Index (formats-bsd 8.5.0 API)

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
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

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(File) - Method in class loci.formats.NumberFilter: Tests if a specified file should be included in a file list.
accept(String) - Method in class loci.formats.NumberFilter: Tests if a specified file should be included in a file list.
ACCESSION_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_CONTEXT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_CONTRAST - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_DEVICE_PROCESSING_CODE - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_DEVICE_PROCESSING_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_DURATION - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_MATRIX - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_START_CONDITION - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_START_CONDITION_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_TERMINATION_CONDITION - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_TERMINATION_CONDITION_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_TIME_SYNCHRONIZED - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITION_TIMESTAMP - Enum constant in enum loci.formats.dicom.DicomAttribute
ACQUISITIONS_IN_SERIES - Enum constant in enum loci.formats.dicom.DicomAttribute
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
ACTUAL_FRAME_DURATION - Enum constant in enum loci.formats.dicom.DicomAttribute
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
addAnnotation(MetadataStore, SlideBook7Reader.CAnnotation70, int, int, int) - Method in class loci.formats.in.SlideBook7Reader
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
ADDITIONAL_DRUG_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
ADDITIONAL_PATIENT_HISTORY - Enum constant in enum loci.formats.dicom.DicomAttribute
ADMITTING_DIAGNOSES_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
ADMITTING_DIAGNOSES_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
AE - Enum constant in enum loci.formats.dicom.DicomVR
alphabeticIndexCount(String) - Static method in class loci.formats.ResourceNamer
alreadyChecked() - Method in class loci.formats.UpgradeChecker: Return true if an upgrade check has already been performed in this JVM session.
ALT_JPEG - Enum constant in enum loci.formats.tiff.TiffCompression
ALT_JPEG2000 - Enum constant in enum loci.formats.tiff.TiffCompression
ALTERNATE_REPRESENTATION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
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
ANATOMIC_REGION_MODIFIER_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
ANATOMIC_REGION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
ANATOMIC_STRUCTURE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
ANGIO_FLAG - Enum constant in enum loci.formats.dicom.DicomAttribute
ANGULAR_POSITION - Enum constant in enum loci.formats.dicom.DicomAttribute
ANGULAR_STEP - Enum constant in enum loci.formats.dicom.DicomAttribute
anim - Variable in class loci.formats.gui.ImageViewer
ANIMATION - Enum constant in enum loci.formats.codec.CompressionType
ANIMATION_KEY - Static variable in class loci.formats.gui.ImageViewer
ANODE_TARGET_MATERIAL - Enum constant in enum loci.formats.dicom.DicomAttribute
APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
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.
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 - Enum constant in enum loci.formats.dicom.ResolutionStrategy
APPLICABLE_FRAME_RANGE - Enum constant in enum loci.formats.dicom.DicomAttribute
ARTIST - Static variable in class loci.formats.tiff.IFD
AS - Enum constant in enum loci.formats.dicom.DicomVR
ascii - Variable in class loci.formats.tools.AmiraParameters
ASCII - Enum constant in enum loci.formats.tiff.IFDType
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
ASSOCIATION - Enum constant in enum loci.formats.codec.JPEG2000BoxType
AT - Enum constant in enum loci.formats.dicom.DicomVR
attribute - Variable in class loci.formats.dicom.DicomTag
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.
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.
autoUpdate - Variable in class loci.formats.cache.Cache: Whether the cache should automatically update when a parameter changes.
AVERAGE_PULSE_WIDTH - Enum constant in enum loci.formats.dicom.DicomAttribute
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
AWTImageTools - Class in loci.formats.gui: A utility class with convenience methods for manipulating images in BufferedImage form.
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.
axisTypes - Variable in class loci.formats.AxisGuesser: Guessed axis types.

B

BACKWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
BARCODE_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
Base64Codec - Class in loci.formats.codec: Implements encoding (compress) and decoding (decompress) methods for Base64.
Base64Codec() - Constructor for class loci.formats.codec.Base64Codec
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
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.
BBOX - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
BDV_MAGIC_STRING - Static variable in class loci.formats.in.BDVReader
BDVReader - Class in loci.formats.in: Reader for BDV files.
BDVReader() - Constructor for class loci.formats.in.BDVReader: Constructs a new BDV reader.
BEAT_REJECTION_FLAG - Enum constant in enum loci.formats.dicom.DicomAttribute
bgrToRgb(byte[], boolean, int, int) - Static method in class loci.formats.ImageTools
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_TIFF - Static variable in class loci.formats.tiff.IFD
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.tiff.TiffConstants: 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
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
BIPLANE_ACQUISITION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
BitBuffer - Class in loci.formats.codec: Deprecated.
Use loci.common.RandomAccessInputStream instead
BitBuffer(byte[]) - Constructor for class loci.formats.codec.BitBuffer: Deprecated.

Default constructor.
BITS_ALLOCATED - Enum constant in enum loci.formats.dicom.DicomAttribute
BITS_PER_COMPONENT - Enum constant in enum loci.formats.codec.JPEG2000BoxType
BITS_PER_SAMPLE - Static variable in class loci.formats.tiff.IFD
BITS_STORED - Enum constant in enum loci.formats.dicom.DicomAttribute
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.
BLACK_IS_ZERO - Enum constant in enum loci.formats.tiff.PhotoInterp
blankImage(int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Creates a blank image with the given dimensions and transfer type.
BLOCK_END - Static variable in class loci.formats.FilePatternBlock: Identifies the end of a block.
BLOCK_START - Static variable in class loci.formats.FilePatternBlock: Identifies the start of a block.
BLUE_LUT_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
BLUE_LUT_DESCRIPTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
BMP_MAGIC_STRING - Static variable in class loci.formats.in.BMPReader
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.
BODY_PART_EXAMINED - Enum constant in enum loci.formats.dicom.DicomAttribute
BODY_PART_THICKNESS - Enum constant in enum loci.formats.dicom.DicomAttribute
BONE_THERMAL_INDEX - Enum constant in enum loci.formats.dicom.DicomAttribute
BooleanIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.BooleanIM3Record
BORDER_DENSITY - Enum constant in enum loci.formats.dicom.DicomAttribute
BOX_SIZE - Static variable in class loci.formats.in.FakeReader
BRANCH_OF_SERVICE - Enum constant in enum loci.formats.dicom.DicomAttribute
BRIGHTNESS_VALUE - Static variable in class loci.formats.tiff.IFD
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.
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.
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.
buildFileFilters(IFormatHandler) - Static method in class loci.formats.gui.GUITools: Constructs a list of file filters for the given file format handler.
BURNED_IN_ANNOTATION - Enum constant in enum loci.formats.dicom.DicomAttribute
BYTE - Enum constant in enum loci.formats.tiff.IFDType
ByteArraySource - Class in loci.formats.cache: Retrieves byte arrays from a data source (e.g., a file) using Bio-Formats.
ByteArraySource(String) - Constructor for class loci.formats.cache.ByteArraySource: Constructs a byte array source that draws from the given file.
ByteArraySource(IFormatReader) - Constructor for class loci.formats.cache.ByteArraySource: Constructs a byte array source from the given Bio-Formats reader.
bytes - Variable in class loci.formats.tiff.TiffSaver: Output bytes.
BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants: The number of bytes in each IFD entry.
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(byte[]) - Constructor for class loci.formats.codec.ByteVector
ByteVector(int) - Constructor for class loci.formats.codec.ByteVector

C

c - Variable in class loci.formats.tools.AmiraParameters
C_AXIS - Static variable in class loci.formats.AxisGuesser: Axis type for channels.
C_PREFIXES - Static variable in class loci.formats.AxisGuesser: Prefixes indicating channel dimension.
cache - Variable in class loci.formats.cache.Cache: Master array containing cached objects.
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.
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.
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 Class in loci.formats.cache: CacheException is the exception thrown when something goes wrong performing a cache operation.
CacheException() - Constructor for exception class loci.formats.cache.CacheException
CacheException(String) - Constructor for exception class loci.formats.cache.CacheException
CacheException(String, Throwable) - Constructor for exception class loci.formats.cache.CacheException
CacheException(Throwable) - Constructor for exception class loci.formats.cache.CacheException
CacheIndicator - Class in loci.formats.gui: Indicator GUI component showing which planes are currently in the cache for a given dimensional axis at a particular dimensional position.
CacheIndicator(Cache, int) - Constructor for class loci.formats.gui.CacheIndicator: Creates a new cache indicator for the given cache.
CacheIndicator(Cache, int, Component, int, int) - Constructor for class loci.formats.gui.CacheIndicator: Creates a new cache indicator.
CacheListener - Interface in loci.formats.cache: A listener for cache updates.
CacheReporter - Interface in loci.formats.cache: Interface for components capable of reporting cache updates.
CacheSource - Class in loci.formats.cache: Superclass of cache sources that retrieve image planes from a data source (e.g., a file) using Bio-Formats.
CacheSource(String) - Constructor for class loci.formats.cache.CacheSource: Constructs a cache source that draws from the given file.
CacheSource(IFormatReader) - Constructor for class loci.formats.cache.CacheSource: Constructs a cache source from the given Bio-Formats reader.
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
canChangePattern() - Method in class loci.formats.FileStitcher
canCloseReader - Variable in class loci.formats.gui.ImageViewer
canDetectBigTiff - Variable in class loci.formats.out.TiffWriter: Whether or not BigTIFF can be used automatically.
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.DicomWriter
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.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
canDoUpgradeCheck() - Method in class loci.formats.UpgradeChecker: Return whether or not we are ever allowed to perform an upgrade check.
canMerge() - Method in class loci.formats.ChannelMerger: Determines whether the channels in the file can be merged.
canSeparateSeries - Variable in class loci.formats.in.MinimalTiffReader: Whether or not IFDs with different dimensions can be split into separate series.
CAPTURE_RESOLUTION - Enum constant in enum loci.formats.codec.JPEG2000BoxType
CARDIAC_NUMBER_OF_IMAGES - Enum constant in enum loci.formats.dicom.DicomAttribute
CASSETTE_ORIENTATION - Enum constant in enum loci.formats.dicom.DicomAttribute
CASSETTE_SIZE - Enum constant in enum loci.formats.dicom.DicomAttribute
CCITT_1D - Enum constant in enum loci.formats.tiff.TiffCompression
CELL_LENGTH - Static variable in class loci.formats.tiff.IFD
CELL_WIDTH - Static variable in class loci.formats.tiff.IFD
CellH5Constants() - Constructor for class loci.formats.in.CellH5Reader.CellH5Constants
CellH5Reader - Class in loci.formats.in: Reader for CellH5 (HDF) files.
CellH5Reader() - Constructor for class loci.formats.in.CellH5Reader: Constructs a new CellH5 HDF reader.
CellH5Reader.CellH5Constants - Class in loci.formats.in
CellH5Reader.CellH5Coordinate - Class in loci.formats.in
CellH5Writer - Class in loci.formats.out: CellH5Writer is the file format writer for CellH5 format.
CellH5Writer() - Constructor for class loci.formats.out.CellH5Writer
CellH5Writer(String, String[]) - Constructor for class loci.formats.out.CellH5Writer
CENTER_OF_CIRCULAR_COLLIMATOR - Enum constant in enum loci.formats.dicom.DicomAttribute
CENTER_OF_CIRCULAR_SHUTTER - Enum constant in enum loci.formats.dicom.DicomAttribute
CENTER_OF_ROTATION_OFFSET - Enum constant in enum loci.formats.dicom.DicomAttribute
CENTERED_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
certain - Variable in class loci.formats.AxisGuesser: Whether the guesser is confident that all axis types are correct.
CFA_ARRAY - Enum constant in enum loci.formats.tiff.PhotoInterp
CFA_PATTERN - Static variable in class loci.formats.tiff.IFD
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 loci.formats.dicom.DicomTile
CHANNEL_DEFINITION - Enum constant in enum loci.formats.codec.JPEG2000BoxType
CHANNEL_DESCRIPTION_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
CHANNEL_PREFIX - Static variable in class loci.formats.in.KLBReader: Prefixes indicating dimensions and projections
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.
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.
channelNames - Variable in class loci.formats.dicom.DicomFileInfo
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.
CHARSET_OF_FILE_SET_DESCRIPTOR_FILE - Enum constant in enum loci.formats.dicom.DicomAttribute
checkHeader() - Method in class loci.formats.tiff.TiffParser: Checks the TIFF header.
checkParams - Variable in class loci.formats.out.TiffWriter: Whether or not to check the parameters passed to saveBytes.
children - Variable in class loci.formats.dicom.DicomTag
CI_SERVER - Static variable in class loci.formats.UpgradeChecker: Location of the OME continuous integration server.
CIE_LAB - Enum constant in enum loci.formats.tiff.PhotoInterp
CINE_RATE - Enum constant in enum loci.formats.dicom.DicomAttribute
CINEPAK - Enum constant in enum loci.formats.codec.CompressionType
CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
CLASSES_IN_STUDY - Enum constant in enum loci.formats.dicom.DicomAttribute
cleanup() - Method in class loci.formats.Memoizer
clear() - Method in class loci.formats.codec.ByteVector
CLINICAL_TRIAL_COORDINATING_CENTER - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_PROTOCOL_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_PROTOCOL_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_SITE_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_SITE_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_SPONSOR_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_SUBJECT_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_SUBJECT_READING_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_TIME_POINT_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
CLINICAL_TRIAL_TIME_POINT_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
clone() - Method in class loci.formats.SwappableMetadata
clone(IFormatReader, int) - Method in class loci.formats.SwappableMetadata
close() - Method in class loci.formats.codec.JPEGTileDecoder
close() - Method in class loci.formats.FileStitcher
close() - Method in class loci.formats.gui.PreviewPane: Closes the underlying image reader.
close() - Method in class loci.formats.Memoizer
close() - Method in interface loci.formats.Memoizer.Deser
close() - Method in class loci.formats.Memoizer.KryoDeser
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.DicomWriter
close() - Method in class loci.formats.out.ICSWriter
close() - Method in class loci.formats.out.JavaWriter
close() - Method in class loci.formats.out.OMETiffWriter
close() - Method in class loci.formats.out.OMEXMLWriter
close() - Method in class loci.formats.out.PyramidOMETiffWriter
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 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: Free resources associated with the initialized stream.
close() - Method in class loci.formats.services.JPEGTurboServiceImpl
close() - Method in class loci.formats.tiff.OnDemandLongArray
close() - Method in class loci.formats.tiff.TiffParser: Close the underlying stream, if this TiffParser was constructed with a file path.
close() - Method in class loci.formats.tiff.TiffSaver: Closes the output stream if not null.
close(boolean) - Method in class loci.formats.ChannelSeparator
close(boolean) - Method in class loci.formats.FileStitcher
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.BDVReader
close(boolean) - Method in class loci.formats.in.BMPReader
close(boolean) - Method in class loci.formats.in.CellH5Reader
close(boolean) - Method in class loci.formats.in.DicomReader
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.FitsReader
close(boolean) - Method in class loci.formats.in.FlowSightReader
close(boolean) - Method in class loci.formats.in.GIFReader
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.ImageIOReader
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.KLBReader
close(boolean) - Method in class loci.formats.in.MicromanagerReader
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.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.PCXReader
close(boolean) - Method in class loci.formats.in.PGMReader
close(boolean) - Method in class loci.formats.in.PictReader
close(boolean) - Method in class loci.formats.in.QTReader
close(boolean) - Method in class loci.formats.in.SlideBook7Reader
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.ZipReader
close(boolean) - Method in class loci.formats.Memoizer
close(boolean) - Method in class loci.formats.MinMaxCalculator
CMYK - Enum constant in enum loci.formats.tiff.PhotoInterp
COC - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
COD - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
CODE_MEANING - Enum constant in enum loci.formats.dicom.DicomAttribute
CODE_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
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 - Variable in class loci.formats.codec.Base64Codec
codec - Variable in class loci.formats.codec.HuffmanCodec
codec - Variable in class loci.formats.codec.JPEG2000Codec
codec - Variable in class loci.formats.codec.JPEGCodec
codec - Variable in class loci.formats.codec.LosslessJPEGCodec
codec - Variable in class loci.formats.codec.LZOCodec
codec - Variable in class loci.formats.codec.LZWCodec
codec - Variable in class loci.formats.codec.MJPBCodec
codec - Variable in class loci.formats.codec.MSRLECodec
codec - Variable in class loci.formats.codec.MSVideoCodec
codec - Variable in class loci.formats.codec.PackbitsCodec
codec - Variable in class loci.formats.codec.PassthroughCodec
codec - Variable in class loci.formats.codec.QTRLECodec
codec - Variable in class loci.formats.codec.RPZACodec
codec - Variable in class loci.formats.codec.ZlibCodec
codec - Variable in class loci.formats.codec.ZstdCodec
codec - Variable in class loci.formats.out.QTWriter: The codec to use.
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.
CODING_SCHEME_DESIGNATOR - Enum constant in enum loci.formats.dicom.DicomAttribute
CODING_SCHEME_EXTERNAL_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
CODING_SCHEME_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
CODING_SCHEME_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
CODING_SCHEME_REGISTRY - Enum constant in enum loci.formats.dicom.DicomAttribute
CODING_SCHEME_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
CODING_SCHEME_VERSION - Enum constant in enum loci.formats.dicom.DicomAttribute
COLLIMATOR_GRID_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
COLLIMATOR_LEFT_VERTICAL_EDGE - Enum constant in enum loci.formats.dicom.DicomAttribute
COLLIMATOR_LOWER_HORIZONTAL_EDGE - Enum constant in enum loci.formats.dicom.DicomAttribute
COLLIMATOR_RIGHT_VERTICAL_EDGE - Enum constant in enum loci.formats.dicom.DicomAttribute
COLLIMATOR_SHAPE - Enum constant in enum loci.formats.dicom.DicomAttribute
COLLIMATOR_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
COLLIMATOR_UPPER_HORIZONTAL_EDGE - Enum constant in enum loci.formats.dicom.DicomAttribute
COLOR_MAP - Static variable in class loci.formats.tiff.IFD
COLOR_SPACE - Enum constant in enum loci.formats.dicom.DicomAttribute
COLOR_SPACE - Static variable in class loci.formats.tiff.IFD
COLOUR_SPECIFICATION - Enum constant in enum loci.formats.codec.JPEG2000BoxType
column - Variable in class loci.formats.tools.AmiraParameters
COLUMN_ANGULATION - Enum constant in enum loci.formats.dicom.DicomAttribute
COLUMN_POSITION_IN_MATRIX - Enum constant in enum loci.formats.dicom.DicomAttribute
COLUMNS - Enum constant in enum loci.formats.dicom.DicomAttribute
COM - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
ComboFileFilter - Class in loci.formats.gui: A file filter that recognizes files from a union of other filters.
ComboFileFilter(FileFilter[], String) - Constructor for class loci.formats.gui.ComboFileFilter: Constructs a new filter from a list of other filters.
COMPANION_KEY - Static variable in class loci.formats.out.OMETiffWriter
COMPANION_SUFFIXES - Static variable in class loci.formats.in.TiffReader
compare(Object, Object) - Method in class loci.formats.cache.CacheStrategy: Default comparator orders dimensional positions based on distance from the current position, taking into account axis priorities and planar ordering.
compareTo(Object) - Method in class loci.formats.gui.ComboFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.ExtensionFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.FormatFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.NoExtensionFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.tiff.TiffIFDEntry
compareTo(DicomFileInfo) - Method in class loci.formats.dicom.DicomFileInfo
compareTo(DicomTag) - Method in class loci.formats.dicom.DicomTag
compareTo(TiffRational) - Method in class loci.formats.tiff.TiffRational: Compares this object with the specified object for order.
COMPLEX_IMAGE_COMPONENT - Enum constant in enum loci.formats.dicom.DicomAttribute
COMPONENT_MAPPING - Enum constant in enum loci.formats.codec.JPEG2000BoxType
COMPONENTS_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec: 2D data block encoding default implementation.
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.Base64Codec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.JPEG2000Codec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.JPEGCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.LosslessJPEGCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.LZOCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.LZWCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.MJPBCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.MSRLECodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.MSVideoCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.PackbitsCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.PassthroughCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.QTRLECodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.RPZACodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.ZlibCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.ZstdCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.NikonCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.Base64Codec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEG2000Codec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.LosslessJPEGCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.LZOCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.LZWCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.MJPBCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.MSRLECodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.MSVideoCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.PackbitsCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.PassthroughCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.QTRLECodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.RPZACodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.ZlibCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.ZstdCodec
compress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression: Encodes a strip of data.
compressBuffer(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer: Compresses the buffer.
COMPRESSED_BITS_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
COMPRESSION - Static variable in class loci.formats.tiff.IFD
COMPRESSION_FORCE - Enum constant in enum loci.formats.dicom.DicomAttribute
COMPRESSION_J2K - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_J2K_LOSSY - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_JPEG - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_LZW - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_UNCOMPRESSED - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_ZLIB - Static variable in class loci.formats.out.TiffWriter
CompressionType - Enum in loci.formats.codec: An enumeration of compression types.
computeAxisLengths() - Method in class loci.formats.FileStitcher: Computes axis length arrays, and total axis lengths.
computeIndices(int) - Method in class loci.formats.FileStitcher: Gets the file index, and image index into that file, corresponding to the given global image index.
CONCATENATION_FRAME_OFFSET_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
concatenationIndex - Variable in class loci.formats.dicom.DicomFileInfo
CONDENSER_LENS_POWER - Enum constant in enum loci.formats.dicom.DicomAttribute
constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class loci.formats.gui.AWTImageTools: Creates an image with the given DataBuffer.
constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class loci.formats.gui.AWTImageTools: Creates an image with the given DataBuffer.
CONTAINER_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTAINER_ID_ISSUER_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTAINER_TYPE_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTENT_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTENT_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTEXT_GROUP_EXTENSION_CREATOR - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTEXT_GROUP_EXTENSION_FLAG - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTEXT_GROUP_LOCAL_VERSION - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTEXT_GROUP_VERSION - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTEXT_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTIGUOUS_CODESTREAM - Enum constant in enum loci.formats.codec.JPEG2000BoxType
CONTRAST - Static variable in class loci.formats.tiff.IFD
CONTRAST_ALLERGIES - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_ADMIN_ROUTE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_AGENT - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_AGENT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_INGREDIENT - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_ROUTE - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_START_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_STOP_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_TOTAL_DOSE - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_BOLUS_VOLUME - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_FLOW_DURATION - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_FLOW_RATE - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_FRAME_AVERAGING - Enum constant in enum loci.formats.dicom.DicomAttribute
CONTRAST_INGREDIENT_CONCENTRATION - Enum constant in enum loci.formats.dicom.DicomAttribute
CONVERSION_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
convertRenderedImage(RenderedImage) - Static method in class loci.formats.gui.AWTImageTools: Converts a java.awt.image.RenderedImage into a java.awt.image.BufferedImage.
CONVOLUTION_KERNEL - Enum constant in enum loci.formats.dicom.DicomAttribute
COPYRIGHT - Static variable in class loci.formats.tiff.IFD
copyScaled(BufferedImage, BufferedImage, Object) - Static method in class loci.formats.gui.AWTImageTools: Copies the source image into the target, applying scaling.
copyTile(IFD, byte[], int, int) - Method in class loci.formats.in.MinimalTiffReader
coreIndexToSeries(int) - Method in class loci.formats.FileStitcher
coreMetadata - Variable in class loci.formats.dicom.DicomFileInfo
CORRECTED_IMAGE - Enum constant in enum loci.formats.dicom.DicomAttribute
COUNT_RATE - Enum constant in enum loci.formats.dicom.DicomAttribute
COUNTRY_OF_RESIDENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
COUNTS_ACCUMULATED - Enum constant in enum loci.formats.dicom.DicomAttribute
CRANIAL_THERMAL_INDEX - Enum constant in enum loci.formats.dicom.DicomAttribute
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.Index16ColorModel
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.SignedColorModel
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
created - Variable in class loci.formats.out.QTWriter: Time the file was created.
createGroup(String) - Method in interface loci.formats.services.JHDFService: Writes an array as sub-slice into an existing HDF5 dataset
createGroup(String) - Method in class loci.formats.services.JHDFServiceImpl
createInputStream() - Method in class loci.formats.out.TiffWriter
createTiffSaver() - Method in class loci.formats.out.TiffWriter
CREATION_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
CREATION_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
CREATOR_KEY - Static variable in class loci.formats.out.OMETiffWriter
CREATOR_KEY - Static variable in class loci.formats.out.OMEXMLWriter
CREATOR_VERSION_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
CRG - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
CrosshairStrategy - Class in loci.formats.cache: A crosshair strategy caches planes extending from the the current dimensional position along each individual axis, but not combinations of axes.
CrosshairStrategy(int[]) - Constructor for class loci.formats.cache.CrosshairStrategy: Constructs a crosshair strategy.
CS - Enum constant in enum loci.formats.dicom.DicomVR
CS_2C - Static variable in class loci.formats.gui.TwoChannelColorSpace
cSlider - Variable in class loci.formats.gui.ImageViewer
currentPos - Variable in class loci.formats.cache.Cache: Current dimensional position.
curve - Variable in class loci.formats.codec.NikonCodecOptions
CURVE_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
CURVE_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
CUSTOM_RENDERED - Static variable in class loci.formats.tiff.IFD

