Index (SCIFIO Core 0.48.0 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

A

AbstractArrayLoader<A> - Class in io.scif.img.cell.loaders: Abstract superclass for all SCIFIOArrayLoader implementations.
AbstractArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.AbstractArrayLoader
AbstractChecker - Class in io.scif: Abstract superclass of all SCIFIO Checker implementations.
AbstractChecker() - Constructor for class io.scif.AbstractChecker
AbstractCodec - Class in io.scif.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.
AbstractCodec() - Constructor for class io.scif.codec.AbstractCodec
AbstractFilter<T> - Class in io.scif.filters: Abstract superclass for Filter implementations.
AbstractFilter(Class<? extends T>) - Constructor for class io.scif.filters.AbstractFilter
AbstractFormat - Class in io.scif: Abstract superclass of all SCIFIO Format implementations.
AbstractFormat() - Constructor for class io.scif.AbstractFormat
AbstractGroupable - Class in io.scif: Abstract super-class for all Groupable components.
AbstractGroupable() - Constructor for class io.scif.AbstractGroupable
AbstractHasFormat - Class in io.scif: Abstract superclass for all classes that implement HasFormat.
AbstractHasFormat() - Constructor for class io.scif.AbstractHasFormat
AbstractHasSource - Class in io.scif: Abstract implementation of the HasSource interface.
AbstractHasSource() - Constructor for class io.scif.AbstractHasSource
AbstractImageMetadata - Class in io.scif: Abstract superclass of all ImageMetadata implementations.
AbstractImageMetadata() - Constructor for class io.scif.AbstractImageMetadata
AbstractImageMetadata(ImageMetadata) - Constructor for class io.scif.AbstractImageMetadata
AbstractImgIOComponent - Class in io.scif.img: Abstract superclass for ImgIOComponents (such as ImgOpener or ImgSaver).
AbstractImgIOComponent() - Constructor for class io.scif.img.AbstractImgIOComponent
AbstractImgIOComponent(Context) - Constructor for class io.scif.img.AbstractImgIOComponent
AbstractMetadata - Class in io.scif: Abstract superclass of all SCIFIO Metadata implementations.
AbstractMetadata() - Constructor for class io.scif.AbstractMetadata
AbstractMetadata(Metadata) - Constructor for class io.scif.AbstractMetadata
AbstractMetadata(List<ImageMetadata>) - Constructor for class io.scif.AbstractMetadata
AbstractMetadataWrapper - Class in io.scif.filters: Abstract superclass for concrete implementations of MetadataWrapper.
AbstractMetadataWrapper() - Constructor for class io.scif.filters.AbstractMetadataWrapper
AbstractMetadataWrapper(Metadata) - Constructor for class io.scif.filters.AbstractMetadataWrapper
AbstractParser<M extends TypedMetadata> - Class in io.scif: Abstract superclass of all SCIFIO Parser implementations.
AbstractParser() - Constructor for class io.scif.AbstractParser
AbstractPlane<T,P extends DataPlane<T>> - Class in io.scif: Abstract superclass for Plane implementations in SCIFIO.
AbstractPlane() - Constructor for class io.scif.AbstractPlane
AbstractPlane(ImageMetadata, Interval) - Constructor for class io.scif.AbstractPlane
AbstractPlaneConverter - Class in io.scif.img.converters: Abstract superclass for PlaneConverter implementations.
AbstractPlaneConverter() - Constructor for class io.scif.img.converters.AbstractPlaneConverter
AbstractReader<M extends TypedMetadata,P extends DataPlane<?>> - Class in io.scif: Abstract superclass of all SCIFIO Reader implementations.
AbstractReader(Class<P>) - Constructor for class io.scif.AbstractReader: Constructs a reader and stores a reference to its plane type
AbstractReaderFilter - Class in io.scif.filters: Abstract superclass for all Filter that delegate to Reader instances.
AbstractReaderFilter() - Constructor for class io.scif.filters.AbstractReaderFilter
AbstractReaderFilter(Class<? extends MetadataWrapper>) - Constructor for class io.scif.filters.AbstractReaderFilter
AbstractSCIFIOPlugin - Class in io.scif: Abstract superclass of all SCIFIOPlugin implementations.
AbstractSCIFIOPlugin() - Constructor for class io.scif.AbstractSCIFIOPlugin
AbstractTranslator<M extends Metadata,N extends Metadata> - Class in io.scif: Abstract superclass of all SCIFIO Translator components.
AbstractTranslator() - Constructor for class io.scif.AbstractTranslator
AbstractWriter<M extends TypedMetadata> - Class in io.scif: Abstract superclass of all SCIFIO Writer implementations.
AbstractWriter() - Constructor for class io.scif.AbstractWriter
accept(File) - Method in class io.scif.gui.ComboFileFilter: Accepts files with the proper filename prefix.
accept(File) - Method in class io.scif.gui.FormatFileFilter: Accepts files in accordance with the associated format's Checker.
accept(String) - Method in class io.scif.NumberFilter: Tests if a specified file should be included in a file list.
accept(File) - Method in class io.scif.NumberFilter: Tests if a specified file should be included in a file list.
actionPerformed(ActionEvent) - Method in class io.scif.gui.ImageViewer: Handles menu commands.
ACTLChunk() - Constructor for class io.scif.formats.APNGFormat.ACTLChunk
add(ImageMetadata) - Method in class io.scif.AbstractMetadata
add(byte) - Method in class io.scif.codec.ByteVector
add(byte[]) - Method in class io.scif.codec.ByteVector
add(byte[], int, int) - Method in class io.scif.codec.ByteVector
add(ImageMetadata, boolean) - Method in class io.scif.filters.AbstractMetadataWrapper
add(ImageMetadata) - Method in class io.scif.filters.AbstractMetadataWrapper
add(ImageMetadata, boolean) - Method in interface io.scif.filters.MetadataWrapper
add(ImageMetadata) - Method in interface io.scif.Metadata: Adds the provided image metadata to this dataset metadata
addAxis(CalibratedAxis) - Method in class io.scif.AbstractImageMetadata
addAxis(CalibratedAxis, long) - Method in class io.scif.AbstractImageMetadata
addAxis(AxisType, long) - Method in class io.scif.AbstractImageMetadata
addAxis(CalibratedAxis) - Method in interface io.scif.ImageMetadata: Appends the provided CalibratedAxis to the metadata's list of axes, with a length of 1.
addAxis(CalibratedAxis, long) - Method in interface io.scif.ImageMetadata: Appends the provided CalibratedAxis to the current CalibratedAxis array and creates a corresponding entry with the specified value in axis lengths.
addAxis(AxisType, long) - Method in interface io.scif.ImageMetadata: As ImageMetadata.addAxis(CalibratedAxis, long) using the default calibration value, per FormatTools.createAxis(AxisType).
addChunk(APNGFormat.FDATChunk) - Method in class io.scif.formats.APNGFormat.FCTLChunk
addComponents(Format) - Method in class io.scif.services.DefaultFormatService
addComponents(Format) - Method in interface io.scif.services.FormatService: Creates mappings between this Format and its components.
addCubeChannel(Map<Integer, String>) - Method in class io.scif.formats.ICSFormat.Metadata
addFormat(Format) - Method in class io.scif.services.DefaultFormatService
addFormat(Format) - Method in interface io.scif.services.FormatService: Makes the provided Format available for image IO operations in this context.
addIdat(APNGFormat.IDATChunk) - Method in class io.scif.formats.APNGFormat.Metadata
addLaserWavelength(Map<Integer, Integer>) - Method in class io.scif.formats.ICSFormat.Metadata
addLocation(int) - Method in class io.scif.formats.DICOMFormat.DICOMTag
addRange(AxisType, String) - Method in class io.scif.img.ImageRegion
addStepChannel(Map<Integer, String>) - Method in class io.scif.formats.ICSFormat.Metadata
ALL_DOMAINS - Static variable in class io.scif.util.FormatTools: List of all supported domains.
ALT_ZVI - Static variable in class io.scif.common.DateTools
ALT_ZVI_EPOCH - Static variable in class io.scif.common.DateTools
APERTURE_VALUE - Static variable in class io.scif.formats.tiff.IFD
APNGChunk(byte[]) - Constructor for class io.scif.formats.APNGFormat.APNGChunk
APNGFormat - Class in io.scif.formats: SCIFIO Format supporting the PNG and APNG image formats.
APNGFormat() - Constructor for class io.scif.formats.APNGFormat
APNGFormat.ACTLChunk - Class in io.scif.formats: Represents the acTL chunk of the APNG image format.
APNGFormat.APNGChunk - Class in io.scif.formats: A parent class for all APNG Chunk classes.
APNGFormat.APNGTranslator - Class in io.scif.formats: This class can be used for translating any io.scif.Metadata to Metadata for writing Animated Portable Network Graphics (APNG) files.
APNGFormat.Checker - Class in io.scif.formats: File format SCIFIO Checker for Animated Portable Network Graphics (APNG) images.
APNGFormat.FCTLChunk - Class in io.scif.formats: Represents the fcTL chunk of the APNG image format.
APNGFormat.FDATChunk - Class in io.scif.formats: Represents the fdAT chunk of the APNG image format.
APNGFormat.IDATChunk - Class in io.scif.formats: Represents the IDAT chunk of the APNG image format.
APNGFormat.IENDChunk - Class in io.scif.formats: This class represents the critical IEND chunk that signifies the end of a PNG stream.
APNGFormat.IHDRChunk - Class in io.scif.formats: Represents the IHDR chunk of the APNG image format.
APNGFormat.Metadata - Class in io.scif.formats: File format SCIFIO Metadata for Animated Portable Network Graphics (APNG) images.
APNGFormat.Parser - Class in io.scif.formats: File format SCIFIO Parser for Animated Portable Network Graphics (APNG) images.
