A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ 

A

a - Variable in class jj2000.j2k.entropy.decoder.MQDecoder
The current interval
a - Variable in class jj2000.j2k.entropy.encoder.MQCoder
The current interval
a00 - Variable in class ome.xml.model.AffineTransform
 
a01 - Variable in class ome.xml.model.AffineTransform
 
a02 - Variable in class ome.xml.model.AffineTransform
 
a10 - Variable in class ome.xml.model.AffineTransform
 
a11 - Variable in class ome.xml.model.AffineTransform
 
a12 - Variable in class ome.xml.model.AffineTransform
 
A4_PAPERSIZE - Static variable in class loci.poi.hssf.usermodel.HSSFPrintSetup
 
A5_PAPERSIZE - Static variable in class loci.poi.hssf.usermodel.HSSFPrintSetup
 
abort() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
Abort(String) - Method in class loci.poi.hssf.model.FormulaParser
Report Error and Halt
abortable - Variable in class loci.poi.hssf.eventmodel.EventRecordFactory
instance is abortable or not
abortable - Variable in class loci.poi.hssf.eventmodel.ListenerWrapper
 
AbortableHSSFListener - Class in loci.poi.hssf.eventusermodel
Interface for use with the HSSFRequest and HSSFEventFactory.
AbortableHSSFListener() - Constructor for class loci.poi.hssf.eventusermodel.AbortableHSSFListener
 
abortableProcessEvents(HSSFRequest, InputStream) - Method in class loci.poi.hssf.eventusermodel.HSSFEventFactory
Processes a DocumentInputStream into essentially Record events.
abortableProcessRecord(Record) - Method in class loci.poi.hssf.eventusermodel.AbortableHSSFListener
Process an HSSF Record.
abortableProcessWorkbookEvents(HSSFRequest, POIFSFileSystem) - Method in class loci.poi.hssf.eventusermodel.HSSFEventFactory
Processes a file into essentially record events.
About - Class in loci.plugins
Displays a small information dialog about the Bio-Formats Plugins package.
About() - Constructor for class loci.plugins.About
 
about() - Static method in class loci.plugins.About
 
abs() - Method in class loci.plugins.util.RecordedImageProcessor
 
absoluteDay(Calendar) - Static method in class loci.poi.hssf.usermodel.HSSFDateUtil
Given a Calendar, return the number of days since 1900/12/31.
absoluteTime - Variable in class loci.formats.in.PrairieMetadata.Frame
absoluteTime attribute of this <Frame>.
AbstractEscherHolderRecord - Class in loci.poi.hssf.record
The escher container record is used to hold escher records.
AbstractEscherHolderRecord() - Constructor for class loci.poi.hssf.record.AbstractEscherHolderRecord
 
AbstractEscherHolderRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.AbstractEscherHolderRecord
Constructs a Bar record and sets its fields appropriately.
AbstractFunctionPtg - Class in loci.poi.hssf.record.formula
This class provides the base functionality for Excel sheet functions There are two kinds of function Ptgs - tFunc and tFuncVar Therefore, this class will have ONLY two subclasses
AbstractFunctionPtg() - Constructor for class loci.poi.hssf.record.formula.AbstractFunctionPtg
 
AbstractNIOHandle - Class in loci.common
A wrapper for buffered NIO logic that implements the IRandomAccess interface.
AbstractNIOHandle() - Constructor for class loci.common.AbstractNIOHandle
 
AbstractOMEModelObject - Class in ome.xml.model
 
AbstractOMEModelObject() - Constructor for class ome.xml.model.AbstractOMEModelObject
 
AbstractOMEXMLMetadata - Class in loci.formats.ome
 
AbstractOMEXMLMetadata() - Constructor for class loci.formats.ome.AbstractOMEXMLMetadata
 
AbstractOMEXMLMetadata - Class in ome.xml.meta
A utility class for constructing and manipulating OME-XML DOMs.
AbstractOMEXMLMetadata() - Constructor for class ome.xml.meta.AbstractOMEXMLMetadata
Creates a new OME-XML metadata object.
AbstractService - Class in loci.common.services
 
AbstractService() - Constructor for class loci.common.services.AbstractService
 
AbstractShape - Class in loci.poi.hssf.model
An abstract shape is the lowlevel model for a shape.
AbstractShape() - Constructor for class loci.poi.hssf.model.AbstractShape
 
ac - Variable in class loci.formats.in.FakeReader
Channel of last opened image plane.
accept(File) - Method in class loci.formats.gui.ComboFileFilter
Accepts files with the proper filename prefix.
accept(File) - Method in class loci.formats.gui.ExtensionFileFilter
Accepts files with the proper extensions.
accept(File) - Method in class loci.formats.gui.FormatFileFilter
Accepts files in accordance with the file format reader.
accept(File) - Method in class loci.formats.gui.NoExtensionFileFilter
Accepts files with no extension.
accept(String) - Method in class loci.formats.NumberFilter
Tests if a specified file should be included in a file list.
accept(File) - Method in class loci.formats.NumberFilter
Tests if a specified file should be included in a file list.
ACCESS_TIME - Static variable in class loci.tests.testng.Configuration
 
accumulate - Variable in class loci.formats.in.SDTInfo
 
ACCUMULATION - Static variable in class loci.formats.in.CellSensReader
 
ACCUMULATION_MODE - Static variable in class loci.formats.in.CellSensReader
 
acquire - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
 
acquiredDate - Variable in class loci.formats.in.LIFReader
 
acquiredDate - Variable in class loci.formats.in.ZeissCZIReader
 
acquiredDate - Variable in class loci.formats.in.ZeissLSMReader
 
ACQUISITION_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
 
ACQUISITION_FILE - Static variable in class loci.formats.in.ScanrReader
 
ACQUISITION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
ACQUISITION_TIME_TAG - Static variable in class loci.formats.in.FlowSightReader
 
acquisitionDate - Variable in class loci.formats.in.BioRadSCNReader
 
acquisitionDate - Variable in class loci.formats.in.SISReader
 
acquisitionDate - Variable in class ome.xml.model.Image
 
acquisitionDates - Variable in class loci.formats.in.FlexReader
 
acquisitionMode - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
acquisitionMode - Variable in class ome.xml.model.Channel
 
AcquisitionMode - Enum in ome.xml.model.enums
 
AcquisitionMode(String) - Constructor for enum ome.xml.model.enums.AcquisitionMode
 
AcquisitionModeEnumHandler - Class in ome.xml.model.enums.handlers
Enumeration handler for AcquisitionMode.
AcquisitionModeEnumHandler() - Constructor for class ome.xml.model.enums.handlers.AcquisitionModeEnumHandler
 
acquisitions - Variable in class loci.formats.in.ZeissCZIReader
 
acquisitionTime - Variable in class loci.formats.in.CellSensReader.Pyramid
 
act - Variable in class loci.formats.in.GIFReader
Active color table.
actionPerformed(ActionEvent) - Method in class loci.formats.gui.CacheComponent
Handles combo box changes.
actionPerformed(ActionEvent) - Method in class loci.formats.gui.DataConverter
 
actionPerformed(ActionEvent) - Method in class loci.formats.gui.ImageViewer
Handles menu commands.
actionPerformed(ActionEvent) - Method in class loci.formats.tools.EditTiffG
 
actionPerformed(ActionEvent) - Method in class loci.plugins.config.ConfigWindow
 
actionPerformed(ActionEvent) - Method in class loci.plugins.in.SeriesDialog
 
actionPerformed(ActionEvent) - Method in class loci.plugins.shortcut.ShortcutPanel
Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.plugins.util.DataBrowser
 
actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow
 
actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
 
active - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
active - Variable in class loci.formats.in.LeicaHandler.Detector
 
active - Variable in class loci.formats.in.LeicaReader.Detector
 
ACTIVE_CHANNEL - Static variable in class loci.formats.in.CellSensReader
 
ACTIVE_LAYER_INDEX_VECTOR - Static variable in class loci.formats.in.CellSensReader
 
ACTIVE_LAYER_VECTOR - Static variable in class loci.formats.in.CellSensReader
 
ACTIVE_PANE_LOWER_LEFT - Static variable in class loci.poi.hssf.record.PaneRecord
 
ACTIVE_PANE_LOWER_RIGHT - Static variable in class loci.poi.hssf.record.PaneRecord
 
ACTIVE_PANE_UPER_LEFT - Static variable in class loci.poi.hssf.record.PaneRecord
 
ACTIVE_PANE_UPPER_RIGHT - Static variable in class loci.poi.hssf.record.PaneRecord
 
ACTIVE_STACK_DIMENSION - Static variable in class loci.formats.in.CellSensReader
 
activeChannelIndices - Variable in class loci.formats.in.LeicaReader
 
activeChannels - Variable in class loci.formats.in.PrairieMetadata
Set of active channel indices.
activeDetector - Variable in class loci.formats.in.LIFReader
 
activePane - Variable in class loci.poi.hssf.util.PaneInformation
 
activePlane - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
activeSrcHeight - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
The height of the source region that will actually be copied into the destination image, taking into account all susbampling, offsetting, and clipping.
activeSrcMinX - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
The X coordinate of the upper-left source pixel that will actually be copied into the destination image, taking into account all subsampling, offsetting, and clipping.
activeSrcMinY - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
The Y coordinate of the upper-left source pixel that will actually be copied into the destination image, taking into account all subsampling, offsetting, and clipping.
activeSrcWidth - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
The width of the source region that will actually be copied into the destination image, taking into account all susbampling, offsetting, and clipping.
ACTUAL_TEMPERATURE - Static variable in class loci.formats.in.FluoviewReader
 
actualBytes - Variable in class jj2000.j2k.entropy.encoder.EBCOTLayer
The actual number of bytes which are consumed by the the current and any previous layers.
adcDE - Variable in class loci.formats.in.SDTInfo
ADC sample delay (SPC-930).
adcRE - Variable in class loci.formats.in.SDTInfo
 
adcResShift - Variable in class loci.formats.in.SPCReader
 
adcZoom - Variable in class loci.formats.in.SDTInfo
 
add(byte) - Method in class loci.formats.codec.ByteVector
 
add(byte[]) - Method in class loci.formats.codec.ByteVector
 
add(byte[], int, int) - Method in class loci.formats.codec.ByteVector
 
add(byte[], int, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder.TileCache
 
add(int[], int, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder.TileCache
 
add(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
add(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
Add() - Method in class loci.poi.hssf.model.FormulaParser
Recognize and Translate an Add
add(int, Record) - Method in class loci.poi.hssf.model.WorkbookRecordList
 
ADD - Static variable in class loci.poi.hssf.record.formula.AddPtg
 
ADD - Static variable in class loci.poi.hssf.record.formula.UnaryPlusPtg
 
add(int, double) - Method in class loci.poi.util.DoubleList
add the specfied value at the specified index
add(double) - Method in class loci.poi.util.DoubleList
Appends the specified element to the end of this list
add(int, int) - Method in class loci.poi.util.IntList
add the specfied value at the specified index
add(int) - Method in class loci.poi.util.IntList
Appends the specified element to the end of this list
add(Object) - Method in class loci.poi.util.IntMapper
Appends the specified element to the end of this list
add(int, short) - Method in class loci.poi.util.ShortList
add the specfied value at the specified index
add(short) - Method in class loci.poi.util.ShortList
Appends the specified element to the end of this list
add(Integer) - Method in class ome.units.unit.Unit
Increase the scaling offset in this unit by a scalar.
add(Double) - Method in class ome.units.unit.Unit
Increase the scaling offset in this unit by a scalar.
add(T) - Method in class ome.xml.model.ReferenceList
 
add(int, T) - Method in class ome.xml.model.ReferenceList
 
add1DBits(byte[], int, int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Get code for run and add to compressed bitstream.
add2DBits(byte[], int, int[][], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Place entry from mode table into compressed bitstream.
addAll(DoubleList) - Method in class loci.poi.util.DoubleList
Appends all of the elements in the specified collection to the end of this list, in the order that they are returned by the specified collection's iterator.
addAll(int, DoubleList) - Method in class loci.poi.util.DoubleList
Inserts all of the elements in the specified collection into this list at the specified position.
addAll(IntList) - Method in class loci.poi.util.IntList
Appends all of the elements in the specified collection to the end of this list, in the order that they are returned by the specified collection's iterator.
addAll(int, IntList) - Method in class loci.poi.util.IntList
Inserts all of the elements in the specified collection into this list at the specified position.
addAll(ShortList) - Method in class loci.poi.util.ShortList
Appends all of the elements in the specified collection to the end of this list, in the order that they are returned by the specified collection's iterator.
addAll(int, ShortList) - Method in class loci.poi.util.ShortList
Inserts all of the elements in the specified collection into this list at the specified position.
addAll(Collection<? extends T>) - Method in class ome.xml.model.ReferenceList
 
addAll(int, Collection<? extends T>) - Method in class ome.xml.model.ReferenceList
 
addAllowedTagSet(TIFFTagSet) - Method in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam
Adds a TIFFTagSet object to the list of allowed tag sets.
addArea(int, short, int, short) - Method in class loci.poi.hssf.record.MergeCellsRecord
Add an area to consider a merged cell.
addArgumentPointer() - Method in class loci.poi.hssf.model.FormulaParser
Adds a pointer to the last token to the latest function argument list.
addBinData(BinData) - Method in class ome.xml.model.Pixels
 
addBooleanAnnotation(BooleanAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addBreak(short, short, short) - Method in class loci.poi.hssf.record.PageBreakRecord
Adds the page break at the specified parameters
addBSERecord(EscherBSERecord) - Method in class loci.poi.hssf.model.Workbook
 
addByteArray(byte[], int, int) - Method in class jj2000.j2k.entropy.decoder.ByteInputBuffer
Adds the specified data to the end of the byte array stream.
addCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
 
addCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter
Adds a listener for status update events.
addCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
 
addCell(HSSFCell) - Method in class loci.poi.hssf.usermodel.HSSFRow
used internally to add a cell.
addCellOffset(short) - Method in class loci.poi.hssf.record.DBCellRecord
 
addChannel(Channel) - Method in class ome.xml.model.Pixels
 
addChar(char, int) - Method in class loci.poi.hssf.usermodel.FontDetails
 
addChars(char[], int[]) - Method in class loci.poi.hssf.usermodel.FontDetails
 
AddCharString(short, byte) - Method in class com.sun.media.imageioimpl.common.LZWStringTable
 
addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
Adds a checkbox to the given dialog object corresponding to the boolean option identified by the specified key.
addChild(Property) - Method in class loci.poi.poifs.property.DirectoryProperty
Add a new child to the collection of children
addChild(Property) - Method in interface loci.poi.poifs.property.Parent
Add a new child to the collection of children
addChildNode(IIOMetadataNode, String, Object) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
addChildNode(IIOMetadataNode, String, Object) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadata
 
addChildRecord(EscherRecord) - Method in class loci.poi.ddf.EscherContainerRecord
 
addChildRecord(EscherRecord) - Method in class loci.poi.ddf.UnknownEscherRecord
 
addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
Adds a choice to the given dialog object corresponding to the string option identified by the specified key.
addClass(int, Class<? extends T>) - Method in class loci.formats.ClassList
Adds the given class, which must be assignable to the base class, to the list.
addClass(Class<? extends T>) - Method in class loci.formats.ClassList
Adds the given class, which must be assignable to the base class, to the list.
addCluster(int, int) - Method in class loci.poi.ddf.EscherDggRecord
 
addColor(byte, byte, byte) - Method in class loci.poi.hssf.usermodel.HSSFPalette
Adds a new color into an empty color slot.
addColumn(Object) - Method in class mdbtools.dbengine.sql.Select
 
addComment(String) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
addCommentAnnotation(CommentAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addDataset(Dataset) - Method in class ome.xml.model.OME
 
addDbcell(int) - Method in class loci.poi.hssf.record.IndexRecord
 
addDetector(Detector) - Method in class ome.xml.model.Instrument
 
addDichroic(Dichroic) - Method in class ome.xml.model.Instrument
 
addDirectory(String, int) - Method in class loci.formats.in.L2DReader
Recursively add all of the files in the given directory to the used file list.
addDirectory(DirectoryProperty) - Method in class loci.poi.poifs.filesystem.POIFSFileSystem
add a new DirectoryProperty
addDocument(POIFSDocument) - Method in class loci.poi.poifs.filesystem.POIFSFileSystem
add a new POIFSDocument
addDoubleAnnotation(DoubleAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addElements() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
Adds the elements into this format object based on the XML schema and DTD.
addElements() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat
Adds the elements into this format object based on the XML schema and DTD.
addEntry(Comparable<Object>, DefaultListModel) - Static method in class loci.plugins.config.ConfigWindow
 
addEOFB(byte[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Add an End-of-Facsimile-Block (EOFB == 0x001001) to the compressed bitstream.
addEOL(boolean, boolean, boolean, byte[], int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Add an End-of-Line (EOL == 0x001) to the compressed bitstream with optional byte alignment.
addEscherProperty(EscherProperty) - Method in class loci.poi.ddf.EscherOptRecord
Add a property to this record.
addEscherRecord(int, EscherRecord) - Method in class loci.poi.hssf.record.AbstractEscherHolderRecord
 
addEscherRecord(EscherRecord) - Method in class loci.poi.hssf.record.AbstractEscherHolderRecord
 
addExperiment(Experiment) - Method in class ome.xml.model.OME
 
addExperimenter(Experimenter) - Method in class ome.xml.model.OME
 
addExperimenterGroup(ExperimenterGroup) - Method in class ome.xml.model.OME
 
addFileAnnotation(FileAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addFileToList(String, boolean) - Method in class loci.formats.in.DicomReader
Determine if the given file belongs in the same dataset as this file.
addFilter(Filter) - Method in class ome.xml.model.Instrument
 
addFilterSet(FilterSet) - Method in class ome.xml.model.Instrument
 
addFolder(Folder) - Method in class ome.xml.model.OME
 
addFormatRun(UnicodeString.FormatRun) - Method in class loci.poi.hssf.record.UnicodeString
Adds a font run to the formatted string.
addGlobalMeta(String, Object) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, boolean) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, byte) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, short) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, int) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, long) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, float) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, double) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, char) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMetaList(String, Object) - Method in class loci.formats.FormatReader
Add the given key/value pair to the global metadata hashtable.
addGroupBy(FQColumn) - Method in class mdbtools.dbengine.sql.Select
 
addImage(Image) - Method in class ome.xml.model.OME
 
addInfo(int, String) - Method in class loci.formats.in.DicomReader
 
addInfo(int, int) - Method in class loci.formats.in.DicomReader
 
addInfoRecord(ExtSSTInfoSubRecord) - Method in class loci.poi.hssf.record.ExtSSTRecord
 
addInstrument(Instrument) - Method in class ome.xml.model.OME
 
additionalMakeup - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
addLightSource(LightSource) - Method in class ome.xml.model.Instrument
 
addLightSourceSettings(LightSourceSettings) - Method in class ome.xml.model.MicrobeamManipulation
 
addListAnnotation(ListAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addListener(HSSFListener, short) - Method in class loci.poi.hssf.eventusermodel.HSSFRequest
add an event listener for a particular record type.
addListenerForAllRecords(HSSFListener) - Method in class loci.poi.hssf.eventusermodel.HSSFRequest
This is the equivilent of calling addListener(myListener, sid) for EVERY record in the loci.poi.hssf.record package.
addLongAnnotation(LongAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addMapAnnotation(MapAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addMergedRegion(int, short, int, short) - Method in class loci.poi.hssf.model.Sheet
 
addMergedRegion(Region) - Method in class loci.poi.hssf.usermodel.HSSFSheet
adds a merged region of cells (hence those cells form one)
addMeta(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
Adds an entry to the specified Hashtable.
addMetadataOnly(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in interface loci.formats.services.OMEXMLService
Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
 
addMetaList(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
Add the given key/value pair to the given hashtable.
addMicrobeamManipulation(MicrobeamManipulation) - Method in class ome.xml.model.Experiment
 
addModelObject(String, OMEModelObject) - Method in interface ome.xml.model.OMEModel
 
addModelObject(String, OMEModelObject) - Method in class ome.xml.model.OMEModelImpl
 
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in interface loci.formats.services.OMEXMLService
Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
addName(NameRecord) - Method in class loci.poi.hssf.model.Workbook
creates new name
addNode(Box) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
addNTP(int, int) - Method in class jj2000.j2k.codestream.reader.CBlkInfo
Adds the number of new truncation for specified layer.
addObjective(Objective) - Method in class ome.xml.model.Instrument
 
addOption(String, String) - Method in class loci.formats.ClassList
Add a key/value pair to the list of options.
addOptPoint(float, int) - Method in class jj2000.j2k.entropy.encoder.LayersInfo
Adds a new optimization point, with target bitrate 'brate' and with 'elyrs' (unoptimized) extra layers after it.
addOrderBy(OrderBy) - Method in class mdbtools.dbengine.sql.Select
 
addPicture(byte[], int) - Method in class loci.poi.hssf.usermodel.HSSFWorkbook
Adds a picture to the workbook.
addPlane(Plane) - Method in class ome.xml.model.Pixels
 
addPlate(Plate) - Method in class ome.xml.model.OME
 
addPlateAcquisition(PlateAcquisition) - Method in class ome.xml.model.Plate
 
addPossible(String) - Method in class loci.plugins.prefs.StringOption
Adds a possible value to the list.
addProject(Project) - Method in class ome.xml.model.OME
 
addProp(HashMap<String, String>, String, String, HashMap<String, String>) - Method in class loci.plugins.config.ConfigWindow
 
addProp(int, EscherPropertyMetaData) - Static method in class loci.poi.ddf.EscherProperties
 
addProperty(Property) - Method in class loci.poi.poifs.property.PropertyTable
Add a property to the list of properties we manage
AddPtg - Class in loci.poi.hssf.record.formula
Addition operator PTG the "+" binomial operator.
AddPtg() - Constructor for class loci.poi.hssf.record.formula.AddPtg
Creates new AddPtg
AddPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AddPtg
 
addPtyFiles() - Method in class loci.formats.in.FV1000Reader
 
addReagent(Reagent) - Method in class ome.xml.model.Screen
 
addReference(OMEModelObject, Reference) - Method in interface ome.xml.model.OMEModel
 
addReference(OMEModelObject, Reference) - Method in class ome.xml.model.OMEModelImpl
 
addREFRecord(ExternSheetSubRecord) - Method in class loci.poi.hssf.record.ExternSheetRecord
adds REF struct (ExternSheetSubRecord)
addRenderingHints(Map) - Method in class loci.poi.hssf.usermodel.DummyGraphics2d
 
addRenderingHints(Map) - Method in class loci.poi.hssf.usermodel.EscherGraphics2d
 
addROI(ROI) - Method in class ome.xml.model.OME
 
addRow(RowRecord) - Method in class loci.poi.hssf.model.Sheet
Adds a row record to the sheet
addRow(HSSFRow, boolean) - Method in class loci.poi.hssf.usermodel.HSSFSheet
add a row to the sheet
addRow(Object[]) - Method in class mdbtools.dbengine.MemoryData
Add a row of data
addScreen(Screen) - Method in class ome.xml.model.OME
 
addScrollBars(Container) - Static method in class loci.plugins.util.WindowTools
Adds AWT scroll bars to the given container.
addSection(Section) - Method in class loci.poi.hpsf.MutablePropertySet
Adds a section to this property set.
addSection(Section) - Method in class loci.poi.hpsf.SpecialPropertySet
 
addSeriesMeta(String, Object) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, boolean) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, byte) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, short) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, int) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, long) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, float) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, double) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, char) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMetaList(String, Object) - Method in class loci.formats.FormatReader
Add the given key/value pair to the current series metadata hashtable.
addShape(Shape) - Method in class ome.xml.model.Union
 
addSheetIndexToExternSheet(short) - Method in class loci.poi.hssf.model.Workbook
 
addSheetReference(String, int) - Method in class loci.poi.hssf.util.SheetReferences
 
addShortOrLongField(int, int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadata
 
addSSTString(UnicodeString) - Method in class loci.poi.hssf.model.Workbook
Adds a string to the SST table and returns its index (if its a duplicate just returns its index and update the counts) ASSUMES compressed unicode (meaning 8bit)
addSSTString(String) - Method in class loci.poi.hssf.usermodel.HSSFWorkbook
Deprecated.
Do not call this method from your applications. Use the methods available in the HSSFRow to add string HSSFCells
addStandardOptions(HSSFShape, EscherOptRecord) - Method in class loci.poi.hssf.model.AbstractShape
Add standard properties to the opt record.
addStandardOptions(HSSFShape, EscherOptRecord) - Method in class loci.poi.hssf.model.CommentShape
Sets standard escher options for a comment.
addStatusListener(StatusListener) - Method in interface loci.common.StatusReporter
 
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
 
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
 
addString(UnicodeString) - Method in class loci.poi.hssf.record.SSTRecord
Add a string.
addStringToTable(byte[], byte) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
Add a new string to the string table.
addStringToTable(byte[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
Add a new string to the string table.
addStringToTable(byte[], byte) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
Add a new string to the string table.
addStringToTable(byte[]) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
Add a new string to the string table.
addSubRecord(int, Object) - Method in class loci.poi.hssf.record.ObjRecord
 
addSubRecord(Object) - Method in class loci.poi.hssf.record.ObjRecord
 
addTable(Object) - Method in class mdbtools.dbengine.sql.Select
 
addTagAnnotation(TagAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addTagSet(TIFFTagSet) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory
Adds an element to the group of TIFFTagSets of which this directory is aware.
addTermAnnotation(TermAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addTiffData(TiffData) - Method in class ome.xml.model.Pixels
 
addTIFFField(TIFFField) - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory
Adds a TIFF field to the directory.
addTimestampAnnotation(TimestampAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addToAll(int[], int) - Method in class loci.poi.hssf.usermodel.EscherGraphics
 
addToHashtable() - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
addToSSTIfRequired() - Method in class loci.poi.hssf.usermodel.HSSFRichTextString
 
addToStringTable(IntMapper, UnicodeString) - Static method in class loci.poi.hssf.record.SSTDeserializer
 
addUsedFile(String, String) - Method in class loci.formats.in.PerkinElmerReader
Add the given file to the used files list.
addUserCommentMeta(Element, int) - Method in class loci.formats.in.LIFReader
 
addValueName(int, String) - Method in class com.sun.media.imageio.plugins.tiff.TIFFTag
Adds a mnemonic name for a particular value that this tag's data may take on.
addValueRecord(int, CellValueRecordInterface) - Method in class loci.poi.hssf.model.Sheet
Adds a value record to the sheet's contained binary records (i.e.
addWell(Well) - Method in class ome.xml.model.Plate
 
addWellSample(WellSample) - Method in class ome.xml.model.Well
 
addXMLAnnotation(XMLAnnotation) - Method in class ome.xml.model.StructuredAnnotations
 
addXYZPoints(IIOMetadataNode, String, double, double, double) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
adjust - Variable in class loci.formats.in.SlidebookReader
 
adjustBitDepths - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
adjustEndianness - Variable in class loci.formats.in.GatanReader
 
adjustForWhiteBalance(short, int) - Method in class loci.formats.in.DNGReader
 
adjustForWhiteBalance(short, int) - Method in class loci.formats.in.NikonReader
 
adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser
 
adjustWellDimensions() - Method in class loci.formats.in.ScanrReader
 
advanceBlock() - Method in class loci.formats.in.APNGReader.PNGInputStream
 
AE - Static variable in class loci.formats.in.DicomReader
 
AffineTransform - Class in ome.xml.model
 
AffineTransform() - Constructor for class ome.xml.model.AffineTransform
Default constructor.
AffineTransform(Element, OMEModel) - Constructor for class ome.xml.model.AffineTransform
Constructs AffineTransform recursively from an XML DOM tree.
AffineTransform(AffineTransform) - Constructor for class ome.xml.model.AffineTransform
Copy constructor.
AFIReader - Class in loci.formats.in
AFIReader is the file format reader for Aperio AFI files.
AFIReader() - Constructor for class loci.formats.in.AFIReader
Constructs a new AFI reader.
AFIReader.AFIHandler - Class in loci.formats.in
 