D

DA - Enum constant in enum loci.formats.dicom.DicomVR
DAILY_BUILD - Static variable in class loci.formats.UpgradeChecker: Location of the JAR artifacts for Bio-Formats' daily build.
DATA_COLLECTION_DIAMETER - Enum constant in enum loci.formats.dicom.DicomAttribute
DATA_POINT_COLUMNS - Enum constant in enum loci.formats.dicom.DicomAttribute
DATA_POINT_ROWS - Enum constant in enum loci.formats.dicom.DicomAttribute
DATA_REPRESENTATION - Enum constant in enum loci.formats.dicom.DicomAttribute
DataConverter - Class in loci.formats.gui: A utility for reorganizing and converting QuickTime movies, TIFF series and other 4D datasets.
DataConverter() - Constructor for class loci.formats.gui.DataConverter
DATASET_SUBTYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
DATE_FORMAT - Static variable in class loci.formats.in.MicromanagerReader
DATE_FORMATS - Static variable in class loci.formats.in.BaseTiffReader
DATE_FORMATS - Static variable in class loci.formats.in.ICSReader
DATE_OF_LAST_CALIBRATION - Enum constant in enum loci.formats.dicom.DicomAttribute
DATE_OF_LAST_DETECTOR_CALIBRATION - Enum constant in enum loci.formats.dicom.DicomAttribute
DATE_OF_SECONDARY_CAPTURE - Enum constant in enum loci.formats.dicom.DicomAttribute
DATE_TIME - Static variable in class loci.formats.tiff.IFD
DATE_TIME_DIGITIZED - Static variable in class loci.formats.tiff.IFD
DATE_TIME_ORIGINAL - Static variable in class loci.formats.tiff.IFD
DB_DT - Enum constant in enum loci.formats.dicom.DicomAttribute
decompress(byte[]) - Method in class loci.formats.codec.BaseCodec
decompress(byte[]) - Method in class loci.formats.codec.Base64Codec
decompress(byte[]) - Method in class loci.formats.codec.HuffmanCodec
decompress(byte[]) - Method in class loci.formats.codec.JPEG2000Codec
decompress(byte[]) - Method in class loci.formats.codec.JPEGCodec
decompress(byte[]) - Method in class loci.formats.codec.LosslessJPEGCodec
decompress(byte[]) - Method in class loci.formats.codec.LZOCodec
decompress(byte[]) - Method in class loci.formats.codec.LZWCodec
decompress(byte[]) - Method in class loci.formats.codec.MJPBCodec
decompress(byte[]) - Method in class loci.formats.codec.MSRLECodec
decompress(byte[]) - Method in class loci.formats.codec.MSVideoCodec
decompress(byte[]) - Method in class loci.formats.codec.PackbitsCodec
decompress(byte[]) - Method in class loci.formats.codec.PassthroughCodec
decompress(byte[]) - Method in class loci.formats.codec.QTRLECodec
decompress(byte[]) - Method in class loci.formats.codec.RPZACodec
decompress(byte[]) - Method in class loci.formats.codec.ZlibCodec
decompress(byte[]) - Method in class loci.formats.codec.ZstdCodec
decompress(byte[]) - Method in interface loci.formats.services.JPEGXRService: Decompress the given JPEG-XR compressed byte array and return as a byte array.
decompress(byte[]) - Method in class loci.formats.services.JPEGXRServiceImpl
decompress(byte[][]) - Method in class loci.formats.codec.BaseCodec
decompress(byte[][]) - Method in class loci.formats.codec.Base64Codec
decompress(byte[][]) - Method in class loci.formats.codec.HuffmanCodec
decompress(byte[][]) - Method in class loci.formats.codec.JPEG2000Codec
decompress(byte[][]) - Method in class loci.formats.codec.JPEGCodec
decompress(byte[][]) - Method in class loci.formats.codec.LosslessJPEGCodec
decompress(byte[][]) - Method in class loci.formats.codec.LZOCodec
decompress(byte[][]) - Method in class loci.formats.codec.LZWCodec
decompress(byte[][]) - Method in class loci.formats.codec.MJPBCodec
decompress(byte[][]) - Method in class loci.formats.codec.MSRLECodec
decompress(byte[][]) - Method in class loci.formats.codec.MSVideoCodec
decompress(byte[][]) - Method in class loci.formats.codec.PackbitsCodec
decompress(byte[][]) - Method in class loci.formats.codec.PassthroughCodec
decompress(byte[][]) - Method in class loci.formats.codec.QTRLECodec
decompress(byte[][]) - Method in class loci.formats.codec.RPZACodec
decompress(byte[][]) - Method in class loci.formats.codec.ZlibCodec
decompress(byte[][]) - Method in class loci.formats.codec.ZstdCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec: 2D data block decoding default implementation.
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.Base64Codec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.JPEG2000Codec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.JPEGCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.LosslessJPEGCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.LZOCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.LZWCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.MJPBCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.MSRLECodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.MSVideoCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.PackbitsCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.PassthroughCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.QTRLECodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.RPZACodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.ZlibCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.ZstdCodec
decompress(byte[], int, int) - Method in class loci.formats.codec.ZstdCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.BaseCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec: The CodecOptions parameter should have the following fields set: maxBytes interleaved bitsPerSample littleEndian width height
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.Base64Codec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEG2000Codec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.LosslessJPEGCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.LZOCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.LZWCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.MJPBCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.MSRLECodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.MSVideoCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.PackbitsCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.PassthroughCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.QTRLECodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.RPZACodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.ZlibCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.ZstdCodec
decompress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression: Decodes a strip of data.
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.BaseCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.NikonCodec: The CodecOptions parameter must be an instance of NikonCodecOptions, and should have the following fields set: lossless vPredictor curve split bitsPerSample maxBytes width height
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.TargaRLECodec: The CodecOptions parameter should have the following fields set: maxBytes CodecOptions.bitsPerSample
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.Base64Codec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEG2000Codec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEGCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.LosslessJPEGCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.LZOCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.LZWCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.MJPBCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.MSRLECodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.MSVideoCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.PackbitsCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.PassthroughCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.QTRLECodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.RPZACodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.ZlibCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.ZstdCodec
DEFAULT_CALLER - Static variable in class loci.formats.UpgradeChecker: Value of "bioformats.caller" for Bio-Formats utilities.
DEFAULT_DIMENSION_ORDER - Static variable in class loci.formats.in.FakeReader
DEFAULT_DISPLAY_RESOLUTION - Enum constant in enum loci.formats.codec.JPEG2000BoxType
DEFAULT_MINIMUM_ELAPSED - Static variable in class loci.formats.Memoizer: Default value for Memoizer.minimumElapsed if none is provided in the constructor.
DEFAULT_PIXEL_TYPE - Static variable in class loci.formats.in.FakeReader
DEFAULT_RANGE - Static variable in class loci.formats.cache.CacheStrategy: Default cache range.
DEFAULT_RESOLUTION_SCALE - Static variable in class loci.formats.in.FakeReader
DEFAULT_RGB_CHANNEL_COUNT - Static variable in class loci.formats.in.FakeReader
DEFAULT_RGB_DIMENSION_ORDER - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_C - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_T - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_X - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_Y - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_Z - Static variable in class loci.formats.in.FakeReader
DEFAULT_UNCOMPRESSED - Enum constant in enum loci.formats.tiff.TiffCompression
DefaultJPEGReader() - Constructor for class loci.formats.in.JPEGReader.DefaultJPEGReader
DEFINITION - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
DEFLATE - Enum constant in enum loci.formats.tiff.TiffCompression
deleteMemo() - Method in class loci.formats.Memoizer: Force the current memo file to be deleted, if it exists.
deleteQuietly(File) - Method in class loci.formats.Memoizer: Attempts to delete an existing file, logging at warn if the deletion returns false or at error if an exception is thrown.
denom - Variable in class loci.formats.tiff.TiffRational: Components of the rational's fractional representation.
depth - Variable in class loci.formats.tools.AmiraParameters
DEPTH_OF_SCAN_FIELD - Enum constant in enum loci.formats.dicom.DicomAttribute
DERIVATION_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
DERIVATION_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
DERIVATION_IMAGE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_ACTIVATION_OFFSET - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_ACTIVE_DIMENSIONS - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_ACTIVE_ORIGIN - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_ACTIVE_SHAPE - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_ACTIVE_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_BINNING - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_CONDITIONS_NOMINAL_FLAG - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_CONFIGURATION - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_ELEMENT_PHYSICAL_SIZE - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_ELEMENT_SPACING - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_MANUFACTURER_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_MODE - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_MODEL_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_PRIMARY_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_SECONDARY_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_TEMPERATURE - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_TIME_SINCE_LAST_EXPOSURE - Enum constant in enum loci.formats.dicom.DicomAttribute
DETECTOR_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
DEVICE_SERIAL_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
DICOM_MAGIC_STRING - Static variable in class loci.formats.in.DicomReader
DicomAttribute - Enum in loci.formats.dicom: Describes a DICOM attribute (integer tag, associated description, and expected VR).
DicomFileInfo - Class in loci.formats.dicom: Structure containing metadata for one DICOM file (instance).
DicomFileInfo() - Constructor for class loci.formats.dicom.DicomFileInfo: Construct an empty object to be populated later.
DicomFileInfo(String) - Constructor for class loci.formats.dicom.DicomFileInfo: Construct an object from the given file.
DicomJSONProvider - Class in loci.formats.dicom: Provide DICOM tags from a file containing JSON.
DicomJSONProvider() - Constructor for class loci.formats.dicom.DicomJSONProvider
DicomReader - Class in loci.formats.in: DicomReader is the file format reader for DICOM files.
DicomReader() - Constructor for class loci.formats.in.DicomReader: Constructs a new DICOM reader.
DicomTag - Class in loci.formats.dicom: Represents a complete DICOM tag, including the dictionary attribute, actual VR, value, and any "child" tags (in the case of a sequence).
DicomTag(int, DicomVR) - Constructor for class loci.formats.dicom.DicomTag
DicomTag(RandomAccessInputStream, boolean, long, boolean) - Constructor for class loci.formats.dicom.DicomTag: Read a complete tag and value from the given input stream.
DicomTag(RandomAccessInputStream, boolean, long, boolean, boolean) - Constructor for class loci.formats.dicom.DicomTag: Read a complete tag and optionally a value from the given input stream.
DicomTag(DicomAttribute) - Constructor for class loci.formats.dicom.DicomTag
DicomTag(DicomAttribute, DicomVR) - Constructor for class loci.formats.dicom.DicomTag
DicomTile - Class in loci.formats.dicom: Represents a tile stored in a DICOM file.
DicomTile() - Constructor for class loci.formats.dicom.DicomTile
DicomVR - Enum in loci.formats.dicom: Enumeration of valid DICOM value representations (VRs).
DicomWriter - Class in loci.formats.out: DicomWriter is the file format writer for DICOM files.
DicomWriter() - Constructor for class loci.formats.out.DicomWriter
difference(byte[], IFD) - Static method in enum loci.formats.tiff.TiffCompression: Performs in-place differencing according to the given predictor value.
DIGITAL_IMAGE_FORMAT_ACQUIRED - Enum constant in enum loci.formats.dicom.DicomAttribute
DIGITAL_ZOOM_RATIO - Static variable in class loci.formats.tiff.IFD
DIGITIZING_DEVICE_TRANSPORT_DIRECTION - Enum constant in enum loci.formats.dicom.DicomAttribute
DIMENSION_DESCRIPTION_LABEL - Enum constant in enum loci.formats.dicom.DicomAttribute
DIMENSION_INDEX_POINTER - Enum constant in enum loci.formats.dicom.DicomAttribute
DIMENSION_INDEX_PRIVATE_CREATOR - Enum constant in enum loci.formats.dicom.DicomAttribute
DIMENSION_INDEX_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
DIMENSION_INDEX_VALUES - Enum constant in enum loci.formats.dicom.DicomAttribute
DIMENSION_ORGANIZATION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
DIMENSION_ORGANIZATION_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
DIMENSION_ORGANIZATION_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
DimensionSwapper - Class in loci.formats: Handles swapping the dimension order of an image series.
DimensionSwapper() - Constructor for class loci.formats.DimensionSwapper: Constructs a DimensionSwapper around a new image reader.
DimensionSwapper(IFormatReader) - Constructor for class loci.formats.DimensionSwapper: Constructs a DimensionSwapper with the given reader.
dimOrder - Variable in class loci.formats.AxisGuesser: Original ordering of internal dimensional axes.
DIRECTORY_RECORD_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
DIRECTORY_RECORD_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
DISPLAY_WINDOW_LABEL_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
dispose() - Method in class loci.formats.gui.CacheComponent
distance(int, int) - Method in class loci.formats.cache.CacheStrategy: Computes the distance from the given axis value to the axis center, taking into account the axis ordering scheme.
DISTANCE_BETWEEN_FOCAL_PLANES - Enum constant in enum loci.formats.dicom.DicomAttribute
DISTANCE_SOURCE_TO_DETECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
DISTANCE_SOURCE_TO_PATIENT - Enum constant in enum loci.formats.dicom.DicomAttribute
DOCUMENT_NAME - Static variable in class loci.formats.tiff.IFD
DOPPLER_CORRECTION_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
DOPPLER_SAMPLE_VOLUME_X_POSITION - Enum constant in enum loci.formats.dicom.DicomAttribute
DOPPLER_SAMPLE_VOLUME_Y_POSITION - Enum constant in enum loci.formats.dicom.DicomAttribute
DOT - Static variable in class loci.formats.ResourceNamer
DOT_RANGE - Static variable in class loci.formats.tiff.IFD
DOUBLE - Enum constant in enum loci.formats.tiff.IFDType
DOUBLE_FLOAT_PIXEL_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
doubleValue() - Method in class loci.formats.tiff.TiffRational: Returns the value of the specified number as a double.
DS - Enum constant in enum loci.formats.dicom.DicomVR
DT - Enum constant in enum loci.formats.dicom.DicomVR

E

ECHO_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
ECHO_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
ECHO_TRAIN_LENGTH - Enum constant in enum loci.formats.dicom.DicomAttribute
edf - Variable in class loci.formats.dicom.DicomFileInfo
EditTiffG - Class in loci.formats.tools: Provides a GUI for editing TIFF file comments.
EditTiffG() - Constructor for class loci.formats.tools.EditTiffG
EFFECTIVE_DURATION - Enum constant in enum loci.formats.dicom.DicomAttribute
elementLength - Variable in class loci.formats.dicom.DicomTag
endOffset - Variable in class loci.formats.dicom.DicomTile
entryToString(Object, String) - Static method in class loci.formats.tools.AmiraParameters
EOC - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
EPH - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
EPSReader - Class in loci.formats.in: Reader is the file format reader for Encapsulated PostScript (EPS) files.
EPSReader() - Constructor for class loci.formats.in.EPSReader: Constructs a new EPS reader.
EPSWriter - Class in loci.formats.out: EPSWriter is the file format writer for Encapsulated PostScript (EPS) files.
EPSWriter() - Constructor for class loci.formats.out.EPSWriter
equals(Object) - Method in class loci.formats.tiff.TiffRational: Indicates whether some other object is "equal to" this one.
equalStrips - Variable in class loci.formats.in.MinimalTiffReader
ESTIMATED_RADIOGRAPHIC_MAG_FACTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
ETHNIC_GROUP - Enum constant in enum loci.formats.dicom.DicomAttribute
EVENT_ELAPSED_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
EVENT_TIMER_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
EXIF - Static variable in class loci.formats.tiff.IFD
EXIF_VERSION - Static variable in class loci.formats.tiff.IFD
EXIFService - Interface in loci.formats.services
EXIFServiceImpl - Class in loci.formats.services
EXIFServiceImpl() - Constructor for class loci.formats.services.EXIFServiceImpl
exists(String) - Method in interface loci.formats.services.JHDFService: Checks if path in HDF5 file exists.
exists(String) - Method in class loci.formats.services.JHDFServiceImpl
exit() - Method in class loci.formats.tools.EditTiffG
EXPOSURE - Enum constant in enum loci.formats.dicom.DicomAttribute
EXPOSURE_BIAS_VALUE - Static variable in class loci.formats.tiff.IFD
EXPOSURE_CONTROL_MODE - Enum constant in enum loci.formats.dicom.DicomAttribute
EXPOSURE_IN_UAS - Enum constant in enum loci.formats.dicom.DicomAttribute
EXPOSURE_INDEX - Static variable in class loci.formats.tiff.IFD
EXPOSURE_MODE - Static variable in class loci.formats.tiff.IFD
EXPOSURE_PROGRAM - Static variable in class loci.formats.tiff.IFD
EXPOSURE_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
EXPOSURE_TIME - Static variable in class loci.formats.tiff.IFD: EXIF tags.
EXPOSURES_ON_PLATE - Enum constant in enum loci.formats.dicom.DicomAttribute
EXTENDED_DEPTH_OF_FIELD - Enum constant in enum loci.formats.dicom.DicomAttribute
EXTENDED_OFFSET_TABLE - Enum constant in enum loci.formats.dicom.DicomAttribute
EXTENDED_OFFSET_TABLE_LENGTHS - Enum constant in enum loci.formats.dicom.DicomAttribute
ExtensionFileFilter - Class in loci.formats.gui: A file filter based on file extensions, for use with a JFileChooser.
ExtensionFileFilter(String[], String) - Constructor for class loci.formats.gui.ExtensionFileFilter: Constructs a new filter that accepts the given extensions.
ExtensionFileFilter(String, String) - Constructor for class loci.formats.gui.ExtensionFileFilter: Constructs a new filter that accepts the given extension.
EXTRA_SAMPLES - Static variable in class loci.formats.tiff.IFD
extractCoreMetaData() - Method in class loci.formats.tools.AmiraParameters

F

F_NUMBER - Static variable in class loci.formats.tiff.IFD
FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.OMETiffReader
FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.OMETiffReader
FAILED_SOP_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
FAILED_SOP_UID_LIST - Enum constant in enum loci.formats.dicom.DicomAttribute
failOnMissingTIFF() - Method in class loci.formats.in.OMETiffReader
FAILURE_REASON - Enum constant in enum loci.formats.dicom.DicomAttribute
FAKE_EXT - Static variable in class loci.formats.ResourceNamer
FakeImage - Class in loci.formats.tools: Generates fake image structures.
FakeImage(Location) - Constructor for class loci.formats.tools.FakeImage
FakeReader - Class in loci.formats.in: FakeReader is the file format reader for faking input data.
FakeReader() - Constructor for class loci.formats.in.FakeReader: Constructs a new fake reader.
FD - Enum constant in enum loci.formats.dicom.DicomVR
FEATURE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
FIELD - Static variable in class loci.formats.ResourceNamer
file - Variable in class loci.formats.dicom.DicomFileInfo
file - Variable in class loci.formats.dicom.DicomTile
FILE - Enum constant in enum loci.formats.codec.JPEG2000BoxType
FILE_META_INFO_GROUP_LENGTH - Enum constant in enum loci.formats.dicom.DicomAttribute
FILE_META_INFO_VERSION - Enum constant in enum loci.formats.dicom.DicomAttribute
FILE_SET_CONSISTENCY_FLAG - Enum constant in enum loci.formats.dicom.DicomAttribute
FILE_SET_DESCRIPTOR_FILE_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
FILE_SET_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
FILE_SOURCE - Static variable in class loci.formats.tiff.IFD
fileGroupOption(String) - Method in class loci.formats.in.DicomReader
fileGroupOption(String) - Method in class loci.formats.in.ICSReader
fileGroupOption(String) - Method in class loci.formats.in.KLBReader
fileGroupOption(String) - Method in class loci.formats.in.MicromanagerReader
fileGroupOption(String) - Method in class loci.formats.in.NRRDReader
fileGroupOption(String) - Method in class loci.formats.in.OMETiffReader
fileIndex - Variable in class loci.formats.dicom.DicomTile
filename - Variable in class loci.formats.gui.ImageViewer
filename - Variable in class loci.formats.tiff.TiffSaver: Output filename.
fileOffset - Variable in class loci.formats.dicom.DicomTile
FilePattern - Class in loci.formats: Represents a collection of files meant to be part of the same data series.
FilePattern(String) - Constructor for class loci.formats.FilePattern: Creates a pattern object for files with the given pattern string.
FilePattern(String, String) - Constructor for class loci.formats.FilePattern: Creates a pattern object using the given filename and directory path as a template.
FilePattern(Location) - Constructor for class loci.formats.FilePattern: Creates a pattern object using the given file as a template.
FilePatternBlock - Class in loci.formats: FilePatternBlock represents a single block in a FilePattern.
FilePatternBlock(String) - Constructor for class loci.formats.FilePatternBlock: Builds a FilePatternBlock from a block string.
FilePatternReader - Class in loci.formats.in
FilePatternReader() - Constructor for class loci.formats.in.FilePatternReader: Constructs a new pattern reader.
fileReader - Variable in class loci.formats.gui.ImageViewer: Reader for files on disk.
fileSave - Variable in class loci.formats.gui.ImageViewer
FileStitcher - Class in loci.formats: Logic to stitch together files with similar names.
FileStitcher() - Constructor for class loci.formats.FileStitcher: Constructs a FileStitcher around a new image reader.
FileStitcher(boolean) - Constructor for class loci.formats.FileStitcher: Constructs a FileStitcher around a new image reader.
FileStitcher(IFormatReader) - Constructor for class loci.formats.FileStitcher: Constructs a FileStitcher with the given reader.
FileStitcher(IFormatReader, boolean) - Constructor for class loci.formats.FileStitcher: Constructs a FileStitcher with the given reader.
fileView - Variable in class loci.formats.gui.ImageViewer
fileWriter - Variable in class loci.formats.gui.ImageViewer: Writer for files on disk.
FILL_ORDER - Static variable in class loci.formats.tiff.IFD
filled - Variable in class loci.formats.ChannelFiller: Whether to fill in the indices.
fillInIFD(IFD) - Method in class loci.formats.tiff.TiffParser: Fill in IFD entries that are stored at an arbitrary offset.
FILTER_MATERIAL - Enum constant in enum loci.formats.dicom.DicomAttribute
FILTER_THICKNESS_MAX - Enum constant in enum loci.formats.dicom.DicomAttribute
FILTER_THICKNESS_MIN - Enum constant in enum loci.formats.dicom.DicomAttribute
FILTER_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
findPattern(File) - Static method in class loci.formats.FilePattern: Identifies the group pattern from a given file within that group.
findPattern(String) - Static method in class loci.formats.FilePattern: Identifies the group pattern from a given file within that group.
findPattern(String) - Method in class loci.formats.FileStitcher
findPattern(String[]) - Static method in class loci.formats.FilePattern: Generate a pattern from a list of file names.
findPattern(String, String) - Static method in class loci.formats.FilePattern: Identifies the group pattern from a given filename and directory.
findPattern(String, String, String[]) - Static method in class loci.formats.FilePattern: Identifies the group pattern from a given filename, directory and list of candidate filenames.
findPattern(String, String, String[], int[]) - Static method in class loci.formats.FilePattern: Identifies the group pattern from a given filename, directory and list of candidate filenames.
findPattern(Location) - Static method in class loci.formats.FilePattern: Identifies the group pattern from a given file within that group.
findPatterns(String) - Method in class loci.formats.FileStitcher: Finds the file pattern for the given ID, based on the state of the file stitcher.
findSeriesPatterns(String) - Static method in class loci.formats.FilePattern: Works like FilePattern.findSeriesPatterns(String, String, String[]), but dir and nameList are inferred from the given file's absolute path.
findSeriesPatterns(String, String, String[]) - Static method in class loci.formats.FilePattern: Similar to FilePattern.findPattern(String, String, String[]), but this does not merge series indices into a pattern block.
firstDataStream - Variable in class loci.formats.tools.AmiraParameters
FitsReader - Class in loci.formats.in: FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
FitsReader() - Constructor for class loci.formats.in.FitsReader: Constructs a new FitsReader.
FL - Enum constant in enum loci.formats.dicom.DicomVR
FLASH - Static variable in class loci.formats.tiff.IFD
FLASH_ENERGY - Static variable in class loci.formats.tiff.IFD
FLASH_PIX_VERSION - Static variable in class loci.formats.tiff.IFD
FLIP_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
FLOAT - Enum constant in enum loci.formats.tiff.IFDType
FLOAT_PIXEL_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
FloatIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.FloatIM3Record
floatValue() - Method in class loci.formats.tiff.TiffRational: Returns the value of the specified number as a float.
FlowSightReader - Class in loci.formats.in
FlowSightReader() - Constructor for class loci.formats.in.FlowSightReader
FOCAL_DISTANCE - Enum constant in enum loci.formats.dicom.DicomAttribute
FOCAL_LENGTH - Static variable in class loci.formats.tiff.IFD
FOCAL_LENGTH_35MM_FILM - Static variable in class loci.formats.tiff.IFD
FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
FOCAL_PLANE_X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
FOCAL_PLANE_Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
FOCAL_SPOTS - Enum constant in enum loci.formats.dicom.DicomAttribute
FOCUS_DEPTH - Enum constant in enum loci.formats.dicom.DicomAttribute
FOCUS_METHOD - Enum constant in enum loci.formats.dicom.DicomAttribute
FormatFileFilter - Class in loci.formats.gui: A file filter for a biological file format, for use with a JFileChooser.
FormatFileFilter(IFormatReader) - Constructor for class loci.formats.gui.FormatFileFilter: Constructs a new filter that accepts files of the given reader's type.
FormatFileFilter(IFormatReader, boolean) - Constructor for class loci.formats.gui.FormatFileFilter: Constructs a new filter that accepts files of the given reader's type, allowing the reader to open files only if the allowOpen flag is set.
formatFixedWidth(double, int) - Static method in class loci.formats.out.DicomWriter: Format the given double as a string with no more than width characters.
formatLabel - Variable in class loci.formats.gui.PreviewPane: Labels containing thumbnail and dimensional information.
formatTag(int) - Static method in enum loci.formats.dicom.DicomAttribute: Format the given tag as a pair of comma-separated hex strings.
formatText - Variable in class loci.formats.gui.PreviewPane
formatTip - Variable in class loci.formats.gui.PreviewPane
FORWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
FOV_DIMENSIONS - Enum constant in enum loci.formats.dicom.DicomAttribute
FOV_HORIZONTAL_FLIP - Enum constant in enum loci.formats.dicom.DicomAttribute
FOV_ORIGIN - Enum constant in enum loci.formats.dicom.DicomAttribute
FOV_ROTATION - Enum constant in enum loci.formats.dicom.DicomAttribute
FOV_SHAPE - Enum constant in enum loci.formats.dicom.DicomAttribute
fp - Variable in class loci.formats.AxisGuesser: File pattern identifying dimensional axis blocks.
fps - Variable in class loci.formats.gui.ImageViewer
FRAME_ACQUISITION_DATETIME - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_ACQUISITION_DURATION - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_CONTENT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_DELAY - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_DIMENSION_POINTER - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_INCREMENT_POINTER - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_LABEL_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_NUMBERS_OF_INTEREST - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_OF_INTEREST_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_OF_INTEREST_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_OF_REFERENCE_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_PRIMARY_ANGLE_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_REFERENCE_DATETIME - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_SECONDARY_ANGLE_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_TIME_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAME_VOI_LUT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
FRAMING_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
FREE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
FREE_OFFSETS - Static variable in class loci.formats.tiff.IFD
fromCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
fromRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
FUNCTIONAL_GROUP_POINTER - Enum constant in enum loci.formats.dicom.DicomAttribute
FUNCTIONAL_GROUP_PRIVATE_CREATOR - Enum constant in enum loci.formats.dicom.DicomAttribute

G

GAIN_CONTROL - Static variable in class loci.formats.tiff.IFD
GANTRY_DETECTOR_SKEW - Enum constant in enum loci.formats.dicom.DicomAttribute
GANTRY_DETECTOR_TILT - Enum constant in enum loci.formats.dicom.DicomAttribute
generateMemo(String) - Method in class loci.formats.Memoizer: Convenience method to generate (or regenerate) the memo file for a given file.
generateScreen(int, int, int, int, int) - Method in class loci.formats.tools.FakeImage: Creates a fake SPW file/directory structure.
GENERATOR_POWER - Enum constant in enum loci.formats.dicom.DicomAttribute
get(int) - Method in class loci.formats.codec.ByteVector
get(int) - Static method in enum loci.formats.codec.CompressionType: Retrieves the compression by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.codec.JPEG2000BoxType: Retrieves the box type by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.codec.JPEG2000SegmentMarker: Retrieves the segment marker by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.dicom.DicomAttribute: Lookup the attribute for the given tag.
get(int) - Static method in enum loci.formats.dicom.DicomVR
get(int) - Static method in enum loci.formats.tiff.IFDType: Retrieves a IFD type by reverse lookup of its "code".
get(int) - Method in class loci.formats.tiff.OnDemandLongArray
get(int) - Static method in enum loci.formats.tiff.PhotoInterp: Retrieves a photometric interpretation by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.tiff.TiffCompression: Retrieves a TIFF compression instance by code.
get(Codec) - Static method in enum loci.formats.codec.CompressionType: Look up the compression type by Codec instance.
get16BitLookupTable() - Method in class loci.formats.ChannelFiller
get16BitLookupTable() - Method in class loci.formats.FileStitcher
get16BitLookupTable() - Method in class loci.formats.in.DicomReader
get16BitLookupTable() - Method in class loci.formats.in.FakeReader
get16BitLookupTable() - Method in class loci.formats.in.FilePatternReader
get16BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
get16BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
get16BitLookupTable() - Method in class loci.formats.in.OMETiffReader
get16BitLookupTable() - Method in class loci.formats.in.ZipReader
get8BitLookupTable() - Method in class loci.formats.ChannelFiller
get8BitLookupTable() - Method in class loci.formats.FileStitcher
get8BitLookupTable() - Method in class loci.formats.in.APNGReader
get8BitLookupTable() - Method in class loci.formats.in.AVIReader
get8BitLookupTable() - Method in class loci.formats.in.BDVReader
get8BitLookupTable() - Method in class loci.formats.in.BMPReader
get8BitLookupTable() - Method in class loci.formats.in.CellH5Reader
get8BitLookupTable() - Method in class loci.formats.in.DicomReader
get8BitLookupTable() - Method in class loci.formats.in.FakeReader
get8BitLookupTable() - Method in class loci.formats.in.FilePatternReader
get8BitLookupTable() - Method in class loci.formats.in.GIFReader
get8BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
get8BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
get8BitLookupTable() - Method in class loci.formats.in.OMETiffReader
get8BitLookupTable() - Method in class loci.formats.in.PCXReader
get8BitLookupTable() - Method in class loci.formats.in.PictReader
get8BitLookupTable() - Method in class loci.formats.in.ZipReader
get8BitLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools: Converts an IndexColorModel to a 2D byte array.
getAdjustedIndex(int) - Method in class loci.formats.FileStitcher: Gets the local reader index for use with the given image plane.
getAdjustedOrder() - Method in class loci.formats.AxisGuesser: Gets the adjusted dimension order.
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
getAdvancedUsedFiles(boolean) - Method in class loci.formats.FileStitcher
getAlpha(int) - Method in class loci.formats.gui.Index16ColorModel
getAlpha(int) - Method in class loci.formats.gui.SignedColorModel
getAlpha(int) - Method in class loci.formats.gui.UnsignedIntColorModel
getAlpha(Object) - Method in class loci.formats.gui.SignedColorModel
getAlpha(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
getAlphas() - Method in class loci.formats.gui.Index16ColorModel: Return the array of alpha color components.
getAvailableOptions() - Method in class loci.formats.in.OMETiffReader
getAxisCount(int) - Method in class loci.formats.AxisGuesser: Gets the number of axes in the pattern of the given type.
getAxisCountC() - Method in class loci.formats.AxisGuesser: Gets the number of C axes in the pattern.
getAxisCountS() - Method in class loci.formats.AxisGuesser: Gets the number of S axes in the pattern.
getAxisCountT() - Method in class loci.formats.AxisGuesser: Gets the number of T axes in the pattern.
getAxisCountZ() - Method in class loci.formats.AxisGuesser: Gets the number of Z axes in the pattern.
getAxisGuesser() - Method in class loci.formats.FileStitcher: Gets the axis guesser object used to guess which dimensional axes are which.
getAxisType(String) - Static method in class loci.formats.AxisGuesser: Convert the given label to an axis type.
getAxisTypes() - Method in class loci.formats.AxisGuesser: Gets the guessed axis type for each dimensional block.
getAxisTypes() - Method in class loci.formats.FileStitcher: Gets the axis type for each dimensional block.
getBits(int) - Method in class loci.formats.codec.BitBuffer: Deprecated.

Returns an int value representing the value of the bits read from the byte array, from the current position.
getBitsPerPixel() - Method in class loci.formats.ChannelFiller
getBitsPerPixel() - Method in class loci.formats.FileStitcher
getBitsPerSample() - Method in class loci.formats.tiff.IFD: Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
getBlock() - Method in class loci.formats.FilePatternBlock: Gets the block string.
getBlock(int) - Method in class loci.formats.FilePattern: Gets the specified file pattern block (e.g., <0-9>).
getBlocks() - Method in class loci.formats.FilePattern: Gets all file pattern blocks.
getBlue(int) - Method in class loci.formats.gui.Index16ColorModel
getBlue(int) - Method in class loci.formats.gui.SignedColorModel
getBlue(int) - Method in class loci.formats.gui.UnsignedIntColorModel
getBlue(Object) - Method in class loci.formats.gui.SignedColorModel
getBlue(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
getBlues() - Method in class loci.formats.gui.Index16ColorModel: Return the array of blue color components.
getByteBuffer() - Method in class loci.formats.codec.BitBuffer: Deprecated.

