Package loci.formats.in

Class CellSensReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.CellSensReader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class CellSensReader
extends FormatReader

CellSensReader is the file format reader for cellSens .vsi files.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	CellSensReader.Pyramid
(package private) class	CellSensReader.TileCoordinate

Field Summary

Fields

Modifier and Type	Field	Description
private static final int	ACCUMULATION
private static final int	ACCUMULATION_MODE
private static final int	ACQUISITION_PROPERTIES
private static final int	ACTIVE_CHANNEL
private static final int	ACTIVE_LAYER_INDEX_VECTOR
private static final int	ACTIVE_LAYER_VECTOR
private static final int	ACTIVE_STACK_DIMENSION
private static final int	ANDOR_SHIFT_SPEED
private static final int	AUTOEXPOSURE
private static final int	AVERAGING
private HashMap<Integer,byte[]>	backgroundColor
private static final int	BASELINE_OFFSET_CLAMP
private boolean[]	bgr
private static final int	BGR
private static final int	BIT_DEPTH
private static final int	BLUE_GAIN
private static final int	BLUE_OFFSET
private static final int	BMP
private static final int	BOOLEAN
private static final int	BRIGHTNESS
private static final int	C
private static final int	CALIBRATION
private static final int	CAMERA_GAIN
private static final int	CAMERA_GAMMA
private static final int	CAMERA_OFFSET
private static final int	CANVAS_COLOR_1
private static final int	CANVAS_COLOR_2
private static final int	CCD_SENSITIVITY
private static final int	CHAINED_LAYERS
private static final int	CHANNEL_CONTRAST_BRIGHTNESS
private static final int	CHANNEL_DIM
private static final int	CHANNEL_GAMMA_CORRECTION
private static final int	CHANNEL_INFO_PROPERTIES
private static final int	CHANNEL_NAME
private static final int	CHANNEL_OVERFLOW
private static final int	CHANNEL_PROPERTIES
private static final int	CHANNEL_TRANSPARENCY_VALUE
private static final int	CHANNEL_VISIBLE
private int	channelCount
private static final int	CHAR
private static final int	CLIPPING
private static final int	CLIPPING_STATE
private static final int	COARSE_FRAME_IFD
private static final int	COARSE_PYRAMID_LEVEL
private static final int	COLLECTION_VOLUME
private static final int	COLOR_SPACE
private static final int	COLORSPACE
private ArrayList<Integer>	cols
private static final int	COMPLEX
private ArrayList<Integer>	compressionType
private static final int	CONTRAST
private static final int	CONTRAST_BRIGHTNESS
private static final int	CONTRAST_TARGET
private static final int	COOLING_ON
private static final int	CREATION_TIME
private static final int	CUSTOM_GRAYSCALE
private static final int	DATE
private static final int	DEFAULT_BACKGROUND_COLOR
private static final int	DEFAULT_IMAGE
private static final int	DEFAULT_SAMPLE_IFD
private static final int	DEVICE_ID
private static final int	DEVICE_MANUFACTURER
private static final int	DEVICE_NAME
private static final int	DEVICE_SUBTYPE
private static final int	DIM_INDEX_1
private static final int	DIM_INDEX_2
private static final int	DIMENSION_DESCRIPTION_VOLUME
private static final int	DIMENSION_INCREMENT_ID
private static final int	DIMENSION_MEANING
private static final int	DIMENSION_NAME
private static final int	DIMENSION_SIZE
private static final int	DIMENSION_START_ID
private static final int	DIMENSION_VALUE_ID
private int	dimensionTag
private static final int	DISPLAY_COLOR
private static final int	DISPLAY_CONTRAST_BRIGHTNESS
private static final int	DISPLAY_GAMMA_CORRECTION
private static final int	DISPLAY_LIMITS
private static final int	DISPLAY_LUT
private static final int	DISPLAY_MAPPING_VOLUME
private static final int	DISPLAY_PROCESSOR_TYPE
private static final int	DISPLAY_STACK_ID
private static final int	DISPLAY_STACK_INDEX
private static final int	DISPLAY_VISIBLE
private static final int	DISPLAYED_LUT_ID
private static final int	DOCUMENT_AUTHOR
private static final int	DOCUMENT_COMPANY
private static final int	DOCUMENT_CREATOR_BUILD_NUMBER
private static final int	DOCUMENT_CREATOR_MAJOR_VERSION
private static final int	DOCUMENT_CREATOR_MINOR_VERSION
private static final int	DOCUMENT_CREATOR_NAME
private static final int	DOCUMENT_CREATOR_PACKAGE
private static final int	DOCUMENT_CREATOR_SUB_VERSION
private static final int	DOCUMENT_NAME
private static final int	DOCUMENT_NOTE
private static final int	DOCUMENT_PRODUCT
private static final int	DOCUMENT_PRODUCT_NAME
private static final int	DOCUMENT_PRODUCT_VERSION
private static final int	DOCUMENT_PROPERTIES
private static final int	DOCUMENT_THUMB
private static final int	DOCUMENT_TIME
private static final int	DOCUMENT_TYPE_HINT
private static final int	DOUBLE
private static final int	DOUBLE_2
private static final int	DOUBLE_2_2
private static final int	DOUBLE_3
private static final int	DOUBLE_3_3
private static final int	DOUBLE_4
private static final int	DOUBLE_4_4
private static final int	DOUBLE_ARRAY_2
private static final int	DOUBLE_ARRAY_3
private static final int	DOUBLE_INTERVAL
private static final int	DOUBLE_RECT
private static final int	DP80_FRAME_CENTERING
private static final int	DWORD
private static final int	DYNAMIC_PROPERTIES
private static final int	EFI_HEIGHT_MAP
private static final int	EFI_SHARPNESS_MAP
private static final int	EFI_STACK
private static final int	EFI_TEXTURE_MAP
private static final int	EM_GAIN
private static final int	ENHANCED_DYNAMIC_RANGE
private boolean	expectETS
private static final int	EXPOSURE_METERING_MODE
private static final int	EXPOSURE_TIME
private static final int	EXTERNAL_DATA_VOLUME
private static final int	EXTERNAL_FILE_PROPERTIES
private static final int	EXTRA_SAMPLES
private static final int	EXTRA_SAMPLES_PROPERTIES
private ArrayList<String>	extraFiles
static final boolean	FAIL_ON_MISSING_DEFAULT
static final String	FAIL_ON_MISSING_KEY
private static final int	FAN_SPEED
private static final int	FIELD_TYPE
private HashMap<Integer,String>	fileMap
private static final int	FLOAT
private static final int	FOCUS_IMAGE
private boolean	foundChannelTag
private static final int	FRAME_ORIGIN