AFIReader.AFIHandler() - Constructor for class loci.formats.in.AFIReader.AFIHandler
 
afterRecordSerialize(int, short, int, EscherRecord) - Method in interface loci.poi.ddf.EscherSerializationListener
Fired after a record has been serialized.
afterRecordSerialize(int, short, int, EscherRecord) - Method in class loci.poi.ddf.NullEscherSerializationListener
 
ag - Variable in class loci.formats.FileStitcher.ExternalSeries
 
Aggregate - Interface in mdbtools.dbengine.functions
 
aggregateDrawingRecords(DrawingManager2) - Method in class loci.poi.hssf.model.Sheet
 
AggregateMetadata - Class in ome.xml.meta
A metadata store which delegates the actual storage to one or more sub metadata stores.
AggregateMetadata(List<BaseMetadata>) - Constructor for class ome.xml.meta.AggregateMetadata
Creates a new instance.
aggregateQuery(Data) - Method in class mdbtools.dbengine.SelectEngine
execute an aggregate query
AggregateQuery - Class in mdbtools.dbengine.tasks
resolve the columns, num rows not the same
AggregateQuery(Task, Select, int[]) - Constructor for class mdbtools.dbengine.tasks.AggregateQuery
 
AHZ - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.ATTOHERTZ instead.
AIMReader - Class in loci.formats.in
AIMReader is the file format reader for .aim files.
AIMReader() - Constructor for class loci.formats.in.AIMReader
Constructs a new AIM reader.
airPressure - Variable in class loci.formats.in.ZeissCZIReader
 
airPressure - Variable in class ome.xml.model.ImagingEnvironment
 
AISF - Static variable in class loci.formats.in.VolocityClippingReader
 
AL3D_MAGIC_STRING - Static variable in class loci.formats.in.AliconaReader
 
AliconaReader - Class in loci.formats.in
AliconaReader is the file format reader for Alicona AL3D files.
AliconaReader() - Constructor for class loci.formats.in.AliconaReader
Constructs a new Alicona reader.
ALIGN_CENTER - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
center horizontal alignment
ALIGN_CENTER_SELECTION - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
center-selection? horizontal alignment
ALIGN_FILL - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
fill? horizontal alignment
ALIGN_GENERAL - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
general (normal) horizontal alignment
ALIGN_JUSTIFY - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
justified horizontal alignment
ALIGN_LEFT - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
left-justified horizontal alignment
ALIGN_RIGHT - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
right-justified horizontal alignment
ALIGNMENT - Static variable in class loci.formats.in.ZeissCZIReader
 
alignROI - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
By specifying this parameter, the ROI mask will be limited to covering only entire code-blocks.
aLine - Variable in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
all_data - Variable in class loci.poi.hssf.record.FormulaRecord
 
ALL_DOMAINS - Static variable in class loci.formats.FormatTools
List of all supported domains.
ALL_TYPES - Static variable in class loci.formats.gui.GUITools
String to use for "all types" combination filter.
allBlockLengths - Variable in class loci.formats.in.SDTInfo
 
allBlockOffsets - Variable in class loci.formats.in.SDTInfo
 
allFiles - Variable in class loci.formats.in.BrukerReader
 
allFiles - Variable in class loci.formats.in.PerkinElmerReader
List of all files to open
allFiles - Variable in class loci.formats.in.SPCReader
List of all files to open
allocate(int...) - Static method in class loci.common.DataTools
Allocates a 1-dimensional byte array matching the product of the given sizes.
allocate(long, int) - Method in class loci.common.NIOByteBufferProvider
Allocates or maps the desired file data into memory.
allocateDirect(long, int) - Method in class loci.common.NIOByteBufferProvider
Allocates memory and copies the desired file data into it.
allocatedSize - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
allocateMappedByteBuffer(long, int) - Method in class loci.common.NIOByteBufferProvider
Memory maps the desired file data into memory.
allocateRate() - Method in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Allocates output bit-rate for each tile in parsing mode: The allocator simulates the truncation of a virtual layer-resolution progressive codestream.
allocateShapeId(short) - Method in class loci.poi.hssf.model.DrawingManager
Allocates new shape id for the new drawing group id.
allocateShapeId(short) - Method in class loci.poi.hssf.model.DrawingManager2
Allocates new shape id for the new drawing group id.
allocateSpace(int) - Method in class loci.poi.poifs.storage.BlockAllocationTableWriter
Allocate space for a block of indices
allowedTagsByName - Variable in class com.sun.media.imageio.plugins.tiff.TIFFTagSet
 
allowedTagsByNumber - Variable in class com.sun.media.imageio.plugins.tiff.TIFFTagSet
 
allowedTagSets - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageReadParam
 
allowOpen - Variable in class loci.formats.gui.FormatFileFilter
Whether it is ok to open a file to determine its type.
allowOpen - Variable in class loci.formats.ImageReader
 
allowShow - Variable in class loci.plugins.util.DataBrowser
 
ALPHA - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
The value of the first lifting step coefficient
ALPHA - Static variable in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
The value of the first lifting step coefficient
ALPHABET_LENGTH - Static variable in class loci.formats.ResourceNamer
 
alphabeticIndexCount(String) - Static method in class loci.formats.ResourceNamer
 
alphaChannel - Variable in enum ome.jxr.ifd.PixelFormat
Deprecated.
 
alphaImagePlaneFlag - Variable in class ome.jxr.parser.DatastreamParser
Deprecated.
 
alphaMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
alphaMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
ALPHANUM - Static variable in class loci.tests.IOTester
 
alphaShort - Variable in class loci.formats.gui.Index16ColorModel
Lookup tables.
alreadyChecked() - Method in class loci.formats.UpgradeChecker
Return true if an upgrade check has already been performed in this JVM session.
ALT_BARS - Static variable in class loci.poi.hssf.record.ExtendedFormatRecord
 
ALT_BARS - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
Wide dots
alt_pg_buf - Variable in class mdbtools.libmdb.MdbHandle
 
ALT_ZVI - Static variable in class loci.common.DateTools
 
ALT_ZVI_EPOCH - Static variable in class loci.common.DateTools
 
altCodec - Variable in class loci.formats.in.NativeQTReader
Some movies use two video codecs -- this is the second codec.
ALTERNATE_MD5 - Static variable in class loci.tests.testng.Configuration
 
alternateCenter - Variable in class loci.formats.in.LeicaHandler
 
alternateCenter - Variable in class loci.formats.in.LIFReader
 
alternateexpression - Static variable in class loci.poi.hssf.record.WSBoolRecord
 
alternateformula - Static variable in class loci.poi.hssf.record.WSBoolRecord
 
ALTITUDE_REF_SEA_LEVEL - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSAltitudeRef" tag.
ALTITUDE_REF_SEA_LEVEL_REFERENCE - Static variable in class com.sun.media.imageio.plugins.tiff.EXIFGPSTagSet
A value to be used with the "GPSAltitudeRef" tag.
altPlanes - Variable in class loci.formats.in.NativeQTReader
Number of frames that use the alternate codec.
alwaysCalc - Variable in class loci.poi.hssf.record.FormulaRecord
 
AM - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.ATTOMETRE instead.
AmiraParameters - Class in loci.formats.tools
AmiraParameters handles parsing and writing of AmiraMesh headers.
AmiraParameters(String) - Constructor for class loci.formats.tools.AmiraParameters
 
AmiraParameters(RandomAccessInputStream) - Constructor for class loci.formats.tools.AmiraParameters
 
AmiraReader - Class in loci.formats.in
This is a file format reader for AmiraMesh data.
AmiraReader() - Constructor for class loci.formats.in.AmiraReader
 
AmiraReader.ASCII - Class in loci.formats.in
This class provides a not-quite-efficient, but simple reader for planes stored in ASCII-encoded numbers.
AmiraReader.ASCII(int, int) - Constructor for class loci.formats.in.AmiraReader.ASCII
 
AmiraReader.HxRLE - Class in loci.formats.in
This is the reader for RLE-compressed AmiraMeshes.
AmiraReader.HxRLE(int, long) - Constructor for class loci.formats.in.AmiraReader.HxRLE
 
AmiraReader.HxZip - Class in loci.formats.in
This is the reader for GZip-compressed AmiraMeshes.
AmiraReader.HxZip(long) - Constructor for class loci.formats.in.AmiraReader.HxZip
 
AmiraReader.PlaneReader - Interface in loci.formats.in
This is the common interface for all formats, compressed or not.
amplificationGain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
amplificationGain - Variable in class ome.xml.model.Detector
 
analysisFiles - Variable in class loci.formats.in.MIASReader
 
analyze_hpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter
Filters the input signal by this analysis filter, decomposing it in a low-pass and a high-pass signal.
analyze_hpf(float[], int, int, int, float[], int, int, float[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat
A specific version of the analyze_hpf() method that works on int data.
analyze_hpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat
The general version of the analyze_hpf() method, it just calls the specialized version.
analyze_hpf(float[], int, int, int, float[], int, int, float[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
An implementation of the analyze_hpf() method that works on int data, for the forward 9x7 wavelet transform using the lifting scheme.
analyze_hpf(int[], int, int, int, int[], int, int, int[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt
A specific version of the analyze_hpf() method that works on int data.
analyze_hpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt
The general version of the analyze_hpf() method, it just calls the specialized version.
analyze_hpf(int[], int, int, int, int[], int, int, int[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
An implementation of the analyze_hpf() method that works on int data, for the forward 5x3 wavelet transform using the lifting scheme.
analyze_lpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilter
Filters the input signal by this analysis filter, decomposing it in a low-pass and a high-pass signal.
analyze_lpf(float[], int, int, int, float[], int, int, float[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat
A specific version of the analyze_lpf() method that works on int data.
analyze_lpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloat
The general version of the analyze_lpf() method, it just calls the specialized version.
analyze_lpf(float[], int, int, int, float[], int, int, float[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
An implementation of the analyze_lpf() method that works on int data, for the forward 9x7 wavelet transform using the lifting scheme.
analyze_lpf(int[], int, int, int, int[], int, int, int[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt
A specific version of the analyze_lpf() method that works on int data.
analyze_lpf(Object, int, int, int, Object, int, int, Object, int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterInt
The general version of the analyze_lpf() method, it just calls the specialized version.
analyze_lpf(int[], int, int, int, int[], int, int, int[], int, int) - Method in class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
An implementation of the analyze_lpf() method that works on int data, for the forward 5x3 wavelet transform using the lifting scheme.
AnalyzeReader - Class in loci.formats.in
AnalyzeReader is the file format reader for Analyze 7.5 files.
AnalyzeReader() - Constructor for class loci.formats.in.AnalyzeReader
Constructs a new Analyze reader.
anbytes - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent
Actual number of read bytes
anchor - Variable in class loci.poi.hssf.usermodel.HSSFShape
 
ANCHOR_ID_CHART_TITLE - Static variable in class loci.poi.hssf.record.ObjectLinkRecord
 
ANCHOR_ID_SERIES_OR_POINT - Static variable in class loci.poi.hssf.record.ObjectLinkRecord
 
ANCHOR_ID_X_AXIS - Static variable in class loci.poi.hssf.record.ObjectLinkRecord
 
ANCHOR_ID_Y_AXIS - Static variable in class loci.poi.hssf.record.ObjectLinkRecord
 
ANCHOR_ID_Z_AXIS - Static variable in class loci.poi.hssf.record.ObjectLinkRecord
 
anchorType - Variable in class loci.poi.hssf.usermodel.HSSFClientAnchor
 
and(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
AND - Static variable in class mdbtools.dbengine.sql.Condition
 
ANDOR_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
 
ANDOR_SHIFT_SPEED - Static variable in class loci.formats.in.CellSensReader
 
andTable - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
andTable - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
anGainExp - Variable in class jj2000.j2k.wavelet.Subband
The base 2 exponent of the analysis gain of the subband.
ANGLE - Static variable in class loci.formats.in.ZeissLSMReader
 
angle - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
Angle - Class in ome.units.quantity
Angle quantity.
Angle(Number, Unit<Angle>) - Constructor for class ome.units.quantity.Angle
Create an Angle.
angles - Variable in class loci.formats.in.ZeissCZIReader
 
ANGSTROM - Static variable in class ome.units.UNITS
 
anim - Variable in class loci.formats.gui.ImageViewer
 
anim - Variable in class loci.plugins.util.DataBrowser
 
animate - Variable in class loci.plugins.util.DataBrowser
 
ANIMATION_KEY - Static variable in class loci.formats.gui.ImageViewer
 
ANN_BOOLEAN_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_COMMENT_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_DOUBLE_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_LONG_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_TAG_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_TERM_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_TIME_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_XML_VALUE_END - Static variable in class loci.formats.in.FakeReader
 
ANN_XML_VALUE_START - Static variable in class loci.formats.in.FakeReader
 
annBool - Variable in class loci.formats.in.FakeReader
 
annComment - Variable in class loci.formats.in.FakeReader
 
annDouble - Variable in class loci.formats.in.FakeReader
 
annLong - Variable in class loci.formats.in.FakeReader
 
annMap - Variable in class loci.formats.in.FakeReader
 
Annotation - Class in ome.xml.model
 
Annotation() - Constructor for class ome.xml.model.Annotation
Default constructor.
Annotation(Element, OMEModel) - Constructor for class ome.xml.model.Annotation
Constructs Annotation recursively from an XML DOM tree.
Annotation(Annotation) - Constructor for class ome.xml.model.Annotation
Copy constructor.
ANNOTATION_NAMESPACE - Static variable in class loci.formats.in.FakeReader
 
ANNOTATION_PREFIX - Static variable in class loci.formats.in.FakeReader
 
annotationBoolCount - Variable in class loci.formats.in.FakeReader
 
annotationCommentCount - Variable in class loci.formats.in.FakeReader
 
annotationCount - Variable in class loci.formats.in.FakeReader
 
annotationDoubleCount - Variable in class loci.formats.in.FakeReader
 
annotationLinks - Variable in class ome.xml.model.Annotation
 
annotationLinks - Variable in class ome.xml.model.Channel
 
annotationLinks - Variable in class ome.xml.model.Dataset
 
annotationLinks - Variable in class ome.xml.model.Detector
 
annotationLinks - Variable in class ome.xml.model.Dichroic
 
annotationLinks - Variable in class ome.xml.model.Experimenter
 
annotationLinks - Variable in class ome.xml.model.ExperimenterGroup
 
annotationLinks - Variable in class ome.xml.model.Filter
 
annotationLinks - Variable in class ome.xml.model.Folder
 
annotationLinks - Variable in class ome.xml.model.Image
 
annotationLinks - Variable in class ome.xml.model.Instrument
 
annotationLinks - Variable in class ome.xml.model.LightPath
 
annotationLinks - Variable in class ome.xml.model.LightSource
 
annotationLinks - Variable in class ome.xml.model.Objective
 
annotationLinks - Variable in class ome.xml.model.Plane
 
annotationLinks - Variable in class ome.xml.model.Plate
 
annotationLinks - Variable in class ome.xml.model.PlateAcquisition
 
annotationLinks - Variable in class ome.xml.model.Project
 
annotationLinks - Variable in class ome.xml.model.Reagent
 
annotationLinks - Variable in class ome.xml.model.ROI
 
annotationLinks - Variable in class ome.xml.model.Screen
 
annotationLinks - Variable in class ome.xml.model.Shape
 
annotationLinks - Variable in class ome.xml.model.Well
 
annotationLongCount - Variable in class loci.formats.in.FakeReader
 
annotationMapCount - Variable in class loci.formats.in.FakeReader
 
AnnotationRef - Class in ome.xml.model
 
AnnotationRef() - Constructor for class ome.xml.model.AnnotationRef
Default constructor.
AnnotationRef(Element, OMEModel) - Constructor for class ome.xml.model.AnnotationRef
Constructs AnnotationRef recursively from an XML DOM tree.
AnnotationRef(AnnotationRef) - Constructor for class ome.xml.model.AnnotationRef
Copy constructor.
ANNOTATIONS - Static variable in class ome.specification.XMLMockObjects
The supported types of annotations.
annotationTagCount - Variable in class loci.formats.in.FakeReader
 
annotationTermCount - Variable in class loci.formats.in.FakeReader
 
annotationTimeCount - Variable in class loci.formats.in.FakeReader
 
annotationXmlCount - Variable in class loci.formats.in.FakeReader
 
annotator - Variable in class ome.xml.model.Annotation
 
annTag - Variable in class loci.formats.in.FakeReader
 
annTerm - Variable in class loci.formats.in.FakeReader
 
annTime - Variable in class loci.formats.in.FakeReader
 
annXml - Variable in class loci.formats.in.FakeReader
 
ANO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
ANSI_CHARSET - Static variable in class loci.poi.hssf.usermodel.HSSFFont
ANSI character set
AnWTFilter - Class in jj2000.j2k.wavelet.analysis
This abstract class defines the methods of all analysis wavelet filters.
AnWTFilter() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilter
 
AnWTFilterFloat - Class in jj2000.j2k.wavelet.analysis
This extends the analysis wavelet filter general definitions of AnWTFilter by adding methods that work for float data specifically.
AnWTFilterFloat() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterFloat
 
AnWTFilterFloatLift9x7 - Class in jj2000.j2k.wavelet.analysis
This class inherits from the analysis wavelet filter definition for int data.
AnWTFilterFloatLift9x7() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
 
AnWTFilterInt - Class in jj2000.j2k.wavelet.analysis
This extends the analysis wavelet filter general definitions of AnWTFilter by adding methods that work for int data specifically.
AnWTFilterInt() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterInt
 
AnWTFilterIntLift5x3 - Class in jj2000.j2k.wavelet.analysis
This class inherits from the analysis wavelet filter definition for int data.
AnWTFilterIntLift5x3() - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterIntLift5x3
 
AnWTFilterSpec - Class in jj2000.j2k.wavelet.analysis
This class extends ModuleSpec class for analysis filters specification holding purpose.
AnWTFilterSpec(int, int, byte, QuantTypeSpec, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.wavelet.analysis.AnWTFilterSpec
Constructs a new 'AnWTFilterSpec' for the specified number of components and tiles.
APA - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.ATTOPASCAL instead.
APERIO_IMAGE_DESCRIPTION_PREFIX - Static variable in class loci.formats.in.SVSReader
TIFF image description prefix for Aperio SVS files.
APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
 
APLReader - Class in loci.formats.in
APLReader is the file format reader for Olympus APL files.
APLReader() - Constructor for class loci.formats.in.APLReader
Constructs a new APL reader.
APNGReader - Class in loci.formats.in
APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.
APNGReader() - Constructor for class loci.formats.in.APNGReader
Constructs a new APNGReader.
APNGReader.PNGBlock - Class in loci.formats.in
 
APNGReader.PNGBlock() - Constructor for class loci.formats.in.APNGReader.PNGBlock
 
APNGReader.PNGInputStream - Class in loci.formats.in
InputStream implementation that stitches together IDAT blocks into a seamless zlib stream.
APNGReader.PNGInputStream(String) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
 
APNGReader.PNGInputStream(String, int) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
 
APNGWriter - Class in loci.formats.out
APNGWriter is the file format writer for PNG and APNG files.
APNGWriter() - Constructor for class loci.formats.out.APNGWriter
 
append(ClassList<T>) - Method in class loci.formats.ClassList
Appends a class list which must be assignable to the base class
append(List<Class<? extends T>>) - Method in class loci.formats.ClassList
Appends a list of classes which must be assignable to the base class
append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer
 
appendChild(Node) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
appendedCompressionType - Variable in class com.sun.media.imageio.plugins.tiff.TIFFImageWriteParam
 
appendServerMap(String, String) - Static method in class loci.formats.in.FlexReader
Add the path 'realName' to the mapping for the server named 'alias'.
applicationData - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
applicationIDs - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator
Applies spatial calibrations to an image stack.
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer
 
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
 
applyDisplayRanges(ImagePlus, int) - Method in class loci.plugins.in.Colorizer
 
applyFont(int, int, short) - Method in class loci.poi.hssf.usermodel.HSSFRichTextString
Applies a font to the specified characters of a string.
applyFont(int, int, HSSFFont) - Method in class loci.poi.hssf.usermodel.HSSFRichTextString
Applies a font to the specified characters of a string.
applyFont(HSSFFont) - Method in class loci.poi.hssf.usermodel.HSSFRichTextString
Sets the font of the entire string.
applyFont(short) - Method in class loci.poi.hssf.usermodel.HSSFRichTextString
Applies the specified font to the entire string.
applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor
 
applystyles - Static variable in class loci.poi.hssf.record.WSBoolRecord
 
applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
approximation - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ColorSpecificationBox
 
arabic - Variable in class loci.poi.hssf.record.WindowTwoRecord
 
arate - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent
Actual decoding rate in bpp
ArbROIMaskGenerator - Class in jj2000.j2k.roi.encoder
This class generates the ROI bit-mask when, at least, one ROI is not rectangular.
ArbROIMaskGenerator(ROI[], int, Quantizer) - Constructor for class jj2000.j2k.roi.encoder.ArbROIMaskGenerator
The constructor of the arbitrary mask generator
arbShape - Variable in class jj2000.j2k.roi.encoder.ROI
Where or not the ROI shape is arbitrary
Arc - Class in ome.xml.model
 
Arc() - Constructor for class ome.xml.model.Arc
Default constructor.
Arc(Element, OMEModel) - Constructor for class ome.xml.model.Arc
Constructs Arc recursively from an XML DOM tree.
Arc(Arc) - Constructor for class ome.xml.model.Arc
Copy constructor.
ARC_TYPE - Static variable in class ome.specification.XMLMockObjects
The default type of an arc.
ARCHIVE - Static variable in class loci.formats.in.FlexReader
 
ArcType - Enum in ome.xml.model.enums
 
ArcType(String) - Constructor for enum ome.xml.model.enums.ArcType
 
ArcTypeEnumHandler - Class in ome.xml.model.enums.handlers
Enumeration handler for ArcType.
ArcTypeEnumHandler() - Constructor for class ome.xml.model.enums.handlers.ArcTypeEnumHandler
 
Area3DPtg - Class in loci.poi.hssf.record.formula
Title: Area 3D Ptg - 3D referecnce (Sheet + Area)
Area3DPtg() - Constructor for class loci.poi.hssf.record.formula.Area3DPtg
Creates new AreaPtg
Area3DPtg(String, short) - Constructor for class loci.poi.hssf.record.formula.Area3DPtg
 
Area3DPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.Area3DPtg
 
AreaAPtg - Class in loci.poi.hssf.record.formula
Specifies a rectangular area of cells A1:A4 for instance.
AreaAPtg() - Constructor for class loci.poi.hssf.record.formula.AreaAPtg
 
AreaAPtg(short, short, short, short, boolean, boolean, boolean, boolean) - Constructor for class loci.poi.hssf.record.formula.AreaAPtg
 
AreaAPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AreaAPtg
 
AreaErrPtg - Class in loci.poi.hssf.record.formula
AreaErr - handles deleted cell area references.
AreaErrPtg() - Constructor for class loci.poi.hssf.record.formula.AreaErrPtg
 
AreaErrPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AreaErrPtg
 
AreaFormatRecord - Class in loci.poi.hssf.record
The area format record is used to define the colours and patterns for an area.
AreaFormatRecord() - Constructor for class loci.poi.hssf.record.AreaFormatRecord
 
AreaFormatRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.AreaFormatRecord
Constructs a AreaFormat record and sets its fields appropriately.
AreaNAPtg - Class in loci.poi.hssf.record.formula
Specifies a rectangular area of cells A1:A4 for instance.
AreaNAPtg() - Constructor for class loci.poi.hssf.record.formula.AreaNAPtg
 
AreaNAPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AreaNAPtg
 
AreaNPtg - Class in loci.poi.hssf.record.formula
Specifies a rectangular area of cells A1:A4 for instance.
AreaNPtg() - Constructor for class loci.poi.hssf.record.formula.AreaNPtg
 
AreaNPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AreaNPtg
 
AreaNVPtg - Class in loci.poi.hssf.record.formula
Specifies a rectangular area of cells A1:A4 for instance.
AreaNVPtg() - Constructor for class loci.poi.hssf.record.formula.AreaNVPtg
 
AreaNVPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AreaNVPtg
 
AreaPtg - Class in loci.poi.hssf.record.formula
Specifies a rectangular area of cells A1:A4 for instance.
AreaPtg() - Constructor for class loci.poi.hssf.record.formula.AreaPtg
 
AreaPtg(String) - Constructor for class loci.poi.hssf.record.formula.AreaPtg
 
AreaPtg(short, short, short, short, boolean, boolean, boolean, boolean) - Constructor for class loci.poi.hssf.record.formula.AreaPtg
 
AreaPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AreaPtg
 
AreaRecord - Class in loci.poi.hssf.record
The area record is used to define a area chart.
AreaRecord() - Constructor for class loci.poi.hssf.record.AreaRecord
 
AreaRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.AreaRecord
Constructs a Area record and sets its fields appropriately.
AreaReference - Class in loci.poi.hssf.util
 
AreaReference(String) - Constructor for class loci.poi.hssf.util.AreaReference
Create an area ref from a string representation
areas - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
AreaVPtg - Class in loci.poi.hssf.record.formula
Specifies a rectangular area of cells A1:A4 for instance.
AreaVPtg() - Constructor for class loci.poi.hssf.record.formula.AreaVPtg
 
AreaVPtg(short, short, short, short, boolean, boolean, boolean, boolean) - Constructor for class loci.poi.hssf.record.formula.AreaVPtg
 
AreaVPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AreaVPtg
 
areIntArraysEqual(int[], int[]) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
areSampleSizesEqual(SampleModel) - Static method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
Returns whether all samples have the same number of bits.
ARFReader - Class in loci.formats.in
ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.
ARFReader() - Constructor for class loci.formats.in.ARFReader
Constructs a new ARF reader.
arg - Variable in class loci.plugins.LociExporter
Argument passed to setup method.
arg - Variable in class loci.plugins.Slicer
Plugin options.
args - Static variable in class loci.plugins.shortcut.ShortcutPanel
Details for installed plugins.
args - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
 
argument - Variable in class mdbtools.dbengine.sql.FunctionDef
 
Arguments() - Method in class loci.poi.hssf.model.FormulaParser
get arguments to a function
ARRAY - Static variable in class loci.formats.in.GatanReader
Data types.
array_to_string(int[], int) - Static method in class mdbtools.libmdb.Money
 
arraycopy(byte[], int, byte[], int, int) - Static method in class loci.poi.util.ArrayUtil
This is really a debugging version of System.arraycopy().
arrayMoveWithin(Object[], int, int, int) - Static method in class loci.poi.util.ArrayUtil
Moves a number of entries in an array to another point in the array, shifting those inbetween as required.
ArrayPtg - Class in loci.poi.hssf.record.formula
ArrayPtg - handles arrays The ArrayPtg is a little wierd, the size of the Ptg when parsing initially only includes the Ptg sid and the reserved bytes.
ArrayPtg() - Constructor for class loci.poi.hssf.record.formula.ArrayPtg
 
ArrayPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.ArrayPtg
 
ArrayPtgA - Class in loci.poi.hssf.record.formula
ArrayPtgA - handles arrays
ArrayPtgA() - Constructor for class loci.poi.hssf.record.formula.ArrayPtgA
 
ArrayPtgA(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.ArrayPtgA
 
ArrayPtgV - Class in loci.poi.hssf.record.formula
ArrayPtg - handles arrays The ArrayPtg is a little wierd, the size of the Ptg when parsing initially only includes the Ptg sid and the reserved bytes.
ArrayPtgV() - Constructor for class loci.poi.hssf.record.formula.ArrayPtgV
 
ArrayPtgV(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.ArrayPtgV
 
arrayToString(Array) - Method in class loci.formats.services.NetCDFServiceImpl
 
ArrayUtil - Class in jj2000.j2k.util
This class contains a colleaction of utility static methods for arrays.
ArrayUtil() - Constructor for class jj2000.j2k.util.ArrayUtil
 
ArrayUtil - Class in loci.poi.util
Utility classes for dealing with arrays.
ArrayUtil() - Constructor for class loci.poi.util.ArrayUtil
 
ARROW - Static variable in class loci.formats.in.FV1000Reader
 
ARROW - Static variable in class loci.formats.in.LeicaHandler.ROI
 
ARROW - Static variable in class loci.formats.in.LIFReader.ROI
 
ARTIST - Static variable in class loci.formats.tiff.IFD
 
AS - Static variable in class loci.formats.in.DicomReader
 
AS - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.ATTOSECOND instead.
ascending - Variable in class mdbtools.dbengine.sql.OrderBy
 
ascii - Variable in class loci.formats.in.AmiraReader
 
ascii - Variable in class loci.formats.tools.AmiraParameters
 
AsciiImage - Class in loci.formats.tools
A utility class for outputting a BufferedImage as ASCII text.
AsciiImage(BufferedImage) - Constructor for class loci.formats.tools.AsciiImage
 
asDateTime(DateTimeZone) - Method in class ome.xml.model.primitives.Timestamp
Returns the timestamp as a Joda DateTime type.
asInstant() - Method in class ome.xml.model.primitives.Timestamp
Returns the timestamp as a Joda DateTime type.
asMap() - Method in class loci.formats.in.DeltavisionReader.DVExtHdrFields
 
asRetrieve(MetadataStore) - Method in interface loci.formats.services.OMEXMLService
Gets the given MetadataStore object as a MetadataRetrieve.
asRetrieve(MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
 
assertBlock(int, int, int, int, int) - Method in class loci.tests.testng.OpenBytesPerformanceTest
 
assertCompression(TiffCompression, boolean) - Method in class loci.tests.testng.CompressDecompressTest
Tests the writing of the tiles.
assertId(String, boolean, int) - Static method in class loci.formats.FormatTools
Asserts that the current file is either null, or not, according to the given flag.
assertRows(int) - Method in class loci.tests.testng.OpenBytesPerformanceTest
 
assertSeries(int) - Method in class loci.tests.testng.OpenBytesPerformanceTest
 
assertStep(ImportStep) - Method in class loci.plugins.in.ImportProcess
 
assertTiles(String, String, int, int, boolean) - Method in class loci.tests.testng.TiffWriterTest
Tests the writing of the tiles.
assertUnevenTiles(String, String, int, int, boolean) - Method in class loci.tests.testng.TiffWriterTest
Tests the writing of the tiles.
assignL2Norm(float) - Method in class jj2000.j2k.wavelet.analysis.SubbandAn
Assigns the given L2-norm to the first leaf that does not have an L2-norm value yet (i.e.
assignPlaneIndices() - Method in class loci.formats.in.ZeissCZIReader
 
assignValues(double[]) - Method in class loci.formats.in.TextReader
Assigns values from the given row into the data array.
associations - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
 
associations - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
 
assoicateShapeToObjRecord(EscherRecord, Record) - Method in class loci.poi.hssf.record.EscherAggregate
Associates an escher record to an OBJ record or a TXO record.
asStore(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
Gets the given MetadataRetrieve object as a MetadataStore.
asStore(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
 
ASTRONOMICALUNIT - Static variable in class ome.units.UNITS
 
ASTRONOMY_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the astronomy domain.
asXMLElement(Document) - Method in class ome.xml.model.AbstractOMEModelObject
 
asXMLElement(Document, Element) - Method in class ome.xml.model.AbstractOMEModelObject
Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
asXMLElement(Document) - Method in class ome.xml.model.AffineTransform
 
asXMLElement(Document, Element) - Method in class ome.xml.model.AffineTransform
 
asXMLElement(Document) - Method in class ome.xml.model.Annotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Annotation
 
asXMLElement(Document) - Method in class ome.xml.model.AnnotationRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.AnnotationRef
 
asXMLElement(Document) - Method in class ome.xml.model.Arc
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Arc
 
asXMLElement(Document) - Method in class ome.xml.model.BasicAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.BasicAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.BinaryFile
 
asXMLElement(Document, Element) - Method in class ome.xml.model.BinaryFile
 
asXMLElement(Document) - Method in class ome.xml.model.BinaryOnly
 
asXMLElement(Document, Element) - Method in class ome.xml.model.BinaryOnly
 
asXMLElement(Document) - Method in class ome.xml.model.BinData
 
asXMLElement(Document, Element) - Method in class ome.xml.model.BinData
 
asXMLElement(Document) - Method in class ome.xml.model.BooleanAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.BooleanAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.Channel
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Channel
 
asXMLElement(Document) - Method in class ome.xml.model.ChannelRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ChannelRef
 
asXMLElement(Document) - Method in class ome.xml.model.CommentAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.CommentAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.Dataset
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Dataset
 
asXMLElement(Document) - Method in class ome.xml.model.DatasetRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.DatasetRef
 
asXMLElement(Document) - Method in class ome.xml.model.Detector
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Detector
 
asXMLElement(Document) - Method in class ome.xml.model.DetectorSettings
 
asXMLElement(Document, Element) - Method in class ome.xml.model.DetectorSettings
 
asXMLElement(Document) - Method in class ome.xml.model.Dichroic
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Dichroic
 
asXMLElement(Document) - Method in class ome.xml.model.DichroicRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.DichroicRef
 
asXMLElement(Document) - Method in class ome.xml.model.DoubleAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.DoubleAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.Ellipse
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Ellipse
 
asXMLElement(Document) - Method in class ome.xml.model.EmissionFilterRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.EmissionFilterRef
 
asXMLElement(Document) - Method in class ome.xml.model.ExcitationFilterRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ExcitationFilterRef
 
asXMLElement(Document) - Method in class ome.xml.model.Experiment
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Experiment
 
asXMLElement(Document) - Method in class ome.xml.model.Experimenter
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Experimenter
 
asXMLElement(Document) - Method in class ome.xml.model.ExperimenterGroup
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ExperimenterGroup
 
asXMLElement(Document) - Method in class ome.xml.model.ExperimenterGroupRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ExperimenterGroupRef
 
asXMLElement(Document) - Method in class ome.xml.model.ExperimenterRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ExperimenterRef
 
asXMLElement(Document) - Method in class ome.xml.model.ExperimentRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ExperimentRef
 
asXMLElement(Document) - Method in class ome.xml.model.External
 
asXMLElement(Document, Element) - Method in class ome.xml.model.External
 
asXMLElement(Document) - Method in class ome.xml.model.Filament
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Filament
 
asXMLElement(Document) - Method in class ome.xml.model.FileAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.FileAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.Filter
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Filter
 
asXMLElement(Document) - Method in class ome.xml.model.FilterRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.FilterRef
 
asXMLElement(Document) - Method in class ome.xml.model.FilterSet
 
asXMLElement(Document, Element) - Method in class ome.xml.model.FilterSet
 
asXMLElement(Document) - Method in class ome.xml.model.FilterSetRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.FilterSetRef
 
asXMLElement(Document) - Method in class ome.xml.model.Folder
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Folder
 
asXMLElement(Document) - Method in class ome.xml.model.FolderRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.FolderRef
 
asXMLElement(Document) - Method in class ome.xml.model.GenericExcitationSource
 
asXMLElement(Document, Element) - Method in class ome.xml.model.GenericExcitationSource
 
asXMLElement(Document) - Method in class ome.xml.model.Image
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Image
 
asXMLElement(Document) - Method in class ome.xml.model.ImageRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ImageRef
 
asXMLElement(Document) - Method in class ome.xml.model.ImagingEnvironment
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ImagingEnvironment
 
asXMLElement(Document) - Method in class ome.xml.model.Instrument
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Instrument
 
asXMLElement(Document) - Method in class ome.xml.model.InstrumentRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.InstrumentRef
 
asXMLElement(Document) - Method in class ome.xml.model.Label
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Label
 
asXMLElement(Document) - Method in class ome.xml.model.Laser
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Laser
 
asXMLElement(Document) - Method in class ome.xml.model.Leader
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Leader
 
asXMLElement(Document) - Method in class ome.xml.model.LightEmittingDiode
 
asXMLElement(Document, Element) - Method in class ome.xml.model.LightEmittingDiode
 
asXMLElement(Document) - Method in class ome.xml.model.LightPath
 
asXMLElement(Document, Element) - Method in class ome.xml.model.LightPath
 
asXMLElement(Document) - Method in class ome.xml.model.LightSource
 
asXMLElement(Document, Element) - Method in class ome.xml.model.LightSource
 
asXMLElement(Document) - Method in class ome.xml.model.LightSourceSettings
 
asXMLElement(Document, Element) - Method in class ome.xml.model.LightSourceSettings
 
asXMLElement(Document) - Method in class ome.xml.model.Line
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Line
 
asXMLElement(Document) - Method in class ome.xml.model.ListAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ListAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.LongAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.LongAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.ManufacturerSpec
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ManufacturerSpec
 
asXMLElement(Document) - Method in class ome.xml.model.MapAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.MapAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.Mask
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Mask
 
asXMLElement(Document) - Method in class ome.xml.model.MetadataOnly
 
asXMLElement(Document, Element) - Method in class ome.xml.model.MetadataOnly
 
asXMLElement(Document) - Method in class ome.xml.model.MicrobeamManipulation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.MicrobeamManipulation
 
asXMLElement(Document) - Method in class ome.xml.model.MicrobeamManipulationRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.MicrobeamManipulationRef
 
asXMLElement(Document) - Method in class ome.xml.model.Microscope
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Microscope
 
asXMLElement(Document) - Method in class ome.xml.model.NumericAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.NumericAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.Objective
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Objective
 
asXMLElement(Document) - Method in class ome.xml.model.ObjectiveSettings
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ObjectiveSettings
 
asXMLElement(Document) - Method in class ome.xml.model.OME
 
asXMLElement(Document, Element) - Method in class ome.xml.model.OME
 
asXMLElement(Document) - Method in interface ome.xml.model.OMEModelObject
Takes the entire object hierarchy and produces an XML DOM tree.
asXMLElement(Document) - Method in class ome.xml.model.Pixels
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Pixels
 
asXMLElement(Document) - Method in class ome.xml.model.Plane
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Plane
 
asXMLElement(Document) - Method in class ome.xml.model.Plate
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Plate
 
asXMLElement(Document) - Method in class ome.xml.model.PlateAcquisition
 
asXMLElement(Document, Element) - Method in class ome.xml.model.PlateAcquisition
 
asXMLElement(Document) - Method in class ome.xml.model.PlateRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.PlateRef
 
asXMLElement(Document) - Method in class ome.xml.model.Point
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Point
 
asXMLElement(Document) - Method in class ome.xml.model.Polygon
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Polygon
 
asXMLElement(Document) - Method in class ome.xml.model.Polyline
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Polyline
 
asXMLElement(Document) - Method in class ome.xml.model.Project
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Project
 
asXMLElement(Document) - Method in class ome.xml.model.ProjectRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ProjectRef
 
asXMLElement(Document) - Method in class ome.xml.model.Pump
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Pump
 
asXMLElement(Document) - Method in class ome.xml.model.Reagent
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Reagent
 
asXMLElement(Document) - Method in class ome.xml.model.ReagentRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ReagentRef
 
asXMLElement(Document) - Method in class ome.xml.model.Rectangle
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Rectangle
 
asXMLElement(Document) - Method in class ome.xml.model.Reference
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Reference
 
asXMLElement(Document) - Method in class ome.xml.model.Rights
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Rights
 
asXMLElement(Document) - Method in class ome.xml.model.ROI
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ROI
 
asXMLElement(Document) - Method in class ome.xml.model.ROIRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.ROIRef
 
asXMLElement(Document) - Method in class ome.xml.model.Screen
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Screen
 
asXMLElement(Document) - Method in class ome.xml.model.Settings
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Settings
 
asXMLElement(Document) - Method in class ome.xml.model.Shape
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Shape
 
asXMLElement(Document) - Method in class ome.xml.model.StageLabel
 
asXMLElement(Document, Element) - Method in class ome.xml.model.StageLabel
 
asXMLElement(Document) - Method in class ome.xml.model.StructuredAnnotations
 
asXMLElement(Document, Element) - Method in class ome.xml.model.StructuredAnnotations
 
asXMLElement(Document) - Method in class ome.xml.model.TagAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.TagAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.TermAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.TermAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.TextAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.TextAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.TiffData
 
asXMLElement(Document, Element) - Method in class ome.xml.model.TiffData
 
asXMLElement(Document) - Method in class ome.xml.model.TimestampAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.TimestampAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.TransmittanceRange
 
asXMLElement(Document, Element) - Method in class ome.xml.model.TransmittanceRange
 
asXMLElement(Document) - Method in class ome.xml.model.TypeAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.TypeAnnotation
 
asXMLElement(Document) - Method in class ome.xml.model.Union
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Union
 
asXMLElement(Document) - Method in class ome.xml.model.UUID
 
asXMLElement(Document, Element) - Method in class ome.xml.model.UUID
 
asXMLElement(Document) - Method in class ome.xml.model.Well
 
asXMLElement(Document, Element) - Method in class ome.xml.model.Well
 
asXMLElement(Document) - Method in class ome.xml.model.WellSample
 
asXMLElement(Document, Element) - Method in class ome.xml.model.WellSample
 
asXMLElement(Document) - Method in class ome.xml.model.WellSampleRef
 
asXMLElement(Document, Element) - Method in class ome.xml.model.WellSampleRef
 
asXMLElement(Document) - Method in class ome.xml.model.XMLAnnotation
 
asXMLElement(Document, Element) - Method in class ome.xml.model.XMLAnnotation
 
AT - Static variable in class loci.formats.in.DicomReader
 
atEOD() - Method in class loci.poi.poifs.filesystem.DocumentInputStream
 
aTile - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
The raster for a destination tile
ATM - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.ATMOSPHERE instead.
ATMOSPHERE - Static variable in class ome.units.UNITS
 
attachCompanionFiles() - Method in class loci.formats.in.DicomReader
DICOM datasets produced by: http://www.ct-imaging.de/index.php/en/ct-systeme-e/mikro-ct-e.html contain a bunch of extra metadata and log files.
attachListeners(List<TextField>, List<Panel>) - Method in class loci.plugins.in.ColorDialog
 
attachment - Variable in class loci.formats.in.ZeissCZIReader.Attachment
 
attachment - Variable in class loci.formats.in.ZeissCZIReader.Metadata
 
attachmentData - Variable in class loci.formats.in.ZeissCZIReader.Attachment
 
attachmentDirectoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
attachmentSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
attenuation - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
attenuation - Variable in class ome.xml.model.LightSourceSettings
 
ATTO(Unit<T>) - Static method in class ome.units.UNITS
 
ATTOHERTZ - Static variable in class ome.units.UNITS
 
ATTOMETER - Static variable in class ome.units.UNITS
 
ATTOMETRE - Static variable in class ome.units.UNITS
 
ATTOPASCAL - Static variable in class ome.units.UNITS
 
ATTOSECOND - Static variable in class ome.units.UNITS
 
ATTOVOLT - Static variable in class ome.units.UNITS
 
ATTOWATT - Static variable in class ome.units.UNITS
 
attr(Element, String) - Method in class loci.formats.in.PrairieMetadata
Gets the attribute value with the given name, or null if not defined.
ATTR_NAME - Static variable in class loci.poi.hssf.record.formula.AbstractFunctionPtg
 
ATTR_NAME_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
 
ATTR_NAME_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
 
ATTR_VALUE_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
 
ATTR_VALUE_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
 
attributeList - Variable in class loci.formats.services.NetCDFServiceImpl
 
attributeNames - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
attrInfoMap - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFMetadataFormat
 
AttrPtg - Class in loci.poi.hssf.record.formula
"Special Attributes" This seems to be a Misc Stuff and Junk record.
AttrPtg() - Constructor for class loci.poi.hssf.record.formula.AttrPtg
 
AttrPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.AttrPtg
 
authenticationCodes - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
author - Variable in class loci.poi.hssf.usermodel.HSSFComment
 
auto - Variable in class loci.poi.hssf.record.LineFormatRecord
 
autoBackground - Variable in class loci.poi.hssf.record.TextRecord
 
autobreaks - Static variable in class loci.poi.hssf.record.WSBoolRecord
 
autoColor - Variable in class loci.poi.hssf.record.TextRecord
 
autoContinue - Variable in class loci.poi.hssf.record.RecordInputStream
 
AUTOEXPOSURE - Static variable in class loci.formats.in.CellSensReader
 
autofill - Variable in class loci.poi.hssf.record.CommonObjectDataSubRecord
 
autoGeneratedText - Variable in class loci.poi.hssf.record.TextRecord
 
autoLabelDeleted - Variable in class loci.poi.hssf.record.TextRecord
 
autoline - Variable in class loci.poi.hssf.record.CommonObjectDataSubRecord
 
automatic - Variable in class loci.poi.hssf.record.AreaFormatRecord
 
AUTOMATIC - Static variable in class loci.poi.hssf.record.CalcModeRecord
automatically calculate formulas (1)
AUTOMATIC_EXCEPT_TABLES - Static variable in class loci.poi.hssf.record.CalcModeRecord
automatically calculate formulas except for tables (-1)
automaticCategoryCrossing - Variable in class loci.poi.hssf.record.ValueRangeRecord
 
automaticMajor - Variable in class loci.poi.hssf.record.ValueRangeRecord
 
automaticMaximum - Variable in class loci.poi.hssf.record.ValueRangeRecord
 
automaticMinimum - Variable in class loci.poi.hssf.record.ValueRangeRecord
 
automaticMinor - Variable in class loci.poi.hssf.record.ValueRangeRecord
 
autoPlotArea - Variable in class loci.poi.hssf.record.SheetPropertiesRecord
 
autoPosition - Variable in class loci.poi.hssf.record.FrameRecord
 
autoPosition - Variable in class loci.poi.hssf.record.LegendRecord
 
autorotate - Variable in class loci.poi.hssf.record.TickRecord
 
autoscale(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Perform autoscaling on the given BufferedImage.
autoscale(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools
Perform autoscaling on the given BufferedImage; map min to 0 and max to 255.
autoscale(byte[], int, int, int, boolean) - Static method in class loci.formats.ImageTools
Perform autoscaling on the given byte array; map min to 0 and max to 255.
autoscaleBox - Variable in class loci.plugins.in.MainDialog
 
autoSeries - Variable in class loci.poi.hssf.record.LegendRecord
 
autoSize - Variable in class loci.poi.hssf.record.FrameRecord
 
autoSizeColumn(short) - Method in class loci.poi.hssf.usermodel.HSSFSheet
Adjusts the column width to fit the contents.
autoTextBackground - Variable in class loci.poi.hssf.record.TickRecord
 
autoTextColor - Variable in class loci.poi.hssf.record.TickRecord
 
autoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
autoUpdate - Variable in class loci.formats.cache.Cache
Whether the cache should automatically update when a parameter changes.
autoXPositioning - Variable in class loci.poi.hssf.record.LegendRecord
 
autoYPositioning - Variable in class loci.poi.hssf.record.LegendRecord
 
AV - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.ATTOVOLT instead.
available() - Method in class loci.common.NIOInputStream
 
available() - Method in class loci.common.RandomAccessInputStream
 
available() - Method in class loci.formats.in.APNGReader.PNGInputStream
 
available() - Method in class loci.poi.poifs.filesystem.DocumentInputStream
Returns the number of bytes that can be read (or skipped over) from this input stream without blocking by the next caller of a method for this input stream.
available() - Method in class loci.poi.util.BlockingInputStream
 
availMem - Variable in class loci.plugins.in.MemoryDialog
Remaining memory for the JVM.
avbits - Variable in class jj2000.j2k.codestream.writer.BitOutputBuffer
The number of available bits in the current byte
AVERAGE - Static variable in class loci.formats.in.APNGReader
 
AVERAGING - Static variable in class loci.formats.in.CellSensReader
 
AVI_MAGIC_STRING - Static variable in class loci.formats.in.AVIReader
 
AVIReader - Class in loci.formats.in
AVIReader is the file format reader for AVI files.
AVIReader() - Constructor for class loci.formats.in.AVIReader
Constructs a new AVI reader.
AVIWriter - Class in loci.formats.out
AVIWriter is the file format writer for AVI files.
AVIWriter() - Constructor for class loci.formats.out.AVIWriter
 
avoidUndeclaredNamespaces(String) - Static method in class loci.common.xml.XMLTools
Replaces NS:tag with NS_tag for undeclared namespaces
AW - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.ATTOWATT instead.
AWTImageTools - Class in loci.formats.gui
A utility class with convenience methods for manipulating images in BufferedImage form.
AWTImageTools() - Constructor for class loci.formats.gui.AWTImageTools
 
ax - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent
The horizontal coordinate of the image origin in the canvas system, on the reference grid.
axis - Variable in class loci.formats.gui.CacheIndicator
 
AXIS_TYPE_AXIS_LINE - Static variable in class loci.poi.hssf.record.AxisLineFormatRecord
 
AXIS_TYPE_CATEGORY_OR_X_AXIS - Static variable in class loci.poi.hssf.record.AxisRecord
 
AXIS_TYPE_MAIN - Static variable in class loci.poi.hssf.record.AxisParentRecord
 
AXIS_TYPE_MAJOR_GRID_LINE - Static variable in class loci.poi.hssf.record.AxisLineFormatRecord
 
AXIS_TYPE_MINOR_GRID_LINE - Static variable in class loci.poi.hssf.record.AxisLineFormatRecord
 
AXIS_TYPE_SECONDARY - Static variable in class loci.poi.hssf.record.AxisParentRecord
 
AXIS_TYPE_SERIES_AXIS - Static variable in class loci.poi.hssf.record.AxisRecord
 
AXIS_TYPE_VALUE_AXIS - Static variable in class loci.poi.hssf.record.AxisRecord
 
AXIS_TYPE_WALLS_OR_FLOOR - Static variable in class loci.poi.hssf.record.AxisLineFormatRecord
 
AxisGuesser - Class in loci.formats
AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T, C or S), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
AxisGuesser(FilePattern, String, int, int, int, boolean) - Constructor for class loci.formats.AxisGuesser
Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide.
AxisLineFormatRecord - Class in loci.poi.hssf.record
The axis line format record defines the axis type details.
AxisLineFormatRecord() - Constructor for class loci.poi.hssf.record.AxisLineFormatRecord
 
AxisLineFormatRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.AxisLineFormatRecord
Constructs a AxisLineFormat record and sets its fields appropriately.
AxisOptionsRecord - Class in loci.poi.hssf.record
The axis options record provides unit information and other various tidbits about the axis.
AxisOptionsRecord() - Constructor for class loci.poi.hssf.record.AxisOptionsRecord
 
AxisOptionsRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.AxisOptionsRecord
Constructs a AxisOptions record and sets its fields appropriately.
AxisParentRecord - Class in loci.poi.hssf.record
The axis size and location NOTE: This source is automatically generated please do not modify this file.
AxisParentRecord() - Constructor for class loci.poi.hssf.record.AxisParentRecord
 
AxisParentRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.AxisParentRecord
Constructs a AxisParent record and sets its fields appropriately.
AxisRecord - Class in loci.poi.hssf.record
The axis record defines the type of an axis.
AxisRecord() - Constructor for class loci.poi.hssf.record.AxisRecord
 
AxisRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.AxisRecord
Constructs a Axis record and sets its fields appropriately.
axisTypes - Variable in class loci.formats.AxisGuesser
Guessed axis types.
AxisUsedRecord - Class in loci.poi.hssf.record
The number of axes used on a chart.
AxisUsedRecord() - Constructor for class loci.poi.hssf.record.AxisUsedRecord
 
AxisUsedRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.AxisUsedRecord
Constructs a AxisUsed record and sets its fields appropriately.
ay - Variable in class jj2000.j2k.codestream.reader.BitstreamReaderAgent
The vertical coordinate of the image origin in the canvas system, on the reference grid.