Return the backing byte array.
getByteCount(boolean) - Method in class loci.formats.tiff.IFD: Get the maximum number of bytes needed to represent this IFD.
getBytes(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools: Get the bytes from an image, merging the channels as necessary.
getBytes(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytesPerElement() - Method in enum loci.formats.tiff.IFDType: Retrieves the number of bytes per element.
getBytesPerSample() - Method in class loci.formats.tiff.IFD: Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
getC() - Method in class loci.formats.gui.ImageViewer: Gets the C value of the currently displayed image.
getCache() - Method in class loci.formats.gui.CacheComponent
getCacheListeners() - Method in class loci.formats.cache.Cache
getCacheListeners() - Method in interface loci.formats.cache.CacheReporter: Gets a list of all registered status update listeners.
getCacheListeners() - Method in class loci.formats.cache.CacheStrategy
getChannelGlobalMaximum(int) - Method in class loci.formats.MinMaxCalculator: Retrieves a specified channel's global maximum.
getChannelGlobalMinimum(int) - Method in class loci.formats.MinMaxCalculator: Retrieves a specified channel's global minimum.
getChannelKnownMaximum(int) - Method in class loci.formats.MinMaxCalculator: Retrieves the specified channel's maximum based on the images that have been read.
getChannelKnownMinimum(int) - Method in class loci.formats.MinMaxCalculator: Retrieves the specified channel's minimum based on the images that have been read.
getChannelLabel(int) - Method in class loci.formats.in.TextReader: Gets the label for the given channel.
getChannelNames() - Method in class loci.formats.in.DicomReader
getCode() - Method in enum loci.formats.codec.CompressionType: Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.codec.JPEG2000BoxType: Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.codec.JPEG2000SegmentMarker: Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.dicom.DicomVR
getCode() - Method in enum loci.formats.tiff.IFDType
getCode() - Method in enum loci.formats.tiff.PhotoInterp
getCode() - Method in enum loci.formats.tiff.TiffCompression
getCodec() - Method in class loci.formats.out.DicomWriter
getCodec() - Method in class loci.formats.out.TiffWriter
getCodec() - Method in enum loci.formats.tiff.TiffCompression
getCodecName() - Method in enum loci.formats.tiff.TiffCompression: Retrieves the name of the TIFF compression codec.
getCodecOptions() - Method in class loci.formats.tiff.TiffParser: Retrieves the current set of codec options being used to decompress pixel data.
getCodestreamOffset() - Method in class loci.formats.in.JPEG2000MetadataParser: Retrieves the offset to the first contiguous codestream.
getCodestreamPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the pixel type as specified in the header.
getCodestreamSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the number of channels the image has as specified in the header.
getCodestreamSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the width of the image as specified in the header.
getCodestreamSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the height of the image as specified in the header.
getColorMap(IFD) - Method in class loci.formats.tiff.TiffParser: Retrieve the color map associated with the given IFD.
getComment() - Method in class loci.formats.tiff.IFD: Convenience method for obtaining the ImageDescription from this IFD.
getComment() - Method in class loci.formats.tiff.TiffParser: Convenience method for obtaining a stream's first ImageDescription.
getComments() - Method in class loci.formats.in.JPEG2000MetadataParser: Retrieves the list of comments stored in the file.
getCompanion() - Method in class loci.formats.out.OMETiffWriter: Get the value of the OMETiffWriter.COMPANION_KEY option.
getCompressedByteCount(IFD, int, int) - Method in class loci.formats.in.MinimalTiffReader
getCompressedTile(byte[], int, int) - Method in interface loci.formats.services.JPEGTurboService: Similar to getTile(int, int), but returns the JPEG-compressed bytes.
getCompressedTile(byte[], int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
getCompressedTile(int, int) - Method in interface loci.formats.services.JPEGTurboService: Similar to getTile(int, int), but returns the JPEG-compressed bytes.
getCompressedTile(int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
getCompression() - Method in enum loci.formats.codec.CompressionType: Returns the compression.
getCompression() - Method in class loci.formats.tiff.IFD: Retrieves the image's compression type (TIFF tag Compression) from this IFD.
getCompressionCodecOptions(IFD) - Method in enum loci.formats.tiff.TiffCompression: Creates a set of codec options for compression.
getCompressionCodecOptions(IFD, CodecOptions) - Method in enum loci.formats.tiff.TiffCompression: Creates a set of codec options for compression.
getConcatenationIndex() - Method in class loci.formats.in.DicomReader
getCoreIndex() - Method in class loci.formats.FileStitcher
getCoreMetadataList() - Method in class loci.formats.DimensionSwapper
getCoreMetadataList() - Method in class loci.formats.FileStitcher
getCoreMetadataList() - Method in class loci.formats.in.FilePatternReader
getCount() - Method in class loci.formats.FilePattern: Gets the number of elements for each pattern block.
getCreationDate() - Method in interface loci.formats.services.EXIFService
getCreationDate() - Method in class loci.formats.services.EXIFServiceImpl
getCurrentPos() - Method in class loci.formats.cache.Cache: Gets the current dimensional position.
getData() - Method in class loci.formats.gui.SignedByteBuffer
getData() - Method in class loci.formats.gui.SignedShortBuffer
getData() - Method in class loci.formats.gui.UnsignedIntBuffer
getData(int) - Method in class loci.formats.gui.SignedByteBuffer
getData(int) - Method in class loci.formats.gui.SignedShortBuffer
getData(int) - Method in class loci.formats.gui.UnsignedIntBuffer
getDataElements(int, Object) - Method in class loci.formats.gui.Index16ColorModel
getDataElements(int, Object) - Method in class loci.formats.gui.SignedColorModel
getDataElements(int, Object) - Method in class loci.formats.gui.UnsignedIntColorModel
getDefaultConfiguration() - Static method in class loci.formats.gui.AWTImageTools: Gets the default graphics configuration for the environment.
getDefaultOptions() - Static method in class loci.formats.codec.JPEG2000CodecOptions: Return JPEG2000CodecOptions with reasonable default values.
getDefaultOptions(CodecOptions) - Static method in class loci.formats.codec.JPEG2000CodecOptions: Return JPEG2000CodecOptions using the given CodecOptions as the default.
getDefaultVR() - Method in enum loci.formats.dicom.DicomAttribute: Get the known default VR for this attribute, or IMPLICIT if our dictionary does not include a default VR.
getDefaultVR(int) - Static method in enum loci.formats.dicom.DicomAttribute
getDenominator() - Method in class loci.formats.tiff.TiffRational: Gets this number's denominator.
getDescription() - Method in enum loci.formats.dicom.DicomAttribute: Get the human-readable description associated with this attribute.
getDescription() - Method in class loci.formats.gui.ComboFileFilter: Returns the filter's description.
getDescription() - Method in class loci.formats.gui.ExtensionFileFilter: Gets the filter's description.
getDescription() - Method in class loci.formats.gui.FormatFileFilter: Gets the filter's description.
getDescription() - Method in class loci.formats.gui.NoExtensionFileFilter: Gets the filter's description.
getDescription(int) - Static method in enum loci.formats.dicom.DicomAttribute
getDeser() - Method in class loci.formats.Memoizer: Returns a configured Kryo instance.
getDimensionOrder() - Method in class loci.formats.ChannelMerger
getDimensionOrder() - Method in class loci.formats.ChannelSeparator
getDimensionOrder() - Method in class loci.formats.DimensionSwapper
getDimensionOrder() - Method in class loci.formats.FileStitcher
getDocument() - Method in class loci.formats.gui.XMLWindow: Gets the XML document currently being displayed within the window.
getDomains() - Method in class loci.formats.in.ICSReader
getDomains() - Method in class loci.formats.in.OMETiffReader
getDomains() - Method in class loci.formats.in.OMEXMLReader
getDoubles(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getElem(int) - Method in class loci.formats.gui.SignedByteBuffer
getElem(int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
getElem(int, int) - Method in class loci.formats.gui.SignedShortBuffer
getElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElemDouble(int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElemDouble(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElements() - Method in class loci.formats.FilePattern: Gets individual elements for each pattern block.
getElements() - Method in class loci.formats.FilePatternBlock: Gets all block elements.
getElementSize(String) - Method in interface loci.formats.services.JHDFService: Retrieves the Element Size of a dataset in Byte.
getElementSize(String) - Method in class loci.formats.services.JHDFServiceImpl
getElemFloat(int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElemFloat(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
getEndPointer() - Method in class loci.formats.dicom.DicomTag: Get the file pointer at which the value ends (useful for sequences and byte streams).
getEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record: Return all entries as an array
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record: Get the boolean value at the given index
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.FloatIM3Record: Get the floating-point value at the given index
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.IntIM3Record: Get the integer value at the given index
getErrorMessage() - Method in class loci.formats.FilePattern: Gets the file pattern error message, if any.
getExifIFDs() - Method in class loci.formats.tiff.TiffParser: Returns EXIF IFDs.
getExifTagName(int) - Static method in class loci.formats.in.BaseTiffReader
getExtension() - Method in class loci.formats.gui.ExtensionFileFilter: Gets the filter's first valid extension.
getExtensions() - Method in class loci.formats.gui.ExtensionFileFilter: Gets the filter's valid extensions.
getFieldName(int) - Static method in class loci.formats.tiff.IFD: This method uses reflection to scan the values of this class's static fields, returning the first matching field's name.
getFile() - Method in interface loci.formats.services.JHDFService: Retrieves the current initialized file path.
getFile() - Method in class loci.formats.services.JHDFServiceImpl
getFilePattern() - Method in class loci.formats.AxisGuesser: Gets the file pattern.
getFilePattern() - Method in class loci.formats.FileStitcher: Gets the file pattern object used to build the list of files.
getFiles() - Method in class loci.formats.FilePattern: Gets a listing of all files matching this file pattern.
getFilters() - Method in class loci.formats.gui.ComboFileFilter: Gets the list of file filters forming this filter combination.
getFirst() - Method in class loci.formats.FilePattern: Gets the START element for all blocks.
getFirst() - Method in class loci.formats.FilePatternBlock: Gets the first element in a range block.
getFirstIFD() - Method in class loci.formats.tiff.TiffParser: Gets the first IFD within the TIFF file, or null if the input source is not a valid TIFF file.
getFirstIFDEntry(int) - Method in class loci.formats.tiff.TiffParser: Retrieve a given entry from the first IFD in the stream.
getFirstOffset() - Method in class loci.formats.tiff.TiffParser: Gets offset to the first IFD, or -1 if stream is not TIFF.
getFloats(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getGreen(int) - Method in class loci.formats.gui.Index16ColorModel
getGreen(int) - Method in class loci.formats.gui.SignedColorModel
getGreen(int) - Method in class loci.formats.gui.UnsignedIntColorModel
getGreen(Object) - Method in class loci.formats.gui.SignedColorModel
getGreen(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
getGreens() - Method in class loci.formats.gui.Index16ColorModel: Return the array of green color components.
getHeaderPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the pixel type as specified in the header.
getHeaderSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the number of channels the image has as specified in the header.
getHeaderSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the width of the image as specified in the header.
getHeaderSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the height of the image as specified in the header.
getHeight() - Method in class loci.formats.codec.JPEGTileDecoder
getHelper() - Method in class loci.formats.in.FilePatternReader
getIFD(long) - Method in class loci.formats.tiff.TiffParser: Gets the IFD stored at the given offset.
getIFDIntArray(int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry values in int format from this IFD, performing some error checking.
getIFDIntValue(int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry value in int format from this IFD, or -1 if the given directory does not exist.
getIFDIntValue(int, int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry value in int format from this IFD, performing some error checking.
getIFDLongArray(int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry values in long format from this IFD, performing some error checking.
getIFDLongValue(int, long) - Method in class loci.formats.tiff.IFD: Gets the given directory entry value in long format from this IFD, performing some error checking.
getIFDOffsets() - Method in class loci.formats.tiff.TiffParser: Gets the offsets to every IFD in the file.
getIFDRationalValue(int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry value in rational format from this IFD, performing some error checking.
getIFDs() - Method in class loci.formats.in.MinimalTiffReader: Gets the list of IFDs associated with the current TIFF's image planes.
getIFDs() - Method in class loci.formats.tiff.TiffParser: Deprecated.
Use TiffParser.getMainIFDs() and TiffParser.getSubIFDs(IFD) instead.
getIFDShortArray(int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry values in short format from this IFD, performing some error checking.
getIFDStringValue(int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry value as a string from this IFD, performing some error checking.
getIFDTagName(int) - Static method in class loci.formats.tiff.IFD: Gets the name of the IFD tag encoded by the given number.
getIFDTextValue(int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry value as a string (regardless of type).
getIFDValue(int) - Method in class loci.formats.tiff.IFD: Gets the given directory entry value from this IFD.
getIFDValue(int, Class) - Method in class loci.formats.tiff.IFD: Gets the given directory entry value from this IFD, performing some error checking.
getIFDValue(TiffIFDEntry) - Method in class loci.formats.tiff.TiffParser: Retrieve the value corresponding to the given TiffIFDEntry.
getImage() - Method in class loci.formats.gui.ImageViewer: Gets the currently displayed image.
getImageCount() - Method in class loci.formats.ChannelMerger
getImageCount() - Method in class loci.formats.ChannelSeparator
getImageCount() - Method in class loci.formats.FileStitcher
getImageCreationDate() - Method in class loci.formats.in.BaseTiffReader: Retrieves the image creation date.
getImageIndex() - Method in class loci.formats.gui.ImageViewer: Gets the index of the currently displayed image.
getImageLength() - Method in class loci.formats.tiff.IFD: Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
getImageType() - Method in class loci.formats.in.DicomReader
getImageWidth() - Method in class loci.formats.tiff.IFD: Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
getIndex() - Method in class loci.formats.cache.CacheEvent: Gets the index relevant to the cache update, if any.
getIndex(int, int, int) - Method in class loci.formats.ChannelMerger
getIndex(int, int, int) - Method in class loci.formats.ChannelSeparator
getIndex(int, int, int) - Method in class loci.formats.DimensionSwapper
getIndex(int, int, int) - Method in class loci.formats.FileStitcher
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelMerger
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
getIndex(int, int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
getIndex(int, int, int, int, int, int) - Method in class loci.formats.FileStitcher
getInputOrder() - Method in class loci.formats.DimensionSwapper
getInstance(int) - Static method in class loci.formats.gui.TwoChannelColorSpace
getInts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of signed integers, one per channel.
getLast() - Method in class loci.formats.FilePattern: Gets the STOP element for all blocks.
getLast() - Method in class loci.formats.FilePatternBlock: Gets the last element in a range block.
getLengths() - Method in class loci.formats.cache.CacheStrategy
getLengths() - Method in interface loci.formats.cache.ICacheStrategy: Gets the lengths of all the axes.
getLetter() - Method in class loci.formats.ResourceNamer: Returns a String representing a single letter (in the case where the class instance has been initialized with a resource count lower than 26) or a concatenation of two letters (if resource count is higher than 26).
getLoadList(int[]) - Method in class loci.formats.cache.CacheStrategy
getLoadList(int[]) - Method in interface loci.formats.cache.ICacheStrategy: Gets the indices of the objects to cache, surrounding the object at the given position.
getLocationFromResourceName(Location, String, int, String) - Method in class loci.formats.ResourceNamer: Creates a new Location instance using the provided parent path and child node name.
getLookupTable() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the color lookup table stored in the file, or null if a lookup table is not present.
getLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools: Convers an Index16ColorModel to a 2D short array.
getMagnitudes() - Method in class loci.formats.in.IM3Reader.Spectrum
getMainIFDs() - Method in class loci.formats.tiff.TiffParser: Returns the main list of IFDs in the file.
getMap() - Method in class loci.formats.tools.AmiraParameters
getMaximumSize() - Method in class loci.formats.gui.CacheIndicator
getMember(String) - Method in interface loci.formats.services.JHDFService: Retrieves the all members of a group.
getMember(String) - Method in class loci.formats.services.JHDFServiceImpl
getMemoFile() - Method in class loci.formats.Memoizer
getMemoFile(String) - Method in class loci.formats.Memoizer: Constructs a File object from id string.
getMetadataStore() - Method in class loci.formats.FileStitcher
getMetadataStore() - Method in class loci.formats.in.FilePatternReader
getMetadataStore() - Method in class loci.formats.Memoizer
getMetadataStoreForConversion() - Method in class loci.formats.in.OMETiffReader: Deprecated.
Use the general FormatReader.getMetadataStore() method.
getMetadataStoreForDisplay() - Method in class loci.formats.in.OMETiffReader: Deprecated.
Use the general FormatReader.getMetadataStore() method.
getMetadataStoreRoot() - Method in class loci.formats.FileStitcher
getMetadataType() - Method in enum loci.formats.tiff.PhotoInterp: Retrieves the metadata type of the photometric interpretation.
getMinimumSize() - Method in class loci.formats.gui.CacheIndicator
getMinMaxStore() - Method in class loci.formats.MinMaxCalculator: Retrieves the current active min-max store for the calculator.
getName() - Method in enum loci.formats.codec.JPEG2000BoxType: Returns the name of the box type.
getName() - Method in enum loci.formats.codec.JPEG2000SegmentMarker: Returns the name of the segment marker.
getName() - Method in class loci.formats.in.IM3Reader.Spectrum
getName() - Method in enum loci.formats.tiff.PhotoInterp: Retrieves the given name of the photometric interpretation.
getName(int) - Method in class loci.formats.gui.TwoChannelColorSpace
getNativeDataType() - Method in class loci.formats.ChannelFiller
getNativeDataType() - Method in class loci.formats.ChannelMerger
getNativeDataType() - Method in class loci.formats.ChannelSeparator
getNativeDataType() - Method in class loci.formats.in.BIFormatReader
getNativeDataType() - Method in class loci.formats.in.TextReader
getNativeDataType() - Method in class loci.formats.MinMaxCalculator
getNativeDataType() - Method in class loci.formats.out.ImageIOWriter
getNonThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser: Returns non-thumbnail IFDs.
getNumber(String) - Method in class loci.formats.NumberFilter: Gets numbers filling the asterisk positions.
getNumberValue() - Method in class loci.formats.dicom.DicomTag: Get a number representation of the current value, or null if not a number.
getNumComponents() - Method in class loci.formats.gui.TwoChannelColorSpace
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record: Get the # of boolean values in this record
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record: Get the # of floating-point values in this record
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.IntIM3Record: Get the # of integer values in this record
getNumerator() - Method in class loci.formats.tiff.TiffRational: Gets this number's numerator.
getObject(int) - Method in class loci.formats.cache.ByteArraySource
getObject(int) - Method in class loci.formats.cache.CacheSource
getObject(int) - Method in interface loci.formats.cache.ICacheSource: Get the object corresponding to the given index.
getObject(int) - Method in class loci.formats.gui.BufferedImageSource
getObject(int[]) - Method in class loci.formats.cache.Cache: Gets the cached object at the given dimensional position.
getObjectCount() - Method in class loci.formats.cache.CacheSource
getObjectCount() - Method in interface loci.formats.cache.ICacheSource: Get the total number of objects that this source can retrieve.
getObjectCount() - Method in class loci.formats.gui.BufferedImageSource
getOmeXmlMetadata() - Method in class loci.formats.in.FakeReader
getOmeXmlService() - Method in class loci.formats.in.FakeReader
getOnDemandStripOffsets() - Method in class loci.formats.tiff.IFD
getOptimalTileHeight() - Method in class loci.formats.in.CellH5Reader
getOptimalTileHeight() - Method in class loci.formats.in.DicomReader
getOptimalTileHeight() - Method in class loci.formats.in.EPSReader
getOptimalTileHeight() - Method in class loci.formats.in.ImageIOReader
getOptimalTileHeight() - Method in class loci.formats.in.MicromanagerReader
getOptimalTileHeight() - Method in class loci.formats.in.MinimalTiffReader
getOptimalTileHeight() - Method in class loci.formats.in.NRRDReader
getOptimalTileHeight() - Method in class loci.formats.in.OMETiffReader
getOptimalTileWidth() - Method in class loci.formats.in.DicomReader
getOptimalTileWidth() - Method in class loci.formats.in.EPSReader
getOptimalTileWidth() - Method in class loci.formats.in.MicromanagerReader
getOptimalTileWidth() - Method in class loci.formats.in.MinimalTiffReader
getOptimalTileWidth() - Method in class loci.formats.in.OMETiffReader
getOptions(CodecOptions) - Static method in class loci.formats.codec.Base64Codec
getOptions(CodecOptions) - Static method in class loci.formats.codec.HuffmanCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.JPEG2000Codec
getOptions(CodecOptions) - Static method in class loci.formats.codec.JPEGCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.LosslessJPEGCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.LZOCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.LZWCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.MJPBCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.MSRLECodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.MSVideoCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.PackbitsCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.PassthroughCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.QTRLECodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.RPZACodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.ZlibCodec
getOptions(CodecOptions) - Static method in class loci.formats.codec.ZstdCodec
getOrder() - Method in class loci.formats.cache.CacheStrategy
getOrder() - Method in interface loci.formats.cache.ICacheStrategy: Retrieves the order in which objects should be loaded along each axis.
getOriginalIndex(int) - Method in class loci.formats.ChannelMerger: Returns the image number in the original dataset that corresponds to the given image number.
getOriginalIndex(int) - Method in class loci.formats.ChannelSeparator: Returns the image number in the original dataset that corresponds to the given image number.
getOriginalOrder() - Method in class loci.formats.AxisGuesser: Gets the original dimension order.
getPathToImageData() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
getPathToSegmentationData() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
getPattern() - Method in class loci.formats.FilePattern: Gets the file pattern string.
getPhotometricInterpretation() - Method in class loci.formats.tiff.IFD: Retrieves the image's photometric interpretation (TIFF tag PhotometricInterpretation) from this IFD.
getPixelBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools: Return a 2D array of bytes representing the image.
getPixelBytes(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Return a 2D array of bytes representing the image.
getPixelBytes(WritableRaster, boolean) - Static method in class loci.formats.gui.AWTImageTools: Return a 2D array of bytes representing the image.
getPixelBytes(WritableRaster, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Return a 2D array of bytes representing the image.
getPixels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Gets the image's pixel data as arrays of primitives, one per channel.
getPixels(BufferedImage, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Gets the image's pixel data as arrays of primitives, one per channel.
getPixels(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools: Gets the raster's pixel data as arrays of primitives, one per channel.
getPixels(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Gets the raster's pixel data as arrays of primitives, one per channel.
getPixelSizeX() - Method in class loci.formats.in.DicomReader
getPixelSizeY() - Method in class loci.formats.in.DicomReader
getPixelSizeZ() - Method in class loci.formats.in.DicomReader
getPixelType() - Method in class loci.formats.FileStitcher
getPixelType() - Method in class loci.formats.tiff.IFD: Retrieves the image's pixel type based on the BitsPerSample tag.
getPixelType(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Gets the pixel type of the given image.
getPixelTypes(String) - Method in class loci.formats.out.APNGWriter
getPixelTypes(String) - Method in class loci.formats.out.AVIWriter
getPixelTypes(String) - Method in class loci.formats.out.CellH5Writer
getPixelTypes(String) - Method in class loci.formats.out.DicomWriter
getPixelTypes(String) - Method in class loci.formats.out.EPSWriter
getPixelTypes(String) - Method in class loci.formats.out.ICSWriter
getPixelTypes(String) - Method in class loci.formats.out.ImageIOWriter
getPixelTypes(String) - Method in class loci.formats.out.JavaWriter
getPixelTypes(String) - Method in class loci.formats.out.JPEG2000Writer: Overridden to return the formats supported by the writer.
getPixelTypes(String) - Method in class loci.formats.out.JPEGWriter
getPixelTypes(String) - Method in class loci.formats.out.OMEXMLWriter
getPixelTypes(String) - Method in class loci.formats.out.QTWriter
getPixelTypes(String) - Method in class loci.formats.out.TiffWriter
getPixelTypes(String) - Method in class loci.formats.out.V3DrawWriter
getPlanarConfiguration() - Method in class loci.formats.tiff.IFD: Retrieves the image's planar configuration (TIFF tag PlanarConfiguration) from this IFD.
getPlaneCount() - Method in class loci.formats.out.CellH5Writer
getPlaneCount() - Method in class loci.formats.out.TiffWriter
getPlaneMaximum(int) - Method in class loci.formats.MinMaxCalculator: Retrieves the maximum pixel value for the specified plane.
getPlaneMinimum(int) - Method in class loci.formats.MinMaxCalculator: Retrieves the minimum pixel value for the specified plane.
getPositionX() - Method in class loci.formats.in.DicomReader
getPositionY() - Method in class loci.formats.in.DicomReader
getPositionZ() - Method in class loci.formats.in.DicomReader
getPossiblePositions() - Method in class loci.formats.cache.CacheStrategy: Gets positions to consider for possible inclusion in the cache, assuming a current position at the origin (0).
getPossiblePositions() - Method in class loci.formats.cache.CrosshairStrategy
getPossiblePositions() - Method in class loci.formats.cache.RectangleStrategy
getPreferredSize() - Method in class loci.formats.gui.CacheIndicator
getPreferredSize() - Method in class loci.formats.gui.PreviewPane
getPrefix() - Method in class loci.formats.FilePattern: Gets the pattern's substring that comes before any block sections.
getPrefix(int) - Method in class loci.formats.FilePattern: Gets the pattern's substring between block i-1 (or the beginning of the pattern, if i is 0) and block i.
getPrefixes() - Method in class loci.formats.FilePattern: Gets all block prefixes.
getPriorities() - Method in class loci.formats.cache.CacheStrategy
getPriorities() - Method in interface loci.formats.cache.ICacheStrategy: Retrieves the priority for caching each axis.
getRange() - Method in class loci.formats.cache.CacheStrategy
getRange() - Method in interface loci.formats.cache.ICacheStrategy: Retrieves the number of objects to cache along each axis.
getReader() - Method in class loci.formats.FileStitcher: Gets the wrapped reader prototype.
getReader() - Method in class loci.formats.gui.FormatFileFilter: Returns the filter's reader.
getReader(int) - Method in class loci.formats.FileStitcher: Gets the reader appropriate for use with the given image plane.
getReader(int, int) - Method in class loci.formats.FileStitcher: Gets the reader that should be used with the given series and image plane.
getRed(int) - Method in class loci.formats.gui.Index16ColorModel
getRed(int) - Method in class loci.formats.gui.SignedColorModel
getRed(int) - Method in class loci.formats.gui.UnsignedIntColorModel
getRed(Object) - Method in class loci.formats.gui.SignedColorModel
getRed(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
getReds() - Method in class loci.formats.gui.Index16ColorModel: Return the array of red color components.
getRequiredDirectories(String[]) - Method in class loci.formats.FileStitcher
getRequiredDirectories(String[]) - Method in class loci.formats.in.DicomReader
getRequiredDirectories(String[]) - Method in class loci.formats.in.OMETiffReader
getResolution() - Method in class loci.formats.FileStitcher
getResolutionLevels() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the number of resolution levels the file JPEG 2000 data has.
getResolutionMultiplier() - Method in class loci.formats.tiff.IFD: Retrieve the value by which to multiply the X and Y resolution so that the resolutions are in microns per pixel.
getRestartMarkers() - Method in interface loci.formats.services.JPEGTurboService
getRestartMarkers() - Method in class loci.formats.services.JPEGTurboServiceImpl
getRowsPerStrip() - Method in class loci.formats.tiff.IFD: Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip) from this IFD.
getSample(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
getSample(BitBuffer, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec: Deprecated.
getSamples(IFD, byte[]) - Method in class loci.formats.tiff.TiffParser
getSamples(IFD, byte[], int, int, long, long) - Method in class loci.formats.tiff.TiffParser
getSamples(IFD, byte[], int, int, long, long, int, int) - Method in class loci.formats.tiff.TiffParser
getSamplesPerPixel() - Method in class loci.formats.tiff.IFD: Retrieves the number of samples per pixel for the image (TIFF tag SamplesPerPixel) from this IFD.
getScanline(int) - Method in class loci.formats.codec.JPEGTileDecoder
getSeries() - Method in class loci.formats.FileStitcher
getSeriesCount() - Method in class loci.formats.FileStitcher
getSeriesMetadata() - Method in class loci.formats.FileStitcher
getSeriesUsedFiles() - Method in class loci.formats.FileStitcher
getSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DicomReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FakeReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ICSReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JPEGReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicromanagerReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NRRDReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OMETiffReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.QTReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TiffReader
getService() - Method in class loci.formats.Memoizer
getShape(String) - Method in interface loci.formats.services.JHDFService: Retrieves the shape of a dataset.
getShape(String) - Method in class loci.formats.services.JHDFServiceImpl
getShorts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of unsigned shorts, one per channel.
getShorts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of unsigned shorts, one per channel.
getShorts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of unsigned shorts, one per channel.
getSize(Image) - Static method in class loci.formats.gui.AWTImageTools: Gets the width and height of the given AWT image, waiting for it to finish loading if necessary.
getSizeC() - Method in class loci.formats.ChannelFiller
getSizeC() - Method in class loci.formats.DimensionSwapper
getSizeC() - Method in class loci.formats.FileStitcher
getSizeT() - Method in class loci.formats.DimensionSwapper
getSizeT() - Method in class loci.formats.FileStitcher
getSizeX() - Method in class loci.formats.DimensionSwapper
getSizeX() - Method in class loci.formats.FileStitcher
getSizeY() - Method in class loci.formats.DimensionSwapper
getSizeY() - Method in class loci.formats.FileStitcher
getSizeZ() - Method in class loci.formats.DimensionSwapper
getSizeZ() - Method in class loci.formats.FileStitcher
getSource() - Method in class loci.formats.cache.Cache: Gets the cache's caching source.
getSource() - Method in class loci.formats.cache.CacheEvent: Gets the source of the cache update.
getSpectra() - Method in class loci.formats.in.IM3Reader: If a Nuance file is a spectral library set (.csl) file, there is a spectral library inside that contains a profile of spectral bin magnitudes for each of several measured fluorophores (or auto fluorescence).
getStep() - Method in class loci.formats.FilePattern: Gets the STEP element for all blocks.
getStep() - Method in class loci.formats.FilePatternBlock: Gets the difference between consecutive elements in a range block.
getStrategy() - Method in class loci.formats.cache.Cache: Gets the cache's caching strategy.
getStream() - Method in class loci.formats.tiff.OnDemandLongArray
getStream() - Method in class loci.formats.tiff.TiffParser: Gets the stream from which TIFF data is being parsed.
getStream() - Method in class loci.formats.tiff.TiffSaver: Gets the stream from which TIFF data is being saved.
getStreams() - Method in class loci.formats.tools.AmiraParameters
getStringValue() - Method in class loci.formats.dicom.DicomTag: Get a string representation of the current value.
getStripByteCounts() - Method in class loci.formats.tiff.IFD: Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from this IFD.
getStripOffsets() - Method in class loci.formats.tiff.IFD: Retrieves the strip offsets for the image (TIFF tag StripOffsets) from this IFD.
getSubIFDs(IFD) - Method in class loci.formats.tiff.TiffParser: Returns the SUBIFDS belonging to a given IFD.
getSubimage(byte[], byte[], int, int, int, int, int, int, int, int, boolean) - Static method in class loci.formats.ImageTools
getSubimage(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Returns a subimage of the specified image.
getSuffix() - Method in class loci.formats.FilePattern: Gets the pattern's substring that comes after all block sections.
getT() - Method in class loci.formats.gui.ImageViewer: Gets the T value of the currently displayed image.
getTag() - Method in enum loci.formats.dicom.DicomAttribute: Get the 4 byte integer tag.
getTag() - Method in class loci.formats.tiff.TiffIFDEntry: Retrieves the entry's Tag value.
getTag(String) - Static method in enum loci.formats.dicom.DicomAttribute
getTags() - Method in class loci.formats.dicom.DicomJSONProvider
getTags() - Method in interface loci.formats.dicom.ITagProvider: Retrieve the tags defined by this provider.
getTags() - Method in class loci.formats.in.DicomReader: Provide the complete hierarchy of DICOM tags.
getTags() - Method in interface loci.formats.services.EXIFService
getTags() - Method in class loci.formats.services.EXIFServiceImpl
getThumbnailIFDs() - Method in class loci.formats.in.MinimalTiffReader: Gets the list of IFDs associated with the current TIFF's thumbnails.
getThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser: Returns thumbnail IFDs.
getThumbSizeX() - Method in class loci.formats.FileStitcher
getThumbSizeX() - Method in class loci.formats.in.MinimalTiffReader
getThumbSizeY() - Method in class loci.formats.FileStitcher
getThumbSizeY() - Method in class loci.formats.in.MinimalTiffReader
getTile(byte[], int, int, int, int) - Method in interface loci.formats.services.JPEGTurboService: Get the uncompressed bytes representing the given bounding box.
getTile(byte[], int, int, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
getTile(int, int) - Method in interface loci.formats.services.JPEGTurboService: Get the uncompressed bytes representing the given tile index.
getTile(int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
getTile(IFD, byte[], int, int) - Method in class loci.formats.tiff.TiffParser
getTileCodec(int) - Method in class loci.formats.ChannelFiller
getTileCodec(int) - Method in class loci.formats.ChannelMerger
getTileCodec(int) - Method in class loci.formats.ChannelSeparator
getTileCodec(int) - Method in class loci.formats.DimensionSwapper
getTileCodec(int) - Method in class loci.formats.FileStitcher
getTileCodec(int) - Method in class loci.formats.in.DicomReader
getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelFiller
getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelMerger
getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelSeparator
getTileCodecOptions(int, int, int) - Method in class loci.formats.DimensionSwapper
getTileCodecOptions(int, int, int) - Method in class loci.formats.FileStitcher
getTileCodecOptions(int, int, int) - Method in class loci.formats.in.DicomReader
getTileColumns() - Method in interface loci.formats.services.JPEGTurboService
getTileColumns() - Method in class loci.formats.services.JPEGTurboServiceImpl
getTileColumns(int) - Method in class loci.formats.in.DicomReader
getTileHeight() - Method in interface loci.formats.services.JPEGTurboService
getTileHeight() - Method in class loci.formats.services.JPEGTurboServiceImpl
getTileIndex(IFD, int, int) - Method in class loci.formats.in.MinimalTiffReader: Get the index of the tile corresponding to given IFD (plane) and tile XY indexes.
getTileLength() - Method in class loci.formats.tiff.IFD: Returns the length of an image tile.
getTileRows() - Method in interface loci.formats.services.JPEGTurboService
getTileRows() - Method in class loci.formats.services.JPEGTurboServiceImpl
getTileRows(int) - Method in class loci.formats.in.DicomReader
getTiles() - Method in class loci.formats.in.DicomReader
getTileSizeX() - Method in class loci.formats.out.DicomWriter
getTileSizeX() - Method in class loci.formats.out.TiffWriter
getTileSizeY() - Method in class loci.formats.out.DicomWriter
getTileSizeY() - Method in class loci.formats.out.TiffWriter
getTilesPerColumn() - Method in class loci.formats.tiff.IFD: Returns the number of image tiles per column.
getTilesPerRow() - Method in class loci.formats.tiff.IFD: Returns the number of image tiles per row.
getTileWidth() - Method in interface loci.formats.services.JPEGTurboService
getTileWidth() - Method in class loci.formats.services.JPEGTurboServiceImpl
getTileWidth() - Method in class loci.formats.tiff.IFD: Returns the width of an image tile.
getTimestamp() - Method in class loci.formats.in.DicomReader
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class loci.formats.gui.XMLCellRenderer
getType() - Method in class loci.formats.cache.CacheEvent: Gets the type of cache update.
getType() - Method in class loci.formats.gui.TwoChannelColorSpace
getType() - Method in class loci.formats.tiff.TiffIFDEntry: Retrieves the entry's Type value.
getType(Object, boolean) - Static method in enum loci.formats.tiff.IFDType: Get the type corresponding to the given value.
getUIDRoot() - Method in class loci.formats.out.DicomWriter
getUnderlyingReaders() - Method in class loci.formats.FileStitcher
getUsedFiles() - Method in class loci.formats.FileStitcher
getUsedFiles(boolean) - Method in class loci.formats.FileStitcher
getUsedFiles(boolean) - Method in class loci.formats.in.BDVReader
getUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
getUsedFiles(boolean) - Method in class loci.formats.in.KLBReader
getUsedFiles(boolean) - Method in class loci.formats.in.SlideBook7Reader
getValue(IRandomAccess) - Method in class loci.formats.in.IM3Reader.StringIM3Record: Return the string value for this record
getValueCount() - Method in class loci.formats.tiff.TiffIFDEntry: Retrieves the entry's ValueCount value.
getValueOffset() - Method in class loci.formats.tiff.TiffIFDEntry: Retrieves the entry's ValueOffset value.
getValueStartPointer() - Method in class loci.formats.dicom.DicomTag: Get the file pointer at which the value starts (useful for sequences and byte streams).
getWavelengths() - Method in class loci.formats.in.IM3Reader.Spectrum
getWidth() - Method in class loci.formats.codec.JPEGTileDecoder
getWidth() - Method in enum loci.formats.dicom.DicomVR
getXML() - Method in class loci.formats.tools.EditTiffG
getXResolution() - Method in class loci.formats.tiff.IFD: Retrieve the X resolution (TIFF tag XResolution) from this IFD.
getYResolution() - Method in class loci.formats.tiff.IFD: Retrieve the Y resolution (TIFF tag YResolution) from this IFD.
getZ() - Method in class loci.formats.gui.ImageViewer: Gets the Z value of the currently displayed image.
getZCTCoords(int) - Method in class loci.formats.ChannelMerger
getZCTCoords(int) - Method in class loci.formats.ChannelSeparator
getZCTCoords(int) - Method in class loci.formats.DimensionSwapper
getZCTCoords(int) - Method in class loci.formats.FileStitcher
getZCTModuloCoords(int) - Method in class loci.formats.ChannelMerger
getZCTModuloCoords(int) - Method in class loci.formats.ChannelSeparator
getZCTModuloCoords(int) - Method in class loci.formats.DimensionSwapper
getZCTModuloCoords(int) - Method in class loci.formats.FileStitcher
getZOffsets() - Method in class loci.formats.in.DicomReader
GIF_MAGIC_STRING - Static variable in class loci.formats.in.GIFReader
GIFReader - Class in loci.formats.in: GIFReader is the file format reader for Graphics Interchange Format (GIF) files.
GIFReader() - Constructor for class loci.formats.in.GIFReader: Constructs a new GIF reader.
GRAY_RESPONSE_CURVE - Static variable in class loci.formats.tiff.IFD
GRAY_RESPONSE_UNIT - Static variable in class loci.formats.tiff.IFD
GREEN_LUT_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
GREEN_LUT_DESCRIPTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
GRID - Enum constant in enum loci.formats.dicom.DicomAttribute
GRID_ABSORBING_MATERIAL - Enum constant in enum loci.formats.dicom.DicomAttribute
GRID_ASPECT_RATIO - Enum constant in enum loci.formats.dicom.DicomAttribute
GRID_FOCAL_DISTANCE - Enum constant in enum loci.formats.dicom.DicomAttribute
GRID_PERIOD - Enum constant in enum loci.formats.dicom.DicomAttribute
GRID_PITCH - Enum constant in enum loci.formats.dicom.DicomAttribute
GRID_SPACING_MATERIAL - Enum constant in enum loci.formats.dicom.DicomAttribute
GRID_THICKNESS - Enum constant in enum loci.formats.dicom.DicomAttribute
GROUP_3_FAX - Enum constant in enum loci.formats.tiff.TiffCompression
GROUP_4_FAX - Enum constant in enum loci.formats.tiff.TiffCompression
GUITools - Class in loci.formats.gui: A utility class for working with graphical user interfaces.