APNGFormat.PLTEChunk - Class in io.scif.formats: Represents the PLTE chunk of the APNG image format.
APNGFormat.Reader - Class in io.scif.formats: File format SCIFIO Reader for Animated Portable Network Graphics (APNG) images.
APNGFormat.Writer - Class in io.scif.formats: The SCIFIO file format writer for PNG and APNG files.
APNGTranslator() - Constructor for class io.scif.formats.APNGFormat.APNGTranslator
ArrayDataAccessConverter - Class in io.scif.img.converters: PlaneConverter implementation specialized for populating ArrayImg instances.
ArrayDataAccessConverter() - Constructor for class io.scif.img.converters.ArrayDataAccessConverter
ARTIST - Static variable in class io.scif.formats.tiff.IFD
asBrowsableLocation(Location) - Method in class io.scif.AbstractHasFormat: Safely casts a Location to a BrowsableLocation, throwing a FormatException if the cast is not possible.
asBrowsableLocation(DataHandle<Location>) - Method in class io.scif.AbstractHasFormat: Convenience overload of AbstractHasFormat.asBrowsableLocation(Location) that operates on a handle.
assertId(Object, boolean, int) - Static method in class io.scif.util.FormatTools: Asserts that the current file is either null, or not, according to the given flag.
assertStream(DataHandle<Location>, boolean, int) - Static method in class io.scif.util.FormatTools: Asserts that the current file is either null, or not, according to the given flag.
ASTRONOMY_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the astronomy domain.
autoscale(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Perform autoscaling on the given BufferedImage.
autoscale(BufferedImage, int, int) - Static method in class io.scif.gui.AWTImageTools: Perform autoscaling on the given BufferedImage; map min to 0 and max to 255.
autoscale(byte[], int, int, int, boolean) - Static method in class io.scif.util.ImageTools: Perform autoscaling on the given byte array; map min to 0 and max to 255.
AVI_MAGIC_STRING - Static variable in class io.scif.formats.AVIFormat.Checker
AVIFormat - Class in io.scif.formats: AVIReader is the file format reader for AVI files.
AVIFormat() - Constructor for class io.scif.formats.AVIFormat
AVIFormat.Checker - Class in io.scif.formats
AVIFormat.Metadata - Class in io.scif.formats
AVIFormat.Parser - Class in io.scif.formats
AVIFormat.Reader - Class in io.scif.formats
AVIFormat.Translator - Class in io.scif.formats
AVIFormat.Writer - Class in io.scif.formats
avoidUndeclaredNamespaces(String) - Method in class io.scif.xml.DefaultXMLService
avoidUndeclaredNamespaces(String) - Method in interface io.scif.xml.XMLService: Replaces NS:tag with NS_tag for undeclared namespaces
AWTImageTools - Class in io.scif.gui: A utility class with convenience methods for manipulating images in BufferedImage form.
axes(String...) - Method in class io.scif.io.location.TestImgLocation.Builder
AxisGuesser - Class in io.scif: AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T or C), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
AxisGuesser(FilePattern, AxisType[], long, long, long, boolean) - Constructor for class io.scif.AxisGuesser: Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide.
AxisValue(AxisType, long) - Constructor for class io.scif.util.SCIFIOMetadataTools.AxisValue

B

Base64Codec - Class in io.scif.codec: Implements encoding (compress) and decoding (decompress) methods for Base64.
Base64Codec() - Constructor for class io.scif.codec.Base64Codec
BaseHandler - Class in io.scif.xml: Top-level SAX handler.
BaseHandler(LogService) - Constructor for class io.scif.xml.BaseHandler
baseTiff - Variable in class io.scif.formats.MicromanagerFormat.Position
BaseTIFFParser() - Constructor for class io.scif.formats.TIFFFormat.BaseTIFFParser
bgrToRgb(byte[], boolean, int, int) - Static method in class io.scif.util.ImageTools: Reorganizes the provided BGR buffer to be in RGB order.
BIG - Static variable in class io.scif.formats.tiff.TiffConstants
BIG_TIFF - Static variable in class io.scif.formats.tiff.IFD
BIG_TIFF_BYTES_PER_ENTRY - Static variable in class io.scif.formats.tiff.TiffConstants: The number of bytes in each IFD entry of a BigTIFF file.
BIG_TIFF_KEY - Static variable in class io.scif.formats.TIFFFormat.Writer
BIG_TIFF_MAGIC_NUMBER - Static variable in class io.scif.formats.tiff.TiffConstants
binning - Variable in class io.scif.formats.MicromanagerFormat.Position
BitBuffer - Class in io.scif.codec: A class for reading arbitrary numbers of bits from a byte array.
BitBuffer(byte[]) - Constructor for class io.scif.codec.BitBuffer: Default constructor.
BITS_PER_SAMPLE - Static variable in class io.scif.formats.tiff.IFD
bitsPerSample - Variable in class io.scif.codec.CodecOptions: Number of bits per channel.
BitWriter - Class in io.scif.codec: A class for writing arbitrary numbers of bits to a byte array.
BitWriter() - Constructor for class io.scif.codec.BitWriter: Constructs a new bit writer.
BitWriter(int) - Constructor for class io.scif.codec.BitWriter: Constructs a new bit writer with the given initial buffer size.
blankImage(ImageMetadata, long[], int) - Static method in class io.scif.gui.AWTImageTools: Creates a blank image with the given dimensions and transfer type.
blankPlane(Interval) - Method in class io.scif.AbstractPlane
blankPlane(Interval) - Method in class io.scif.BufferedImagePlane
blankPlane(Interval) - Method in class io.scif.ByteArrayPlane
BLOCK_END - Static variable in class io.scif.FilePatternBlock
BLOCK_START - Static variable in class io.scif.FilePatternBlock
BMP_MAGIC_STRING - Static variable in class io.scif.formats.BMPFormat
BMPFormat - Class in io.scif.formats: BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
BMPFormat() - Constructor for class io.scif.formats.BMPFormat
BMPFormat.Checker - Class in io.scif.formats
BMPFormat.Metadata - Class in io.scif.formats
BMPFormat.Parser - Class in io.scif.formats
BMPFormat.Reader - Class in io.scif.formats
BRIGHTNESS_VALUE - Static variable in class io.scif.formats.tiff.IFD
BufferedImagePlane - Class in io.scif: A Plane implementation using a BufferedImage for the underlying data representation.
BufferedImagePlane() - Constructor for class io.scif.BufferedImagePlane
BufferedImagePlane(ImageMetadata, Interval) - Constructor for class io.scif.BufferedImagePlane
BufferedImageReader<M extends TypedMetadata> - Class in io.scif.gui: BufferedImageReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
BufferedImageReader() - Constructor for class io.scif.gui.BufferedImageReader: Constructs a new BIFormatReader.
BufferedImageTools - Class in io.scif.gui: Collection of static utility methods for working with BufferedImage.
BufferedImageTools() - Constructor for class io.scif.gui.BufferedImageTools
bufferedReadingEnabled() - Method in class io.scif.config.SCIFIOConfig
build() - Method in class io.scif.io.location.TestImgLocation.Builder
builder() - Static method in class io.scif.io.location.TestImgLocation
Builder() - Constructor for class io.scif.io.location.TestImgLocation.Builder
buildFileChooser(Collection<Format>) - Method in class io.scif.gui.DefaultGUIService
buildFileChooser(Collection<Format>, boolean) - Method in class io.scif.gui.DefaultGUIService
buildFileChooser(FileFilter[]) - Method in class io.scif.gui.DefaultGUIService
buildFileChooser(FileFilter[], boolean) - Method in class io.scif.gui.DefaultGUIService
buildFileChooser(Collection<Format>) - Method in interface io.scif.gui.GUIService: Constructs a file chooser for the given file format handler.
buildFileChooser(Collection<Format>, boolean) - Method in interface io.scif.gui.GUIService: Constructs a file chooser for the given file format handler.
buildFileChooser(FileFilter[]) - Method in interface io.scif.gui.GUIService: Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter.
buildFileChooser(FileFilter[], boolean) - Method in interface io.scif.gui.GUIService: Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter, if one is not already specified.
buildFileFilters(Collection<Format>) - Method in class io.scif.gui.DefaultGUIService
buildFileFilters(Collection<Format>) - Method in interface io.scif.gui.GUIService: Constructs a list of file filters for the given file format handler.
ByteAccessLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for ByteAccess types.
ByteAccessLoader(Reader, ImageRegion, IntFunction<ByteAccess>) - Constructor for class io.scif.img.cell.loaders.ByteAccessLoader
ByteArrayLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for ByteArray types.
ByteArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.ByteArrayLoader
ByteArrayPlane - Class in io.scif: A naive Plane implementation that uses byte[] for its underlying data type.
ByteArrayPlane() - Constructor for class io.scif.ByteArrayPlane
ByteArrayPlane(ImageMetadata, Interval) - Constructor for class io.scif.ByteArrayPlane
ByteArrayReader<M extends TypedMetadata> - Class in io.scif: Abstract superclass for all Reader implementations that return a ByteArrayPlane when reading datasets.
ByteArrayReader() - Constructor for class io.scif.ByteArrayReader
BYTES_PER_ENTRY - Static variable in class io.scif.formats.tiff.TiffConstants: The number of bytes in each IFD entry.
byteValue() - Method in class io.scif.formats.tiff.TiffRational: Returns the value of the specified number as a byte.
ByteVector - Class in io.scif.codec: A growable array of bytes.