B

b - Variable in class jj2000.j2k.entropy.decoder.MQDecoder
The last byte read
b - Variable in class jj2000.j2k.entropy.encoder.MQCoder
The last encoded byte of data
b(String) - Method in class loci.formats.in.PrairieMetadata
Converts the given string to a boolean.
ba - Variable in class mdbtools.libmdb.Holder
 
BACK_MASK - Static variable in class loci.common.RandomAccessInputStream
Various bitmasks for the 0000xxxx side of a byte.
BACK_MASK - Static variable in class loci.formats.codec.BitBuffer
Deprecated.
Various bitmasks for the 0000xxxx side of a byte.
backend - Class in mdbtools.libmdb
 
backend() - Constructor for class mdbtools.libmdb.backend
 
backend_name - Variable in class mdbtools.libmdb.MdbFile
 
backend_name - Variable in class mdbtools.libmdb.MdbHandle
 
background - Variable in class loci.poi.hssf.usermodel.EscherGraphics
 
BACKGROUND_TABLE - Static variable in class loci.formats.in.LiFlimReader
 
backgroundC - Variable in class loci.formats.in.LiFlimReader
 
backgroundColor - Variable in class loci.formats.in.CellSensReader
 
backgroundColorIndex - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadata
 
backgroundDatatype - Variable in class loci.formats.in.LiFlimReader
 
backgroundF - Variable in class loci.formats.in.LiFlimReader
 
backgroundP - Variable in class loci.formats.in.LiFlimReader
 
backgroundT - Variable in class loci.formats.in.LiFlimReader
 
backgroundX - Variable in class loci.formats.in.LiFlimReader
 
backgroundY - Variable in class loci.formats.in.LiFlimReader
 
backgroundZ - Variable in class loci.formats.in.LiFlimReader
 
backingBuffer - Variable in class loci.tests.testng.ConversionTest.Plane
 
backingSet - Variable in class ome.xml.model.ReferenceList
 
backupHandler - Variable in class loci.formats.in.NativeND2Reader
 
backuppos - Variable in class loci.poi.hssf.model.WorkbookRecordList
 
BackupRecord - Class in loci.poi.hssf.record
Title: Backup Record
BackupRecord() - Constructor for class loci.poi.hssf.record.BackupRecord
 
BackupRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BackupRecord
Constructs a BackupRecord and sets its fields appropriately
BACKWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
 
backwardsStage - Variable in class loci.formats.in.DeltavisionReader
Whether or not the stage moved backwards.
BAD_DATE - Static variable in class loci.poi.hssf.usermodel.HSSFDateUtil
 
badFontHeight - Static variable in class loci.poi.hssf.record.RowRecord
 
bais - Variable in class jj2000.j2k.codestream.reader.PktHeaderBitReader
The byte array that is the source of data if the PktHeaderBitReader is instantiated with a buffer instead of a RandomAccessIO
bak_lblock - Variable in class jj2000.j2k.codestream.writer.PktEncoder
The saved base number of bits for sending code-block length information.
bak_prevtIdxs - Variable in class jj2000.j2k.codestream.writer.PktEncoder
The saved last encoded truncation point for each code-block.
baknBytes - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Backup of the number of bytes allocated to each tile.
bandOffsets - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
bandsPresent - Variable in class ome.jxr.parser.DatastreamParser
Deprecated.
 
bandStride - Variable in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
The strides for pixel, band, and scanline.
bankData - Variable in class loci.formats.gui.SignedByteBuffer
 
bankData - Variable in class loci.formats.gui.UnsignedIntBuffer
 
baos - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFBaseJPEGCompressor
 
baos - Variable in class jj2000.j2k.codestream.writer.HeaderEncoder
The ByteArrayOutputStream to store header data.
BAR - Static variable in class ome.units.UNITS
 
barcode - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
barr - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
Buffer for the 3 components of each pixel(in the current block)
BarRecord - Class in loci.poi.hssf.record
The bar record is used to define a bar chart.
BarRecord() - Constructor for class loci.poi.hssf.record.BarRecord
 
BarRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BarRecord
Constructs a Bar record and sets its fields appropriately.
barrierFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
base - Variable in class loci.common.CBZip2InputStream.Data
 
base - Variable in class loci.formats.ClassList
Base class to which all classes are assignable.
base64Alphabet - Static variable in class loci.formats.codec.Base64Codec
 
base64Binary - Variable in class ome.xml.model.BinData
 
Base64Codec - Class in loci.formats.codec
Implements encoding (compress) and decoding (decompress) methods for Base64.
Base64Codec() - Constructor for class loci.formats.codec.Base64Codec
 
BASE_BLOCK_SIZE - Static variable in class loci.common.CBZip2InputStream
 
BASE_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
 
BaseCodec - Class in loci.formats.codec
BaseCodec contains default implementation and testing for classes implementing the Codec interface, and acts as a base class for any of the compression classes.
BaseCodec() - Constructor for class loci.formats.codec.BaseCodec
 
baseConfigName - Static variable in class loci.tests.testng.TestTools
 
basedir - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
BaseHandler - Class in loci.common.xml
Top-level SAX handler.
BaseHandler() - Constructor for class loci.common.xml.BaseHandler
 
BASELINE_CLAMP - Static variable in class loci.formats.in.FluoviewReader
 
BASELINE_OFFSET - Static variable in class loci.formats.in.FluoviewReader
 
BASELINE_OFFSET_CLAMP - Static variable in class loci.formats.in.CellSensReader
 
BaselineTIFFTagSet - Class in com.sun.media.imageio.plugins.tiff
A class representing the set of tags found in the baseline TIFF specification as well as some common additional tags.
BaselineTIFFTagSet() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet
 
BaselineTIFFTagSet.Artist - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Artist() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Artist
 
BaselineTIFFTagSet.BitsPerSample - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.BitsPerSample() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.BitsPerSample
 
BaselineTIFFTagSet.CellLength - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.CellLength() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.CellLength
 
BaselineTIFFTagSet.CellWidth - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.CellWidth() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.CellWidth
 
BaselineTIFFTagSet.ColorMap - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.ColorMap() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ColorMap
 
BaselineTIFFTagSet.Compression - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Compression() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Compression
 
BaselineTIFFTagSet.Copyright - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Copyright() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Copyright
 
BaselineTIFFTagSet.DateTime - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.DateTime() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.DateTime
 
BaselineTIFFTagSet.DocumentName - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.DocumentName() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.DocumentName
 
BaselineTIFFTagSet.DotRange - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.DotRange() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.DotRange
 
BaselineTIFFTagSet.ExtraSamples - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.ExtraSamples() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ExtraSamples
 
BaselineTIFFTagSet.FillOrder - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.FillOrder() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.FillOrder
 
BaselineTIFFTagSet.FreeByteCounts - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.FreeByteCounts() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.FreeByteCounts
 
BaselineTIFFTagSet.FreeOffsets - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.FreeOffsets() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.FreeOffsets
 
BaselineTIFFTagSet.GrayResponseCurve - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.GrayResponseCurve() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.GrayResponseCurve
 
BaselineTIFFTagSet.GrayResponseUnit - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.GrayResponseUnit() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.GrayResponseUnit
 
BaselineTIFFTagSet.HalftoneHints - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.HalftoneHints() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.HalftoneHints
 
BaselineTIFFTagSet.HostComputer - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.HostComputer() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.HostComputer
 
BaselineTIFFTagSet.ICCProfile - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.ICCProfile() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ICCProfile
 
BaselineTIFFTagSet.ImageDescription - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.ImageDescription() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ImageDescription
 
BaselineTIFFTagSet.ImageLength - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.ImageLength() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ImageLength
 
BaselineTIFFTagSet.ImageWidth - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.ImageWidth() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ImageWidth
 
BaselineTIFFTagSet.InkNames - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.InkNames() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.InkNames
 
BaselineTIFFTagSet.InkSet - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.InkSet() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.InkSet
 
BaselineTIFFTagSet.JPEGACTables - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGACTables() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGACTables
 
BaselineTIFFTagSet.JPEGDCTables - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGDCTables() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGDCTables
 
BaselineTIFFTagSet.JPEGInterchangeFormat - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGInterchangeFormat() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGInterchangeFormat
 
BaselineTIFFTagSet.JPEGInterchangeFormatLength - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGInterchangeFormatLength() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGInterchangeFormatLength
 
BaselineTIFFTagSet.JPEGLosslessPredictors - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGLosslessPredictors() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGLosslessPredictors
 
BaselineTIFFTagSet.JPEGPointTransforms - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGPointTransforms() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGPointTransforms
 
BaselineTIFFTagSet.JPEGProc - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGProc() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGProc
 
BaselineTIFFTagSet.JPEGQTables - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGQTables() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGQTables
 
BaselineTIFFTagSet.JPEGRestartInterval - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGRestartInterval() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGRestartInterval
 
BaselineTIFFTagSet.JPEGTables - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.JPEGTables() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.JPEGTables
 
BaselineTIFFTagSet.Make - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Make() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Make
 
BaselineTIFFTagSet.MaxSampleValue - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.MaxSampleValue() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.MaxSampleValue
 
BaselineTIFFTagSet.MinSampleValue - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.MinSampleValue() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.MinSampleValue
 
BaselineTIFFTagSet.Model - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Model() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Model
 
BaselineTIFFTagSet.NewSubfileType - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.NewSubfileType() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.NewSubfileType
 
BaselineTIFFTagSet.NumberOfInks - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.NumberOfInks() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.NumberOfInks
 
BaselineTIFFTagSet.Orientation - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Orientation() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Orientation
 
BaselineTIFFTagSet.PageName - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.PageName() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PageName
 
BaselineTIFFTagSet.PageNumber - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.PageNumber() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PageNumber
 
BaselineTIFFTagSet.PhotometricInterpretation - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.PhotometricInterpretation() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PhotometricInterpretation
 
BaselineTIFFTagSet.PlanarConfiguration - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.PlanarConfiguration() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PlanarConfiguration
 
BaselineTIFFTagSet.Predictor - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Predictor() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Predictor
 
BaselineTIFFTagSet.PrimaryChromaticities - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.PrimaryChromaticities() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.PrimaryChromaticities
 
BaselineTIFFTagSet.ReferenceBlackWhite - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.ReferenceBlackWhite() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ReferenceBlackWhite
 
BaselineTIFFTagSet.ResolutionUnit - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.ResolutionUnit() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.ResolutionUnit
 
BaselineTIFFTagSet.RowsPerStrip - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.RowsPerStrip() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.RowsPerStrip
 
BaselineTIFFTagSet.SampleFormat - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.SampleFormat() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SampleFormat
 
BaselineTIFFTagSet.SamplesPerPixel - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.SamplesPerPixel() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SamplesPerPixel
 
BaselineTIFFTagSet.SMaxSampleValue - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.SMaxSampleValue() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SMaxSampleValue
 
BaselineTIFFTagSet.SMinSampleValue - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.SMinSampleValue() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SMinSampleValue
 
BaselineTIFFTagSet.Software - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Software() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Software
 
BaselineTIFFTagSet.StripByteCounts - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.StripByteCounts() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.StripByteCounts
 
BaselineTIFFTagSet.StripOffsets - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.StripOffsets() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.StripOffsets
 
BaselineTIFFTagSet.SubfileType - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.SubfileType() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.SubfileType
 
BaselineTIFFTagSet.T4Options - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.T4Options() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.T4Options
 
BaselineTIFFTagSet.T6Options - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.T6Options() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.T6Options
 
BaselineTIFFTagSet.TargetPrinter - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.TargetPrinter() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.TargetPrinter
 
BaselineTIFFTagSet.Threshholding - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.Threshholding() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.Threshholding
 
BaselineTIFFTagSet.TileByteCounts - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.TileByteCounts() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.TileByteCounts
 
BaselineTIFFTagSet.TileLength - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.TileLength() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.TileLength
 
BaselineTIFFTagSet.TileOffsets - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.TileOffsets() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.TileOffsets
 
BaselineTIFFTagSet.TileWidth - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.TileWidth() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.TileWidth
 
BaselineTIFFTagSet.TransferFunction - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.TransferFunction() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.TransferFunction
 
BaselineTIFFTagSet.TransferRange - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.TransferRange() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.TransferRange
 
BaselineTIFFTagSet.WhitePoint - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.WhitePoint() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.WhitePoint
 
BaselineTIFFTagSet.XPosition - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.XPosition() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.XPosition
 
BaselineTIFFTagSet.XResolution - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.XResolution() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.XResolution
 
BaselineTIFFTagSet.YCbCrCoefficients - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.YCbCrCoefficients() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.YCbCrCoefficients
 
BaselineTIFFTagSet.YCbCrPositioning - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.YCbCrPositioning() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.YCbCrPositioning
 
BaselineTIFFTagSet.YCbCrSubSampling - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.YCbCrSubSampling() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.YCbCrSubSampling
 
BaselineTIFFTagSet.YPosition - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.YPosition() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.YPosition
 
BaselineTIFFTagSet.YResolution - Class in com.sun.media.imageio.plugins.tiff
 
BaselineTIFFTagSet.YResolution() - Constructor for class com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet.YResolution
 
BaseMetadata - Interface in loci.formats.meta
 
BaseMetadata - Interface in ome.xml.meta
A proxy capable of bidirectional communication of biological image data to and from a particular storage medium.
basename - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
 
baseReader - Variable in class loci.plugins.in.ImportProcess
 
baseTiff - Variable in class loci.formats.in.MicromanagerReader.Position
 
BaseTiffReader - Class in loci.formats.in
BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
BaseTiffReader(String, String) - Constructor for class loci.formats.in.BaseTiffReader
Constructs a new BaseTiffReader.
BaseTiffReader(String, String[]) - Constructor for class loci.formats.in.BaseTiffReader
Constructs a new BaseTiffReader.
baseURI - Variable in class loci.common.xml.LSInputI
 
BaseZeissReader - Class in loci.formats.in
BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.
BaseZeissReader(String, String) - Constructor for class loci.formats.in.BaseZeissReader
Constructs a new ZeissZVI reader.
BaseZeissReader(String, String[]) - Constructor for class loci.formats.in.BaseZeissReader
Constructs a new ZeissZVI reader.
BaseZeissReader.Charset - Enum in loci.formats.in
 
BaseZeissReader.Charset(int, String) - Constructor for enum loci.formats.in.BaseZeissReader.Charset
 
BaseZeissReader.Context - Enum in loci.formats.in
 
BaseZeissReader.Context() - Constructor for enum loci.formats.in.BaseZeissReader.Context
 
BaseZeissReader.DrawStyle - Enum in loci.formats.in
Line drawing styles.
BaseZeissReader.DrawStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.DrawStyle
 
BaseZeissReader.FeatureType - Enum in loci.formats.in
Feature types.
BaseZeissReader.FeatureType(int, int) - Constructor for enum loci.formats.in.BaseZeissReader.FeatureType
 
BaseZeissReader.FillStyle - Enum in loci.formats.in
Fill styles.
BaseZeissReader.FillStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.FillStyle
 
BaseZeissReader.Layer - Class in loci.formats.in
Layer class representing an AxioVision layer; used to contain a collection of shapes.
BaseZeissReader.Layer() - Constructor for class loci.formats.in.BaseZeissReader.Layer
 
BaseZeissReader.LineEndPositions - Enum in loci.formats.in
 
BaseZeissReader.LineEndPositions(int) - Constructor for enum loci.formats.in.BaseZeissReader.LineEndPositions
 
BaseZeissReader.LineEndStyle - Enum in loci.formats.in
Line ending styles.
BaseZeissReader.LineEndStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.LineEndStyle
 
BaseZeissReader.PointStyle - Enum in loci.formats.in
Point styles.
BaseZeissReader.PointStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.PointStyle
 
BaseZeissReader.Shape - Class in loci.formats.in
Shape class representing the metadata within an AxioVision Shape ROI
BaseZeissReader.Shape() - Constructor for class loci.formats.in.BaseZeissReader.Shape
 
BaseZeissReader.Tag - Class in loci.formats.in
Content of a single tag from a Tags block.
BaseZeissReader.Tag(int, BaseZeissReader.Context) - Constructor for class loci.formats.in.BaseZeissReader.Tag
Constructor.
BaseZeissReader.Tag(int, String, BaseZeissReader.Context) - Constructor for class loci.formats.in.BaseZeissReader.Tag
Constructor.
BaseZeissReader.TextAlignment - Enum in loci.formats.in
 
BaseZeissReader.TextAlignment(int) - Constructor for enum loci.formats.in.BaseZeissReader.TextAlignment
 
BasicAnnotation - Class in ome.xml.model
 
BasicAnnotation() - Constructor for class ome.xml.model.BasicAnnotation
Default constructor.
BasicAnnotation(Element, OMEModel) - Constructor for class ome.xml.model.BasicAnnotation
Constructs BasicAnnotation recursively from an XML DOM tree.
BasicAnnotation(BasicAnnotation) - Constructor for class ome.xml.model.BasicAnnotation
Copy constructor.
BATBlock - Class in loci.poi.poifs.storage
A block of block allocation table entries.
BATBlock(int) - Constructor for class loci.poi.poifs.storage.BATBlock
Create a single instance initialized with default values
BATBlock(int[], int, int, int) - Constructor for class loci.poi.poifs.storage.BATBlock
Create a single instance initialized (perhaps partially) with entries
BATManaged - Interface in loci.poi.poifs.filesystem
This interface defines behaviors for objects managed by the Block Allocation Table (BAT).
batsInHeader - Variable in class loci.poi.poifs.storage.HeaderBlockReader
 
baxcel - Variable in class loci.poi.hssf.record.formula.AttrPtg
 
bayerPattern - Variable in class loci.formats.in.MRWReader
 
bbox - Variable in class loci.formats.in.CellH5Reader
 
BBOX - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
bBox - Variable in class loci.formats.services.WlzServiceImpl
 
bbuf - Variable in class jj2000.j2k.codestream.reader.PktHeaderBitReader
The current bit buffer
bbuf - Variable in class jj2000.j2k.entropy.decoder.ByteToBitInput
The bit buffer
bbuf - Variable in class jj2000.j2k.entropy.encoder.BitToByteOutput
The bit buffer
BDReader - Class in loci.formats.in
BDReader is the file format reader for BD Pathway datasets.
BDReader() - Constructor for class loci.formats.in.BDReader
Constructs a new ScanR reader.
BEAM_SPLITTER_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
 
BEAM_SPLITTER_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
 
BEBufferedRandomAccessFile - Class in jj2000.j2k.io
This class defines a Buffered Random Access File, where all I/O is considered to be big-endian, and extends the BufferedRandomAccessFile class.
BEBufferedRandomAccessFile(File, String, int) - Constructor for class jj2000.j2k.io.BEBufferedRandomAccessFile
Constructor.
BEBufferedRandomAccessFile(File, String) - Constructor for class jj2000.j2k.io.BEBufferedRandomAccessFile
Constructor.
BEBufferedRandomAccessFile(String, String, int) - Constructor for class jj2000.j2k.io.BEBufferedRandomAccessFile
Constructor.
BEBufferedRandomAccessFile(String, String) - Constructor for class jj2000.j2k.io.BEBufferedRandomAccessFile
Constructor.
beforeRecordSerialize(int, short, EscherRecord) - Method in interface loci.poi.ddf.EscherSerializationListener
Fired before a given escher record is serialized.
beforeRecordSerialize(int, short, EscherRecord) - Method in class loci.poi.ddf.NullEscherSerializationListener
 
begin - Variable in class loci.formats.FilePatternBlock
 
beginDecoding() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
This routine is called prior to a sequence of calls to the decode method, in order to allow any necessary tables or other structures to be initialized based on metadata values.
beginDecoding() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
Invokes the superclass method and then sets instance variables on the basis of the metadata set on this decompressor.
beginDecoding() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGDecompressor
 
beginDecoding() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFNullDecompressor
 
beginDecoding() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
BeginRecord - Class in loci.poi.hssf.record
The begin record defines the start of a block of records for a (grpahing data object.
BeginRecord() - Constructor for class loci.poi.hssf.record.BeginRecord
 
BeginRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BeginRecord
Constructs a BeginRecord record and sets its fields appropriately.
BETA - Static variable in class jj2000.j2k.wavelet.analysis.AnWTFilterFloatLift9x7
The value of the second lifting step coefficient
BETA - Static variable in class jj2000.j2k.wavelet.synthesis.SynWTFilterFloatLift9x7
The value of the second lifting step coefficient
BEZIER_WITH_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
 
BF - Class in loci.plugins
Miscellaneous plugins utility methods.
BF() - Constructor for class loci.plugins.BF
 
bf_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor
output destination for bit codes
BFVirtualStack - Class in loci.plugins.util
Subclass of VirtualStack that uses Bio-Formats to read planes on demand.
BFVirtualStack(String, IFormatReader, boolean, boolean, boolean) - Constructor for class loci.plugins.util.BFVirtualStack
 
BGR - Static variable in class loci.formats.in.CellSensReader
 
BGR_24 - Static variable in class loci.formats.in.ZeissCZIReader
 
BGR_48 - Static variable in class loci.formats.in.ZeissCZIReader
 
BGR_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
 
BGRA_8 - Static variable in class loci.formats.in.ZeissCZIReader
 
bgrToRgb(byte[], boolean, int, int) - Static method in class loci.formats.ImageTools
 
BH_HEADER_CHKSUM - Static variable in class loci.formats.in.SDTInfo
 
BH_HEADER_NOT_VALID - Static variable in class loci.formats.in.SDTInfo
 
BH_HEADER_VALID - Static variable in class loci.formats.in.SDTInfo
 
bi - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
The destination image.
bi - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
The destination image.
BI_BITFIELDS - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_JPEG - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_PNG - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_RGB - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_RLE4 - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
BI_RLE8 - Static variable in interface com.sun.media.imageioimpl.plugins.bmp.BMPConstants
 
BiffViewer - Class in loci.poi.hssf.dev
Utillity for reading in BIFF8 records and displaying data from them.
BiffViewer(String[]) - Constructor for class loci.poi.hssf.dev.BiffViewer
Creates new BiffViewer
BiffViewer.BiffviewRecordInputStream - Class in loci.poi.hssf.dev
 
BiffViewer.BiffviewRecordInputStream(InputStream) - Constructor for class loci.poi.hssf.dev.BiffViewer.BiffviewRecordInputStream
 
BiffViewer.RecordDetails - Class in loci.poi.hssf.dev
This record supports dumping of completed continue records.
BiffViewer.RecordDetails(short, short, int, Record) - Constructor for class loci.poi.hssf.dev.BiffViewer.RecordDetails
 
BIFormatReader - Class in loci.formats.in
BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
BIFormatReader(String, String) - Constructor for class loci.formats.in.BIFormatReader
Constructs a new BIFormatReader.
BIFormatReader(String, String[]) - Constructor for class loci.formats.in.BIFormatReader
Constructs a new BIFormatReader.
BIG - Static variable in class loci.formats.tiff.TiffConstants
 
BIG_ENDIAN - Static variable in interface jj2000.j2k.io.EndianType
Identifier for big-endian byte ordering (i.e.
BIG_ENDIAN_ATTRIBUTE - Static variable in class ome.specification.XMLWriter
Identifies the BigEndian attribute.
BIG_SPOTS - Static variable in class loci.poi.hssf.record.ExtendedFormatRecord
 
BIG_SPOTS - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
Large spots
BIG_TIFF - Static variable in class loci.formats.tiff.IFD
 
BIG_TIFF - Static variable in class loci.tests.testng.TiffWriterTest
The big tiff flags.
BIG_TIFF_BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants
The number of bytes in each IFD entry of a BigTIFF file.
BIG_TIFF_CUTOFF - Static variable in class loci.formats.out.TiffWriter
Number of bytes at which to automatically switch to BigTIFF This is approximately 3.9 GB instead of 4 GB, to allow space for the IFDs.
BIG_TIFF_MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
 
BIG_TIFF_SUFFIXES - Static variable in class loci.formats.out.TiffWriter
 
BigBlock - Class in loci.poi.poifs.storage
 
BigBlock() - Constructor for class loci.poi.poifs.storage.BigBlock
 
bigBlocks - Variable in class loci.poi.poifs.filesystem.POIFSDocument.BigBlockStore
 
bigBlockSize - Variable in class loci.poi.poifs.eventfilesystem.POIFSReader
 
bigBlockSize - Variable in class loci.poi.poifs.filesystem.POIFSDocument
 
bigBlockSize - Variable in class loci.poi.poifs.filesystem.POIFSFileSystem
 
bigBlockSize - Variable in class loci.poi.poifs.storage.HeaderBlockWriter
 
bigBlockSize - Variable in class loci.poi.poifs.storage.RawDataBlockList
 
bigEndian - Variable in class ome.xml.model.BinData
 
bigEndian - Variable in class ome.xml.model.Pixels
 
bigEndianString - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
bigEndianTransferSyntax - Variable in class loci.formats.in.DicomReader
 
bigImage - Variable in class loci.tests.testng.OpenBytesPerformanceTest
 
bigTiff - Variable in class loci.formats.tiff.TiffParser
Whether or not the TIFF file contains BigTIFF data.
bigTiff - Variable in class loci.formats.tiff.TiffSaver
Whether or not to write BigTIFF data.
bin - Variable in class jj2000.j2k.codestream.reader.PktDecoder
The wrapper to read bits for the packet heads
bin - Variable in class jj2000.j2k.entropy.decoder.StdEntropyDecoder
The bit based input for arithmetic coding bypass (i.e.
bin - Variable in class loci.formats.in.InCellReader
 
BIN_DATA_TAG - Static variable in class ome.specification.XMLWriter
Identifies the BinData tag.
binary - Variable in class loci.formats.in.EPSReader
Flag indicating binary data.
BINARY_SETUP - Static variable in class loci.formats.in.SDTInfo
 
BinaryDataInput - Interface in jj2000.j2k.io
This interface defines the input of binary data from streams and/or files.
BinaryDataOutput - Interface in jj2000.j2k.io
This interface defines the output of binary data to streams and/or files.
BinaryFile - Class in ome.xml.model
 
BinaryFile() - Constructor for class ome.xml.model.BinaryFile
Default constructor.
BinaryFile(Element, OMEModel) - Constructor for class ome.xml.model.BinaryFile
Constructs BinaryFile recursively from an XML DOM tree.
BinaryFile(BinaryFile) - Constructor for class ome.xml.model.BinaryFile
Copy constructor.
binaryFile - Variable in class ome.xml.model.FileAnnotation
 
BinaryOnly - Class in ome.xml.model
 
BinaryOnly() - Constructor for class ome.xml.model.BinaryOnly
Default constructor.
BinaryOnly(Element, OMEModel) - Constructor for class ome.xml.model.BinaryOnly
Constructs BinaryOnly recursively from an XML DOM tree.
BinaryOnly(BinaryOnly) - Constructor for class ome.xml.model.BinaryOnly
Copy constructor.
binaryOnly - Variable in class ome.xml.model.OME
 
BinaryTree - Class in loci.poi.util
Red-Black tree-based implementation of Map.
BinaryTree() - Constructor for class loci.poi.util.BinaryTree
Construct a new BinaryTree
BinaryTree(Map) - Constructor for class loci.poi.util.BinaryTree
Constructs a new BinaryTree from an existing Map, with keys and values sorted
BinaryTree.BinaryTreeIterator - Class in loci.poi.util
 
BinaryTree.BinaryTreeIterator(int) - Constructor for class loci.poi.util.BinaryTree.BinaryTreeIterator
Constructor
BinaryTree.Node - Class in loci.poi.util
 
BinaryTree.Node(Comparable, Comparable) - Constructor for class loci.poi.util.BinaryTree.Node
Make a new cell with given key and value, and with null links, and black (true) colors.
bind_ptr - Variable in class mdbtools.libmdb.MdbColumn
 
binData - Variable in class loci.formats.in.OMEXMLReader
 
binData - Variable in class ome.xml.model.BinaryFile
 
BinData - Class in ome.xml.model
 
BinData() - Constructor for class ome.xml.model.BinData
Default constructor.
BinData(Element, OMEModel) - Constructor for class ome.xml.model.BinData
Constructs BinData recursively from an XML DOM tree.
BinData(BinData) - Constructor for class ome.xml.model.BinData
Copy constructor.
binData - Variable in class ome.xml.model.Mask
 
binDataBlocks - Variable in class ome.xml.model.Pixels
 
binDataOffsets - Variable in class loci.formats.in.OMEXMLReader
 
binning - Variable in class loci.formats.in.BDReader
 
binning - Variable in class loci.formats.in.BioRadSCNReader
 
binning - Variable in class loci.formats.in.MetamorphHandler
 
binning - Variable in class loci.formats.in.MetamorphReader
 
binning - Variable in class loci.formats.in.MicromanagerReader.Position
 
binning - Variable in class loci.formats.in.ND2Handler
 
binning - Variable in class loci.formats.in.PCIReader
 
binning - Variable in class loci.formats.in.SimplePCITiffReader
 
binning - Variable in class loci.formats.in.ZeissLSMReader
 
binning - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
BINNING - Static variable in class ome.specification.XMLMockObjects
The default binning value.
binning - Variable in class ome.xml.model.DetectorSettings
 