H

H_263 - Enum constant in enum loci.formats.codec.CompressionType
HALFTONE_HINTS - Static variable in class loci.formats.tiff.IFD
handleMetadataStore(IFormatReader) - Method in class loci.formats.Memoizer: Return the IFormatReader instance that is passed in or null if it has been invalidated, which will include the instance being closed.
HARDCOPY_CREATION_DEVICE_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
HARDCOPY_DEVICE_MANUFACTURER - Enum constant in enum loci.formats.dicom.DicomAttribute
HARDCOPY_DEVICE_MODEL_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
HARDCOPY_DEVICE_SOFTWARE_VERSION - Enum constant in enum loci.formats.dicom.DicomAttribute
hasCompanionFiles() - Method in class loci.formats.in.FilePatternReader
hasFlattenedResolutions() - Method in class loci.formats.in.FilePatternReader
hashCode() - Method in class loci.formats.tiff.TiffRational: Reasonable hash value for use with hashtables.
HDF_MAGIC_STRING - Static variable in class loci.formats.in.BDVReader
HDF_MAGIC_STRING - Static variable in class loci.formats.in.CellH5Reader
HEADER - Enum constant in enum loci.formats.codec.JPEG2000BoxType
HEADER_LENGTH - Static variable in class loci.formats.in.DicomReader
HEART_RATE - Enum constant in enum loci.formats.dicom.DicomAttribute
height - Variable in class loci.formats.tools.AmiraParameters
HIGH_BIT - Enum constant in enum loci.formats.dicom.DicomAttribute
HIGH_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
HIGH_RR_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
HOST_COMPUTER - Static variable in class loci.formats.tiff.IFD
HuffmanCodec - Class in loci.formats.codec: This class implements Huffman decoding.
HuffmanCodec() - Constructor for class loci.formats.codec.HuffmanCodec
HuffmanCodecOptions - Class in loci.formats.codec: Options for compressing and decompressing Huffman data.
HuffmanCodecOptions() - Constructor for class loci.formats.codec.HuffmanCodecOptions

I

ICacheSource - Interface in loci.formats.cache: Interface for cache sources.
ICacheStrategy - Interface in loci.formats.cache: Interface for cache strategies.
ICC_PROFILE - Enum constant in enum loci.formats.dicom.DicomAttribute
icon - Variable in class loci.formats.gui.ImageViewer
icon - Variable in class loci.formats.gui.PreviewPane
ICON_IMAGE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
iconLabel - Variable in class loci.formats.gui.ImageViewer
iconLabel - Variable in class loci.formats.gui.PreviewPane: Labels containing thumbnail and dimensional information.
iconText - Variable in class loci.formats.gui.PreviewPane
iconTip - Variable in class loci.formats.gui.PreviewPane
ICSReader - Class in loci.formats.in: ICSReader is the file format reader for ICS (Image Cytometry Standard) files.
ICSReader() - Constructor for class loci.formats.in.ICSReader: Constructs a new ICSReader.
ICSWriter - Class in loci.formats.out: ICSWriter is the file format writer for ICS files.
ICSWriter() - Constructor for class loci.formats.out.ICSWriter
IExtraMetadataWriter - Interface in loci.formats.out
IFD - Class in loci.formats.tiff: Data structure for working with TIFF Image File Directories (IFDs).
IFD - Enum constant in enum loci.formats.tiff.IFDType
IFD() - Constructor for class loci.formats.tiff.IFD
IFD(IFD) - Constructor for class loci.formats.tiff.IFD
IFD8 - Enum constant in enum loci.formats.tiff.IFDType
IFDList - Class in loci.formats.tiff: Data structure for working with a list of TIFF IFDs.
IFDList() - Constructor for class loci.formats.tiff.IFDList
ifds - Variable in class loci.formats.in.MinimalTiffReader: List of IFDs for the current TIFF.
IFDType - Enum in loci.formats.tiff: An enumeration of IFD types.
IGNORE - Enum constant in enum loci.formats.dicom.ResolutionStrategy
IllegalBlockException - Exception Class in loci.formats: Exception thrown when FilePatternBlock encounters an invalid pattern.
IllegalBlockException() - Constructor for exception class loci.formats.IllegalBlockException
IllegalBlockException(String) - Constructor for exception class loci.formats.IllegalBlockException
IllegalBlockException(String, Throwable) - Constructor for exception class loci.formats.IllegalBlockException
IllegalBlockException(Throwable) - Constructor for exception class loci.formats.IllegalBlockException
ILLUMINATION_COLOR_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
ILLUMINATION_TYPE_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
ILLUMINATION_WAVELENGTH - Enum constant in enum loci.formats.dicom.DicomAttribute
ILLUMINATOR_TYPE_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
IM3Reader - Class in loci.formats.in
IM3Reader() - Constructor for class loci.formats.in.IM3Reader: Construct an uninitialized reader of .im3 files.
IM3Reader.BooleanIM3Record - Class in loci.formats.in: A record containing boolean values
IM3Reader.ContainerRecord - Class in loci.formats.in
IM3Reader.FloatIM3Record - Class in loci.formats.in
IM3Reader.IM3Record - Class in loci.formats.in
IM3Reader.IntIM3Record - Class in loci.formats.in
IM3Reader.Spectrum - Class in loci.formats.in
IM3Reader.StringIM3Record - Class in loci.formats.in
IMAGE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
IMAGE_AREA_DOSE_PRODUCT - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_DESCRIPTION - Static variable in class loci.formats.tiff.IFD
IMAGE_GEOMETRY_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_HEADER - Enum constant in enum loci.formats.codec.JPEG2000BoxType
IMAGE_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_LENGTH - Static variable in class loci.formats.tiff.IFD
IMAGE_ORIENTATION_PATIENT - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
IMAGE_PATH_FILTER_PASS_BAND - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_PATH_FILTER_PASSTHROUGH_WAVELENGTH - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_PATH_FILTER_TYPE_STACK_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_POSITION - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_POSITION_PATIENT - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_TRIGGER_DELAY - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGE_WIDTH - Static variable in class loci.formats.tiff.IFD
IMAGED_NUCLEUS - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGED_VOLUME_DEPTH - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGED_VOLUME_HEIGHT - Enum constant in enum loci.formats.dicom.DicomAttribute
IMAGED_VOLUME_WIDTH - Enum constant in enum loci.formats.dicom.DicomAttribute
ImageIOReader - Class in loci.formats.in: ImageIOReader is the superclass for file format readers that use the javax.imageio package.
ImageIOReader(String, String) - Constructor for class loci.formats.in.ImageIOReader: Constructs a new ImageIOReader.
ImageIOReader(String, String[]) - Constructor for class loci.formats.in.ImageIOReader: Constructs a new ImageIOReader.
ImageIOWriter - Class in loci.formats.out: ImageIOWriter is the superclass for file format writers that use the javax.imageio library.
ImageIOWriter(String, String[], String) - Constructor for class loci.formats.out.ImageIOWriter: Constructs an ImageIO-based writer with the given name, default suffixes and output type (e.g., png, jpeg).
ImageIOWriter(String, String, String) - Constructor for class loci.formats.out.ImageIOWriter: Constructs an ImageIO-based writer with the given name, default suffix and output type (e.g., png, jpeg).
IMAGEJ_TAG - Static variable in class loci.formats.in.TiffReader
IMAGER_PIXEL_SPACING - Enum constant in enum loci.formats.dicom.DicomAttribute
images - Variable in class loci.formats.gui.ImageViewer
ImageTools - Class in loci.formats: A utility class with convenience methods for manipulating images in primitive array form.
imageType - Variable in class loci.formats.dicom.DicomFileInfo
ImageViewer - Class in loci.formats.gui: ImageViewer is a simple viewer/converter for the Bio-Formats image formats.
ImageViewer() - Constructor for class loci.formats.gui.ImageViewer: Constructs an image viewer.
ImageViewer(boolean) - Constructor for class loci.formats.gui.ImageViewer: Constructs an image viewer.
IMAGING_FREQUENCY - Enum constant in enum loci.formats.dicom.DicomAttribute
IMPLANT_PRESENT - Enum constant in enum loci.formats.dicom.DicomAttribute
IMPLEMENTATION_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
IMPLEMENTATION_VERSION - Enum constant in enum loci.formats.dicom.DicomAttribute
IMPLICIT - Enum constant in enum loci.formats.dicom.DicomVR
in - Variable in class loci.formats.gui.ImageViewer
in - Variable in class loci.formats.out.TiffWriter: Input stream to use when overwriting data.
in - Variable in class loci.formats.tiff.TiffParser: Input source from which to parse TIFF data.
in - Variable in class loci.formats.tools.AmiraParameters
IN_CONCATENATION_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
inCache - Variable in class loci.formats.cache.Cache: Whether each position is currently supposed to be cached.
index - Variable in class loci.formats.cache.CacheEvent: Relevant index to the event, if any.
Index16ColorModel - Class in loci.formats.gui: ColorModel that handles 16 bits per channel lookup tables.
Index16ColorModel(int, int, short[][], boolean) - Constructor for class loci.formats.gui.Index16ColorModel
indexedToRGB(byte[][], byte[]) - Static method in class loci.formats.ImageTools: Converts a LUT and an array of indices into an array of RGB tuples.
indexedToRGB(short[][], byte[], boolean) - Static method in class loci.formats.ImageTools: Converts a LUT and an array of indices into an array of RGB tuples.
indexedToRGB(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools: Converts an indexed color BufferedImage to an RGB BufferedImage.
INDIVIDUAL_JARS - Static variable in class loci.formats.UpgradeChecker: Names of the individual JARs.
info - Variable in class loci.formats.in.OMETiffReader: Mapping from series and plane numbers to files and IFD entries.
initFile(String) - Method in class loci.formats.FileStitcher: Initializes the given file or file pattern.
initFile(String) - Method in class loci.formats.in.APNGReader
initFile(String) - Method in class loci.formats.in.AVIReader
initFile(String) - Method in class loci.formats.in.BaseTiffReader
initFile(String) - Method in class loci.formats.in.BDVReader
initFile(String) - Method in class loci.formats.in.BMPReader
initFile(String) - Method in class loci.formats.in.CellH5Reader
initFile(String) - Method in class loci.formats.in.DicomReader
initFile(String) - Method in class loci.formats.in.EPSReader
initFile(String) - Method in class loci.formats.in.FakeReader
initFile(String) - Method in class loci.formats.in.FilePatternReader
initFile(String) - Method in class loci.formats.in.FitsReader
initFile(String) - Method in class loci.formats.in.FlowSightReader
initFile(String) - Method in class loci.formats.in.GIFReader
initFile(String) - Method in class loci.formats.in.ICSReader
initFile(String) - Method in class loci.formats.in.IM3Reader
initFile(String) - Method in class loci.formats.in.ImageIOReader
initFile(String) - Method in class loci.formats.in.JPEG2000Reader
initFile(String) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
initFile(String) - Method in class loci.formats.in.KLBReader
initFile(String) - Method in class loci.formats.in.MicromanagerReader
initFile(String) - Method in class loci.formats.in.MinimalTiffReader
initFile(String) - Method in class loci.formats.in.MNGReader
initFile(String) - Method in class loci.formats.in.NRRDReader
initFile(String) - Method in class loci.formats.in.OBFReader
initFile(String) - Method in class loci.formats.in.OMETiffReader
initFile(String) - Method in class loci.formats.in.OMEXMLReader
initFile(String) - Method in class loci.formats.in.PCXReader
initFile(String) - Method in class loci.formats.in.PGMReader
initFile(String) - Method in class loci.formats.in.PictReader
initFile(String) - Method in class loci.formats.in.QTReader
initFile(String) - Method in class loci.formats.in.SlideBook7Reader
initFile(String) - Method in class loci.formats.in.TextReader
initFile(String) - Method in class loci.formats.in.TiffJAIReader
initFile(String) - Method in class loci.formats.in.TileJPEGReader
initFile(String) - Method in class loci.formats.in.ZipReader
initialize(String) - Method in interface loci.formats.services.EXIFService
initialize(String) - Method in class loci.formats.services.EXIFServiceImpl
initialize(String, int) - Method in class loci.formats.codec.JPEGTileDecoder
initialize(RandomAccessInputStream, int) - Method in class loci.formats.codec.JPEGTileDecoder
initialize(RandomAccessInputStream, int, int) - Method in interface loci.formats.services.JPEGTurboService: Initialize the given stream, which represents an image of the given width and height.
initialize(RandomAccessInputStream, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
initialize(RandomAccessInputStream, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder
initImage() - Method in class loci.formats.in.ImageIOReader
initIntArray(String, long[], long) - Method in interface loci.formats.services.JHDFService: Creates an HDF5 dataset in path consisting of integers specified by bytes per pixel bpp.
initIntArray(String, long[], long) - Method in class loci.formats.services.JHDFServiceImpl
initMetadata() - Method in class loci.formats.in.BaseTiffReader: Populates the metadata hashtable and metadata store.
initMetadataStore() - Method in class loci.formats.in.BaseTiffReader: Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself.
initMetadataStore() - Method in class loci.formats.in.TiffReader
initMinMax() - Method in class loci.formats.MinMaxCalculator: Ensures internal min/max variables are initialized properly.
initReader(int, int) - Method in class loci.formats.FileStitcher
initStandardMetadata() - Method in class loci.formats.in.BaseTiffReader: Parses standard metadata.
initStandardMetadata() - Method in class loci.formats.in.TiffReader
initTiffParser() - Method in class loci.formats.in.MinimalTiffReader: Reinitialize the underlying TiffParser.
INK_NAMES - Static variable in class loci.formats.tiff.IFD
INK_SET - Static variable in class loci.formats.tiff.IFD
INPLANE_PHASE_ENCODING_DIRECTION - Enum constant in enum loci.formats.dicom.DicomAttribute
inputOrder - Variable in class loci.formats.SwappableMetadata: Order in which dimensions are stored.
install(String, String) - Method in class loci.formats.UpgradeChecker: Download and install a JAR file from the given URL.
installIndividualJars(String, String) - Method in class loci.formats.UpgradeChecker: Download and install all of the individual JAR files into the given directory.
INSTANCE_AVAILABILITY - Enum constant in enum loci.formats.dicom.DicomAttribute
INSTANCE_CREATOR - Enum constant in enum loci.formats.dicom.DicomAttribute
INSTANCE_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
INSTITUTION_ADDRESS - Enum constant in enum loci.formats.dicom.DicomAttribute
INSTITUTION_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
INSTITUTION_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
INSTITUTIONAL_DEPARTMENT_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
INTELLECTUAL_PROPERTY - Enum constant in enum loci.formats.codec.JPEG2000BoxType
INTENSIFIER_SIZE - Enum constant in enum loci.formats.dicom.DicomAttribute
interlaced - Variable in class loci.formats.codec.MJPBCodecOptions: Indicates whether or not channels are interlaced.
interpolate(short[], byte[], int[], int, int, boolean) - Static method in class loci.formats.ImageTools
INTERVALS_ACQUIRED - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVALS_REJECTED - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_DRUG_DOSE - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_DRUG_INFORMATION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_DRUG_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_DRUG_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_DRUG_START_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_DRUG_STOP_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
INTERVENTION_STATUS - Enum constant in enum loci.formats.dicom.DicomAttribute
IntIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IntIM3Record
intValue() - Method in class loci.formats.tiff.TiffRational: Returns the value of the specified number as an int.
INVALID - Enum constant in enum loci.formats.dicom.DicomAttribute
INVALID_PIXEL_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
INVERSION_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
IS - Enum constant in enum loci.formats.dicom.DicomVR
isBigTiff - Variable in class loci.formats.out.TiffWriter: Whether or not the output file is a BigTIFF file.
isBigTiff() - Method in class loci.formats.tiff.IFD: Gets whether this is a BigTIFF IFD.
isBigTiff() - Method in class loci.formats.tiff.TiffParser: Returns whether or not the current TIFF file contains BigTIFF data.
isBigTiff() - Method in class loci.formats.tiff.TiffSaver: Returns whether or not we are writing BigTIFF data.
isBitOnByteBoundary() - Method in class loci.formats.codec.BitBuffer: Deprecated.