ByteVector() - Constructor for class io.scif.codec.ByteVector
ByteVector(int) - Constructor for class io.scif.codec.ByteVector
ByteVector(byte[]) - Constructor for class io.scif.codec.ByteVector

C

c() - Method in class io.scif.gui.XYCTuple
C_AXIS - Static variable in class io.scif.AxisGuesser: Axis type for channels.
calibrate(Metadata, int, double[]) - Static method in class io.scif.util.FormatTools: Applies the given scale value, and an origin of 0.0, to each LinearAxis in the provided Metadata.
calibrate(Metadata, int, double[], double[]) - Static method in class io.scif.util.FormatTools: Applies the given scale and origin values to each LinearAxis in the provided Metadata.
calibrate(CalibratedAxis, double, double) - Static method in class io.scif.util.FormatTools: Applies the given scale and origin to the provided CalibratedAxis , if it is a LinearAxis.
calibrate(CalibratedAxis, double, double, String) - Static method in class io.scif.util.FormatTools: As FormatTools.calibrate(CalibratedAxis, double, double) but also sets the unit of the axis.
cameraMode - Variable in class io.scif.formats.MicromanagerFormat.Position
cameraRef - Variable in class io.scif.formats.MicromanagerFormat.Position
CAN_GROUP - Static variable in class io.scif.util.FormatTools
canChangePattern() - Method in class io.scif.filters.FileStitcher
canConvert(Class<?>, Class<?>) - Method in class io.scif.convert.FileToDatasetConverter
canConvert(Object, Class<?>) - Method in class io.scif.convert.FileToDatasetConverter
canConvert(Object, Type) - Method in class io.scif.convert.FileToDatasetConverter
canConvert(Object, Class<?>) - Method in class io.scif.convert.StringToDatasetConverter
canConvert(Object, Type) - Method in class io.scif.convert.StringToDatasetConverter
canDoQT() - Method in class io.scif.formats.qt.DefaultQTJavaService
canDoQT() - Method in interface io.scif.formats.qt.QTJavaService: Whether QuickTime is available to this JVM.
canDoStacks() - Method in class io.scif.AbstractWriter
canDoStacks() - Method in class io.scif.formats.APNGFormat.Writer
canDoStacks() - Method in class io.scif.formats.AVIFormat.Writer
canDoStacks() - Method in class io.scif.formats.ICSFormat.Writer
canDoStacks() - Method in class io.scif.formats.JPEG2000Format.Writer: Overridden to indicate that stacks are not supported.
canDoStacks() - Method in class io.scif.formats.qt.LegacyQTFormat.Writer
canDoStacks() - Method in class io.scif.formats.qt.NativeQTFormat.Writer
canDoStacks() - Method in class io.scif.formats.TIFFFormat.Writer
canDoStacks() - Method in interface io.scif.Writer
CANNOT_GROUP - Static variable in class io.scif.util.FormatTools
canOpen(Location) - Method in interface io.scif.services.DatasetIOService: Determines whether the given source can be opened as a Dataset using the DatasetIOService.open(Location) method.
canOpen(String) - Method in interface io.scif.services.DatasetIOService: Determines whether the given source can be opened as a Dataset using the DatasetIOService.open(Location) method.
canOpen(Location) - Method in class io.scif.services.DefaultDatasetIOService
canOpen(String) - Method in class io.scif.services.DefaultDatasetIOService
canSave(Location) - Method in interface io.scif.services.DatasetIOService: Determines whether the given destination can be used to save a Dataset using the DatasetIOService.save(Dataset, Location) method.
canSave(Location) - Method in class io.scif.services.DefaultDatasetIOService
castMeta(Metadata) - Static method in class io.scif.util.SCIFIOMetadataTools: Casts the provided Metadata object to the generic type of this method.
castToTypedPlane(Plane) - Method in class io.scif.AbstractReader
castToTypedPlane(Plane) - Method in class io.scif.filters.AbstractReaderFilter
castToTypedPlane(Plane) - Method in interface io.scif.Reader: Convenience method for casting Plane implementations to the type associated with this Reader.
CELL_LENGTH - Static variable in class io.scif.formats.tiff.IFD
CELL_WIDTH - Static variable in class io.scif.formats.tiff.IFD
CFA_PATTERN - Static variable in class io.scif.formats.tiff.IFD
CHANNEL_NAME - Static variable in class io.scif.util.FormatTools
CHANNEL_NUM - Static variable in class io.scif.util.FormatTools
ChannelFiller - Class in io.scif.filters: For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
ChannelFiller() - Constructor for class io.scif.filters.ChannelFiller
ChannelFillerMetadata - Class in io.scif.filters: MetadataWrapper implementation specifically for use with the ChannelFiller.
ChannelFillerMetadata() - Constructor for class io.scif.filters.ChannelFillerMetadata
channels - Variable in class io.scif.codec.CodecOptions: Number of channels.
channels - Variable in class io.scif.formats.MicromanagerFormat.Position
CharAccessLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for CharArray types.
CharAccessLoader(Reader, ImageRegion, IntFunction<CharAccess>) - Constructor for class io.scif.img.cell.loaders.CharAccessLoader
CharArrayLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for CharArray types.
CharArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.CharArrayLoader
checkBufferSize(int, Metadata, int) - Static method in class io.scif.util.FormatTools: Checks that the given buffer length is long enough to hold planes of the specified image index, using the provided Reader.
checkBufferSize(Metadata, int, Interval, int) - Static method in class io.scif.util.FormatTools: Checks that the given buffer size is large enough to hold an image with the given planar lengths.
Checker - Interface in io.scif: Interface for all SCIFIO Checker components.
Checker() - Constructor for class io.scif.formats.APNGFormat.Checker
Checker() - Constructor for class io.scif.formats.AVIFormat.Checker
Checker() - Constructor for class io.scif.formats.BMPFormat.Checker
Checker() - Constructor for class io.scif.formats.DICOMFormat.Checker
Checker() - Constructor for class io.scif.formats.GIFFormat.Checker
Checker() - Constructor for class io.scif.formats.JPEG2000Format.Checker
Checker() - Constructor for class io.scif.formats.JPEGFormat.Checker
Checker() - Constructor for class io.scif.formats.KontronFormat.Checker
Checker() - Constructor for class io.scif.formats.MicromanagerFormat.Checker
Checker() - Constructor for class io.scif.formats.MinimalTIFFFormat.Checker
Checker() - Constructor for class io.scif.formats.MNGFormat.Checker
Checker() - Constructor for class io.scif.formats.NRRDFormat.Checker
Checker() - Constructor for class io.scif.formats.PCXFormat.Checker
Checker() - Constructor for class io.scif.formats.PGMFormat.Checker
Checker() - Constructor for class io.scif.formats.qt.NativeQTFormat.Checker
Checker() - Constructor for class io.scif.formats.ScancoISQFormat.Checker
Checker() - Constructor for class io.scif.formats.StratecPQCTFormat.Checker
Checker() - Constructor for class io.scif.formats.TestImgFormat.Checker
checkerIsOpen() - Method in class io.scif.config.SCIFIOConfig
checkerSetOpen(boolean) - Method in class io.scif.config.SCIFIOConfig
checkHeader(byte[]) - Method in class io.scif.AbstractChecker
checkHeader(byte[]) - Method in interface io.scif.Checker: Checks if the given bytes are a valid header for this Format.
checkHeader() - Method in class io.scif.formats.tiff.TiffParser: Checks the TIFF header.
checkLocation(DataHandle<Location>, SCIFIOConfig) - Method in class io.scif.AbstractWriter: Validate that the given output is consistent with the given configuration.
checkParams(int, long, byte[], Interval) - Method in class io.scif.AbstractWriter: Ensure that the arguments that are being passed to saveBytes(...) are valid.
checkPlaneForReading(Metadata, int, long, int, Interval) - Static method in class io.scif.util.FormatTools: As FormatTools.checkPlaneForWriting(io.scif.Metadata, int, long, int, net.imglib2.Interval) but also asserts that the Metadata has a non-null source attached.
checkPlaneForWriting(Metadata, int, long, int, Interval) - Static method in class io.scif.util.FormatTools: Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given Metadata.
checkPlaneNumber(Metadata, int, long) - Static method in class io.scif.util.FormatTools: Checks that the given plane number is valid for the given reader.
checkQTLibrary() - Method in class io.scif.formats.qt.DefaultQTJavaService
checkQTLibrary() - Method in interface io.scif.formats.qt.QTJavaService: Checks whether QTJava is available, throwing an exception if not.
checkSuffix(String, String) - Static method in class io.scif.util.FormatTools: Performs suffix matching for the given filename.
checkSuffix(String, String[]) - Static method in class io.scif.util.FormatTools: Performs suffix matching for the given filename.
checkTileSize(Metadata, Interval, int) - Static method in class io.scif.util.FormatTools: Checks that the given tile size is valid for the given reader.