private static final int	FRAME_PROPERTIES
private static final int	FRAME_SCALE
private static final int	FRAME_SIZE
private static final int	FRAME_TRANSFER
private static final int	FRAME_TYPE
private static final int	GAIN_UNIT
private static final int	GAMMA_CORRECTION
private static final int	GRADIENT_LUT
private static final int	GREEN_GAIN
private static final int	GREEN_OFFSET
private static final int	HAS_EXTERNAL_FILE
private static final int	HDRI_EXPOSURE_RANGE
private static final int	HDRI_FRAMES
private static final int	HDRI_MAP_MODE
private static final int	HDRI_ON
private static final int	HIDDEN_LAYER
private static final int	HOT_PIXEL_CORRECTION
private static final int	ICC_ENABLED
private IFDList	ifds
private static final int	IMAGE_BOUNDARY
private static final int	IMAGE_COLLECTION_PROPERTIES
private static final int	IMAGE_FRAME_VOLUME
private boolean	inDimensionProperties
private static final int	INT
private static final int	INT_2
private static final int	INT_3
private static final int	INT_4
private static final int	INT_ARRAY_2
private static final int	INT_ARRAY_3
private static final int	INT_ARRAY_4
private static final int	INT_ARRAY_5
private static final int	INT_INTERVAL
private static final int	INT_RECT
private static final int	IS_TRANSMISSION
private static final int	ISO_SENSITIVITY
private boolean	jpeg
private static final int	JPEG
private static final int	JPEG_2000
private static final int	JPEG_LOSSLESS
private static final int	LAMBDA
private static final int	LAMBDA_INCREMENT
private static final int	LAMBDA_START
private static final int	LAMBDA_VALUE
private static final int	LAYER_INFO_PROPERTIES
private static final int	LAYER_SELECTION
private static final int	LAYER_SELECTION_INDEX
private static final int	LAYER_XY_FIXED
private static final int	LIVE_OVERFLOW
private static final int	LONG
private static final int	MACRO_IMAGE
private static final int	MAGNIFICATION
private static final int	MEM_MODEL
private int	metadataIndex
private static final int	MIRROR_H
private static final int	MIRROR_V
private static final int	MULTIDIM_IMAGE_VOLUME
private static final int	MULTIDIM_STACK_PROPERTIES
private ArrayList<Integer>	nDimensions
private static final int	NEW_MDIM_VOLUME_HEADER
private static final int	NEW_VOLUME_HEADER
private static final int	NOISE_REDUCTION
private static final int	NUMERICAL_APERTURE
private static final int	OBJECTIVE_MAG
private static final int	OBJECTIVE_NAME
private static final int	OBJECTIVE_TYPE
private static final int	OPTICAL_PATH
private static final int	ORIGINAL_FRAME_RATE
private static final int	OVERVIEW_IMAGE
private TiffParser	parser
private static final int	PHASE
private static final int	PHOTOBLEACHING
private static final int	PHOTON_IMAGING_MODE
private static final int	PIXEL_CLOCK
private static final int	PIXEL_INFO_TYPE
private static final int	PLANE_ORIGIN_RWC
private static final int	PLANE_SCALE_RWC
private static final int	PLANE_UNIT
private static final int	PNG
private static final int	PREAMP_GAIN_VALUE
private int	previousTag
private static final int	PROPERTY_SET_VOLUME
private ArrayList<CellSensReader.Pyramid>	pyramids
private static final int	RAW
private static final int	RED_GAIN
private static final int	RED_OFFSET
private static final int	REFRACTIVE_INDEX
private static final int	RENDER_OPERATION_ID
private static final int	RGB
private ArrayList<Integer>	rows
private static final int	RWC_FRAME_ORIGIN
private static final int	RWC_FRAME_SCALE
private static final int	RWC_FRAME_UNIT
private static final int	SAMPLE_FLAGS_LIST
private static final int	SAMPLE_ID_LIST
private static final int	SAMPLE_MASK
private static final int	SATURATION
private static final int	SELECTED_CHANNELS
private static final int	SELECTED_FRAMES
private static final int	SERIALIZED_MASK
private static final int	SHADING_MUL
private static final int	SHADING_SUB
private static final int	SHARPNESS
private static final int	SHORT
private static final int	SIGNAL_OUTPUT
private static final int	SLIDE_INFO
private static final int	SLIDE_NAME
private static final int	SLIDE_PREPARATION
private static final int	SLIDE_PROPERTIES
private static final int	SLIDE_SPECIMEN
private static final int	SLIDE_STAINING
private static final int	SLIDE_TISSUE
private static final int	SPURIOUS_NOISE_REMOVAL
private static final int	STACK_DISPLAY_LUT
private static final int	STACK_NAME
private static final int	STACK_TYPE
private static final int	T
private static final int	TCHAR
private static final int	TEMPERATURE_TARGET
private static final int	THIRD_ID
private static final int	TIFF_IFD
private static final int	TILE_ORIGIN
private static final int	TILE_SYSTEM
private ArrayList<ArrayList<CellSensReader.TileCoordinate>>	tileMap
private ArrayList<Long[]>	tileOffsets
private ArrayList<Integer>	tileX
private ArrayList<Integer>	tileY
private static final int	TIME_INCREMENT
private static final int	TIME_START
private static final int	TIME_VALUE
private static final int	TIMESTAMP
private static final int	TRANSPARENCY_ID
private static final int	TRANSPARENCY_VALUE
private static final int	UCHAR
private static final int	UINT
private static final int	ULONG
private static final int	UNICODE_TCHAR
private static final int	UNKNOWN
private static final int	UNKNOWN_BLOBS_VOLUME
private static final int	USE_ORIGINAL_FRAME_RATE
private String[]	usedFiles
private static final int	USHORT
private static final int	VALUE
private static final int	VCLOCK_AMPLITUDE
private static final int	VECTOR_DATA
private static final int	VECTOR_LAYER_VOLUME
private static final int	VERSION_NUMBER
private static final int	VOLUME_INDEX
private static final int	WB_MODE
private static final int	WB_PRESET_ID
private static final int	WB_PRESET_NAME
private static final int	WIDER
private static final int	WIDER_ENABLED
private static final int	WORKING_DISTANCE
private static final int	X_BINNING
private static final int	Y_BINNING
private static final int	Y_DIMENSION_UNIT
private static final int	Y_PLANE_DIMENSION_UNIT
private static final int	Z
private static final int	Z_INCREMENT
private static final int	Z_START
private static final int	Z_VALUE
private int	zCount