Binning - Enum in ome.xml.model.enums
 
Binning(String) - Constructor for enum ome.xml.model.enums.Binning
 
BinningEnumHandler - Class in ome.xml.model.enums.handlers
Enumeration handler for Binning.
BinningEnumHandler() - Constructor for class ome.xml.model.enums.handlers.BinningEnumHandler
 
binnings - Variable in class loci.formats.in.FlexReader
 
binnings - Variable in class loci.formats.in.ZeissCZIReader
 
binningX - Variable in class loci.formats.in.CellSensReader.Pyramid
 
binningY - Variable in class loci.formats.in.CellSensReader.Pyramid
 
binSize - Variable in class loci.formats.in.SPCReader
 
binX - Variable in class loci.formats.in.FlexReader
Camera binning values.
binX - Variable in class loci.formats.in.IvisionReader
 
binY - Variable in class loci.formats.in.FlexReader
Camera binning values.
binY - Variable in class loci.formats.in.IvisionReader
 
BioFormatsExtensionPrinter - Class in loci.formats.tools
This class is used to generate a text file containing all of the image file extensions supported by Bio-Formats.
BioFormatsExtensionPrinter() - Constructor for class loci.formats.tools.BioFormatsExtensionPrinter
 
BioRadGelReader - Class in loci.formats.in
BioRadGelReader is the file format reader for Bio-Rad gel files.
BioRadGelReader() - Constructor for class loci.formats.in.BioRadGelReader
Constructs a new Bio-Rad gel reader.
BioRadReader - Class in loci.formats.in
BioRadReader is the file format reader for Bio-Rad PIC files.
BioRadReader() - Constructor for class loci.formats.in.BioRadReader
Constructs a new BioRadReader.
BioRadReader.BioRadHandler - Class in loci.formats.in
SAX handler for parsing XML.
BioRadReader.BioRadHandler() - Constructor for class loci.formats.in.BioRadReader.BioRadHandler
 
BioRadReader.Note - Class in loci.formats.in
 
BioRadReader.Note() - Constructor for class loci.formats.in.BioRadReader.Note
 
BioRadSCNReader - Class in loci.formats.in
BioRadSCNReader is the reader for Bio-Rad .scn files
BioRadSCNReader() - Constructor for class loci.formats.in.BioRadSCNReader
Constructs a new Bio-Rad .scn reader.
BioRadSCNReader.SCNHandler - Class in loci.formats.in
 
BioRadSCNReader.SCNHandler() - Constructor for class loci.formats.in.BioRadSCNReader.SCNHandler
 
biReader - Variable in class loci.formats.gui.DataConverter
 
bit - Variable in class loci.formats.codec.BitWriter
Deprecated.
Bit index into current byte of the buffer.
BIT - Static variable in class loci.formats.FormatTools
Identifies the BIT data type used to store pixel values.
BIT_DEPTH - Static variable in class loci.formats.in.CellSensReader
 
BitBuffer - Class in loci.formats.codec
Deprecated.
Use loci.common.RandomAccessInputStream instead
BitBuffer(byte[]) - Constructor for class loci.formats.codec.BitBuffer
Deprecated.
Default constructor.
bitDepth - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.HeaderBox
 
bitDepth - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.PaletteBox
 
bitDepth - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
bitDepth - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
 
bitDepth - Variable in class loci.formats.in.CellSensReader.Pyramid
 
BitDepth - Enum in ome.jxr.image
Deprecated.
BitDepth(Integer...) - Constructor for enum ome.jxr.image.BitDepth
Deprecated.
 
bitDepths - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
Various bit depth
bitDepthScale - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
BitField - Class in loci.poi.util
Manage operations dealing with bit-mapped fields.
BitField(int) - Constructor for class loci.poi.util.BitField
Create a BitField instance
BitFieldFactory - Class in loci.poi.util
Returns immutable Btfield instances.
BitFieldFactory() - Constructor for class loci.poi.util.BitFieldFactory
 
BitFile - Class in com.sun.media.imageioimpl.common
Came from GIFEncoder initially.
BitFile(ImageOutputStream, boolean) - Constructor for class com.sun.media.imageioimpl.common.BitFile
 
bitmapFileSize - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
bitmapOffset - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
BITMASK_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
 
bitMasks - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
BitOutputBuffer - Class in jj2000.j2k.codestream.writer
This class implements a buffer for writing bits, with the required bit stuffing policy for the packet headers.
BitOutputBuffer() - Constructor for class jj2000.j2k.codestream.writer.BitOutputBuffer
Creates a new BitOutputBuffer width a buffer of length 'SZ_INIT'.
bitPointer - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
bitPos - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
bits - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
Output bit buffer.
bits - Variable in class loci.formats.in.TargaReader
 
bits - Variable in enum ome.jxr.ifd.PixelType
Deprecated.
 
BITS_ALLOCATED - Static variable in class loci.formats.in.DicomReader
 
BITS_PER_COMPONENT_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
BITS_PER_SAMPLE - Static variable in class loci.formats.tiff.IFD
 
bitsLeft_ - Variable in class com.sun.media.imageioimpl.common.BitFile
 
BitsPerComponentBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000
This class is defined to represent a Bits Per Component Box of JPEG JP2 file format.
BitsPerComponentBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.BitsPerComponentBox
Counstructs a BitsPerComponentBox from the provided byte array containing the bit depths of each color component.
BitsPerComponentBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.BitsPerComponentBox
Constructs a BitsPerComponentBox based on the provide org.w3c.dom.Node.
bitsPerPixel - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
bitsPerPixel - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
bitsPerPixel - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXMetadata
 
bitsPerPixel - Variable in class loci.formats.CoreMetadata
Number of valid bits per pixel.
bitsPerPixel - Variable in class loci.formats.in.DicomReader
Bits per pixel.
bitsPerPixel - Variable in class loci.formats.in.NativeQTReader
Pixel depth.
bitsPerSample - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
The value of the BitsPerSample tag.
bitsPerSample - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
bitsPerSample - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
bitsPerSample - Variable in class loci.formats.codec.CodecOptions
Number of bits per channel.
bitsPerSampleCache - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
 
bitsPerScanline - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
bitsToGet - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWDecompressor
 
bitsToGet - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFLZWUtil
 
BitstreamReaderAgent - Class in jj2000.j2k.codestream.reader
This is the generic interface for bit stream reader agents.
BitstreamReaderAgent(HeaderDecoder, DecoderSpecs) - Constructor for class jj2000.j2k.codestream.reader.BitstreamReaderAgent
Initializes members of this class.
BitToByteOutput - Class in jj2000.j2k.entropy.encoder
This class provides an adapter to perform bit based output on byte based output objects that inherit from a 'ByteOutputBuffer' class.
BitToByteOutput(ByteOutputBuffer) - Constructor for class jj2000.j2k.entropy.encoder.BitToByteOutput
Instantiates a new 'BitToByteOutput' object that uses 'out' as the underlying byte based output.
BitWriter - Class in loci.formats.codec
Deprecated.
Use loci.common.RandomAccessOutputStream instead
BitWriter() - Constructor for class loci.formats.codec.BitWriter
Deprecated.
Constructs a new bit writer.
BitWriter(int) - Constructor for class loci.formats.codec.BitWriter
Deprecated.
Constructs a new bit writer with the given initial buffer size.
biWriter - Variable in class loci.formats.gui.DataConverter
 
bizarreMultichannelAcquisition - Variable in class loci.formats.in.MetamorphReader
 
BLACK - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
The CCITT numerical definition of black.
black - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
blank(byte[]) - Method in class loci.formats.in.PrairieReader
Blanks out and returns the given buffer.
blankImage(int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Creates a blank image with the given dimensions and transfer type.
BlankRecord - Class in loci.poi.hssf.record
Title: Blank cell record
BlankRecord() - Constructor for class loci.poi.hssf.record.BlankRecord
Creates a new instance of BlankRecord
BlankRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BlankRecord
Constructs a BlankRecord and sets its fields appropriately
blankThumbBytes - Variable in class loci.formats.FileStitcher.ExternalSeries
 
blip - Variable in class loci.poi.hssf.usermodel.HSSFPictureData
Underlying escher blip record containing the bitmap data.
BLIP__BLIPFILENAME - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__BLIPFLAGS - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__BLIPTODISPLAY - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__BRIGHTNESSSETTING - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__CONTRASTSETTING - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__CROPFROMBOTTOM - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__CROPFROMLEFT - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__CROPFROMRIGHT - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__CROPFROMTOP - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__DOUBLEMOD - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__GAMMA - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__NOHITTESTPICTURE - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PICTUREACTIVE - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PICTUREBILEVEL - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PICTUREFILLMOD - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PICTUREGRAY - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PICTUREID - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PICTURELINE - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PRINTBLIP - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PRINTBLIPFILENAME - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__PRINTFLAGS - Static variable in class loci.poi.ddf.EscherProperties
 
BLIP__TRANSPARENTCOLOR - Static variable in class loci.poi.ddf.EscherProperties
 
BlkImgDataSrc - Interface in jj2000.j2k.image
This interface defines the methods to transfer image data in blocks, without following any particular order (random access).
block - Variable in class loci.formats.FilePatternBlock
String representation of this block.
block0 - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf
Block used to request component with index 0
block0 - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf
Block used to request component 0
block1 - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf
Block used to request component with index 1
block1 - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf
Block used to request component 1
block2 - Variable in class jj2000.j2k.image.forwcomptransf.ForwCompTransf
Block used to request component with index 2
block2 - Variable in class jj2000.j2k.image.invcomptransf.InvCompTransf
Block used to request component 2
BLOCK_END - Static variable in class loci.formats.FilePatternBlock
Identifies the end of a block.
BLOCK_SIZE - Static variable in class loci.poi.hssf.record.DBCellRecord
 
BLOCK_START - Static variable in class loci.formats.FilePatternBlock
Identifies the start of a block.
blockAligned - Variable in class jj2000.j2k.roi.encoder.ROIScaler
Flag indicating if block aligned ROIs are used
BlockAllocationTableReader - Class in loci.poi.poifs.storage
This class manages and creates the Block Allocation Table, which is basically a set of linked lists of block indices.
BlockAllocationTableReader(int, int[], int, int, BlockList, int) - Constructor for class loci.poi.poifs.storage.BlockAllocationTableReader
create a BlockAllocationTableReader for an existing filesystem.
BlockAllocationTableReader(ListManagedBlock[], BlockList, int) - Constructor for class loci.poi.poifs.storage.BlockAllocationTableReader
create a BlockAllocationTableReader from an array of raw data blocks
BlockAllocationTableReader() - Constructor for class loci.poi.poifs.storage.BlockAllocationTableReader
Constructor BlockAllocationTableReader
BlockAllocationTableWriter - Class in loci.poi.poifs.storage
This class manages and creates the Block Allocation Table, which is basically a set of linked lists of block indices.
BlockAllocationTableWriter() - Constructor for class loci.poi.poifs.storage.BlockAllocationTableWriter
create a BlockAllocationTableWriter
blockData - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
 
BlockingInputStream - Class in loci.poi.util
Implementation of a BlockingInputStream to provide data to RawDataBlock that expects data in 512 byte chunks.
BlockingInputStream(InputStream) - Constructor for class loci.poi.util.BlockingInputStream
 
blockLength - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
blockLength - Variable in class loci.formats.in.PQBinReader
No of timeBins pre-loaded as a block
blockLength - Variable in class loci.formats.in.SDTInfo
reserved2 now contains block (set) length.
blockLength - Variable in class loci.formats.in.SDTReader
No of timeBins pre-loaded as a block
BlockList - Interface in loci.poi.poifs.storage
Interface for lists of blocks that are mapped by block allocation tables
BlockListImpl - Class in loci.poi.poifs.storage
A simple implementation of BlockList
BlockListImpl() - Constructor for class loci.poi.poifs.storage.BlockListImpl
Constructor BlockListImpl
blockNo - Variable in class loci.formats.in.SDTInfo
Number of the block in the file.
blockPointer - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
blockRandomised - Variable in class loci.common.CBZip2InputStream
 
blocks - Variable in class loci.formats.FilePattern
List of pattern blocks for this file pattern.
blocks - Variable in class loci.formats.in.APNGReader
 
blocks_ - Variable in class com.sun.media.imageioimpl.common.BitFile
note this also indicates gif format BITFile.
blockSize - Variable in class loci.formats.in.GIFReader
Block size.
blockSize - Variable in class loci.formats.in.VolocityReader.Stack
 
blockSize - Variable in class loci.poi.poifs.storage.BATBlock
 
blockSize - Variable in class loci.poi.poifs.storage.DocumentBlock
 
blockSize - Variable in class loci.poi.poifs.storage.PropertyBlock
 
blockSize - Variable in class loci.poi.poifs.storage.RawDataBlock
 
blockSize100k - Variable in class loci.common.CBZip2InputStream
always: in the range 0 ..
blockType - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
blockType - Variable in class loci.formats.in.SDTInfo
See blockType defines below.
BlockWritable - Interface in loci.poi.poifs.storage
An interface for persisting block storage of POIFS components.
blue - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
blue - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
blue - Variable in class loci.poi.hssf.record.PColor
 
blue - Variable in class loci.poi.hssf.usermodel.HSSFPalette.CustomColor
 
BLUE_GAIN - Static variable in class loci.formats.in.CellSensReader
 
BLUE_MIN - Static variable in class loci.plugins.in.Colorizer
 
BLUE_OFFSET - Static variable in class loci.formats.in.CellSensReader
 
BLUE_TO_GREEN_MIN - Static variable in class loci.plugins.in.Colorizer
 
blueGain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
blueMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
blueMask - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
blueOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
 
blueOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
blueShort - Variable in class loci.formats.gui.Index16ColorModel
Lookup tables.
blueX - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
blueY - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
blueZ - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
BMP - Static variable in class loci.formats.in.CellSensReader
 
BMP_MAGIC_STRING - Static variable in class loci.formats.in.BMPReader
 
bmpBitsPerPixel - Variable in class loci.formats.in.AVIReader
 
bmpColorsUsed - Variable in class loci.formats.in.AVIReader
 
bmpCompression - Variable in class loci.formats.in.AVIReader
 
BMPConstants - Interface in com.sun.media.imageioimpl.plugins.bmp
 
BMPImageReader - Class in com.sun.media.imageioimpl.plugins.bmp
This class is the Java Image IO plugin reader for BMP images.
BMPImageReader(ImageReaderSpi) - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
Constructs BMPImageReader from the provided ImageReaderSpi.
BMPImageReader.EmbeddedProgressAdapter - Class in com.sun.media.imageioimpl.plugins.bmp
 
BMPImageReader.EmbeddedProgressAdapter() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader.EmbeddedProgressAdapter
 
BMPImageReaderSpi - Class in com.sun.media.imageioimpl.plugins.bmp
 
BMPImageReaderSpi() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
BMPImageWriteParam - Class in com.sun.media.imageio.plugins.bmp
A subclass of ImageWriteParam for encoding images in the BMP format.
BMPImageWriteParam(Locale) - Constructor for class com.sun.media.imageio.plugins.bmp.BMPImageWriteParam
Constructs a BMPImageWriteParam set to use a given Locale and with default values for all parameters.
BMPImageWriteParam() - Constructor for class com.sun.media.imageio.plugins.bmp.BMPImageWriteParam
Constructs an BMPImageWriteParam object with default values for all parameters and a null Locale.
BMPImageWriter - Class in com.sun.media.imageioimpl.plugins.bmp
The Java Image IO plugin writer for encoding a binary RenderedImage into a BMP format.
BMPImageWriter(ImageWriterSpi) - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
Constructs BMPImageWriter based on the provided ImageWriterSpi.
BMPImageWriter.IIOWriteProgressAdapter - Class in com.sun.media.imageioimpl.plugins.bmp
 
BMPImageWriter.IIOWriteProgressAdapter() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter.IIOWriteProgressAdapter
 
BMPImageWriterSpi - Class in com.sun.media.imageioimpl.plugins.bmp
 
BMPImageWriterSpi() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
BMPMetadata - Class in com.sun.media.imageioimpl.plugins.bmp
 
BMPMetadata() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
BMPMetadata(IIOMetadata) - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
BMPMetadataFormat - Class in com.sun.media.imageioimpl.plugins.bmp
 
BMPMetadataFormat() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormat
 
BMPMetadataFormatResources - Class in com.sun.media.imageioimpl.plugins.bmp
 
BMPMetadataFormatResources() - Constructor for class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormatResources
 
BMPReader - Class in loci.formats.in
BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
BMPReader() - Constructor for class loci.formats.in.BMPReader
Constructs a new BMP reader.
bmpScanLineSize - Variable in class loci.formats.in.AVIReader
 
bmpVersion - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
bmpWidth - Variable in class loci.formats.in.AVIReader
 
bms - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder
By-pass mode specifications
BOFRecord - Class in loci.poi.hssf.record
Title: Beginning Of File
BOFRecord() - Constructor for class loci.poi.hssf.record.BOFRecord
Constructs an empty BOFRecord with no fields set.
BOFRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BOFRecord
Constructs a BOFRecord and sets its fields appropriately
BogusColorSpace - Class in com.sun.media.imageioimpl.common
A dummy ColorSpace to enable ColorModel for image data which do not have an innate color representation.
BogusColorSpace(int) - Constructor for class com.sun.media.imageioimpl.common.BogusColorSpace
Constructs a bogus ColorSpace.
bold - Variable in class loci.formats.in.BaseZeissReader.Shape
 
BOLDWEIGHT_BOLD - Static variable in class loci.poi.hssf.usermodel.HSSFFont
Bold boldness (bold)
BOLDWEIGHT_NORMAL - Static variable in class loci.poi.hssf.usermodel.HSSFFont
Normal boldness (not bold)
book - Variable in class loci.poi.hssf.model.FormulaParser
 
book - Variable in class loci.poi.hssf.usermodel.HSSFCell
 
book - Variable in class loci.poi.hssf.usermodel.HSSFName
 
book - Variable in class loci.poi.hssf.usermodel.HSSFRichTextString
 
book - Variable in class loci.poi.hssf.usermodel.HSSFRow
reference to containing low level Workbook
book - Variable in class loci.poi.hssf.usermodel.HSSFSheet
 
BookBoolRecord - Class in loci.poi.hssf.record
Title: Save External Links record (BookBool)
BookBoolRecord() - Constructor for class loci.poi.hssf.record.BookBoolRecord
 
BookBoolRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BookBoolRecord
Constructs a BookBoolRecord and sets its fields appropriately
BOOLEAN - Static variable in class loci.formats.in.CellSensReader
 
BooleanAnnotation - Class in ome.xml.model
 
BooleanAnnotation() - Constructor for class ome.xml.model.BooleanAnnotation
Default constructor.
BooleanAnnotation(Element, OMEModel) - Constructor for class ome.xml.model.BooleanAnnotation
Constructs BooleanAnnotation recursively from an XML DOM tree.
BooleanAnnotation(BooleanAnnotation) - Constructor for class ome.xml.model.BooleanAnnotation
Copy constructor.
booleanAnnotations - Variable in class ome.xml.model.StructuredAnnotations
 
BooleanOption - Class in loci.plugins.prefs
A boolean option for one of the plugins.
BooleanOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.BooleanOption
Constructs a boolean option with the parameters from the given map.
BooleanOption(String, boolean, String, String, boolean) - Constructor for class loci.plugins.prefs.BooleanOption
Constructs a boolean option with the given parameters.
BoolErrRecord - Class in loci.poi.hssf.record
Creates new BoolErrRecord.
BoolErrRecord() - Constructor for class loci.poi.hssf.record.BoolErrRecord
Creates new BoolErrRecord
BoolErrRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BoolErrRecord
Constructs a BoolErr record and sets its fields appropriately.
BoolPtg - Class in loci.poi.hssf.record.formula
Boolean (boolean) Stores a (java) boolean value in a formula.
BoolPtg() - Constructor for class loci.poi.hssf.record.formula.BoolPtg
 
BoolPtg(RecordInputStream) - Constructor for class loci.poi.hssf.record.formula.BoolPtg
 
BoolPtg(String) - Constructor for class loci.poi.hssf.record.formula.BoolPtg
 
BORDER - Static variable in class loci.plugins.shortcut.ShortcutPanel
Number of pixels for window border.
border - Variable in class loci.poi.hssf.record.DatRecord
 
BORDER_DASH_DOT - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
dash-dot border
BORDER_DASH_DOT_DOT - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
dash-dot-dot border
BORDER_DASHED - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
dash border
BORDER_DOTTED - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
hair-line border
BORDER_DOUBLE - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
double-line border
BORDER_HAIR - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
dot border
BORDER_MEDIUM - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
Medium border
BORDER_MEDIUM_DASH_DOT - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
medium dash-dot border
BORDER_MEDIUM_DASH_DOT_DOT - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
medium dash-dot-dot border
BORDER_MEDIUM_DASHED - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
Medium dashed border
BORDER_NONE - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
No border
BORDER_SLANTED_DASH_DOT - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
slanted dash-dot border
BORDER_THICK - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
Thick border
BORDER_THIN - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
Thin border
BORDER_TYPE_REGULAR - Static variable in class loci.poi.hssf.record.FrameRecord
 
BORDER_TYPE_SHADOW - Static variable in class loci.poi.hssf.record.FrameRecord
 
bordL - Variable in class loci.formats.in.SDTInfo
 
bordU - Variable in class loci.formats.in.SDTInfo
 
bottomHalfSize - Variable in class loci.tests.testng.OpenBytesPerformanceTest
 
bottomLeftQuarterSize - Variable in class loci.tests.testng.OpenBytesPerformanceTest
 
BottomMargin - Static variable in class loci.poi.hssf.model.Sheet
 
BottomMargin - Static variable in class loci.poi.hssf.usermodel.HSSFSheet
 
bottomMargin - Variable in class ome.jxr.parser.DatastreamParser
Deprecated.
 
BottomMarginRecord - Class in loci.poi.hssf.record
Record for the bottom margin.
BottomMarginRecord() - Constructor for class loci.poi.hssf.record.BottomMarginRecord
 
BottomMarginRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BottomMarginRecord
Constructs a BottomMargin record and sets its fields appropriately.
bottomRightQuarterSize - Variable in class loci.tests.testng.OpenBytesPerformanceTest
 
BoundSheetRecord - Class in loci.poi.hssf.record
Title: Bound Sheet Record (aka BundleSheet)
BoundSheetRecord() - Constructor for class loci.poi.hssf.record.BoundSheetRecord
 
BoundSheetRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.BoundSheetRecord
Constructs a BoundSheetRecord and sets its fields appropriately
boundsheets - Variable in class loci.poi.hssf.model.Workbook
holds the "boundsheet" records (aka bundlesheet) so that they can have their reference to their "BOF" marker
boundValues - Variable in class loci.formats.services.MDBServiceImpl
 
boutT - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder
The raw bit output used, for each thread
Box - Class in com.sun.media.imageioimpl.plugins.jpeg2000
This class is defined to create the box of JP2 file format.
Box(int, int, byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.Box
Constructs a Box instance using the provided the box type and the box content in byte array format.
Box(int, int, long, byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.Box
Constructs a Box instance using the provided the box type, the box extra length, and the box content in byte array format.
Box(ImageInputStream, int) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.Box
Constructs a Box instance from the provided ImageInputStream at the specified position.
Box(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.Box
Constructs a Box from an "unknown" Node.
BOX_SIZE - Static variable in class loci.formats.in.FakeReader
 
boxClasses - Static variable in class com.sun.media.imageioimpl.plugins.jpeg2000.Box
A Hashtable contains the class names for each type of the boxes.
boxes - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
The boxes of JP2 file used as meta data, i.
boxes - Variable in class loci.plugins.in.SeriesDialog
 
bpc - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter
Bits per component
BPC_LENGTH - Static variable in class jj2000.j2k.fileformat.writer.FileFormatWriter
base length of Bits Per Component box
bpcVaries - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter
Flag indicating whether number of bits per component varies
bpixels - Variable in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
bpos - Variable in class jj2000.j2k.codestream.reader.PktHeaderBitReader
The position of the next bit to read in the bit buffer (0 means empty, 8 full)
bpos - Variable in class jj2000.j2k.entropy.decoder.ByteToBitInput
The position of the next bit to get from the byte buffer.
bpos - Variable in class jj2000.j2k.entropy.encoder.BitToByteOutput
The position of the next bit to put in the bit buffer.
bpp - Variable in class loci.formats.in.BaseZeissReader
Number of bytes per pixel.
bpp - Variable in class loci.formats.in.BMPReader
Number of bits per pixel.
bpp - Variable in class loci.formats.in.MIASReader
 
bpp - Variable in class loci.formats.in.SPCReader
 
bpp - Variable in class loci.formats.out.CellH5Writer
 
bpp - Variable in class loci.tests.testng.OpenBytesPerformanceTest
 
branch - Variable in class loci.formats.codec.HuffmanCodec.Decoder
 
brand - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.FileTypeBox
The element values.
breader - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
BreakMap - Variable in class loci.poi.hssf.record.PageBreakRecord
 
breaks - Variable in class loci.poi.hssf.record.PageBreakRecord
 
BRICKS - Static variable in class loci.poi.hssf.record.ExtendedFormatRecord
 
BRICKS - Static variable in class loci.poi.hssf.usermodel.HSSFCellStyle
Brick-like layout
BRIGHT_FIELD - Static variable in class loci.formats.in.LegacyND2Reader
 
BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
 
BRIGHTNESS_VALUE - Static variable in class loci.formats.tiff.IFD
 
brokenNotes - Variable in class loci.formats.in.BioRadReader
 
BrowserOptionsWindow - Class in loci.plugins.util
Extension of JFrame that allows the user to adjust caching settings.
BrowserOptionsWindow(String, Cache, String[]) - Constructor for class loci.plugins.util.BrowserOptionsWindow
 
BrukerReader - Class in loci.formats.in
BrukerReader is the file format reader for Bruker MRI files.
BrukerReader() - Constructor for class loci.formats.in.BrukerReader
Constructs a new Bruker reader.
bsBuff - Variable in class loci.common.CBZip2InputStream
 
bsGetBit() - Method in class loci.common.CBZip2InputStream
 
bsGetInt() - Method in class loci.common.CBZip2InputStream
 
bsGetUByte() - Method in class loci.common.CBZip2InputStream
 
bsLive - Variable in class loci.common.CBZip2InputStream
 
bspos - Variable in class loci.poi.hssf.model.WorkbookRecordList
 
bsR(int) - Method in class loci.common.CBZip2InputStream
 
BSTORE_CONTAINER - Static variable in class loci.poi.ddf.EscherContainerRecord
 
bsWriter - Variable in class jj2000.j2k.entropy.encoder.PostCompRateAllocator
The bit-stream writer
BT_DIB - Static variable in class loci.poi.ddf.EscherBSERecord
 