CleaningRef - Interface in io.scif.refs: Interface for Reference subclasses that have some operation that should be performed after they are enqueued in a ReferenceQueue.
cleanUp() - Method in class io.scif.filters.AbstractReaderFilter: Helper method that is always called by the AbstractReaderFilter.close(boolean) method, if the fileOnly flag is false.
cleanUp() - Method in class io.scif.filters.ChannelFiller
cleanUp() - Method in class io.scif.filters.FileStitcher
cleanUp() - Method in class io.scif.filters.PlaneSeparator
cleanup() - Method in class io.scif.img.ImgPlusCtxCleaningProvider.ImgPlusCtxCleaner
cleanup() - Method in interface io.scif.refs.CleaningRef: Hook for cleaning up resources when this reference is removed from a ReferenceQueue.
clear() - Method in class io.scif.codec.ByteVector
clone() - Method in class io.scif.config.SCIFIOConfig
close() - Method in class io.scif.AbstractHasSource
close(boolean) - Method in class io.scif.AbstractMetadata
close(boolean) - Method in class io.scif.AbstractParser
close(boolean) - Method in class io.scif.AbstractReader
close(boolean) - Method in class io.scif.AbstractWriter
close() - Method in class io.scif.codec.JPEGTileDecoder
close(boolean) - Method in class io.scif.filters.AbstractMetadataWrapper
close(boolean) - Method in class io.scif.filters.AbstractReaderFilter
close() - Method in class io.scif.filters.AbstractReaderFilter
close(boolean) - Method in class io.scif.filters.MinMaxFilter
close(boolean) - Method in class io.scif.formats.APNGFormat.Metadata
close(boolean) - Method in class io.scif.formats.APNGFormat.Reader
close(boolean) - Method in class io.scif.formats.APNGFormat.Writer
close(boolean) - Method in class io.scif.formats.AVIFormat.Metadata
close() - Method in class io.scif.formats.AVIFormat.Writer
close(boolean) - Method in class io.scif.formats.BMPFormat.Metadata
close(boolean) - Method in class io.scif.formats.DICOMFormat.Metadata
close(boolean) - Method in class io.scif.formats.EPSFormat.Metadata
close() - Method in class io.scif.formats.FITSFormat.Metadata
close(boolean) - Method in class io.scif.formats.GIFFormat.Metadata
close(boolean) - Method in class io.scif.formats.ICSFormat.Metadata
close(boolean) - Method in class io.scif.formats.ICSFormat.Reader
close(int) - Method in class io.scif.formats.ICSFormat.Writer
close(boolean) - Method in class io.scif.formats.ImageIOFormat.Metadata
close(boolean) - Method in class io.scif.formats.JPEG2000Format.Metadata
close(boolean) - Method in class io.scif.formats.JPEGFormat.Metadata
close(boolean) - Method in class io.scif.formats.JPEGTileFormat.Metadata
close(boolean) - Method in class io.scif.formats.MicromanagerFormat.Metadata
close(boolean) - Method in class io.scif.formats.MicromanagerFormat.Reader
close(boolean) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
close(boolean) - Method in class io.scif.formats.MNGFormat.Metadata
close(boolean) - Method in class io.scif.formats.NRRDFormat.Metadata
close(boolean) - Method in class io.scif.formats.PCXFormat.Metadata
close(boolean) - Method in class io.scif.formats.PGMFormat.Metadata
close(boolean) - Method in class io.scif.formats.qt.LegacyQTFormat.Metadata
close(boolean) - Method in class io.scif.formats.qt.LegacyQTFormat.Reader
close() - Method in class io.scif.formats.qt.LegacyQTFormat.Writer
close(boolean) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
close() - Method in class io.scif.formats.qt.NativeQTFormat.Writer
close(boolean) - Method in class io.scif.formats.qt.PICTFormat.Metadata
close() - Method in class io.scif.formats.tiff.OnDemandLongArray
close() - Method in class io.scif.formats.tiff.TiffParser
close(boolean) - Method in class io.scif.formats.TIFFFormat.Metadata
close() - Method in class io.scif.formats.TIFFFormat.Writer
close() - Method in class io.scif.gui.PreviewPane: Closes the underlying image reader.
close(boolean) - Method in interface io.scif.HasSource: Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
close() - Method in interface io.scif.HasSource: Closes the image source(s) associated with this component and resets the component to its default state.
COBOL - Static variable in class io.scif.common.DateTools
COBOL_EPOCH - Static variable in class io.scif.common.DateTools
codeBlockSize - Variable in class io.scif.codec.JPEG2000CodecOptions: The maximum code-block size to use per tile-component as it would be provided to: J2KImageWriteParam#setCodeBlockSize(int[]) (WRITE).
Codec - Interface in io.scif.codec: This class is an interface for any kind of compression or decompression.
codec() - Method in class io.scif.SCIFIO: Gets this application context's CodecService.
CODEC_ANIMATION - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Animation codec.
CODEC_CINEPAK - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Cinepak codec.
CODEC_H_263 - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating H.263 codec.
CODEC_MOTION_JPEG_B - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Motion JPEG-B codec.
CODEC_MPEG_4 - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating MPEG-4 codec.
CODEC_RAW - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Raw codec.
CODEC_SORENSON - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Sorenson codec.
CODEC_SORENSON_3 - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Sorenson 3 codec.
CodecOptions - Class in io.scif.codec: Options for compressing and decompressing data.
CodecOptions() - Constructor for class io.scif.codec.CodecOptions: Construct a new CodecOptions.
CodecOptions(CodecOptions) - Constructor for class io.scif.codec.CodecOptions: Construct a new CodecOptions using the given CodecOptions.
CodecService - Interface in io.scif.codec: Interface for service which manages available Codecs.
CodedEnum - Interface in io.scif.enumeration: Enumeration which is coded.
COLOR_MAP - Static variable in class io.scif.formats.tiff.IFD
COLOR_SPACE - Static variable in class io.scif.formats.tiff.IFD
colorModel - Variable in class io.scif.codec.CodecOptions: Color model to use when constructing an image (WRITE).
COM - Static variable in class io.scif.codec.LosslessJPEGCodec
ComboFileFilter - Class in io.scif.gui: A file filter that recognizes files from a union of other filters.
ComboFileFilter(FileFilter[], String) - Constructor for class io.scif.gui.ComboFileFilter: Constructs a new filter from a list of other filters.
comment - Variable in class io.scif.formats.MicromanagerFormat.Position
COMPANION_SUFFIXES - Static variable in class io.scif.formats.TIFFFormat
compareTo(Object) - Method in class io.scif.formats.tiff.TiffIFDEntry
compareTo(TiffRational) - Method in class io.scif.formats.tiff.TiffRational: Compares this object with the specified object for order.
compareTo(Object) - Method in class io.scif.gui.ComboFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(FileFilter) - Method in class io.scif.gui.FormatFileFilter: Compares two FileFilter objects alphanumerically.
COMPONENTS_CONFIGURATION - Static variable in class io.scif.formats.tiff.IFD
compress(byte[][], CodecOptions) - Method in class io.scif.codec.AbstractCodec: 2D data block encoding default implementation.
compress(byte[], CodecOptions) - Method in class io.scif.codec.Base64Codec
compress(byte[], CodecOptions) - Method in interface io.scif.codec.Codec: Compresses a block of data.
compress(byte[][], CodecOptions) - Method in interface io.scif.codec.Codec: Compresses a block of data.
compress(byte[], CodecOptions) - Method in class io.scif.codec.HuffmanCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.JPEG2000Codec: The CodecOptions parameter should have the following fields set: width height bitsPerSample channels interleaved littleEndian lossless
compress(byte[], CodecOptions) - Method in class io.scif.codec.JPEGCodec: The CodecOptions parameter should have the following fields set: width height channels bitsPerSample interleaved littleEndian signed
compress(byte[], CodecOptions) - Method in class io.scif.codec.LosslessJPEGCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.LuraWaveCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.LZWCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.MJPBCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.MSRLECodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.MSVideoCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.NikonCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.PackbitsCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.PassthroughCodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.QTRLECodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.RPZACodec
compress(byte[], CodecOptions) - Method in class io.scif.codec.ZlibCodec
compress(CodecService, byte[], CodecOptions) - Method in enum io.scif.formats.tiff.TiffCompression: Encodes a strip of data.
compressBuffer(int, long, Plane, Interval) - Method in class io.scif.formats.JPEG2000Format.Writer: Compresses the buffer.
COMPRESSED_BITS_PER_PIXEL - Static variable in class io.scif.formats.tiff.IFD
COMPRESSION - Static variable in class io.scif.formats.tiff.IFD
COMPRESSION_J2K - Static variable in class io.scif.formats.TIFFFormat.Writer
COMPRESSION_J2K_LOSSY - Static variable in class io.scif.formats.TIFFFormat.Writer
COMPRESSION_JPEG - Static variable in class io.scif.formats.TIFFFormat.Writer
COMPRESSION_LZW - Static variable in class io.scif.formats.TIFFFormat.Writer
COMPRESSION_SUFFIXES - Static variable in class io.scif.util.FormatTools
COMPRESSION_UNCOMPRESSED - Static variable in class io.scif.formats.TIFFFormat.Writer
COMPRESSION_ZLIB - Static variable in class io.scif.formats.TIFFFormat.Writer
CompressionType - Enum in io.scif.codec: An enumeration of compression types.
Constants - Class in io.scif.common: Constants that are used within many classes in io.scif.common.
Constants() - Constructor for class io.scif.common.Constants
constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class io.scif.gui.AWTImageTools: Creates an image with the given DataBuffer.
constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class io.scif.gui.AWTImageTools: Creates an image with the given DataBuffer.
contains(Object) - Method in class io.scif.img.Range
CONTRAST - Static variable in class io.scif.formats.tiff.IFD
convert(Object, Class<T>) - Method in class io.scif.convert.FileToDatasetConverter
convert(Reader, Writer, String) - Static method in class io.scif.util.FormatTools: Convenience method for writing all of the images and metadata obtained from the specified Reader into the specified Writer.
convert(Reader, Writer, String, SCIFIOConfig) - Static method in class io.scif.util.FormatTools: As FormatTools.convert(Reader, Writer, String), with configuration options.
convertBytes(A, byte[], int) - Method in class io.scif.img.cell.loaders.AbstractArrayLoader: Type-specific conversion method.
