFunctions - Class in loci.plugins.macro
-
Convenience class that simplifies implemention of ImageJ macro extensions.
- MacroFunctions() - Constructor for class loci.plugins.macro.MacroFunctions
-
- mag - Variable in class loci.formats.in.FluoviewReader
-
- mag - Variable in class loci.formats.in.GatanReader
-
- mag - Variable in class loci.formats.in.ND2Handler
-
- MAG_MULTIPLIER - Static variable in class loci.formats.in.FEITiffReader
-
- MAGIC - Static variable in class loci.formats.in.AnalyzeReader
-
- MAGIC - Static variable in class loci.formats.in.BioRadSCNReader
-
- MAGIC - Static variable in class loci.formats.in.ColumbusReader
-
- MAGIC - Static variable in class loci.formats.in.HitachiReader
-
- MAGIC_BYTES - Static variable in class loci.formats.in.BioRadGelReader
-
- MAGIC_NUMBER - Static variable in class loci.formats.in.OBFReader
-
- MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
-
- MAGIC_STRING - Static variable in class loci.formats.in.HRDGDFReader
-
- MAGIC_STRING - Static variable in class loci.formats.in.IMODReader
-
- MAGIC_STRING - Static variable in class loci.formats.in.ImspectorReader
-
The header for each file contains this string.
- MAGIC_STRING - Static variable in class loci.formats.in.KodakReader
-
- MAGIC_STRING - Static variable in class loci.formats.in.MolecularImagingReader
-
- MAGIC_STRING - Static variable in class loci.formats.in.SIFReader
-
- MAGIC_STRING - Static variable in class loci.formats.in.SimplePCITiffReader
-
- MAGNIFICATION - Static variable in class loci.formats.in.CellSensReader
-
- magnification - Variable in class loci.formats.in.CellSensReader.Pyramid
-
- magnification - Variable in class loci.formats.in.FEITiffReader
-
- magnification - Variable in class loci.formats.in.FV1000Reader
-
- magnification - Variable in class loci.formats.in.IvisionReader
-
- magnification - Variable in class loci.formats.in.LIFReader
-
- magnification - Variable in class loci.formats.in.NDPIReader
-
- magnification - Variable in class loci.formats.in.NikonTiffReader
-
- magnification - Variable in class loci.formats.in.OIRReader.Objective
-
- magnification - Variable in class loci.formats.in.OperettaReader.Plane
-
- magnification - Variable in class loci.formats.in.SimplePCITiffReader
-
- magnification - Variable in class loci.formats.in.SISReader
-
- magnification - Variable in class loci.formats.in.SVSReader
-
- magnification - Variable in class loci.formats.in.VolocityReader.Stack
-
- magnification - Variable in class loci.formats.in.ZeissLSMReader.Recording
-
- MAGNIFICATION_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
-
- magnitudes - Variable in class loci.formats.in.IM3Reader.Spectrum
-
- main(String[]) - Static method in class loci.formats.codec.BitBuffer
-
Deprecated.
Testing method.
- main(String[]) - Static method in class loci.formats.codec.BitWriter
-
Deprecated.
Tests the BitWriter class.
- main(String[]) - Static method in class loci.formats.gui.DataConverter
-
- main(String[]) - Static method in class loci.formats.gui.ImageViewer
-
- main(String[]) - Static method in class loci.formats.gui.XMLWindow
-
- main(String[]) - Static method in class loci.formats.in.IM3Reader
-
Write a summary of each record to STDOUT
- main(String[]) - Static method in class loci.formats.Memoizer
-
- main(String[]) - Static method in class loci.formats.tools.AmiraParameters
-
- main(String[]) - Static method in class loci.formats.tools.BioFormatsExtensionPrinter
-
- main(String[]) - Static method in class loci.formats.tools.CacheConsole
-
Interactive interpreter for testing Bio-Formats caching implementation.
- main(String[]) - Static method in class loci.formats.tools.EditTiffG
-
- main(String[]) - Static method in class loci.formats.tools.MakeTestOmeTiff
-
- main(String[]) - Static method in class loci.formats.tools.UpgradeCheck
-
- main(String[]) - Static method in class loci.plugins.About
-
- main(String[]) - Static method in class loci.plugins.config.LociConfig
-
- main(String[]) - Static method in class loci.plugins.in.Importer
-
Main method, for testing.
- main_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
-
- MainDialog - Class in loci.plugins.in
-
Bio-Formats Importer general options dialog box.
- MainDialog(ImportProcess) - Constructor for class loci.plugins.in.MainDialog
-
Creates a general options dialog for the Bio-Formats Importer.
- majorVersion - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
-
- MAKE - Static variable in class loci.formats.tiff.IFD
-
- make24Bits(Object, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools
-
Convert an arbitrary primitive type array with 3 samples per pixel to
a 3 x (width * height) byte array.
- make24Bits(Object, int, int, boolean, boolean, Double, Double) - Static method in class loci.formats.ImageTools
-
Convert an arbitrary primitive type array with 3 samples per pixel to
a 3 x (width * height) byte array.
- make24Bits(Object, int, int, boolean) - Static method in class loci.formats.ImageTools
-
Convert an arbitrary primitive type array with 3 samples per pixel to
an int array, i.e.
- make24Bits(Object, int, int, boolean, Double, Double) - Static method in class loci.formats.ImageTools
-
Convert an arbitrary primitive type array with 3 samples per pixel to
an int array, i.e.
- makeBitArray(int, int) - Static method in class loci.formats.gui.SignedColorModel
-
- makeBitArray(int, int) - Static method in class loci.formats.gui.UnsignedIntColorModel
-
- makeBuffered(Image) - Static method in class loci.formats.gui.AWTImageTools
-
Creates a buffered image from the given AWT image object.
- makeBuffered(Image, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Creates a buffered image possessing the given color model,
from the specified AWT image object.
- makeBufferedImageReader(IFormatReader) - Static method in class loci.formats.gui.BufferedImageReader
-
Converts the given reader into a BufferedImageReader, wrapping if needed.
- makeBufferedImageWriter(IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter
-
Converts the given writer into a BufferedImageWriter, wrapping if needed.
- makeChannelFiller(IFormatReader) - Static method in class loci.formats.ChannelFiller
-
Converts the given reader into a ChannelFiller, wrapping if needed.
- makeChannelMerger(IFormatReader) - Static method in class loci.formats.ChannelMerger
-
Converts the given reader into a ChannelMerger, wrapping if needed.
- makeChannelSeparator(IFormatReader) - Static method in class loci.formats.ChannelSeparator
-
Converts the given reader into a ChannelSeparator, wrapping if needed.
- makeColorModel(int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Gets a color model for the given number of color components.
- makeColorSpace(int) - Static method in class loci.formats.gui.AWTImageTools
-
Gets a color space for the given number of color components.
- makeComboFilter(FileFilter[]) - Static method in class loci.formats.gui.GUITools
-
Creates an "All supported file types" combo filter
encompassing all of the given filters.
- makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities
-
Aligns the first rows * cols
components of parent in
a grid.
- makeCompatible(BufferedImage, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools
-
Creates a buffered image compatible with the given graphics
configuration, using the given buffered image as a source.
- makeDimensionSwapper(IFormatReader) - Static method in class loci.formats.DimensionSwapper
-
Converts the given reader into a DimensionSwapper, wrapping if needed.
- makeDimensionTable() - Static method in class loci.formats.in.LeicaReader
-
- makeDummySlider() - Static method in class loci.plugins.util.DataBrowser
-
- makeFileList() - Method in class loci.formats.in.DicomReader
-
- makeFilterMetadata() - Method in class loci.formats.FormatReader
-
Return a properly configured loci.formats.meta.FilterMetadata.
- makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities
-
Aligns the first rows * cols
components of parent in
a grid.
- makeHeavyPanel(Component) - Static method in class loci.plugins.util.DataBrowser
-
Makes AWT play nicely with Swing components.
- makeImage(byte[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel byte data.
- makeImage(short[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel short data.
- makeImage(int[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel int data.
- makeImage(float[], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel float data.
- makeImage(double[], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel double data.
- makeImage(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given byte data.
- makeImage(short[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given short data.
- makeImage(int[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given int data.
- makeImage(float[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given float data.
- makeImage(double[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given double data.
- makeImage(byte[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given byte data.
- makeImage(short[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given short data.
- makeImage(int[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given int data.
- makeImage(float[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-precision floating point data.
- makeImage(double[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given double-precision floating point data.
- makeImage(byte[], boolean, MetadataRetrieve, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given raw byte array, obtaining the
dimensional parameters from the specified metadata object.
- makeImage(byte[], int, int, int, boolean, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given raw byte array,
performing any necessary type conversions.
- makeImage(byte[][], int, int, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given raw byte array,
performing any necessary type conversions.
- makeImage(String) - Method in class loci.formats.gui.PreviewPane
-
Creates a blank image with the given message painted on top (e.g.,
a loading or error message), matching the size of the active reader's
thumbnails.
- makeImageName(int) - Method in class loci.formats.in.MetamorphReader
-
Create an appropriate name for the given series.
- makeImageProcessorReader(IFormatReader) - Static method in class loci.plugins.util.ImageProcessorReader
-
Converts the given reader into a ImageProcessorReader, wrapping if needed.
- makeImageReader() - Static method in class loci.plugins.util.LociPrefs
-
Creates an image reader according to the current configuration settings,
including which format readers are currently enabled, as well as
format-specific configuration settings.
- makeJTree(Document) - Static method in class loci.formats.gui.XMLCellRenderer
-
Constructs a Swing JTree that displays the given XML DOM document.
- makeLabel(String, boolean) - Method in class loci.plugins.config.ConfigWindow
-
- makeLabel(String, int, int) - Method in class loci.plugins.in.ColorDialog
-
- makeList(DefaultListModel) - Method in class loci.plugins.config.ConfigWindow
-
- makeLUT(int, int) - Method in class loci.plugins.in.Colorizer
-
- makeLUT(Color) - Method in class loci.plugins.in.Colorizer
-
- makeLUTs(ColorModel[], boolean) - Method in class loci.plugins.in.Colorizer
-
- makeLUTs(int) - Method in class loci.plugins.in.Colorizer
-
- makeMinMaxCalculator(IFormatReader) - Static method in class loci.formats.MinMaxCalculator
-
Converts the given reader into a MinMaxCalculator, wrapping if needed.
- makeModuloElement(Document) - Method in class loci.formats.meta.ModuloAnnotation
-
Construct a DOM element for this annotation using
the given Document as the root.
- makeOmeTiff(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
-
- makeOmeTiff(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
-
- makeOmeTiffExtensions(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
-
- makeOriginalMetadata(Document) - Method in class loci.formats.meta.OriginalMetadataAnnotation
-
Create a DOM element for this annotation with the given document
as the parent.
- makePixelTypes() - Static method in class loci.formats.FormatTools
-
- MAKER_NOTE - Static variable in class loci.formats.tiff.IFD
-
- MAKER_WHITE_BALANCE - Static variable in class loci.formats.in.NikonReader
-
- makeRGBImage(byte[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
- makeRGBImage(byte[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
- makerNoteOffset - Variable in class loci.formats.in.NikonReader
-
Offset to the Nikon Maker Note.
- makeSamples() - Method in class loci.formats.tools.MakeTestOmeTiff
-
- makeSaneDimensionOrder(String) - Static method in class loci.formats.MetadataTools
-
Adjusts the given dimension order as needed so that it contains exactly
one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
- makeSplitPane(JList, JPanel) - Method in class loci.plugins.config.ConfigWindow
-
- makeStack(ImageStack) - Method in class loci.plugins.Slicer
-
Returns a new ImageStack using the given ImageStack as a template.
- MakeTestOmeTiff - Class in loci.formats.tools
-
Creates sample OME-TIFF datasets according to the given parameters.
- MakeTestOmeTiff() - Constructor for class loci.formats.tools.MakeTestOmeTiff
-
- MakeTestOmeTiff.TextLine - Class in loci.formats.tools
-
- makeTextField() - Static method in class loci.plugins.config.ConfigWindow
-
- makeTileStitcher(IFormatReader) - Static method in class loci.formats.TileStitcher
-
Converts the given reader into a TileStitcher, wrapping if needed.
- makeTreeNode(Node) - Static method in class loci.formats.gui.XMLCellRenderer
-
Recursively builds JTree node structure from DOM node structure.
- makeUnsigned(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Converts the given BufferedImage into an image with unsigned pixel data.
- makeValidIFD(IFD, int, int) - Method in class loci.formats.tiff.TiffSaver
-
Makes a valid IFD.
- map - Variable in class loci.formats.in.EPSReader
-
- map - Variable in class loci.formats.tools.AmiraParameters
-
- mapFile - Variable in class loci.formats.in.HamamatsuVMSReader
-
- mapOIBFiles() - Method in class loci.formats.in.FV1000Reader
-
- mappedFiles - Variable in class loci.formats.in.ZipReader
-
- mapServer(String, String) - Static method in class loci.formats.in.FlexReader
-
Map the server named 'alias' to the path 'realName'.
- mapServer(String, String[]) - Static method in class loci.formats.in.FlexReader
-
Map the server named 'alias' to the paths in 'realNames'.
- mapServersFromConfigurationFile(String) - Static method in class loci.formats.in.FlexReader
-
Read a configuration file with lines of the form:
<server alias>=<real server name>
and call mapServer(String, String) accordingly.
- MARKER - Static variable in class loci.formats.in.ZeissLMSReader
-
- Marker() - Constructor for class loci.formats.in.ZeissLSMReader.Marker
-
- MARKER_0 - Static variable in class loci.formats.in.TillVisionReader
-
- MARKER_1 - Static variable in class loci.formats.in.TillVisionReader
-
- MARKER_2 - Static variable in class loci.formats.in.TillVisionReader
-
- MARKER_3 - Static variable in class loci.formats.in.TillVisionReader
-
- MARKER_TAG - Static variable in class loci.formats.in.NDPIReader
-
- masks - Variable in class loci.formats.in.FakeReader
-
- masterClock - Variable in class loci.formats.in.SDTInfo
-
Use or not Master Clock (SPC140 multi-module).
- matchFilename(String) - Method in class loci.formats.in.CellomicsReader
-
- matchFiles(String[], NumberFilter) - Static method in class loci.formats.FilePattern
-
- matrix - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
-
- max - Variable in class loci.formats.gui.SignedColorModel
-
- max(double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- MAX_APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
-
- MAX_BLOCK_SIZE - Static variable in class loci.formats.services.POIServiceImpl
-
- MAX_COMPONENTS - Static variable in class loci.plugins.in.SeriesDialog
-
- MAX_HEADER_SIZE - Static variable in class loci.formats.in.QuesantReader
-
- MAX_JPEG_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
-
- MAX_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
-
- MAX_READERS - Static variable in class loci.formats.FileStitcher
-
- MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
-
- MAX_SERIES_THUMBS - Static variable in class loci.plugins.in.SeriesDialog
-
- MAX_SERIES_TOGGLES - Static variable in class loci.plugins.in.SeriesDialog
-
- MAX_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
-
- MAX_SIZE - Static variable in class loci.formats.in.JPEGReader
-
- MAX_SIZE - Static variable in class loci.formats.in.NDPIReader
-
- MAX_STACK_SIZE - Static variable in class loci.formats.in.GIFReader
-
Maximum buffer size.
- MAX_TRIES - Static variable in class loci.plugins.util.LuraWave
-
- maxAdcRate - Variable in class loci.formats.in.SDTInfo
-
- maxBytes - Variable in class loci.formats.codec.CodecOptions
-
If compressing, this is the maximum number of raw bytes to compress.
- maxCfdRate - Variable in class loci.formats.in.SDTInfo
-
(-1.0 - not set).
- MAXIMAL_NUMBER_OF_DIMENSIONS - Static variable in class loci.formats.in.OBFReader
-
- maximumReadOffset - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Maximum read offset within in the stream.
- maxInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Maxiumum intensity.
- maxOffsetIndex - Variable in class loci.formats.in.AmiraReader.HxRLE
-
- maxPixelRange - Variable in class loci.formats.in.DicomReader
-
- maxResolution - Variable in class loci.formats.in.ZeissCZIReader
-
- maxSyncRate - Variable in class loci.formats.in.SDTInfo
-
Maximum rates during the measurement.
- maxTacRate - Variable in class loci.formats.in.SDTInfo
-
- maxValue() - Method in class loci.plugins.util.RecordedImageProcessor
-
- maxX - Variable in class loci.formats.in.ImarisHDFReader
-
- maxY - Variable in class loci.formats.in.ImarisHDFReader
-
- maxZ - Variable in class loci.formats.in.ImarisHDFReader
-
- mcsPoints - Variable in class loci.formats.in.SDTInfo
-
No of MCS values.
- mcstaPoints - Variable in class loci.formats.in.SDTInfo
-
Number of MCS_TA points.
- mcsTime - Variable in class loci.formats.in.SDTInfo
-
Interval time [ms] for MCS histogram.
- mcuHeight - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
- mcuWidth - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
- MD_FILE_UNITS - Static variable in class loci.formats.in.GelReader
-
- MD_FILETAG - Static variable in class loci.formats.in.GelReader
-
- MD_LAB_NAME - Static variable in class loci.formats.in.GelReader
-
- MD_PREP_DATE - Static variable in class loci.formats.in.GelReader
-
- MD_PREP_TIME - Static variable in class loci.formats.in.GelReader
-
- MD_SAMPLE_INFO - Static variable in class loci.formats.in.GelReader
-
- MD_SCALE_PIXEL - Static variable in class loci.formats.in.GelReader
-
- mdb - Variable in class loci.formats.services.MDBServiceImpl
-
- MDB_SUFFIX - Static variable in class loci.formats.in.ZeissLSMReader
-
- MDBService - Interface in loci.formats.services
-
Interface defining methods for parsing MDB database files.
- MDBServiceImpl - Class in loci.formats.services
-
Implementation of
MDBService for parsing MDB database files.
- MDBServiceImpl() - Constructor for class loci.formats.services.MDBServiceImpl
-
Default constructor.
- MEA_SUFFIX - Static variable in class loci.formats.in.FlexReader
-
- MeaHandler() - Constructor for class loci.formats.in.FlexReader.MeaHandler
-
- measDescBlockLength - Variable in class loci.formats.in.SDTInfo
-
- measDescBlockNo - Variable in class loci.formats.in.SDTInfo
-
Number of the measurement description block
corresponding to this data block.
- measDescBlockOffs - Variable in class loci.formats.in.SDTInfo
-
- measMode - Variable in class loci.formats.in.SDTInfo
-
- MEASUREMENT_SUFFIXES - Static variable in class loci.formats.in.FlexReader
-
- measurementFiles - Variable in class loci.formats.in.FlexReader
-
- measurementFolder - Variable in class loci.formats.in.CellVoyagerReader
-
- MeasurementHandler() - Constructor for class loci.formats.in.ColumbusReader.MeasurementHandler
-
- measurementID - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- measurementID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- measurementName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- measurementResultFile - Variable in class loci.formats.in.CellVoyagerReader
-
- measurementTime - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- medianFilter() - Method in class loci.plugins.util.RecordedImageProcessor
-
- MEDICAL_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the medical imaging domain.
- medium - Variable in class loci.formats.in.ZeissCZIReader
-
- medium - Variable in class loci.formats.in.ZeissLSMReader.Laser
-
- MEM_MODEL - Static variable in class loci.formats.in.CellSensReader
-
- memBank - Variable in class loci.formats.in.SDTInfo
-
- memoFile - Variable in class loci.formats.Memoizer
-
- Memoizer - Class in loci.formats
-
- Memoizer() - Constructor for class loci.formats.Memoizer
-
- Memoizer(long) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around a new
ImageReader creating memo
files under the same directory as the original file only if the call to
Memoizer.setId(java.lang.String) takes longer than
minimumElapsed in milliseconds.
- Memoizer(long, File) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around a new
ImageReader creating memo file
files under the
directory argument including the full path of the
original file only if the call to
Memoizer.setId(java.lang.String) takes longer than
minimumElapsed in milliseconds.
- Memoizer(IFormatReader) - Constructor for class loci.formats.Memoizer
-
- Memoizer(IFormatReader, long) - Constructor for class loci.formats.Memoizer
-
- Memoizer(IFormatReader, long, File) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around the given
IFormatReader creating
memo files under the
directory argument including the full path
of the original file only if the call to
Memoizer.setId(java.lang.String) takes longer than
minimumElapsed in milliseconds.
- Memoizer.Deser - Interface in loci.formats
-
- Memoizer.KryoDeser - Class in loci.formats
-
- Memoizer.RandomAccessDeser - Class in loci.formats
-
Helper implementation that can be used to implement
Memoizer.Deser
classes for libraries working solely with byte arrays.
- MemoryDialog - Class in loci.plugins.in
-
Bio-Formats Importer memory usage confirmation dialog box.
- MemoryDialog(ImportProcess) - Constructor for class loci.plugins.in.MemoryDialog
-
Creates a memory confirmation dialog for the Bio-Formats Importer.
- merge(Map<String, Object>, Map<String, Object>, String) - Static method in class loci.formats.MetadataTools
-
Merges the given lists of metadata, prepending the
specified prefix for the destination keys.
- merge - Variable in class loci.plugins.util.BFVirtualStack
-
- MERGE_NAMES - Static variable in class loci.formats.in.BioRadReader
-
List of merge types.
- mergeChannels(BufferedImage[]) - Static method in class loci.formats.gui.AWTImageTools
-
Merges the given images into a single multi-channel image.
- message - Variable in enum loci.plugins.in.ImportStep
-
- meta - Variable in class loci.formats.in.OMETiffReader
-
- meta - Variable in class loci.formats.in.PrairieReader
-
Format-specific metadata.
- meta - Variable in class loci.plugins.in.ImportProcess
-
- META_EXT - Static variable in class loci.formats.in.BDReader
-
- metadata - Variable in class loci.formats.FormatReader
-
Hashtable containing metadata key/value pairs.
- metadata - Variable in class loci.formats.in.MetamorphHandler
-
- METADATA - Static variable in class loci.formats.in.MicromanagerReader
-
File containing extra metadata.
- metadata - Variable in class loci.formats.in.ND2Handler
-
- Metadata() - Constructor for class loci.formats.in.ZeissCZIReader.Metadata
-
- metadata - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- metadata - Variable in class loci.plugins.in.ImportProcess
-
- metadata - Variable in class loci.plugins.util.DataBrowser
-
- METADATA_KEYS - Static variable in class loci.formats.in.ZeissLSMReader
-
- METADATA_LEVEL_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
-
- METADATA_LEVEL_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
-
- METADATA_SUFFIXES - Static variable in class loci.formats.in.APLReader
-
- METADATA_SUFFIXES - Static variable in class loci.formats.in.InCellReader
-
- METADATA_SUFFIXES - Static variable in class loci.formats.in.ScanrReader
-
- METADATA_TAG - Static variable in class loci.formats.in.NDPIReader
-
- METADATA_XML_TAG - Static variable in class loci.formats.in.FlowSightReader
-
- metadataComplete - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not we are confident that all of the metadata stored
within the file has been parsed.
- MetadataConverter - Class in loci.formats.meta
-
- MetadataConverter() - Constructor for class loci.formats.meta.MetadataConverter
-
Deprecated.
Private constructor; all methods in MetadataConverter
are static, so this should not be called.