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
CellSensReader()	Constructs a new cellSens reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
private int	convertPixelType(int pixelType)
private byte[]	decodeTile(int no, int row, int col)
boolean	failOnMissingETS()
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
protected ArrayList<String>	getAvailableOptions()	Returns the list of available metadata options.
private CellSensReader.Pyramid	getCurrentPyramid()	Get an object representing the pyramid which contains the current series/resolution.
private int	getCurrentPyramidIndex()	Get an index to the pyramid which contains the current series/resolution.
private String	getDeviceSubtype(String type)
private int	getIFDIndex()
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth()	Returns the optimal sub-image width for use with openBytes.
private int	getResolutionIndex()	Get the current pyramid resolution, accounting for flattened resolutions as needed.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
private String	getStackType(String type)
private String	getTagName(int tag)
private int	getTileSize()	Get the expected decompressed size of a single tile, in bytes.
private String	getVolumeName(int tag)
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
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.
byte[]	openThumbBytes(int no)	Obtains a thumbnail for the specified image plane from the current file, as a byte array.
private boolean	parseETSFile(loci.common.RandomAccessInputStream etsFile, String file, int s, boolean hasOrphanEtsFiles)
private void	readTags(loci.common.RandomAccessInputStream vsi, boolean populateMetadata, String tagPrefix)
void	reopenFile()	Reopen any files that were closed, and which are expected to be open while the reader is open.

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, 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, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

FAIL_ON_MISSING_KEY

public static final String FAIL_ON_MISSING_KEY

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• Constant Field Values

FAIL_ON_MISSING_DEFAULT

public static final boolean FAIL_ON_MISSING_DEFAULT

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RAW

private static final int RAW

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JPEG

private static final int JPEG

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JPEG_2000

private static final int JPEG_2000

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JPEG_LOSSLESS

private static final int JPEG_LOSSLESS

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PNG

private static final int PNG

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BMP

private static final int BMP

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CHAR

private static final int CHAR

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UCHAR

private static final int UCHAR

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SHORT

private static final int SHORT

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USHORT

private static final int USHORT

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INT

private static final int INT

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UINT

private static final int UINT

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LONG

private static final int LONG

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ULONG

private static final int ULONG

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FLOAT

private static final int FLOAT

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DOUBLE

private static final int DOUBLE

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COMPLEX

private static final int COMPLEX

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BOOLEAN

private static final int BOOLEAN

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TCHAR

private static final int TCHAR

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DWORD

private static final int DWORD

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TIMESTAMP

private static final int TIMESTAMP

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DATE

private static final int DATE

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INT_2

private static final int INT_2

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INT_3

private static final int INT_3

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INT_4

private static final int INT_4

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INT_RECT

private static final int INT_RECT

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DOUBLE_2

private static final int DOUBLE_2

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DOUBLE_3

private static final int DOUBLE_3

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DOUBLE_4

private static final int DOUBLE_4

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DOUBLE_RECT

private static final int DOUBLE_RECT

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DOUBLE_2_2

private static final int DOUBLE_2_2

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DOUBLE_3_3

private static final int DOUBLE_3_3

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DOUBLE_4_4

private static final int DOUBLE_4_4

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INT_INTERVAL

private static final int INT_INTERVAL

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DOUBLE_INTERVAL

private static final int DOUBLE_INTERVAL

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RGB

private static final int RGB

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BGR

private static final int BGR

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FIELD_TYPE

private static final int FIELD_TYPE

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MEM_MODEL

private static final int MEM_MODEL

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COLOR_SPACE

private static final int COLOR_SPACE

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INT_ARRAY_2

private static final int INT_ARRAY_2

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INT_ARRAY_3

private static final int INT_ARRAY_3

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INT_ARRAY_4

private static final int INT_ARRAY_4

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INT_ARRAY_5

private static final int INT_ARRAY_5

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DOUBLE_ARRAY_2

private static final int DOUBLE_ARRAY_2

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DOUBLE_ARRAY_3

private static final int DOUBLE_ARRAY_3

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UNICODE_TCHAR

private static final int UNICODE_TCHAR

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DIM_INDEX_1

private static final int DIM_INDEX_1

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DIM_INDEX_2

private static final int DIM_INDEX_2

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VOLUME_INDEX

private static final int VOLUME_INDEX

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PIXEL_INFO_TYPE

private static final int PIXEL_INFO_TYPE

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NEW_VOLUME_HEADER

private static final int NEW_VOLUME_HEADER

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PROPERTY_SET_VOLUME

private static final int PROPERTY_SET_VOLUME

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NEW_MDIM_VOLUME_HEADER

private static final int NEW_MDIM_VOLUME_HEADER

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TIFF_IFD

private static final int TIFF_IFD

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VECTOR_DATA

private static final int VECTOR_DATA

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COLLECTION_VOLUME

private static final int COLLECTION_VOLUME

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MULTIDIM_IMAGE_VOLUME

private static final int MULTIDIM_IMAGE_VOLUME

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IMAGE_FRAME_VOLUME

private static final int IMAGE_FRAME_VOLUME

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DIMENSION_SIZE

private static final int DIMENSION_SIZE

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IMAGE_COLLECTION_PROPERTIES

private static final int IMAGE_COLLECTION_PROPERTIES

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MULTIDIM_STACK_PROPERTIES

private static final int MULTIDIM_STACK_PROPERTIES

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FRAME_PROPERTIES

private static final int FRAME_PROPERTIES

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DIMENSION_DESCRIPTION_VOLUME

private static final int DIMENSION_DESCRIPTION_VOLUME

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CHANNEL_PROPERTIES

private static final int CHANNEL_PROPERTIES

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DISPLAY_MAPPING_VOLUME

private static final int DISPLAY_MAPPING_VOLUME

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LAYER_INFO_PROPERTIES

private static final int LAYER_INFO_PROPERTIES

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CHANNEL_INFO_PROPERTIES

private static final int CHANNEL_INFO_PROPERTIES

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DEFAULT_SAMPLE_IFD

private static final int DEFAULT_SAMPLE_IFD

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VECTOR_LAYER_VOLUME

private static final int VECTOR_LAYER_VOLUME

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EXTERNAL_FILE_PROPERTIES

private static final int EXTERNAL_FILE_PROPERTIES

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COARSE_FRAME_IFD

private static final int COARSE_FRAME_IFD

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COARSE_PYRAMID_LEVEL

private static final int COARSE_PYRAMID_LEVEL

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SERIALIZED_MASK

private static final int SERIALIZED_MASK

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UNKNOWN_BLOBS_VOLUME

private static final int UNKNOWN_BLOBS_VOLUME

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SAMPLE_ID_LIST

private static final int SAMPLE_ID_LIST

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EXTRA_SAMPLES

private static final int EXTRA_SAMPLES

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EXTRA_SAMPLES_PROPERTIES

private static final int EXTRA_SAMPLES_PROPERTIES

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SAMPLE_FLAGS_LIST

private static final int SAMPLE_FLAGS_LIST

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FRAME_TYPE

private static final int FRAME_TYPE

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DEFAULT_BACKGROUND_COLOR

private static final int DEFAULT_BACKGROUND_COLOR

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VERSION_NUMBER

private static final int VERSION_NUMBER

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DOCUMENT_PROPERTIES

private static final int DOCUMENT_PROPERTIES

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DOCUMENT_NAME

private static final int DOCUMENT_NAME

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DOCUMENT_NOTE

private static final int DOCUMENT_NOTE

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DOCUMENT_TIME

private static final int DOCUMENT_TIME

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DOCUMENT_AUTHOR

private static final int DOCUMENT_AUTHOR

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DOCUMENT_COMPANY

private static final int DOCUMENT_COMPANY

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DOCUMENT_CREATOR_NAME

private static final int DOCUMENT_CREATOR_NAME

See Also:

• Constant Field Values

DOCUMENT_CREATOR_MAJOR_VERSION

private static final int DOCUMENT_CREATOR_MAJOR_VERSION

See Also:

• Constant Field Values

DOCUMENT_CREATOR_MINOR_VERSION

private static final int DOCUMENT_CREATOR_MINOR_VERSION

See Also:

• Constant Field Values

DOCUMENT_CREATOR_SUB_VERSION

private static final int DOCUMENT_CREATOR_SUB_VERSION

See Also:

• Constant Field Values

DOCUMENT_CREATOR_BUILD_NUMBER

private static final int DOCUMENT_CREATOR_BUILD_NUMBER

See Also:

• Constant Field Values

DOCUMENT_CREATOR_PACKAGE

private static final int DOCUMENT_CREATOR_PACKAGE

See Also:

• Constant Field Values

DOCUMENT_PRODUCT

private static final int DOCUMENT_PRODUCT

See Also:

• Constant Field Values

DOCUMENT_PRODUCT_NAME

private static final int DOCUMENT_PRODUCT_NAME

See Also:

• Constant Field Values

DOCUMENT_PRODUCT_VERSION

private static final int DOCUMENT_PRODUCT_VERSION

See Also:

• Constant Field Values

DOCUMENT_TYPE_HINT

private static final int DOCUMENT_TYPE_HINT

See Also:

• Constant Field Values

DOCUMENT_THUMB

private static final int DOCUMENT_THUMB

See Also:

• Constant Field Values

SLIDE_PROPERTIES

private static final int SLIDE_PROPERTIES

See Also:

• Constant Field Values

SLIDE_SPECIMEN

private static final int SLIDE_SPECIMEN

See Also:

• Constant Field Values

SLIDE_TISSUE

private static final int SLIDE_TISSUE

See Also:

• Constant Field Values

SLIDE_PREPARATION

private static final int SLIDE_PREPARATION

See Also:

• Constant Field Values

SLIDE_STAINING

private static final int SLIDE_STAINING

See Also:

• Constant Field Values

SLIDE_INFO

private static final int SLIDE_INFO

See Also:

• Constant Field Values

SLIDE_NAME

private static final int SLIDE_NAME

See Also:

• Constant Field Values

DYNAMIC_PROPERTIES

private static final int DYNAMIC_PROPERTIES

See Also:

• Constant Field Values

MAGNIFICATION

private static final int MAGNIFICATION

See Also:

• Constant Field Values

IMAGE_BOUNDARY

private static final int IMAGE_BOUNDARY

See Also:

• Constant Field Values

TILE_SYSTEM

private static final int TILE_SYSTEM

See Also:

• Constant Field Values

HAS_EXTERNAL_FILE

private static final int HAS_EXTERNAL_FILE

See Also:

• Constant Field Values

EXTERNAL_DATA_VOLUME

private static final int EXTERNAL_DATA_VOLUME

See Also:

• Constant Field Values

TILE_ORIGIN

private static final int TILE_ORIGIN

See Also:

• Constant Field Values

EXPOSURE_TIME

private static final int EXPOSURE_TIME

See Also:

• Constant Field Values

CAMERA_GAIN

private static final int CAMERA_GAIN

See Also:

• Constant Field Values

CAMERA_OFFSET

private static final int CAMERA_OFFSET

See Also:

• Constant Field Values

CAMERA_GAMMA

private static final int CAMERA_GAMMA

See Also:

• Constant Field Values

SHARPNESS

private static final int SHARPNESS

See Also:

• Constant Field Values

RED_GAIN

private static final int RED_GAIN

See Also:

• Constant Field Values

GREEN_GAIN

private static final int GREEN_GAIN

See Also:

• Constant Field Values

BLUE_GAIN

private static final int BLUE_GAIN

See Also:

• Constant Field Values

RED_OFFSET

private static final int RED_OFFSET

See Also:

• Constant Field Values

GREEN_OFFSET

private static final int GREEN_OFFSET

See Also:

• Constant Field Values

BLUE_OFFSET

private static final int BLUE_OFFSET

See Also:

• Constant Field Values

SHADING_SUB

private static final int SHADING_SUB

See Also:

• Constant Field Values

SHADING_MUL

private static final int SHADING_MUL

See Also:

• Constant Field Values

X_BINNING

private static final int X_BINNING

See Also:

• Constant Field Values

Y_BINNING

private static final int Y_BINNING

See Also:

• Constant Field Values

CLIPPING

private static final int CLIPPING

See Also:

• Constant Field Values

MIRROR_H

private static final int MIRROR_H

See Also:

• Constant Field Values

MIRROR_V

private static final int MIRROR_V

See Also:

• Constant Field Values

CLIPPING_STATE

private static final int CLIPPING_STATE

See Also:

• Constant Field Values

ICC_ENABLED

private static final int ICC_ENABLED

See Also:

• Constant Field Values

BRIGHTNESS

private static final int BRIGHTNESS

See Also:

• Constant Field Values

CONTRAST

private static final int CONTRAST

See Also:

• Constant Field Values

CONTRAST_TARGET

private static final int CONTRAST_TARGET

See Also:

• Constant Field Values

ACCUMULATION

private static final int ACCUMULATION

See Also:

• Constant Field Values

AVERAGING

private static final int AVERAGING

See Also:

• Constant Field Values

ISO_SENSITIVITY

private static final int ISO_SENSITIVITY

See Also:

• Constant Field Values

ACCUMULATION_MODE

private static final int ACCUMULATION_MODE

See Also:

• Constant Field Values

AUTOEXPOSURE

private static final int AUTOEXPOSURE

See Also:

• Constant Field Values

EXPOSURE_METERING_MODE

private static final int EXPOSURE_METERING_MODE

See Also:

• Constant Field Values

FRAME_SIZE

private static final int FRAME_SIZE

See Also:

• Constant Field Values

BIT_DEPTH

private static final int BIT_DEPTH

See Also:

• Constant Field Values

HDRI_ON

private static final int HDRI_ON

See Also:

• Constant Field Values

HDRI_FRAMES

private static final int HDRI_FRAMES

See Also:

• Constant Field Values

HDRI_EXPOSURE_RANGE

private static final int HDRI_EXPOSURE_RANGE

See Also:

• Constant Field Values

HDRI_MAP_MODE

private static final int HDRI_MAP_MODE

See Also:

• Constant Field Values

CUSTOM_GRAYSCALE

private static final int CUSTOM_GRAYSCALE

See Also:

• Constant Field Values

SATURATION

private static final int SATURATION

See Also:

• Constant Field Values

WB_PRESET_ID

private static final int WB_PRESET_ID

See Also:

• Constant Field Values

WB_PRESET_NAME

private static final int WB_PRESET_NAME

See Also:

• Constant Field Values

WB_MODE

private static final int WB_MODE

See Also:

• Constant Field Values

CCD_SENSITIVITY

private static final int CCD_SENSITIVITY

See Also:

• Constant Field Values

ENHANCED_DYNAMIC_RANGE

private static final int ENHANCED_DYNAMIC_RANGE

See Also:

• Constant Field Values

PIXEL_CLOCK

private static final int PIXEL_CLOCK

See Also:

• Constant Field Values

COLORSPACE

private static final int COLORSPACE

See Also:

• Constant Field Values

COOLING_ON

private static final int COOLING_ON

See Also:

• Constant Field Values

FAN_SPEED

private static final int FAN_SPEED

See Also:

• Constant Field Values

TEMPERATURE_TARGET

private static final int TEMPERATURE_TARGET

See Also:

• Constant Field Values

GAIN_UNIT

private static final int GAIN_UNIT

See Also:

• Constant Field Values

EM_GAIN

private static final int EM_GAIN

See Also:

• Constant Field Values

PHOTON_IMAGING_MODE

private static final int PHOTON_IMAGING_MODE

See Also:

• Constant Field Values

FRAME_TRANSFER

private static final int FRAME_TRANSFER

See Also:

• Constant Field Values

ANDOR_SHIFT_SPEED

private static final int ANDOR_SHIFT_SPEED

See Also:

• Constant Field Values

VCLOCK_AMPLITUDE

private static final int VCLOCK_AMPLITUDE

See Also:

• Constant Field Values

SPURIOUS_NOISE_REMOVAL

private static final int SPURIOUS_NOISE_REMOVAL

See Also:

• Constant Field Values

SIGNAL_OUTPUT

private static final int SIGNAL_OUTPUT

See Also:

• Constant Field Values

BASELINE_OFFSET_CLAMP

private static final int BASELINE_OFFSET_CLAMP

See Also:

• Constant Field Values

DP80_FRAME_CENTERING

private static final int DP80_FRAME_CENTERING

See Also:

• Constant Field Values

HOT_PIXEL_CORRECTION

private static final int HOT_PIXEL_CORRECTION

See Also:

• Constant Field Values

NOISE_REDUCTION

private static final int NOISE_REDUCTION

See Also:

• Constant Field Values

WIDER

private static final int WIDER

See Also:

• Constant Field Values

PHOTOBLEACHING

private static final int PHOTOBLEACHING

See Also:

• Constant Field Values

PREAMP_GAIN_VALUE

private static final int PREAMP_GAIN_VALUE

See Also:

• Constant Field Values

WIDER_ENABLED

private static final int WIDER_ENABLED

See Also:

• Constant Field Values

Z_START

private static final int Z_START

See Also:

• Constant Field Values

Z_INCREMENT

private static final int Z_INCREMENT

See Also:

• Constant Field Values

Z_VALUE

private static final int Z_VALUE

See Also:

• Constant Field Values

TIME_START

private static final int TIME_START

See Also:

• Constant Field Values

TIME_INCREMENT

private static final int TIME_INCREMENT

See Also:

• Constant Field Values

TIME_VALUE

private static final int TIME_VALUE

See Also:

• Constant Field Values

LAMBDA_START

private static final int LAMBDA_START

See Also:

• Constant Field Values

LAMBDA_INCREMENT

private static final int LAMBDA_INCREMENT

See Also:

• Constant Field Values

LAMBDA_VALUE

private static final int LAMBDA_VALUE

See Also:

• Constant Field Values

DIMENSION_NAME

private static final int DIMENSION_NAME

See Also:

• Constant Field Values

DIMENSION_MEANING

private static final int DIMENSION_MEANING

See Also:

• Constant Field Values

DIMENSION_START_ID

private static final int DIMENSION_START_ID

See Also:

• Constant Field Values

DIMENSION_INCREMENT_ID

private static final int DIMENSION_INCREMENT_ID

See Also:

• Constant Field Values

DIMENSION_VALUE_ID

private static final int DIMENSION_VALUE_ID

See Also:

• Constant Field Values

CHANNEL_NAME

private static final int CHANNEL_NAME

See Also:

• Constant Field Values

Z

private static final int Z

See Also:

• Constant Field Values

T

private static final int T

See Also:

• Constant Field Values

LAMBDA

private static final int LAMBDA

See Also:

• Constant Field Values

C

private static final int C

See Also:

• Constant Field Values

UNKNOWN

private static final int UNKNOWN

See Also:

• Constant Field Values

PHASE

private static final int PHASE

See Also:

• Constant Field Values

DISPLAY_LIMITS

private static final int DISPLAY_LIMITS

See Also:

• Constant Field Values

STACK_DISPLAY_LUT

private static final int STACK_DISPLAY_LUT

See Also:

• Constant Field Values

GAMMA_CORRECTION

private static final int GAMMA_CORRECTION

See Also:

• Constant Field Values

FRAME_ORIGIN

private static final int FRAME_ORIGIN

See Also:

• Constant Field Values

FRAME_SCALE

private static final int FRAME_SCALE

See Also:

• Constant Field Values

DISPLAY_COLOR

private static final int DISPLAY_COLOR

See Also:

• Constant Field Values

CREATION_TIME

private static final int CREATION_TIME

See Also:

• Constant Field Values

RWC_FRAME_ORIGIN

private static final int RWC_FRAME_ORIGIN

See Also:

• Constant Field Values

RWC_FRAME_SCALE

private static final int RWC_FRAME_SCALE

See Also:

• Constant Field Values

RWC_FRAME_UNIT

private static final int RWC_FRAME_UNIT

See Also:

• Constant Field Values

STACK_NAME

private static final int STACK_NAME

See Also:

• Constant Field Values

CHANNEL_DIM

private static final int CHANNEL_DIM

See Also:

• Constant Field Values

OPTICAL_PATH

private static final int OPTICAL_PATH

See Also:

• Constant Field Values

STACK_TYPE

private static final int STACK_TYPE

See Also:

• Constant Field Values

LIVE_OVERFLOW

private static final int LIVE_OVERFLOW

See Also:

• Constant Field Values

IS_TRANSMISSION

private static final int IS_TRANSMISSION

See Also:

• Constant Field Values

CONTRAST_BRIGHTNESS

private static final int CONTRAST_BRIGHTNESS

See Also:

• Constant Field Values

ACQUISITION_PROPERTIES

private static final int ACQUISITION_PROPERTIES

See Also:

• Constant Field Values

GRADIENT_LUT

private static final int GRADIENT_LUT

See Also:

• Constant Field Values

CALIBRATION

private static final int CALIBRATION

See Also:

• Constant Field Values

DEFAULT_IMAGE

private static final int DEFAULT_IMAGE

See Also:

• Constant Field Values

OVERVIEW_IMAGE

private static final int OVERVIEW_IMAGE

See Also:

• Constant Field Values

SAMPLE_MASK

private static final int SAMPLE_MASK

See Also:

• Constant Field Values

FOCUS_IMAGE

private static final int FOCUS_IMAGE

See Also:

• Constant Field Values

EFI_SHARPNESS_MAP

private static final int EFI_SHARPNESS_MAP

See Also:

• Constant Field Values

EFI_HEIGHT_MAP

private static final int EFI_HEIGHT_MAP

See Also:

• Constant Field Values

EFI_TEXTURE_MAP

private static final int EFI_TEXTURE_MAP

See Also:

• Constant Field Values

EFI_STACK

private static final int EFI_STACK

See Also:

• Constant Field Values

MACRO_IMAGE

private static final int MACRO_IMAGE

See Also:

• Constant Field Values

DISPLAY_PROCESSOR_TYPE

private static final int DISPLAY_PROCESSOR_TYPE

See Also:

• Constant Field Values

RENDER_OPERATION_ID

private static final int RENDER_OPERATION_ID

See Also:

• Constant Field Values

DISPLAY_STACK_ID

private static final int DISPLAY_STACK_ID

See Also:

• Constant Field Values

TRANSPARENCY_ID

private static final int TRANSPARENCY_ID

See Also:

• Constant Field Values

THIRD_ID

private static final int THIRD_ID

See Also:

• Constant Field Values

DISPLAY_VISIBLE

private static final int DISPLAY_VISIBLE

See Also:

• Constant Field Values

TRANSPARENCY_VALUE

private static final int TRANSPARENCY_VALUE

See Also:

• Constant Field Values

DISPLAY_LUT

private static final int DISPLAY_LUT

See Also:

• Constant Field Values

DISPLAY_STACK_INDEX

private static final int DISPLAY_STACK_INDEX

See Also:

• Constant Field Values

CHANNEL_TRANSPARENCY_VALUE

private static final int CHANNEL_TRANSPARENCY_VALUE

See Also:

• Constant Field Values

CHANNEL_VISIBLE

private static final int CHANNEL_VISIBLE

See Also:

• Constant Field Values

SELECTED_CHANNELS

private static final int SELECTED_CHANNELS

See Also:

• Constant Field Values

DISPLAY_GAMMA_CORRECTION

private static final int DISPLAY_GAMMA_CORRECTION

See Also:

• Constant Field Values

CHANNEL_GAMMA_CORRECTION

private static final int CHANNEL_GAMMA_CORRECTION

See Also:

• Constant Field Values

DISPLAY_CONTRAST_BRIGHTNESS

private static final int DISPLAY_CONTRAST_BRIGHTNESS

See Also:

• Constant Field Values

CHANNEL_CONTRAST_BRIGHTNESS

private static final int CHANNEL_CONTRAST_BRIGHTNESS

See Also:

• Constant Field Values

ACTIVE_STACK_DIMENSION

private static final int ACTIVE_STACK_DIMENSION

See Also:

• Constant Field Values

SELECTED_FRAMES

private static final int SELECTED_FRAMES

See Also:

• Constant Field Values

DISPLAYED_LUT_ID

private static final int DISPLAYED_LUT_ID

See Also:

• Constant Field Values

HIDDEN_LAYER

private static final int HIDDEN_LAYER

See Also:

• Constant Field Values

LAYER_XY_FIXED

private static final int LAYER_XY_FIXED

See Also:

• Constant Field Values

ACTIVE_LAYER_VECTOR

private static final int ACTIVE_LAYER_VECTOR

See Also:

• Constant Field Values

ACTIVE_LAYER_INDEX_VECTOR

private static final int ACTIVE_LAYER_INDEX_VECTOR

See Also:

• Constant Field Values

CHAINED_LAYERS

private static final int CHAINED_LAYERS

See Also:

• Constant Field Values

LAYER_SELECTION

private static final int LAYER_SELECTION

See Also:

• Constant Field Values

LAYER_SELECTION_INDEX

private static final int LAYER_SELECTION_INDEX

See Also:

• Constant Field Values

CANVAS_COLOR_1

private static final int CANVAS_COLOR_1

See Also:

• Constant Field Values

CANVAS_COLOR_2

private static final int CANVAS_COLOR_2

See Also:

• Constant Field Values

ORIGINAL_FRAME_RATE

private static final int ORIGINAL_FRAME_RATE

See Also:

• Constant Field Values

USE_ORIGINAL_FRAME_RATE

private static final int USE_ORIGINAL_FRAME_RATE

See Also:

• Constant Field Values

ACTIVE_CHANNEL

private static final int ACTIVE_CHANNEL

See Also:

• Constant Field Values

PLANE_UNIT

private static final int PLANE_UNIT

See Also:

• Constant Field Values

Y_PLANE_DIMENSION_UNIT

private static final int Y_PLANE_DIMENSION_UNIT

See Also:

• Constant Field Values

Y_DIMENSION_UNIT

private static final int Y_DIMENSION_UNIT

See Also:

• Constant Field Values

PLANE_ORIGIN_RWC

private static final int PLANE_ORIGIN_RWC

See Also:

• Constant Field Values

PLANE_SCALE_RWC

private static final int PLANE_SCALE_RWC

See Also:

• Constant Field Values

CHANNEL_OVERFLOW

private static final int CHANNEL_OVERFLOW

See Also:

• Constant Field Values

OBJECTIVE_MAG

private static final int OBJECTIVE_MAG

See Also:

• Constant Field Values

NUMERICAL_APERTURE

private static final int NUMERICAL_APERTURE

See Also:

• Constant Field Values

WORKING_DISTANCE

private static final int WORKING_DISTANCE

See Also:

• Constant Field Values

OBJECTIVE_NAME

private static final int OBJECTIVE_NAME

See Also:

• Constant Field Values

OBJECTIVE_TYPE

private static final int OBJECTIVE_TYPE

See Also:

• Constant Field Values

REFRACTIVE_INDEX

private static final int REFRACTIVE_INDEX

See Also:

• Constant Field Values

DEVICE_NAME

private static final int DEVICE_NAME

See Also:

• Constant Field Values

DEVICE_ID

private static final int DEVICE_ID

See Also:

• Constant Field Values

DEVICE_SUBTYPE

private static final int DEVICE_SUBTYPE

See Also:

• Constant Field Values

DEVICE_MANUFACTURER

private static final int DEVICE_MANUFACTURER

See Also:

• Constant Field Values

VALUE

private static final int VALUE

See Also:

• Constant Field Values

usedFiles

private String[] usedFiles

extraFiles

private ArrayList<String> extraFiles

fileMap

private HashMap<Integer,String> fileMap

parser

private TiffParser parser

ifds

private IFDList ifds

tileOffsets

private ArrayList<Long[]> tileOffsets

jpeg

private boolean jpeg

rows

private ArrayList<Integer> rows

cols

private ArrayList<Integer> cols

compressionType

private ArrayList<Integer> compressionType

tileX

private ArrayList<Integer> tileX

tileY

private ArrayList<Integer> tileY

tileMap

private ArrayList<ArrayList<CellSensReader.TileCoordinate>> tileMap

nDimensions

private ArrayList<Integer> nDimensions

inDimensionProperties

private boolean inDimensionProperties

foundChannelTag

private boolean foundChannelTag

dimensionTag

private int dimensionTag

backgroundColor

private HashMap<Integer,byte[]> backgroundColor

metadataIndex

private int metadataIndex

previousTag

private int previousTag

pyramids

private ArrayList<CellSensReader.Pyramid> pyramids

bgr

private boolean[] bgr

expectETS

private transient boolean expectETS

channelCount

private transient int channelCount

zCount

private transient int zCount

Constructor Details

CellSensReader

public CellSensReader()

Constructs a new cellSens reader.

Method Details

failOnMissingETS

public boolean failOnMissingETS()

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Parameters:

id - a file in the multi-file dataset

Returns:

an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).

Throws:

FormatException

IOException

See Also:

• FormatTools.MUST_GROUP
• FormatTools.CAN_GROUP
• FormatTools.CANNOT_GROUP

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

openThumbBytes

public byte[] openThumbBytes(int no)
                      throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a thumbnail for the specified image plane from the current file, as a byte array.

Specified by:

openThumbBytes in interface IFormatReader

Overrides:

openThumbBytes in class FormatReader

Throws:

FormatException

IOException

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

Returns:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

IOException - if there was a problem reading the file.

See Also:

• IFormatReader.openBytes(int, byte[], int, int, int, int)

reopenFile

public void reopenFile()
                throws IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

IOException

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

IOException

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Description copied from class: FormatReader

Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.

Overrides:

initFile in class FormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

IOException - if an I/O error occurs processing the file

getTileSize

private int getTileSize()

Get the expected decompressed size of a single tile, in bytes.

getCurrentPyramidIndex

private int getCurrentPyramidIndex()

Get an index to the pyramid which contains the current series/resolution. Accounts for flattened resolutions as needed.

getCurrentPyramid

private CellSensReader.Pyramid getCurrentPyramid()

Get an object representing the pyramid which contains the current series/resolution. Accounts for flattened resolutions as needed.

getResolutionIndex

private int getResolutionIndex()

Get the current pyramid resolution, accounting for flattened resolutions as needed.

decodeTile

private byte[] decodeTile(int no,
 int row,
 int col)
                   throws FormatException,
IOException

Throws:

FormatException

IOException

parseETSFile

private boolean parseETSFile(loci.common.RandomAccessInputStream etsFile,
 String file,
 int s,
 boolean hasOrphanEtsFiles)
                      throws FormatException,
IOException

Throws:

FormatException

IOException

convertPixelType

private int convertPixelType(int pixelType)
                      throws FormatException

Throws:

FormatException

readTags

private void readTags(loci.common.RandomAccessInputStream vsi,
 boolean populateMetadata,
 String tagPrefix)

getVolumeName

private String getVolumeName(int tag)

getTagName

private String getTagName(int tag)

getDeviceSubtype

private String getDeviceSubtype(String type)

getStackType

private String getStackType(String type)

getIFDIndex

private int getIFDIndex()