convertBytes(ByteAccess, byte[], int) - Method in class io.scif.img.cell.loaders.ByteAccessLoader
convertBytes(ByteArray, byte[], int) - Method in class io.scif.img.cell.loaders.ByteArrayLoader
convertBytes(CharAccess, byte[], int) - Method in class io.scif.img.cell.loaders.CharAccessLoader
convertBytes(CharArray, byte[], int) - Method in class io.scif.img.cell.loaders.CharArrayLoader
convertBytes(DoubleAccess, byte[], int) - Method in class io.scif.img.cell.loaders.DoubleAccessLoader
convertBytes(DoubleArray, byte[], int) - Method in class io.scif.img.cell.loaders.DoubleArrayLoader
convertBytes(FloatAccess, byte[], int) - Method in class io.scif.img.cell.loaders.FloatAccessLoader
convertBytes(FloatArray, byte[], int) - Method in class io.scif.img.cell.loaders.FloatArrayLoader
convertBytes(IntAccess, byte[], int) - Method in class io.scif.img.cell.loaders.IntAccessLoader
convertBytes(IntArray, byte[], int) - Method in class io.scif.img.cell.loaders.IntArrayLoader
convertBytes(LongAccess, byte[], int) - Method in class io.scif.img.cell.loaders.LongAccessLoader
convertBytes(LongArray, byte[], int) - Method in class io.scif.img.cell.loaders.LongArrayLoader
convertBytes(ShortAccess, byte[], int) - Method in class io.scif.img.cell.loaders.ShortAccessLoader
convertBytes(ShortArray, byte[], int) - Method in class io.scif.img.cell.loaders.ShortArrayLoader
convertDate(long, int) - Static method in class io.scif.common.DateTools: Converts the given timestamp into an ISO8601 date.
convertDate(long, int, String) - Static method in class io.scif.common.DateTools: Converts the given timestamp into a date string with the given format.
convertDate(long, int, String, boolean) - Static method in class io.scif.common.DateTools: Converts the given timestamp into a date string with the given format.
convertRenderedImage(RenderedImage) - Static method in class io.scif.gui.AWTImageTools: Converts a java.awt.image.RenderedImage into a java.awt.image.BufferedImage.
copy(ImageMetadata) - Method in class io.scif.AbstractImageMetadata
copy() - Method in class io.scif.DefaultImageMetadata
copy() - Method in interface io.scif.ImageMetadata
copy(ImageMetadata) - Method in interface io.scif.ImageMetadata: Populates this ImageMetadata using the provided instance.
copy() - Method in class io.scif.img.cell.SCIFIOCellImg
copy() - Method in class io.scif.img.SCIFIOImgPlus
COPYRIGHT - Static variable in class io.scif.formats.tiff.IFD
copyScaled(BufferedImage, BufferedImage, Object) - Static method in class io.scif.gui.AWTImageTools: Copies the source image into the target, applying scaling.
CRC - Class in io.scif.common: Holds and calculates a CRC for verifying data integrity.
CRC() - Constructor for class io.scif.common.CRC
CRC_32_TABLE - Static variable in class io.scif.common.CRC
create(long...) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
create(Dimensions) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
create(int[]) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
create(long[], T) - Method in class io.scif.img.cell.SCIFIOCellImgFactory: Deprecated.
createAxes(AxisType...) - Static method in class io.scif.util.FormatTools: Creates an array, wrapping all provided AxisTypes as CalibratedAxis with calibration = 1.0.
createAxis(AxisType) - Static method in class io.scif.util.FormatTools: Wraps the provided AxisType in a CalibratedAxis with calibration = 1.0.
createChecker() - Method in class io.scif.AbstractFormat
createChecker() - Method in interface io.scif.Format: Create an instance of the Checker associated with this format.
createCompatibleWritableRaster(int, int) - Method in class io.scif.gui.Index16ColorModel
createCompatibleWritableRaster(int, int) - Method in class io.scif.gui.SignedColorModel
createCompatibleWritableRaster(int, int) - Method in class io.scif.gui.UnsignedIntColorModel
createDomainArray() - Method in class io.scif.AbstractReader: Helper method to lazily create the domain array for this reader instance, to avoid constantly re-creating the array.
createDomainArray() - Method in class io.scif.DefaultReader
createDomainArray() - Method in class io.scif.formats.APNGFormat.Reader
createDomainArray() - Method in class io.scif.formats.AVIFormat.Reader
createDomainArray() - Method in class io.scif.formats.BMPFormat.Reader
createDomainArray() - Method in class io.scif.formats.DICOMFormat.Reader
createDomainArray() - Method in class io.scif.formats.EPSFormat.Reader
createDomainArray() - Method in class io.scif.formats.FITSFormat.Reader
createDomainArray() - Method in class io.scif.formats.GIFFormat.Reader
createDomainArray() - Method in class io.scif.formats.ICSFormat.Reader
createDomainArray() - Method in class io.scif.formats.ImageIOFormat.Reader
createDomainArray() - Method in class io.scif.formats.JPEG2000Format.Reader
createDomainArray() - Method in class io.scif.formats.JPEGTileFormat.Reader
createDomainArray() - Method in class io.scif.formats.KontronFormat.Reader
createDomainArray() - Method in class io.scif.formats.MicromanagerFormat.Reader
createDomainArray() - Method in class io.scif.formats.MinimalTIFFFormat.Reader
createDomainArray() - Method in class io.scif.formats.MNGFormat.Reader
createDomainArray() - Method in class io.scif.formats.NRRDFormat.Reader
createDomainArray() - Method in class io.scif.formats.PCXFormat.Reader
createDomainArray() - Method in class io.scif.formats.PGMFormat.Reader
createDomainArray() - Method in class io.scif.formats.qt.LegacyQTFormat.Reader
createDomainArray() - Method in class io.scif.formats.qt.NativeQTFormat.Reader
createDomainArray() - Method in class io.scif.formats.qt.PICTFormat.Reader
createDomainArray() - Method in class io.scif.formats.ScancoISQFormat.Reader
createDomainArray() - Method in class io.scif.formats.StratecPQCTFormat.Reader
createDomainArray() - Method in class io.scif.formats.TestImgFormat.Reader
createDomainArray() - Method in class io.scif.formats.TIFFJAIFormat.Reader
createFactory(Metadata, SCIFIOConfig.ImgMode[], T) - Method in class io.scif.img.DefaultImgFactoryHeuristic
createFactory(Metadata, SCIFIOConfig.ImgMode[], T) - Method in interface io.scif.img.ImgFactoryHeuristic
createImageMetadata(int) - Method in class io.scif.AbstractMetadata
createImageMetadata(int) - Method in class io.scif.formats.TIFFFormat.Metadata
createImageMetadata(int) - Method in interface io.scif.Metadata: Creates the specified number of blank ImageMetadata.
createIndexMaps(int[][], int[][]) - Static method in class io.scif.formats.TestImgFormat.TestImgUtils: Populates a mapping between indicies and color values, and the inverse mapping of color values to indicies.
createIndexValueMap(int[][]) - Static method in class io.scif.formats.TestImgFormat.TestImgUtils: Populates the given array with a random mapping of indices to values.
createInverseIndexMap(int[][], int[][]) - Static method in class io.scif.formats.TestImgFormat.TestImgUtils: Populates an array with inverse mapping of values and indices, drawn from a base index:value mapping.
createMetadata() - Method in class io.scif.AbstractFormat
createMetadata() - Method in interface io.scif.Format: Create an instance of the Metadata associated with this format.
createParser() - Method in class io.scif.AbstractFormat
createParser() - Method in interface io.scif.Format: Create an instance of the Parser associated with this format.
createPlane(Interval) - Method in class io.scif.ByteArrayReader
createPlane(ImageMetadata, Interval) - Method in class io.scif.ByteArrayReader
createPlane(Interval) - Method in class io.scif.filters.AbstractReaderFilter
createPlane(ImageMetadata, Interval) - Method in class io.scif.filters.AbstractReaderFilter
createPlane(Interval) - Method in class io.scif.gui.BufferedImageReader
createPlane(ImageMetadata, Interval) - Method in class io.scif.gui.BufferedImageReader
createPlane(Interval) - Method in interface io.scif.Reader: Creates a blank plane compatible with this reader.
createPlane(ImageMetadata, Interval) - Method in interface io.scif.Reader: Creates a blank plane compatible with this reader.
createPlane(Interval) - Method in interface io.scif.TypedReader
createReader() - Method in class io.scif.AbstractFormat
createReader() - Method in interface io.scif.Format: Creates an instance of the Reader associated with this format.
createWriter() - Method in class io.scif.AbstractFormat
createWriter() - Method in interface io.scif.Format: Creates an instance of the Writer associated with this format.
CS_2C - Static variable in class io.scif.gui.TwoChannelColorSpace
curve - Variable in class io.scif.codec.NikonCodecOptions
CUSTOM_RENDERED - Static variable in class io.scif.formats.tiff.IFD

D

DAC - Static variable in class io.scif.codec.LosslessJPEGCodec
DataPlane<T> - Interface in io.scif: Extension of the base Plane interface.
datasetIO() - Method in class io.scif.SCIFIO: Gets this application context's DatasetIOService.
DatasetIOPlugin - Class in io.scif.io: I/O plugin for Datasets.
DatasetIOPlugin() - Constructor for class io.scif.io.DatasetIOPlugin
DatasetIOService - Interface in io.scif.services: A service for opening and saving Datasets using SCIFIO.
DATE_FORMAT - Static variable in class io.scif.formats.MicromanagerFormat.Parser
DATE_FORMATS - Static variable in class io.scif.formats.ICSFormat.ICSUtils
DATE_FORMATS - Static variable in class io.scif.formats.TIFFFormat.BaseTIFFParser
DATE_TIME - Static variable in class io.scif.formats.tiff.IFD
DATE_TIME_DIGITIZED - Static variable in class io.scif.formats.tiff.IFD
DATE_TIME_ORIGINAL - Static variable in class io.scif.formats.tiff.IFD
DateTools - Class in io.scif.common: A utility class with convenience methods for working with dates.
decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) - Method in interface io.scif.services.LuraWaveService: Wraps com.luratech.lwf.lwfDecoder#decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) .
decodeToMemoryGray8(byte[], int, int, int) - Method in interface io.scif.services.LuraWaveService: Wraps com.luratech.lwf.lwfDecoder#decodeToMemoryGray8(byte[], int, int, int) .
decodeWord(byte[], int, int, boolean) - Method in class io.scif.img.DefaultImgUtilityService
decodeWord(byte[], int, int, boolean) - Method in interface io.scif.img.ImgUtilityService
decompress(byte[]) - Method in class io.scif.codec.AbstractCodec
decompress(byte[][]) - Method in class io.scif.codec.AbstractCodec
decompress(byte[], CodecOptions) - Method in class io.scif.codec.AbstractCodec
decompress(byte[][], CodecOptions) - Method in class io.scif.codec.AbstractCodec: 2D data block decoding default implementation.