- metadataFile - Variable in class loci.formats.in.MicromanagerReader.Position
-
- metadataFile - Variable in class loci.formats.in.OMETiffReader
-
- metadataFiles - Variable in class loci.formats.in.BDReader
-
- metadataFiles - Variable in class loci.formats.in.ColumbusReader
-
- metadataFiles - Variable in class loci.formats.in.InCellReader
-
- metadataFiles - Variable in class loci.formats.in.L2DReader
-
List of all metadata files in the dataset.
- metadataFiles - Variable in class loci.formats.in.ScanrReader
-
- metadataIndex - Variable in class loci.formats.in.CellSensReader
-
- metadataInPlanes - Variable in class loci.formats.in.SlidebookReader
-
- metadataLevel - Variable in class loci.formats.in.DefaultMetadataOptions
-
- MetadataLevel - Enum in loci.formats.in
-
- MetadataLevel() - Constructor for enum loci.formats.in.MetadataLevel
-
- metadataOffsets - Variable in class loci.formats.in.SlidebookReader
-
- metadataOptions - Variable in class loci.formats.FormatHandler
-
Metadata parsing options.
- MetadataOptions - Interface in loci.formats.in
-
Holds metadata-related options.
- metadataPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
-
- metadataRetrieve - Variable in class loci.formats.FormatWriter
-
Current metadata retrieval object.
- MetadataRetrieve - Interface in loci.formats.meta
-
- metadataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- metadataStore - Variable in class loci.formats.FormatReader
-
Current metadata store.
- MetadataStore - Interface in loci.formats.meta
-
- MetadataTools - Class in loci.formats
-
- MetadataTools() - Constructor for class loci.formats.MetadataTools
-
- metadataType - Variable in enum loci.formats.tiff.PhotoInterp
-
Metadata type of the photometric interpretation.
- metaFile - Variable in class loci.formats.in.OMETiffReader
-
- MetakitService - Interface in loci.formats.services
-
Interface defining methods for interacting with the OME Metakit library.
- MetakitServiceImpl - Class in loci.formats.services
-
Implementation of MetakitService for interacting with the
OME Metakit library.
- MetakitServiceImpl() - Constructor for class loci.formats.services.MetakitServiceImpl
-
- METAMORPH_ID - Static variable in class loci.formats.in.MetamorphReader
-
- MetamorphHandler - Class in loci.formats.in
-
MetamorphTiffReader is the file format reader for TIFF files produced by
Metamorph software version 7.5 and above.
- MetamorphHandler() - Constructor for class loci.formats.in.MetamorphHandler
-
- MetamorphHandler(Hashtable) - Constructor for class loci.formats.in.MetamorphHandler
-
- MetamorphReader - Class in loci.formats.in
-
Reader is the file format reader for Metamorph STK files.
- MetamorphReader() - Constructor for class loci.formats.in.MetamorphReader
-
Constructs a new Metamorph reader.
- MetamorphTiffReader - Class in loci.formats.in
-
MetamorphTiffReader is the file format reader for TIFF files produced by
Metamorph software version 7.5 and above.
- MetamorphTiffReader() - Constructor for class loci.formats.in.MetamorphTiffReader
-
Constructs a new Metamorph TIFF reader.
- MetamorphTiffReader.NumericComparator - Class in loci.formats.in
-
- MetamorphTiffReader.Well - Class in loci.formats.in
-
- metaWindow - Variable in class loci.plugins.util.DataBrowser
-
- METERING_MODE - Static variable in class loci.formats.tiff.IFD
-
- method - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
-
- MethodEntry() - Constructor for class loci.plugins.util.RecordedImageProcessor.MethodEntry
-
- methodStack - Variable in class loci.plugins.util.RecordedImageProcessor
-
- methodStacks - Variable in class loci.plugins.util.BFVirtualStack
-
- MIASReader - Class in loci.formats.in
-
MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.
- MIASReader() - Constructor for class loci.formats.in.MIASReader
-
Constructs a new MIAS reader.
- MIASReader.AnalysisFile - Class in loci.formats.in
-
- MicromanagerHandler() - Constructor for class loci.formats.in.MicromanagerReader.MicromanagerHandler
-
- MicromanagerReader - Class in loci.formats.in
-
MicromanagerReader is the file format reader for Micro-Manager files.
- MicromanagerReader() - Constructor for class loci.formats.in.MicromanagerReader
-
Constructs a new Micromanager reader.
- MicromanagerReader.Index - Class in loci.formats.in
-
- MicromanagerReader.MicromanagerHandler - Class in loci.formats.in
-
SAX handler for parsing Acqusition.xml.
- MicromanagerReader.Position - Class in loci.formats.in
-
- microscopeModel - Variable in class loci.formats.in.FEITiffReader
-
- microscopeModels - Variable in class loci.formats.in.LIFReader
-
- microscopyMode - Variable in class loci.formats.in.ImarisHDFReader
-
- microSecPerFrame - Variable in class loci.formats.out.AVIWriter
-
- min(double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- MIN_BROWSER_WIDTH - Static variable in class loci.plugins.util.DataBrowser
-
- MIN_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
-
- MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
-
- minAdcRate - Variable in class loci.formats.in.SDTInfo
-
- minCfdRate - Variable in class loci.formats.in.SDTInfo
-
(-1.0 - not set).
- MINCReader - Class in loci.formats.in
-
MINCReader is the file format reader for MINC MRI files.
- MINCReader() - Constructor for class loci.formats.in.MINCReader
-
Constructs a new MINC reader.
- MINIMAL_TAGS - Static variable in class loci.formats.in.FlowSightReader
-
The tags that must be present for this reader
to function properly
- MinimalInCellHandler() - Constructor for class loci.formats.in.InCellReader.MinimalInCellHandler
-
- MinimalTiffReader - Class in loci.formats.in
-
MinimalTiffReader is the superclass for file format readers compatible with
or derived from the TIFF 6.0 file format.
- MinimalTiffReader() - Constructor for class loci.formats.in.MinimalTiffReader
-
Constructs a new MinimalTiffReader.
- MinimalTiffReader(String, String) - Constructor for class loci.formats.in.MinimalTiffReader
-
Constructs a new MinimalTiffReader.
- MinimalTiffReader(String, String[]) - Constructor for class loci.formats.in.MinimalTiffReader
-
Constructs a new MinimalTiffReader.
- MINIMUM_MEMORY_PADDING - Static variable in class loci.plugins.in.MemoryDialog
-
Minimum amount of wiggle room for available memory, in bytes.
- minimumElapsed - Variable in class loci.formats.Memoizer
-
- minInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Minimum intensity
- MinMaxCalculator - Class in loci.formats
-
Logic to compute minimum and maximum values for each channel.
- MinMaxCalculator() - Constructor for class loci.formats.MinMaxCalculator
-
Constructs a MinMaxCalculator around a new image reader.
- MinMaxCalculator(IFormatReader) - Constructor for class loci.formats.MinMaxCalculator
-
Constructs a MinMaxCalculator with the given reader.
- minMaxCalculator - Variable in class loci.plugins.in.ImportProcess
-
- minMaxDone - Variable in class loci.formats.MinMaxCalculator
-
Number of planes for which min/max computations have been completed.
- minMaxStore - Variable in class loci.formats.MinMaxCalculator
-
Consumer of channel global minima and maxima
- minorVersion - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
-
- minSyncRate - Variable in class loci.formats.in.SDTInfo
-
Minimum rates during the measurement.
- minTacRate - Variable in class loci.formats.in.SDTInfo
-
- minValue() - Method in class loci.plugins.util.RecordedImageProcessor
-
- minX - Variable in class loci.formats.in.ImarisHDFReader
-
- minY - Variable in class loci.formats.in.ImarisHDFReader
-
- minZ - Variable in class loci.formats.in.ImarisHDFReader
-
- MIRROR_H - Static variable in class loci.formats.in.CellSensReader
-
- MIRROR_V - Static variable in class loci.formats.in.CellSensReader
-
- MISSING - Static variable in class loci.plugins.config.LibraryEntry
-
HTML markup for missing library.
- MISSING_VERSION_CODE - Static variable in class loci.plugins.config.LibraryEntry
-
Version code to indicate a missing library.
- MissingLibraryException - Exception in loci.formats
-
MissingLibraryException is the exception thrown when a particular data
stream or filename requires a library that is not present on the system.
- MissingLibraryException() - Constructor for exception loci.formats.MissingLibraryException
-
- MissingLibraryException(String) - Constructor for exception loci.formats.MissingLibraryException
-
- MissingLibraryException(String, Throwable) - Constructor for exception loci.formats.MissingLibraryException
-
- MissingLibraryException(Throwable) - Constructor for exception loci.formats.MissingLibraryException
-
- MJPBCodec - Class in loci.formats.codec
-
Methods for compressing and decompressing QuickTime Motion JPEG-B data.
- MJPBCodec() - Constructor for class loci.formats.codec.MJPBCodec
-
- MJPBCodecOptions - Class in loci.formats.codec
-
Options for compressing and decompressing MJPB data.
- MJPBCodecOptions() - Constructor for class loci.formats.codec.MJPBCodecOptions
-
- MJPEG_HUFFMAN_TABLE - Static variable in class loci.formats.in.AVIReader
-
Huffman table for MJPEG data.
- MM_JSON_TAG - Static variable in class loci.formats.in.MicromanagerReader
-
- MMHEADER - Static variable in class loci.formats.in.FluoviewReader
-
Private TIFF tags
- mmPlanes - Variable in class loci.formats.in.MetamorphReader
-
- MMSTAMP - Static variable in class loci.formats.in.FluoviewReader
-
- MNG_MAGIC_BYTES - Static variable in class loci.formats.in.MNGReader
-
- MNGReader - Class in loci.formats.in
-
MNGReader is the file format reader for Multiple-image Network Graphics
(MNG) files.
- MNGReader() - Constructor for class loci.formats.in.MNGReader
-
Constructs a new MNG reader.
- MNGReader.SeriesInfo - Class in loci.formats.in
-
- mod - Variable in class loci.formats.in.SDTInfo
-
Module number.
- modality - Variable in class loci.formats.in.ND2Handler
-
- model - Variable in class loci.formats.in.BioRadSCNReader
-
- MODEL - Static variable in class loci.formats.in.FluoviewReader
-
- model - Variable in class loci.formats.in.FluoviewReader
-
- model - Variable in class loci.formats.in.LeicaHandler.Detector
-
- model - Variable in class loci.formats.in.ZeissLSMReader.Laser
-
- MODEL - Static variable in class loci.formats.tiff.IFD
-
- modFpgaVer - Variable in class loci.formats.in.SDTInfo
-
New in v.8.4.
- modSerNo - Variable in class loci.formats.in.SDTInfo
-
Serial number of the module.
- modType - Variable in class loci.formats.in.SDTInfo
-
Module type.
- modTypeCode - Variable in class loci.formats.in.SDTInfo
-
- modulo - Variable in class loci.formats.meta.ModuloAnnotation
-
- Modulo - Class in loci.formats
-
Represents a subdimension of Z, C, or T as needed for supporting Modulo
annotations.
- Modulo(String) - Constructor for class loci.formats.Modulo
-
- Modulo(Modulo) - Constructor for class loci.formats.Modulo
-
- MODULO_NS - Static variable in class loci.formats.meta.ModuloAnnotation
-
- ModuloAnnotation - Class in loci.formats.meta
-
- ModuloAnnotation() - Constructor for class loci.formats.meta.ModuloAnnotation
-
- moduloC - Variable in class loci.formats.CoreMetadata
-
- moduloT - Variable in class loci.formats.CoreMetadata
-
- moduloZ - Variable in class loci.formats.CoreMetadata
-
- MolecularImagingReader - Class in loci.formats.in
-
MolecularImagingReader is the file format reader for Molecular Imaging files.
- MolecularImagingReader() - Constructor for class loci.formats.in.MolecularImagingReader
-
Constructs a new Molecular Imaging reader.
- montageIndex - Variable in class loci.formats.in.FluoviewReader
-
- montageOffsets - Variable in class loci.formats.in.FluoviewReader
-
- mosaics - Variable in class loci.formats.in.ZeissCZIReader
-
- mouseClicked(MouseEvent) - Method in class loci.plugins.in.MainDialog
-
- mouseDragged(MouseEvent) - Method in class loci.formats.gui.ImageViewer
-
Handles cursor probes.
- mouseEntered(MouseEvent) - Method in class loci.plugins.in.MainDialog
-
Focuses the component upon mouseover.
- mouseExited(MouseEvent) - Method in class loci.plugins.in.MainDialog
-
- mouseMoved(MouseEvent) - Method in class loci.formats.gui.ImageViewer
-
Handles cursor probes.
- mousePressed(MouseEvent) - Method in class loci.plugins.in.MainDialog
-
- mouseReleased(MouseEvent) - Method in class loci.plugins.in.MainDialog
-
- mouseWheelMoved(MouseWheelEvent) - Method in class loci.plugins.util.DataBrowser
-
- moveTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- MRC_SUFFIXES - Static variable in class loci.formats.in.MRCReader
-
- MRCReader - Class in loci.formats.in
-
MRCReader is the file format reader for MRC files.
- MRCReader() - Constructor for class loci.formats.in.MRCReader
-
Constructs a new MRC reader.
- mReserved1 - Variable in class loci.formats.in.SDTInfo
-
- mReserved2 - Variable in class loci.formats.in.SDTInfo
-
- MRW_MAGIC_STRING - Static variable in class loci.formats.in.MRWReader
-
- MRWReader - Class in loci.formats.in
-
MRWReader is the file format reader for Minolta MRW files.
- MRWReader() - Constructor for class loci.formats.in.MRWReader
-
Constructs a new MRW reader.
- MS_VIDEO - Static variable in class loci.formats.in.AVIReader
-
- msg - Variable in class loci.formats.FilePattern
-
Error message generated during file pattern construction.
- msg(String) - Method in class loci.formats.gui.DataConverter
-
- MSRLE - Static variable in class loci.formats.in.AVIReader
-
Supported compression types.
- MSRLECodec - Class in loci.formats.codec
-
Methods for compressing and decompressing data using Microsoft RLE.
- MSRLECodec() - Constructor for class loci.formats.codec.MSRLECodec
-
- MSVideoCodec - Class in loci.formats.codec
-
Methods for compressing and decompressing data using Microsoft Video 1.
- MSVideoCodec() - Constructor for class loci.formats.codec.MSVideoCodec
-
- mtResol - Variable in class loci.formats.in.SDTInfo
-
Macro time clock in 0.1 ns units.
- MULTI_PHOTON - Static variable in class loci.formats.in.LegacyND2Reader
-
- MultiBand() - Constructor for class loci.formats.in.LeicaHandler.MultiBand
-
- multiBands - Variable in class loci.formats.in.LeicaHandler
-
- MULTIDIM_IMAGE_VOLUME - Static variable in class loci.formats.in.CellSensReader
-
- MULTIDIM_STACK_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- multifile - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
-
- multiply(double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- MUST_GROUP - Static variable in class loci.formats.FormatTools
-
File grouping options.
- MUST_GROUP - Static variable in interface loci.formats.IFormatReader
-
File grouping options.
- myReader - Variable in class loci.formats.gui.ImageViewer
-
Current format reader.
- myWriter - Variable in class loci.formats.gui.ImageViewer
-
Current format writer.
- p - Variable in class loci.formats.in.BioRadReader.Note
-
- p - Variable in class loci.plugins.in.SeriesDialog
-
- p - Variable in class loci.plugins.in.ThumbLoader
-
- P_KEY - Static variable in class loci.formats.in.LiFlimReader
-
- pack() - Method in class loci.plugins.util.DataBrowser
-
Overridden pack method to allow us to delay initial window sizing.
- PACKBITS - Static variable in class loci.formats.in.PhotoshopTiffReader
-
- PackbitsCodec - Class in loci.formats.codec
-
This class implements packbits decompression.
- PackbitsCodec() - Constructor for class loci.formats.codec.PackbitsCodec
-
- pad - Variable in class loci.formats.out.QTWriter
-
Number of padding bytes in each row.
- PAD - Static variable in class loci.plugins.config.ConfigWindow
-
- padding - Variable in class loci.formats.in.UBMReader
-
- PADDING_BYTES - Static variable in class loci.formats.out.AVIWriter
-
- paddingZeros - Variable in class loci.plugins.in.FilePatternDialog
-
- padImage(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Pads (or crops) the image to the given width and height.
- padImage(byte[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the byte array to the given width and height.
- padImage(short[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the short array to the given width and height.
- padImage(int[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the int array to the given width and height.
- padImage(float[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the float array to the given width and height.
- padImage(double[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the double array to the given width and height.
- PAETH - Static variable in class loci.formats.in.APNGReader
-
- page - Variable in class loci.formats.in.SDTInfo
-
- PAGE_NAME - Static variable in class loci.formats.tiff.IFD
-
- PAGE_NUMBER - Static variable in class loci.formats.tiff.IFD
-
- paintComponent(Graphics) - Method in class loci.formats.gui.CacheIndicator
-
- palette - Variable in class loci.formats.in.BMPReader
-
The palette for indexed color images.
- PALETTE - Static variable in class loci.formats.in.ZeissLSMReader
-
- pane - Variable in class loci.formats.gui.ImageViewer
-
- panel - Variable in class loci.plugins.util.SearchableWindow
-
- PARAMETER_KEYS - Static variable in class loci.formats.in.ICSReader
-
- parameterFile - Variable in class loci.formats.in.JEOLReader
-
- paramFile - Variable in class loci.formats.in.PCORAWReader
-
- PARAMS - Static variable in class loci.plugins.config.ConfigWindow
-
- parentDimension - Variable in class loci.formats.Modulo
-
- parentNames - Variable in class loci.formats.in.FEITiffReader.FEIHandler
-
- parentQName - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- parentType - Variable in class loci.formats.Modulo
-
- parse(int, long, long) - Method in class loci.formats.in.NativeQTReader
-
Parse all of the atoms in the file.
- parse(Element) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Parses metadata from the given Frame element.
- parse(Element) - Method in class loci.formats.in.PrairieMetadata.PFile
-
Parses metadata from the given File element.
- parse(Element) - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Parses metadata from the given Sequence element.
- parseApplicationTags() - Method in class loci.formats.in.ZeissLSMReader
-
- parseArg(String) - Method in class loci.plugins.in.ImporterOptions
-
Parses the plugin argument for parameter values.
- parseArray(String) - Method in class loci.formats.in.VarianFDFReader
-
Split a String that represents an array into individual elements.
- parseAttributes() - Method in class loci.formats.in.ImarisHDFReader
-
- parseAttributesAndVariables(List<Group>) - Method in class loci.formats.services.NetCDFServiceImpl
-
Recursively parses attribute and variable paths, filling
attributeList and variableList.
- parseAxis(Element) - Method in class loci.formats.in.OIRReader
-
- parseBoxes() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Parses the JPEG 2000 JP2 metadata boxes.
- parseCellObjects() - Method in class loci.formats.in.CellH5Reader
-
- parseCFG(Document) - Method in class loci.formats.in.PrairieMetadata
-
Parses metadata from Prairie CFG file.
- parseChannel(Element, boolean) - Method in class loci.formats.in.OIRReader
-
- parseChannelData(Location) - Method in class loci.formats.in.BDReader
-
- parseChannels() - Method in class loci.formats.in.PrairieMetadata
-
- parseChannelTag() - Method in class loci.formats.in.LeicaReader
-
- parseChunks(IRandomAccess) - Method in class loci.formats.in.IM3Reader.ContainerRecord
-
Parse and return the sub-records for the record container
- parseColor(byte, byte, byte) - Static method in class loci.formats.in.BaseZeissReader
-
- parseColor(String) - Method in class loci.formats.in.FakeReader
-
- parseColor(byte, byte, byte) - Static method in class loci.formats.in.ZeissTIFFHandler
-
- parseComment() - Method in class loci.formats.in.FluoviewReader
-
- parseCommentGeneric(String) - Method in class loci.formats.in.TiffReader
-
- parseCommentImageJ(String) - Method in class loci.formats.in.TiffReader
-
- parseCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
-
- parseContiguousCodestream(long) - Method in class loci.formats.in.JPEG2000MetadataParser
-
Parses the JPEG 2000 codestream metadata.
- parseCSVFile(String) - Method in class loci.formats.in.PerkinElmerReader
-
- parseDatabase() - Method in interface loci.formats.services.MDBService
-
Read all tables from a pre-initialized .mdb files.
- parseDatabase() - Method in class loci.formats.services.MDBServiceImpl
-
- parseDeconvolutionLog(MetadataStore) - Method in class loci.formats.in.DeltavisionReader
-
Parse deconvolution output, if it exists.
- parseDimension(String) - Method in class loci.formats.in.APLReader
-
Parse an integer from the given dimension String.
- parseDimensionSizes(String[], String[]) - Method in class loci.formats.in.NikonTiffReader
-
- parseDimensionTag(int) - Method in class loci.formats.in.LeicaReader
-
- parseDOM(Location) - Method in class loci.formats.in.PrairieReader
-
Parses a
Document from the data in the given file.
- parseDouble(String) - Method in class loci.formats.in.LeicaHandler
-
- parseDouble(String) - Method in class loci.formats.in.LIFReader
-
- parseDouble(String) - Method in class loci.formats.in.TiffReader
-
- parseDouble(String) - Static method in class loci.formats.in.ZeissTIFFHandler
-
Parse a Double from a String.
- parseENV(Document) - Method in class loci.formats.in.PrairieMetadata
-
Parses metadata from Prairie ENV file.
- parseETSFile(String, int) - Method in class loci.formats.in.CellSensReader
-
- parseExperimentTag() - Method in class loci.formats.in.LeicaReader
-
- parseExtraTags() - Method in class loci.formats.in.GatanDM2Reader
-
- parseFDF(String) - Method in class loci.formats.in.VarianFDFReader
-
- parseFile(String, Class<?>) - Method in class loci.formats.ClassList
-
Parses a list of classes from a configuration file.
- parseFile(String, MetamorphHandler) - Method in class loci.formats.in.MetamorphTiffReader
-
- parseFile(DirectoryEntry) - Method in class loci.formats.services.POIServiceImpl
-
- parseFileHeader(List<String>) - Method in class loci.formats.in.TextReader
-
Parses the file looking for the file header.
- parseFilename(String[], int, int) - Method in class loci.formats.in.APLReader
-
- parseFilenames(int) - Method in class loci.formats.in.LeicaReader
-
- parseFlexFile(int, int, int, int, boolean, MetadataStore) - Method in class loci.formats.in.FlexReader
-
Parses XML metadata from the Flex file corresponding to the given well.
- parseFrameProperties(Element) - Method in class loci.formats.in.OIRReader
-
- parseHeader() - Method in class loci.formats.in.LiFlimReader
-
- parseHeaderRow(String[]) - Method in class loci.formats.in.TextReader
-
Populates rowLength, xIndex, yIndex, and channels.
- parseImageNames(int) - Method in class loci.formats.in.OpenlabReader
-
- parseImageProperties(Element) - Method in class loci.formats.in.OIRReader
-
- parseImageTag(int) - Method in class loci.formats.in.LeicaReader
-
- parseImageXML(String, int) - Method in class loci.formats.in.ColumbusReader
-
- parseInstrumentData(MetadataStore, int) - Method in class loci.formats.in.LeicaReader
-
- parseInt(String) - Static method in class loci.formats.in.BaseZeissReader
-
Parse an Integer from a String.
- parseInt(String, int) - Static method in class loci.formats.in.BaseZeissReader
-
Parse an Integer from a String.