BT_EMF - Static variable in class loci.poi.ddf.EscherBSERecord
 
BT_ERROR - Static variable in class loci.poi.ddf.EscherBSERecord
 
BT_JPEG - Static variable in class loci.poi.ddf.EscherBSERecord
 
BT_PICT - Static variable in class loci.poi.ddf.EscherBSERecord
 
BT_PNG - Static variable in class loci.poi.ddf.EscherBSERecord
 
BT_UNKNOWN - Static variable in class loci.poi.ddf.EscherBSERecord
 
BT_WMF - Static variable in class loci.poi.ddf.EscherBSERecord
 
BUBBLE_SERIES_TYPE_DATES - Static variable in class loci.poi.hssf.record.SeriesRecord
 
BUBBLE_SERIES_TYPE_NUMERIC - Static variable in class loci.poi.hssf.record.SeriesRecord
 
BUBBLE_SERIES_TYPE_SEQUENCE - Static variable in class loci.poi.hssf.record.SeriesRecord
 
BUBBLE_SERIES_TYPE_TEXT - Static variable in class loci.poi.hssf.record.SeriesRecord
 
bucketAbsoluteOffsets - Variable in class loci.poi.hssf.record.SSTRecord
Offsets from the beginning of the SST record (even across continuations)
bucketAbsoluteOffsets - Variable in class loci.poi.hssf.record.SSTSerializer
Offsets from the beginning of the SST record (even across continuations)
bucketRelativeOffsets - Variable in class loci.poi.hssf.record.SSTRecord
Offsets relative the start of the current SST or continue record
bucketRelativeOffsets - Variable in class loci.poi.hssf.record.SSTSerializer
Offsets relative the start of the current SST or continue record
buf - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
The line buffer.
buf - Variable in class jj2000.j2k.codestream.writer.BitOutputBuffer
The buffer where we store the data
buf - Variable in class jj2000.j2k.entropy.decoder.ByteInputBuffer
The byte array containing the data
buf - Variable in class jj2000.j2k.entropy.encoder.ByteOutputBuffer
The buffer where the data is stored
buf - Variable in class jj2000.j2k.image.input.ImgReaderPGM
The line buffer.
buf - Variable in class jj2000.j2k.util.ISRandomAccessIO
 
buf - Variable in class loci.formats.codec.BitWriter
Deprecated.
Buffer storing all bits written thus far.
BUF_DEF_LEN - Static variable in class jj2000.j2k.entropy.encoder.ByteOutputBuffer
The default initial buffer size
BUF_INC - Static variable in class jj2000.j2k.entropy.encoder.ByteOutputBuffer
The buffer increase size
buffer - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
buffer - Variable in class loci.common.ByteArrayHandle
Backing ByteBuffer.
buffer - Variable in class loci.common.NIOFileHandle
The buffer itself.
buffer(long, int) - Method in class loci.common.NIOFileHandle
Aligns the NIO buffer, maps it if it is not currently and sets all relevant positions and offsets.
buffer_ - Variable in class com.sun.media.imageioimpl.common.BitFile
 
BUFFER_SIZE - Static variable in class loci.formats.in.NativeND2Reader
 
BUFFER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
 
BufferedImageReader - Class in loci.formats.gui
A reader wrapper for reading image planes as BufferedImage objects.
BufferedImageReader() - Constructor for class loci.formats.gui.BufferedImageReader
Constructs a BufferedImageReader around a new image reader.
BufferedImageReader(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageReader
Constructs a BufferedImageReader with the given reader.
BufferedImageSource - Class in loci.formats.gui
Retrieves BufferedImages from a data source using Bio-Formats.
BufferedImageSource(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageSource
 
BufferedImageWriter - Class in loci.formats.gui
A writer wrapper for writing image planes from BufferedImage objects.
BufferedImageWriter() - Constructor for class loci.formats.gui.BufferedImageWriter
Constructs a BufferedImageWriter around a new image writer.
BufferedImageWriter(IFormatWriter) - Constructor for class loci.formats.gui.BufferedImageWriter
Constructs a BufferedImageWriter with the given writer.
BufferedRandomAccessFile - Class in jj2000.j2k.io
This class defines a Buffered Random Access File.
BufferedRandomAccessFile(File, String, int) - Constructor for class jj2000.j2k.io.BufferedRandomAccessFile
Constructor.
BufferedRandomAccessFile(File, String) - Constructor for class jj2000.j2k.io.BufferedRandomAccessFile
Constructor.
BufferedRandomAccessFile(String, String, int) - Constructor for class jj2000.j2k.io.BufferedRandomAccessFile
Constructor.
BufferedRandomAccessFile(String, String) - Constructor for class jj2000.j2k.io.BufferedRandomAccessFile
Constructor.
bufferSize - Variable in class loci.common.NIOFileHandle
The buffer size.
bufferStartPosition - Variable in class loci.common.NIOFileHandle
The absolute position of the start of the buffer.
bufLength - Variable in class loci.formats.in.SPCReader
 
bufSize(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ
Returns the maximum size of the buffer (in bytes) required to hold a JPEG image with the given width and height, and level of chrominance subsampling.
bufSizeYUV(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ
Returns the size of the buffer (in bytes) required to hold a YUV planar image with the given width, height, and level of chrominance subsampling.
bugaddr - Static variable in class jj2000.j2k.JJ2KInfo
The bug reporting e-mail address
BUILD - Static variable in class loci.poi.hssf.record.BOFRecord
suggested default 0x10d3
BUILD_YEAR - Static variable in class loci.poi.hssf.record.BOFRecord
suggested default 0x07CC (1996)
buildAndWriteLayers() - Method in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator
This method builds all the bit stream layers and then writes them to the output bit stream.
buildCondition(Object, int, Object) - Method in class mdbtools.dbengine.Tests
 
buildDB() - Method in class mdbtools.dbengine.Tests
 
buildEquation(Object, int, Object) - Method in class mdbtools.dbengine.Tests
 
BUILDER - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
 
builder - Variable in class ome.xml.meta.AbstractOMEXMLMetadata
 
buildExtensions() - Method in class loci.plugins.macro.MacroFunctions
Builds the list of extensions, using reflection, from public methods of this class.
buildFileChooser(IFormatHandler) - Static method in class loci.formats.gui.GUITools
Constructs a file chooser for the given file format handler.
buildFileChooser(IFormatHandler, boolean) - Static method in class loci.formats.gui.GUITools
Constructs a file chooser for the given file format handler.
buildFileChooser(FileFilter[]) - Static method in class loci.formats.gui.GUITools
Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter.
buildFileChooser(FileFilter[], boolean) - Static method in class loci.formats.gui.GUITools
Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter, if one is not already specified.
buildFileFilters(IFormatHandler) - Static method in class loci.formats.gui.GUITools
Constructs a list of file filters for the given file format handler.
buildFiles(String, int, List<String>) - Method in class loci.formats.FilePattern
 
buildFontCharactersProperty(String) - Static method in class loci.poi.hssf.usermodel.FontDetails
 
buildFontHeightProperty(String) - Static method in class loci.poi.hssf.usermodel.FontDetails
 
buildFontWidthsProperty(String) - Static method in class loci.poi.hssf.usermodel.FontDetails
 
buildFunction(Function, Object) - Method in class mdbtools.dbengine.Tests
 
buildFunction(Aggregate, Object) - Method in class mdbtools.dbengine.Tests
 
buildJoin(Object, int, Table, Equation) - Method in class mdbtools.dbengine.Tests
 
buildPalette() - Method in class com.sun.media.imageioimpl.common.PaletteBuilder
 
buildSelect(Object[], Object[], Object, FQColumn[], Object[][]) - Method in class mdbtools.dbengine.Tests
 
buildTestCases() - Method in class mdbtools.dbengine.Tests
 
buildTIFFList(int) - Method in class loci.formats.in.MicromanagerReader
 
buildTIFFList(int, String) - Method in class loci.formats.in.MicromanagerReader
Populate the list of TIFF files using the given file name as a pattern.
buildTime - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator
The wall time for the building of layers.
buildTypes() - Static method in class loci.formats.in.DicomReader
Assemble the data dictionary.
BUILTIN_AUTO_ACTIVATE - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_AUTO_CLOSE - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_AUTO_DEACTIVATE - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_AUTO_OPEN - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_CONSOLIDATE_AREA - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_CRITERIA - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_DATA_FORM - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_DATABASE - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_PRINT_AREA - Static variable in class loci.poi.hssf.record.NameRecord
 
BUILTIN_PRINT_TITLE - Static variable in class loci.poi.hssf.record.NameRecord
 
BUILTIN_RECORDER - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
BUILTIN_SHEET_TITLE - Static variable in class loci.poi.hssf.record.NameRecord
Included for completeness sake, not implemented
builtinFormats - Static variable in class loci.poi.hssf.usermodel.HSSFDataFormat
 
BurleighReader - Class in loci.formats.in
BurleighReader is the file format reader for Burleigh .img files.
BurleighReader() - Constructor for class loci.formats.in.BurleighReader
Constructs a new Burleigh reader.
bypass - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Uses the lazy coding mode with the entropy coder.
BYTE - Static variable in class loci.formats.in.GatanReader
 
BYTE_COUNT_OFFSET - Static variable in class loci.formats.out.QTWriter
Seek to this offset to update the total number of pixel bytes.
BYTE_ORDER_ASSERTION - Static variable in class loci.poi.hpsf.PropertySet
The "byteOrder" field must equal this value.
BYTE_SIZE - Static variable in interface loci.poi.util.LittleEndianConsts
 
ByteArrayHandle - Class in loci.common
A wrapper for a byte array that implements the IRandomAccess interface.
ByteArrayHandle(byte[]) - Constructor for class loci.common.ByteArrayHandle
Creates a random access byte stream to read from, and write to, the bytes specified by the byte[] argument.
ByteArrayHandle(ByteBuffer) - Constructor for class loci.common.ByteArrayHandle
 
ByteArrayHandle(int) - Constructor for class loci.common.ByteArrayHandle
Creates a random access byte stream to read from, and write to.
ByteArrayHandle() - Constructor for class loci.common.ByteArrayHandle
Creates a random access byte stream to write to a byte array.
byteArraySet(byte[], byte) - Static method in class jj2000.j2k.util.ArrayUtil
Reinitializes a byte array to the given value in an optimized way.
ByteArraySource - Class in loci.formats.cache
Retrieves byte arrays from a data source (e.g., a file) using Bio-Formats.
ByteArraySource(IFormatReader) - Constructor for class loci.formats.cache.ByteArraySource
Constructs a byte array source from the given Bio-Formats reader.
ByteArraySource(String) - Constructor for class loci.formats.cache.ByteArraySource
Constructs a byte array source that draws from the given file.
bytebuf - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
byteBuffer - Variable in class com.sun.media.imageio.stream.FileChannelImageOutputStream
A ByteBuffer used for writing to the channel.
byteBuffer - Variable in class jj2000.j2k.io.BufferedRandomAccessFile
Buffer of bytes containing the part of the file that is currently being accessed
byteBuffer - Variable in class loci.formats.codec.BitBuffer
Deprecated.
 
byteBufferChanged - Variable in class jj2000.j2k.io.BufferedRandomAccessFile
Boolean keeping track of whether the byte buffer has been changed since it was read.
byteBufferProvider - Variable in class loci.common.NIOFileHandle
Provider class for NIO byte buffers, allocated or memory mapped.
byteCount - Variable in class com.sun.media.imageio.plugins.tiff.TIFFDecompressor
The number of bytes of data from the source ImageInputStream to be decompressed.
ByteField - Class in loci.poi.util
representation of a byte (8-bit) field at a fixed location within a byte array
ByteField(int) - Constructor for class loci.poi.util.ByteField
construct the ByteField with its offset into its containing byte array and a default value of 0
ByteField(int, byte) - Constructor for class loci.poi.util.ByteField
construct the ByteField with its offset into its containing byte array and initialize its value
ByteField(int, byte[]) - Constructor for class loci.poi.util.ByteField
Construct the ByteField with its offset into its containing byte array and initialize its value from its byte array
ByteField(int, byte, byte[]) - Constructor for class loci.poi.util.ByteField
construct the ByteField with its offset into its containing byte array, initialize its value, and write its value to its byte array
byteIn() - Method in class jj2000.j2k.entropy.decoder.MQDecoder
This function gets one byte of compressed bits from the in-stream.
ByteInputBuffer - Class in jj2000.j2k.entropy.decoder
This class provides a byte input facility from byte buffers.
ByteInputBuffer(byte[]) - Constructor for class jj2000.j2k.entropy.decoder.ByteInputBuffer
Creates a new byte array input stream that reads data from the specified byte array.
ByteInputBuffer(byte[], int, int) - Constructor for class jj2000.j2k.entropy.decoder.ByteInputBuffer
Creates a new byte array input stream that reads data from the specified byte array.
byteOffset - Variable in class loci.poi.hssf.usermodel.HSSFPalette.CustomColor
 
byteOrder - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
byteOrder - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadata
 
byteOrder - Variable in class loci.poi.hpsf.PropertySet
Specifies this PropertySet's byte order.
byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
byteOrdering - Variable in class jj2000.j2k.io.BufferedRandomAccessFile
 
byteOut() - Method in class jj2000.j2k.entropy.encoder.MQCoder
This function puts one byte of compressed bits in the out out stream.
ByteOutputBuffer - Class in jj2000.j2k.entropy.encoder
This class provides a buffering output stream similar to ByteArrayOutputStream, with some additional methods.
ByteOutputBuffer() - Constructor for class jj2000.j2k.entropy.encoder.ByteOutputBuffer
Creates a new byte array output stream.
ByteOutputBuffer(int) - Constructor for class jj2000.j2k.entropy.encoder.ByteOutputBuffer
Creates a new byte array output stream, with a buffer capacity of the specified size, in bytes.
bytePointer - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
bytes - Variable in class loci.formats.in.OBFReader.Frame
 
bytes - Variable in class loci.formats.tiff.TiffSaver
Output bytes.
bytes - Variable in class loci.poi.hpsf.ClassID
The bytes making out the class ID in correct order, i.e.
BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants
The number of bytes in each IFD entry.
BYTES_PER_PIXEL - Static variable in class ome.specification.XMLMockObjects
The number of bytes per pixels.
bytesFromReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
bytesPerAxis - Variable in class loci.formats.in.LeicaHandler
 
bytesPerElement - Variable in enum loci.formats.tiff.IFDType
Number of bytes per element of this type.
bytesPerLine - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
bytesPerLine - Variable in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriter
 
bytesPerLine - Variable in class loci.formats.in.PCXReader
Number of bytes per scan line - may be different than image width.
bytesPerPixel - Variable in class loci.formats.in.AmiraReader.ASCII
 
bytesPerPixel - Variable in class loci.formats.in.GatanReader
 
bytesPerPixel - Variable in class loci.formats.in.OpenlabRawReader
Number of bytes per pixel.
bytesPerPixel - Variable in class loci.formats.out.AVIWriter
 
bytesPerPixel - Variable in class loci.tests.testng.Jpeg2000GrindTest
 
bytesPerPlane - Variable in class loci.formats.in.AVIReader
 
bytesToDouble(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a double.
bytesToDouble(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
bytesToDouble(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array to a double.
bytesToDouble(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a double.
bytesToDouble(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
bytesToDouble(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array to a double.
bytesToFloat(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a float.
bytesToFloat(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
bytesToFloat(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array to a float.
bytesToFloat(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond a given offset to a float.
bytesToFloat(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
bytesToFloat(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array to a float.
bytesToHex(byte[]) - Static method in class loci.common.DataTools
Translates the given byte array into a String of hexadecimal digits.
bytesToInt(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to an int.
bytesToInt(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
bytesToInt(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array to an int.
bytesToInt(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to an int.
bytesToInt(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
bytesToInt(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array to an int.
bytesToLong(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a long.
bytesToLong(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
bytesToLong(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array to a long.
bytesToLong(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a long.
bytesToLong(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
bytesToLong(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array to a long.
bytesToShort(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a short.
bytesToShort(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 2 bytes of a byte array beyond the given offset to a short.
bytesToShort(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 2 bytes of a byte array to a short.
bytesToShort(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array byond the given offset to a short.
bytesToShort(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 2 bytes of a byte array byond the given offset to a short.
bytesToShort(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 2 bytes of a byte array to a short.
byteStream - Variable in class loci.common.xml.LSInputI
 
byteTable - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxCompressor
 
ByteToBitInput - Class in jj2000.j2k.entropy.decoder
This class provides an adapter to perform bit based input on byte based output obejcts that inherit from a 'ByteInputBuffer' class.
ByteToBitInput(ByteInputBuffer) - Constructor for class jj2000.j2k.entropy.decoder.ByteToBitInput
Instantiates a new 'ByteToBitInput' object that uses 'in' as the underlying byte based input.
byteValue() - Method in class loci.formats.tiff.TiffRational
Returns the value of the specified number as a byte.
ByteVector - Class in loci.formats.codec
A growable array of bytes.
ByteVector() - Constructor for class loci.formats.codec.ByteVector
 
ByteVector(int) - Constructor for class loci.formats.codec.ByteVector
 
ByteVector(byte[]) - Constructor for class loci.formats.codec.ByteVector
 
BZip2Handle - Class in loci.common
StreamHandle implementation for reading from BZip2-compressed files or byte arrays.
BZip2Handle(String) - Constructor for class loci.common.BZip2Handle
Construct a new BZip2Handle corresponding to the given file.

C

c - Variable in class jj2000.j2k.entropy.decoder.MQDecoder
The current bit code
c - Variable in class jj2000.j2k.entropy.encoder.MQCoder
The current bit code
c - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor
The component on which to compress
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
 
c - Variable in class loci.tests.testng.Jpeg2000GrindTest.TileRunnable
 
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 - Static variable in class loci.common.CaseInsensitiveLocation
 
cache - Variable in class loci.common.CaseInsensitiveLocation.Cache
Mapping of directory names to directory content, the content being a mapping of case insensitive name to case sensitive (real) name on disc.
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
 
cachedDecoders - Variable in class loci.formats.codec.HuffmanCodec
 
cacheDirectoryListings(boolean) - Static method in class loci.common.Location
Turn cacheing of directory listings on or off.
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.
cacheListings - Static variable in class loci.common.Location
 
cacheNanos - Static variable in class loci.common.Location
 
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
 
calcBasisWaveForms(float[][]) - Method in class jj2000.j2k.wavelet.analysis.SubbandAn
Calculates the basis waveform of the first leaf for which the L2-norm has not been calculated yet.
CalcCountRecord - Class in loci.poi.hssf.record
Title: Calc Count Record Description: Specifies the maximum times the gui should perform a formula recalculation.
CalcCountRecord() - Constructor for class loci.poi.hssf.record.CalcCountRecord
 
CalcCountRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.CalcCountRecord
Constructs a CalcCountRecord and sets its fields appropriately
calcExtSSTRecordSize() - Method in class loci.poi.hssf.record.SSTRecord
Calculates the size in bytes of the EXTSST record as it would be if the record was serialized.
calcL2Norms() - Method in class jj2000.j2k.wavelet.analysis.SubbandAn
Calculates the L2-norm of the sythesis waveforms of every leaf in the tree.
calcMaxMagBits(J2KImageWriteParamJava) - Method in class jj2000.j2k.roi.encoder.ROIScaler
Calculates the maximum amount of magnitude bits for each tile-component, and stores it in the 'maxMagBits' array.
calcMixedBitDepths(int[], int, int[]) - Static method in class jj2000.j2k.image.forwcomptransf.ForwCompTransf
Calculates the bitdepths of the transformed components, given the bitdepth of the un-transformed components and the component tranformation type.
calcMixedBitDepths(int[], int, int[]) - Static method in class jj2000.j2k.image.invcomptransf.InvCompTransf
Calculates the bitdepths of the transformed components, given the bitdepth of the un-transformed components and the component tranformation type.
CalcModeRecord - Class in loci.poi.hssf.record
Title: Calc Mode Record
CalcModeRecord() - Constructor for class loci.poi.hssf.record.CalcModeRecord
 
CalcModeRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.CalcModeRecord
Constructs a CalcModeRecord and sets its fields appropriately
calcOnLoad - Variable in class loci.poi.hssf.record.FormulaRecord
 
calcPhotons - Variable in class loci.formats.in.SDTInfo
No of photons.
calcSbParams(SubbandAn, int) - Method in class jj2000.j2k.quantization.quantizer.Quantizer
Calculates the parameters of the SubbandAn objects that depend on the Quantizer.
calcSbParams(SubbandAn, int) - Method in class jj2000.j2k.quantization.quantizer.StdQuantizer
Calculates the parameters of the SubbandAn objects that depend on the Quantizer.
calcSize() - Method in class loci.poi.hpsf.MutableSection
Calculates the section's size.
calcSize(int) - Static method in class loci.poi.poifs.storage.SmallDocumentBlock
Calculate the storage size of a set of SmallDocumentBlocks
calcSkipMSBP(CBlkWTData, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder
Calculates the number of magnitude bit-planes that are to be skipped, because they are non-significant.
calculateDimensions() - Method in class loci.formats.in.ZeissCZIReader
 
calculateIFDOffset() - Method in class ome.jxr.parser.FileParser
Deprecated.
 
calculateStorageRequirements(int, int) - Static method in class loci.poi.poifs.storage.BATBlock
Calculate how many BATBlocks are needed to hold a specified number of BAT entries.
calculateXBATStorageRequirements(int, int) - Static method in class loci.poi.poifs.storage.BATBlock
Calculate how many XBATBlocks are needed to hold a specified number of BAT entries.
calculateXBATStorageRequirements(int, int) - Static method in class loci.poi.poifs.storage.HeaderBlockWriter
For a given number of BAT blocks, calculate how many XBAT blocks will be needed
calibratedMagnification - Variable in class ome.xml.model.Objective
 
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
 
CALLER - Static variable in class loci.common.LogbackTools
 
callLegacyReader() - Method in class loci.formats.DelegateReader
 
CALLOUT__CALLOUTACCENTBAR - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__CALLOUTANGLE - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__CALLOUTDROPSPECIFIED - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__CALLOUTDROPTYPE - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__CALLOUTLENGTHSPECIFIED - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__CALLOUTMINUSX - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__CALLOUTMINUSY - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__CALLOUTTEXTBORDER - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__CALLOUTTYPE - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__DROPAUTO - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__ISCALLOUT - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__LENGTHSPECIFIED - Static variable in class loci.poi.ddf.EscherProperties
 
CALLOUT__XYCALLOUTGAP - Static variable in class loci.poi.ddf.EscherProperties
 
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
 
canCreatePalette(ImageTypeSpecifier) - Static method in class com.sun.media.imageioimpl.common.PaletteBuilder
Returns true if PaletteBuilder is able to create palette for given image type.
canCreatePalette(RenderedImage) - Static method in class com.sun.media.imageioimpl.common.PaletteBuilder
Returns true if PaletteBuilder is able to create palette for given rendered image.
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReaderSpi
 
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
 
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReaderSpi
 
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReaderSpi
 
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReaderSpi
 
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReaderSpi
 
canDecodeInput(Object) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReaderSpi
 
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.
canEncodeImage(ImageWriter, ImageTypeSpecifier) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
Checks that the provided ImageWriter can encode the provided ImageTypeSpecifier or not.
canEncodeImage(ImageWriter, ColorModel, SampleModel) - Static method in class com.sun.media.imageioimpl.common.ImageUtil
Checks that the provided ImageWriter can encode the provided ColorModel and SampleModel.
canEncodeImage(int, ColorModel, SampleModel) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
canEncodeImage(int, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriterSpi
 
canEncodeImage(ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriterSpi
 
canFitInMemory(long) - Static method in class loci.tests.testng.TestTools
Returns true if a byte buffer of the given size will fit in memory.
canImport(JComponent, DataFlavor[]) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
 
canInsertEmpty(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
canInsertImage(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
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.
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.gif.GIFStreamMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFStreamMetadataFormat
 
canNodeAppear(String, ImageTypeSpecifier) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPMetadataFormat
 
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
 
canRead() - Method in class loci.common.Location
If the underlying location is a URL, this method will return true if the URL exists.
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
canReadRaster() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
canReplacePixels(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
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
 
canWrite() - Method in class loci.common.Location
If the underlying location is a URL, this method will always return false.
canWriteEmpty() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageWriter
 
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageWriter
 
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageWriter
 
canWriteRasters() - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
canWriteSequence() - Method in class com.sun.media.imageioimpl.plugins.gif.GIFImageWriter
 
canWriteSequence() - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
CAPTURE_EDITOR_DATA - Static variable in class loci.formats.in.NikonReader
 
CAPTURE_RESOLUTION_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
CaseInsensitiveLocation - Class in loci.common
Case insensitive variant of Location.
CaseInsensitiveLocation(String) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation(Location) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation(File) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation(String, String) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation(CaseInsensitiveLocation, String) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation.Cache - Class in loci.common
Caching for CaseInsensitiveLocation.
CaseInsensitiveLocation.Cache() - Constructor for class loci.common.CaseInsensitiveLocation.Cache
The constructor.
cast(Class<?>) - Method in class loci.formats.ClassList
Cast the given class to something that extends the base class.
cat(byte[][]) - Static method in class loci.poi.hpsf.Util
Concatenates the contents of several byte arrays into a single one.
cat - Variable in class loci.poi.util.SystemOutLogger
 
Catalog - Class in mdbtools.libmdb
 
Catalog() - Constructor for class mdbtools.libmdb.Catalog
 
catalog - Variable in class mdbtools.libmdb.MdbHandle
 
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
 
CATEGORY_DATA_TYPE_ALL_TEXT_CHARACTERISTIC - Static variable in class loci.poi.hssf.record.DefaultDataLabelTextPropertiesRecord
 
CATEGORY_DATA_TYPE_DATES - Static variable in class loci.poi.hssf.record.SeriesRecord
 
CATEGORY_DATA_TYPE_NUMERIC - Static variable in class loci.poi.hssf.record.SeriesRecord
 
CATEGORY_DATA_TYPE_SEQUENCE - Static variable in class loci.poi.hssf.record.SeriesRecord
 
CATEGORY_DATA_TYPE_SHOW_LABELS_CHARACTERISTIC - Static variable in class loci.poi.hssf.record.DefaultDataLabelTextPropertiesRecord
 
CATEGORY_DATA_TYPE_TEXT - Static variable in class loci.poi.hssf.record.SeriesRecord
 
CATEGORY_DATA_TYPE_VALUE_AND_PERCENTAGE_CHARACTERISTIC - Static variable in class loci.poi.hssf.record.DefaultDataLabelTextPropertiesRecord
 
CategorySeriesAxisRecord - Class in loci.poi.hssf.record
This record refers to a category or series axis and is used to specify label/tickmark frequency.
CategorySeriesAxisRecord() - Constructor for class loci.poi.hssf.record.CategorySeriesAxisRecord
 
CategorySeriesAxisRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.CategorySeriesAxisRecord
Constructs a CategorySeriesAxis record and sets its fields appropriately.
causalCXInfo - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Uses vertically stripe causal context formation.
cb0x - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder
The horizontal code-block partition origin
cb0x - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull
The horizontal coordinate of the code-block partition origin on the reference grid
cb0y - Variable in class jj2000.j2k.codestream.reader.HeaderDecoder
The vertical code-block partition origin
cb0y - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull
The vertical coordinate of the code-block partition on the reference grid
CBAR - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.CENTIBAR instead.
cBegin - Variable in class loci.plugins.in.ImporterOptions
 
cbI - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
Array containing info.
cbLength - Variable in class jj2000.j2k.codestream.reader.PktInfo
The length of the code-block in this packet (in bytes)
cblk - Variable in class jj2000.j2k.codestream.PrecInfo
Code-blocks belonging to this precinct in each subbands of the resolution level
CBlkCoordInfo - Class in jj2000.j2k.codestream
This class is used to store the coordinates of code-blocks.
CBlkCoordInfo() - Constructor for class jj2000.j2k.codestream.CBlkCoordInfo
Constructor.
CBlkCoordInfo(int, int) - Constructor for class jj2000.j2k.codestream.CBlkCoordInfo
Constructor.
CBlkInfo - Class in jj2000.j2k.codestream.reader
This class contains location of code-blocks' piece of codewords (there is one piece per layer) and some other information.
CBlkInfo(int, int, int, int, int) - Constructor for class jj2000.j2k.codestream.reader.CBlkInfo
Constructs a new instance with specified number of layers and code-block coordinates.
CBlkQuantDataSrcDec - Interface in jj2000.j2k.quantization.dequantizer
This interface defines a source of quantized wavelet coefficients and methods to transfer them in a code-block by code-block basis, fro the decoder side.
CBlkQuantDataSrcEnc - Interface in jj2000.j2k.quantization.quantizer
This interface defines a source of quantized wavelet coefficients and methods to transfer them in a code-block by code-block basis.
CBlkRateDistStats - Class in jj2000.j2k.entropy.encoder
This class stores coded (compressed) code-blocks with their associated rate-distortion statistics.
CBlkRateDistStats() - Constructor for class jj2000.j2k.entropy.encoder.CBlkRateDistStats
Creates a new CBlkRateDistStats object without allocating any space for 'truncRates', 'truncSlopes', 'truncDists' and 'truncIdxs' or 'data'.
CBlkRateDistStats(int, int, int, byte[], int[], double[], boolean[], int, boolean) - Constructor for class jj2000.j2k.entropy.encoder.CBlkRateDistStats
Creates a new CBlkRateDistStats object and initializes the valid truncation points, their rates and their slopes, from the 'rates' and 'dist' arrays.
cblks - Variable in class jj2000.j2k.codestream.reader.PktDecoder
List of code-blocks found in last read packet head (one list per subband)
cblks - Variable in class jj2000.j2k.decoder.DecoderSpecs
Code-blocks sizes specification
cblks - Variable in class jj2000.j2k.entropy.encoder.EBCOTRateAllocator
5D Array containing all the coded code-blocks: 1st index: tile index 2nd index: component index 3rd index: resolution level index 4th index: subband index 5th index: code-block index
cblks - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder
The code-block size specifications
cblks - Variable in class jj2000.j2k.wavelet.analysis.ForwWTFull
The code-block size specifications
CBlkSizeSpec - Class in jj2000.j2k.entropy
This class extends ModuleSpec class for code-blocks sizes holding purposes.
CBlkSizeSpec(int, int, byte) - Constructor for class jj2000.j2k.entropy.CBlkSizeSpec
Creates a new CBlkSizeSpec object for the specified number of tiles and components.
CBlkSizeSpec(int, int, byte, J2KImageWriteParamJava, String) - Constructor for class jj2000.j2k.entropy.CBlkSizeSpec
Creates a new CBlkSizeSpec object for the specified number of tiles and components and the parameters instance.
cblkToDecode - Variable in class jj2000.j2k.wavelet.synthesis.InvWTFull
The total number of code-blocks to decode
CBlkWTData - Class in jj2000.j2k.wavelet.analysis
This is a generic abstract class to store a code-block of wavelet data, be it quantized or not.
CBlkWTData() - Constructor for class jj2000.j2k.wavelet.analysis.CBlkWTData
 
CBlkWTDataFloat - Class in jj2000.j2k.wavelet.analysis
This is an implementation of the 'CBlkWTData' abstract class for 32 bit floating point data (float).
CBlkWTDataFloat() - Constructor for class jj2000.j2k.wavelet.analysis.CBlkWTDataFloat
 
CBlkWTDataInt - Class in jj2000.j2k.wavelet.analysis
This is an implementation of the 'CBlkWTData' abstract class for signed 32 bit integer data.
CBlkWTDataInt() - Constructor for class jj2000.j2k.wavelet.analysis.CBlkWTDataInt
 
CBlkWTDataSrc - Interface in jj2000.j2k.wavelet.analysis
This abstract class defines methods to transfer wavelet data in a code-block by code-block basis.
CBlkWTDataSrcDec - Interface in jj2000.j2k.wavelet.synthesis
This abstract class defines methods to transfer wavelet data in a code-block by code-block basis, for the decoder side.
cbOff - Variable in class jj2000.j2k.codestream.reader.PktInfo
The code-block offset in the codestream (for this packet)
CBZip2InputStream - Class in loci.common
An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.
CBZip2InputStream(InputStream) - Constructor for class loci.common.CBZip2InputStream
Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
CBZip2InputStream.Data - Class in loci.common
 
CBZip2InputStream.Data(int) - Constructor for class loci.common.CBZip2InputStream.Data
 
ccb - Variable in class jj2000.j2k.entropy.encoder.StdEntropyCoder.Compressor
The object where to store the compressed code-block
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
 
ccoc - Variable in class jj2000.j2k.codestream.HeaderInfo.COC
 
ccom - Variable in class jj2000.j2k.codestream.HeaderInfo.COM
 
cdata - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
cdata - Variable in class loci.formats.in.ZeissTIFFHandler
 
cdstreamStart - Variable in class jj2000.j2k.codestream.reader.FileBitstreamReaderAgent
 
ce - Variable in class jj2000.j2k.entropy.Progression
Component index for the end of a progression.
CELL_LENGTH - Static variable in class loci.formats.tiff.IFD
 
CELL_TYPE_BLANK - Static variable in class loci.poi.hssf.usermodel.HSSFCell
Blank Cell type (3)
CELL_TYPE_BOOLEAN - Static variable in class loci.poi.hssf.usermodel.HSSFCell
Boolean Cell type (4)
CELL_TYPE_ERROR - Static variable in class loci.poi.hssf.usermodel.HSSFCell
Error Cell type (5)
CELL_TYPE_FORMULA - Static variable in class loci.poi.hssf.usermodel.HSSFCell
Formula Cell type (2)
CELL_TYPE_NUMERIC - Static variable in class loci.poi.hssf.usermodel.HSSFCell
Numeric Cell type (0)
CELL_TYPE_STRING - Static variable in class loci.poi.hssf.usermodel.HSSFCell
String Cell type (1)
CELL_WIDTH - Static variable in class loci.formats.tiff.IFD
 
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.CellH5Constants() - Constructor for class loci.formats.in.CellH5Reader.CellH5Constants
 
CellH5Reader.CellH5Coordinate - Class in loci.formats.in
 
CellH5Reader.CellH5Coordinate(String, String, String) - Constructor for class loci.formats.in.CellH5Reader.CellH5Coordinate
 
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
 
cellIterator() - Method in class loci.poi.hssf.usermodel.HSSFRow
 
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.
CellReference - Class in loci.poi.hssf.util
 
CellReference(String) - Constructor for class loci.poi.hssf.util.CellReference
 
CellReference(int, int) - Constructor for class loci.poi.hssf.util.CellReference
 
CellReference(int, int, boolean, boolean) - Constructor for class loci.poi.hssf.util.CellReference
 
cells - Variable in class loci.poi.hssf.model.Sheet
 
cells - Variable in class loci.poi.hssf.usermodel.HSSFRow
 
cells - Variable in class loci.poi.hssf.util.AreaReference
 
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.Pyramid() - Constructor for class loci.formats.in.CellSensReader.Pyramid
 
CellSensReader.TileCoordinate - Class in loci.formats.in
 
CellSensReader.TileCoordinate(int) - Constructor for class loci.formats.in.CellSensReader.TileCoordinate
 
cellType - Variable in class loci.poi.hssf.usermodel.HSSFCell
 
CellValueRecordInterface - Interface in loci.poi.hssf.record
The cell value record interface is implemented by all classes of type Record that contain cell values.
CellVoyagerReader - Class in loci.formats.in
A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
CellVoyagerReader() - Constructor for class loci.formats.in.CellVoyagerReader
 
CellVoyagerReader.AreaInfo - Class in loci.formats.in
 
CellVoyagerReader.AreaInfo() - Constructor for class loci.formats.in.CellVoyagerReader.AreaInfo
 
CellVoyagerReader.ChannelInfo - Class in loci.formats.in
 
CellVoyagerReader.ChannelInfo() - Constructor for class loci.formats.in.CellVoyagerReader.ChannelInfo
 
CellVoyagerReader.FieldInfo - Class in loci.formats.in
 
CellVoyagerReader.FieldInfo() - Constructor for class loci.formats.in.CellVoyagerReader.FieldInfo
 
CellVoyagerReader.WellInfo - Class in loci.formats.in
 
CellVoyagerReader.WellInfo() - Constructor for class loci.formats.in.CellVoyagerReader.WellInfo
 
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.
CELSIUS - Static variable in class ome.units.UNITS
 
cEnd - Variable in class loci.plugins.in.ImporterOptions
 
CENTER - Static variable in class loci.poi.hssf.record.ExtendedFormatRecord
 
center - Variable in class loci.poi.hssf.usermodel.HSSFFooter
 
center - Variable in class loci.poi.hssf.usermodel.HSSFHeader
 
CENTER_SELECTION - Static variable in class loci.poi.hssf.record.ExtendedFormatRecord
 
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
 
CENTI(Unit<T>) - Static method in class ome.units.UNITS
 
CENTIBAR - Static variable in class ome.units.UNITS
 
CENTIHERTZ - Static variable in class ome.units.UNITS
 
CENTIMETER - Static variable in class ome.units.UNITS
 
CENTIMETRE - Static variable in class ome.units.UNITS
 
CENTIPASCAL - Static variable in class ome.units.UNITS
 
CENTISECOND - Static variable in class ome.units.UNITS
 
CENTIVOLT - Static variable in class ome.units.UNITS
 
CENTIWATT - Static variable in class ome.units.UNITS
 
cepoc - Variable in class jj2000.j2k.codestream.HeaderInfo.POC
 
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.
certifiedText - Variable in class loci.common.xml.LSInputI
 
cf - Variable in class org.libjpegturbo.turbojpeg.TJTransform
Custom filter instance
CF_BITMAP - Static variable in class loci.poi.hpsf.Thumbnail
Clipboard Format - Bitmap
CF_DIB - Static variable in class loci.poi.hpsf.Thumbnail
Clipboard Format - Device Independent Bitmap
CF_ENHMETAFILE - Static variable in class loci.poi.hpsf.Thumbnail
Clipboard Format - Enhanced Windows metafile format
CF_METAFILEPICT - Static variable in class loci.poi.hpsf.Thumbnail
Clipboard Format - Windows metafile format.
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.
cftab - Variable in class loci.common.CBZip2InputStream.Data
 
CFTAG_FMTID - Static variable in class loci.poi.hpsf.Thumbnail
Clipboard Format Tag - Format ID
CFTAG_MACINTOSH - Static variable in class loci.poi.hpsf.Thumbnail
Clipboard Format Tag - Macintosh clipboard format
CFTAG_NODATA - Static variable in class loci.poi.hpsf.Thumbnail
Clipboard Format Tag - No Data
CFTAG_WINDOWS - Static variable in class loci.poi.hpsf.Thumbnail
Clipboard Format Tag - Windows clipboard format
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
 
changeName(String, String) - Method in class loci.poi.poifs.filesystem.DirectoryNode
Change a contained Entry's name
changeName(Property, String) - Method in class loci.poi.poifs.property.DirectoryProperty
Change a Property's name
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
 
changingElemSize - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFFaxDecompressor
 
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 - Variable in class com.sun.media.imageio.stream.FileChannelImageInputStream
The FileChannel data source.
channel - Variable in class com.sun.media.imageio.stream.FileChannelImageOutputStream
The FileChannel data destination.
channel - Variable in class loci.common.NIOByteBufferProvider
File channel to allocate or map data from.
channel - Variable in class loci.common.NIOFileHandle
The file channel backed by the random access file.
channel - Variable in class loci.common.NIOInputStream
The file channel backed by the random access file.
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.LeicaHandler.Detector
 
channel - Variable in class loci.formats.in.LeicaHandler.MultiBand
 
channel - Variable in class loci.formats.in.PrairieMetadata.PFile
channel of this <File>.
channel - Variable in class loci.formats.in.SPCReader
 
Channel - Class in ome.xml.model
 
Channel() - Constructor for class ome.xml.model.Channel
Default constructor.
Channel(Element, OMEModel) - Constructor for class ome.xml.model.Channel
Constructs Channel recursively from an XML DOM tree.
Channel(Channel) - Constructor for class ome.xml.model.Channel
Copy constructor.
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 - Static variable in class loci.tests.testng.Configuration
 
CHANNEL_COUNT_TAG - Static variable in class loci.formats.in.FlowSightReader
 
CHANNEL_DEFINITION_BOX - Static variable in interface jj2000.j2k.fileformat.FileFormatBoxes
 
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_NAME - Static variable in class loci.tests.testng.Configuration
 
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.LeicaReader
 
channelColor - Variable in class loci.formats.in.ZeissLSMReader
 
channelColors - Variable in class loci.formats.in.BaseZeissReader
 
channelColors - Variable in class loci.formats.in.NativeND2Reader
 
ChannelDefinitionBox - Class in com.sun.media.imageioimpl.plugins.jpeg2000
This class is designed to represent a Channel Definition Box of JPEG JP2 file format.
ChannelDefinitionBox(ColorModel) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Constructs a ChannelDefinitionBox based on the provided ColorModel.
ChannelDefinitionBox(byte[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Constructs a ChannelDefinitionBox based on the provided content in byte array.
ChannelDefinitionBox(short[], short[], short[]) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Constructs a ChannelDefinitionBox based on the provided channel definitions.
ChannelDefinitionBox(Node) - Constructor for class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
Constructs a ChannelDefinitionBox based on the provided org.w3c.dom.Node.
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
 
ChannelImageInputStreamSpi - Class in com.sun.media.imageioimpl.stream
 
ChannelImageInputStreamSpi() - Constructor for class com.sun.media.imageioimpl.stream.ChannelImageInputStreamSpi
 
ChannelImageOutputStreamSpi - Class in com.sun.media.imageioimpl.stream
 
ChannelImageOutputStreamSpi() - Constructor for class com.sun.media.imageioimpl.stream.ChannelImageOutputStreamSpi
 
channelIndices - Variable in class loci.formats.in.BaseZeissReader
 
channelInfos - Variable in class loci.formats.in.CellVoyagerReader
 
channelLengths - Variable in class loci.formats.in.ICSReader
The length of each channel axis.
channelLinks - Variable in class ome.xml.model.Annotation
 
channelMap - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
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.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.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
 
ChannelRef - Class in ome.xml.model
 
ChannelRef() - Constructor for class ome.xml.model.ChannelRef
Default constructor.
ChannelRef(Element, OMEModel) - Constructor for class ome.xml.model.ChannelRef
Constructs ChannelRef recursively from an XML DOM tree.
ChannelRef(ChannelRef) - Constructor for class ome.xml.model.ChannelRef
Copy constructor.
channels - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.ChannelDefinitionBox
 
channels - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
Channel definitions
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.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
 
channels - Variable in class ome.xml.model.FilterSet
 
channels - Variable in class ome.xml.model.Pixels
 
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
 
character - Variable in class loci.poi.hssf.record.UnicodeString.FormatRun
 
characterCellHeight - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
characterCellWidth - Variable in class com.sun.media.imageioimpl.plugins.gif.GIFImageMetadata
 
characters(char[], int, int) - Method in class loci.common.xml.MetadataHandler
 
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.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
 
characterStream - Variable in class loci.common.xml.LSInputI
 
charData - Variable in class loci.formats.in.FlexReader.FlexHandler
 
CHARS - Static variable in class loci.formats.tools.AsciiImage
 
charset - Variable in class loci.formats.in.BaseZeissReader.Shape
 
ChartFormatRecord - Class in loci.poi.hssf.record
Class ChartFormatRecord
ChartFormatRecord() - Constructor for class loci.poi.hssf.record.ChartFormatRecord
 
ChartFormatRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.ChartFormatRecord
Constructs a ChartFormatRecord record and sets its fields appropriately.
ChartRecord - Class in loci.poi.hssf.record
The chart record is used to define the location and size of a chart.
ChartRecord() - Constructor for class loci.poi.hssf.record.ChartRecord
 
ChartRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.ChartRecord
Constructs a Chart record and sets its fields appropriately.
chartTypeManuallyFormatted - Variable in class loci.poi.hssf.record.SheetPropertiesRecord
 
charWidths - Variable in class loci.poi.hssf.usermodel.FontDetails
 
CHECK - Static variable in class loci.formats.in.ZeissLMSReader
 
check(int) - Method in class loci.poi.util.CommonsLogger
Check if a logger is enabled to log at the specified level
check(int) - Method in class loci.poi.util.NullLogger
Check if a logger is enabled to log at the specified level
check(int) - Method in class loci.poi.util.POILogger
Check if a logger is enabled to log at the specified level
check(int) - Method in class loci.poi.util.SystemOutLogger
Check if a logger is enabled to log at the specified level
checkBounds(int) - Method in class loci.poi.hssf.usermodel.HSSFCell
 
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.
checkBytePadding() - Method in class jj2000.j2k.entropy.decoder.ByteToBitInput
Checks for past errors in the decoding process by verifying the byte padding with an alternating sequence of 0's and 1's.
checkCells() - Method in class loci.poi.hssf.model.Sheet
 
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.common.services.AbstractService
Checks a given class dependency at runtime to ensure that a given class will be 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
 
checkComplexData(byte[]) - Static method in class loci.poi.ddf.EscherArrayProperty
 
checkDefaultBackgroundFills() - Method in class loci.poi.hssf.usermodel.HSSFCellStyle
Checks if the background and foreground fills are set correctly when one or the other is set to the default color.
checkDimsLoc(Record, int) - Method in class loci.poi.hssf.model.Sheet
in the event the record is a dimensions record, resets both the loc index and dimsloc index
checkElement(Element, String) - Method in class loci.formats.in.PrairieMetadata
Checks that the given element has the specified name.
checkEndOfPassFF(byte[], int[], boolean[], int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder
Ensures that at the end of a non-terminated coding pass there is not a 0xFF byte, modifying the stored rates if necessary.
checkExternSheet(int) - Method in class loci.poi.hssf.model.Workbook
returns the extern sheet number for specific sheet number , if this sheet doesn't exist in extern sheet , add it
checkFileSize() - Method in class ome.jxr.parser.FileParser
Deprecated.
 
checkFileStructureVersion() - Method in class ome.jxr.parser.FileParser
Deprecated.
 
checkGDISignaturePresence() - Method in class ome.jxr.parser.DatastreamParser
Deprecated.
 
checkHeader() - Method in class loci.formats.tiff.TiffParser
Checks the TIFF header.
checkHeaderBOM() - Method in class ome.jxr.parser.FileParser
Deprecated.
 
checkHeaderLength() - Method in class ome.jxr.parser.FileParser
Deprecated.
 
checkIfValidJpegXr() - Method in class ome.jxr.parser.FileParser
Deprecated.
 
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.
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPImageReader
 
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
 
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.pcx.PCXImageReader
 
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMImageReader
 
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawImageReader
 
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageReader
 
checkIndex(int) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageReader
 
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.
checkKey(Object) - Static method in class loci.poi.util.BinaryTree
check a key for validity (non-null and implements Comparable)
checkKeyAndValue(Object, Object) - Static method in class loci.poi.util.BinaryTree
check a key and a value for validity (non-null and implements Comparable)
checkLatest(String, String) - Static method in class loci.plugins.config.InstallWizard
 
checkLibrary() - Static method in class jj2000.j2k.util.NativeServices
Checks if the library SHLIB_NAME is already loaded and attempts to load if not yet loaded.
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).
checkMarkerLength(DataInputStream, String) - Method in class jj2000.j2k.codestream.reader.HeaderDecoder
Checks that the marker segment length is correct.
checkMismatch(boolean, boolean, int, String) - Static method in class loci.tests.testng.FormatWriterTest
 
checkMismatch(int, int, int, String) - Static method in class loci.tests.testng.FormatWriterTest
 
checkMismatch(String, String, int, String) - Static method in class loci.tests.testng.FormatWriterTest
 
checkMissing(HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
Reports missing libraries in the given hash set to the user.
checkNonNullComparable(Object, int) - Static method in class loci.poi.util.BinaryTree
check if an object is fit to be proper input ...
checkObsoleteOptions() - Method in class loci.plugins.in.ImporterOptions
Handles obsolete macro keys, for backward compatibility.
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.
checkParamsEmpty(ImageTypeSpecifier, int, int, List) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFImageWriter
 
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
 
checkPredTerm() - Method in class jj2000.j2k.entropy.decoder.MQDecoder
Checks for past errors in the decoding process using the predictable error resilient termination.
checkProgMode(String) - Method in class jj2000.j2k.entropy.ProgressionSpec
Check if the progression mode exists and if so, return its integer value.
checkQTLibrary() - Method in class loci.formats.gui.LegacyQTTools
Checks whether QTJava is available, throwing an exception if not.
checkRange(int, int, int, String) - Method in class loci.poi.hssf.usermodel.HSSFClientAnchor
 
checkReadParamBandSettingsWrapper(ImageReadParam, int, int) - Static method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
Wrapper for the protected method checkReadParamBandSettings.
checkRecordPosition() - Method in class loci.poi.hssf.record.RecordInputStream
 
checkRows() - Method in class loci.poi.hssf.model.Sheet
 
checkSampleModel(SampleModel) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
 
checkSampleModel(SampleModel) - Method in class com.sun.media.imageioimpl.plugins.wbmp.WBMPImageWriter
 
checkSheets(int) - Method in class loci.poi.hssf.model.Workbook
if we're trying to address one more sheet than we have, go ahead and add it! if we're trying to address >1 more than we have throw an exception!
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.
checkTargetErrors() - Method in class jj2000.j2k.util.ThreadPool
Checks that no error or runtime exception in any target have occurred so far.
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.
checkUTF8(InputStream) - Static method in class loci.common.xml.XMLTools
Checks the given stream for a UTF-8 BOM header, skipping it if present.
checkUUIDInfoBox(Node, String) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
Check whether the child with a name childName exists.
checkValidId(String) - Static method in class loci.common.Location
Checks that the given id points at a valid data stream.
checkValue(Object) - Static method in class loci.poi.util.BinaryTree
check a value for validity (non-null and implements Comparable)
Child - Interface in loci.poi.poifs.property
This interface defines methods for finding and setting sibling Property instances
childCount - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
childNames - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
childPolicy - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFElementInfo
 
childRecords - Variable in class loci.poi.ddf.EscherContainerRecord
 
childRecords - Variable in class loci.poi.ddf.UnknownEscherRecord
 
children - Variable in class com.sun.media.imageioimpl.common.PaletteBuilder.ColorNode
 
children - Variable in class loci.poi.hssf.model.Node
 
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
 
chosenDocumentDescriptors - Variable in class loci.poi.poifs.eventfilesystem.POIFSReaderRegistry
 
CHROMA_SUBSAMPLING - Static variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFJPEGCompressor
 
chromaCenteringX - Variable in class ome.jxr.parser.DatastreamParser
Deprecated.
 
chromaCenteringY - Variable in class ome.jxr.parser.DatastreamParser
Deprecated.
 
chromaSubsampleH - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
chromaSubsampleV - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
CHUNK_SIZE - Static variable in class loci.formats.UpgradeChecker
Number of bytes to read from the CI server at a time.
chunkSizes - Variable in class loci.formats.in.NativeQTReader
Number of bytes in each plane.
CHZ - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.CENTIHERTZ instead.
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
 
clamp(float) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFCIELabColorConverter
 
clamp(int) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
clamp2(float) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFCIELabColorConverter
 
CLASS_ARRAY - Static variable in class loci.poi.hssf.record.formula.Ptg
 
CLASS_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions
 
CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
CLASS_REF - Static variable in class loci.poi.hssf.record.formula.Ptg
 
CLASS_VALUE - Static variable in class loci.poi.hssf.record.formula.Ptg
 
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
 
ClassID - Class in loci.poi.hpsf
Represents a class ID (16 bytes).
ClassID(byte[], int) - Constructor for class loci.poi.hpsf.ClassID
Creates a ClassID and reads its value from a byte array.
ClassID() - Constructor for class loci.poi.hpsf.ClassID
Creates a ClassID and initializes its value with 0x00 bytes.
classID - Variable in class loci.poi.hpsf.PropertySet
Specifies this PropertySet's "classID" field.
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
 
CLEAN_FAX_DATA_ERRORS_CORRECTED - Static variable in class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet
A value to be used with the "CleanFaxData" tag.
CLEAN_FAX_DATA_ERRORS_UNCORRECTED - Static variable in class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet
A value to be used with the "CleanFaxData" tag.
CLEAN_FAX_DATA_NO_ERRORS - Static variable in class com.sun.media.imageio.plugins.tiff.FaxTIFFTagSet
A value to be used with the "CleanFaxData" tag.
cleanStaleCacheEntries() - Static method in class loci.common.Location
Remove any cached directory listings that have expired.
cleanup() - Method in class loci.formats.Memoizer
 
cleanup() - Method in class loci.tests.testng.SubResolutionTest
 
cleanuppass(DataBlk, MQDecoder, int, int[], int[], boolean) - Method in class jj2000.j2k.entropy.decoder.StdEntropyDecoder
Performs the cleanup pass on the specified data and bit-plane.
cleanuppass(CBlkWTData, MQCoder, boolean, int, int[], int[], int[], int[], int[], int[], int, int, int) - Static method in class jj2000.j2k.entropy.encoder.StdEntropyCoder
Performs the cleanup pass on the specified data and bit-plane.
clear() - Method in class loci.formats.codec.ByteVector
 
clear() - Method in class loci.poi.hpsf.MutableSection
Removes all properties from the section including 0 (dictionary) and 1 (codepage).
clear() - Method in class loci.poi.hssf.record.EscherAggregate
 
clear() - Method in class loci.poi.util.BinaryTree
Removes all mappings from this map
clear(int) - Method in class loci.poi.util.BitField
Clear the bits.
clear() - Method in class loci.poi.util.DoubleList
Removes all of the elements from this list.
clear() - Method in class loci.poi.util.IntList
Removes all of the elements from this list.
clear() - Method in class loci.poi.util.ShortList
Removes all of the elements from this list.
clear() - Method in class ome.xml.model.ReferenceList
 