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.Base64Codec
decompress(byte[], CodecOptions) - Method in interface io.scif.codec.Codec: Decompresses a block of data.
decompress(byte[][], CodecOptions) - Method in interface io.scif.codec.Codec: Decompresses a block of data.
decompress(byte[]) - Method in interface io.scif.codec.Codec: Decompresses a block of data.
decompress(byte[][]) - Method in interface io.scif.codec.Codec: Decompresses a block of data.
decompress(DataHandle<Location>, CodecOptions) - Method in interface io.scif.codec.Codec: Decompresses data from the given DataHandle.
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.HuffmanCodec: The CodecOptions parameter must be an instance of HuffmanCodecOptions, and should have the following fields set: table bitsPerSample maxBytes
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.JPEG2000Codec: The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(byte[], CodecOptions) - Method in class io.scif.codec.JPEG2000Codec: The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.JPEGCodec: The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.LosslessJPEGCodec: The CodecOptions parameter should have the following fields set: interleaved littleEndian
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.LuraWaveCodec
decompress(byte[], CodecOptions) - Method in class io.scif.codec.LuraWaveCodec: The CodecOptions parameter should have the following fields set: maxBytes
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.LZWCodec: The CodecOptions parameter should have the following fields set: maxBytes
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.MJPBCodec: The CodecOptions parameter must be an instance of MJPBCodecOptions, and should have the following fields set: interlaced width height bitsPerSample littleEndian interleaved
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.MSRLECodec: The CodecOptions parameter should have the following fields set: width height previousImage
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.MSVideoCodec: The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.NikonCodec: The CodecOptions parameter must be an instance of NikonCodecOptions , and should have the following fields set: vPredictor curve split bitsPerSample maxBytes width height
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.PackbitsCodec: The CodecOptions parameter should have the following fields set: maxBytes
decompress(byte[], CodecOptions) - Method in class io.scif.codec.PassthroughCodec
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.PassthroughCodec
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.QTRLECodec
decompress(byte[], CodecOptions) - Method in class io.scif.codec.QTRLECodec: The CodecOptions parameter should have the following fields set: width height bitsPerSample previousImage
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.RPZACodec: The CodecOptions parameter should have the following fields set: width height
decompress(DataHandle<Location>, CodecOptions) - Method in class io.scif.codec.ZlibCodec
decompress(CodecService, byte[], CodecOptions) - Method in enum io.scif.formats.tiff.TiffCompression: Decodes a strip of data.
DEFAULT_DATE - Static variable in class io.scif.formats.StratecPQCTFormat.Metadata: Date used when parsing fails
DEFAULT_KEY - Static variable in class io.scif.formats.APNGFormat.Metadata
DefaultChecker - Class in io.scif: Default Checker implementation.
DefaultChecker() - Constructor for class io.scif.DefaultChecker
DefaultCodecService - Class in io.scif.codec: Default service for managing available Codecs.
DefaultCodecService() - Constructor for class io.scif.codec.DefaultCodecService
DefaultComponent - Interface in io.scif: Marker interface for default class implementations.
DefaultDatasetIOService - Class in io.scif.services: Default DatasetIOService implementation.
DefaultDatasetIOService() - Constructor for class io.scif.services.DefaultDatasetIOService
DefaultFilePatternService - Class in io.scif.services: Default FilePatternService implementation.
DefaultFilePatternService() - Constructor for class io.scif.services.DefaultFilePatternService
DefaultFormatService - Class in io.scif.services: Default FormatService implementation
DefaultFormatService() - Constructor for class io.scif.services.DefaultFormatService
DefaultGUIService - Class in io.scif.gui: Basic GUIService implementation.
DefaultGUIService() - Constructor for class io.scif.gui.DefaultGUIService
DefaultImageMetadata - Class in io.scif: Default implementation of ImageMetadata.
DefaultImageMetadata() - Constructor for class io.scif.DefaultImageMetadata
DefaultImageMetadata(ImageMetadata) - Constructor for class io.scif.DefaultImageMetadata
DefaultImgFactoryHeuristic - Class in io.scif.img: Default ImgFactoryHeuristic implementation.
DefaultImgFactoryHeuristic() - Constructor for class io.scif.img.DefaultImgFactoryHeuristic
DefaultImgUtilityService - Class in io.scif.img: Helper methods for converting between SCIFIO and ImgLib2 data structures.
DefaultImgUtilityService() - Constructor for class io.scif.img.DefaultImgUtilityService
DefaultInitializeService - Class in io.scif.services: Default InitializeService implementation.
DefaultInitializeService() - Constructor for class io.scif.services.DefaultInitializeService
DefaultMetadata - Class in io.scif: A dummy Metadata implementation.
DefaultMetadata() - Constructor for class io.scif.DefaultMetadata
DefaultMetadata(Metadata) - Constructor for class io.scif.DefaultMetadata
DefaultMetadata(List<ImageMetadata>) - Constructor for class io.scif.DefaultMetadata
DefaultMetadataService - Class in io.scif: Default service for working with SCIFIO metadata.
DefaultMetadataService() - Constructor for class io.scif.DefaultMetadataService
DefaultMetaTable - Class in io.scif: Default MetaTable implementation.
DefaultMetaTable() - Constructor for class io.scif.DefaultMetaTable
DefaultMetaTable(boolean) - Constructor for class io.scif.DefaultMetaTable: Basic constructor
DefaultMetaTable(Map<String, Object>) - Constructor for class io.scif.DefaultMetaTable: Construct a MetaTable and populate it using an existing map.
defaultMinMax(int) - Static method in class io.scif.util.FormatTools: Get the default range for the specified pixel type.
defaultMinMax(int, boolean) - Static method in class io.scif.util.FormatTools: Get the default range for the specified bits per pixel.
defaultMinMax(int, int) - Static method in class io.scif.util.FormatTools: Helper method to delegate to FormatTools.defaultMinMax(int, boolean) or FormatTools.defaultMinMax(int) based on the given parameters.
defaultMinMax(ImageMetadata) - Static method in class io.scif.util.FormatTools: Helper method to get the default range for the specified ImageMetadata.
DefaultParser - Class in io.scif: Default Parser implementation.
DefaultParser() - Constructor for class io.scif.DefaultParser
DefaultPlaneConverterService - Class in io.scif.img.converters: Default PlaneConverterService implementation.
DefaultPlaneConverterService() - Constructor for class io.scif.img.converters.DefaultPlaneConverterService
DefaultQTJavaService - Class in io.scif.formats.qt: Default service for working with QuickTime for Java.
DefaultQTJavaService() - Constructor for class io.scif.formats.qt.DefaultQTJavaService
DefaultReader - Class in io.scif: Non-functional default Reader implementation.
DefaultReader() - Constructor for class io.scif.DefaultReader
DefaultRefManagerService - Class in io.scif.refs: Default RefManagerService implementation.
DefaultRefManagerService() - Constructor for class io.scif.refs.DefaultRefManagerService
defaultTestImg() - Static method in class io.scif.io.location.TestImgLocation
DefaultTiffService - Class in io.scif.formats.tiff: Default service for working with TIFF files.
DefaultTiffService() - Constructor for class io.scif.formats.tiff.DefaultTiffService
DefaultTranslator - Class in io.scif: Basic Translator implementation.
DefaultTranslator() - Constructor for class io.scif.DefaultTranslator
DefaultTranslatorService - Class in io.scif.services: Default TranslatorService implementation.
DefaultTranslatorService() - Constructor for class io.scif.services.DefaultTranslatorService
DefaultWriter - Class in io.scif: Non-functional default Writer implementation.
DefaultWriter() - Constructor for class io.scif.DefaultWriter
DefaultXMLService - Class in io.scif.xml: Default service for working with XML.
DefaultXMLService() - Constructor for class io.scif.xml.DefaultXMLService
DependencyException - Exception in io.scif: Exception thrown when there is an object instantiation error or error processing dependencies.
DependencyException(String) - Constructor for exception io.scif.DependencyException: Default constructor.
DependencyException(String, Class<? extends Service>) - Constructor for exception io.scif.DependencyException: Default constructor.
DependencyException(String, Class<? extends Service>, Throwable) - Constructor for exception io.scif.DependencyException: Default constructor.
DependencyException(Throwable) - Constructor for exception io.scif.DependencyException: Default constructor.
dest() - Method in class io.scif.DefaultTranslator
dest() - Method in class io.scif.formats.APNGFormat.APNGTranslator
dest() - Method in class io.scif.formats.AVIFormat.Translator
dest() - Method in class io.scif.formats.EPSFormat.EPSTranslator
dest() - Method in class io.scif.formats.ICSFormat.ICSTranslator
dest() - Method in class io.scif.formats.ImageIOFormat.ImageIOTranslator
dest() - Method in class io.scif.formats.MicromanagerFormat.MicromanagerTranslator
dest() - Method in class io.scif.formats.qt.LegacyQTFormat.LegacyQTTranslator
dest() - Method in class io.scif.formats.qt.NativeQTFormat.NativeQTTranslator
dest() - Method in class io.scif.formats.TestImgFormat.TestImgTranslator
dest() - Method in class io.scif.formats.TIFFFormat.TIFFTranslator
dest() - Method in interface io.scif.Translator
detectorID - Variable in class io.scif.formats.MicromanagerFormat.Position
detectorManufacturer - Variable in class io.scif.formats.MicromanagerFormat.Position
detectorModel - Variable in class io.scif.formats.MicromanagerFormat.Position
DEVICE_NAME_INDEX - Static variable in class io.scif.formats.StratecPQCTFormat: Index of device name in the header
DHP - Static variable in class io.scif.codec.LosslessJPEGCodec
DHT - Static variable in class io.scif.codec.LosslessJPEGCodec
DICOM_MAGIC_STRING - Static variable in class io.scif.formats.DICOMFormat
DICOMDictionary - Class in io.scif.formats.dicom: Data dictionary of DICOM types.