Checks if the current position is on a byte boundary, that is the next bit in the byte array is the first bit in a byte.
isCertain() - Method in class loci.formats.AxisGuesser: Gets whether the guesser is confident that all axes are correct.
isCompatibleRaster(Raster) - Method in class loci.formats.gui.Index16ColorModel
isCompatibleRaster(Raster) - Method in class loci.formats.gui.SignedColorModel
isCompatibleRaster(Raster) - Method in class loci.formats.gui.UnsignedIntColorModel
isCS_sRGB() - Method in class loci.formats.gui.TwoChannelColorSpace
isDeflate - Variable in class loci.formats.dicom.DicomTile
isExtendedDepthOfField() - Method in class loci.formats.in.DicomReader
isFalseColor() - Method in class loci.formats.FileStitcher
isFilled() - Method in class loci.formats.ChannelFiller: Returns true if the indices are being factored out.
isFixed() - Method in class loci.formats.FilePatternBlock: Whether or not this is a fixed-width block.
isGroupFiles() - Method in class loci.formats.FileStitcher
isGroupFiles() - Method in class loci.formats.in.FilePatternReader
isInCache(int) - Method in class loci.formats.cache.Cache: Returns true if the object at the given index is in the cache.
isInCache(int[]) - Method in class loci.formats.cache.Cache: Returns true if the object at the given dimensional position is in the cache.
isIndexed() - Method in class loci.formats.ChannelFiller
isIndexed() - Method in class loci.formats.ChannelMerger
isIndexed() - Method in class loci.formats.FileStitcher
isInterleaved() - Method in class loci.formats.ChannelMerger
isInterleaved() - Method in class loci.formats.FileStitcher
isInterleaved(int) - Method in class loci.formats.FileStitcher
isInterleaved(int) - Method in class loci.formats.in.ICSReader
isJP2K - Variable in class loci.formats.dicom.DicomTile
isJPEG - Variable in class loci.formats.dicom.DicomTile
isLibraryLoaded() - Method in interface loci.formats.services.JPEGTurboService
isLibraryLoaded() - Method in class loci.formats.services.JPEGTurboServiceImpl
isLittleEndian() - Method in class loci.formats.FileStitcher
isLittleEndian() - Method in class loci.formats.tiff.IFD: Gets whether the TIFF information in this IFD is little-endian.
isLittleEndian() - Method in class loci.formats.tiff.TiffSaver: Returns whether or not we are writing little-endian data.
isLoadedFromMemo() - Method in class loci.formats.Memoizer: Returns whether the ReaderWrapper.reader instance currently active was loaded from the memo file during Memoizer.setId(String).
isMetadataFiltered() - Method in class loci.formats.in.FilePatternReader
isMinMaxPopulated() - Method in class loci.formats.MinMaxCalculator: Returns true if the values returned by getChannelGlobalMinimum/Maximum can be trusted.
isModulo - Variable in class loci.formats.tools.MakeTestOmeTiff
isNormalized() - Method in class loci.formats.in.FilePatternReader
isNumeric() - Method in class loci.formats.FilePatternBlock: Whether or not this is a numeric block.
ISO_SPEED_RATINGS - Static variable in class loci.formats.tiff.IFD
isOrderCertain() - Method in class loci.formats.FileStitcher
isOriginalMetadataPopulated() - Method in class loci.formats.in.FilePatternReader
isPrivateContentCreator() - Method in class loci.formats.dicom.DicomTag: See https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_7.8.html
isRawCodestream() - Method in class loci.formats.in.JPEG2000MetadataParser: Whether or not the codestream is raw and not JP2 boxed.
isRegex() - Method in class loci.formats.FilePattern: Returns whether or not this pattern is a regular expression.
isRGB() - Method in class loci.formats.ChannelFiller
isRGB() - Method in class loci.formats.ChannelMerger
isRGB() - Method in class loci.formats.ChannelSeparator
isRGB() - Method in class loci.formats.FileStitcher
isRLE - Variable in class loci.formats.dicom.DicomTile
isSavedToMemo() - Method in class loci.formats.Memoizer: Returns whether the ReaderWrapper.reader instance currently active was saved to the memo file during Memoizer.setId(String).
isSingleFile(String) - Method in class loci.formats.in.FakeReader
isSingleFile(String) - Method in class loci.formats.in.FilePatternReader
isSingleFile(String) - Method in class loci.formats.in.ICSReader
isSingleFile(String) - Method in class loci.formats.in.MicromanagerReader
isSingleFile(String) - Method in class loci.formats.in.NRRDReader
isSingleFile(String) - Method in class loci.formats.in.OMETiffReader
isSingleFile(String) - Method in class loci.formats.in.SlideBook7Reader
ISSUER_OF_PATIENT_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
isThisType(String) - Method in class loci.formats.out.PyramidOMETiffWriter
isThisType(String, boolean) - Method in class loci.formats.in.BDVReader
isThisType(String, boolean) - Method in class loci.formats.in.CellH5Reader
isThisType(String, boolean) - Method in class loci.formats.in.DicomReader
isThisType(String, boolean) - Method in class loci.formats.in.FakeReader
isThisType(String, boolean) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
isThisType(String, boolean) - Method in class loci.formats.in.MicromanagerReader
isThisType(String, boolean) - Method in class loci.formats.in.NRRDReader
isThisType(String, boolean) - Method in class loci.formats.in.OMETiffReader
isThisType(String, boolean) - Method in class loci.formats.in.OMEXMLReader
isThisType(String, boolean) - Method in class loci.formats.in.SlideBook7Reader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.APNGReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AVIReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BDVReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BMPReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellH5Reader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DicomReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FlowSightReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GIFReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IM3Reader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEG2000Reader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MicromanagerReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MinimalTiffReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MNGReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NRRDReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMETiffReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMEXMLReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCXReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PGMReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.QTReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlideBook7Reader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TextReader
isThumbnailSeries() - Method in class loci.formats.FileStitcher
isTiled() - Method in class loci.formats.tiff.IFD
isUsingPatternIds() - Method in class loci.formats.FileStitcher: Gets whether the reader is using file patterns for IDs.
isValid() - Method in class loci.formats.FilePattern: Returns whether or not the file pattern is valid.
isValidHeader() - Method in class loci.formats.tiff.TiffParser: Tests this stream to see if it represents a TIFF file.
isValidRange(int, int, int) - Static method in class loci.formats.tools.FakeImage
isVersionChecking() - Method in class loci.formats.Memoizer: Returns whether or not version checking is done based upon major/minor version numbers.
isWritableDirectory(File) - Method in class loci.formats.Memoizer: Test if the given File instance is a writable directory.
ITagProvider - Interface in loci.formats.dicom: Interface used to provide DICOM tags.
ITEM - Enum constant in enum loci.formats.dicom.DicomAttribute
ITEM_DELIMITATION_ITEM - Enum constant in enum loci.formats.dicom.DicomAttribute
IVUS_ACQUISITION - Enum constant in enum loci.formats.dicom.DicomAttribute
IVUS_GATED_RATE - Enum constant in enum loci.formats.dicom.DicomAttribute
IVUS_PULLBACK_RATE - Enum constant in enum loci.formats.dicom.DicomAttribute
IVUS_PULLBACK_START_FRAME_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
IVUS_PULLBACK_STOP_FRAME_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute

J

J2K - Enum constant in enum loci.formats.codec.CompressionType
J2K_LOSSY - Enum constant in enum loci.formats.codec.CompressionType
JAIIIOService - Interface in loci.formats.services: Interface defining methods for reading data using JAI Image I/O.
JAIIIOServiceImpl - Class in loci.formats.services: Implementation of JAIIIOService for reading and writing JPEG-2000 data.
JAIIIOServiceImpl() - Constructor for class loci.formats.services.JAIIIOServiceImpl: Default constructor.
JavaWriter - Class in loci.formats.out: JavaWriter is the file format writer for Java source code.
JavaWriter() - Constructor for class loci.formats.out.JavaWriter
JHDFService - Interface in loci.formats.services: Utility class for working with NetCDF/HDF files.
JHDFServiceImpl - Class in loci.formats.services: Utility class for working with HDF files.
JHDFServiceImpl() - Constructor for class loci.formats.services.JHDFServiceImpl: Default constructor.
JPEG - Enum constant in enum loci.formats.codec.CompressionType
JPEG - Enum constant in enum loci.formats.tiff.TiffCompression
JPEG_2000 - Enum constant in enum loci.formats.tiff.TiffCompression
JPEG_2000_LOSSY - Enum constant in enum loci.formats.tiff.TiffCompression
JPEG_AC_TABLES - Static variable in class loci.formats.tiff.IFD
JPEG_DC_TABLES - Static variable in class loci.formats.tiff.IFD
JPEG_INTERCHANGE_FORMAT - Static variable in class loci.formats.tiff.IFD
JPEG_INTERCHANGE_FORMAT_LENGTH - Static variable in class loci.formats.tiff.IFD
JPEG_LOSSLESS_PREDICTORS - Static variable in class loci.formats.tiff.IFD
JPEG_POINT_TRANSFORMS - Static variable in class loci.formats.tiff.IFD
JPEG_PROC - Static variable in class loci.formats.tiff.IFD
JPEG_Q_TABLES - Static variable in class loci.formats.tiff.IFD
JPEG_RESTART_INTERVAL - Static variable in class loci.formats.tiff.IFD
JPEG_TABLES - Static variable in class loci.formats.tiff.IFD
JPEG2000BoxType - Enum in loci.formats.codec: An enumeration of JPEG 2000 box types.
JPEG2000Codec - Class in loci.formats.codec: This class implements JPEG 2000 compression and decompression.
JPEG2000Codec() - Constructor for class loci.formats.codec.JPEG2000Codec
JPEG2000CodecOptions - Class in loci.formats.codec: Options for compressing and decompressing JPEG-2000 data.
JPEG2000CodecOptions() - Constructor for class loci.formats.codec.JPEG2000CodecOptions: Creates a new instance.
JPEG2000CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.JPEG2000CodecOptions: Creates a new instance with options.
JPEG2000MetadataParser - Class in loci.formats.in: A parser for JPEG 2000 metadata.
JPEG2000MetadataParser(RandomAccessInputStream) - Constructor for class loci.formats.in.JPEG2000MetadataParser: Constructs a new JPEG2000MetadataParser.
JPEG2000MetadataParser(RandomAccessInputStream, long) - Constructor for class loci.formats.in.JPEG2000MetadataParser: Constructs a new JPEG2000MetadataParser.
JPEG2000Reader - Class in loci.formats.in: JPEG2000Reader is the file format reader for JPEG-2000 images.
JPEG2000Reader() - Constructor for class loci.formats.in.JPEG2000Reader: Constructs a new JPEG2000Reader.
JPEG2000SegmentMarker - Enum in loci.formats.codec: An enumeration of JPEG 2000 segment markers.
JPEG2000Writer - Class in loci.formats.out: JPEG2000Writer is the file format writer for JPEG2000 files.
JPEG2000Writer() - Constructor for class loci.formats.out.JPEG2000Writer: Creates a new instance.
JPEGCodec - Class in loci.formats.codec: This class implements JPEG compression and decompression.
JPEGCodec() - Constructor for class loci.formats.codec.JPEGCodec
JPEGReader - Class in loci.formats.in: JPEGReader is the file format reader for JPEG images.
JPEGReader() - Constructor for class loci.formats.in.JPEGReader: Constructs a new JPEGReader.
JPEGReader.DefaultJPEGReader - Class in loci.formats.in
JPEGTileDecoder - Class in loci.formats.codec
JPEGTileDecoder() - Constructor for class loci.formats.codec.JPEGTileDecoder
JPEGTurboService - Interface in loci.formats.services
JPEGTurboServiceImpl - Class in loci.formats.services: Based upon the NDPI to OME-TIFF converter by Matthias Baldauf: http://matthias-baldauf.at/software/ndpi_converter/
JPEGTurboServiceImpl() - Constructor for class loci.formats.services.JPEGTurboServiceImpl
JPEGWriter - Class in loci.formats.out: JPEGWriter is the file format writer for JPEG files.
JPEGWriter() - Constructor for class loci.formats.out.JPEGWriter
JPEGXR - Enum constant in enum loci.formats.tiff.TiffCompression
JPEGXRCodec - Class in loci.formats.codec
JPEGXRCodec() - Constructor for class loci.formats.codec.JPEGXRCodec
JPEGXRService - Interface in loci.formats.services: Interface defining methods for working with JPEG-XR data
JPEGXRServiceImpl - Class in loci.formats.services: Interface defining methods for working with JPEG-XR data
JPEGXRServiceImpl() - Constructor for class loci.formats.services.JPEGXRServiceImpl

K

key - Variable in class loci.formats.dicom.DicomTag
keyPressed(KeyEvent) - Method in class loci.formats.gui.ImageViewer: Handles key presses.
keyReleased(KeyEvent) - Method in class loci.formats.gui.ImageViewer
keyTyped(KeyEvent) - Method in class loci.formats.gui.ImageViewer
kind - Variable in class loci.formats.out.ImageIOWriter
KLBReader - Class in loci.formats.in: Reader for Keller Lab Block (KLB) files.
KLBReader() - Constructor for class loci.formats.in.KLBReader: Constructs a new BDV reader.
kryo - Variable in class loci.formats.Memoizer.KryoDeser
KryoDeser() - Constructor for class loci.formats.Memoizer.KryoDeser
KVP - Enum constant in enum loci.formats.dicom.DicomAttribute

L

LABEL - Enum constant in enum loci.formats.codec.JPEG2000BoxType
LABEL_TEXT - Enum constant in enum loci.formats.dicom.DicomAttribute
LARGEST_IMAGE_PIXEL_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
LARGEST_IMAGE_PIXEL_VALUE_IN_PLANE - Enum constant in enum loci.formats.dicom.DicomAttribute
LARGEST_PIXEL_VALUE_IN_SERIES - Enum constant in enum loci.formats.dicom.DicomAttribute
last - Variable in class loci.formats.dicom.DicomTile
LAST_MENSTRUAL_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
lastId - Variable in class loci.formats.gui.PreviewPane: Last ID loaded.
lastPlane - Variable in class loci.formats.in.MinimalTiffReader
length() - Method in class loci.formats.cache.CacheStrategy: Shortcut for computing total number of positions.
lengths - Variable in class loci.formats.cache.CacheStrategy: Length of each dimensional axis.
LENSES_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
LESION_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
LIGHT_PATH_FILTER_PASS_BAND - Enum constant in enum loci.formats.dicom.DicomAttribute
LIGHT_PATH_FILTER_PASSTHROUGH_WAVELENGTH - Enum constant in enum loci.formats.dicom.DicomAttribute
LIGHT_PATH_FILTER_TYPE_STACK_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
LIGHT_SOURCE - Static variable in class loci.formats.tiff.IFD
listeners - Variable in class loci.formats.cache.Cache: List of cache event listeners.
listeners - Variable in class loci.formats.cache.CacheStrategy: List of cache event listeners.
LITTLE - Static variable in class loci.formats.tiff.TiffConstants
LITTLE_ENDIAN - Static variable in class loci.formats.tiff.IFD
littleEndian - Variable in class loci.formats.tools.AmiraParameters
LO - Enum constant in enum loci.formats.dicom.DicomVR
loader - Variable in class loci.formats.gui.PreviewPane: Thumbnail loading thread.
loaderAlive - Variable in class loci.formats.gui.PreviewPane: Flag indicating whether loader thread should keep running.
loadId - Variable in class loci.formats.gui.PreviewPane: Current ID to load.
loadImage(Image) - Static method in class loci.formats.gui.AWTImageTools: Ensures the given AWT image is fully loaded.
loadMemo() - Method in class loci.formats.Memoizer: Load a memo file if possible, returning a null if not.
loadReader() - Method in interface loci.formats.Memoizer.Deser
loadReader() - Method in class loci.formats.Memoizer.KryoDeser
loadReleaseVersion() - Method in interface loci.formats.Memoizer.Deser
loadReleaseVersion() - Method in class loci.formats.Memoizer.KryoDeser
loadRevision() - Method in interface loci.formats.Memoizer.Deser
loadRevision() - Method in class loci.formats.Memoizer.KryoDeser
loadStart(File) - Method in interface loci.formats.Memoizer.Deser
loadStart(File) - Method in class loci.formats.Memoizer.KryoDeser
loadStop() - Method in interface loci.formats.Memoizer.Deser
loadStop() - Method in class loci.formats.Memoizer.KryoDeser
loadVersion() - Method in interface loci.formats.Memoizer.Deser
loadVersion() - Method in class loci.formats.Memoizer.KryoDeser
LOCATION - Enum constant in enum loci.formats.dicom.DicomAttribute
loci.formats - package loci.formats
loci.formats.cache - package loci.formats.cache: Package containing Bio-Formats caching logic, for managing subsets of large collections of image planes in memory.
loci.formats.codec - package loci.formats.codec
loci.formats.dicom - package loci.formats.dicom
loci.formats.gui - package loci.formats.gui: Package containing Bio-Formats graphical user interface code.
loci.formats.in - package loci.formats.in
loci.formats.out - package loci.formats.out: Package containing Bio-Formats file format writers.
loci.formats.services - package loci.formats.services
loci.formats.tiff - package loci.formats.tiff: Package containing Bio-Formats TIFF code of general utility.
loci.formats.tools - package loci.formats.tools: Package containing utility methods corresponding to the Bio-Formats command line tools.
LOGGER - Static variable in class loci.formats.codec.BaseCodec
LOGGER - Static variable in class loci.formats.in.BaseTiffReader: Logger for this class.
LOGGER - Static variable in class loci.formats.in.SlideBook7Reader
LONG - Enum constant in enum loci.formats.tiff.IFDType
LONG8 - Enum constant in enum loci.formats.tiff.IFDType
longValue() - Method in class loci.formats.tiff.TiffRational: Returns the value of the specified number as a long.
lookup - Variable in class loci.formats.in.PictReader: Color lookup table for palette color images.
lookupChild(DicomAttribute) - Method in class loci.formats.dicom.DicomTag: Find the first child tag with the given attribute, or null if one does not exist.
LosslessJPEGCodec - Class in loci.formats.codec: Decompresses lossless JPEG images.
LosslessJPEGCodec() - Constructor for class loci.formats.codec.LosslessJPEGCodec
LOSSY_IMAGE_COMPRESSION - Enum constant in enum loci.formats.dicom.DicomAttribute
LOSSY_IMAGE_COMPRESSION_METHOD - Enum constant in enum loci.formats.dicom.DicomAttribute
LOSSY_IMAGE_COMPRESSION_RATIO - Enum constant in enum loci.formats.dicom.DicomAttribute
LOW_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
LOW_RR_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
LT - Enum constant in enum loci.formats.dicom.DicomVR
LUMA_BLUE - Static variable in enum loci.formats.tiff.PhotoInterp
LUMA_GREEN - Static variable in enum loci.formats.tiff.PhotoInterp
LUMA_RED - Static variable in enum loci.formats.tiff.PhotoInterp: Default luminance values for YCbCr data.
LUT_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
LUT_DESCRIPTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
LUT_EXPLANATION - Enum constant in enum loci.formats.dicom.DicomAttribute
lutLength - Variable in class loci.formats.ChannelFiller: Number of LUT components.
LZOCodec - Class in loci.formats.codec: This class implements LZO decompression.
LZOCodec() - Constructor for class loci.formats.codec.LZOCodec
LZW - Enum constant in enum loci.formats.codec.CompressionType
LZW - Enum constant in enum loci.formats.tiff.TiffCompression
LZWCodec - Class in loci.formats.codec: This is an optimized LZW codec for use with TIFF files.
LZWCodec() - Constructor for class loci.formats.codec.LZWCodec

M

MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
MAGNETIC_FIELD_STRENGTH - Enum constant in enum loci.formats.dicom.DicomAttribute
main(String[]) - Static method in class loci.formats.codec.BitBuffer: Deprecated.

Testing method.
main(String[]) - Static method in class loci.formats.codec.BitWriter: Deprecated.

Tests the BitWriter class.
main(String[]) - Static method in class loci.formats.gui.DataConverter
main(String[]) - Static method in class loci.formats.gui.ImageViewer
main(String[]) - Static method in class loci.formats.gui.XMLWindow
main(String[]) - Static method in class loci.formats.in.IM3Reader: Write a summary of each record to STDOUT
main(String[]) - Static method in class loci.formats.Memoizer
main(String[]) - Static method in class loci.formats.tools.AmiraParameters
main(String[]) - Static method in class loci.formats.tools.BioFormatsExtensionPrinter
main(String[]) - Static method in class loci.formats.tools.CacheConsole: Interactive interpreter for testing Bio-Formats caching implementation.
main(String[]) - Static method in class loci.formats.tools.EditTiffG
main(String[]) - Static method in class loci.formats.tools.MakeTestOmeTiff
main(String[]) - Static method in class loci.formats.tools.UpgradeCheck
MAKE - Static variable in class loci.formats.tiff.IFD
make24Bits(Object, int, int, boolean) - Static method in class loci.formats.ImageTools: Convert an arbitrary primitive type array with 3 samples per pixel to an int array, i.e.
make24Bits(Object, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools: Convert an arbitrary primitive type array with 3 samples per pixel to a 3 x (width * height) byte array.
make24Bits(Object, int, int, boolean, boolean, Double, Double) - Static method in class loci.formats.ImageTools: Convert an arbitrary primitive type array with 3 samples per pixel to a 3 x (width * height) byte array.
make24Bits(Object, int, int, boolean, Double, Double) - Static method in class loci.formats.ImageTools: Convert an arbitrary primitive type array with 3 samples per pixel to an int array, i.e.
makeBuffered(Image) - Static method in class loci.formats.gui.AWTImageTools: Creates a buffered image from the given AWT image object.
makeBuffered(Image, ColorModel) - Static method in class loci.formats.gui.AWTImageTools: Creates a buffered image possessing the given color model, from the specified AWT image object.
makeBufferedImageReader(IFormatReader) - Static method in class loci.formats.gui.BufferedImageReader: Converts the given reader into a BufferedImageReader, wrapping if needed.
makeBufferedImageWriter(IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter: Converts the given writer into a BufferedImageWriter, wrapping if needed.
makeChannelFiller(IFormatReader) - Static method in class loci.formats.ChannelFiller: Converts the given reader into a ChannelFiller, wrapping if needed.
makeChannelMerger(IFormatReader) - Static method in class loci.formats.ChannelMerger: Converts the given reader into a ChannelMerger, wrapping if needed.
makeChannelSeparator(IFormatReader) - Static method in class loci.formats.ChannelSeparator: Converts the given reader into a ChannelSeparator, wrapping if needed.
makeColorModel(int, int) - Static method in class loci.formats.gui.AWTImageTools: Gets a color model for the given number of color components.
makeColorSpace(int) - Static method in class loci.formats.gui.AWTImageTools: Gets a color space for the given number of color components.
makeCompatible(BufferedImage, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools: Creates a buffered image compatible with the given graphics configuration, using the given buffered image as a source.
makeDimensionSwapper(IFormatReader) - Static method in class loci.formats.DimensionSwapper: Converts the given reader into a DimensionSwapper, wrapping if needed.
makeIFD() - Method in class loci.formats.out.PyramidOMETiffWriter
makeIFD() - Method in class loci.formats.out.TiffWriter
makeImage(byte[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given byte data.
makeImage(byte[][], int, int, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given raw byte array, performing any necessary type conversions.
makeImage(byte[], boolean, MetadataRetrieve, int) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given raw byte array, obtaining the dimensional parameters from the specified metadata object.
makeImage(byte[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given single-channel byte data.
makeImage(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given byte data.
makeImage(byte[], int, int, int, boolean, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given raw byte array, performing any necessary type conversions.
makeImage(double[][], int, int) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given double-precision floating point data.
makeImage(double[], int, int) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given single-channel double data.
makeImage(double[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given double data.
makeImage(float[][], int, int) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given single-precision floating point data.
makeImage(float[], int, int) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given single-channel float data.
makeImage(float[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given float data.
makeImage(int[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given int data.
makeImage(int[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given single-channel int data.
makeImage(int[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given int data.
makeImage(short[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given short data.
makeImage(short[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given single-channel short data.
makeImage(short[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given short data.
makeJTree(Document) - Static method in class loci.formats.gui.XMLCellRenderer: Constructs a Swing JTree that displays the given XML DOM document.
makeMinMaxCalculator(IFormatReader) - Static method in class loci.formats.MinMaxCalculator: Converts the given reader into a MinMaxCalculator, wrapping if needed.
makeOmeTiff(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
makeOmeTiff(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
makeOmeTiffExtensions(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
MAKER_NOTE - Static variable in class loci.formats.tiff.IFD
makeRGBImage(byte[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
makeRGBImage(byte[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
makeSamples() - Method in class loci.formats.tools.MakeTestOmeTiff
MakeTestOmeTiff - Class in loci.formats.tools: Creates sample OME-TIFF datasets according to the given parameters.
MakeTestOmeTiff() - Constructor for class loci.formats.tools.MakeTestOmeTiff
makeUnsigned(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Converts the given BufferedImage into an image with unsigned pixel data.
makeValidIFD(IFD, int, int) - Method in class loci.formats.tiff.TiffSaver: Makes a valid IFD.
MANUFACTURER - Enum constant in enum loci.formats.dicom.DicomAttribute
MANUFACTURER_MODEL_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
map - Variable in class loci.formats.tools.AmiraParameters
MAPPING_RESOURCE - Enum constant in enum loci.formats.dicom.DicomAttribute
MASK_FRAME_NUMBERS - Enum constant in enum loci.formats.dicom.DicomAttribute
MASK_OPERATION - Enum constant in enum loci.formats.dicom.DicomAttribute
MASK_OPERATION_EXPLANATION - Enum constant in enum loci.formats.dicom.DicomAttribute
MASK_SUBPIXEL_SHIFT - Enum constant in enum loci.formats.dicom.DicomAttribute
MASK_SUBTRACTION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
MAX_APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
MAX_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
MECHANICAL_INDEX - Enum constant in enum loci.formats.dicom.DicomAttribute
MEDIA_SOP_CLASS_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
MEDIA_SOP_INSTANCE_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
MEDICAL_ALERTS - Enum constant in enum loci.formats.dicom.DicomAttribute
MEDICAL_RECORD_LOCATOR - Enum constant in enum loci.formats.dicom.DicomAttribute
Memoizer - Class in loci.formats: ReaderWrapper implementation which caches the state of the delegate (including and other ReaderWrapper instances) after Memoizer.setId(String) has been called.
Memoizer() - Constructor for class loci.formats.Memoizer: Constructs a memoizer around a new ImageReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than 100L in milliseconds.
Memoizer(long) - Constructor for class loci.formats.Memoizer: Constructs a memoizer around a new ImageReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer(long, File) - Constructor for class loci.formats.Memoizer: Constructs a memoizer around a new ImageReader creating memo files under the directory argument including the full path of the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer(IFormatReader) - Constructor for class loci.formats.Memoizer: Constructs a memoizer around the given IFormatReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than 100L in milliseconds.
Memoizer(IFormatReader, long) - Constructor for class loci.formats.Memoizer: Constructs a memoizer around the given IFormatReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer(IFormatReader, long, File) - Constructor for class loci.formats.Memoizer: Constructs a memoizer around the given IFormatReader creating memo files under the directory argument including the full path of the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer(IFormatReader, File) - Constructor for class loci.formats.Memoizer: Constructs a memoizer around the given IFormatReader creating memo file under the directory argument including the full path of the original file only if the call to Memoizer.setId(java.lang.String) takes longer than 100L in milliseconds.
Memoizer.Deser - Interface in loci.formats
Memoizer.KryoDeser - Class in loci.formats
mergeChannels(BufferedImage[]) - Static method in class loci.formats.gui.AWTImageTools: Merges the given images into a single multi-channel image.
mergeSubIFDs - Variable in class loci.formats.in.MinimalTiffReader: Merge SubIFDs into the main IFD list.
METERING_MODE - Static variable in class loci.formats.tiff.IFD
MicromanagerReader - Class in loci.formats.in: MicromanagerReader is the file format reader for Micro-Manager files.
MicromanagerReader() - Constructor for class loci.formats.in.MicromanagerReader: Constructs a new Micromanager reader.
MILITARY_RANK - Enum constant in enum loci.formats.dicom.DicomAttribute
MIN_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
MinimalTiffReader - Class in loci.formats.in: MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
MinimalTiffReader() - Constructor for class loci.formats.in.MinimalTiffReader: Constructs a new MinimalTiffReader.
MinimalTiffReader(String, String) - Constructor for class loci.formats.in.MinimalTiffReader: Constructs a new MinimalTiffReader.
MinimalTiffReader(String, String[]) - Constructor for class loci.formats.in.MinimalTiffReader: Constructs a new MinimalTiffReader.
MinMaxCalculator - Class in loci.formats: Logic to compute minimum and maximum values for each channel.
MinMaxCalculator() - Constructor for class loci.formats.MinMaxCalculator: Constructs a MinMaxCalculator around a new image reader.
MinMaxCalculator(IFormatReader) - Constructor for class loci.formats.MinMaxCalculator: Constructs a MinMaxCalculator with the given reader.
minMaxDone - Variable in class loci.formats.MinMaxCalculator: Number of planes for which min/max computations have been completed.
minMaxStore - Variable in class loci.formats.MinMaxCalculator: Consumer of channel global minima and maxima
MJPBCodec - Class in loci.formats.codec: Methods for compressing and decompressing QuickTime Motion JPEG-B data.
MJPBCodec() - Constructor for class loci.formats.codec.MJPBCodec
MJPBCodecOptions - Class in loci.formats.codec: Options for compressing and decompressing MJPB data.
MJPBCodecOptions() - Constructor for class loci.formats.codec.MJPBCodecOptions
MNG_MAGIC_BYTES - Static variable in class loci.formats.in.MNGReader
MNGReader - Class in loci.formats.in: MNGReader is the file format reader for Multiple-image Network Graphics (MNG) files.
MNGReader() - Constructor for class loci.formats.in.MNGReader: Constructs a new MNG reader.
MODALITIES_IN_STUDY - Enum constant in enum loci.formats.dicom.DicomAttribute
MODALITY - Enum constant in enum loci.formats.dicom.DicomAttribute
MODALITY_LUT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
MODALITY_LUT_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
MODEL - Static variable in class loci.formats.tiff.IFD
mouseDragged(MouseEvent) - Method in class loci.formats.gui.ImageViewer: Handles cursor probes.
mouseMoved(MouseEvent) - Method in class loci.formats.gui.ImageViewer: Handles cursor probes.
MPEG_4 - Enum constant in enum loci.formats.codec.CompressionType
MR_ACQUISITION_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
MRDR_RECORD_OFFSET - Enum constant in enum loci.formats.dicom.DicomAttribute
MSRLECodec - Class in loci.formats.codec: Methods for compressing and decompressing data using Microsoft RLE.
MSRLECodec() - Constructor for class loci.formats.codec.MSRLECodec
MSVideoCodec - Class in loci.formats.codec: Methods for compressing and decompressing data using Microsoft Video 1.
MSVideoCodec() - Constructor for class loci.formats.codec.MSVideoCodec
MULTIPLEX_GROUP_TIME_OFFSET - Enum constant in enum loci.formats.dicom.DicomAttribute
myReader - Variable in class loci.formats.gui.ImageViewer: Current format reader.
myWriter - Variable in class loci.formats.gui.ImageViewer: Current format writer.

N

NEW_SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
newOrder - Variable in class loci.formats.AxisGuesser: Adjusted ordering of internal dimensional axes.
newVersionAvailable(String) - Method in class loci.formats.UpgradeChecker: Contact the OME registry and return true if a new version is available.
newVersionAvailable(String, String) - Method in class loci.formats.UpgradeChecker: Contact the OME registry and return true if a new version is available.
nextLetter() - Method in class loci.formats.ResourceNamer: Increments the internal alphabet pointer to the next element of the alphabet.
NIKON - Enum constant in enum loci.formats.tiff.TiffCompression
NikonCodec - Class in loci.formats.codec: This class implements Nikon decompression.
NikonCodec() - Constructor for class loci.formats.codec.NikonCodec
NikonCodecOptions - Class in loci.formats.codec: Options for compressing and decompressing Nikon NEF data.
NikonCodecOptions() - Constructor for class loci.formats.codec.NikonCodecOptions
NL - Static variable in class loci.formats.in.ICSReader: Newline characters.
NO_J2K_MSG - Static variable in class loci.formats.services.JAIIIOServiceImpl
NO_JHDF_MSG - Static variable in class loci.formats.services.JHDFServiceImpl
NoExtensionFileFilter - Class in loci.formats.gui: A file filter that selects files with no extension, for use with a JFileChooser.
NoExtensionFileFilter() - Constructor for class loci.formats.gui.NoExtensionFileFilter
NOMINAL_INTERVAL - Enum constant in enum loci.formats.dicom.DicomAttribute
NOMINAL_SCANNED_PIXEL_SPACING - Enum constant in enum loci.formats.dicom.DicomAttribute
NORMAL_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
noSubresolutions - Variable in class loci.formats.in.MinimalTiffReader
notifyListeners(CacheEvent) - Method in class loci.formats.cache.Cache: Informs listeners of a cache update.
notifyListeners(CacheEvent) - Method in class loci.formats.cache.CacheStrategy: Informs listeners of a cache update.
NRRD_MAGIC_STRING - Static variable in class loci.formats.in.NRRDReader
NRRDReader - Class in loci.formats.in: File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
NRRDReader() - Constructor for class loci.formats.in.NRRDReader: Constructs a new NRRD reader.
nSlider - Variable in class loci.formats.gui.ImageViewer
nStreams - Variable in class loci.formats.tools.AmiraParameters
NTP_SOURCE_ADDRESS - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_AVERAGES - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_DETECTORS - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_ENERGY_WINDOWS - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_EVENT_TIMERS - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_FOCAL_PLANES - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_FRAMES - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_INKS - Static variable in class loci.formats.tiff.IFD
NUMBER_OF_PHASE_ENCODING_STEPS - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_REFERENCES - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_ROTATIONS - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_SLICES - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_STAGES - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_TABLE_BREAK_POINTS - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_TABLE_ENTRIES - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_TOMOSYNTHESIS_SOURCE_IMAGES - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OF_VIEWS_STAGE - Enum constant in enum loci.formats.dicom.DicomAttribute
NUMBER_OPTICAL_PATHS - Enum constant in enum loci.formats.dicom.DicomAttribute
NumberFilter - Class in loci.formats: NumberFilter is a helper filter for FilePattern.findPattern().
NumberFilter(String, String) - Constructor for class loci.formats.NumberFilter: Creates a filter for files containing a numerical block, sandwiched between the given strings.
numBytes - Variable in class loci.formats.out.QTWriter: Total number of pixel bytes.
numDecompositionLevels - Variable in class loci.formats.codec.JPEG2000CodecOptions: The number of decomposition levels as would be provided to: J2KImageWriteParam.setNumDecompositionLevels(int) (WRITE).
numer - Variable in class loci.formats.tiff.TiffRational: Components of the rational's fractional representation.