- parseInt(String) - Method in class loci.formats.in.TiffReader
-
- parseKeyAndValue(String, String, int, int, int) - Method in class loci.formats.in.MicromanagerReader
-
- parseKeyAndValue(String, String, String) - Method in class loci.formats.in.ND2Handler
-
- parseKeys(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata
-
Parses <Key> elements beneath the given element, into the specified
table.
- parseKeyValue(String, String) - Method in class loci.formats.in.PerkinElmerReader
-
- parseLength(String, String) - Method in class loci.formats.in.FakeReader
-
- parseLine(String) - Method in class loci.formats.ClassList
-
Parses a class from a string including options and comments.
- parseList(String) - Static method in class loci.plugins.prefs.StringOption
-
Parses a string of comma-separated values into a list of tokens.
- parseLogFile(MetadataStore) - Method in class loci.formats.in.DeltavisionReader
-
Extract metadata from associated log file, if it exists.
- parseLUT(int) - Method in class loci.formats.in.LeicaReader
-
- parseLUT(Element, String) - Method in class loci.formats.in.OIRReader
-
- parseMainTags(int, MetadataStore, ArrayList<BaseZeissReader.Tag>) - Method in class loci.formats.in.BaseZeissReader
-
- parseMasks - Variable in class loci.formats.in.MIASReader
-
Whether or not mask pixel data should be parsed in setId.
- parseMasks(MetadataStore) - Method in class loci.formats.in.MIASReader
-
Parse masks into a separate overlay-specific MetadataStore.
- parseMasks(MetadataStore, int, int, String) - Method in class loci.formats.in.MIASReader
-
Parse Mask ROIs from the given TIFF and place them in the given
MetadataStore.
- parseMDB(String) - Method in class loci.formats.in.ZeissLSMReader
-
Parse a .mdb file and return a list of referenced .lsm files.
- parseMetadata() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
-
- parseNotes(MetadataStore) - Method in class loci.formats.in.BioRadReader
-
- parseObjectives(NodeList) - Method in class loci.formats.in.ZeissCZIReader
-
- parseOption(String) - Method in class loci.plugins.prefs.BooleanOption
-
- parseOption(String) - Method in class loci.plugins.prefs.DoubleOption
-
- parseOption(String) - Method in class loci.plugins.prefs.Option
-
Parses the option's value from the given argument string.
- parseOption(String) - Method in class loci.plugins.prefs.StringOption
-
- parseOptions(String) - Method in class loci.formats.ClassList
-
Parses one or more options from a string.
- parseOptions(String) - Method in class loci.plugins.in.Importer
-
Parses core options.
- parseOptions(String) - Method in class loci.plugins.prefs.OptionsList
-
Parses option values from the given argument string.
- parseOriginalMetadata(Node) - Method in class loci.formats.in.OIRReader
-
- parseOverlays(int, long, String, MetadataStore) - Method in class loci.formats.in.ZeissLSMReader
-
Parses overlay-related fields.
- parsePageName() - Method in class loci.formats.in.FluoviewReader
-
- parsePixelsSizeZFromKey(String) - Method in class loci.formats.in.ND2Handler
-
Parses the physical size from a key.
- parsePoints(String) - Static method in class loci.plugins.util.ROIHandler
-
Parse (x, y) coordinates from a String returned by
MetadataRetrieve.getPolygonpoints(...) or
MetadataRetrieve.getPolylinepoints(...)
- parsePosition(int) - Method in class loci.formats.in.MicromanagerReader
-
- parsePosition(String, int) - Method in class loci.formats.in.MicromanagerReader
-
- parsePrairieMetadata() - Method in class loci.formats.in.PrairieReader
-
This step parses the Prairie metadata files into the Prairie-specific
metadata structure,
PrairieReader.meta.
- parsePVStateShard(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata
-
Parses the <PVStateShard> element beneath the given element, into
the specified table.
- parser - Variable in class loci.formats.in.APLReader
-
- parser - Variable in class loci.formats.in.CellSensReader
-
- parser - Variable in class loci.formats.in.FV1000Reader
-
- parser - Variable in class loci.formats.in.ZeissCZIReader
-
- parseRecord(IRandomAccess) - Static method in class loci.formats.in.IM3Reader
-
Parse an IM3 record at the current file pointer location
- parseResFile(String) - Method in class loci.formats.in.FlexReader
-
- parseROIFile(String, MetadataStore, int, int) - Method in class loci.formats.in.FV1000Reader
-
- parseROIs(MetadataStore) - Method in class loci.formats.in.BDReader
-
- parseROIs(int) - Method in class loci.formats.in.CellH5Reader
-
- parseROIs(MetadataStore) - Method in class loci.formats.in.TrestleReader
-
- parseROIs(int, String, MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
-
Parse ROI data from the given RandomAccessInputStream and store it in the
given MetadataStore.
- parseROIString(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
-
- parseSeriesTag() - Method in class loci.formats.in.LeicaReader
-
- parseSetup(String, String) - Method in class loci.formats.in.SPCReader
-
- parseSpectrumRecord(IRandomAccess, IM3Reader.ContainerRecord) - Method in class loci.formats.in.IM3Reader.Spectrum
-
Parse the spectrum record
- parseString(IRandomAccess) - Static method in class loci.formats.in.IM3Reader
-
Parse a string from the IM3 file at the current file pointer loc
- parseStructure() - Method in class loci.formats.in.CellH5Reader
-
- parseTableData(List<String>, int) - Method in class loci.formats.in.TextReader
-
Reads the tabular data into the data array.
- parseTags(int, String, String) - Method in class loci.formats.in.GatanReader
-
Parses Gatan DM3 tags.
- parseTags(MetadataStore) - Method in class loci.formats.in.IPLabReader
-
- parseTags(int, String, MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
-
Parse all of the tags in a stream.
- parseTemplateFile(MetadataStore) - Method in class loci.formats.in.MIASReader
-
Parse metadata from the Nugenesistemplate.txt file.
- parseText(String, int, boolean) - Method in class loci.formats.in.NativeND2Reader
-
- parseTimestamp(String) - Method in class loci.formats.in.BaseZeissReader
-
Parse timestamp from string.
- parseTimeTag(int) - Method in class loci.formats.in.LeicaReader
-
- parseTimFile(String) - Method in class loci.formats.in.PerkinElmerReader
-
- parseUIC1Tags(long, int) - Method in class loci.formats.in.MetamorphReader
-
UIC1 entry parser
- parseUIC2Tags(long) - Method in class loci.formats.in.MetamorphReader
-
Populates metadata fields with some contained in MetaMorph UIC2 Tag.
- parseUIC4Tags(long) - Method in class loci.formats.in.MetamorphReader
-
UIC4 metadata parser
UIC4 Table contains per-plane blocks of metadata
stage X/Y positions,
camera chip offsets,
stage labels...
- parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.CellWorxReader
-
Parse metadata from a well log file.
- parseXML(String, long) - Method in class loci.formats.in.OIRReader
-
- parseXML(Document) - Method in class loci.formats.in.PrairieMetadata
-
Parses metadata from Prairie XML file.
- parseXMLFile() - Method in class loci.formats.in.MicromanagerReader
-
Parse metadata values from the Acqusition.xml file.
- parseZpoFile(String) - Method in class loci.formats.in.PerkinElmerReader
-
- PASS_HEIGHTS - Static variable in class loci.formats.in.APNGReader
-
- PASS_WIDTHS - Static variable in class loci.formats.in.APNGReader
-
Interlacing pass dimensions.
- PassthroughCodec - Class in loci.formats.codec
-
A codec which just returns the exact data it was given, performing no
compression or decompression.
- PassthroughCodec() - Constructor for class loci.formats.codec.PassthroughCodec
-
- path - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
-
- path - Variable in class loci.plugins.config.ConfigWindow
-
- path - Variable in class loci.plugins.config.LibraryEntry
-
- pathToImageData - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
-
- pathToPosition - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
-
- pathToSegmentationData - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
-
- pattern - Variable in class loci.formats.FilePattern
-
The file pattern string.
- pattern - Variable in class loci.formats.FileStitcher.ExternalSeries
-
- PATTERN_D - Static variable in class loci.formats.in.CellomicsReader
-
- PATTERN_O - Static variable in class loci.formats.in.CellomicsReader
-
- patternIds - Variable in class loci.formats.FileStitcher
-
Whether string ids given should be treated
as file patterns rather than single file paths.
- PCI_MAGIC_BYTES - Static variable in class loci.formats.in.PCIReader
-
- PCIReader - Class in loci.formats.in
-
PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
- PCIReader() - Constructor for class loci.formats.in.PCIReader
-
Constructs a new SimplePCI reader.
- PCORAWReader - Class in loci.formats.in
-
PCORAWReader is the file format reader for PCORAW files.
- PCORAWReader() - Constructor for class loci.formats.in.PCORAWReader
-
Constructs a new PCORAW reader.
- PCX_MAGIC_BYTE - Static variable in class loci.formats.in.PCXReader
-
- PCXReader - Class in loci.formats.in
-
PCXReader is the file format reader for PCX files (originally used by
PC Paintbrush; now used in Zeiss' LSM Image Browser).
- PCXReader() - Constructor for class loci.formats.in.PCXReader
-
Constructs a new PCX reader.
- PDS_MAGIC_STRING - Static variable in class loci.formats.in.PDSReader
-
- PDSReader - Class in loci.formats.in
-
PDSReader is the file format reader for Perkin Elmer densitometer files.
- PDSReader() - Constructor for class loci.formats.in.PDSReader
-
Constructs a new PDS reader.
- PerkinElmerReader - Class in loci.formats.in
-
PerkinElmerReader is the file format reader for PerkinElmer files.
- PerkinElmerReader() - Constructor for class loci.formats.in.PerkinElmerReader
-
Constructs a new PerkinElmer reader.
- PerkinElmerReader.PixelsFile - Class in loci.formats.in
-
- pf(Double, String) - Method in class loci.formats.in.PrairieReader
-
Converts the given double to a PositiveFloat, or
null if incompatible.
- PF_ABGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
ABGR pixel format.
- PF_ARGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
ARGB pixel format.
- PF_BGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
BGR pixel format.
- PF_BGRA - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
BGRA pixel format.
- PF_BGRX - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
BGRX pixel format.
- PF_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Grayscale pixel format.
- PF_RGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
RGB pixel format.
- PF_RGBA - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
RGBA pixel format.
- PF_RGBX - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
RGBX pixel format.
- PF_XBGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
XBGR pixel format.
- PF_XRGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
XRGB pixel format.
- PFile(PrairieMetadata.Frame, Element) - Constructor for class loci.formats.in.PrairieMetadata.PFile
-
Creates a new file by parsing the given <File> element.
- pfsOffset - Variable in class loci.formats.in.NativeND2Reader
-
- pfsStateOffset - Variable in class loci.formats.in.NativeND2Reader
-
- PGM_MAGIC_CHAR - Static variable in class loci.formats.in.PGMReader
-
- PGMReader - Class in loci.formats.in
-
PGMReader is the file format reader for Portable Gray Map (PGM) images.
- PGMReader() - Constructor for class loci.formats.in.PGMReader
-
Constructs a new PGMReader.
- PHASE - Static variable in class loci.formats.FormatTools
-
Identifies the Phase dimensional type,
representing a dimension consisting of phases.
- PHASE - Static variable in class loci.formats.in.CellSensReader
-
- phaseLabels - Variable in class loci.formats.in.ZeissCZIReader
-
- phases - Variable in class loci.formats.in.LiFlimReader
-
- phases - Variable in class loci.formats.in.ZeissCZIReader
-
- phases - Variable in class loci.formats.in.ZeissLSMReader
-
- PHOTOBLEACHING - Static variable in class loci.formats.in.CellSensReader
-
- PhotoInterp - Enum in loci.formats.tiff
-
Utility class for working with TIFF photometric interpretations.
- PhotoInterp(int, String, String) - Constructor for enum loci.formats.tiff.PhotoInterp
-
Default constructor.
- PHOTOMETRIC_INTERPRETATION - Static variable in class loci.formats.in.DicomReader
-
- PHOTOMETRIC_INTERPRETATION - Static variable in class loci.formats.tiff.IFD
-
- photon(int) - Method in class loci.formats.in.SPCReader
-
- PHOTON_IMAGING_MODE - Static variable in class loci.formats.in.CellSensReader
-
- photosensorReading - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Photosensor reading.
- PhotoshopTiffReader - Class in loci.formats.in
-
PhotoshopTiffReader is the file format reader for
Adobe Photoshop TIFF files.
- PhotoshopTiffReader() - Constructor for class loci.formats.in.PhotoshopTiffReader
-
Constructs a new Photoshop TIFF reader.
- PHYSICAL_SIZE_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
-
- physicalSizes - Variable in class loci.formats.in.LeicaReader
-
- physicalSizeX - Variable in class loci.formats.in.BaseZeissReader
-
- physicalSizeX - Variable in class loci.formats.in.BioRadSCNReader
-
- physicalSizeX - Variable in class loci.formats.in.CellSensReader.Pyramid
-
- physicalSizeX - Variable in class loci.formats.in.FakeReader
-
- physicalSizeX - Variable in class loci.formats.in.LeicaHandler
-
- physicalSizeX - Variable in class loci.formats.in.NikonTiffReader
-
- physicalSizeX - Variable in class loci.formats.in.OIRReader
-
- physicalSizeX - Variable in class loci.formats.in.SISReader
-
- physicalSizeXs - Variable in class loci.formats.in.LIFReader
-
- physicalSizeY - Variable in class loci.formats.in.BaseZeissReader
-
- physicalSizeY - Variable in class loci.formats.in.BioRadSCNReader
-
- physicalSizeY - Variable in class loci.formats.in.CellSensReader.Pyramid
-
- physicalSizeY - Variable in class loci.formats.in.FakeReader
-
- physicalSizeY - Variable in class loci.formats.in.LeicaHandler
-
- physicalSizeY - Variable in class loci.formats.in.NikonTiffReader
-
- physicalSizeY - Variable in class loci.formats.in.OIRReader
-
- physicalSizeY - Variable in class loci.formats.in.SISReader
-
- physicalSizeYs - Variable in class loci.formats.in.LIFReader
-
- physicalSizeZ - Variable in class loci.formats.in.BaseZeissReader
-
- physicalSizeZ - Variable in class loci.formats.in.FakeReader
-
- physicalSizeZ - Variable in class loci.formats.in.NikonTiffReader
-
- physicalSizeZ - Variable in class loci.formats.in.OIRReader
-
- physicalSizeZ - Variable in class loci.formats.in.TiffReader
-
- physicalX - Variable in class loci.formats.in.VolocityReader.Stack
-
- physicalY - Variable in class loci.formats.in.VolocityReader.Stack
-
- physicalZ - Variable in class loci.formats.in.VolocityReader.Stack
-
- PIC_FILE_ID - Static variable in class loci.formats.in.BioRadReader
-
Numerical ID of a valid Bio-Rad PIC file.
- PIC_SUFFIX - Static variable in class loci.formats.in.BioRadReader
-
- picFiles - Variable in class loci.formats.in.BioRadReader
-
- pict - Variable in class loci.formats.in.OpenlabReader
-
Helper reader to read PICT data.
- pict - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
-
- PICT_9A - Static variable in class loci.formats.in.PictReader
-
- PICT_BITSRECT - Static variable in class loci.formats.in.PictReader
-
- PICT_BITSRGN - Static variable in class loci.formats.in.PictReader
-
- PICT_CLIP_RGN - Static variable in class loci.formats.in.PictReader
-
- PICT_END - Static variable in class loci.formats.in.PictReader
-
- PICT_JPEG - Static variable in class loci.formats.in.PictReader
-
- PICT_LONGCOMMENT - Static variable in class loci.formats.in.PictReader
-
- PICT_PACKBITSRECT - Static variable in class loci.formats.in.PictReader
-
- PICT_PACKBITSRGN - Static variable in class loci.formats.in.PictReader
-
- PICT_TYPE_1 - Static variable in class loci.formats.in.PictReader
-
- PICT_TYPE_2 - Static variable in class loci.formats.in.PictReader
-
- PictReader - Class in loci.formats.in
-
PictReader is the file format reader for Apple PICT files.
- PictReader() - Constructor for class loci.formats.in.PictReader
-
Constructs a new PICT reader.
- pictToImage(byte[]) - Method in class loci.formats.gui.LegacyQTTools
-
Converts the given byte array in PICT format to a Java image.
- PictWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats PICT support.
- PictWidgets() - Constructor for class loci.plugins.config.PictWidgets
-
- pinhole - Variable in class loci.formats.in.ImarisHDFReader
-
- pinhole - Variable in class loci.formats.in.LeicaHandler
-
- pinhole - Variable in class loci.formats.in.LeicaReader
-
- pinhole - Variable in class loci.formats.in.OIRReader.Channel
-
- pinhole - Variable in class loci.formats.in.ZeissCZIReader.Channel
-
- pinhole - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
-
- pinholes - Variable in class loci.formats.in.LIFReader
-
- pinholeSize - Variable in class loci.formats.in.FV1000Reader
-
- pinholeSize - Variable in class loci.formats.in.ND2Handler
-
- pinholeSize - Variable in class loci.formats.in.NikonTiffReader
-
- pix - Variable in class loci.formats.in.CanonRawReader
-
- pixClk - Variable in class loci.formats.in.SDTInfo
-
- PIXEL_CLOCK - Static variable in class loci.formats.in.CellSensReader
-
- PIXEL_DATA - Static variable in class loci.formats.in.DicomReader
-
- PIXEL_INFO_TYPE - Static variable in class loci.formats.in.CellSensReader
-
- PIXEL_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
-
- PIXEL_OFFSET - Static variable in class loci.formats.in.VGSAMReader
-
- PIXEL_REPRESENTATION - Static variable in class loci.formats.in.DicomReader
-
- PIXEL_SIGN - Static variable in class loci.formats.in.DicomReader
-
- PIXEL_SPACING - Static variable in class loci.formats.in.DicomReader
-
- PIXEL_X_DIMENSION - Static variable in class loci.formats.tiff.IFD
-
- PIXEL_Y_DIMENSION - Static variable in class loci.formats.tiff.IFD
-
- pixelBits - Variable in class loci.formats.gui.SignedColorModel
-
- PixelBlock() - Constructor for class loci.formats.in.OIRReader.PixelBlock
-
- pixelBlocks - Variable in class loci.formats.in.OIRReader
-
- pixelBytes - Variable in class loci.formats.in.NativeQTReader
-
Total number of bytes of pixel data.
- pixelData - Variable in class loci.formats.in.MINCReader
-
- pixelFile - Variable in class loci.formats.in.AnalyzeReader
-
File containing the pixel data.
- pixelFile - Variable in class loci.formats.in.NiftiReader
-
File containing the pixel data.
- pixelLengths - Variable in class loci.formats.in.SlidebookReader
-
- pixelOffset - Variable in class loci.formats.in.AIMReader
-
- pixelOffset - Variable in class loci.formats.in.AnalyzeReader
-
Offset to the pixel data in the .img file.
- pixelOffset - Variable in class loci.formats.in.FitsReader
-
- pixelOffset - Variable in class loci.formats.in.GatanReader
-
Offset to pixel data.
- pixelOffset - Variable in class loci.formats.in.HISReader
-
Offsets to pixel data for each series.
- pixelOffset - Variable in class loci.formats.in.JEOLReader
-
- pixelOffset - Variable in class loci.formats.in.KodakReader
-
- pixelOffset - Variable in class loci.formats.in.MolecularImagingReader
-
- pixelOffset - Variable in class loci.formats.in.NativeQTReader
-
Offset to start of pixel data.
- pixelOffset - Variable in class loci.formats.in.NiftiReader
-
Offset to the pixel data in the .img file.
- pixelOffset - Variable in class loci.formats.in.RHKReader
-
- pixelOffset - Variable in class loci.formats.in.SIFReader
-
- pixelOffset - Variable in class loci.formats.in.TopometrixReader
-
- pixelOffset - Variable in class loci.formats.in.VolocityClippingReader
-
- pixelOffset - Variable in class loci.formats.out.ICSWriter
-
- pixelOffset - Variable in class loci.formats.out.V3DrawWriter
-
- pixelOffsets - Variable in class loci.formats.in.JPXReader
-
- pixelOffsets - Variable in class loci.formats.in.SlidebookReader
-
- pixelOffsets - Variable in class loci.formats.in.VarianFDFReader
-
- pixelOffsets - Variable in class loci.formats.in.VisitechReader
-
- pixels - Variable in class loci.formats.in.AFIReader
-
- pixels - Variable in class loci.formats.in.GIFReader
-
- pixels - Variable in class loci.formats.in.ImagicReader
-
- pixels - Variable in class loci.formats.in.LeicaSCNReader.Image
-
- Pixels(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Pixels
-
- pixels - Variable in class loci.formats.in.ZeissCZIReader
-
- pixels - Variable in class loci.formats.out.ICSWriter
-
- pixels - Variable in class loci.formats.out.V3DrawWriter
-
- pixels2 - Variable in class loci.formats.out.LegacyQTWriter
-
- PIXELS_MARKER - Static variable in class loci.formats.in.VisitechReader
-
- PIXELS_OFFSET - Static variable in class loci.formats.in.ARFReader
-
- PIXELS_OFFSET - Static variable in class loci.formats.in.LIMReader
-
- PIXELS_STRING - Static variable in class loci.formats.in.KodakReader
-
- PIXELS_SUFFIXES - Static variable in class loci.formats.in.InCellReader
-
- PIXELS_TAG - Static variable in class loci.formats.in.ImaconReader
-
- pixelsFile - Variable in class loci.formats.in.FujiReader
-
- pixelsFile - Variable in class loci.formats.in.ImagicReader
-
- pixelsFile - Variable in class loci.formats.in.PDSReader
-
- PixelsFile() - Constructor for class loci.formats.in.PerkinElmerReader.PixelsFile
-
- pixelsFilename - Variable in class loci.formats.in.AnalyzeReader
-
- pixelsFilename - Variable in class loci.formats.in.NiftiReader
-
- pixelsFiles - Variable in class loci.formats.in.BrukerReader
-
- pixelsFiles - Variable in class loci.formats.in.TillVisionReader
-
- pixelsFiles - Variable in class loci.formats.in.VolocityReader.Stack
-
- pixelSize - Variable in class loci.formats.in.FV1000Reader
-
- pixelSize - Variable in class loci.formats.in.IPLabReader
-
- pixelSize - Variable in class loci.formats.in.MicromanagerReader.Position
-
- pixelSize - Variable in class loci.formats.in.ScanrReader
-
- pixelSize - Variable in class loci.formats.in.SVSReader
-
- pixelSize - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
- pixelSizes - Variable in class loci.formats.in.GatanReader
-
List of pixel sizes.