DICOMDictionary() - Constructor for class io.scif.formats.dicom.DICOMDictionary
DICOMFormat - Class in io.scif.formats: DICOMReader is the file format reader for DICOM files.
DICOMFormat() - Constructor for class io.scif.formats.DICOMFormat
DICOMFormat.Checker - Class in io.scif.formats
DICOMFormat.DICOMTag - Class in io.scif.formats
DICOMFormat.Metadata - Class in io.scif.formats
DICOMFormat.Parser - Class in io.scif.formats
DICOMFormat.Reader - Class in io.scif.formats
DICOMTag() - Constructor for class io.scif.formats.DICOMFormat.DICOMTag
difference(byte[], IFD) - Method in class io.scif.formats.tiff.DefaultTiffService
difference(byte[], IFD) - Method in interface io.scif.formats.tiff.TiffService: Performs in-place differencing according to the given predictor value.
DIGITAL_ZOOM_RATIO - Static variable in class io.scif.formats.tiff.IFD
DimensionSwapper - Class in io.scif.filters: Handles swapping the dimension order of an image series.
DimensionSwapper() - Constructor for class io.scif.filters.DimensionSwapper
DimensionSwapperMetadata - Class in io.scif.filters: MetadataWrapper implementation specifically for use with the DimensionSwapper.
DimensionSwapperMetadata() - Constructor for class io.scif.filters.DimensionSwapperMetadata
disable(Class<? extends Filter>) - Method in interface io.scif.filters.MasterFilter: Removes the specified filter from the filter stack, if present.
disable(Class<? extends Filter>) - Method in class io.scif.filters.MasterFilterHelper
disable(Class<? extends Filter>) - Method in class io.scif.filters.ReaderFilter
dispose() - Method in class io.scif.img.cell.SCIFIOCellImg
dispose() - Method in class io.scif.img.SCIFIOImgPlus
dispose() - Method in class io.scif.refs.DefaultRefManagerService: Signal to any active RefCleaner that this service has been disposed.
DNL - Static variable in class io.scif.codec.LosslessJPEGCodec
DOCUMENT_NAME - Static variable in class io.scif.formats.tiff.IFD
DOT_RANGE - Static variable in class io.scif.formats.tiff.IFD
DOUBLE - Static variable in class io.scif.util.FormatTools: Identifies the DOUBLE data type used to store pixel values.
DoubleAccessLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for DoubleArray types.
DoubleAccessLoader(Reader, ImageRegion, IntFunction<DoubleAccess>) - Constructor for class io.scif.img.cell.loaders.DoubleAccessLoader
DoubleArrayLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for DoubleArray types.
DoubleArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.DoubleArrayLoader
doubleValue() - Method in class io.scif.formats.tiff.TiffRational: Returns the value of the specified number as a double.
DQT - Static variable in class io.scif.codec.LosslessJPEGCodec
DRI - Static variable in class io.scif.codec.LosslessJPEGCodec

E

EM_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the electron microscopy domain.
emptyArray(int) - Method in class io.scif.img.cell.loaders.ByteAccessLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.ByteArrayLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.CharAccessLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.CharArrayLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.DoubleAccessLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.DoubleArrayLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.FloatAccessLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.FloatArrayLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.IntAccessLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.IntArrayLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.LongAccessLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.LongArrayLoader
emptyArray(int) - Method in interface io.scif.img.cell.loaders.SCIFIOArrayLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.ShortAccessLoader
emptyArray(int) - Method in class io.scif.img.cell.loaders.ShortArrayLoader
enable(Class<F>) - Method in interface io.scif.filters.MasterFilter: Inserts an instance of the indicated filter class into the filter stack.
enable(Class<F>) - Method in class io.scif.filters.MasterFilterHelper
enable(Class<F>) - Method in class io.scif.filters.ReaderFilter
enableBufferedReading(boolean) - Method in class io.scif.config.SCIFIOConfig
enabledDefault() - Method in class io.scif.filters.AbstractFilter
enabledDefault() - Method in interface io.scif.filters.Filter
ENCODING - Static variable in class io.scif.common.Constants
EnumException - Exception in io.scif.enumeration
EnumException() - Constructor for exception io.scif.enumeration.EnumException
EnumException(String) - Constructor for exception io.scif.enumeration.EnumException
EnumException(String, Throwable) - Constructor for exception io.scif.enumeration.EnumException
EnumException(Throwable) - Constructor for exception io.scif.enumeration.EnumException
EOI - Static variable in class io.scif.codec.LosslessJPEGCodec
EPSFormat - Class in io.scif.formats: Reader is the file format reader for Encapsulated PostScript (EPS) files.
EPSFormat() - Constructor for class io.scif.formats.EPSFormat
EPSFormat.EPSTranslator - Class in io.scif.formats: Necessary dummy translator, so that an EPS-OMEXML translator can be used.
EPSFormat.Metadata - Class in io.scif.formats
EPSFormat.Parser - Class in io.scif.formats
EPSFormat.Reader - Class in io.scif.formats
EPSFormat.Writer - Class in io.scif.formats
EPSTranslator() - Constructor for class io.scif.formats.EPSFormat.EPSTranslator
equals(Object) - Method in class io.scif.formats.tiff.TiffRational: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class io.scif.io.location.TestImgLocation
error(SAXParseException) - Method in class io.scif.xml.ParserErrorHandler
error(SAXParseException) - Method in class io.scif.xml.ValidationErrorHandler
escapeXML(String) - Method in class io.scif.xml.DefaultXMLService
escapeXML(String) - Method in interface io.scif.xml.XMLService: Escape special characters.
EXIF - Static variable in class io.scif.formats.tiff.IFD
EXIF_VERSION - Static variable in class io.scif.formats.tiff.IFD
EXP - Static variable in class io.scif.codec.LosslessJPEGCodec
EXPOSURE_BIAS_VALUE - Static variable in class io.scif.formats.tiff.IFD
EXPOSURE_INDEX - Static variable in class io.scif.formats.tiff.IFD
EXPOSURE_MODE - Static variable in class io.scif.formats.tiff.IFD
EXPOSURE_PROGRAM - Static variable in class io.scif.formats.tiff.IFD
EXPOSURE_TIME - Static variable in class io.scif.formats.tiff.IFD: EXIF tags.
exposureTime - Variable in class io.scif.formats.MicromanagerFormat.Position
EXTRA_SAMPLES - Static variable in class io.scif.formats.tiff.IFD

F

F_NUMBER - Static variable in class io.scif.formats.tiff.IFD
factory() - Method in class io.scif.img.cell.SCIFIOCellImg
falseColor(boolean) - Method in class io.scif.io.location.TestImgLocation.Builder
fatalError(SAXParseException) - Method in class io.scif.xml.ParserErrorHandler
fatalError(SAXParseException) - Method in class io.scif.xml.ValidationErrorHandler
FCTLChunk() - Constructor for class io.scif.formats.APNGFormat.FCTLChunk
FDATChunk() - Constructor for class io.scif.formats.APNGFormat.FDATChunk
Field - Annotation Type in io.scif: Field annotation.
FieldPrinter - Class in io.scif: This class can be used as a flag to ensure all SCIFIO components are printed in a consistent manner via their toString methods.
FieldPrinter(Object) - Constructor for class io.scif.FieldPrinter
FILE_SOURCE - Static variable in class io.scif.formats.tiff.IFD
fileGroupOption(Location) - Method in class io.scif.AbstractGroupable
fileGroupOption(Location) - Method in class io.scif.filters.AbstractReaderFilter
fileGroupOption(Location) - Method in class io.scif.formats.DICOMFormat.Parser
fileGroupOption(Location) - Method in class io.scif.formats.MicromanagerFormat.Parser
fileGroupOption(Location) - Method in class io.scif.formats.NRRDFormat.Parser
fileGroupOption(Location) - Method in class io.scif.formats.NRRDFormat.Reader
fileGroupOption(Location) - Method in interface io.scif.Groupable: Returns an int indicating that we cannot, must, or might group the files in a given dataset.
FilePattern - Class in io.scif: FilePattern is a collection of methods for handling file patterns, a way of succinctly representing a collection of files meant to be part of the same data series.
FilePattern(FilePatternService, BrowsableLocation, DataHandleService) - Constructor for class io.scif.FilePattern: Creates a pattern object using the given file as a template.
FilePattern(FilePatternService, BrowsableLocation, BrowsableLocation, DataHandleService) - Constructor for class io.scif.FilePattern: Creates a pattern object using the given filename and directory path as a template.
FilePattern(BrowsableLocation, String, DataHandleService) - Constructor for class io.scif.FilePattern: Creates a pattern object for files with the given pattern string.
filePattern() - Method in class io.scif.SCIFIO: Gets this application context's FilePatternService.
FilePatternBlock - Class in io.scif: FilePatternBlock represents a single block in a FilePattern.
FilePatternBlock(String) - Constructor for class io.scif.FilePatternBlock
FilePatternService - Interface in io.scif.services: A collection of utility methods to facilitate FilePattern use.
FileStitcher - Class in io.scif.filters: Logic to stitch together files with similar names.
FileStitcher() - Constructor for class io.scif.filters.FileStitcher: Constructs a FileStitcher around a new image reader.