CLEAR_CODE - Static variable in class loci.formats.codec.LZWCodec
 
clearByte(byte) - Method in class loci.poi.util.BitField
Clear the bits.
clearCode_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor
reserved clear code based on code size
clearDestImage() - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
clearDirectoryListingsCache() - Static method in class loci.common.Location
Clear the directory listings cache.
clearEscherRecords() - Method in class loci.poi.hssf.record.AbstractEscherHolderRecord
 
clearFormatting() - Method in class loci.poi.hssf.record.UnicodeString
 
clearFormatting() - Method in class loci.poi.hssf.usermodel.HSSFRichTextString
Removes any formatting that may have been applied to the string.
clearRect(int, int, int, int) - Method in class loci.poi.hssf.usermodel.DummyGraphics2d
 
clearRect(int, int, int, int) - Method in class loci.poi.hssf.usermodel.EscherGraphics
 
clearRect(int, int, int, int) - Method in class loci.poi.hssf.usermodel.EscherGraphics2d
 
clearSections() - Method in class loci.poi.hpsf.MutablePropertySet
Removes all sections from this property set.
clearSections() - Method in class loci.poi.hpsf.SpecialPropertySet
 
clearSeries() - Method in class loci.plugins.in.ImporterOptions
 
clearShort(short) - Method in class loci.poi.util.BitField
Clear the bits.
clearSubRecords() - Method in class loci.poi.hssf.record.ObjRecord
 
ClearTable(int) - Method in class com.sun.media.imageioimpl.common.LZWStringTable
 
clearTargetErrors() - Method in class jj2000.j2k.util.ThreadPool
Clears the current target error conditions, if any.
clearXML() - Method in class loci.formats.in.ZeissCZIReader.Metadata
 
clength - Variable in class jj2000.j2k.fileformat.writer.FileFormatWriter
Length of codestream
cLengths - Variable in class loci.plugins.util.DataBrowser
 
clip(int, int, int) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
clip(int, int, int) - Method in class com.sun.media.imageioimpl.plugins.raw.RawRenderedImage
 
clip(Shape) - Method in class loci.poi.hssf.usermodel.DummyGraphics2d
 
clip(Shape) - Method in class loci.poi.hssf.usermodel.EscherGraphics2d
 
clipDestination(Rectangle) - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState
 
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
 
clipRect(int, int, int, int) - Method in class loci.poi.hssf.usermodel.DummyGraphics2d
 
clipRect(int, int, int, int) - Method in class loci.poi.hssf.usermodel.EscherGraphics
 
clipRect(int, int, int, int) - Method in class loci.poi.hssf.usermodel.EscherGraphics2d
 
CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
 
clone() - Method in class com.sun.media.imageio.plugins.tiff.TIFFDirectory
Clones the directory and all the fields contained therein.
clone() - Method in class com.sun.media.imageioimpl.plugins.bmp.BMPMetadata
 
clone() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KMetadata
 
clone() - Method in class com.sun.media.imageioimpl.plugins.pnm.PNMMetadata
 
clone() - Method in class jj2000.j2k.ModuleSpec
 
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
 
clone() - Method in class loci.poi.ddf.EscherRecord
Escher records may need to be clonable in the future.
clone() - Method in class loci.poi.ddf.EscherTextboxRecord
 
clone() - Method in class loci.poi.ddf.UnknownEscherRecord
 
clone() - Method in class loci.poi.hssf.record.AbstractEscherHolderRecord
 
clone() - Method in class loci.poi.hssf.record.aggregates.ColumnInfoRecordsAggregate
Performs a deep clone of the record
clone() - Method in class loci.poi.hssf.record.aggregates.FormulaRecordAggregate
 
clone() - Method in class loci.poi.hssf.record.aggregates.RowRecordsAggregate
Performs a deep clone of the record
clone() - Method in class loci.poi.hssf.record.aggregates.ValueRecordsAggregate
Performs a deep clone of the record
clone() - Method in class loci.poi.hssf.record.AreaFormatRecord
 
clone() - Method in class loci.poi.hssf.record.AreaRecord
 
clone() - Method in class loci.poi.hssf.record.AxisLineFormatRecord
 
clone() - Method in class loci.poi.hssf.record.AxisOptionsRecord
 
clone() - Method in class loci.poi.hssf.record.AxisParentRecord
 
clone() - Method in class loci.poi.hssf.record.AxisRecord
 
clone() - Method in class loci.poi.hssf.record.AxisUsedRecord
 
clone() - Method in class loci.poi.hssf.record.BarRecord
 
clone() - Method in class loci.poi.hssf.record.BlankRecord
 
clone() - Method in class loci.poi.hssf.record.BOFRecord
 
clone() - Method in class loci.poi.hssf.record.BoolErrRecord
 
clone() - Method in class loci.poi.hssf.record.BottomMarginRecord
 
clone() - Method in class loci.poi.hssf.record.CalcCountRecord
 
clone() - Method in class loci.poi.hssf.record.CalcModeRecord
 
clone() - Method in class loci.poi.hssf.record.CategorySeriesAxisRecord
 
clone() - Method in interface loci.poi.hssf.record.CellValueRecordInterface
 
clone() - Method in class loci.poi.hssf.record.ChartRecord
 
clone() - Method in class loci.poi.hssf.record.ColumnInfoRecord
 
clone() - Method in class loci.poi.hssf.record.CommonObjectDataSubRecord
 
clone() - Method in class loci.poi.hssf.record.ContinueRecord
Clone this record.
clone() - Method in class loci.poi.hssf.record.DataFormatRecord
 
clone() - Method in class loci.poi.hssf.record.DatRecord
 
clone() - Method in class loci.poi.hssf.record.DefaultColWidthRecord
 
clone() - Method in class loci.poi.hssf.record.DefaultDataLabelTextPropertiesRecord
 
clone() - Method in class loci.poi.hssf.record.DefaultRowHeightRecord
 
clone() - Method in class loci.poi.hssf.record.DeltaRecord
 
clone() - Method in class loci.poi.hssf.record.DimensionsRecord
 
clone() - Method in class loci.poi.hssf.record.EndSubRecord
 
clone() - Method in class loci.poi.hssf.record.EOFRecord
 
clone() - Method in class loci.poi.hssf.record.FilePassRecord
 
clone() - Method in class loci.poi.hssf.record.FileSharingRecord
Clone this record.
clone() - Method in class loci.poi.hssf.record.FontBasisRecord
 
clone() - Method in class loci.poi.hssf.record.FontIndexRecord
 
clone() - Method in class loci.poi.hssf.record.FooterRecord
 
clone() - Method in class loci.poi.hssf.record.formula.AddPtg
 
clone() - Method in class loci.poi.hssf.record.formula.Area3DPtg
 
clone() - Method in class loci.poi.hssf.record.formula.AreaAPtg
 
clone() - Method in class loci.poi.hssf.record.formula.AreaErrPtg
 
clone() - Method in class loci.poi.hssf.record.formula.AreaNAPtg
 
clone() - Method in class loci.poi.hssf.record.formula.AreaNPtg
 
clone() - Method in class loci.poi.hssf.record.formula.AreaNVPtg
 
clone() - Method in class loci.poi.hssf.record.formula.AreaPtg
 
clone() - Method in class loci.poi.hssf.record.formula.AreaVPtg
 
clone() - Method in class loci.poi.hssf.record.formula.ArrayPtg
 
clone() - Method in class loci.poi.hssf.record.formula.ArrayPtgA
 
clone() - Method in class loci.poi.hssf.record.formula.ArrayPtgV
 
clone() - Method in class loci.poi.hssf.record.formula.AttrPtg
 
clone() - Method in class loci.poi.hssf.record.formula.BoolPtg
 
clone() - Method in class loci.poi.hssf.record.formula.ConcatPtg
 
clone() - Method in class loci.poi.hssf.record.formula.DividePtg
 
clone() - Method in class loci.poi.hssf.record.formula.EqualPtg
 
clone() - Method in class loci.poi.hssf.record.formula.ErrPtg
 
clone() - Method in class loci.poi.hssf.record.formula.ExpPtg
 
clone() - Method in class loci.poi.hssf.record.formula.FuncPtg
 
clone() - Method in class loci.poi.hssf.record.formula.FuncVarPtg
 
clone() - Method in class loci.poi.hssf.record.formula.GreaterEqualPtg
 
clone() - Method in class loci.poi.hssf.record.formula.GreaterThanPtg
Implementation of clone method from Object
clone() - Method in class loci.poi.hssf.record.formula.IntersectionPtg
 
clone() - Method in class loci.poi.hssf.record.formula.IntPtg
 
clone() - Method in class loci.poi.hssf.record.formula.LessEqualPtg
 
clone() - Method in class loci.poi.hssf.record.formula.LessThanPtg
Implementation of clone method from Object
clone() - Method in class loci.poi.hssf.record.formula.MemAreaPtg
 
clone() - Method in class loci.poi.hssf.record.formula.MemErrPtg
 
clone() - Method in class loci.poi.hssf.record.formula.MemFuncPtg
 
clone() - Method in class loci.poi.hssf.record.formula.MissingArgPtg
 
clone() - Method in class loci.poi.hssf.record.formula.MultiplyPtg
 
clone() - Method in class loci.poi.hssf.record.formula.NamePtg
 
clone() - Method in class loci.poi.hssf.record.formula.NameXPtg
 
clone() - Method in class loci.poi.hssf.record.formula.NotEqualPtg
 
clone() - Method in class loci.poi.hssf.record.formula.NumberPtg
 
clone() - Method in class loci.poi.hssf.record.formula.ParenthesisPtg
 
clone() - Method in class loci.poi.hssf.record.formula.PercentPtg
 
clone() - Method in class loci.poi.hssf.record.formula.PowerPtg
 
clone() - Method in class loci.poi.hssf.record.formula.Ptg
 
clone() - Method in class loci.poi.hssf.record.formula.RangePtg
 
clone() - Method in class loci.poi.hssf.record.formula.Ref3DPtg
 
clone() - Method in class loci.poi.hssf.record.formula.RefAPtg
 
clone() - Method in class loci.poi.hssf.record.formula.ReferencePtg
 
clone() - Method in class loci.poi.hssf.record.formula.RefErrorPtg
 
clone() - Method in class loci.poi.hssf.record.formula.RefNAPtg
 
clone() - Method in class loci.poi.hssf.record.formula.RefNPtg
 
clone() - Method in class loci.poi.hssf.record.formula.RefNVPtg
 
clone() - Method in class loci.poi.hssf.record.formula.RefVPtg
 
clone() - Method in class loci.poi.hssf.record.formula.StringPtg
 
clone() - Method in class loci.poi.hssf.record.formula.SubtractPtg
 
clone() - Method in class loci.poi.hssf.record.formula.UnaryMinusPtg
 
clone() - Method in class loci.poi.hssf.record.formula.UnaryPlusPtg
 
clone() - Method in class loci.poi.hssf.record.formula.UnionPtg
 
clone() - Method in class loci.poi.hssf.record.formula.UnknownPtg
 
clone() - Method in class loci.poi.hssf.record.FormulaRecord
 
clone() - Method in class loci.poi.hssf.record.FrameRecord
 
clone() - Method in class loci.poi.hssf.record.GridsetRecord
 
clone() - Method in class loci.poi.hssf.record.GroupMarkerSubRecord
 
clone() - Method in class loci.poi.hssf.record.GutsRecord
 
clone() - Method in class loci.poi.hssf.record.HCenterRecord
 
clone() - Method in class loci.poi.hssf.record.HeaderRecord
 
clone() - Method in class loci.poi.hssf.record.IndexRecord
 
clone() - Method in class loci.poi.hssf.record.IterationRecord
 
clone() - Method in class loci.poi.hssf.record.LabelRecord
 
clone() - Method in class loci.poi.hssf.record.LabelSSTRecord
 
clone() - Method in class loci.poi.hssf.record.LeftMarginRecord
 
clone() - Method in class loci.poi.hssf.record.LegendRecord
 
clone() - Method in class loci.poi.hssf.record.LineFormatRecord
 
clone() - Method in class loci.poi.hssf.record.LinkedDataFormulaField
 
clone() - Method in class loci.poi.hssf.record.LinkedDataRecord
 
clone() - Method in class loci.poi.hssf.record.MergeCellsRecord
 
clone() - Method in class loci.poi.hssf.record.NumberFormatIndexRecord
 
clone() - Method in class loci.poi.hssf.record.NumberRecord
 
clone() - Method in class loci.poi.hssf.record.ObjectLinkRecord
 
clone() - Method in class loci.poi.hssf.record.ObjectProtectRecord
 
clone() - Method in class loci.poi.hssf.record.ObjRecord
 
clone() - Method in class loci.poi.hssf.record.PageBreakRecord
 
clone() - Method in class loci.poi.hssf.record.PaneRecord
 
clone() - Method in class loci.poi.hssf.record.PasswordRecord
Clone this record.
clone() - Method in class loci.poi.hssf.record.PlotAreaRecord
 
clone() - Method in class loci.poi.hssf.record.PlotGrowthRecord
 
clone() - Method in class loci.poi.hssf.record.PrintGridlinesRecord
 
clone() - Method in class loci.poi.hssf.record.PrintHeadersRecord
 
clone() - Method in class loci.poi.hssf.record.PrintSetupRecord
 
clone() - Method in class loci.poi.hssf.record.ProtectRecord
 
clone() - Method in class loci.poi.hssf.record.Record
 
clone() - Method in class loci.poi.hssf.record.RefModeRecord
 
clone() - Method in class loci.poi.hssf.record.RightMarginRecord
 
clone() - Method in class loci.poi.hssf.record.RKRecord
 
clone() - Method in class loci.poi.hssf.record.RowRecord
 
clone() - Method in class loci.poi.hssf.record.SaveRecalcRecord
 
clone() - Method in class loci.poi.hssf.record.ScenarioProtectRecord
 
clone() - Method in class loci.poi.hssf.record.SCLRecord
 
clone() - Method in class loci.poi.hssf.record.SelectionRecord
 
clone() - Method in class loci.poi.hssf.record.SeriesChartGroupIndexRecord
 
clone() - Method in class loci.poi.hssf.record.SeriesIndexRecord
 
clone() - Method in class loci.poi.hssf.record.SeriesLabelsRecord
 
clone() - Method in class loci.poi.hssf.record.SeriesListRecord
 
clone() - Method in class loci.poi.hssf.record.SeriesRecord
 
clone() - Method in class loci.poi.hssf.record.SeriesTextRecord
 
clone() - Method in class loci.poi.hssf.record.SeriesToChartGroupRecord
 
clone() - Method in class loci.poi.hssf.record.SharedFormulaRecord
 
clone() - Method in class loci.poi.hssf.record.SheetPropertiesRecord
 
clone() - Method in class loci.poi.hssf.record.StringRecord
 
clone() - Method in class loci.poi.hssf.record.TextObjectBaseRecord
 
clone() - Method in class loci.poi.hssf.record.TextRecord
 
clone() - Method in class loci.poi.hssf.record.TickRecord
 
clone() - Method in class loci.poi.hssf.record.TopMarginRecord
 
clone() - Method in class loci.poi.hssf.record.UnicodeString
 
clone() - Method in class loci.poi.hssf.record.UnitsRecord
 
clone() - Method in class loci.poi.hssf.record.UnknownRecord
Unlike the other Record.clone methods this is a shallow clone
clone() - Method in class loci.poi.hssf.record.ValueRangeRecord
 
clone() - Method in class loci.poi.hssf.record.VCenterRecord
 
clone() - Method in class loci.poi.hssf.record.WindowTwoRecord
 
clone() - Method in class loci.poi.hssf.record.WSBoolRecord
 
clone() - Method in class mdbtools.libmdb.MdbColumn
 
clone() - Method in class mdbtools.libmdb.MdbSarg
 
cloneArray(int[]) - Method in class loci.poi.hssf.usermodel.HSSFPolygon
 
cloneImageReadParam(ImageReadParam, boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFRenderedImage
Creates a copy of param.
cloneNode(boolean) - Method in class com.sun.media.imageioimpl.plugins.tiff.TIFFFieldNode
 
cloneSheet() - Method in class loci.poi.hssf.model.Sheet
Clones the low level records of this sheet and returns the new sheet instance.
cloneSheet(HSSFWorkbook) - Method in class loci.poi.hssf.usermodel.HSSFSheet
 
cloneSheet(int) - Method in class loci.poi.hssf.usermodel.HSSFWorkbook
create an HSSFSheet from an existing sheet in the HSSFWorkbook.
cloneStringIfRequired() - Method in class loci.poi.hssf.usermodel.HSSFRichTextString
Called whenever the unicode string is modified.
close() - Method in class com.sun.media.imageio.stream.FileChannelImageInputStream
Invokes the superclass method and sets the internal reference to the source FileChannel to null.
close() - Method in class com.sun.media.imageio.stream.FileChannelImageOutputStream
Invokes the superclass method, writes any unwritten data, and sets the internal reference to the source FileChannel to null.
close() - Method in class com.sun.media.imageio.stream.RawImageInputStream
 
close() - Method in class com.sun.media.imageioimpl.plugins.clib.InputStreamAdapter
 
close() - Method in class com.sun.media.imageioimpl.plugins.clib.OutputStreamAdapter
 
close() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.IISRandomAccessIO
 
close() - Method in class com.sun.media.imageioimpl.plugins.jpeg2000.ImageInputStreamWrapper
 
close() - Method in class jj2000.j2k.codestream.writer.CodestreamWriter
Closes the underlying resource (file, stream, network connection, etc.).
close() - Method in class jj2000.j2k.codestream.writer.FileCodestreamWriter
Writes the EOC marker and closes the underlying stream.
close() - Method in class jj2000.j2k.image.input.ImgReader
Closes the underlying file or network connection from where the image data is being read.
close() - Method in class jj2000.j2k.image.input.ImgReaderPGM
Closes the underlying RandomAccessFile from where the image data is being read.
close() - Method in class jj2000.j2k.io.BufferedRandomAccessFile
Closes the buffered random access file
close() - Method in interface jj2000.j2k.io.RandomAccessIO
Closes the I/O stream.
close() - Method in class jj2000.j2k.util.ISRandomAccessIO
Closes this object for reading as well as the wrapped InputStream, if not already closed.
close() - Method in class loci.common.ByteArrayHandle
 
close() - Method in class loci.common.CBZip2InputStream
 
close() - Method in class loci.common.FileHandle
 
close() - Method in interface loci.common.IRandomAccess
Closes this random access stream and releases any system resources associated with the stream.
close() - Method in class loci.common.NIOFileHandle
 
close() - Method in class loci.common.NIOInputStream
Closes the streams.
close() - Method in class loci.common.RandomAccessInputStream
Closes the streams.
close() - Method in class loci.common.RandomAccessOutputStream
 
close() - Method in class loci.common.StreamHandle
 
close() - Method in class loci.common.ZipHandle
 
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.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.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 loci.poi.poifs.filesystem.DocumentInputStream
Closes this input stream and releases any system resources associated with the stream.
close() - Method in class loci.poi.poifs.filesystem.DocumentOutputStream
Closes this output stream and releases any system resources associated with this stream.
close() - Method in class loci.poi.util.BlockingInputStream
 
close() - Method in class loci.tests.testng.FormatReaderTest
 
close() - Method in class mdbtools.examples.MemoryRandomAccess
 
close() - Method in class mdbtools.jdbc2.File
 
close() - Method in class mdbtools.libmdb.MdbFile
 
close() - Method in class mdbtools.libmdb.MdbHandle
 
close() - Method in interface mdbtools.publicapi.RandomAccess
 
close() - Method in class ome.jxr.JXRReader
Deprecated.
 
close() - Method in class ome.jxr.parser.DatastreamParser
Deprecated.
 
close() - Method in class ome.jxr.parser.FileParser
Deprecated.
 
close() - Method in class ome.jxr.parser.IFDParser
Deprecated.
 
close() - Method in class ome.jxr.parser.Parser
Deprecated.
 
close() - Method in class ome.metakit.MetakitReader
Close the reader and release any resources in use.
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_CURVES - Static variable in class loci.poi.ddf.EscherShapePathProperty
 
CLOSED_POLYGON - Static variable in class loci.poi.ddf.EscherShapePathProperty
 
CLOSED_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
 
closeFileOnly() - Method in class loci.plugins.macro.LociFunctions
 
cm - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
cm - Variable in class loci.formats.FormatWriter
Default color model.
CM - Static variable in class ome.units.UNITS
Deprecated.
Use UNITS.CENTIMETRE instead.
cNames - Variable in class loci.formats.in.ImprovisionTiffReader
 
co - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.RenderedImageSrc
 
co2Percent - Variable in class loci.formats.in.ZeissCZIReader
 
co2Percent - Variable in class ome.xml.model.ImagingEnvironment
 
COARSE_FRAME_IFD - Static variable in class loci.formats.in.CellSensReader
 
COARSE_PYRAMID_LEVEL - Static variable in class loci.formats.in.CellSensReader
 
COBOL - Static variable in class loci.common.DateTools
 
COBOL_EPOCH - Static variable in class loci.common.DateTools
 
coc - Variable in class jj2000.j2k.codestream.HeaderInfo
Reference to the COC marker segments found in main and first tile-part header.
COC - Static variable in interface jj2000.j2k.codestream.Markers
Coding style component (COC): 0xFF53
COC_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder
Flag bit for COC marker segment found
cod - Variable in class jj2000.j2k.codestream.HeaderInfo
Reference to the COD marker segments found in main and first tile-part header.
COD - Static variable in interface jj2000.j2k.codestream.Markers
Coding style default (COD): 0xFF52
COD_FOUND - Static variable in class jj2000.j2k.codestream.reader.HeaderDecoder
Flag bit for COD marker segment found
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 com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam
Specifies the maximum code-block size to use for tile-component.
codeBlockSize - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Specifies the maximum code-block size to use for tile-component.
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.JPEGTileDecoder.TileCache
 
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.
CodedCBlk - Class in jj2000.j2k.entropy
This is the generic class to store coded (compressed) code-block.
CodedCBlk() - Constructor for class jj2000.j2k.entropy.CodedCBlk
Creates a new CodedCBlk object wit the default values and without allocating any space for its members.
CodedCBlk(int, int, int, byte[]) - Constructor for class jj2000.j2k.entropy.CodedCBlk
Creates a new CodedCBlk object with the specified values.
CodedCBlkDataSrcDec - Interface in jj2000.j2k.entropy.decoder
This interface defines a source of entropy coded data and methods to transfer it in a code-block by code-block basis.
CodedCBlkDataSrcEnc - Interface in jj2000.j2k.entropy.encoder
This interface defines a source of entropy coded data and methods to transfer it in a code-block by code-block basis.
CodedEnum - Interface in loci.common.enumeration
Enumeration which is coded.
CODEPAGE - Static variable in class loci.poi.hssf.model.Workbook
constant used to set the "codepage" wherever "codepage" is set in records (which is duplciated in more than one record)
CODEPAGE - Static variable in class loci.poi.hssf.record.CodepageRecord
the likely correct value for CODEPAGE (at least for US versions).
CODEPAGE - Static variable in class loci.poi.hssf.record.InterfaceHdrRecord
suggested (and probably correct) default
CodepageRecord - Class in loci.poi.hssf.record
Title: Codepage Record
CodepageRecord() - Constructor for class loci.poi.hssf.record.CodepageRecord
 
CodepageRecord(RecordInputStream) - Constructor for class loci.poi.hssf.record.CodepageRecord
Constructs a CodepageRecord and sets its fields appropriately
codepageToEncoding(int) - Static method in class loci.poi.hpsf.VariantSupport
Turns a codepage number into the equivalent character encoding's name.
codeSegSymbol - Variable in class com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriteParamJava
Inserts an error resilience segmentation symbol in the MQ codeword at the end of each bit-plane (cleanup pass).
codeSize_ - Variable in class com.sun.media.imageioimpl.common.LZWCompressor
base underlying code size of data being compressed 8 for TIFF, 1 to 8 for GIF
CODESTREAM_VERSION - Static variable in class ome.jxr.constants.File
Deprecated.
 
codeStreamLength - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
The lengths of the codestreams in the fileformat
CodestreamManipulator - Class in jj2000.j2k.util
This class takes a legal JPEG 2000 codestream and performs some manipulation on it.
CodestreamManipulator(File, int, int, boolean, boolean, boolean, boolean) - Constructor for class jj2000.j2k.util.CodestreamManipulator
Instantiates a codestream manipulator..
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..
codeStreamPos - Variable in class jj2000.j2k.fileformat.reader.FileFormatReader
The positions of the codestreams in the fileformat
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.
CodestreamWriter - Class in jj2000.j2k.codestream.writer
This is the abstract class for writing to a bit stream.
CodestreamWriter(int) - Constructor for class jj2000.j2k.codestream.writer.CodestreamWriter
Allocates this object and initializes the maximum numner of bytes.
codeSymbol(int, int) - Method in class jj2000.j2k.entropy.encoder.MQCoder
This function performs the arithmetic encoding of one symbol.
codeSymbols(int[], int[], int) - Method in class jj2000.j2k.entropy.encoder.MQCoder
This function performs the arithmetic encoding of several symbols together.
codingRangeCbCr - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
codingRangeY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrColorConverter
 
codingRangeY - Variable in class com.sun.media.imageioimpl.plugins.tiff.TIFFYCbCrDecompressor
 
col - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
col - Variable in class loci.formats.in.OperettaReader.Plane
 
col - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
col - Variable in class loci.poi.hssf.usermodel.HSSFComment
 
col - Variable in class loci.poi.hssf.util.CellReference
 
col - Variable in class ome.metakit.ColumnMap
 
col1 - Variable in class loci.poi.hssf.usermodel.HSSFClientAnchor
 
col2 - Variable in class loci.poi.hssf.usermodel.HSSFClientAnchor
 
col_fixed_offset - Variable in class mdbtools.libmdb.MdbFormatConstants
 
col_from - Variable in class loci.poi.hssf.record.MergeCellsRecord.MergedRegion
upper right hand corner col
col_num - Variable in class mdbtools.libmdb.MdbColumn
 
col_num_offset - Variable in class mdbtools.libmdb.MdbFormatConstants
 
col_prec - Variable in class mdbtools.libmdb.MdbColumn
 
col_scale - Variable in class mdbtools.libmdb.MdbColumn
 
col_size - Variable in class mdbtools.libmdb.MdbColumn
 
col_size_offset - Variable in class mdbtools.libmdb.MdbFormatConstants
 
col_to - Variable in class loci.poi.hssf.record.MergeCellsRecord.MergedRegion
lower right hand corner col
col_type - Variable in class mdbtools.libmdb.MdbColumn
 
colAbs - Variable in class loci.poi.hssf.util.CellReference
 
colapsed - Static variable in class loci.poi.hssf.record.RowRecord
 
colBreaks - Variable in class loci.poi.hssf.model.Sheet
 
colCount - Variable in class loci.formats.in.BaseZeissReader
 
colFrom - Variable in class loci.poi.hssf.util.Region
 
collapseColInfoRecords(int) - Method in class loci.poi.hssf.record.aggregates.ColumnInfoRecordsAggregate
 
collapseColumn(short) - Method in class loci.poi.hssf.record.aggregates.ColumnInfoRecordsAggregate
 
collapsed - Static variable in class loci.poi.hssf.record.ColumnInfoRecord
 
collapseRow(int) - Method in class loci.poi.hssf.record.aggregates.RowRecordsAggregate
 
collect - Variable in class mdbtools.libmdb.MdbStatistics
 
collection - Variable in class loci.formats.in.LeicaHandler