- pixelSizes - Variable in class loci.formats.in.NRRDReader
-
- pixelSizeT - Variable in class loci.formats.in.FV1000Reader
-
- pixelSizeT - Variable in class loci.formats.in.ImprovisionTiffReader
-
- pixelSizeUnits - Variable in class loci.formats.in.GatanDM2Reader
-
- pixelSizeX - Variable in class loci.formats.in.DicomReader
-
- pixelSizeX - Variable in class loci.formats.in.FV1000Reader
-
- pixelSizeX - Variable in class loci.formats.in.GatanDM2Reader
-
- pixelSizeX - Variable in class loci.formats.in.ImarisHDFReader
-
- pixelSizeX - Variable in class loci.formats.in.ImprovisionTiffReader
-
- pixelSizeX - Variable in class loci.formats.in.MetamorphHandler
-
- pixelSizeX - Variable in class loci.formats.in.ND2Handler
-
- pixelSizeX - Variable in class loci.formats.in.PerkinElmerReader
-
- pixelSizeX - Variable in class loci.formats.in.VarianFDFReader
-
- pixelSizeX - Variable in class loci.formats.in.ZeissLSMReader
-
- pixelSizeY - Variable in class loci.formats.in.DicomReader
-
- pixelSizeY - Variable in class loci.formats.in.FV1000Reader
-
- pixelSizeY - Variable in class loci.formats.in.GatanDM2Reader
-
- pixelSizeY - Variable in class loci.formats.in.ImarisHDFReader
-
- pixelSizeY - Variable in class loci.formats.in.ImprovisionTiffReader
-
- pixelSizeY - Variable in class loci.formats.in.MetamorphHandler
-
- pixelSizeY - Variable in class loci.formats.in.ND2Handler
-
- pixelSizeY - Variable in class loci.formats.in.PerkinElmerReader
-
- pixelSizeY - Variable in class loci.formats.in.VarianFDFReader
-
- pixelSizeY - Variable in class loci.formats.in.ZeissLSMReader
-
- pixelSizeZ - Variable in class loci.formats.in.DicomReader
-
- pixelSizeZ - Variable in class loci.formats.in.FV1000Reader
-
- pixelSizeZ - Variable in class loci.formats.in.ImarisHDFReader
-
- pixelSizeZ - Variable in class loci.formats.in.ImprovisionTiffReader
-
- pixelSizeZ - Variable in class loci.formats.in.ND2Handler
-
- pixelSizeZ - Variable in class loci.formats.in.VarianFDFReader
-
- pixelSizeZ - Variable in class loci.formats.in.ZeissLSMReader
-
- pixelsOffset - Variable in class loci.formats.in.BioRadSCNReader
-
- pixelsOffset - Variable in class loci.formats.in.BurleighReader
-
- pixelsOffset - Variable in class loci.formats.in.InCell3000Reader
-
- pixelsOffset - Variable in class loci.formats.in.JPEG2000Reader
-
- pixelsOffset - Variable in class loci.formats.in.QuesantReader
-
- pixelsOffsets - Variable in class loci.formats.in.ImspectorReader
-
List of offsets to each block of pixel data.
- pixelsPerPlane - Variable in class loci.formats.in.AmiraReader.ASCII
-
- pixelsStream - Variable in class loci.formats.in.TillVisionReader
-
- pixelStack - Variable in class loci.formats.in.GIFReader
-
- pixelType - Variable in class loci.formats.CoreMetadata
-
Describes the number of bytes per pixel.
- pixelType - Variable in class loci.formats.in.AmiraReader.ASCII
-
- pixelType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
-
- pixelType - Variable in class loci.formats.services.WlzServiceImpl
-
- pixelTypeFromBytes(int, boolean, boolean) - Static method in class loci.formats.FormatTools
-
Returns an appropriate pixel type given the number of bytes per pixel.
- pixelTypeFromString(String) - Static method in class loci.formats.FormatTools
-
Takes a string value and maps it to one of the pixel type enumerations.
- pixelTypeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- pixelTypes - Static variable in class loci.formats.FormatTools
-
Human readable pixel type.
- pixelUIDs - Variable in class loci.formats.in.OIRReader
-
- pixTime - Variable in class loci.formats.in.SDTInfo
-
- placeWindow(Window) - Static method in class loci.plugins.util.WindowTools
-
Places the given window at a nice location on screen, either centered
below the ImageJ window if there is one, or else centered on screen.
- PLANAR_CONFIGURATION - Static variable in class loci.formats.in.DicomReader
-
- PLANAR_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
-
- plane - Variable in class loci.formats.in.CanonRawReader
-
- Plane() - Constructor for class loci.formats.in.ColumbusReader.Plane
-
- Plane() - Constructor for class loci.formats.in.OperettaReader.Plane
-
- plane - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
-
- Plane(String, ZeissTIFFHandler.TagSet) - Constructor for class loci.formats.in.ZeissTIFFHandler.Plane
-
Constructor
- Plane() - Constructor for class loci.formats.in.ZeissTIFFReader.Plane
-
- PLANE_ORIGIN_RWC - Static variable in class loci.formats.in.CellSensReader
-
- PLANE_SCALE_RWC - Static variable in class loci.formats.in.CellSensReader
-
- PLANE_UNIT - Static variable in class loci.formats.in.CellSensReader
-
- planeCount() - Method in class loci.formats.out.OMETiffWriter
-
- PlaneData() - Constructor for class loci.formats.in.FV1000Reader.PlaneData
-
- planeDeltaT - Variable in class loci.formats.in.FlexReader
-
- planeExposureTime - Variable in class loci.formats.in.FlexReader
-
- planeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- planeIndexes - Variable in class loci.plugins.util.BFVirtualStack
-
- PlaneInfo() - Constructor for class loci.formats.in.OpenlabReader.PlaneInfo
-
- planeMax - Variable in class loci.formats.MinMaxCalculator
-
Max values for each plane.
- planeMin - Variable in class loci.formats.MinMaxCalculator
-
Min values for each plane.
- planeName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
-
- planeNames - Variable in class loci.formats.in.ZeissTIFFHandler
-
- planeOffset - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
-
- planeOffset - Variable in class loci.formats.in.SlidebookReader
-
- planeOffset - Variable in class loci.formats.out.EPSWriter
-
- planeOffsets - Variable in class loci.formats.in.OpenlabReader
-
- planePadding - Variable in class loci.formats.in.VolocityReader.Stack
-
- planePositionX - Variable in class loci.formats.in.FlexReader
-
- planePositionY - Variable in class loci.formats.in.FlexReader
-
- planePositionZ - Variable in class loci.formats.in.FlexReader
-
- planeReader - Variable in class loci.formats.in.AmiraReader
-
- planes - Variable in class loci.formats.in.ColumbusReader
-
- planes - Variable in class loci.formats.in.FV1000Reader
-
- planes - Variable in class loci.formats.in.OpenlabReader
-
- planes - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- planes - Variable in class loci.formats.in.OperettaReader
-
- planes - Variable in class loci.formats.in.ZeissCZIReader
-
- planes - Variable in class loci.formats.in.ZeissTIFFHandler
-
- planes - Variable in class loci.formats.in.ZeissTIFFReader
-
Image planes
- planeSize - Variable in class loci.formats.in.AmiraReader.HxRLE
-
- planeSize - Variable in class loci.formats.in.AmiraReader.HxZip
-
- planesPerBlock - Variable in class loci.formats.in.ImspectorReader
-
Number of planes in each block of pixel data.
- planesWritten - Variable in class loci.formats.out.AVIWriter
-
- PLATE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- plate - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
-
- plate - Variable in class loci.formats.in.MIASReader.AnalysisFile
-
- PLATE - Static variable in class loci.formats.ResourceNamer
-
- plateAcqStartTime - Variable in class loci.formats.in.FlexReader
-
- plateBarcode - Variable in class loci.formats.in.FlexReader
-
- plateCols - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- plateColumns - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- plateCount - Variable in class loci.formats.in.FlexReader
-
- plateDescription - Variable in class loci.formats.in.BDReader
-
- plateDescription - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- plateID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- plateLogFile - Variable in class loci.formats.in.CellWorxReader
-
- plateMap - Variable in class loci.formats.in.InCellReader
-
- plateMaps - Variable in class loci.formats.in.ScreenReader
-
- plateMetadataFiles - Variable in class loci.formats.in.ScreenReader
-
- plateName - Variable in class loci.formats.in.BDReader
-
- plateName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- plateName - Variable in class loci.formats.in.FlexReader
-
- plateName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- plateName - Variable in class loci.formats.in.ScanrReader
-
- plateRows - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- plateRows - Variable in class loci.formats.in.OperettaReader.OperettaHandler
-
- plateType - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- plugin - Variable in class loci.plugins.in.Importer
-
A handle to the plugin wrapper, for toggling
the canceled and success flags.
- plugin - Variable in class loci.plugins.out.Exporter
-
- plugins - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Details for installed plugins.
- PN - Static variable in class loci.formats.in.DicomReader
-
- PNG - Static variable in class loci.formats.in.CellSensReader
-
- PNG_SIG - Static variable in class loci.formats.out.APNGWriter
-
- PNGBlock() - Constructor for class loci.formats.in.APNGReader.PNGBlock
-
- PNGInputStream(String) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
-
- PNGInputStream(String, int) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
-
- poi - Variable in class loci.formats.in.FV1000Reader
-
- poi - Variable in class loci.formats.in.IPWReader
-
Helper reader - parses embedded files from the OLE document.
- poi - Variable in class loci.formats.in.PCIReader
-
- poi - Variable in class loci.formats.in.ZeissZVIReader
-
- POINT - Static variable in class loci.formats.in.FV1000Reader
-
ROI types.
- pointCount - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- points - Variable in enum loci.formats.in.BaseZeissReader.FeatureType
-
- points - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- points - Variable in class loci.formats.in.FakeReader
-
- points - Variable in class loci.formats.in.IMODReader
-
- points - Variable in class loci.formats.in.LiFlimReader.ROI
-
- pointsToString() - Method in class loci.formats.in.LiFlimReader.ROI
-
- PointStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.PointStyle
-
- pointStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- POIService - Interface in loci.formats.services
-
Interface defining methods for reading Microsoft OLE2 documents using
OME's fork of Apache POI.
- POIServiceImpl - Class in loci.formats.services
-
- POIServiceImpl() - Constructor for class loci.formats.services.POIServiceImpl
-
Default constructor.
- polarityF - Variable in class loci.formats.in.SDTInfo
-
- polarityL - Variable in class loci.formats.in.SDTInfo
-
2 = disabled line markers.
- polarityP - Variable in class loci.formats.in.SDTInfo
-
- POLARIZATION - Static variable in class loci.formats.FormatTools
-
Identifies the Polarization dimensional type,
representing a dimension consisting of polarization states.
- POLYGON - Static variable in class loci.formats.in.FV1000Reader
-
- POLYGON - Static variable in class loci.formats.in.LeicaHandler.ROI
-
- POLYGON - Static variable in class loci.formats.in.LIFReader.ROI
-
- polygons - Variable in class loci.formats.in.FakeReader
-
- POLYLINE - Static variable in class loci.formats.in.FV1000Reader
-
- POLYLINE_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
-
- polylines - Variable in class loci.formats.in.FakeReader
-
- populateCircles(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
-
- populateCore - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- populateCoreMetadata(int, int, int, List<String>) - Method in class loci.formats.in.FlexReader
-
Populate core metadata using the given list of image names.
- populateCoreMetadata() - Method in class loci.formats.in.PrairieReader
-
- populateCoreMetadata(int, int, int, int, int) - Method in class loci.formats.in.TextReader
-
- populateExtendedMetadata() - Method in class loci.formats.in.NiftiReader
-
- populateGlobalMetaData() - Method in class loci.formats.in.SPEReader
-
This function is used to populate values not contained in Core Meta Data to the Global Meta Data
- populateImage(OMEXMLMetadata, int) - Method in class loci.formats.out.OMETiffWriter
-
- populateLines(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
-
- populateMaskPixels(int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader
-
Populate the MaskPixels.BinData attribute for the Mask identified by the
given Image index, ROI index, and Shape index.
- populateMetadata() - Method in class loci.formats.in.MicromanagerReader
-
- populateMetadata(MetadataStore, int, String, CoreMetadata) - Static method in class loci.formats.MetadataTools
-
- populateMetadata(MetadataStore, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
-
Populates the given
MetadataStore, for the specified series, using
the provided values.
- populateMetadata(MetadataStore, String, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
-
Populates the given
MetadataStore, for the specified series, using
the provided values.
- populateMetadataStore(MetadataStore) - Method in class loci.formats.in.FlexReader
-
- populateMetadataStore(MetadataStore, String) - Method in class loci.formats.in.FV1000Reader
-
- populateMetadataStore(String[]) - Method in class loci.formats.in.MicromanagerReader
-
- populateMetadataStore(ND2Handler) - Method in class loci.formats.in.NativeND2Reader
-
- populateMetadataStore() - Method in class loci.formats.in.TillVisionReader
-
- populateMetadataStore(ZeissLSMReader.SubBlock, MetadataStore, int) - Method in class loci.formats.in.ZeissLSMReader
-
- populateMetadataStoreImageJ(MetadataStore) - Method in class loci.formats.in.TiffReader
-
Checks the original metadata table for ImageJ-specific information
to propagate into the metadata store.
- populateObjective(MetadataStore, int) - Method in class loci.formats.in.DeltavisionReader
-
Populate an Objective based upon the lens ID.
- populateOMEMetadata(IniTable, MetadataStore) - Method in class loci.formats.in.HitachiReader
-
- populateOMEMetadata() - Method in class loci.formats.in.PrairieReader
-
- populateOriginalMetadata(Element, Deque<String>) - Method in class loci.formats.in.LIFReader
-
- populateOriginalMetadata() - Method in class loci.formats.in.PrairieReader
-
- populateOriginalMetadata(Element, Deque<String>) - Method in class loci.formats.in.ZeissCZIReader
-
- populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in interface loci.formats.services.OMEXMLService
-
Adds the key/value pairs in the specified Hashtable as new
OriginalMetadata annotations in the given OME-XML metadata object.
- populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in interface loci.formats.services.OMEXMLService
-
Adds the specified key/value pair as a new OriginalMetadata node
to the given OME-XML metadata object.
- populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- populatePixels(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools
-
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
- populatePixels(MetadataStore, IFormatReader, boolean) - Static method in class loci.formats.MetadataTools
-
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
- populatePixels(MetadataStore, IFormatReader, boolean, boolean) - Static method in class loci.formats.MetadataTools
-
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
- populatePixelsOnly(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools
-
- populatePixelsOnly(MetadataStore, int, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
-
- populatePixelType(int) - Method in class loci.formats.in.NiftiReader
-
- populatePolylines(NodeList, int, int, boolean) - Method in class loci.formats.in.ZeissCZIReader
-
- populateRectangles(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
-
- populateROI(List<String>, String[], int, int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader
-
- populateRoiMetaData(MetadataStore) - Method in class loci.formats.in.SPEReader
-
Reads and populates ROI Meta Data values.
- populateROIs(MetadataStore) - Method in class loci.formats.in.ND2Handler
-
- populateSPW(MetadataStore, int, int, int, int, int, int, boolean) - Method in class loci.formats.in.FakeReader
-
- populateTiffData(OMEXMLMetadata, int[], int, int, int) - Method in class loci.formats.out.OMETiffWriter
-
- populateXY - Variable in class loci.formats.in.ND2Handler
-
- pos(int) - Method in class loci.formats.cache.CacheStrategy
-
Shortcut for converting rasterized position to N-D position.
- pos(int, int[]) - Method in class loci.formats.cache.CacheStrategy
-
Shortcut for converting rasterized position to N-D position,
using the given array instead of allocating a new one.
- pos - Variable in class loci.formats.in.AVIReader
-
- position - Variable in class loci.formats.in.MicromanagerReader.Index
-
- Position() - Constructor for class loci.formats.in.MicromanagerReader.Position
-
- position - Variable in class loci.formats.in.NativeND2Reader.ChunkMapEntry
-
- position - Variable in class loci.formats.in.OBFReader.Stack
-
- POSITION_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating an updated current dimensional position.
- positionCount - Variable in class loci.formats.in.NativeND2Reader
-
- positions - Variable in class loci.formats.cache.CacheStrategy
-
The list of dimensional positions to consider caching, in order of
preference based on strategy, axis priority and planar ordering.
- positions - Variable in class loci.formats.in.MicromanagerReader.Position
-
- positions - Variable in class loci.formats.in.MicromanagerReader
-
- positions - Variable in class loci.formats.in.ZeissCZIReader
-
- positionsMatch(int, int) - Method in class loci.formats.in.PrairieReader
-
Verifies that stage coordinates match for all (P, Z) across time.
- positionsX - Variable in class loci.formats.in.ZeissCZIReader
-
- positionsY - Variable in class loci.formats.in.ZeissCZIReader
-
- positionsZ - Variable in class loci.formats.in.ZeissCZIReader
-
- positionToRaster(int[], int[]) - Static method in class loci.formats.FormatTools
-
Computes a unique 1-D index corresponding
to the given multidimensional position.
- positionX - Variable in class loci.formats.in.ColumbusReader.Plane
-
- positionX - Variable in class loci.formats.in.DicomReader
-
- positionX - Variable in class loci.formats.in.FV1000Reader.PlaneData
-
- positionX - Variable in class loci.formats.in.MetamorphHandler
-
- positionX - Variable in class loci.formats.in.OperettaReader.Plane
-
- positionY - Variable in class loci.formats.in.ColumbusReader.Plane
-
- positionY - Variable in class loci.formats.in.DicomReader
-
- positionY - Variable in class loci.formats.in.FV1000Reader.PlaneData
-
- positionY - Variable in class loci.formats.in.MetamorphHandler
-
- positionY - Variable in class loci.formats.in.OperettaReader.Plane
-
- positionZ - Variable in class loci.formats.in.ColumbusReader.Plane
-
- positionZ - Variable in class loci.formats.in.DicomReader
-
- positionZ - Variable in class loci.formats.in.FV1000Reader.PlaneData
-
- positionZ - Variable in class loci.formats.in.OperettaReader.Plane
-
- posNames - Variable in class loci.formats.in.ND2Handler
-
- possibleValues - Variable in class loci.plugins.prefs.StringOption
-
List of possible values.
- post - Variable in class loci.formats.NumberFilter
-
String appearing after the numerical block.
- posX - Variable in class loci.formats.in.GatanReader
-
- posX - Variable in class loci.formats.in.InCellReader
-
- posX - Variable in class loci.formats.in.LIFReader
-
- posX - Variable in class loci.formats.in.NativeND2Reader
-
- posX - Variable in class loci.formats.in.ND2Handler
-
- posY - Variable in class loci.formats.in.GatanReader
-
- posY - Variable in class loci.formats.in.InCellReader
-
- posY - Variable in class loci.formats.in.LIFReader
-
- posY - Variable in class loci.formats.in.NativeND2Reader
-
- posY - Variable in class loci.formats.in.ND2Handler
-
- posZ - Variable in class loci.formats.in.GatanReader
-
- posZ - Variable in class loci.formats.in.LIFReader
-
- posZ - Variable in class loci.formats.in.NativeND2Reader
-
- posZ - Variable in class loci.formats.in.ND2Handler
-
- PovrayReader - Class in loci.formats.in
-
PovrayReader is the file format reader for POV-Ray .df3 files.
- PovrayReader() - Constructor for class loci.formats.in.PovrayReader
-
Constructs a new POV-Ray reader.
- power - Variable in class loci.formats.in.ND2Handler
-
- power - Variable in class loci.formats.in.OIRReader.Laser
-
- power - Variable in class loci.formats.in.ZeissLSMReader.Laser
-
- PQBinReader - Class in loci.formats.in
-
PQBinReader is the file format reader for PicoQuant .bin files.
- PQBinReader() - Constructor for class loci.formats.in.PQBinReader
-
Constructs a new PQBin reader.
- PRAIRIE_SUFFIXES - Static variable in class loci.formats.in.PrairieReader
-
- PRAIRIE_TAG_1 - Static variable in class loci.formats.in.PrairieReader
-
- PRAIRIE_TAG_2 - Static variable in class loci.formats.in.PrairieReader
-
- PRAIRIE_TAG_3 - Static variable in class loci.formats.in.PrairieReader
-
- PrairieMetadata - Class in loci.formats.in
-
Metadata structure for Prairie Technologies' TIFF-based format.
- PrairieMetadata(Document, Document, Document) - Constructor for class loci.formats.in.PrairieMetadata
-
Creates a new Prairie metadata by parsing the given XML, CFG and/or ENV
documents.
- PrairieMetadata.Frame - Class in loci.formats.in
-
A Prairie <Frame>, beneath a <Sequence>.
- PrairieMetadata.PFile - Class in loci.formats.in
-
A Prairie <File> beneath a <Frame>.
- PrairieMetadata.Sequence - Class in loci.formats.in
-
A Prairie <Sequence>.
- PrairieMetadata.Value - Interface in loci.formats.in
-
A value in a Prairie metadata dictionary.
- PrairieMetadata.ValueItem - Class in loci.formats.in
-
- PrairieMetadata.ValueTable - Class in loci.formats.in
-
A table of values.
- PrairieReader - Class in loci.formats.in
-
PrairieReader is the file format reader for
Prairie Technologies' TIFF variant.
- PrairieReader() - Constructor for class loci.formats.in.PrairieReader
-
Constructs a new Prairie TIFF reader.
- pre - Variable in class loci.formats.NumberFilter
-
String appearing before the numerical block.
- PRE_AMP_SETTING - Static variable in class loci.formats.in.FluoviewReader
-
- PREAMP_GAIN_VALUE - Static variable in class loci.formats.in.CellSensReader
-
- PREDICTED_CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- PREDICTOR - Static variable in class loci.formats.tiff.IFD
-
- PREF_CELLSENS_FAIL - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_CZI_ATTACHMENT - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_CZI_AUTOSTITCH - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_LEICA_LIF_PHYSICAL_SIZE - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_ND2_CHUNKMAP - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_ND2_NIKON - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_PICT_QTJAVA - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_QT_QTJAVA - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_READER_ENABLED - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_READER_WINDOWLESS - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_SDT_INTENSITY - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_SLICE_LABEL_BASE_INDEX - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_SLICE_LABEL_PATTERN - Static variable in class loci.plugins.util.LociPrefs
-
- PREF_TIFF_IMAGEIO - Static variable in class loci.plugins.util.LociPrefs
-
- prefix - Variable in class loci.formats.in.GIFReader
-
- prefix - Variable in class loci.formats.in.ND2Handler
-
- PREFIX - Static variable in class loci.formats.in.TCSReader
-
- prefix - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
-
- PREFIX_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- preLoad - Variable in class loci.formats.in.SDTReader
-
Whether to pre-load all lifetime bins for faster loading.
- prepareGZipStream(int) - Method in class loci.formats.in.LiFlimReader
-
- prepareToWriteImage(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter
-
Performs the preparation for work prior to the usage of the TIFF saver.
- prepend(ClassList<T>) - Method in class loci.formats.ClassList
-
Prepends a class list which must be assignable to the base class
- prepend(List<Class<? extends T>>) - Method in class loci.formats.ClassList
-
Prepends a list of classes which must be assignable to the base class
- preprocess(RandomAccessInputStream) - Method in class loci.formats.codec.JPEGTileDecoder
-
Pre-process the stream to make sure that the
image width and height are non-zero.
- PRESCANS - Static variable in class loci.formats.in.FluoviewReader
-
- PRESENT - Static variable in class loci.plugins.config.LibraryEntry
-
HTML markup for installed library.
- prestitched - Variable in class loci.formats.in.ZeissCZIReader
-
- prevBuf - Variable in class loci.formats.in.ZeissLSMReader
-
- prevChannel - Variable in class loci.formats.in.ZeissLSMReader
-
- prevElement - Variable in class loci.formats.in.ND2Handler
-
- PREVIEWNAME_PREFIXES - Static variable in class loci.formats.in.FV1000Reader
-
- previewNames - Variable in class loci.formats.in.FV1000Reader
-
- PreviewPane - Class in loci.formats.gui
-
PreviewPane is a panel for use as a JFileChooser accessory, displaying
a thumbnail for the selected image, loaded in a separate thread.