O

OB - Enum constant in enum loci.formats.dicom.DicomVR
OBFReader - Class in loci.formats.in: OBFReader is the file format reader for Imspector OBF files.
OBFReader() - Constructor for class loci.formats.in.OBFReader
OBJECT - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
OBJECT_DROPPED - Static variable in class loci.formats.cache.CacheEvent: Event type indicating an object has been removed from the cache.
OBJECT_LOADED - Static variable in class loci.formats.cache.CacheEvent: Event type indicating an object has been added to the cache.
OBJECTIVE_LENS_NA - Enum constant in enum loci.formats.dicom.DicomAttribute
OBJECTIVE_LENS_POWER - Enum constant in enum loci.formats.dicom.DicomAttribute
OBS - Static variable in class loci.formats.gui.AWTImageTools: ImageObserver for working with AWT images.
OCCUPATION - Enum constant in enum loci.formats.dicom.DicomAttribute
OD - Enum constant in enum loci.formats.dicom.DicomVR
OECF - Static variable in class loci.formats.tiff.IFD
OF - Enum constant in enum loci.formats.dicom.DicomVR
OFFSET_FIRST_DIRECTORY_RECORD - Enum constant in enum loci.formats.dicom.DicomAttribute
OFFSET_LAST_DIRECTORY_RECORD - Enum constant in enum loci.formats.dicom.DicomAttribute
OFFSET_OF_NEXT_DIRECTORY_RECORD - Enum constant in enum loci.formats.dicom.DicomAttribute
OFFSET_OF_REFERENCED_DIRECTORY - Enum constant in enum loci.formats.dicom.DicomAttribute
offsets - Variable in class loci.formats.out.QTWriter: Vector of plane offsets.
OL - Enum constant in enum loci.formats.dicom.DicomVR
OLD_JPEG - Enum constant in enum loci.formats.tiff.TiffCompression
OLD_TOOLS - Static variable in class loci.formats.UpgradeChecker: Deprecated.
Removed in Bio-Formats 6.9.0
OLYMPUS_JPEG2000 - Enum constant in enum loci.formats.tiff.TiffCompression
OME_TIFF_SUFFIXES - Static variable in class loci.formats.in.OMETiffReader
OME_TOOLS - Static variable in class loci.formats.UpgradeChecker: Name of the OME tools JAR.
omeMeta - Variable in class loci.formats.gui.ImageViewer: Attached OME metadata store, if available.
OMETiffReader - Class in loci.formats.in: OMETiffReader is the file format reader for OME-TIFF files.
OMETiffReader() - Constructor for class loci.formats.in.OMETiffReader: Constructs a new OME-TIFF reader.
OMETiffWriter - Class in loci.formats.out: OMETiffWriter is the file format writer for OME-TIFF files.
OMETiffWriter() - Constructor for class loci.formats.out.OMETiffWriter
OMEXMLReader - Class in loci.formats.in: OMEXMLReader is the file format reader for OME-XML files.
OMEXMLReader() - Constructor for class loci.formats.in.OMEXMLReader: Constructs a new OME-XML reader.
omexmlService - Variable in class loci.formats.gui.ImageViewer: Service for working with OME-XML metadata.
OMEXMLWriter - Class in loci.formats.out: OMEXMLWriter is the file format writer for OME-XML files.
OMEXMLWriter() - Constructor for class loci.formats.out.OMEXMLWriter
OnDemandLongArray - Class in loci.formats.tiff
OnDemandLongArray(RandomAccessInputStream) - Constructor for class loci.formats.tiff.OnDemandLongArray
ONE - Static variable in class loci.formats.AxisGuesser
open() - Method in class loci.formats.tools.EditTiffG
open(String) - Method in class loci.formats.gui.ImageViewer: Opens the given data source using the current format reader.
open(String) - Static method in class loci.formats.tools.EditTiffG
open(String, IFormatReader) - Method in class loci.formats.gui.ImageViewer: Opens from the given data source using the specified reader in a separate thread.
openBufferedImage(int) - Method in class loci.formats.in.TiffJAIReader: Obtains a BufferedImage from the given data source using JAI.
openBytes(int) - Method in class loci.formats.ChannelFiller
openBytes(int) - Method in class loci.formats.ChannelMerger
openBytes(int) - Method in class loci.formats.ChannelSeparator
openBytes(int) - Method in class loci.formats.DimensionSwapper
openBytes(int) - Method in class loci.formats.FileStitcher
openBytes(int) - Method in class loci.formats.MinMaxCalculator
openBytes(int, byte[]) - Method in class loci.formats.ChannelFiller
openBytes(int, byte[]) - Method in class loci.formats.ChannelMerger
openBytes(int, byte[]) - Method in class loci.formats.ChannelSeparator
openBytes(int, byte[]) - Method in class loci.formats.DimensionSwapper
openBytes(int, byte[]) - Method in class loci.formats.FileStitcher
openBytes(int, byte[]) - Method in class loci.formats.MinMaxCalculator
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelFiller
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelMerger
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelSeparator
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.DimensionSwapper
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.FileStitcher
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.APNGReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AVIReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BDVReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BIFormatReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BMPReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellH5Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DicomReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.EPSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FakeReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FitsReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlowSightReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GIFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ICSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IM3Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPEG2000Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KLBReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicromanagerReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MinimalTiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NRRDReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OBFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMETiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMEXMLReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCXReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PGMReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PictReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.QTReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TextReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TiffDelegateReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TileJPEGReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZipReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.MinMaxCalculator
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelFiller
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelMerger
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
openBytes(int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
openBytes(int, int, int, int, int) - Method in class loci.formats.FileStitcher
openBytes(int, int, int, int, int) - Method in class loci.formats.MinMaxCalculator
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelFiller
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelMerger
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelSeparator
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.DimensionSwapper
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.FileStitcher
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.DicomReader
openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelFiller
openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelMerger
openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelSeparator
openCompressedBytes(int, int, int) - Method in class loci.formats.DimensionSwapper
openCompressedBytes(int, int, int) - Method in class loci.formats.FileStitcher
openCompressedBytes(int, int, int) - Method in class loci.formats.in.DicomReader
openFile(File) - Method in class loci.formats.tools.EditTiffG
openFile(File, RandomAccessInputStream) - Method in class loci.formats.tools.EditTiffG
openFile(String) - Static method in class loci.formats.tools.EditTiffG: Deprecated.
openImage(byte[], IFormatReader, int, int) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
openImage(byte[], IFormatReader, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
openImage(int) - Method in class loci.formats.gui.BufferedImageReader: Obtains the specified image from the current file.
openImage(int, int, int, int, int) - Method in class loci.formats.gui.BufferedImageReader: Obtains a sub-image of the specified image, whose upper-left corner is given by (x, y).
openPlane(int, int, int, int, int) - Method in class loci.formats.FileStitcher
openPlane(int, int, int, int, int) - Method in class loci.formats.in.ImageIOReader
openPlane(int, int, int, int, int) - Method in class loci.formats.in.MNGReader
openPlane(int, int, int, int, int) - Method in class loci.formats.in.TextReader
openPlane(int, int, int, int, int) - Method in class loci.formats.in.TiffJAIReader
openRaw() - Method in class loci.formats.in.IM3Reader: Open the current series in raw-mode, returning the interleaved image bytes.
openThumbBytes(int) - Method in class loci.formats.ChannelSeparator
openThumbBytes(int) - Method in class loci.formats.DimensionSwapper
openThumbBytes(int) - Method in class loci.formats.FileStitcher
openThumbBytes(int) - Method in class loci.formats.in.MinimalTiffReader
openThumbImage(int) - Method in class loci.formats.gui.BufferedImageReader: Obtains a thumbnail for the specified image from the current file.
OPERATOR_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
OPERATOR_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
OPTICAL_PATH_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
OPTICAL_PATH_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
OPTICAL_PATH_ID_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
OPTICAL_PATH_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
order - Variable in class loci.formats.cache.CacheStrategy: The order in which planes should be loaded along each axis.
ORDER_CHANGED - Static variable in class loci.formats.cache.CacheEvent: Event type indicating new planar ordering.
ORDER_VALUES - Static variable in class loci.formats.gui.CacheComponent
ORDERS - Static variable in class loci.formats.gui.CacheComponent
ORIENTATION - Static variable in class loci.formats.tiff.IFD
ORIGINAL_SOP_CLASS_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
OTHER_PATIENT_IDS - Enum constant in enum loci.formats.dicom.DicomAttribute
OTHER_PATIENT_NAMES - Enum constant in enum loci.formats.dicom.DicomAttribute
out - Variable in class loci.formats.tiff.TiffSaver: Output stream to use when saving TIFF data.
OUTPUT_POWER - Enum constant in enum loci.formats.dicom.DicomAttribute
OV - Enum constant in enum loci.formats.dicom.DicomVR
OVERLAY_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
OVERLAY_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
overwriteComment(RandomAccessInputStream, Object) - Method in class loci.formats.tiff.TiffSaver: Convenience method for overwriting a file's first ImageDescription.
overwriteIFDOffset(RandomAccessInputStream, long, long) - Method in class loci.formats.tiff.TiffSaver
overwriteIFDValue(RandomAccessInputStream, int, int, Object) - Method in class loci.formats.tiff.TiffSaver: Surgically overwrites an existing IFD value with the given one.
overwriteIFDValue(RandomAccessInputStream, long, int, Object) - Method in class loci.formats.tiff.TiffSaver: Surgically overwrites an existing IFD value with the given one.
overwriteIFDValue(RandomAccessInputStream, long, int, Object, boolean) - Method in class loci.formats.tiff.TiffSaver: Surgically overwrites an existing IFD value with the given one.
overwriteLastIFDOffset(RandomAccessInputStream) - Method in class loci.formats.tiff.TiffSaver
OW - Enum constant in enum loci.formats.dicom.DicomVR

P

PACK_BITS - Enum constant in enum loci.formats.tiff.TiffCompression
PackbitsCodec - Class in loci.formats.codec: This class implements packbits decompression.
PackbitsCodec() - Constructor for class loci.formats.codec.PackbitsCodec
pad - Variable in class loci.formats.out.QTWriter: Number of padding bytes in each row.
padImage(byte[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools: Pads (or crops) the byte array to the given width and height.
padImage(double[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools: Pads (or crops) the double array to the given width and height.
padImage(float[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools: Pads (or crops) the float array to the given width and height.
padImage(int[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools: Pads (or crops) the int array to the given width and height.
padImage(short[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools: Pads (or crops) the short array to the given width and height.
padImage(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools: Pads (or crops) the image to the given width and height.
PAGE_NAME - Static variable in class loci.formats.tiff.IFD
PAGE_NUMBER - Static variable in class loci.formats.tiff.IFD
PAGE_NUMBER_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
paintComponent(Graphics) - Method in class loci.formats.gui.CacheIndicator
PALETTE - Enum constant in enum loci.formats.codec.JPEG2000BoxType
PALETTE_COLOR_LUT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
PALETTE_LUT_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
pane - Variable in class loci.formats.gui.ImageViewer
parent - Variable in class loci.formats.dicom.DicomTag
parseString(IRandomAccess) - Static method in class loci.formats.in.IM3Reader: Parse a string from the IM3 file at the current file pointer loc
PARTIAL_VIEW - Enum constant in enum loci.formats.dicom.DicomAttribute
PARTIAL_VIEW_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
PassthroughCodec - Class in loci.formats.codec: A codec which just returns the exact data it was given, performing no compression or decompression.
PassthroughCodec() - Constructor for class loci.formats.codec.PassthroughCodec
pathToPosition - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
PATIENT_ADDRESS - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_AGE - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_BIRTH_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_BIRTH_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_BIRTH_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_COMMENTS - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_INSURANCE_PLAN_CODE - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_MOTHER_BIRTH_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_ORIENTATION - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_POSITION - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_PRIMARY_LANGUAGE_CODE - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_PRIMARY_LANGUAGE_MODIFIER - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_RELIGIOUS_PREFERENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_SEX - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_SIZE - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_TELEPHONE_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
PATIENT_WEIGHT - Enum constant in enum loci.formats.dicom.DicomAttribute
PCX_MAGIC_BYTE - Static variable in class loci.formats.in.PCXReader
PCXReader - Class in loci.formats.in: PCXReader is the file format reader for PCX files (originally used by PC Paintbrush; now used in Zeiss' LSM Image Browser).
PCXReader() - Constructor for class loci.formats.in.PCXReader: Constructs a new PCX reader.
PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
PERCENT_PHASE_FOV - Enum constant in enum loci.formats.dicom.DicomAttribute
PERCENT_SAMPLING - Enum constant in enum loci.formats.dicom.DicomAttribute
PGM_MAGIC_CHAR - Static variable in class loci.formats.in.PGMReader
PGMReader - Class in loci.formats.in: PGMReader is the file format reader for Portable Gray Map (PGM) images.
PGMReader() - Constructor for class loci.formats.in.PGMReader: Constructs a new PGMReader.
PHOSPHOR_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
PhotoInterp - Enum in loci.formats.tiff: Utility class for working with TIFF photometric interpretations.
PHOTOMETRIC_INTERPRETATION - Enum constant in enum loci.formats.dicom.DicomAttribute
PHOTOMETRIC_INTERPRETATION - Static variable in class loci.formats.tiff.IFD
PHYSICAL_DELTA_X - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICAL_DELTA_Y - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICAL_UNITS_X_DIRECTION - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICAL_UNITS_Y_DIRECTION - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICIAN_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICIAN_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICIAN_READING - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICIAN_READING_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICIANS - Enum constant in enum loci.formats.dicom.DicomAttribute
PHYSICIANS_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
PictReader - Class in loci.formats.in: PictReader is the file format reader for Apple PICT files.
PictReader() - Constructor for class loci.formats.in.PictReader: Constructs a new PICT reader.
PIXEL_ASPECT_RATIO - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_BANDWIDTH - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_COMPONENT_DATA_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_COMPONENT_MASK - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_COMPONENT_ORGANIZATION - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_COMPONENT_PHYSICAL_UNITS - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_COMPONENT_RANGE_START - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_COMPONENT_RANGE_STOP - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_DATA_LENGTH - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_INTENSITY_RELATIONSHIP - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_MEASURES_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_PADDING_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_PRESENTATION - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_REPRESENTATION - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_SIGN - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_SPACING - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_VALUE_TRANSFORMATION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
PIXEL_X_DIMENSION - Static variable in class loci.formats.tiff.IFD
PIXEL_Y_DIMENSION - Static variable in class loci.formats.tiff.IFD
pixelSizeX - Variable in class loci.formats.dicom.DicomFileInfo
pixelSizeY - Variable in class loci.formats.dicom.DicomFileInfo
pixelSizeZ - Variable in class loci.formats.dicom.DicomFileInfo
PLACEHOLDER - Enum constant in enum loci.formats.codec.JPEG2000BoxType
PLANAR_CONFIGURATION - Enum constant in enum loci.formats.dicom.DicomAttribute
PLANAR_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
PLANE_POSITION_SLIDE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
planeMax - Variable in class loci.formats.MinMaxCalculator: Max values for each plane.
planeMin - Variable in class loci.formats.MinMaxCalculator: Min values for each plane.
PLANES - Enum constant in enum loci.formats.dicom.DicomAttribute
plate - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
PLATE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
PLATE - Static variable in class loci.formats.ResourceNamer
PLATE_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
PLATE_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
PLM - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
PLT - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
PN - Enum constant in enum loci.formats.dicom.DicomVR
POC - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
populateMetadataStore(String[]) - Method in class loci.formats.in.MicromanagerReader
pos(int) - Method in class loci.formats.cache.CacheStrategy: Shortcut for converting rasterized position to N-D position.
pos(int, int[]) - Method in class loci.formats.cache.CacheStrategy: Shortcut for converting rasterized position to N-D position, using the given array instead of allocating a new one.
POSITION_CHANGED - Static variable in class loci.formats.cache.CacheEvent: Event type indicating an updated current dimensional position.
POSITIONER_MOTION - Enum constant in enum loci.formats.dicom.DicomAttribute
POSITIONER_PRIMARY_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
POSITIONER_PRIMARY_ANGLE_INCREMENT - Enum constant in enum loci.formats.dicom.DicomAttribute
POSITIONER_SECONDARY_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
POSITIONER_SECONDARY_ANGLE_INCREMENT - Enum constant in enum loci.formats.dicom.DicomAttribute
POSITIONER_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
positionX - Variable in class loci.formats.dicom.DicomFileInfo
positionY - Variable in class loci.formats.dicom.DicomFileInfo
positionZ - Variable in class loci.formats.dicom.DicomFileInfo
POSTPROCESSING_FUNCTION - Enum constant in enum loci.formats.dicom.DicomAttribute
PPM - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
PPT - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
PREDICTED_CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
PREDICTOR - Static variable in class loci.formats.tiff.IFD
PREFERRED_PLAYBACK_SEQUENCING - Enum constant in enum loci.formats.dicom.DicomAttribute
PREFIX_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
PREGNANCY_STATUS - Enum constant in enum loci.formats.dicom.DicomAttribute
prepareToWriteImage(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter: Performs the preparation for work prior to the usage of the TIFF saver.
preprocess(RandomAccessInputStream) - Method in class loci.formats.codec.JPEGTileDecoder: Pre-process the stream to make sure that the image width and height are non-zero.
PRESENTATION_INTENT_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
PRESENTATION_LUT_SHAPE - Enum constant in enum loci.formats.dicom.DicomAttribute
preserveCreator() - Method in class loci.formats.out.OMETiffWriter: Get the value of the OMETiffWriter.CREATOR_KEY option.
preserveCreator() - Method in class loci.formats.out.OMEXMLWriter: Get the value of the OMEXMLWriter.CREATOR_KEY option.
PreviewPane - Class in loci.formats.gui: PreviewPane is a panel for use as a JFileChooser accessory, displaying a thumbnail for the selected image, loaded in a separate thread.
PreviewPane(JFileChooser) - Constructor for class loci.formats.gui.PreviewPane: Constructs a preview pane for the given file chooser.
PRIMARY_ANATOMIC_STRUCTURE_MODIFIER - Enum constant in enum loci.formats.dicom.DicomAttribute
PRIMARY_ANATOMIC_STRUCTURE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
PRIMARY_CHROMATICITIES - Static variable in class loci.formats.tiff.IFD
printIFD() - Method in class loci.formats.tiff.IFD: Prints the contents of this IFD.
priorities - Variable in class loci.formats.cache.CacheStrategy: Priority for caching each axis.
PRIORITIES - Static variable in class loci.formats.gui.CacheComponent
PRIORITIES_CHANGED - Static variable in class loci.formats.cache.CacheEvent: Event type indicating new axis priorities.
PRIORITY_VALUES - Static variable in class loci.formats.gui.CacheComponent
PRIVATE_RECORD_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
probeLabel - Variable in class loci.formats.gui.ImageViewer
PROCEDURE_CODE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
PROCESSING_FUNCTION - Enum constant in enum loci.formats.dicom.DicomAttribute
PROJECTION_EPONYMOUS_NAME_CODE - Enum constant in enum loci.formats.dicom.DicomAttribute
PROJECTION_PREFIX - Static variable in class loci.formats.in.KLBReader
PROJECTION_SUFFIX - Static variable in class loci.formats.in.KLBReader
propertyChange(PropertyChangeEvent) - Method in class loci.formats.gui.PreviewPane: Property change event, to listen for when a new file is selected, or the file chooser closes.
PROPRIETARY_DEFLATE - Enum constant in enum loci.formats.tiff.TiffCompression
PROTOCOL_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
PULSE_REPETITION_FREQUENCY - Enum constant in enum loci.formats.dicom.DicomAttribute
put(String, boolean) - Method in class loci.formats.in.BaseTiffReader
put(String, byte) - Method in class loci.formats.in.BaseTiffReader
put(String, char) - Method in class loci.formats.in.BaseTiffReader
put(String, double) - Method in class loci.formats.in.BaseTiffReader
put(String, float) - Method in class loci.formats.in.BaseTiffReader
put(String, int) - Method in class loci.formats.in.BaseTiffReader
put(String, long) - Method in class loci.formats.in.BaseTiffReader
put(String, short) - Method in class loci.formats.in.BaseTiffReader
put(String, Object) - Method in class loci.formats.in.BaseTiffReader
put(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
putDouble(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
putIFDValue(int, int) - Method in class loci.formats.tiff.IFD: Adds a directory entry of type SHORT to this IFD.
putIFDValue(int, long) - Method in class loci.formats.tiff.IFD: Adds a directory entry of type LONG to this IFD.
putIFDValue(int, short) - Method in class loci.formats.tiff.IFD: Adds a directory entry of type BYTE to this IFD.
putIFDValue(int, Object) - Method in class loci.formats.tiff.IFD: Adds a directory entry to this IFD.
putInt(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
putString(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
PVC_REJECTION - Enum constant in enum loci.formats.dicom.DicomAttribute
PyramidOMETiffWriter - Class in loci.formats.out: PyramidOMETiffWriter is the file format writer for pyramid OME-TIFF files.
PyramidOMETiffWriter() - Constructor for class loci.formats.out.PyramidOMETiffWriter

Q

QCC - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
QCD - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
QQ - Enum constant in enum loci.formats.dicom.DicomVR
QTReader - Class in loci.formats.in: QTReader is the file format reader for QuickTime movie files.
QTReader() - Constructor for class loci.formats.in.QTReader: Constructs a new QuickTime reader.
QTRLECodec - Class in loci.formats.codec: Methods for compressing and decompressing data using QuickTime RLE.
QTRLECodec() - Constructor for class loci.formats.codec.QTRLECodec
QTWriter - Class in loci.formats.out: QTWriter is the file format writer for uncompressed QuickTime movie files.
QTWriter() - Constructor for class loci.formats.out.QTWriter
quality - Variable in class loci.formats.out.QTWriter: The quality to use.
QUALITY_CONTROL_IMAGE - Enum constant in enum loci.formats.dicom.DicomAttribute
QUALITY_HIGH - Static variable in class loci.formats.out.QTWriter: Value indicating High quality.
QUALITY_LOW - Static variable in class loci.formats.out.QTWriter: Value indicating Low quality.
QUALITY_MAXIMUM - Static variable in class loci.formats.out.QTWriter: Value indicating Maximum quality.
QUALITY_NORMAL - Static variable in class loci.formats.out.QTWriter: Value indicating Normal quality.
QUERY_LEVEL - Enum constant in enum loci.formats.dicom.DicomAttribute
quit() - Method in class loci.formats.cache.CacheUpdater

