public class FluoviewReader extends BaseTiffReader
Modifier and Type | Field and Description |
---|---|
private static int |
ACQUISITION_CYCLE_TIME |
private static int |
ACTUAL_TEMPERATURE |
private static java.lang.String |
ANDOR_MAGIC_STRING |
private static int |
BASELINE_CLAMP |
private static int |
BASELINE_OFFSET |
private static int |
CAMERA_SERIAL_SETTING |
private java.lang.String[] |
channelNames |
private static int |
CHIP_SIZE_X |
private static int |
CHIP_SIZE_Y |
private static int |
CLOCKWISE |
private java.lang.String |
comment |
private static int |
COUNTER_CLOCKWISE |
private java.lang.String |
date |
private static java.lang.String |
DATE_FORMAT
Date format
|
private java.lang.String |
detectorManufacturer |
private java.lang.String |
dimensionOrder |
private static int |
EM_DAC |
private static int |
EXPOSURE_TIME |
private java.lang.Float |
exposureTime |
private int |
fieldIndex |
private double[][] |
fieldOffsets |
private static java.lang.String |
FLUOVIEW_MAGIC_STRING
String identifying a Fluoview file.
|
private java.lang.String[] |
gains |
private static int |
HORIZONTAL_FLIP |
private static int |
KINETIC_CYCLE_TIME |
private java.lang.String[] |
lensNA |
private java.lang.String |
mag |
private static int |
MMHEADER
Private TIFF tags
|
private static int |
MMSTAMP |
private java.lang.String |
model |
private static int |
MODEL |
private int |
montageIndex |
private double[][] |
montageOffsets |
private static int |
N_ACCUMULATIONS |
private static int |
N_FRAMES |
private java.lang.String |
objectiveManufacturer |
private java.lang.String[] |
offsets |
private static int |
PRE_AMP_SETTING |
private static int |
PRESCANS |
private static int |
READOUT_TIME |
private java.lang.Float |
readoutTime |
private double[][] |
stamps
Timestamps for each plane, in seconds.
|
private java.lang.Float |
temperature |
private static int |
TEMPERATURE |
private int |
timeIndex |
private static int |
VERTICAL_CLOCK_VOLTAGE |
private static int |
VERTICAL_FLIP |
private static int |
VERTICAL_SHIFT_SPEED |
private java.lang.String[] |
voltages |
private double |
voxelC
Pixel dimensions for this file.
|
private double |
voxelT
Pixel dimensions for this file.
|
private double |
voxelX
Pixel dimensions for this file.
|
private double |
voxelY
Pixel dimensions for this file.
|
private double |
voxelZ
Pixel dimensions for this file.
|
private double[] |
zPositions |
DATE_FORMATS, LOGGER
canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit
core
coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
FluoviewReader()
Constructs a new Fluoview TIFF reader.
|
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
private int |
getField(int seriesIndex) |
private int |
getImageIndex(int no) |
private int |
getMontage(int seriesIndex) |
private int[] |
getPos(int seriesIndex) |
private void |
initAlternateMetadata() |
private void |
initAlternateMetadataStore() |
protected void |
initMetadataStore()
Populates the metadata store using the data parsed in
BaseTiffReader.initStandardMetadata() along with some further parsing done in
the method itself. |
protected void |
initStandardMetadata()
Parses standard metadata.
|
boolean |
isThisType(loci.common.RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
|
byte[] |
openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Obtains a sub-image of the specified image plane
into a pre-allocated byte array.
|
private void |
parseComment() |
private void |
parsePageName() |
private void |
readStamps() |
private byte[] |
shortArrayToBytes(short[] s) |
getExifTagName, getImageCreationDate, initFile, initMetadata, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString
get16BitLookupTable, get8BitLookupTable, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, openThumbBytes, reopenFile, setResolutionLevel
coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, fileGroupOption, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, updateMetadataLists
checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFormat, getNativeDataType, getSuffixes
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions
private static final java.lang.String FLUOVIEW_MAGIC_STRING
private static final java.lang.String ANDOR_MAGIC_STRING
private static final int MMHEADER
private static final int MMSTAMP
private static final int TEMPERATURE
private static final int EXPOSURE_TIME
private static final int KINETIC_CYCLE_TIME
private static final int N_ACCUMULATIONS
private static final int ACQUISITION_CYCLE_TIME
private static final int READOUT_TIME
private static final int EM_DAC
private static final int N_FRAMES
private static final int HORIZONTAL_FLIP
private static final int VERTICAL_FLIP
private static final int CLOCKWISE
private static final int COUNTER_CLOCKWISE
private static final int VERTICAL_CLOCK_VOLTAGE
private static final int VERTICAL_SHIFT_SPEED
private static final int PRE_AMP_SETTING
private static final int CAMERA_SERIAL_SETTING
private static final int ACTUAL_TEMPERATURE
private static final int BASELINE_CLAMP
private static final int PRESCANS
private static final int MODEL
private static final int CHIP_SIZE_X
private static final int CHIP_SIZE_Y
private static final int BASELINE_OFFSET
private static final java.lang.String DATE_FORMAT
private double voxelX
private double voxelY
private double voxelZ
private double voxelC
private double voxelT
private java.lang.String dimensionOrder
private java.lang.String date
private int timeIndex
private int fieldIndex
private int montageIndex
private double[][] stamps
private double[] zPositions
private java.lang.String[] gains
private java.lang.String[] voltages
private java.lang.String[] offsets
private java.lang.String[] channelNames
private java.lang.String[] lensNA
private java.lang.String mag
private java.lang.String detectorManufacturer
private java.lang.String objectiveManufacturer
private java.lang.String comment
private java.lang.Float temperature
private java.lang.Float exposureTime
private java.lang.Float readoutTime
private java.lang.String model
private double[][] montageOffsets
private double[][] fieldOffsets
public boolean isThisType(loci.common.RandomAccessInputStream stream) throws java.io.IOException
IFormatReader
isThisType
in interface IFormatReader
isThisType
in class MinimalTiffReader
stream
- A RandomAccessInputStream representing the file to check.
The first byte in the stream is assumed to be the first byte
in the file.java.io.IOException
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, java.io.IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class MinimalTiffReader
no
- the image index within the file.buf
- a pre-allocated buffer.x
- X coordinate of the upper-left corner of the sub-imagey
- Y coordinate of the upper-left corner of the sub-imagew
- width of the sub-imageh
- height of the sub-imagebuf
for convenience.FormatException
- if there was a problem parsing the metadata of the
file.java.io.IOException
- if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class MinimalTiffReader
java.io.IOException
protected void initStandardMetadata() throws FormatException, java.io.IOException
BaseTiffReader
initStandardMetadata
in class BaseTiffReader
FormatException
java.io.IOException
protected void initMetadataStore() throws FormatException
BaseTiffReader
BaseTiffReader.initStandardMetadata()
along with some further parsing done in
the method itself.
All calls to the active MetadataStore
should be made in this
method and only in this method. This is especially important for
sub-classes that override the getters for pixel set array size, etc.initMetadataStore
in class BaseTiffReader
FormatException
private void initAlternateMetadata() throws FormatException, java.io.IOException
FormatException
java.io.IOException
private void initAlternateMetadataStore() throws FormatException
FormatException
private int getImageIndex(int no)
private void readStamps() throws FormatException, java.io.IOException
FormatException
java.io.IOException
private byte[] shortArrayToBytes(short[] s)
private void parsePageName()
private void parseComment()
private int getMontage(int seriesIndex)
private int getField(int seriesIndex)
private int[] getPos(int seriesIndex)
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