- PreviewPane(JFileChooser) - Constructor for class loci.formats.gui.PreviewPane
-
Constructs a preview pane for the given file chooser.
- prevImage - Variable in class loci.formats.in.ICSReader
-
- previousChannel - Variable in class loci.formats.in.ZeissCZIReader
-
- previousImage - Variable in class loci.formats.codec.CodecOptions
-
Pixels for preceding image (READ/WRITE).
- previousTag - Variable in class loci.formats.in.CellSensReader
-
- prevPixels - Variable in class loci.formats.in.NativeQTReader
-
Pixel data for the previous image plane.
- prevPlane - Variable in class loci.formats.in.NativeQTReader
-
Previous plane number.
- prevPlane - Variable in class loci.formats.in.ZeissLSMReader
-
- prevRegion - Variable in class loci.formats.in.ZeissLSMReader
-
- prevRuntype - Variable in class loci.formats.in.ND2Handler
-
- PRIMARY_CHROMATICITIES - Static variable in class loci.formats.tiff.IFD
-
- primaryFileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
-
- print(int, long, String) - Method in class loci.formats.in.NativeQTReader
-
Debugging method; prints information on an atom.
- printArray(String, int[]) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for outputing contents of an int array, used by main.
- printIFD() - Method in class loci.formats.tiff.IFD
-
Prints the contents of this IFD.
- printOrder(String, Cache) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for outputing cache strategy's order, used by main.
- printSizes(Component) - Static method in class loci.plugins.config.SpringUtilities
-
A debugging utility that prints to stdout the component's
minimum, preferred, and maximum sizes.
- printSource(String, Cache) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for outputing cache's associated source, used by main.
- printStrategy(String, Cache) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for outputing cache's associated strategy, used by main.
- priorities - Variable in class loci.formats.cache.CacheStrategy
-
Priority for caching each axis.
- PRIORITIES - Static variable in class loci.formats.gui.CacheComponent
-
- PRIORITIES_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating new axis priorities.
- priority - Variable in class loci.formats.gui.CacheComponent
-
Combo boxes for choosing axis priority.
- PRIORITY_VALUES - Static variable in class loci.formats.gui.CacheComponent
-
- priorityIndex(int) - Method in class loci.formats.gui.CacheComponent
-
Converts enumerated priority value to priority chooser index.
- priorityValue(int) - Method in class loci.formats.gui.CacheComponent
-
Converts priority chooser index to enumerated priority value.
- probeLabel - Variable in class loci.formats.gui.ImageViewer
-
- proc - Variable in class loci.plugins.util.RecordedImageProcessor
-
- process - Variable in class loci.plugins.in.Calibrator
-
- process - Variable in class loci.plugins.in.Colorizer
-
- process - Variable in class loci.plugins.in.DisplayHandler
-
- process - Variable in class loci.plugins.in.ImagePlusReader
-
Import preparation process managing Bio-Formats readers and other state.
- process - Variable in class loci.plugins.in.ImporterDialog
-
- process - Variable in class loci.plugins.in.ImporterPrompter
-
- processBuffer(int) - Method in class loci.formats.in.SPCReader
-
- processElement(String) - Method in class loci.formats.in.FEITiffReader.FEIHandler
-
- progress - Variable in class loci.formats.gui.DataConverter
-
- progress(boolean, int, int) - Static method in class loci.plugins.BF
-
- promptColors() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for color details, if necessary.
- promptCrop() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for cropping details, if necessary.
- promptFilePattern() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for the file pattern, if necessary.
- promptId() - Method in class loci.plugins.in.ImporterPrompter
-
- promptLicenseCode(String, boolean) - Static method in class loci.plugins.util.LuraWave
-
Prompts the user to enter their LuraWave
license code in an ImageJ dialog window.
- promptLocation() - Method in class loci.plugins.in.ImporterPrompter
-
- promptMain() - Method in class loci.plugins.in.ImporterPrompter
-
- promptMemory() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for confirmation of memory usage, if necessary.
- promptRange() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for the range of planes to import, if necessary.
- promptSeries() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for which series to import, if necessary.
- promptSwap() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for dimension swapping parameters, if necessary.
- promptUpgrade() - Method in class loci.plugins.in.ImporterPrompter
-
- PROP_LUT - Static variable in class loci.plugins.in.ImagePlusReader
-
Special property prefix for storing planar LUTs.
- PROP_SERIES - Static variable in class loci.plugins.in.ImagePlusReader
-
Special property for storing series number associated with the image.
- PROPERTY_FILE - Static variable in class loci.formats.FormatTools
-
- PROPERTY_SET_VOLUME - Static variable in class loci.formats.in.CellSensReader
-
- propertyChange(PropertyChangeEvent) - Method in class loci.formats.gui.PreviewPane
-
Property change event, to listen for when a new
file is selected, or the file chooser closes.
- props - Variable in class loci.formats.in.DynamicMetadataOptions
-
- PSD_MAGIC_STRING - Static variable in class loci.formats.in.PSDReader
-
- PSDReader - Class in loci.formats.in
-
PSDReader is the file format reader for Photoshop PSD files.
- PSDReader() - Constructor for class loci.formats.in.PSDReader
-
Constructs a new PSD reader.
- ptyEnd - Variable in class loci.formats.in.FV1000Reader
-
- ptyPattern - Variable in class loci.formats.in.FV1000Reader
-
- ptyStart - Variable in class loci.formats.in.FV1000Reader
-
- put(String, Object) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, int) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, boolean) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, byte) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, char) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, double) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, float) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, long) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, short) - Method in class loci.formats.in.BaseTiffReader
-
- put(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
-
- putColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- putIFDValue(int, Object) - Method in class loci.formats.tiff.IFD
-
Adds a directory entry to this IFD.
- putIFDValue(int, short) - Method in class loci.formats.tiff.IFD
-
Adds a directory entry of type BYTE to this IFD.
- putIFDValue(int, int) - Method in class loci.formats.tiff.IFD
-
Adds a directory entry of type SHORT to this IFD.
- putIFDValue(int, long) - Method in class loci.formats.tiff.IFD
-
Adds a directory entry of type LONG to this IFD.
- putInt(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
-
- putPixel(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- putPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
-
- putPixelValue(int, int, double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- putRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- putString(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
-
- Pyramid() - Constructor for class loci.formats.in.CellSensReader.Pyramid
-
- pyramidHeight - Variable in class loci.formats.in.NDPIReader
-
- pyramids - Variable in class loci.formats.in.CellSensReader
-
- PyramidTiffReader - Class in loci.formats.in
-
PyramidTiffReader is the file format reader for pyramid TIFFs.
- PyramidTiffReader() - Constructor for class loci.formats.in.PyramidTiffReader
-
Constructs a new pyramid TIFF reader.
- pyramidType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
-
- S_AXIS - Static variable in class loci.formats.AxisGuesser
-
Axis type for series.
- S_MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
-
- S_MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
-
- S_PREFIXES - Static variable in class loci.formats.AxisGuesser
-
Prefixes indicating series dimension.
- SAMP_420 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
4:2:0 chrominance subsampling.
- SAMP_422 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
4:2:2 chrominance subsampling.
- SAMP_440 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
4:4:0 chrominance subsampling.
- SAMP_444 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
4:4:4 chrominance subsampling (no chrominance subsampling).
- SAMP_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Grayscale.
- SAMPLE_FLAGS_LIST - Static variable in class loci.formats.in.CellSensReader
-
- SAMPLE_FORMAT - Static variable in class loci.formats.tiff.IFD
-
- SAMPLE_ID_LIST - Static variable in class loci.formats.in.CellSensReader
-
- SAMPLE_MASK - Static variable in class loci.formats.in.CellSensReader
-
- SAMPLES_PER_PIXEL - Static variable in class loci.formats.in.DicomReader
-
- SAMPLES_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
-
- sampleTable - Variable in class loci.formats.in.VolocityReader
-
- sampleTime - Variable in class loci.formats.in.GatanReader
-
- sanitize(String, boolean) - Method in class loci.formats.gui.XMLCellRenderer.XMLItem
-
Sanitizes strings to appear correctly in HTML.
- sanitizeControl(String) - Static method in class loci.formats.in.NativeND2Reader
-
Remove control and invalid characters from the given string.
- sanitizeFile(String, String) - Method in class loci.formats.in.FV1000Reader
-
- sanitizeValue(String) - Method in class loci.formats.in.FV1000Reader
-
- SATURATION - Static variable in class loci.formats.in.CellSensReader
-
- SATURATION - Static variable in class loci.formats.tiff.IFD
-
- save(String) - Method in class loci.formats.gui.ImageViewer
-
Saves the current images to the given destination
using the current format writer.
- save(String, IFormatWriter) - Method in class loci.formats.gui.ImageViewer
-
Saves to the given data destination using the specified writer
in a separate thread.
- save() - Method in class loci.formats.tools.EditTiffG
-
- save - Variable in class loci.plugins.prefs.Option
-
Whether option state should be saved to ImageJ preferences file.
- SAVE_FILE_SIZE - Static variable in class loci.formats.out.AVIWriter
-
- SAVE_JUNK_SIG - Static variable in class loci.formats.out.AVIWriter
-
- SAVE_LIST1_SIZE - Static variable in class loci.formats.out.AVIWriter
-
- SAVE_LIST1_SUBSIZE - Static variable in class loci.formats.out.AVIWriter
-
- SAVE_LIST2_SIZE - Static variable in class loci.formats.out.AVIWriter
-
- SAVE_MOVI - Static variable in class loci.formats.out.AVIWriter
-
- SAVE_STRF_SIZE - Static variable in class loci.formats.out.AVIWriter
-
- SAVE_STRN_POS - Static variable in class loci.formats.out.AVIWriter
-
- saveBytes(int, byte[]) - Method in class loci.formats.FormatWriter
-
- saveBytes(int, byte[], Region) - Method in class loci.formats.FormatWriter
-
- saveBytes(int, byte[]) - Method in interface loci.formats.IFormatWriter
-
Saves the given image to the current series in the current file.
- saveBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatWriter
-
Saves the given image tile to the current series in the current file.
- saveBytes(int, byte[], Region) - Method in interface loci.formats.IFormatWriter
-
Saves the given image tile to the current series in the current file.
- saveBytes(int, byte[]) - Method in class loci.formats.ImageWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageWriter
-
- saveBytes(int, byte[], Region) - Method in class loci.formats.ImageWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.APNGWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.AVIWriter
-
- saveBytes(int, byte[]) - Method in class loci.formats.out.CellH5Writer
-
Saves the given image to the specified (possibly already open) file.
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.CellH5Writer
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.EPSWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ICSWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JavaWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.LegacyQTWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
-
- saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMEXMLWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.QTWriter
-
- saveBytes(int, byte[], IFD) - Method in class loci.formats.out.TiffWriter
-
Saves the given image to the specified (possibly already open) file.
- saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter
-
Saves the given image to the specified series in the current file.
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.TiffWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.V3DrawWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.WlzWriter
-
- saveBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.services.WlzService
-
Adds a rectangle of bytes in an x-y plane to the opened Woolz object.
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
-
- saveBytes(int, byte[]) - Method in class loci.formats.WriterWrapper
-
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WriterWrapper
-
- saveBytes(int, byte[], Region) - Method in class loci.formats.WriterWrapper
-
- saveComment(String, String) - Method in class loci.formats.out.OMETiffWriter
-
- savedbLength - Variable in class loci.formats.out.AVIWriter
-
- saveDefaults() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.FILE notification.
- savedToMemo - Variable in class loci.formats.Memoizer
-
- saveFile(File) - Method in class loci.formats.tools.EditTiffG
-
- saveidx1Length - Variable in class loci.formats.out.AVIWriter
-
- saveImage(int, BufferedImage) - Method in class loci.formats.gui.BufferedImageWriter
-
Saves the given BufferedImage to the current file.
- saveImage(int, BufferedImage, int, int, int, int) - Method in class loci.formats.gui.BufferedImageWriter
-
Saves the given BufferedImage to the current file.
- saveLUTs(ImagePlus, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
-
- saveMemo() - Method in class loci.formats.Memoizer
-
Save a reader including all reader wrappers inside a memo file.
- saveOption() - Method in class loci.plugins.prefs.BooleanOption
-
- saveOption() - Method in class loci.plugins.prefs.DoubleOption
-
- saveOption() - Method in class loci.plugins.prefs.Option
-
Saves the option's value to the ImageJ preferences file.
- saveOption() - Method in class loci.plugins.prefs.StringOption
-
- saveOptions() - Method in class loci.plugins.prefs.OptionsList
-
Saves option values to the ImageJ preferences file.
- saveOriginalMetadata - Variable in class loci.formats.FormatReader
-
Whether or not to save proprietary metadata in the MetadataStore.
- savePlane(int, Object) - Method in class loci.formats.FormatWriter
-
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.FormatWriter
-
- savePlane(int, Object, Region) - Method in class loci.formats.FormatWriter
-
- savePlane(int, Object) - Method in interface loci.formats.IFormatWriter
-
Saves the given image plane to the current series in the current file.
- savePlane(int, Object, int, int, int, int) - Method in interface loci.formats.IFormatWriter
-
Saves the given image plane to the current series in the current file.
- savePlane(int, Object, Region) - Method in interface loci.formats.IFormatWriter
-
Saves the given image plane to the current series in the current file.
- savePlane(int, Object) - Method in class loci.formats.ImageWriter
-
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.ImageWriter
-
- savePlane(int, Object, Region) - Method in class loci.formats.ImageWriter
-
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
-
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.out.LegacyQTWriter
-
- savePlane(int, Object) - Method in class loci.formats.WriterWrapper
-
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.WriterWrapper
-
- savePlane(int, Object, Region) - Method in class loci.formats.WriterWrapper
-
- saveReader(IFormatReader) - Method in interface loci.formats.Memoizer.Deser
-
- saveReader(IFormatReader) - Method in class loci.formats.Memoizer.KryoDeser
-
- saveReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- saveReleaseVersion(String) - Method in interface loci.formats.Memoizer.Deser
-
- saveReleaseVersion(String) - Method in class loci.formats.Memoizer.KryoDeser
-
- saveReleaseVersion(String) - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- saveRevision(String) - Method in interface loci.formats.Memoizer.Deser
-
- saveRevision(String) - Method in class loci.formats.Memoizer.KryoDeser
-
- saveRevision(String) - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- saveROIs(MetadataStore) - Static method in class loci.plugins.util.ROIHandler
-
Save ROIs in the ROI manager to the given MetadataStore.
- saveStart(File) - Method in interface loci.formats.Memoizer.Deser
-
- saveStart(File) - Method in class loci.formats.Memoizer.KryoDeser
-
- saveStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- saveStop() - Method in interface loci.formats.Memoizer.Deser
-
- saveStop() - Method in class loci.formats.Memoizer.KryoDeser
-
- saveStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- saveStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
-
- saveVersion(Integer) - Method in interface loci.formats.Memoizer.Deser
-
- saveVersion(Integer) - Method in class loci.formats.Memoizer.KryoDeser
-
- saveVersion(Integer) - Method in class loci.formats.Memoizer.RandomAccessDeser
-
- sb - Variable in class loci.formats.gui.ImageViewer
-
- sb - Variable in class loci.formats.in.FEITiffReader.FEIHandler
-
- SBIGReader - Class in loci.formats.in
-
SBIGReader is the file format reader for SBIG files.
- SBIGReader() - Constructor for class loci.formats.in.SBIGReader
-
Constructs a new SBIG reader.
- scale(BufferedImage, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Scales the image using the most appropriate API, with the resultant image
having the same color model as the original image.
- SCALE - Static variable in class loci.formats.in.FV1000Reader
-
- scale - Variable in class loci.formats.in.NativeQTReader
-
Amount to subtract from each offset.
- scale(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- scale2D(BufferedImage, int, int, Object, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools
-
Scales the image using the Java2D API, with the resultant
image optimized for the given graphics configuration.
- scale2D(BufferedImage, int, int, Object, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Scales the image using the Java2D API, with the
resultant image having the given color model.
- SCALE_BAR - Static variable in class loci.formats.in.LeicaHandler.ROI
-
- SCALE_BAR - Static variable in class loci.formats.in.LIFReader.ROI
-
- SCALE_BAR - Static variable in class loci.formats.in.ZeissLSMReader
-
- scaleAWT(BufferedImage, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Scales the image using the AWT Image API.
- scaleFactor - Variable in class loci.formats.in.FakeReader
-
Scale factor for gradient, if any.
- scaleFactor - Variable in class loci.formats.in.ZeissCZIReader
-
- scaleX - Variable in class loci.formats.in.LeicaHandler.ROI
-
- scaleX - Variable in class loci.formats.in.LIFReader.ROI
-
- scaleY - Variable in class loci.formats.in.LeicaHandler.ROI
-
- scaleY - Variable in class loci.formats.in.LIFReader.ROI
-
- scaling - Variable in class loci.formats.in.SimplePCITiffReader
-
- Scaling() - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling
-
- scalings - Variable in class loci.formats.in.ZeissTIFFHandler
-
- scanData(byte[], int, boolean) - Static method in class loci.formats.ImageTools
-
Scan a plane for the channel min and max values.
- scanDim - Variable in class loci.formats.in.ZeissCZIReader
-
- scanDirectory(Location, boolean) - Method in class loci.formats.in.DicomReader
-
Scan the given directory for files that belong to this dataset.
- scanFormat(String, String) - Static method in class loci.formats.in.FV1000Reader
-
- SCANNERSET - Static variable in class loci.formats.in.LeicaReader
-
- ScanrHandler() - Constructor for class loci.formats.in.ScanrReader.ScanrHandler
-
- ScanrReader - Class in loci.formats.in
-
ScanrReader is the file format reader for Olympus ScanR datasets.
- ScanrReader() - Constructor for class loci.formats.in.ScanrReader
-
Constructs a new ScanR reader.
- ScanrReader.ScanrHandler - Class in loci.formats.in
-
- scanRX - Variable in class loci.formats.in.SDTInfo
-
- scanRY - Variable in class loci.formats.in.SDTInfo
-
- scanValues - Variable in class loci.formats.in.PrairieMetadata
-
Table of key/value pairs at the top level.
- scanX - Variable in class loci.formats.in.SDTInfo
-
- scanY - Variable in class loci.formats.in.SDTInfo
-
- SCENE_CAPTURE_TYPE - Static variable in class loci.formats.tiff.IFD
-
- SCENE_TYPE - Static variable in class loci.formats.tiff.IFD
-
- SCHEMA_2010_03 - Static variable in class loci.formats.in.LeicaSCNReader
-
- SCHEMA_2010_10 - Static variable in class loci.formats.in.LeicaSCNReader
-
- SCHEMA_CLASSPATH_READER - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
Finds OME-XML schema definitions in specifications.jar.
- SCHEMA_PATH - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
- SCHEMA_URL_PATTERN - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
The pattern of system ID URLs for OME-XML schema definitions.
- schemaType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
-
- schemaType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
-
- SCNHandler() - Constructor for class loci.formats.in.BioRadSCNReader.SCNHandler
-
- SCREENING - Static variable in class loci.formats.in.FlexReader
-
- screenName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- ScreenReader - Class in loci.formats.in
-
ScreenReader is a generic reader for files in non-HCS formats that have been
organized into a screen.
- ScreenReader() - Constructor for class loci.formats.in.ScreenReader
-
Constructs a new screen reader.
- SDTInfo - Class in loci.formats.in
-
SDTInfo encapsulates the header information for
Becker & Hickl SPC-Image SDT files.
- SDTInfo(RandomAccessInputStream, Hashtable) - Constructor for class loci.formats.in.SDTInfo
-
Constructs a new SDT header by reading values from the given input source,
populating the given metadata table.
- SDTReader - Class in loci.formats.in
-
SDTReader is the file format reader for
Becker & Hickl SPC-Image SDT files.
- SDTReader() - Constructor for class loci.formats.in.SDTReader
-
Constructs a new SDT reader.
- SDTWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats SDT support.
- SDTWidgets() - Constructor for class loci.plugins.config.SDTWidgets
-
- SearchableWindow - Class in loci.plugins.util
-
Text panel with search capabilities.
- SearchableWindow(String, String, String, int, int) - Constructor for class loci.plugins.util.SearchableWindow
-
- SearchableWindow.SearchBox - Class in loci.plugins.util
-
- SearchBox(SearchableWindow) - Constructor for class loci.plugins.util.SearchableWindow.SearchBox
-
- searchBox - Variable in class loci.plugins.util.SearchableWindow.SearchBox
-
- searchPane - Variable in class loci.plugins.util.SearchableWindow.SearchBox
-
- SEED - Static variable in class loci.formats.in.FakeReader
-
- seekStartOfPlane(int, long, long) - Method in class loci.formats.in.LIFReader
-
- seekToNextMarker() - Method in class loci.formats.in.ZeissLMSReader
-
- seekToPlaneOffset(long, int, int) - Method in class loci.formats.FormatWriter
-
Seek to the given (x, y) coordinate of the image that starts at
the given offset.
- Segment() - Constructor for class loci.formats.in.ZeissCZIReader.Segment
-
- Segment(String) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
-
- Segment(ZeissCZIReader.Segment) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
-
- SEGMENTATION_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- segments - Variable in class loci.formats.in.ZeissCZIReader
-
- SeikoReader - Class in loci.formats.in
-
SeikoReader is the file format reader for Seiko .xqd/.xqf files.
- SeikoReader() - Constructor for class loci.formats.in.SeikoReader
-
Constructs a new Seiko reader.
- SELECTED_CHANNELS - Static variable in class loci.formats.in.CellSensReader
-
- SELECTED_FRAMES - Static variable in class loci.formats.in.CellSensReader
-
- selectLine(int) - Method in class loci.plugins.util.SearchableWindow
-
- SEM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the scanning electron microscopy domain.
- SENSING_METHOD - Static variable in class loci.formats.tiff.IFD
-
- SENSOR_KEYS - Static variable in class loci.formats.in.ICSReader
-
- sensorHeight - Variable in class loci.formats.in.MRWReader
-
- sensorWidth - Variable in class loci.formats.in.MRWReader
-
- separatedFork - Variable in class loci.formats.in.NativeQTReader
-
Flag indicating whether the resource and data fork are separated.
- SEQ_FILTERSET - Static variable in class loci.formats.in.LeicaReader
-
- SEQ_FILTERSET_END - Static variable in class loci.formats.in.LeicaReader
-
- SEQ_SCANNERSET - Static variable in class loci.formats.in.LeicaReader
-
- SEQ_SCANNERSET_END - Static variable in class loci.formats.in.LeicaReader
-
- SEQReader - Class in loci.formats.in
-
SEQReader is the file format reader for Image-Pro Sequence files.
- SEQReader() - Constructor for class loci.formats.in.SEQReader
-
Constructs a new Image-Pro SEQ reader.
- sequence - Variable in class loci.formats.in.PrairieMetadata.Frame
-
The <Sequence> containing this <Frame>.
- Sequence(Element) - Constructor for class loci.formats.in.PrairieMetadata.Sequence
-
Creates a new sequence by parsing the given <Sequence> element.
- sequence(int) - Method in class loci.formats.in.PrairieReader
-
Gets the first sequence associated with the given series.
- sequence(int, int) - Method in class loci.formats.in.PrairieReader
-
Gets the sequence associated with the given series and time point.