R

r - Variable in class loci.formats.in.TiffJAIReader: Reflection tool for JAI calls.
R_WAVE_POINTER - Enum constant in enum loci.formats.dicom.DicomAttribute
R_WAVE_TIME_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIAL_POSITION - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIATION_MODE - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIATION_SETTING - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIONUCLIDE_HALF_LIFE - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIONUCLIDE_POSITRON_FRACTION - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIONUCLIDE_TOTAL_DOSE - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIOPHARMACEUTICAL - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIOPHARMACEUTICAL_ROUTE - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIOPHARMACEUTICAL_SPECIFIC_ACTIVITY - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIOPHARMACEUTICAL_START_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIOPHARMACEUTICAL_STOP_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIOPHARMACEUTICAL_VOLUME - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIUS_OF_CIRCULAR_COLLIMATOR - Enum constant in enum loci.formats.dicom.DicomAttribute
RADIUS_OF_CIRCULAR_SHUTTER - Enum constant in enum loci.formats.dicom.DicomAttribute
range - Variable in class loci.formats.cache.CacheStrategy: Number of planes to cache along each axis.
RANGE_CHANGED - Static variable in class loci.formats.cache.CacheEvent: Event type indicating new planar ordering.
raster(int[]) - Method in class loci.formats.cache.CacheStrategy: Shortcut for converting N-D position to rasterized position.
RATIONAL - Enum constant in enum loci.formats.tiff.IFDType
readByte() - Method in class loci.formats.tools.AmiraParameters
readByteArray(String) - Method in interface loci.formats.services.JHDFService: Reads a multi-dimensional byte array from path.
readByteArray(String) - Method in class loci.formats.services.JHDFServiceImpl
readByteBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService: Reads a multi-dimensional sub-block byte array from path.
readByteBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
readCompoundArrayDataMap(String) - Method in interface loci.formats.services.JHDFService: Reads Compound array of any type
readCompoundArrayDataMap(String) - Method in class loci.formats.services.JHDFServiceImpl
readDoubleArray(int) - Method in class loci.formats.tools.AmiraParameters
reader - Variable in class loci.formats.cache.CacheSource: Reader from which to draw image planes.
reader - Variable in class loci.formats.gui.BufferedImageSource: Image reader from which to draw BufferedImages.
reader - Variable in class loci.formats.gui.PreviewPane: Reader for use when loading thumbnails.
readFile(String) - Method in class loci.formats.tools.AmiraParameters
readFile(RandomAccessInputStream) - Method in class loci.formats.tools.AmiraParameters
readImage(InputStream) - Method in interface loci.formats.services.JAIIIOService: Reads an image using JAI Image I/O using the JPEG 2000 codec.
readImage(InputStream) - Method in class loci.formats.services.JAIIIOServiceImpl
readImage(InputStream, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService: Reads an image using JAI Image I/O using the JPEG 2000 codec.
readImage(InputStream, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
readIntArray() - Method in class loci.formats.tools.AmiraParameters
readIntArray(int) - Method in class loci.formats.tools.AmiraParameters
readIntArray(String) - Method in interface loci.formats.services.JHDFService: Reads a multi-dimensional int array from path.
readIntArray(String) - Method in class loci.formats.services.JHDFServiceImpl
readIntBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService: Reads a multi-dimensional sub-block int array from path.
readIntBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
readKey() - Method in class loci.formats.tools.AmiraParameters
readMap() - Method in class loci.formats.tools.AmiraParameters
readNumber() - Method in class loci.formats.tools.AmiraParameters
readNumberArray() - Method in class loci.formats.tools.AmiraParameters
readQuotedString() - Method in class loci.formats.tools.AmiraParameters
readRaster(InputStream) - Method in interface loci.formats.services.JAIIIOService: Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
readRaster(InputStream) - Method in class loci.formats.services.JAIIIOServiceImpl
readRaster(InputStream, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService: Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
readRaster(InputStream, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
readShortBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService: Reads a multi-dimensional sub-block short array from path.
readShortBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
readSpecialPixels(byte[]) - Static method in class loci.formats.in.FakeReader: Read byte-encoded metadata from the given plane.
readSpecialPixels(byte[], int, boolean) - Static method in class loci.formats.in.FakeReader: Read byte-encoded metadata from the given plane.
readSpecialPixels(byte[], int, boolean, int, boolean) - Static method in class loci.formats.in.FakeReader: Read byte-encoded metadata from the given plane.
readStringArray(String) - Method in interface loci.formats.services.JHDFService: Reads String array array from path.
readStringArray(String) - Method in class loci.formats.services.JHDFServiceImpl
readTagSource(String) - Method in class loci.formats.dicom.DicomJSONProvider
readTagSource(String) - Method in interface loci.formats.dicom.ITagProvider: Read tags from the given location.
readTopLevel() - Method in class loci.formats.tools.AmiraParameters
recache() - Method in class loci.formats.cache.Cache: Updates all planes on the load list.
recache(int) - Method in class loci.formats.cache.Cache: Updates the given plane.
RECEIVE_COIL_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
RECOGNITION_CODE - Enum constant in enum loci.formats.dicom.DicomAttribute
RECOMMENDED_ABSENT_PIXEL_CIELAB_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
RECOMMENDED_DISPLAY_FRAMERATE - Enum constant in enum loci.formats.dicom.DicomAttribute
RECOMMENDED_VIEWING_MODE - Enum constant in enum loci.formats.dicom.DicomAttribute
RECONSTRUCTION_DIAMETER - Enum constant in enum loci.formats.dicom.DicomAttribute
RECORD_IN_USE_FLAG - Enum constant in enum loci.formats.dicom.DicomAttribute
RectangleStrategy - Class in loci.formats.cache: A rectangle strategy caches planes extending from the the current dimensional position along each axis and combination of axes.
RectangleStrategy(int[]) - Constructor for class loci.formats.cache.RectangleStrategy: Constructs a rectangle strategy.
RECTIFICATION_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
RED_LUT_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
RED_LUT_DESCRIPTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
reduce() - Method in class loci.formats.tiff.TiffRational: Reduces this rational's fraction to lowest terms.
REFERENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCE_BLACK_WHITE - Static variable in class loci.formats.tiff.IFD
REFERENCE_GRAYSCALE_PRESENTATION_STATE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCE_PIXEL_PHYSICAL_VALUE_X - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCE_PIXEL_PHYSICAL_VALUE_Y - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCE_PIXEL_X0 - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCE_PIXEL_Y0 - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_CURVE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_FILE_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_FRAME_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_IMAGE_EVIDENCE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_IMAGE_NAVIGATION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_IMAGE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_INSTANCE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_OVERLAY_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_PATIENT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_PERFORMED_PROCEDURE_STEP - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_RAW_DATA_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_RELATED_SOP_CLASS_UID_FILE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_RESULTS_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_SERIES_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_SOP_CLASS_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_SOP_CLASS_UID_FILE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_SOP_INSTANCE_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_SOP_INSTANCE_UID_FILE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_SOP_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_STUDY_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_TRANSFER_SYNTAX_UID_FILE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_VISIT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERENCED_WAVEFORM_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERRING_PHYSICIAN_ADDRESS - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERRING_PHYSICIAN_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERRING_PHYSICIAN_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
REFERRING_PHYSICIAN_TELEPHONE - Enum constant in enum loci.formats.dicom.DicomAttribute
refresher - Variable in class loci.formats.gui.PreviewPane: Method for syncing the view to the model.
region - Variable in class loci.formats.dicom.DicomTile
REGION_DATA_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
REGION_FLAGS - Enum constant in enum loci.formats.dicom.DicomAttribute
REGION_LOCATION_MAX_X1 - Enum constant in enum loci.formats.dicom.DicomAttribute
REGION_LOCATION_MAX_Y1 - Enum constant in enum loci.formats.dicom.DicomAttribute
REGION_LOCATION_MIN_X0 - Enum constant in enum loci.formats.dicom.DicomAttribute
REGION_LOCATION_MIN_Y0 - Enum constant in enum loci.formats.dicom.DicomAttribute
REGION_OF_RESIDENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
REGION_SPATIAL_FORMAT - Enum constant in enum loci.formats.dicom.DicomAttribute
REGISTRY - Static variable in class loci.formats.UpgradeChecker: Location of the OME registry.
REGISTRY_IMAGEJ - Static variable in class loci.formats.UpgradeChecker: Registry ID identifying usage of Bio-Formats in ImageJ.
REGISTRY_LIBRARY - Static variable in class loci.formats.UpgradeChecker: Registry ID identifying usage of Bio-Formats as a library in general.
RELATED_SERIES_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
RELATED_SOP_CLASS_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
RELATED_SOUND_FILE - Static variable in class loci.formats.tiff.IFD
RELATIVE_XRAY_EXPOSURE - Enum constant in enum loci.formats.dicom.DicomAttribute
removeCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
removeCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter: Removes a listener for status update events.
removeCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
reopenFile() - Method in class loci.formats.FileStitcher
reopenFile() - Method in class loci.formats.in.BDVReader
reopenFile() - Method in class loci.formats.in.CellH5Reader
reopenFile() - Method in class loci.formats.in.FakeReader
reopenFile() - Method in class loci.formats.in.FlowSightReader
reopenFile() - Method in class loci.formats.in.ICSReader
reopenFile() - Method in class loci.formats.in.MinimalTiffReader
reopenFile() - Method in class loci.formats.in.OMETiffReader
reopenFile() - Method in class loci.formats.in.TileJPEGReader
reopenFile() - Method in class loci.formats.in.ZipReader
reorder(int) - Method in class loci.formats.DimensionSwapper
REPETITION_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
REPLACE - Enum constant in enum loci.formats.dicom.ResolutionStrategy
REPRESENTATIVE_FRAME_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
RESCALE_INTERCEPT - Enum constant in enum loci.formats.dicom.DicomAttribute
RESCALE_SLOPE - Enum constant in enum loci.formats.dicom.DicomAttribute
RESCALE_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
RESERVED - Enum constant in enum loci.formats.dicom.DicomVR
RESERVED_DELIMITER_MARKER_MAX - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
RESERVED_DELIMITER_MARKER_MIN - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
reset() - Method in class loci.formats.cache.Cache: Reallocates the cache.
resLabel - Variable in class loci.formats.gui.PreviewPane: Labels containing thumbnail and dimensional information.
resolution - Variable in class loci.formats.codec.JPEG2000CodecOptions: The resolution level as would be provided to: J2KImageReadParam.setResolution(int) (READ).
RESOLUTION - Enum constant in enum loci.formats.codec.JPEG2000BoxType
RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
ResolutionStrategy - Enum in loci.formats.dicom
ResourceNamer - Class in loci.formats: Utility class helping with generating human-readable resource names based on alphanumeric indexing.
ResourceNamer(int) - Constructor for class loci.formats.ResourceNamer
RESPONSIBLE_ORGANIZATION - Enum constant in enum loci.formats.dicom.DicomAttribute
restartAlphabet() - Method in class loci.formats.ResourceNamer: Resets the internal state of the class so that it starts alphabet generation from the first letter (ASCII A).
resText - Variable in class loci.formats.gui.PreviewPane
resTip - Variable in class loci.formats.gui.PreviewPane
RETRIEVE_TITLE - Enum constant in enum loci.formats.dicom.DicomAttribute
REUSE - Static variable in class loci.formats.tiff.IFD
RGB - Enum constant in enum loci.formats.tiff.PhotoInterp
RGB_PALETTE - Enum constant in enum loci.formats.tiff.PhotoInterp
RGN - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
ROTATION_DIRECTION - Enum constant in enum loci.formats.dicom.DicomAttribute
ROTATION_OF_SCANNED_FILM - Enum constant in enum loci.formats.dicom.DicomAttribute
row - Variable in class loci.formats.tools.AmiraParameters
ROW_POSITION_IN_MATRIX - Enum constant in enum loci.formats.dicom.DicomAttribute
rowBytes - Variable in class loci.formats.in.PictReader: Number of bytes in a row of pixel data (variable).
ROWS - Enum constant in enum loci.formats.dicom.DicomAttribute
ROWS_PER_STRIP - Static variable in class loci.formats.tiff.IFD
RPZACodec - Class in loci.formats.codec: Implements encoding and decoding methods for Apple RPZA.
RPZACodec() - Constructor for class loci.formats.codec.RPZACodec
run() - Method in class loci.formats.cache.CacheUpdater
run() - Method in class loci.formats.gui.DataConverter
run() - Method in class loci.formats.gui.ImageViewer: Handles animation.
run() - Method in class loci.formats.gui.PreviewPane: Thumbnail loading routine.
RUN - Static variable in class loci.formats.ResourceNamer

S

S_AXIS - Static variable in class loci.formats.AxisGuesser: Axis type for series.
S_MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
S_MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
S_PREFIXES - Static variable in class loci.formats.AxisGuesser: Prefixes indicating series dimension.
SAMPLE_FORMAT - Static variable in class loci.formats.tiff.IFD
SAMPLES_PER_PIXEL - Enum constant in enum loci.formats.dicom.DicomAttribute
SAMPLES_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
SAMPLES_PER_PIXEL_USED - Enum constant in enum loci.formats.dicom.DicomAttribute
SAR - Enum constant in enum loci.formats.dicom.DicomAttribute
SATURATION - Static variable in class loci.formats.tiff.IFD
save() - Method in class loci.formats.tools.EditTiffG
save(String) - Method in class loci.formats.gui.ImageViewer: Saves the current images to the given destination using the current format writer.
save(String, IFormatWriter) - Method in class loci.formats.gui.ImageViewer: Saves to the given data destination using the specified writer in a separate thread.
saveBytes(int, byte[]) - Method in class loci.formats.out.CellH5Writer: Saves the given image to the specified (possibly already open) file.
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.APNGWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.AVIWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.CellH5Writer
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.DicomWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.EPSWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ICSWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JavaWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMEXMLWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.QTWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.TiffWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.V3DrawWriter
saveBytes(int, byte[], IFD) - Method in class loci.formats.out.TiffWriter: Saves the given image to the specified (possibly already open) file.
saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.PyramidOMETiffWriter
saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter: Saves the given image to the specified series in the current file.
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.DicomWriter
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.TiffWriter
saveFile(File) - Method in class loci.formats.tools.EditTiffG
saveImage(int, BufferedImage) - Method in class loci.formats.gui.BufferedImageWriter: Saves the given BufferedImage to the current file.
saveImage(int, BufferedImage, int, int, int, int) - Method in class loci.formats.gui.BufferedImageWriter: Saves the given BufferedImage to the current file.
saveMemo() - Method in class loci.formats.Memoizer: Save a reader including all reader wrappers inside a memo file.
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
saveReader(IFormatReader) - Method in interface loci.formats.Memoizer.Deser
saveReader(IFormatReader) - Method in class loci.formats.Memoizer.KryoDeser
saveReleaseVersion(String) - Method in interface loci.formats.Memoizer.Deser
saveReleaseVersion(String) - Method in class loci.formats.Memoizer.KryoDeser
saveRevision(String) - Method in interface loci.formats.Memoizer.Deser
saveRevision(String) - Method in class loci.formats.Memoizer.KryoDeser
saveStart(File) - Method in interface loci.formats.Memoizer.Deser
saveStart(File) - Method in class loci.formats.Memoizer.KryoDeser
saveStop() - Method in interface loci.formats.Memoizer.Deser
saveStop() - Method in class loci.formats.Memoizer.KryoDeser
saveVersion(Integer) - Method in interface loci.formats.Memoizer.Deser
saveVersion(Integer) - Method in class loci.formats.Memoizer.KryoDeser
sb - Variable in class loci.formats.gui.ImageViewer
SBYTE - Enum constant in enum loci.formats.tiff.IFDType
scale(BufferedImage, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools: Scales the image using the most appropriate API, with the resultant image having the same color model as the original image.
scale2D(BufferedImage, int, int, Object, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools: Scales the image using the Java2D API, with the resultant image optimized for the given graphics configuration.
scale2D(BufferedImage, int, int, Object, ColorModel) - Static method in class loci.formats.gui.AWTImageTools: Scales the image using the Java2D API, with the resultant image having the given color model.
scaleAWT(BufferedImage, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Scales the image using the AWT Image API.
SCAN_ARC - Enum constant in enum loci.formats.dicom.DicomAttribute
SCAN_LENGTH - Enum constant in enum loci.formats.dicom.DicomAttribute
SCAN_OPTIONS - Enum constant in enum loci.formats.dicom.DicomAttribute
SCAN_VELOCITY - Enum constant in enum loci.formats.dicom.DicomAttribute
scanData(byte[], int, boolean) - Static method in class loci.formats.ImageTools: Scan a plane for the channel min and max values.
SCANNING_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
SCENE_CAPTURE_TYPE - Static variable in class loci.formats.tiff.IFD
SCENE_TYPE - Static variable in class loci.formats.tiff.IFD
SECONDARY_CAPTURE_DEVICE_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
SECONDARY_CAPTURE_DEVICE_MANUFACTURER - Enum constant in enum loci.formats.dicom.DicomAttribute
SECONDARY_CAPTURE_DEVICE_MODEL_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
SECONDARY_CAPTURE_DEVICE_SOFTWARE_VERSION - Enum constant in enum loci.formats.dicom.DicomAttribute
SEGMENTATION_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
SEGMENTED_BLUE_LUT_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
SEGMENTED_GREEN_LUT_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
SEGMENTED_RED_LUT_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
SENSING_METHOD - Static variable in class loci.formats.tiff.IFD
SENSITIVITY - Enum constant in enum loci.formats.dicom.DicomAttribute
SEQUENCE_DELIMITATION_ITEM - Enum constant in enum loci.formats.dicom.DicomAttribute
SEQUENCE_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
SEQUENCE_OF_ULTRASOUND_REGIONS - Enum constant in enum loci.formats.dicom.DicomAttribute
SEQUENCE_VARIANT - Enum constant in enum loci.formats.dicom.DicomAttribute
ser - Variable in class loci.formats.Memoizer
SERIES_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
SERIES_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
SERIES_INSTANCE_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
SERIES_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
SERIES_PREFIXES - Static variable in class loci.formats.in.KLBReader
SERIES_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
seriesToCoreIndex(int) - Method in class loci.formats.FileStitcher
seriesToIFD - Variable in class loci.formats.in.MinimalTiffReader
setAssumeEqualStrips(boolean) - Method in class loci.formats.tiff.TiffParser: Sets whether or not to assume that strips are of equal size.
setAxisTypes(int[]) - Method in class loci.formats.AxisGuesser: Sets the axis type for each dimensional block.
setAxisTypes(int[]) - Method in class loci.formats.FileStitcher: Sets the axis type for each dimensional block.
setBigTiff(boolean) - Method in class loci.formats.out.DicomWriter: Sets whether or not BigTIFF files should be written.
setBigTiff(boolean) - Method in class loci.formats.out.TiffWriter: Sets whether or not BigTIFF files should be written.
setBigTiff(boolean) - Method in class loci.formats.tiff.TiffSaver: Sets whether or not BigTIFF data should be written.
setCanChangePattern(boolean) - Method in class loci.formats.FileStitcher
setCanDetectBigTiff(boolean) - Method in class loci.formats.out.TiffWriter: Sets whether or not BigTIFF can be used automatically based upon the input data size (true by default).
setCanDoUpgradeCheck(boolean) - Method in class loci.formats.UpgradeChecker: Set whether or not we are ever allowed to perform an upgrade check.
setCodec(int) - Method in class loci.formats.out.QTWriter: Sets the encoded movie's codec.
setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffParser: Sets the codec options to be used when decompressing pixel data.
setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffSaver: Sets the codec options.
setCoreIndex(int) - Method in class loci.formats.FileStitcher
setCurrentPos(int[]) - Method in class loci.formats.cache.Cache: Sets the current dimensional position.
setDoCaching(boolean) - Method in class loci.formats.tiff.TiffParser: Sets whether or not IFD entries should be cached.
setDocument(Document) - Method in class loci.formats.gui.XMLWindow: Displays XML from the given document.
setElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
setElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
setElem(int, int, int) - Method in class loci.formats.gui.SignedByteBuffer
setElem(int, int, int) - Method in class loci.formats.gui.SignedShortBuffer
setElem(int, int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
setElemDouble(int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
setElemDouble(int, int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
setElemFloat(int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
setElemFloat(int, int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
setEncoding(String) - Method in class loci.formats.tiff.TiffParser: Sets the encoding to use for tags with ASCII values.
setExtraMetadata(String) - Method in class loci.formats.out.DicomWriter
setExtraMetadata(String) - Method in interface loci.formats.out.IExtraMetadataWriter: Provide additional metadata that should be written as part of this dataset.
setFile(String) - Method in interface loci.formats.services.JHDFService: Initializes the service on a given file path.
setFile(String) - Method in class loci.formats.services.JHDFServiceImpl
setFileForWrite(String) - Method in interface loci.formats.services.JHDFService: Initializes the service on a given file path.
setFileForWrite(String) - Method in class loci.formats.services.JHDFServiceImpl
setFilled(boolean) - Method in class loci.formats.ChannelFiller: Toggles whether the indices should be factored out.
setFlattenedResolutions(boolean) - Method in class loci.formats.FileStitcher
setFlattenedResolutions(boolean) - Method in class loci.formats.in.FilePatternReader
setGroupFiles(boolean) - Method in class loci.formats.FileStitcher
setGroupFiles(boolean) - Method in class loci.formats.in.FilePatternReader
setGroupFiles(boolean) - Method in class loci.formats.in.ZipReader
setId(String) - Method in class loci.formats.ChannelFiller
setId(String) - Method in class loci.formats.ChannelMerger
setId(String) - Method in class loci.formats.ChannelSeparator
setId(String) - Method in class loci.formats.DimensionSwapper
setId(String) - Method in class loci.formats.FileStitcher
setId(String) - Method in class loci.formats.in.JPEGReader
setId(String) - Method in class loci.formats.in.TiffDelegateReader
setId(String) - Method in class loci.formats.Memoizer
setId(String) - Method in class loci.formats.out.APNGWriter
setId(String) - Method in class loci.formats.out.AVIWriter
setId(String) - Method in class loci.formats.out.CellH5Writer
setId(String) - Method in class loci.formats.out.DicomWriter
setId(String) - Method in class loci.formats.out.ICSWriter
setId(String) - Method in class loci.formats.out.JavaWriter
setId(String) - Method in class loci.formats.out.OMETiffWriter
setId(String) - Method in class loci.formats.out.OMEXMLWriter
setId(String) - Method in class loci.formats.out.QTWriter
setId(String) - Method in class loci.formats.out.TiffWriter
setId(String) - Method in class loci.formats.out.V3DrawWriter
setImages(BufferedImage[]) - Method in class loci.formats.gui.ImageViewer: Sets the viewer to display the given images.
setImages(IFormatReader, BufferedImage[]) - Method in class loci.formats.gui.ImageViewer: Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.
setLittleEndian(boolean) - Method in class loci.formats.tiff.TiffSaver: Sets whether or not little-endian data should be written.
setMetadataFiltered(boolean) - Method in class loci.formats.in.FilePatternReader
setMetadataOptions(MetadataOptions) - Method in class loci.formats.FileStitcher
setMetadataStore(MetadataStore) - Method in class loci.formats.FileStitcher
setMetadataStore(MetadataStore) - Method in class loci.formats.in.FilePatternReader
setMetadataStore(MetadataStore) - Method in class loci.formats.Memoizer
setMinMaxStore(IMinMaxStore) - Method in class loci.formats.MinMaxCalculator: Sets the active min-max store for the calculator.
setNormalized(boolean) - Method in class loci.formats.FileStitcher
setNormalized(boolean) - Method in class loci.formats.in.FilePatternReader
setOrder(int, int) - Method in class loci.formats.cache.CacheStrategy
setOrder(int, int) - Method in interface loci.formats.cache.ICacheStrategy: Sets the order in which objects should be loaded along each axis.
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FileStitcher
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.in.FilePatternReader
setOutputOrder(String) - Method in class loci.formats.DimensionSwapper: Sets the output dimension order according to the given string (e.g., "XYZCT").
setOutputOrder(String) - Method in class loci.formats.out.ICSWriter: Set the order in which dimensions should be written to the file.
setOutputOrder(String) - Method in class loci.formats.out.V3DrawWriter: Set the order in which dimensions should be written to the file.
setPriority(int, int) - Method in class loci.formats.cache.CacheStrategy
setPriority(int, int) - Method in interface loci.formats.cache.ICacheStrategy: Sets the priority for caching the given axis.
setQuality(int) - Method in class loci.formats.out.QTWriter: Sets the quality of the encoded movie.
setRange(int, int) - Method in class loci.formats.cache.CacheStrategy
setRange(int, int) - Method in interface loci.formats.cache.ICacheStrategy: Sets the number of objects to cache along the given axis.
setReaderClassList(ClassList<IFormatReader>) - Method in class loci.formats.FileStitcher: Set the ClassList object to use when constructing any helper readers.
setResolution(int) - Method in class loci.formats.FileStitcher
setResolution(int) - Method in class loci.formats.out.DicomWriter
setResolutionLevel(IFD) - Method in class loci.formats.in.MinimalTiffReader: Sets the resolution level when we have JPEG 2000 compressed data.
setRestartMarkers(long[]) - Method in interface loci.formats.services.JPEGTurboService
setRestartMarkers(long[]) - Method in class loci.formats.services.JPEGTurboServiceImpl
setSeries(int) - Method in class loci.formats.FileStitcher
setSeries(int) - Method in class loci.formats.in.IM3Reader
setSeries(int) - Method in class loci.formats.in.OMETiffReader
setSeries(int) - Method in class loci.formats.out.DicomWriter
setSize(int) - Method in class loci.formats.tiff.OnDemandLongArray
setSource(ICacheSource) - Method in class loci.formats.cache.Cache: Sets the cache's caching source.
setStrategy(ICacheStrategy) - Method in class loci.formats.cache.Cache: Sets the cache's caching strategy.
setStream(RandomAccessInputStream) - Method in class loci.formats.tiff.OnDemandLongArray
setTileSizeX(int) - Method in class loci.formats.out.DicomWriter
setTileSizeX(int) - Method in class loci.formats.out.TiffWriter
setTileSizeY(int) - Method in class loci.formats.out.DicomWriter
setTileSizeY(int) - Method in class loci.formats.out.TiffWriter
setupTiffSaver() - Method in class loci.formats.out.TiffWriter
setUse64BitOffsets(boolean) - Method in class loci.formats.tiff.TiffParser: Sets whether or not 64-bit offsets are used for non-BigTIFF files.
setUsingPatternIds(boolean) - Method in class loci.formats.FileStitcher: Sets whether the reader is using file patterns for IDs.
setVersionChecking(boolean) - Method in class loci.formats.Memoizer: Set whether version checking is done based upon major/minor version numbers.
setVisible(boolean) - Method in class loci.formats.gui.ImageViewer
setWritingSequentially(boolean) - Method in class loci.formats.tiff.TiffSaver: Sets whether or not we know that the planes will be written sequentially.
setXML(File) - Method in class loci.formats.gui.XMLWindow: Displays XML from the given file.
setXML(String) - Method in class loci.formats.gui.XMLWindow: Displays XML from the given string.
setXML(String) - Method in class loci.formats.tools.EditTiffG
setYCbCrCorrection(boolean) - Method in class loci.formats.tiff.TiffParser: Sets whether or not YCbCr color correction is allowed.
SH - Enum constant in enum loci.formats.dicom.DicomVR
SHARED_FUNCTIONAL_GROUPS_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
SHARPNESS - Static variable in class loci.formats.tiff.IFD
SHORT - Enum constant in enum loci.formats.tiff.IFDType
shortValue() - Method in class loci.formats.tiff.TiffRational: Returns the value of the specified number as a short.
showError(Throwable) - Method in class loci.formats.tools.EditTiffG
SHUTTER_LEFT_VERTICAL_EDGE - Enum constant in enum loci.formats.dicom.DicomAttribute
SHUTTER_LOWER_HORIZONTAL_EDGE - Enum constant in enum loci.formats.dicom.DicomAttribute
SHUTTER_OVERLAY_GROUP - Enum constant in enum loci.formats.dicom.DicomAttribute
SHUTTER_PRESENTATION_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
SHUTTER_RIGHT_VERTICAL_EDGE - Enum constant in enum loci.formats.dicom.DicomAttribute
SHUTTER_SHAPE - Enum constant in enum loci.formats.dicom.DicomAttribute
SHUTTER_SPEED_VALUE - Static variable in class loci.formats.tiff.IFD
SHUTTER_UPPER_HORIZONTAL_EDGE - Enum constant in enum loci.formats.dicom.DicomAttribute
SIGNAL_DOMAIN_COLUMNS - Enum constant in enum loci.formats.dicom.DicomAttribute
SIGNAL_DOMAIN_ROWS - Enum constant in enum loci.formats.dicom.DicomAttribute
SIGNATURE - Enum constant in enum loci.formats.codec.JPEG2000BoxType
SIGNATURE_WRONG_ENDIANNESS - Enum constant in enum loci.formats.codec.JPEG2000BoxType
SignedByteBuffer - Class in loci.formats.gui: DataBuffer that stores signed bytes.
SignedByteBuffer(byte[][], int) - Constructor for class loci.formats.gui.SignedByteBuffer: Construct a new buffer of signed bytes using the given 2D byte array.
SignedByteBuffer(byte[], int) - Constructor for class loci.formats.gui.SignedByteBuffer: Construct a new buffer of signed bytes using the given byte array.
SignedColorModel - Class in loci.formats.gui: ColorModel that handles 8, 16 and 32 bits per channel signed data.
SignedColorModel(int, int, int) - Constructor for class loci.formats.gui.SignedColorModel
SignedShortBuffer - Class in loci.formats.gui: DataBuffer that stores signed shorts.
SignedShortBuffer(int) - Constructor for class loci.formats.gui.SignedShortBuffer
SignedShortBuffer(int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
SignedShortBuffer(short[][], int) - Constructor for class loci.formats.gui.SignedShortBuffer
SignedShortBuffer(short[][], int, int[]) - Constructor for class loci.formats.gui.SignedShortBuffer
SignedShortBuffer(short[], int) - Constructor for class loci.formats.gui.SignedShortBuffer
SignedShortBuffer(short[], int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
site - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
SITE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
SIZ - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
size() - Method in class loci.formats.codec.ByteVector
size() - Method in class loci.formats.tiff.OnDemandLongArray
sizeC - Variable in class loci.formats.gui.ImageViewer
sizeCsub - Variable in class loci.formats.tools.MakeTestOmeTiff
sizeT - Variable in class loci.formats.gui.ImageViewer
sizeTsub - Variable in class loci.formats.tools.MakeTestOmeTiff
sizeZ - Variable in class loci.formats.gui.ImageViewer
sizeZsub - Variable in class loci.formats.tools.MakeTestOmeTiff
SKIP_BEATS - Enum constant in enum loci.formats.dicom.DicomAttribute
skipBits(long) - Method in class loci.formats.codec.BitBuffer: Deprecated.

Skips a number of bits in the BitBuffer.
skipComment() - Method in class loci.formats.tools.AmiraParameters
skipSave(boolean) - Method in class loci.formats.Memoizer: Set whether a memo file should be saved if a valid file is not present.
skipWhiteSpace() - Method in class loci.formats.tools.AmiraParameters
SL - Enum constant in enum loci.formats.dicom.DicomVR
SLICE_LOCATION - Enum constant in enum loci.formats.dicom.DicomAttribute
SLICE_LOCATION_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
SLICE_SPACING - Enum constant in enum loci.formats.dicom.DicomAttribute
SLICE_THICKNESS - Enum constant in enum loci.formats.dicom.DicomAttribute
SLICE_VECTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
SLIDE_IMAGE_ORIENTATION - Enum constant in enum loci.formats.dicom.DicomAttribute
SlideBook7Reader - Class in loci.formats.in
SlideBook7Reader() - Constructor for class loci.formats.in.SlideBook7Reader
sliderPanel - Variable in class loci.formats.gui.ImageViewer
SLONG - Enum constant in enum loci.formats.tiff.IFDType
SLONG8 - Enum constant in enum loci.formats.tiff.IFDType
SMALLEST_IMAGE_PIXEL_VALUE - Enum constant in enum loci.formats.dicom.DicomAttribute
SMALLEST_IMAGE_PIXEL_VALUE_IN_PLANE - Enum constant in enum loci.formats.dicom.DicomAttribute
SMALLEST_PIXEL_VALUE_IN_SERIES - Enum constant in enum loci.formats.dicom.DicomAttribute
SMOKING_STATUS - Enum constant in enum loci.formats.dicom.DicomAttribute
SOC - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
SOC_WRONG_ENDIANNESS - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
SOD - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
SOFT_TISSUE_FOCUS_THERMAL_INDEX - Enum constant in enum loci.formats.dicom.DicomAttribute
SOFT_TISSUE_SURFACE_THERMAL_INDEX - Enum constant in enum loci.formats.dicom.DicomAttribute
SOFT_TISSUE_THERMAL_INDEX - Enum constant in enum loci.formats.dicom.DicomAttribute
SOFTCOPY_VOI_LUT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
SOFTWARE - Static variable in class loci.formats.tiff.IFD
SOFTWARE_VERSION - Enum constant in enum loci.formats.dicom.DicomAttribute
SOP - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
SOP_CLASS_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
SOP_CLASSES_SUPPORTED - Enum constant in enum loci.formats.dicom.DicomAttribute
SOP_INSTANCE_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
SORENSON - Enum constant in enum loci.formats.codec.CompressionType
SORENSON_3 - Enum constant in enum loci.formats.codec.CompressionType
sortFilters(Vector) - Static method in class loci.formats.gui.ComboFileFilter: Sorts the given list of file filters, and combines filters with identical descriptions into a combination filter that accepts anything any of its constituant filters do.
sortFilters(FileFilter[]) - Static method in class loci.formats.gui.ComboFileFilter: Sorts the given list of file filters, and combines filters with identical descriptions into a combination filter that accepts anything any of its constituant filters do.
SOT - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
source - Variable in class loci.formats.cache.Cache: Current cache source.
source - Variable in class loci.formats.cache.CacheEvent: Source of the cache update.
SOURCE_APPLICATION - Enum constant in enum loci.formats.dicom.DicomAttribute
SOURCE_CHANGED - Static variable in class loci.formats.cache.CacheEvent: Event type indicating a new cache source.
SOURCE_IMAGE_EVIDENCE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
SOURCE_IMAGE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
SOURCE_PARAMS - Static variable in class loci.formats.gui.CacheComponent
SOURCE_VALUES - Static variable in class loci.formats.gui.CacheComponent
SOURCES - Static variable in class loci.formats.gui.CacheComponent
SPATIAL_FREQUENCY_RESPONSE - Static variable in class loci.formats.tiff.IFD
SPATIAL_RESOLUTION - Enum constant in enum loci.formats.dicom.DicomAttribute
SPECIFIC_CHARSET - Enum constant in enum loci.formats.dicom.DicomAttribute
SPECIMEN_DESCRIPTION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
SPECIMEN_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
SPECIMEN_ID_ISSUER_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
SPECIMEN_LABEL_IN_IMAGE - Enum constant in enum loci.formats.dicom.DicomAttribute
SPECIMEN_PREP_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
SPECIMEN_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
SPECTRAL_SENSITIVITY - Static variable in class loci.formats.tiff.IFD
split - Variable in class loci.formats.codec.NikonCodecOptions
splitChannels(byte[], byte[], int, int, int, boolean, boolean, int) - Static method in class loci.formats.ImageTools: Splits the given multi-channel array into a 2D array.
splitChannels(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools: Splits the given multi-channel array into a 2D array.
splitChannels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Splits the given multi-channel image into single-channel images.
SQ - Enum constant in enum loci.formats.dicom.DicomVR
SRATIONAL - Enum constant in enum loci.formats.tiff.IFDType
SS - Enum constant in enum loci.formats.dicom.DicomVR
SSHORT - Enum constant in enum loci.formats.tiff.IFDType
ST - Enum constant in enum loci.formats.dicom.DicomVR
STABLE_BUILD - Static variable in class loci.formats.UpgradeChecker: Location of the JAR artifacts for the stable releases.
STABLE_VERSION - Static variable in class loci.formats.UpgradeChecker: Deprecated.
As of release 6.6.0
STAGE_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
STAGE_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
START_TRIM - Enum constant in enum loci.formats.dicom.DicomAttribute
stateChanged(ChangeEvent) - Method in class loci.formats.gui.CacheComponent: Handles range spinner changes.
stateChanged(ChangeEvent) - Method in class loci.formats.gui.DataConverter
stateChanged(ChangeEvent) - Method in class loci.formats.gui.ImageViewer: Handles slider events.
STATION_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
STEERING_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
STOP_TRIM - Enum constant in enum loci.formats.dicom.DicomAttribute
stopWatch() - Method in class loci.formats.in.DicomReader
stopWatch() - Method in class loci.formats.Memoizer
stopWatch() - Method in class loci.formats.out.DicomWriter
STRATEGIES - Static variable in class loci.formats.gui.CacheComponent
strategy - Variable in class loci.formats.cache.Cache: Current cache strategy.
strategy - Variable in class loci.formats.dicom.DicomTag
STRATEGY_CHANGED - Static variable in class loci.formats.cache.CacheEvent: Event type indicating a new cache strategy.
STRATEGY_PARAMS - Static variable in class loci.formats.gui.CacheComponent
STRATEGY_VALUES - Static variable in class loci.formats.gui.CacheComponent
streamNames - Variable in class loci.formats.tools.AmiraParameters
streams - Variable in class loci.formats.tools.AmiraParameters
streamTypes - Variable in class loci.formats.tools.AmiraParameters
StringIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.StringIM3Record
STRIP_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
STRIP_OFFSETS - Static variable in class loci.formats.tiff.IFD
strips - Variable in class loci.formats.in.PictReader: Vector of byte arrays representing individual rows.
STUDIES_WITH_REFERENCED_INSTANCES - Enum constant in enum loci.formats.dicom.DicomAttribute
STUDY_DATE - Enum constant in enum loci.formats.dicom.DicomAttribute
STUDY_DESCRIPTION - Enum constant in enum loci.formats.dicom.DicomAttribute
STUDY_ID - Enum constant in enum loci.formats.dicom.DicomAttribute
STUDY_INSTANCE_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
STUDY_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
SUB_IFD - Static variable in class loci.formats.tiff.IFD
SUB_SEC_TIME - Static variable in class loci.formats.tiff.IFD
SUB_SEC_TIME_DIGITIZED - Static variable in class loci.formats.tiff.IFD
SUB_SEC_TIME_ORIGINAL - Static variable in class loci.formats.tiff.IFD
SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
SUBJECT_DISTANCE - Static variable in class loci.formats.tiff.IFD
SUBJECT_DISTANCE_RANGE - Static variable in class loci.formats.tiff.IFD
SUBJECT_LOCATION - Static variable in class loci.formats.tiff.IFD
subResolutionIFDs - Variable in class loci.formats.in.MinimalTiffReader: List of sub-resolution IFDs for each IFD in the current TIFF with the same order as ifds.
SV - Enum constant in enum loci.formats.dicom.DicomVR
swapDimensions(String) - Method in class loci.formats.DimensionSwapper: Sets the input dimension order according to the given string (e.g., "XYZCT").
SwappableMetadata - Class in loci.formats: Extends CoreMetadata to include the notion of an "input order" for planes: the input order being the order planes are stored on disk.
SwappableMetadata() - Constructor for class loci.formats.SwappableMetadata
SwappableMetadata(IFormatReader, int) - Constructor for class loci.formats.SwappableMetadata
SwappableMetadata(SwappableMetadata) - Constructor for class loci.formats.SwappableMetadata
SYNCHRONIZATION_CHANNEL - Enum constant in enum loci.formats.dicom.DicomAttribute
SYNCHRONIZATION_TRIGGER - Enum constant in enum loci.formats.dicom.DicomAttribute
syntaxError(String) - Method in class loci.formats.tools.AmiraParameters
SYRINGE_COUNTS - Enum constant in enum loci.formats.dicom.DicomAttribute