- sequence(int, int, int) - Method in class loci.formats.in.PrairieReader
-
Gets the sequence associated with the given time point and stage position.
- SEQUENCE_DELIMINATION - Static variable in class loci.formats.in.DicomReader
-
- sequences - Variable in class loci.formats.in.PrairieMetadata
-
<Sequence> elements, keyed on each sequence's cycle.
- sequences - Variable in class loci.formats.in.PrairieReader
-
List of Prairie metadata Sequences, ordered by cycle.
- sequenceValues - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
Table of key/value pairs for this <Sequence>.
- sequential - Variable in class loci.formats.FormatWriter
-
Whether or not we are writing planes sequentially.
- sequential - Variable in class loci.formats.in.LeicaReader
-
- SEQUENTIALSET - Static variable in class loci.formats.in.LeicaReader
-
- sequentialTileFilePointer - Variable in class loci.formats.tiff.TiffSaver
-
- sequentialTileOffsets - Variable in class loci.formats.tiff.TiffSaver
-
Store tile offsets and original file pointer when writing sequentially.
- sequentialWrite - Variable in class loci.formats.tiff.TiffSaver
-
- ser - Variable in class loci.formats.Memoizer
-
- SERIALIZED_MASK - Static variable in class loci.formats.in.CellSensReader
-
- serialNumber - Variable in class loci.formats.in.BioRadSCNReader
-
- serialNumber - Variable in class loci.formats.in.LIFReader
-
- serialNumber - Variable in class loci.formats.in.NDPIReader
-
- serialVersionUID - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
- series - Variable in class loci.formats.FileStitcher
-
The number of the current series (non flat).
- series - Variable in class loci.formats.FormatReader
-
The number of the current series (non flat).
- series - Variable in class loci.formats.FormatWriter
-
Current series.
- series - Variable in class loci.formats.gui.DataConverter
-
- series - Variable in class loci.formats.in.ColumbusReader.Plane
-
- SERIES - Static variable in class loci.formats.in.LeicaReader
-
IFD tags.
- series - Variable in class loci.formats.in.OBFReader.Frame
-
- series - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
-
- series - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
-
- series - Variable in class loci.plugins.macro.LociFunctions
-
- series - Variable in class loci.plugins.util.BFVirtualStack
-
- SERIES_NAME - Static variable in class loci.formats.FormatTools
-
- SERIES_NUM - Static variable in class loci.formats.FormatTools
-
Patterns to be used when constructing a pattern for output filenames.
- seriesCount - Variable in class loci.formats.in.CellH5Reader
-
- seriesCount - Variable in class loci.formats.in.ImarisHDFReader
-
- seriesCounts - Variable in class loci.formats.in.ZeissLSMReader
-
- seriesDescriptions - Variable in class loci.formats.in.LeicaReader
-
- SeriesDialog - Class in loci.plugins.in
-
Bio-Formats Importer series chooser dialog box.
- SeriesDialog(ImportProcess) - Constructor for class loci.plugins.in.SeriesDialog
-
Creates a series chooser dialog for the Bio-Formats Importer.
- seriesFiles - Variable in class loci.formats.in.ScanrReader
-
- seriesIndex - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- seriesInfo - Variable in class loci.formats.in.MNGReader
-
- SeriesInfo() - Constructor for class loci.formats.in.MNGReader.SeriesInfo
-
- SeriesInfo(int, int) - Constructor for class loci.plugins.in.ThumbLoader.SeriesInfo
-
- seriesLabels - Variable in class loci.plugins.in.ImportProcess
-
A descriptive label for each series.
- seriesMetadata - Variable in class loci.formats.CoreMetadata
-
Non-core metadata associated with this series.
- seriesNames - Variable in class loci.formats.in.LeicaReader
-
- seriesOn - Variable in class loci.plugins.in.ImporterOptions
-
- seriesRow - Variable in class loci.formats.gui.DataConverter
-
- seriesStream - Variable in class loci.formats.in.BrukerReader
-
- seriesToCoreIndex(int) - Method in class loci.formats.FileStitcher
-
- seriesToCoreIndex(int) - Method in class loci.formats.FormatReader
-
- seriesToCoreIndex(int) - Method in interface loci.formats.IFormatReader
-
Returns the first core index corresponding to the specified series.
- seriesToCoreIndex(int) - Method in class loci.formats.ImageReader
-
- seriesToCoreIndex(int) - Method in class loci.formats.in.FilePatternReader
-
- seriesToCoreIndex(int) - Method in class loci.formats.ReaderWrapper
-
- seriesToIFD - Variable in class loci.formats.in.MinimalTiffReader
-
- seriesToWellArea(int) - Method in class loci.formats.in.CellVoyagerReader
-
- serverMap - Static variable in class loci.formats.in.FlexReader
-
Mapping from server names stored in the .mea file to actual server names.
- service - Variable in class loci.formats.codec.JPEGXRCodec
-
- service - Variable in class loci.formats.FormatReader
-
- service - Variable in class loci.formats.in.CellWorxReader
-
- service - Variable in class loci.formats.in.HamamatsuVMSReader
-
- service - Variable in class loci.formats.in.NDPIReader
-
- service - Variable in class loci.formats.in.OMETiffReader
-
- service - Variable in class loci.formats.in.TileJPEGReader
-
- service - Variable in class loci.formats.Memoizer
-
- service - Variable in class loci.formats.out.OMETiffWriter
-
- service - Variable in class loci.formats.out.OMEXMLWriter
-
- serviceRegistry - Variable in class loci.formats.services.JAIIIOServiceImpl
-
- set(String, String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to value.
- set(List<T>, int, T, T) - Method in class loci.plugins.in.ImporterOptions
-
- set(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- set(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setAllowOpenFiles(boolean) - Method in class loci.formats.ImageReader
-
Toggles whether or not file system access is allowed when doing type
detection.
- setAntialiasedText(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setAssumeEqualStrips(boolean) - Method in class loci.formats.tiff.TiffParser
-
Sets whether or not to assume that strips are of equal size.
- setAutomaticallyParseMasks(boolean) - Method in class loci.formats.in.MIASReader
-
Toggle whether or not Mask pixel data should be parsed in setId.
- setAutoscale(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setAutoThreshold(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setAxisTypes(int[]) - Method in class loci.formats.AxisGuesser
-
Sets the axis type for each dimensional block.
- setAxisTypes(int[]) - Method in class loci.formats.FileStitcher
-
Sets the axis type for each dimensional block.
- setBackgroundValue(double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setBigTiff(boolean) - Method in class loci.formats.out.TiffWriter
-
Sets whether or not BigTIFF files should be written.
- setBigTiff(boolean) - Method in class loci.formats.tiff.TiffSaver
-
Sets whether or not BigTIFF data should be written.
- setBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to Boolean value.
- setByte(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set a Byte value in the SPE header
- setCalibrationTable(float[]) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setCanChangePattern(boolean) - Method in class loci.formats.FileStitcher
-
- setCanDoUpgradeCheck(boolean) - Method in class loci.formats.UpgradeChecker
-
Set whether or not we are ever allowed to perform an upgrade check.
- setCanLookForND(boolean) - Method in class loci.formats.in.MetamorphReader
-
- setCategory(int) - Method in class loci.formats.in.BaseZeissReader.Tag
-
- setCBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- setCEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- setChannelGlobalMinMax(int, double, double, int) - Method in interface loci.formats.meta.IMinMaxStore
-
Populates the channel global minimum and maximum.
- setClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to Class value.
- setClipRect(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setCodec(int) - Method in class loci.formats.out.LegacyQTWriter
-
Sets the encoded movie's codec.
- setCodec(int) - Method in class loci.formats.out.QTWriter
-
Sets the encoded movie's codec.
- setCodec() - Method in class loci.formats.out.QTWriter
-
- setCodecOptions(CodecOptions) - Method in class loci.formats.FormatWriter
-
- setCodecOptions(CodecOptions) - Method in interface loci.formats.IFormatWriter
-
Sets the codec options.
- setCodecOptions(CodecOptions) - Method in class loci.formats.ImageWriter
-
- setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffParser
-
Sets the codec options to be used when decompressing pixel data.
- setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffSaver
-
Sets the codec options.
- setCodecOptions(CodecOptions) - Method in class loci.formats.WriterWrapper
-
- setColor(Color) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setColor(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setColorMode(String) - Method in class loci.plugins.in.ImporterOptions
-
- setColorModel(ColorModel) - Method in class loci.formats.FormatWriter
-
- setColorModel(ColorModel) - Method in interface loci.formats.IFormatWriter
-
Sets the color model.
- setColorModel(ColorModel) - Method in class loci.formats.ImageWriter
-
- setColorModel(ColorModel) - Method in class loci.formats.WriterWrapper
-
- setColorModel(ColorModel) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setCompression(String) - Method in class loci.formats.FormatWriter
-
- setCompression(String) - Method in interface loci.formats.IFormatWriter
-
Sets the current compression type.
- setCompression(String) - Method in class loci.formats.ImageWriter
-
- setCompression(String) - Method in class loci.formats.WriterWrapper
-
- setConcatenate(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setCoreIndex(int) - Method in class loci.formats.DelegateReader
-
- setCoreIndex(int) - Method in class loci.formats.FileStitcher
-
- setCoreIndex(int) - Method in class loci.formats.FormatReader
-
- setCoreIndex(int) - Method in interface loci.formats.IFormatReader
-
Set the current resolution/series (ignores subresolutions).
- setCoreIndex(int) - Method in class loci.formats.ImageReader
-
- setCoreIndex(int) - Method in class loci.formats.in.FilePatternReader
-
- setCoreIndex(int) - Method in class loci.formats.ReaderWrapper
-
- setCrop(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setCropRegion(int, Region) - Method in class loci.plugins.in.ImporterOptions
-
- setCStep(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- setCurrentPos(int[]) - Method in class loci.formats.cache.Cache
-
Sets the current dimensional position.
- setCustomColor(int, int, Color) - Method in class loci.plugins.in.ImporterOptions
-
- setDataType(String) - Method in class loci.formats.in.InveonReader
-
- setDefaultCreationDate(MetadataStore, String, int) - Static method in class loci.formats.MetadataTools
-
Sets a default creation date.
- setDefaultDateEnabled(boolean) - Static method in class loci.formats.MetadataTools
-
Disables the setting of a default creation date.
- setDoCaching(boolean) - Method in class loci.formats.tiff.TiffParser
-
Sets whether or not IFD entries should be cached.
- setDocument(Document) - Method in class loci.formats.gui.XMLWindow
-
Displays XML from the given document.
- setDocumentLocator(Locator) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
-
- setDoRecording(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to Double value.
- setElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
-
- setElem(int, int, int) - Method in class loci.formats.gui.SignedByteBuffer
-
- setElem(int, int, int) - Method in class loci.formats.gui.SignedShortBuffer
-
- setElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- setElem(int, int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- setElemDouble(int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- setElemDouble(int, int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- setElemFloat(int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- setElemFloat(int, int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
-
- setEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to enumerated type value.
- setf(int, float) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setf(int, int, float) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to file object value.
- setFile(String) - Method in interface loci.formats.services.JHDFService
-
Initializes the service on a given file path.
- setFile(String) - Method in class loci.formats.services.JHDFServiceImpl
-
- setFile(String) - Method in interface loci.formats.services.NetCDFService
-
Initializes the service on a given file path.
- setFile(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
- setFileForWrite(String) - Method in interface loci.formats.services.JHDFService
-
Initializes the service on a given file path.
- setFileForWrite(String) - Method in class loci.formats.services.JHDFServiceImpl
-
- setFilled(boolean) - Method in class loci.formats.ChannelFiller
-
Toggles whether the indices should be factored out.
- setFirstTime(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setFixed() - Method in class loci.formats.FilePatternBlock
-
- setFlattenedResolutions(boolean) - Method in class loci.formats.DelegateReader
-
- setFlattenedResolutions(boolean) - Method in class loci.formats.FormatReader
-
- setFlattenedResolutions(boolean) - Method in interface loci.formats.IFormatReader
-
Set whether or not to flatten resolutions into individual series.
- setFlattenedResolutions(boolean) - Method in class loci.formats.ImageReader
-
- setFlattenedResolutions(boolean) - Method in class loci.formats.in.FilePatternReader
-
- setFlattenedResolutions(boolean) - Method in class loci.formats.ReaderWrapper
-
- setFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to Float value.
- setFloatArray(float[][]) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setFont(Font) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setForceThumbnails(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setFramesPerSecond(int) - Method in class loci.formats.FormatWriter
-
- setFramesPerSecond(int) - Method in interface loci.formats.IFormatWriter
-
Sets the frames per second to use when writing.
- setFramesPerSecond(int) - Method in class loci.formats.ImageWriter
-
- setFramesPerSecond(int) - Method in class loci.formats.WriterWrapper
-
- setGroupFiles(boolean) - Method in class loci.formats.DelegateReader
-
- setGroupFiles(boolean) - Method in class loci.formats.FileStitcher
-
- setGroupFiles(boolean) - Method in class loci.formats.FormatReader
-
- setGroupFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Specifies whether or not to force grouping in multi-file formats.
- setGroupFiles(boolean) - Method in class loci.formats.ImageReader
-
- setGroupFiles(boolean) - Method in class loci.formats.in.FilePatternReader
-
- setGroupFiles(boolean) - Method in class loci.formats.in.ZipReader
-
- setGroupFiles(boolean) - Method in class loci.formats.ReaderWrapper
-
- setGroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setGroupFiles(String) - Method in class loci.plugins.macro.LociFunctions
-
- setHeader(byte[]) - Method in class loci.formats.in.SPEReader.SpeHeader
-
- setHistogramRange(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setHistogramSize(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setId(String) - Method in class loci.formats.ChannelFiller
-
- setId(String) - Method in class loci.formats.ChannelSeparator
-
- setId(String) - Method in class loci.formats.DelegateReader
-
- setId(String) - Method in class loci.formats.DimensionSwapper
-
- setId(String) - Method in class loci.formats.FileStitcher
-
- setId(String) - Method in class loci.formats.FormatReader
-
Initializes a reader from the input file name.
- setId(String) - Method in class loci.formats.FormatWriter
-
Initializes a writer from the input file name.
- setId(String) - Method in interface loci.formats.IFormatHandler
-
Sets the current file name.
- setId(String) - Method in class loci.formats.ImageReader
-
- setId(String) - Method in class loci.formats.ImageWriter
-
- setId(String) - Method in class loci.formats.in.JPEGReader
-
- setId(String) - Method in class loci.formats.Memoizer
-
- setId(String) - Method in class loci.formats.out.APNGWriter
-
- setId(String) - Method in class loci.formats.out.AVIWriter
-
- setId(String) - Method in class loci.formats.out.CellH5Writer
-
- setId(String) - Method in class loci.formats.out.ICSWriter
-
- setId(String) - Method in class loci.formats.out.JavaWriter
-
- setId(String) - Method in class loci.formats.out.OMETiffWriter
-
- setId(String) - Method in class loci.formats.out.OMEXMLWriter
-
- setId(String) - Method in class loci.formats.out.QTWriter
-
- setId(String) - Method in class loci.formats.out.TiffWriter
-
- setId(String) - Method in class loci.formats.out.V3DrawWriter
-
- setId(String) - Method in class loci.formats.out.WlzWriter
-
- setId(String) - Method in class loci.formats.ReaderWrapper
-
- setId(String) - Method in class loci.formats.TileStitcher
-
- setId(String) - Method in class loci.formats.WriterWrapper
-
- setId(String) - Method in class loci.plugins.in.ImporterOptions
-
- setId() - Method in class loci.plugins.in.ImportProcess
-
HACK: This method mainly exists to prompt the user for a missing
LuraWave license code, in the case of LWF-compressed Flex.
- setId(String) - Method in class loci.plugins.macro.LociFunctions
-
- setImages(BufferedImage[]) - Method in class loci.formats.gui.ImageViewer
-
Sets the viewer to display the given images.
- setImages(IFormatReader, BufferedImage[]) - Method in class loci.formats.gui.ImageViewer
-
Sets the viewer to display the given images, obtaining
corresponding core metadata from the specified format reader.
- setIndex(int) - Method in class loci.formats.in.BaseZeissReader.Tag
-
- setInputOrder(int, String) - Method in class loci.plugins.in.ImporterOptions
-
- setInt(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set an Integer value in the SPE header
- setIntArray(int[][]) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to Integer value.
- setIntensity(boolean) - Method in class loci.formats.in.SDTReader
-
Toggles whether the reader should return intensity
data only (the sum of each lifetime histogram).
- setInterleaved(boolean) - Method in class loci.formats.FormatWriter
-
- setInterleaved(boolean) - Method in interface loci.formats.IFormatWriter
-
Sets whether or not the channels in an image are interleaved.
- setInterleaved(boolean) - Method in class loci.formats.ImageWriter
-
- setInterleaved(boolean) - Method in class loci.formats.WriterWrapper
-
- setInterpolate(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setJPEGImage(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Associate the JPEG image of length imageSize bytes stored in
jpegImage with this decompressor instance.
- setJPEGQuality(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Set the JPEG image quality level for subsequent compress operations.
- setJustification(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag
-
- setKeyValue(String, String) - Method in class loci.formats.meta.OriginalMetadataAnnotation
-
Set the key/value metadata pair for this annotation.
- setLegacy(boolean) - Method in class loci.formats.DelegateReader
-
Sets whether to use the legacy reader by default.
- setLegacy(boolean) - Method in class loci.formats.in.PictReader
-
Control whether or not legacy reader (QT Java) is used.
- setLicenseCode(String) - Method in interface loci.formats.services.LuraWaveService
-
Overrides the license code to use when initializing the LuraWave decoder.
- setLicenseCode(String) - Method in class loci.formats.services.LuraWaveServiceImpl
-
- setLineWidth(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setLittleEndian(boolean) - Method in class loci.formats.tiff.TiffSaver
-
Sets whether or not little-endian data should be written.
- setLocation(String) - Method in class loci.plugins.in.ImporterOptions
-
- setLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property name to Long value.
- setLong(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set a Long value in the SPE header
- setLutAnimation(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setLUTs(LUT[]) - Method in class loci.plugins.util.VirtualImagePlus
-
- setMask(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setMetadataFiltered(boolean) - Method in class loci.formats.DelegateReader
-
- setMetadataFiltered(boolean) - Method in class loci.formats.FormatReader
-
- setMetadataFiltered(boolean) - Method in interface loci.formats.IFormatReader
-
Specifies whether ugly metadata (entries with unprintable characters,
and extremely large entries) should be discarded from the metadata table.
- setMetadataFiltered(boolean) - Method in class loci.formats.ImageReader
-
- setMetadataFiltered(boolean) - Method in class loci.formats.in.FilePatternReader
-
- setMetadataFiltered(boolean) - Method in class loci.formats.ReaderWrapper
-
- setMetadataFiltered(String) - Method in class loci.plugins.macro.LociFunctions
-
- setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DefaultMetadataOptions
-
- setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DynamicMetadataOptions
-
- setMetadataLevel(MetadataLevel) - Method in interface loci.formats.in.MetadataOptions
-
Set the metadata level.
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.DelegateReader
-
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.FileStitcher
-
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.FormatHandler
-
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageReader
-
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageWriter
-
- setMetadataOptions(MetadataOptions) - Method in interface loci.formats.IMetadataConfigurable
-
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.ReaderWrapper
-
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.WriterWrapper
-
- setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.FormatWriter
-
- setMetadataRetrieve(MetadataRetrieve) - Method in interface loci.formats.IFormatWriter
-
Sets the metadata retrieval object from
which to retrieve standardized metadata.
- setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.ImageWriter
-
- setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.WriterWrapper
-
- setMetadataStore(MetadataStore) - Method in class loci.formats.DelegateReader
-
- setMetadataStore(MetadataStore) - Method in class loci.formats.FileStitcher
-
- setMetadataStore(MetadataStore) - Method in class loci.formats.FormatReader
-
- setMetadataStore(MetadataStore) - Method in interface loci.formats.IFormatReader
-
Sets the default metadata store for this reader.
- setMetadataStore(MetadataStore) - Method in class loci.formats.ImageReader
-
- setMetadataStore(MetadataStore) - Method in class loci.formats.in.FilePatternReader
-
- setMetadataStore(MetadataStore) - Method in class loci.formats.Memoizer
-
- setMetadataStore(MetadataStore) - Method in class loci.formats.ReaderWrapper
-
- setMinAndMax(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setMinMaxStore(IMinMaxStore) - Method in class loci.formats.MinMaxCalculator
-
Sets the active min-max store for the calculator.
- setModulo(OMEXMLMetadata, Modulo) - Method in class loci.formats.meta.ModuloAnnotation
-
Set the value of this annotation using the given Modulo object
- setMustGroup(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setNormalized(boolean) - Method in class loci.formats.DelegateReader
-
- setNormalized(boolean) - Method in class loci.formats.FileStitcher
-
- setNormalized(boolean) - Method in class loci.formats.FormatReader
-
- setNormalized(boolean) - Method in interface loci.formats.IFormatReader
-
Specifies whether or not to normalize float data.
- setNormalized(boolean) - Method in class loci.formats.ImageReader
-
- setNormalized(boolean) - Method in class loci.formats.in.FilePatternReader
-
- setNormalized(boolean) - Method in class loci.formats.ReaderWrapper
-
- setNormalized(Boolean) - Method in class loci.plugins.macro.LociFunctions
-
- setNumeric() - Method in class loci.formats.FilePatternBlock
-
- setOffsetInfo(int, int, int, int) - Method in class loci.formats.in.DeltavisionReader
-
This method calculates the size of a w, t, z section depending on which
sequence is being used (either ZTW, WZT, or ZWT)
- setOpenAllSeries(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setOrder(int, int) - Method in class loci.formats.cache.CacheStrategy
-
- setOrder(int, int) - Method in interface loci.formats.cache.ICacheStrategy
-
Sets the order in which objects should be loaded along each axis.
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.DelegateReader
-
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FileStitcher
-
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FormatReader
-
- setOriginalMetadataPopulated(boolean) - Method in interface loci.formats.IFormatReader
-
Specifies whether or not to save proprietary metadata
in the MetadataStore.
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ImageReader
-
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.in.FilePatternReader
-
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ReaderWrapper
-
- setOriginalMetadataPopulated(Boolean) - Method in class loci.plugins.macro.LociFunctions
-
- setOutputOrder(String) - Method in class loci.formats.DimensionSwapper
-
Sets the output dimension order according to the given string (e.g.,
"XYZCT").
- setOutputOrder(String) - Method in class loci.formats.out.ICSWriter
-
Set the order in which dimensions should be written to the file.
- setOutputOrder(String) - Method in class loci.formats.out.V3DrawWriter
-
Set the order in which dimensions should be written to the file.
- setOutputOrder(String) - Method in class loci.formats.out.WlzWriter
-
Set the order in which dimensions should be written to the file.
- setPixels() - Method in class loci.formats.in.GIFReader
-
- setPixels(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setPlaneIndexes(int[]) - Method in class loci.plugins.util.BFVirtualStack
-
- setPreLoad(boolean) - Method in class loci.formats.in.SDTReader
-
Toggles whether the reader should pre-load data for increased performance.
- setPriority(int, int) - Method in class loci.formats.cache.CacheStrategy
-
- setPriority(int, int) - Method in interface loci.formats.cache.ICacheStrategy
-
Sets the priority for caching the given axis.
- setProgressBar(ProgressBar) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setQuality(int) - Method in class loci.formats.out.LegacyQTWriter
-
Sets the quality of the encoded movie.
- setQuality(int) - Method in class loci.formats.out.QTWriter
-
Sets the quality of the encoded movie.
- setQuiet(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setRange(int, int) - Method in class loci.formats.cache.CacheStrategy
-
- setRange(int, int) - Method in interface loci.formats.cache.ICacheStrategy
-
Sets the number of objects to cache along the given axis.
- setReader(IFormatReader) - Method in class loci.plugins.util.VirtualImagePlus
-
- setReaderClassList(ClassList<IFormatReader>) - Method in class loci.formats.FileStitcher
-
Set the ClassList object to use when constructing any helper readers.
- setReaderEnabled(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
-
- setReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
-
- setReaderWindowless(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
-
- setRefCount(int) - Method in class loci.plugins.util.VirtualReader
-
- setResolution(int) - Method in class loci.formats.DelegateReader
-
- setResolution(int) - Method in class loci.formats.FormatReader
-
- setResolution(int) - Method in interface loci.formats.IFormatReader
-
Set the resolution level.
- setResolution(int) - Method in class loci.formats.ImageReader
-
- setResolution(int) - Method in class loci.formats.in.FilePatternReader
-
- setResolution(int) - Method in class loci.formats.ReaderWrapper
-
- setResolutionLevel(IFD) - Method in class loci.formats.in.MinimalTiffReader
-
Sets the resolution level when we have JPEG 2000 compressed data.
- setRestartMarkers(long[]) - Method in interface loci.formats.services.JPEGTurboService
-
- setRestartMarkers(long[]) - Method in class loci.formats.services.JPEGTurboServiceImpl
-
- setRoi(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setRoi(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setRoi(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setRoi(Roi) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setROIsMode(String) - Method in class loci.plugins.in.ImporterOptions
-
- setSeries(int) - Method in class loci.formats.DelegateReader
-
- setSeries(int) - Method in class loci.formats.FileStitcher
-
- setSeries(int) - Method in class loci.formats.FormatReader
-
- setSeries(int) - Method in class loci.formats.FormatWriter
-
- setSeries(int) - Method in interface loci.formats.IFormatReader
-
Activates the specified series.
- setSeries(int) - Method in interface loci.formats.IFormatWriter
-
Sets the current series.
- setSeries(int) - Method in class loci.formats.ImageReader
-
- setSeries(int) - Method in class loci.formats.ImageWriter
-
- setSeries(int) - Method in class loci.formats.in.FilePatternReader
-
- setSeries(int) - Method in class loci.formats.in.IM3Reader
-
- setSeries(int) - Method in class loci.formats.in.ZeissLSMReader
-
- setSeries(int) - Method in class loci.formats.ReaderWrapper
-
- setSeries(int) - Method in class loci.formats.WriterWrapper
-
- setSeries(Double) - Method in class loci.plugins.macro.LociFunctions
-
- setSeriesList(String) - Method in class loci.plugins.in.ImportProcess
-
- setSeriesOn(int, boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setShort(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set a Short value in the SPE header
- setShowMetadata(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setShowOMEXML(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setShowROIs(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setSize(int) - Method in class loci.formats.tiff.OnDemandLongArray
-
- setSlice(int) - Method in class loci.plugins.util.VirtualImagePlus
-
- setSliceLabelButton - Variable in class loci.plugins.config.ConfigWindow
-
- setSnapshotCopyMode(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setSnapshotPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setSource(ICacheSource) - Method in class loci.formats.cache.Cache
-
Sets the cache's caching source.
- setSourceImage(byte[], int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Associate an uncompressed source image with this compressor instance.
- setSpecifyRanges(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setSplitChannels(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setSplitFocalPlanes(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setSplitTimepoints(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setStackFormat(String) - Method in class loci.plugins.in.ImporterOptions
-
- setStackOrder(String) - Method in class loci.plugins.in.ImporterOptions
-
- setStitchTiles(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setStrategy(ICacheStrategy) - Method in class loci.formats.cache.Cache
-
Sets the cache's caching strategy.
- setStream(RandomAccessInputStream) - Method in class loci.formats.tiff.OnDemandLongArray
-
- setString(int, String) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set a String value in the SPE header
- setSubsamp(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Set the level of chrominance subsampling for subsequent compress/encode
operations.
- setSwapDimensions(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setTBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- setTEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- setThreshold(double, double, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setTileSizeX(int) - Method in class loci.formats.FormatWriter
-
- setTileSizeX(int) - Method in interface loci.formats.IFormatWriter
-
Will attempt to set the tile width to the desired value and return the actual value which will be used
- setTileSizeX(int) - Method in class loci.formats.ImageWriter
-
- setTileSizeX(int) - Method in class loci.formats.out.TiffWriter
-
- setTileSizeX(int) - Method in class loci.formats.WriterWrapper
-
- setTileSizeY(int) - Method in class loci.formats.FormatWriter
-
- setTileSizeY(int) - Method in interface loci.formats.IFormatWriter
-
Will attempt to set the tile height to the desired value and return the actual value which will be used
- setTileSizeY(int) - Method in class loci.formats.ImageWriter
-
- setTileSizeY(int) - Method in class loci.formats.out.TiffWriter
-
- setTileSizeY(int) - Method in class loci.formats.WriterWrapper
-
- setTruncatedFileFlag(boolean) - Method in class loci.formats.in.DeltavisionReader
-
This flag indicates if the file is known to be truncated.
- setTStep(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- setUngroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setup - Variable in class loci.formats.in.SDTInfo
-
- setup(String, ImagePlus) - Method in class loci.plugins.LociExporter
-
Sets up the writer.
- setup(String, ImagePlus) - Method in class loci.plugins.Slicer
-
- SETUP_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
-
For .set files (setup only).
- setUpgradeCheck(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setupLength - Variable in class loci.formats.in.SDTInfo
-
Length of the setup data.
- setupOffs - Variable in class loci.formats.in.SDTInfo
-
Offset of the setup text data
(system parameters, display parameters, trace parameters etc.).
- setupReader() - Method in class loci.formats.in.MicromanagerReader
-
Initialize the TIFF reader with the first file in the current series.
- setupService() - Method in class loci.formats.FormatReader
-
- setupService() - Method in class loci.formats.in.OMETiffReader
-
- setupServiceAndMetadata() - Method in class loci.formats.out.OMETiffWriter
-
- setupTiffSaver() - Method in class loci.formats.out.TiffWriter
-
- setupWrite(int, int, int, int, int, int, int, int, double, double, double, int) - Method in interface loci.formats.services.WlzService
-
Sets up the service, which must have already been opened for writing.
- setupWrite(int, int, int, int, int, int, int, int, double, double, double, int) - Method in class loci.formats.services.WlzServiceImpl
-
- setUse64BitOffsets(boolean) - Method in class loci.formats.tiff.TiffParser
-
Sets whether or not 64-bit offsets are used for non-BigTIFF files.
- setUsingPatternIds(boolean) - Method in class loci.formats.FileStitcher
-
Sets whether the reader is using file patterns for IDs.
- setValidate(boolean) - Method in class loci.formats.in.DefaultMetadataOptions
-
- setValidate(boolean) - Method in class loci.formats.in.DynamicMetadataOptions
-
- setValidate(boolean) - Method in interface loci.formats.in.MetadataOptions
-
Specifies whether or not to validate files when reading.
- setValidBitsPerPixel(int) - Method in class loci.formats.FormatWriter
-
- setValidBitsPerPixel(int) - Method in interface loci.formats.IFormatWriter
-
Sets the number of valid bits per pixel.
- setValidBitsPerPixel(int) - Method in class loci.formats.ImageWriter
-
- setValidBitsPerPixel(int) - Method in class loci.formats.WriterWrapper
-
- setValue(String) - Method in class loci.formats.in.BaseZeissReader.Tag
-
- setValue(boolean) - Method in class loci.plugins.prefs.BooleanOption
-
Sets the current value of the option.
- setValue(double) - Method in class loci.plugins.prefs.DoubleOption
-
Sets the current value of the option.
- setValue(String, boolean) - Method in class loci.plugins.prefs.OptionsList
-
Sets the value of the boolean option with the given key.
- setValue(String, String) - Method in class loci.plugins.prefs.OptionsList
-
Sets the value of the string option with the given key.
- setValue(String) - Method in class loci.plugins.prefs.StringOption
-
Sets the current value of the option.
- setValue(double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- setVersionChecking(boolean) - Method in class loci.formats.Memoizer
-
Set whether version checking is done based upon major/minor version
numbers.
- setView(Attributes) - Method in class loci.formats.in.LeicaSCNReader.Image
-
- setVirtual(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setVisible(boolean) - Method in class loci.formats.gui.ImageViewer
-
- setVisible(boolean) - Method in class loci.plugins.util.DataBrowser
-
Overridden show method to allow us to delay initial window display.
- setWindowless(boolean) - Method in class loci.plugins.in.ImporterOptions
-
- setWriteSequentially(boolean) - Method in class loci.formats.FormatWriter
-
- setWriteSequentially(boolean) - Method in interface loci.formats.IFormatWriter
-
Sets whether or not we know that planes will be written sequentially.
- setWriteSequentially(boolean) - Method in class loci.formats.ImageWriter
-
- setWriteSequentially(boolean) - Method in class loci.formats.WriterWrapper
-
- setWritingSequentially(boolean) - Method in class loci.formats.tiff.TiffSaver
-
Sets whether or not we know that the planes will be written sequentially.
- setXML(String) - Method in class loci.formats.gui.XMLWindow
-
Displays XML from the given string.
- setXML(File) - Method in class loci.formats.gui.XMLWindow
-
Displays XML from the given file.
- setXML(String) - Method in class loci.formats.tools.EditTiffG
-
- setXML(String) - Method in class loci.plugins.util.DataBrowser
-
Sets XML block associated with this window.
- setYCbCrCorrection(boolean) - Method in class loci.formats.tiff.TiffParser
-
Sets whether or not YCbCr color correction is allowed.
- setZBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- setZEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- setZStep(int, int) - Method in class loci.plugins.in.ImporterOptions
-
- SFEG_TAG - Static variable in class loci.formats.in.FEITiffReader
-
- SH - Static variable in class loci.formats.in.DicomReader
-
- SHADING_MUL - Static variable in class loci.formats.in.CellSensReader
-
- SHADING_SUB - Static variable in class loci.formats.in.CellSensReader
-
- Shape() - Constructor for class loci.formats.in.BaseZeissReader.Shape
-
- shape_count - Variable in class loci.formats.in.ZeissTIFFHandler
-
- SHAPE_PREFIX - Static variable in class loci.formats.in.FakeReader
-
- shapes - Variable in class loci.formats.in.BaseZeissReader.Layer
-
- shapes - Variable in class loci.formats.in.GatanReader
-
- sharpen() - Method in class loci.plugins.util.RecordedImageProcessor
-
- SHARPENING - Static variable in class loci.formats.in.NikonReader
-
- SHARPNESS - Static variable in class loci.formats.in.CellSensReader
-
- SHARPNESS - Static variable in class loci.formats.tiff.IFD
-
- SHORT - Static variable in class loci.formats.in.CellSensReader
-
- SHORT - Static variable in class loci.formats.in.GatanReader
-
- SHORT_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader
-
- shortArrayToBytes(short[]) - Method in class loci.formats.in.FluoviewReader
-
- SHORTCUT_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Name of this plugin, ignored when parsing the plugins list.
- ShortcutPanel - Class in loci.plugins.shortcut
-
A plugin that displays a small window containing shortcuts to the
plugins, including the Bio-Formats Importer, Bio-Formats Exporter,
Stack Colorizer and Stack Slicer.
- ShortcutPanel() - Constructor for class loci.plugins.shortcut.ShortcutPanel
-
Constructs a shortcut panel.
- shortcutPanel - Variable in class loci.plugins.shortcut.ShortcutTransferHandler
-
Associated shortcut panel.
- ShortcutTransferHandler - Class in loci.plugins.shortcut
-
Drag and drop transfer handler for Bio-Formats Plugins Shortcut Window.
- ShortcutTransferHandler(ShortcutPanel) - Constructor for class loci.plugins.shortcut.ShortcutTransferHandler
-
Constructs a new shortcut panel drag and drop transfer handler.
- shortLut - Variable in class loci.formats.in.DicomReader
-
- shortValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as a short.
- showDialog() - Method in class loci.plugins.in.ImporterDialog
-
- showDialog() - Method in class loci.plugins.prefs.OptionsDialog
-
Displays the options dialog, returning the status of the operation.
- showDialogs(ImportProcess) - Method in class loci.plugins.in.Importer
-
- showError(Throwable) - Method in class loci.formats.tools.EditTiffG
-
- showMetadataBox - Variable in class loci.plugins.in.MainDialog
-
- showMetadataWindow() - Method in class loci.plugins.util.DataBrowser
-
Displays the OME-XML metadata window onscreen.
- showOMEXMLBox - Variable in class loci.plugins.in.MainDialog
-
- showOptionsWindow() - Method in class loci.plugins.util.DataBrowser
-
Displays the caching options window onscreen.
- showROIs() - Method in class loci.plugins.in.ImporterOptions
-
- showROIsBox - Variable in class loci.plugins.in.MainDialog
-
- shuffle(int, int[]) - Static method in class loci.formats.in.FakeReader
-
Fisher-Yates shuffle with constant seeds to ensure reproducibility.
- shuffleAllTypesToFront(FileFilter[]) - Static method in class loci.formats.gui.GUITools
-
Looks for an "All supported file types" combo filter
and shuffles it to the front of the list.
- shutdown - Variable in class loci.formats.gui.DataConverter
-
- SHUTTER_SPEED_VALUE - Static variable in class loci.formats.tiff.IFD
-
- SIFReader - Class in loci.formats.in
-
SIFReader is the file format reader for Andor SIF files.
- SIFReader() - Constructor for class loci.formats.in.SIFReader
-
Constructs a new SIF reader.
- SIGNAL_OUTPUT - Static variable in class loci.formats.in.CellSensReader
-
- SIGNATURE_SIZE - Static variable in class loci.formats.in.VolocityReader
-
- signed - Variable in class loci.formats.codec.CodecOptions
-
Indicates whether or not the pixel data is signed.
- signed - Variable in class loci.formats.in.GatanReader
-
- SignedByteBuffer - Class in loci.formats.gui
-
DataBuffer that stores signed bytes.
- SignedByteBuffer(byte[], int) - Constructor for class loci.formats.gui.SignedByteBuffer
-
Construct a new buffer of signed bytes using the given byte array.
- SignedByteBuffer(byte[][], int) - Constructor for class loci.formats.gui.SignedByteBuffer
-
Construct a new buffer of signed bytes using the given 2D byte array.
- SignedColorModel - Class in loci.formats.gui
-
ColorModel that handles 8, 16 and 32 bits per channel signed data.
- SignedColorModel(int, int, int) - Constructor for class loci.formats.gui.SignedColorModel
-
- SignedShortBuffer - Class in loci.formats.gui
-
DataBuffer that stores signed shorts.
- SignedShortBuffer(int) - Constructor for class loci.formats.gui.SignedShortBuffer
-
- SignedShortBuffer(int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
-
- SignedShortBuffer(short[], int) - Constructor for class loci.formats.gui.SignedShortBuffer
-
- SignedShortBuffer(short[], int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
-
- SignedShortBuffer(short[][], int) - Constructor for class loci.formats.gui.SignedShortBuffer
-
- SignedShortBuffer(short[][], int, int[]) - Constructor for class loci.formats.gui.SignedShortBuffer
-
- SimplePCITiffReader - Class in loci.formats.in
-
SimplePCITiffReader is the file format reader for TIFF files produced by
SimplePCI software.
- SimplePCITiffReader() - Constructor for class loci.formats.in.SimplePCITiffReader
-
- SINGLE_TIFF_PATH_BUILDER - Static variable in class loci.formats.in.CellVoyagerReader
-
- singleTiffMode - Variable in class loci.formats.in.PrairieReader
-
Flag indicating that the reader is operating in a mode where grouping of
files is disallowed.
- SIS_INI_TAG - Static variable in class loci.formats.in.SISReader
-
- SIS_TAG - Static variable in class loci.formats.in.SISReader
-
- SIS_TAG_2 - Static variable in class loci.formats.in.SISReader
-
- SISReader - Class in loci.formats.in
-
SISReader is the file format reader for Olympus Soft Imaging Solutions
TIFF files.
- SISReader() - Constructor for class loci.formats.in.SISReader
-
- SITE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- site - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
-
- site - Variable in class loci.formats.in.ZeissTIFFReader.Plane
-
- size() - Method in class loci.formats.codec.ByteVector
-
- size - Variable in class loci.formats.in.AVIReader
-
- size - Variable in class loci.formats.in.FV1000Reader
-
- size - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
-
- size - Variable in class loci.formats.tiff.OnDemandLongArray
-
- size() - Method in class loci.formats.tiff.OnDemandLongArray
-
- size - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
-
- sizeC - Variable in class loci.formats.CoreMetadata
-
Number of channels.
- sizeC - Variable in class loci.formats.FileStitcher
-
Dimensional axis lengths per file.
- sizeC - Variable in class loci.formats.gui.ImageViewer
-
- sizeC - Variable in class loci.formats.in.FakeReader
-
- sizeC - Variable in class loci.formats.in.LeicaSCNReader.Pixels
-
- sizeCsub - Variable in class loci.formats.tools.MakeTestOmeTiff
-
- sizeR - Variable in class loci.formats.in.LeicaSCNReader.Pixels
-
- sizeT - Variable in class loci.formats.CoreMetadata
-
Number of timepoints.
- sizeT - Variable in class loci.formats.FileStitcher
-
Dimensional axis lengths per file.
- sizeT - Variable in class loci.formats.gui.ImageViewer
-
- sizeT - Variable in class loci.formats.in.FakeReader
-
- sizeTsub - Variable in class loci.formats.tools.MakeTestOmeTiff
-
- sizeX - Variable in class loci.formats.CoreMetadata
-
Width (in pixels) of images in this series.
- sizeX - Variable in class loci.formats.in.ColumbusReader.Plane
-
- sizeX - Variable in class loci.formats.in.FakeReader
-
- sizeX - Variable in class loci.formats.in.FEITiffReader
-
- sizeX - Variable in class loci.formats.in.LeicaSCNReader.Dimension
-
- sizeX - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
-
- sizeX - Variable in class loci.formats.in.LeicaSCNReader.Pixels
-
- sizeX - Variable in class loci.formats.in.MetamorphReader
-
- sizeX - Variable in class loci.formats.in.TextReader
-
Image width.
- sizeY - Variable in class loci.formats.CoreMetadata
-
Height (in pixels) of images in this series.
- sizeY - Variable in class loci.formats.in.ColumbusReader.Plane
-
- sizeY - Variable in class loci.formats.in.FakeReader
-
- sizeY - Variable in class loci.formats.in.FEITiffReader
-
- sizeY - Variable in class loci.formats.in.LeicaSCNReader.Dimension
-
- sizeY - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
-
- sizeY - Variable in class loci.formats.in.LeicaSCNReader.Pixels
-
- sizeY - Variable in class loci.formats.in.MetamorphReader
-
- sizeY - Variable in class loci.formats.in.TextReader
-
Image height.
- sizeZ - Variable in class loci.formats.CoreMetadata
-
Number of Z sections.
- sizeZ - Variable in class loci.formats.FileStitcher
-
Dimensional axis lengths per file.
- sizeZ - Variable in class loci.formats.gui.ImageViewer
-
- sizeZ - Variable in class loci.formats.in.FakeReader
-
- sizeZ - Variable in class loci.formats.in.LeicaSCNReader.Pixels
-
- sizeZ - Variable in class loci.formats.in.NDPIReader
-
- sizeZsub - Variable in class loci.formats.tools.MakeTestOmeTiff
-
- skip(InputStream, long) - Method in class loci.formats.in.LiFlimReader
-
- skipBits(long) - Method in class loci.formats.codec.BitBuffer
-
Deprecated.
Skips a number of bits in the BitBuffer.
- skipBlocks() - Method in class loci.formats.in.GIFReader
-
- skipComment() - Method in class loci.formats.tools.AmiraParameters
-
- skipData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
-
- skipLoad - Variable in class loci.formats.Memoizer
-
- skipPadding() - Method in class loci.formats.in.GatanReader
-
- skipPixelBlock(boolean) - Method in class loci.formats.in.OIRReader
-
- skipSave - Variable in class loci.formats.Memoizer
-
- skipTagBlock() - Method in class loci.formats.in.ImspectorReader
-
Skip an unknown tag.
- skipTags(int) - Method in class loci.formats.in.ImspectorReader
-
Skip a block of unknown string values.
- skipWhiteSpace() - Method in class loci.formats.in.AmiraReader.ASCII
-
- skipWhiteSpace() - Method in class loci.formats.tools.AmiraParameters
-
- SL - Static variable in class loci.formats.in.DicomReader
-
- SLD_MAGIC_BYTES_1_0 - Static variable in class loci.formats.in.SlidebookReader
-
- SLD_MAGIC_BYTES_1_1 - Static variable in class loci.formats.in.SlidebookReader
-
- SLD_MAGIC_BYTES_1_2 - Static variable in class loci.formats.in.SlidebookReader
-
- SLD_MAGIC_BYTES_2_0 - Static variable in class loci.formats.in.SlidebookReader
-
- SLD_MAGIC_BYTES_2_1 - Static variable in class loci.formats.in.SlidebookReader
-
- SLD_MAGIC_BYTES_3 - Static variable in class loci.formats.in.SlidebookReader
-
- sleep(long) - Method in class loci.plugins.prefs.OptionsDialog
-
Blocks the current thread for the specified number of milliseconds.
- Slice(int) - Constructor for class loci.formats.in.ZeissTIFFReader.Slice
-
- SLICE_SPACING - Static variable in class loci.formats.in.DicomReader
-
- sliceLabel - Variable in class loci.plugins.config.ConfigWindow
-
- Slicer - Class in loci.plugins
-
A plugin for splitting an image stack into separate
channels, focal planes and/or time points.
- Slicer() - Constructor for class loci.plugins.Slicer
-
- slices - Variable in class loci.formats.in.ZeissTIFFReader
-
- sliceSpace - Variable in class loci.formats.in.PerkinElmerReader
-
- sliceThickness - Variable in class loci.formats.in.MicromanagerReader.Position
-
- sliceThickness - Variable in class loci.formats.in.NiftiReader
-
- SLIDE_INFO - Static variable in class loci.formats.in.CellSensReader
-
- SLIDE_NAME - Static variable in class loci.formats.in.CellSensReader
-
- SLIDE_PREPARATION - Static variable in class loci.formats.in.CellSensReader
-
- SLIDE_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- SLIDE_SPECIMEN - Static variable in class loci.formats.in.CellSensReader
-
- SLIDE_STAINING - Static variable in class loci.formats.in.CellSensReader
-
- SLIDE_TISSUE - Static variable in class loci.formats.in.CellSensReader
-
- SLIDEBOOK_MAGIC_STRING - Static variable in class loci.formats.in.SlidebookTiffReader
-
- SlidebookReader - Class in loci.formats.in
-
SlidebookReader is the file format reader for 3I Slidebook files.
- SlidebookReader() - Constructor for class loci.formats.in.SlidebookReader
-
Constructs a new Slidebook reader.