T

T_AXIS - Static variable in class loci.formats.AxisGuesser: Axis type for time points.
T_PREFIXES - Static variable in class loci.formats.AxisGuesser: Prefixes indicating time dimension.
T4_OPTIONS - Static variable in class loci.formats.tiff.IFD
T6_OPTIONS - Static variable in class loci.formats.tiff.IFD
table - Variable in class loci.formats.codec.HuffmanCodecOptions
TABLE_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_HEIGHT - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_LATERAL_INCREMENT - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_LONGITUDINAL_INCREMENT - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_MOTION - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_OF_PARAMETER_VALUES - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_OF_PIXEL_VALUES - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_OF_X_BREAK_POINTS - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_OF_Y_BREAK_POINTS - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_TRAVERSE - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
TABLE_VERTICAL_INCREMENT - Enum constant in enum loci.formats.dicom.DicomAttribute
tag - Variable in class loci.formats.dicom.DicomTag
TargaRLECodec - Class in loci.formats.codec: This class implements Targa RLE decompression.
TargaRLECodec() - Constructor for class loci.formats.codec.TargaRLECodec
TARGET_PRINTER - Static variable in class loci.formats.tiff.IFD
test() - Method in class loci.formats.codec.BaseCodec: Main testing method default implementation.
TextReader - Class in loci.formats.in: Reader for text files containing tables of data.
TextReader() - Constructor for class loci.formats.in.TextReader: Constructs a new text reader.
THREE - Static variable in class loci.formats.AxisGuesser
THRESHHOLDING - Static variable in class loci.formats.tiff.IFD
thumbnailIFDs - Variable in class loci.formats.in.MinimalTiffReader: List of thumbnail IFDs for the current TIFF.
THUNDERSCAN - Enum constant in enum loci.formats.tiff.TiffCompression
TID_OFFSET - Enum constant in enum loci.formats.dicom.DicomAttribute
TIFF_KEY - Static variable in class loci.formats.out.DicomWriter: Option for turning off TIFF metadata.
TIFF_SUFFIXES - Static variable in class loci.formats.in.TiffReader
TiffCompression - Enum in loci.formats.tiff: Utility class for performing compression operations with a TIFF file.
TiffConstants - Class in loci.formats.tiff: Generally useful TIFF-related constants.
TiffDelegateReader - Class in loci.formats.in: TiffDelegateReader is a file format reader for TIFF files.
TiffDelegateReader() - Constructor for class loci.formats.in.TiffDelegateReader: Constructs a new TIFF reader.
TiffIFDEntry - Class in loci.formats.tiff: This class represents a single raw TIFF IFD entry.
TiffIFDEntry(int, IFDType, int, long) - Constructor for class loci.formats.tiff.TiffIFDEntry
TiffJAIReader - Class in loci.formats.in: TiffJAIReader is a file format reader for TIFF images.
TiffJAIReader() - Constructor for class loci.formats.in.TiffJAIReader: Constructs a new TIFF reader that uses Java Image I/O.
tiffParser - Variable in class loci.formats.in.MinimalTiffReader
TiffParser - Class in loci.formats.tiff: Parses TIFF data from an input source.
TiffParser(String) - Constructor for class loci.formats.tiff.TiffParser: Constructs a new TIFF parser from the given file name.
TiffParser(RandomAccessInputStream) - Constructor for class loci.formats.tiff.TiffParser: Constructs a new TIFF parser from the given input source.
TiffRational - Class in loci.formats.tiff: A rational number (numerator over denominator).
TiffRational(long, long) - Constructor for class loci.formats.tiff.TiffRational: Constructs a rational number.
TiffReader - Class in loci.formats.in: TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.
TiffReader() - Constructor for class loci.formats.in.TiffReader: Constructs a new Tiff reader.
tiffSaver - Variable in class loci.formats.out.TiffWriter: The TiffSaver that will do most of the writing.
TiffSaver - Class in loci.formats.tiff: Parses TIFF data from an input source.
TiffSaver(String) - Constructor for class loci.formats.tiff.TiffSaver: Constructs a new TIFF saver from the given filename.
TiffSaver(RandomAccessOutputStream, String) - Constructor for class loci.formats.tiff.TiffSaver: Constructs a new TIFF saver from the given output source.
TiffSaver(RandomAccessOutputStream, ByteArrayHandle) - Constructor for class loci.formats.tiff.TiffSaver: Constructs a new TIFF saver from the given output source.
TiffWriter - Class in loci.formats.out: TiffWriter is the file format writer for TIFF files.
TiffWriter() - Constructor for class loci.formats.out.TiffWriter
TiffWriter(String, String[]) - Constructor for class loci.formats.out.TiffWriter
TILE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
TILE_LENGTH - Static variable in class loci.formats.tiff.IFD
TILE_OFFSETS - Static variable in class loci.formats.tiff.IFD
TILE_WIDTH - Static variable in class loci.formats.tiff.IFD
TileJPEGReader - Class in loci.formats.in: Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
TileJPEGReader() - Constructor for class loci.formats.in.TileJPEGReader
tiles - Variable in class loci.formats.dicom.DicomFileInfo
tileSizeX - Variable in class loci.formats.out.TiffWriter: The tile width which will be used for writing.
tileSizeY - Variable in class loci.formats.out.TiffWriter: The tile height which will be used for writing.
TIME_DISTRIBUTION_PROTOCOL - Enum constant in enum loci.formats.dicom.DicomAttribute
TIME_OF_LAST_CALIBRATION - Enum constant in enum loci.formats.dicom.DicomAttribute
TIME_OF_LAST_DETECTOR_CALIBRATION - Enum constant in enum loci.formats.dicom.DicomAttribute
TIME_OF_SECONDARY_CAPTURE - Enum constant in enum loci.formats.dicom.DicomAttribute
TIME_PREFIX - Static variable in class loci.formats.in.KLBReader
TIME_SOURCE - Enum constant in enum loci.formats.dicom.DicomAttribute
TIME_SUFFIX - Static variable in class loci.formats.in.KLBReader
timestamp - Variable in class loci.formats.dicom.DicomFileInfo
TIMEZONE_OFFSET_UTC - Enum constant in enum loci.formats.dicom.DicomAttribute
TITLE - Static variable in class loci.formats.gui.ImageViewer
TLM - Enum constant in enum loci.formats.codec.JPEG2000SegmentMarker
TM - Enum constant in enum loci.formats.dicom.DicomVR
TM_LINE_POSITION_X0 - Enum constant in enum loci.formats.dicom.DicomAttribute
TM_LINE_POSITION_X1 - Enum constant in enum loci.formats.dicom.DicomAttribute
TM_LINE_POSITION_Y0 - Enum constant in enum loci.formats.dicom.DicomAttribute
TM_LINE_POSITION_Y1 - Enum constant in enum loci.formats.dicom.DicomAttribute
toArray() - Method in class loci.formats.tiff.OnDemandLongArray
toByteArray() - Method in class loci.formats.codec.BitWriter: Deprecated.

Gets an array containing all bits written thus far.
toByteArray() - Method in class loci.formats.codec.ByteVector
toBytes(BufferedImage, IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter
toCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
TOMO_ANGLE - Enum constant in enum loci.formats.dicom.DicomAttribute
TOMO_CLASS - Enum constant in enum loci.formats.dicom.DicomAttribute
TOMO_LAYER_HEIGHT - Enum constant in enum loci.formats.dicom.DicomAttribute
TOMO_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
TOMO_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
TOOLS - Static variable in class loci.formats.UpgradeChecker: Name of the ueber tools JAR.
toRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
toString() - Method in class loci.formats.cache.CacheEvent
toString() - Method in class loci.formats.dicom.DicomTag
toString() - Method in class loci.formats.gui.ComboFileFilter: Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.ExtensionFileFilter: Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.FormatFileFilter: Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.NoExtensionFileFilter: Gets a string representation of this file filter.
toString() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
toString() - Method in class loci.formats.in.IM3Reader.IM3Record
toString() - Method in class loci.formats.tiff.TiffIFDEntry
toString() - Method in class loci.formats.tiff.TiffRational: Returns a string representation of the object.
toString() - Method in class loci.formats.tools.AmiraParameters
toString() - Method in class loci.formats.tools.AsciiImage
toString(Map, String) - Static method in class loci.formats.tools.AmiraParameters
TOTAL_PIXEL_MATRIX_COLUMNS - Enum constant in enum loci.formats.dicom.DicomAttribute
TOTAL_PIXEL_MATRIX_FOCAL_PLANES - Enum constant in enum loci.formats.dicom.DicomAttribute
TOTAL_PIXEL_MATRIX_ORIGIN_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
TOTAL_PIXEL_MATRIX_ROWS - Enum constant in enum loci.formats.dicom.DicomAttribute
TRAILING_PADDING - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSACTION_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSDUCER_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSDUCER_FREQUENCY - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSDUCER_ORIENTATION_MODIFIER - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSDUCER_ORIENTATION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSDUCER_POSITION_MODIFIER_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSDUCER_POSITION_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSDUCER_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSFER_FUNCTION - Static variable in class loci.formats.tiff.IFD
TRANSFER_RANGE - Static variable in class loci.formats.tiff.IFD
TRANSFER_SYNTAX_UID - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSMIT_COIL_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
TRANSPARENCY_MASK - Enum constant in enum loci.formats.tiff.PhotoInterp
TRIGGER_SAMPLE_POSITION - Enum constant in enum loci.formats.dicom.DicomAttribute
TRIGGER_SOURCE_OR_TYPE - Enum constant in enum loci.formats.dicom.DicomAttribute
TRIGGER_TIME - Enum constant in enum loci.formats.dicom.DicomAttribute
TRIGGER_TIME_OFFSET - Enum constant in enum loci.formats.dicom.DicomAttribute
TRIGGER_WINDOW - Enum constant in enum loci.formats.dicom.DicomAttribute
TRUNK_BUILD - Static variable in class loci.formats.UpgradeChecker: Location of the JAR artifacts for Bio-Formats' trunk build.
tSlider - Variable in class loci.formats.gui.ImageViewer
TWO - Static variable in class loci.formats.AxisGuesser
TwoChannelColorSpace - Class in loci.formats.gui: ColorSpace for 2-channel images.
TwoChannelColorSpace(int, int) - Constructor for class loci.formats.gui.TwoChannelColorSpace
type - Variable in class loci.formats.cache.CacheEvent: Type of cache event.
TYPE_OF_DETECTOR_MOTION - Enum constant in enum loci.formats.dicom.DicomAttribute
TYPE_OF_FILTERS - Enum constant in enum loci.formats.dicom.DicomAttribute
typeLabel - Variable in class loci.formats.gui.PreviewPane: Labels containing thumbnail and dimensional information.
typeText - Variable in class loci.formats.gui.PreviewPane
typeTip - Variable in class loci.formats.gui.PreviewPane

U

UC - Enum constant in enum loci.formats.dicom.DicomVR
UI - Enum constant in enum loci.formats.dicom.DicomVR
UID_DEFAULT_ROOT - Static variable in class loci.formats.out.DicomWriter
UID_ROOT_KEY - Static variable in class loci.formats.out.DicomWriter: Option for setting the organization root for UIDs.
UL - Enum constant in enum loci.formats.dicom.DicomVR
ULTRASOUND_COLOR_DATA_PRESENT - Enum constant in enum loci.formats.dicom.DicomAttribute
UN - Enum constant in enum loci.formats.dicom.DicomVR
UNCOMPRESSED - Enum constant in enum loci.formats.codec.CompressionType
UNCOMPRESSED - Enum constant in enum loci.formats.tiff.TiffCompression
UNDEFINED - Enum constant in enum loci.formats.tiff.IFDType
undifference(byte[], IFD) - Static method in enum loci.formats.tiff.TiffCompression: Undoes in-place differencing according to the given predictor value.
UNKNOWN_AXIS - Static variable in class loci.formats.AxisGuesser: Axis type for unclassified axes.
unpackBytes(byte[], int, byte[], IFD) - Static method in class loci.formats.tiff.TiffParser: Extracts pixel information from the given byte array according to the bits per sample, photometric interpretation and color map IFD directory entry values, and the specified byte ordering.
UnsignedIntBuffer - Class in loci.formats.gui: DataBuffer that stores unsigned ints.
UnsignedIntBuffer(int[][], int) - Constructor for class loci.formats.gui.UnsignedIntBuffer: Construct a new buffer of unsigned ints using the given 2D int array.
UnsignedIntBuffer(int[], int) - Constructor for class loci.formats.gui.UnsignedIntBuffer: Construct a new buffer of unsigned ints using the given int array.
UnsignedIntColorModel - Class in loci.formats.gui: ColorModel that handles unsigned 32 bit data.
UnsignedIntColorModel(int, int, int) - Constructor for class loci.formats.gui.UnsignedIntColorModel
updateLabel(int, int) - Method in class loci.formats.gui.ImageViewer: Updates cursor probe label.
updateMinMax(int, byte[], int) - Method in class loci.formats.MinMaxCalculator: Updates min/max values based on the given byte array.
UpgradeCheck - Class in loci.formats.tools: Utility that checks for a new stable version, and optionally installs a new version of Bio-Formats ueber tools.
UpgradeCheck() - Constructor for class loci.formats.tools.UpgradeCheck
UpgradeChecker - Class in loci.formats: Class that allows checking for new versions of Bio-Formats, as well as updating to the latest stable, daily, or trunk version.
UpgradeChecker() - Constructor for class loci.formats.UpgradeChecker
UR - Enum constant in enum loci.formats.dicom.DicomVR
URL - Enum constant in enum loci.formats.codec.JPEG2000BoxType
US - Enum constant in enum loci.formats.dicom.DicomVR
use64Bit - Variable in class loci.formats.in.MinimalTiffReader
used - Variable in class loci.formats.in.OMETiffReader: List of used files.
USER_COMMENT - Static variable in class loci.formats.tiff.IFD
UT - Enum constant in enum loci.formats.dicom.DicomVR
UUID - Enum constant in enum loci.formats.codec.JPEG2000BoxType
UUID_INFO - Enum constant in enum loci.formats.codec.JPEG2000BoxType
UUID_LIST - Enum constant in enum loci.formats.codec.JPEG2000BoxType
UV - Enum constant in enum loci.formats.dicom.DicomVR

V

V3DrawWriter - Class in loci.formats.out: V3DrawWriter writes images in the .v3draw format for rapid I/O in Vaa3D, an open-source 3D visualization and analysis toolkit.
V3DrawWriter() - Constructor for class loci.formats.out.V3DrawWriter
validate(List<DicomTag>) - Method in class loci.formats.dicom.DicomTag: Check this tag against a list of existing tags.
validateValue() - Method in class loci.formats.dicom.DicomTag: Compare the value type to the VR.
value - Variable in class loci.formats.dicom.DicomTag
valueOf(String) - Static method in enum loci.formats.codec.CompressionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.codec.JPEG2000BoxType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.codec.JPEG2000SegmentMarker: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.dicom.DicomAttribute: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.dicom.DicomVR: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.dicom.ResolutionStrategy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.tiff.IFDType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.tiff.PhotoInterp: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.tiff.TiffCompression: Returns the enum constant of this type with the specified name.
values() - Static method in enum loci.formats.codec.CompressionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.codec.JPEG2000BoxType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.codec.JPEG2000SegmentMarker: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.dicom.DicomAttribute: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.dicom.DicomVR: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.dicom.ResolutionStrategy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.tiff.IFDType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.tiff.PhotoInterp: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.tiff.TiffCompression: Returns an array containing the constants of this enum type, in the order they are declared.
VARIABLE_FLIP_ANGLE_FLAG - Enum constant in enum loci.formats.dicom.DicomAttribute
VARIABLE_PIXEL_DATA - Enum constant in enum loci.formats.dicom.DicomAttribute
VERSION - Static variable in class loci.formats.Memoizer: Default file version.
versionMismatch() - Method in class loci.formats.Memoizer: Returns true if the version of the memo file as returned by Memoizer.Deser.loadReleaseVersion() and Memoizer.Deser.loadRevision() do not match the current version as specified by FormatTools.VERSION.
versionOne - Variable in class loci.formats.in.PictReader: Whether or not the file is PICT v1.
VERTICES_OF_POLYGONAL_COLLIMATOR - Enum constant in enum loci.formats.dicom.DicomAttribute
VERTICES_OF_POLYGONAL_SHUTTER - Enum constant in enum loci.formats.dicom.DicomAttribute
VIDEO_IMAGE_FORMAT_ACQUIRED - Enum constant in enum loci.formats.dicom.DicomAttribute
VIEW_NAME - Enum constant in enum loci.formats.dicom.DicomAttribute
VIEW_NUMBER - Enum constant in enum loci.formats.dicom.DicomAttribute
VIEW_POSITION - Enum constant in enum loci.formats.dicom.DicomAttribute
VOI_LUT_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
VOLUME_BASED_CALCULATION_TECHNIQUE - Enum constant in enum loci.formats.dicom.DicomAttribute
VOLUMETRIC_PROPERTIES - Enum constant in enum loci.formats.dicom.DicomAttribute
vPredictor - Variable in class loci.formats.codec.NikonCodecOptions
vr - Variable in class loci.formats.dicom.DicomTag

W

wait(boolean) - Method in class loci.formats.gui.ImageViewer: Toggles wait cursor.
well - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
WELL - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
WELL - Static variable in class loci.formats.ResourceNamer
WHITE_BALANCE - Static variable in class loci.formats.tiff.IFD
WHITE_IS_ZERO - Enum constant in enum loci.formats.tiff.PhotoInterp
WHITE_POINT - Static variable in class loci.formats.tiff.IFD
WHOLE_BODY_TECHNIQUE - Enum constant in enum loci.formats.dicom.DicomAttribute
WHOLE_SLIDE_FRAME_TYPE_SEQUENCE - Enum constant in enum loci.formats.dicom.DicomAttribute
width - Variable in class loci.formats.tools.AmiraParameters
WINDOW_CENTER - Enum constant in enum loci.formats.dicom.DicomAttribute
WINDOW_CENTER_AND_WIDTH_EXPLANATION - Enum constant in enum loci.formats.dicom.DicomAttribute
WINDOW_WIDTH - Enum constant in enum loci.formats.dicom.DicomAttribute
windowActivated(WindowEvent) - Method in class loci.formats.gui.ImageViewer
windowClosed(WindowEvent) - Method in class loci.formats.gui.ImageViewer
windowClosing(WindowEvent) - Method in class loci.formats.gui.ImageViewer
windowDeactivated(WindowEvent) - Method in class loci.formats.gui.ImageViewer
windowDeiconified(WindowEvent) - Method in class loci.formats.gui.ImageViewer
windowIconified(WindowEvent) - Method in class loci.formats.gui.ImageViewer
windowOpened(WindowEvent) - Method in class loci.formats.gui.ImageViewer
write(int, int) - Method in class loci.formats.codec.BitWriter: Deprecated.

Writes the given value using the given number of bits.
write(String) - Method in class loci.formats.codec.BitWriter: Deprecated.

Writes the bits represented by a bit string to the buffer.
writeArraySlice(String, MDByteArray, long[]) - Method in interface loci.formats.services.JHDFService: Writes an array as sub-slice into an existing HDF5 dataset
writeArraySlice(String, MDByteArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
writeArraySlice(String, MDIntArray, long[]) - Method in interface loci.formats.services.JHDFService: Writes an array as sub-slice into an existing HDF5 dataset
writeArraySlice(String, MDIntArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
writeArraySlice(String, MDShortArray, long[]) - Method in interface loci.formats.services.JHDFService: Writes an array as sub-slice into an existing HDF5 dataset
writeArraySlice(String, MDShortArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
writeBox - Variable in class loci.formats.codec.JPEG2000CodecOptions: Whether or not to write a boxed stream, i.e.
writeDualPersonality() - Method in class loci.formats.out.DicomWriter: Checks the writer's associated MetadataOptions to see if dual personality writing has been explicitly enabled or disabled.
writeFooter() - Method in class loci.formats.out.JavaWriter
writeHeader() - Method in class loci.formats.out.JavaWriter
writeHeader() - Method in class loci.formats.tiff.TiffSaver: Writes the TIFF file header.
writeIFD(IFD, long) - Method in class loci.formats.tiff.TiffSaver: Write the given IFD to the open stream.
writeIFD(IFD, long, boolean) - Method in class loci.formats.tiff.TiffSaver: Write the given IFD to the open stream.
writeIFDValue(RandomAccessOutputStream, long, int, Object) - Method in class loci.formats.tiff.TiffSaver: Writes the given IFD value to the given output object.
writeImage(byte[][], IFDList, int) - Method in class loci.formats.tiff.TiffSaver
writeImage(byte[], IFD, int, int, boolean) - Method in class loci.formats.tiff.TiffSaver
writeImage(byte[], IFD, int, int, int, int, int, int, boolean) - Method in class loci.formats.tiff.TiffSaver: Writes to any rectangle from the passed block.
writeImage(byte[], IFD, int, int, int, int, int, int, boolean, Integer, boolean) - Method in class loci.formats.tiff.TiffSaver
writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService: Writes an image using JAI Image I/O using the JPEG 2000 codec.
writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
writeImageIFD(IFD, int, byte[][], int, boolean, int, int) - Method in class loci.formats.tiff.TiffSaver: Performs the actual work of dealing with IFD data and writing it to the TIFF for a given image or sub-image.
writePlane(String, byte[], int, int) - Method in class loci.formats.out.JavaWriter
writePlane(String, double[], int, int) - Method in class loci.formats.out.JavaWriter
writePlane(String, float[], int, int) - Method in class loci.formats.out.JavaWriter
writePlane(String, int[], int, int) - Method in class loci.formats.out.JavaWriter
writePlane(String, long[], int, int) - Method in class loci.formats.out.JavaWriter
writePlane(String, short[], int, int) - Method in class loci.formats.out.JavaWriter
writeSummary() - Method in class loci.formats.in.IM3Reader: Write a summary of each field in the IM3 file to the writer
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.ContainerRecord
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.IM3Record: Write a summary of the contents of the record
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.IntIM3Record
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.StringIM3Record

X

X_FOCUS_CENTER - Enum constant in enum loci.formats.dicom.DicomAttribute
X_OFFSET_IN_SLIDE - Enum constant in enum loci.formats.dicom.DicomAttribute
X_POSITION - Static variable in class loci.formats.tiff.IFD
X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
x0 - Variable in class loci.formats.tools.AmiraParameters
x1 - Variable in class loci.formats.tools.AmiraParameters
XML - Enum constant in enum loci.formats.codec.JPEG2000BoxType
XMLCellRenderer - Class in loci.formats.gui: A tree cell renderer for displaying syntax highlighted XML in a JTree.
XMLCellRenderer() - Constructor for class loci.formats.gui.XMLCellRenderer
XMLWindow - Class in loci.formats.gui: A window containing syntax highlighted XML as a tree.
XMLWindow() - Constructor for class loci.formats.gui.XMLWindow
XMLWindow(String) - Constructor for class loci.formats.gui.XMLWindow
XRAY_TUBE_CURRENT - Enum constant in enum loci.formats.dicom.DicomAttribute

Y

Y_CB_CR - Enum constant in enum loci.formats.tiff.PhotoInterp
Y_CB_CR_COEFFICIENTS - Static variable in class loci.formats.tiff.IFD
Y_CB_CR_POSITIONING - Static variable in class loci.formats.tiff.IFD
Y_CB_CR_SUB_SAMPLING - Static variable in class loci.formats.tiff.IFD
Y_FOCUS_CENTER - Enum constant in enum loci.formats.dicom.DicomAttribute
Y_OFFSET_IN_SLIDE - Enum constant in enum loci.formats.dicom.DicomAttribute
Y_POSITION - Static variable in class loci.formats.tiff.IFD
Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
y0 - Variable in class loci.formats.tools.AmiraParameters
y1 - Variable in class loci.formats.tools.AmiraParameters

Z

Z_AXIS - Static variable in class loci.formats.AxisGuesser: Axis type for focal planes.
Z_OFFSET_IN_SLIDE - Enum constant in enum loci.formats.dicom.DicomAttribute
Z_PREFIXES - Static variable in class loci.formats.AxisGuesser: Prefixes indicating space dimension.
z0 - Variable in class loci.formats.tools.AmiraParameters
z1 - Variable in class loci.formats.tools.AmiraParameters
zctLabel - Variable in class loci.formats.gui.PreviewPane: Labels containing thumbnail and dimensional information.
zctText - Variable in class loci.formats.gui.PreviewPane
zctTip - Variable in class loci.formats.gui.PreviewPane
ZipReader - Class in loci.formats.in: Reader for Zip files.
ZipReader() - Constructor for class loci.formats.in.ZipReader
ZLIB - Enum constant in enum loci.formats.codec.CompressionType
ZlibCodec - Class in loci.formats.codec: This class implements ZLIB decompression.
ZlibCodec() - Constructor for class loci.formats.codec.ZlibCodec
zOffset - Variable in class loci.formats.dicom.DicomTile
zOffsets - Variable in class loci.formats.dicom.DicomFileInfo
ZOOM_CENTER - Enum constant in enum loci.formats.dicom.DicomAttribute
ZOOM_FACTOR - Enum constant in enum loci.formats.dicom.DicomAttribute
zSlider - Variable in class loci.formats.gui.ImageViewer
ZSTD - Enum constant in enum loci.formats.tiff.TiffCompression
ZstdCodec - Class in loci.formats.codec
ZstdCodec() - Constructor for class loci.formats.codec.ZstdCodec

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