- SlidebookTiffReader - Class in loci.formats.in
-
- SlidebookTiffReader() - Constructor for class loci.formats.in.SlidebookTiffReader
-
- sliderName - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- sliderPanel - Variable in class loci.formats.gui.ImageViewer
-
- SMC_MAGIC - Static variable in class loci.formats.in.SMCameraReader
-
- SMCameraReader - Class in loci.formats.in
-
SMCameraReader is the file format reader for SM camera files.
- SMCameraReader() - Constructor for class loci.formats.in.SMCameraReader
-
Constructs a new SM camera reader.
- smooth() - Method in class loci.plugins.util.RecordedImageProcessor
-
- snapshot() - Method in class loci.plugins.util.RecordedImageProcessor
-
- SOF0 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
-
- SOFTWARE - Static variable in class loci.formats.tiff.IFD
-
- sortFilters(FileFilter[]) - Static method in class loci.formats.gui.ComboFileFilter
-
Sorts the given list of file filters, and combines filters with identical
descriptions into a combination filter that accepts anything any of its
constituant filters do.
- sortFilters(Vector) - Static method in class loci.formats.gui.ComboFileFilter
-
Sorts the given list of file filters, and combines filters with identical
descriptions into a combination filter that accepts anything any of its
constituant filters do.
- sortFilters(FileFilter[]) - Static method in class loci.formats.gui.GUITools
-
Sorts the given list of file filters, keeping the "All supported
file types" combo filter (if any) at the front of the list.
- sortFilters(Vector) - Static method in class loci.formats.gui.GUITools
-
Sorts the given list of file filters, keeping the "All supported
file types" combo filter (if any) at the front of the list.
- SOS - Static variable in class loci.formats.services.JPEGTurboServiceImpl
-
- sos - Variable in class loci.formats.services.JPEGTurboServiceImpl
-
- source - Variable in class loci.formats.cache.Cache
-
Current cache source.
- source - Variable in class loci.formats.cache.CacheEvent
-
Source of the cache update.
- SOURCE_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating a new cache source.
- SOURCE_LENS - Static variable in class loci.formats.in.NDPIReader
-
- SOURCE_PARAMS - Static variable in class loci.formats.gui.CacheComponent
-
- SOURCE_VALUES - Static variable in class loci.formats.gui.CacheComponent
-
- sourceChooser - Variable in class loci.formats.gui.CacheComponent
-
Combo box for choosing cache source.
- sourceIndex(ICacheSource) - Method in class loci.formats.gui.CacheComponent
-
Converts cache source to source chooser index.
- SOURCES - Static variable in class loci.formats.gui.CacheComponent
-
- sourceValue(int) - Method in class loci.formats.gui.CacheComponent
-
Generates a new cache source matching the source chooser index.
- SPATIAL_FREQUENCY_RESPONSE - Static variable in class loci.formats.tiff.IFD
-
- spatialUnit - Variable in class loci.formats.in.NiftiReader
-
- spcId - Variable in class loci.formats.in.SPCReader
-
- SPCReader - Class in loci.formats.in
-
SPCReader is the file format reader for
Becker & Hickl SPC-Image SPC FIFO files.
- SPCReader() - Constructor for class loci.formats.in.SPCReader
-
Constructs a new SPC reader.
- specialPlateNames - Variable in class loci.formats.in.OpenlabReader
-
- specifyRangesBox - Variable in class loci.plugins.in.MainDialog
-
- SPECTRA - Static variable in class loci.formats.FormatTools
-
Identifies the Spectra dimensional type,
representing a dimension consisting of spectral channels.
- spectra - Variable in class loci.formats.in.IM3Reader
-
- SPECTRAL_SENSITIVITY - Static variable in class loci.formats.tiff.IFD
-
- spectralMode - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
SpectralMode of this <Sequence>.
- Spectrum(IRandomAccess, IM3Reader.ContainerRecord) - Constructor for class loci.formats.in.IM3Reader.Spectrum
-
Construct a spectrum by parsing a Spectrum record
- speed - Variable in class loci.formats.in.ND2Handler
-
- SpeHeader(byte[]) - Constructor for class loci.formats.in.SPEReader.SpeHeader
-
Constructor for SpeHeader
- SpeHeaderEntry(int, SPEReader.SpeHeaderType) - Constructor for enum loci.formats.in.SPEReader.SpeHeaderEntry
-
Constructor for SpeHeaderEntry
- SpeHeaderType() - Constructor for enum loci.formats.in.SPEReader.SpeHeaderType
-
- SPEReader - Class in loci.formats.in
-
SPEReader is the file format reader for Princeton Instruments SPE .spe files.
- SPEReader() - Constructor for class loci.formats.in.SPEReader
-
Constructs a new SPE reader.
- SPEReader.SpeHeader - Class in loci.formats.in
-
SpeHeader holds a byte array containing the SPE binary data header along
with associated methods for reading SPE Header Entry values in various formats
- SPEReader.SpeHeaderEntry - Enum in loci.formats.in
-
SpeHeaderEntry is an Enum which provides a list of all available SPE header entries along
with the offset value from the top of the header in bytes and their associated data type
- SPEReader.SpeHeaderType - Enum in loci.formats.in
-
SpeHeaderType is an Enum representing the available data types stored in the SPE header
- SPEReader.SpeROI - Class in loci.formats.in
-
Private class to represent the data for a single ROI in the SPE format
- SpeROI(int, int, int, int, int, int) - Constructor for class loci.formats.in.SPEReader.SpeROI
-
Constructor for SpeROI objects
- SpiderReader - Class in loci.formats.in
-
SpiderReader is the file format reader for SPIDER files.
- SpiderReader() - Constructor for class loci.formats.in.SpiderReader
-
Constructs a new SPIDER reader.
- SPIN_DISK_CONFOCAL - Static variable in class loci.formats.in.LegacyND2Reader
-
- split - Variable in class loci.formats.codec.NikonCodecOptions
-
- split - Variable in class loci.formats.in.NativeND2Reader
-
- split - Variable in class loci.formats.in.NikonReader
-
- SPLIT_LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
-
- SPLIT_LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
-
- splitCBox - Variable in class loci.plugins.in.MainDialog
-
- splitChannels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Splits the given multi-channel image into single-channel images.
- splitChannels(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools
-
Splits the given multi-channel array into a 2D array.
- splitChannels(byte[], byte[], int, int, int, boolean, boolean, int) - Static method in class loci.formats.ImageTools
-
Splits the given multi-channel array into a 2D array.
- splitDims(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
-
- splitDoubles(String) - Method in class loci.formats.in.ICSReader
-
Splits the given string into a list of
Doubles.
- splitPlanes - Variable in class loci.formats.in.ZeissLSMReader
-
- splitTBox - Variable in class loci.plugins.in.MainDialog
-
- splitZBox - Variable in class loci.plugins.in.MainDialog
-
- SPM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the scanning probe microscopy domain.
- SpringUtilities - Class in loci.plugins.config
-
A 1.4 file that provides utility methods for
creating form- or grid-style layouts with SpringLayout.
- SpringUtilities() - Constructor for class loci.plugins.config.SpringUtilities
-
- SPURIOUS_NOISE_REMOVAL - Static variable in class loci.formats.in.CellSensReader
-
- SQ - Static variable in class loci.formats.in.DicomReader
-
- sqr() - Method in class loci.plugins.util.RecordedImageProcessor
-
- sqrt() - Method in class loci.plugins.util.RecordedImageProcessor
-
- SQUARE_ROOT - Static variable in class loci.formats.in.GelReader
-
- squareRoot - Variable in class loci.formats.in.IvisionReader
-
- srcBuf - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
-
- srcHeight - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
-
- srcPitch - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
-
- srcPixelFormat - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
-
- srcWidth - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
-
- SS - Static variable in class loci.formats.in.DicomReader
-
- ST - Static variable in class loci.formats.in.DicomReader
-
- STABLE - Static variable in class loci.plugins.Updater
-
- STABLE_BUILD - Static variable in class loci.formats.UpgradeChecker
-
Location of the JAR artifacts for the stable releases.
- STABLE_VERSION - Static variable in class loci.formats.UpgradeChecker
-
Version number of the latest stable release.
- Stack() - Constructor for class loci.formats.in.OBFReader.Stack
-
- Stack() - Constructor for class loci.formats.in.VolocityReader.Stack
-
- STACK_DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
-
- STACK_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
-
- STACK_NAME - Static variable in class loci.formats.in.CellSensReader
-
- STACK_TYPE - Static variable in class loci.formats.in.CellSensReader
-
- stackFormatChoice - Variable in class loci.plugins.in.MainDialog
-
- stackOrderChoice - Variable in class loci.plugins.in.MainDialog
-
- stacks - Variable in class loci.formats.in.OBFReader
-
- stacks - Variable in class loci.formats.in.VolocityReader
-
- stageLabel - Variable in class loci.formats.in.MetamorphHandler
-
- stageLabels - Variable in class loci.formats.in.MetamorphReader
-
- stageNames - Variable in class loci.formats.in.MetamorphReader
-
- stageX - Variable in class loci.formats.in.BaseZeissReader
-
- stageX - Variable in class loci.formats.in.FEITiffReader
-
- stageX - Variable in class loci.formats.in.MetamorphReader
-
- stageX - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- stageXCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
X stage coordinates.
- stageY - Variable in class loci.formats.in.BaseZeissReader
-
- stageY - Variable in class loci.formats.in.FEITiffReader
-
- stageY - Variable in class loci.formats.in.MetamorphReader
-
- stageY - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- stageYCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Y stage coordinates.
- stageZ - Variable in class loci.formats.in.FEITiffReader
-
- stageZ - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- stageZCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Z stage coordinates.
- stamps - Variable in class loci.formats.in.FluoviewReader
-
Timestamps for each plane, in seconds.
- stampValues - Variable in class loci.formats.in.LiFlimReader
-
- start - Variable in class loci.formats.in.EPSReader
-
Starting line of pixel data.
- start - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
-
- start - Variable in class loci.formats.Modulo
-
- start - Variable in class loci.formats.tiff.OnDemandLongArray
-
- START_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
-
- START_TIME - Static variable in class loci.formats.in.ZeissLSMReader
-
- startCoordinate - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.AFIReader.AFIHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadReader.BioRadHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.FEITiffReader.FEIHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.FlexHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.MeaHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.ResHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ImaconReader.ImaconHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.InCellHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.MinimalInCellHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.IvisionReader.IvisionHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.MetamorphHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.MicromanagerReader.MicromanagerHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.OperettaReader.OperettaHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ScanrReader.ScanrHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ZeissTIFFHandler
-
- startElement(String, String, String, Attributes) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
-
- startIndex - Variable in class loci.formats.FilePattern
-
Indices into the pattern indicating the start of a numerical block.
- startingPosition - Variable in class loci.formats.in.ZeissCZIReader.Segment
-
- startTime - Variable in class loci.formats.in.PerkinElmerReader
-
- startTime - Variable in class loci.formats.in.ZeissLSMReader.Recording
-
- startTime - Variable in class loci.plugins.in.ImagePlusReader
-
- startTiming() - Method in class loci.plugins.in.ImagePlusReader
-
- startX - Variable in class loci.formats.in.SPEReader.SpeROI
-
- startY - Variable in class loci.formats.in.SPEReader.SpeROI
-
- state - Variable in class loci.formats.services.WlzServiceImpl
-
- stateChanged(ChangeEvent) - Method in class loci.formats.gui.CacheComponent
-
Handles range spinner changes.
- stateChanged(ChangeEvent) - Method in class loci.formats.gui.DataConverter
-
- stateChanged(ChangeEvent) - Method in class loci.formats.gui.ImageViewer
-
Handles slider events.
- stateChanged(ChangeEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
-
- status - Variable in class loci.formats.in.BioRadReader.Note
-
- status - Variable in class loci.formats.in.SDTInfo
-
Last SPC_test_state return value (status).
- status(boolean, String) - Static method in class loci.plugins.BF
-
- status - Variable in class loci.plugins.config.ConfigWindow
-
- status - Variable in class loci.plugins.config.LibraryEntry
-
- STATUS_CANCELED - Static variable in class loci.plugins.prefs.OptionsDialog
-
- STATUS_FINISHED - Static variable in class loci.plugins.prefs.OptionsDialog
-
- STATUS_OK - Static variable in class loci.plugins.prefs.OptionsDialog
-
- statusUpdated(StatusEvent) - Method in class loci.plugins.in.DisplayHandler
-
Reports status updates via ImageJ's status bar mechanism.
- statusUpdated(StatusEvent) - Method in class loci.plugins.in.ImporterPrompter
-
- step - Variable in class loci.formats.FilePatternBlock
-
- step - Variable in class loci.formats.Modulo
-
- step - Variable in class loci.plugins.in.ImportProcess
-
Current step in the import preparation process.
- step(ImportStep) - Method in class loci.plugins.in.ImportProcess
-
- step - Variable in enum loci.plugins.in.ImportStep
-
- STEP_TABLE - Static variable in enum loci.plugins.in.ImportStep
-
- steps - Variable in class loci.formats.in.SDTInfo
-
- stepSize - Variable in class loci.formats.in.MetamorphReader
-
- stitchTilesBox - Variable in class loci.plugins.in.MainDialog
-
- STK_SUFFIX - Static variable in class loci.formats.in.MetamorphReader
-
- stkReaders - Variable in class loci.formats.in.MetamorphReader
-
- stks - Variable in class loci.formats.in.MetamorphReader
-
List of STK files in the dataset.
- stop - Variable in class loci.plugins.in.ThumbLoader
-
- stop() - Method in class loci.plugins.in.ThumbLoader
-
Instructs the thumbnail loader to stop loading thumbnails.
- stopt - Variable in class loci.formats.in.SDTInfo
-
- stopTime - Variable in class loci.formats.in.SDTInfo
-
Time from start to - disarm (simple measurement)
- or to the end of the cycle (for complex measurement).
- stopWatch() - Method in class loci.formats.Memoizer
-
- storageMethod - Variable in class loci.formats.in.MRWReader
-
- store - Variable in class loci.formats.FileStitcher
-
- store - Variable in class loci.formats.in.CellH5Reader
-
- store - Variable in class loci.formats.in.FlexReader.FlexHandler
-
- store - Variable in class loci.formats.in.InCellReader.InCellHandler
-
- store - Variable in class loci.formats.in.LeicaHandler
-
- store - Variable in class loci.formats.in.ZeissCZIReader
-
- storedChannel - Variable in class loci.formats.in.SDTReader
-
- storedChannel - Variable in class loci.formats.in.SPCReader
-
- storedRGB - Variable in class loci.formats.in.ICSReader
-
- storedSeries - Variable in class loci.formats.in.SDTReader
-
- storedSize - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
-
- storedT - Variable in class loci.formats.in.SPCReader
-
- storeKeyValue(Hashtable, String, String) - Method in class loci.formats.in.LeicaHandler
-
- storeLine(Line, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Line ROI into the specified metadata store.
- storeOval(OvalRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Oval ROI into the specified metadata store.
- storePoint(PointRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Point ROI into the specified metadata store.
- storePolygon(PolygonRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Polygon ROI into the specified metadata store.
- storeRectangle(Roi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Rectangle ROI into the specified metadata store.
- storeROI(MetadataStore, int, int) - Method in class loci.formats.in.LeicaHandler.ROI
-
- storeROI(MetadataStore, int, int, int) - Method in class loci.formats.in.LIFReader.ROI
-
- storeROIs(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Store basic dimensions in model
- storeSeriesHashtable(int, Hashtable) - Method in class loci.formats.in.LeicaHandler
-
- storeText(TextRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the text ROI into the metadata stored.
- STRATEGIES - Static variable in class loci.formats.gui.CacheComponent
-
- strategy - Variable in class loci.formats.cache.Cache
-
Current cache strategy.
- STRATEGY_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating a new cache strategy.
- STRATEGY_PARAMS - Static variable in class loci.formats.gui.CacheComponent
-
- STRATEGY_VALUES - Static variable in class loci.formats.gui.CacheComponent
-
- strategyChooser - Variable in class loci.formats.gui.CacheComponent
-
Combo box for choosing cache strategy.
- strategyIndex(ICacheStrategy) - Method in class loci.formats.gui.CacheComponent
-
Converts cache strategy to strategy chooser index.
- strategyValue(int) - Method in class loci.formats.gui.CacheComponent
-
Generates a new cache strategy matching the strategy chooser index.
- stream - Variable in class loci.formats.in.ZeissCZIReader.Segment
-
- stream - Variable in class loci.formats.services.POIServiceImpl
-
- stream - Variable in class loci.formats.tiff.OnDemandLongArray
-
- streamNames - Variable in class loci.formats.tools.AmiraParameters
-
- streams - Variable in class loci.formats.tools.AmiraParameters
-
- streamTypes - Variable in class loci.formats.tools.AmiraParameters
-
- strikeout - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- StringIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.StringIM3Record
-
- StringOption - Class in loci.plugins.prefs
-
A string option for one of the plugins.
- StringOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.StringOption
-
Constructs a string option with the parameters from the given map.
- StringOption(String, boolean, String, String, String, Vector<String>) - Constructor for class loci.plugins.prefs.StringOption
-
Constructs a string option with the given parameters.
- stringTable - Variable in class loci.formats.in.VolocityReader
-
- STRIP_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
-
- STRIP_OFFSETS - Static variable in class loci.formats.tiff.IFD
-
- stripHeader() - Method in class loci.formats.in.NativeQTReader
-
Cut off header bytes from a resource fork file.
- strips - Variable in class loci.formats.in.PictReader
-
Vector of byte arrays representing individual rows.
- strokeColor - Variable in class loci.formats.in.GatanReader.ROIShape
-
- STRUCTURE_LABELS_1 - Static variable in class loci.formats.in.BioRadReader
-
Structure labels.
- STRUCTURE_LABELS_2 - Static variable in class loci.formats.in.BioRadReader
-
- STRUCTURE_LABELS_3 - Static variable in class loci.formats.in.BioRadReader
-
- STRUCTURE_LABELS_4 - Static variable in class loci.formats.in.BioRadReader
-
- STRUCTURE_LABELS_5 - Static variable in class loci.formats.in.BioRadReader
-
- STRUCTURE_LABELS_6 - Static variable in class loci.formats.in.BioRadReader
-
- STUB_FIELD - Static variable in class loci.formats.services.LuraWaveServiceImpl
-
Identifying field in stub class.
- SUB - Static variable in class loci.formats.in.APNGReader
-
- SUB_IFD - Static variable in class loci.formats.tiff.IFD
-
- SUB_SEC_TIME - Static variable in class loci.formats.tiff.IFD
-
- SUB_SEC_TIME_DIGITIZED - Static variable in class loci.formats.tiff.IFD
-
- SUB_SEC_TIME_ORIGINAL - Static variable in class loci.formats.tiff.IFD
-
- SubBlock() - Constructor for class loci.formats.in.ZeissCZIReader.SubBlock
-
- SubBlock(ZeissCZIReader.SubBlock) - Constructor for class loci.formats.in.ZeissCZIReader.SubBlock
-
- SubBlock() - Constructor for class loci.formats.in.ZeissLSMReader.SubBlock
-
- SUBBLOCK_BEAM_SPLITTER - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBBLOCK_DATA_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBBLOCK_DETECTION_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBBLOCK_END - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBBLOCK_ILLUMINATION_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBBLOCK_LASER - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBBLOCK_MARKER - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBBLOCK_RECORDING - Static variable in class loci.formats.in.ZeissLSMReader
-
Subblock types.
- SUBBLOCK_TIMER - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBBLOCK_TRACK - Static variable in class loci.formats.in.ZeissLSMReader
-
- SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
-
- SUBJECT_DISTANCE - Static variable in class loci.formats.tiff.IFD
-
- SUBJECT_DISTANCE_RANGE - Static variable in class loci.formats.tiff.IFD
-
- SUBJECT_LOCATION - Static variable in class loci.formats.tiff.IFD
-
- subResolutionIFDs - Variable in class loci.formats.in.MinimalTiffReader
-
List of sub-resolution IFDs for each IFD in the current TIFF with the
same order as ifds.
- subsamp - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
-
- substringsBetween(String, String, String) - Static method in class loci.plugins.in.ImagePlusReader
-
- subTag - Variable in class loci.formats.in.OpenlabReader
-
- success - Variable in class loci.plugins.LociImporter
-
Flag indicating whether last operation was successful.
- suffix - Variable in class loci.formats.in.GIFReader
-
- SUFFIX - Static variable in class loci.formats.in.TCSReader
-
- suffixes - Variable in class loci.formats.FormatHandler
-
Valid suffixes for this file format.
- SUFFIXES - Static variable in class loci.formats.gui.LegacyQTTools
-
- suffixes - Variable in class loci.formats.ImageReader
-
Valid suffixes for this file format.
- suffixes - Variable in class loci.formats.ImageWriter
-
Valid suffixes for all file format writers.
- SUFFIXES - Static variable in class loci.formats.in.FlexReader
-
- suffixes - Variable in class loci.plugins.config.FormatEntry
-
- suffixNecessary - Variable in class loci.formats.FormatReader
-
Whether the file extension matching one of the reader's suffixes
is necessary to identify the file as an instance of this format.
- suffixSufficient - Variable in class loci.formats.FormatReader
-
Whether the file extension matching one of the reader's suffixes
is sufficient to identify the file as an instance of this format.
- surfaceWind - Variable in class loci.formats.in.HRDGDFReader
-
- SVSReader - Class in loci.formats.in
-
SVSReader is the file format reader for Aperio SVS TIFF files.
- SVSReader() - Constructor for class loci.formats.in.SVSReader
-
Constructs a new SVS reader.
- swap - Variable in class loci.formats.gui.DataConverter
-
- SwapDialog - Class in loci.plugins.in
-
Bio-Formats Importer dimension swapper dialog box.
- SwapDialog(ImportProcess) - Constructor for class loci.plugins.in.SwapDialog
-
Creates a dimension swapper dialog for the Bio-Formats Importer.
- swapDimensions(String) - Method in class loci.formats.DimensionSwapper
-
Sets the input dimension order according to the given string (e.g.,
"XYZCT").
- swapDimsBox - Variable in class loci.plugins.in.MainDialog
-
- SwappableMetadata - Class in loci.formats
-
Extends
CoreMetadata to include the notion of an "input order" for planes:
the input order being the order planes are stored on disk.
- SwappableMetadata() - Constructor for class loci.formats.SwappableMetadata
-
- SwappableMetadata(IFormatReader, int) - Constructor for class loci.formats.SwappableMetadata
-
- SwappableMetadata(SwappableMetadata) - Constructor for class loci.formats.SwappableMetadata
-
- swapPixelArrays() - Method in class loci.plugins.util.RecordedImageProcessor
-
- SWATCH_SIZE - Static variable in class loci.plugins.in.ColorDialog
-
- SWEPT_FIELD_CONFOCAL - Static variable in class loci.formats.in.LegacyND2Reader
-
- syncPlane() - Method in class loci.plugins.util.DataBrowser
-
Updates the ImagePlus's displayed plane to match the slider values.
- syncSliders() - Method in class loci.plugins.util.DataBrowser
-
Updates the slider values to match the ImagePlus's displayed plane.
- synFD - Variable in class loci.formats.in.SDTInfo
-
- synHF - Variable in class loci.formats.in.SDTInfo
-
- syntaxError(String) - Method in class loci.formats.tools.AmiraParameters
-
- synTH - Variable in class loci.formats.in.SDTInfo
-
- synZC - Variable in class loci.formats.in.SDTInfo
-