FileStitcher(boolean) - Constructor for class io.scif.filters.FileStitcher: Constructs a FileStitcher with the given reader.
FileStitcherMetadata - Class in io.scif.filters
FileStitcherMetadata() - Constructor for class io.scif.filters.FileStitcherMetadata
FileToDatasetConverter - Class in io.scif.convert: Converter for loading Datasets from Files.
FileToDatasetConverter() - Constructor for class io.scif.convert.FileToDatasetConverter
FILL_ORDER - Static variable in class io.scif.formats.tiff.IFD
fillInIFD(IFD) - Method in class io.scif.formats.tiff.TiffParser: Fill in IFD entries that are stored at an arbitrary offset.
FillOrder - Enum in io.scif.formats.tiff: Utility class for working with TIFF fill orders.
Filter - Interface in io.scif.filters: Interface for modifying object behavior.
filterType() - Method in class io.scif.filters.ChannelFillerMetadata
filterType() - Method in class io.scif.filters.DimensionSwapperMetadata
filterType() - Method in class io.scif.filters.FileStitcherMetadata
filterType() - Method in interface io.scif.filters.MetadataWrapper
filterType() - Method in class io.scif.filters.PlaneSeparatorMetadata
findImagePatterns(BrowsableLocation) - Method in class io.scif.services.DefaultFilePatternService
findImagePatterns(BrowsableLocation, BrowsableLocation, Collection<BrowsableLocation>) - Method in class io.scif.services.DefaultFilePatternService
findImagePatterns(BrowsableLocation) - Method in interface io.scif.services.FilePatternService: Finds the list of names matching the provided base and generates all patterns that match the list.
findImagePatterns(BrowsableLocation, BrowsableLocation, Collection<BrowsableLocation>) - Method in interface io.scif.services.FilePatternService: Generates a list of all the patterns that match the provided list of file names.
findPattern(BrowsableLocation) - Method in class io.scif.filters.FileStitcher: Constructs a new FilePattern around the pattern extracted from the given id.
findPattern(String) - Method in class io.scif.services.DefaultFilePatternService
findPattern(BrowsableLocation) - Method in class io.scif.services.DefaultFilePatternService
findPattern(BrowsableLocation, BrowsableLocation) - Method in class io.scif.services.DefaultFilePatternService
findPattern(BrowsableLocation, BrowsableLocation, Collection<BrowsableLocation>) - Method in class io.scif.services.DefaultFilePatternService
findPattern(BrowsableLocation, BrowsableLocation, Collection<BrowsableLocation>, int[]) - Method in class io.scif.services.DefaultFilePatternService
findPattern(String[]) - Method in class io.scif.services.DefaultFilePatternService
findPattern(String) - Method in interface io.scif.services.FilePatternService: Identifies the group pattern from a given file within that group.
findPattern(BrowsableLocation) - Method in interface io.scif.services.FilePatternService: Identifies the group pattern from a given file within that group.
findPattern(BrowsableLocation, BrowsableLocation) - Method in interface io.scif.services.FilePatternService: Identifies the group pattern from a given file within that group.
findPattern(BrowsableLocation, BrowsableLocation, Collection<BrowsableLocation>) - Method in interface io.scif.services.FilePatternService: Identifies the group pattern from a given file within that group.
findPattern(BrowsableLocation, BrowsableLocation, Collection<BrowsableLocation>, int[]) - Method in interface io.scif.services.FilePatternService: Identifies the group pattern from a given file within that group.
findPattern(String[]) - Method in interface io.scif.services.FilePatternService: Generate a pattern from a list of file names.
findPatterns(BrowsableLocation) - Method in class io.scif.filters.FileStitcher: Finds the file pattern for the given ID, based on the state of the file stitcher.
findTranslator(Metadata, Metadata, boolean) - Method in class io.scif.services.DefaultTranslatorService
findTranslator(Class<? extends Metadata>, Class<? extends Metadata>, boolean) - Method in class io.scif.services.DefaultTranslatorService
findTranslator(Metadata, Metadata, boolean) - Method in interface io.scif.services.TranslatorService: Returns a translator capable of translating from the source Metadata to the dest Metadata type, or null if no such Translator exists.
findTranslator(Class<? extends Metadata>, Class<? extends Metadata>, boolean) - Method in interface io.scif.services.TranslatorService: Returns a translator capable of translating from the source Metadata to the dest Metadata type, or null if no such Translator exists.
FITSFormat - Class in io.scif.formats: FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
FITSFormat() - Constructor for class io.scif.formats.FITSFormat
FITSFormat.Metadata - Class in io.scif.formats
FITSFormat.Parser - Class in io.scif.formats
FITSFormat.Reader - Class in io.scif.formats
FLASH - Static variable in class io.scif.formats.tiff.IFD
FLASH_ENERGY - Static variable in class io.scif.formats.tiff.IFD
FLASH_PIX_VERSION - Static variable in class io.scif.formats.tiff.IFD
flattenIntoHashMap() - Method in class io.scif.common.IniList: Flattens all of the INI tables into a single HashMap whose keys are of the format "[table name] table key".
FLIM_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the fluorescence-lifetime domain.
FLOAT - Static variable in class io.scif.util.FormatTools: Identifies the FLOAT data type used to store pixel values.
FloatAccessLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for FloatAccess types.
FloatAccessLoader(Reader, ImageRegion, IntFunction<FloatAccess>) - Constructor for class io.scif.img.cell.loaders.FloatAccessLoader
FloatArrayLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for FloatArray types.
FloatArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.FloatArrayLoader
floatValue() - Method in class io.scif.formats.tiff.TiffRational: Returns the value of the specified number as a float.
FOCAL_LENGTH - Static variable in class io.scif.formats.tiff.IFD
FOCAL_LENGTH_35MM_FILM - Static variable in class io.scif.formats.tiff.IFD
FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class io.scif.formats.tiff.IFD
FOCAL_PLANE_X_RESOLUTION - Static variable in class io.scif.formats.tiff.IFD
FOCAL_PLANE_Y_RESOLUTION - Static variable in class io.scif.formats.tiff.IFD
Format - Interface in io.scif: Interface for all SCIFIO formats.
format() - Method in class io.scif.SCIFIO: Gets this application context's FormatService.
formatDate(String, String) - Static method in class io.scif.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String, boolean) - Static method in class io.scif.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String[]) - Static method in class io.scif.common.DateTools: Formats the given date as an ISO 8601 date.
formatDate(String, String[], boolean) - Static method in class io.scif.common.DateTools: Formats the given date as an ISO 8601 date.
FormatException - Exception in io.scif: FormatException is the exception thrown when something goes wrong performing a file format operation.
FormatException() - Constructor for exception io.scif.FormatException
FormatException(String) - Constructor for exception io.scif.FormatException
FormatException(String, Throwable) - Constructor for exception io.scif.FormatException
FormatException(Throwable) - Constructor for exception io.scif.FormatException
FormatFileFilter - Class in io.scif.gui: A file filter for identifying the files supported by an associated Formats.
FormatFileFilter(Format) - Constructor for class io.scif.gui.FormatFileFilter: Constructs a new filter that accepts files of the given format's type.
FormatService - Interface in io.scif.services: A collection of methods for finding Format instances given a child class, discovering available formats, and managing the list of available formats.
FormatTools - Class in io.scif.util: A collection of constants and utility methods applicable for all cycles of image processing within SCIFIO.
FREE_BYTE_COUNTS - Static variable in class io.scif.formats.tiff.IFD
FREE_OFFSETS - Static variable in class io.scif.formats.tiff.IFD
FREQUENCY - Static variable in class io.scif.img.axes.SCIFIOAxes: Identifies the Frequency dimensional type, representing a dimension consisting of frequencies.
fromCIEXYZ(float[]) - Method in class io.scif.gui.TwoChannelColorSpace
fromMap(Map<String, Object>) - Static method in class io.scif.io.location.TestImgLocation: Creates a TestImgLocation with the values from the map set default values
fromRGB(float[]) - Method in class io.scif.gui.TwoChannelColorSpace

G

gain - Variable in class io.scif.formats.MicromanagerFormat.Position
GAIN_CONTROL - Static variable in class io.scif.formats.tiff.IFD
GEL_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the gel and blot imaging domain.
generateSuffixes() - Static method in class io.scif.formats.StratecPQCTFormat
get(int) - Method in class io.scif.AbstractMetadata
get(int) - Method in class io.scif.codec.ByteVector
get(int) - Static method in enum io.scif.codec.CompressionType: Retrieves the compression by reverse lookup of its "code".
get(int) - Static method in enum io.scif.codec.JPEG2000BoxType: Retrieves the box type by reverse lookup of its "code".
get(int) - Static method in enum io.scif.codec.JPEG2000SegmentMarker: Retrieves the segment marker by reverse lookup of its "code".
get(int) - Method in class io.scif.filters.FileStitcherMetadata
get() - Method in class io.scif.formats.DICOMFormat.DICOMTag
get(String) - Method in class io.scif.formats.ICSFormat.Metadata: Convenience method to directly access the hashtable.
get(int) - Static method in enum io.scif.formats.tiff.FillOrder: Retrieves a fill order by reverse lookup of its "code".
get(int) - Static method in enum io.scif.formats.tiff.IFDType: Retrieves a IFD type by reverse lookup of its "code".
get(int) - Method in class io.scif.formats.tiff.OnDemandLongArray
get(int) - Static method in enum io.scif.formats.tiff.PhotoInterp: Retrieves a photometric interpretation by reverse lookup of its "code".
get(int) - Static method in enum io.scif.formats.tiff.ResolutionUnit: Retrieves a resolution unit by reverse lookup of its "code".
get(int) - Static method in enum io.scif.formats.tiff.TiffCompression: Retrieves a TIFF compression instance by code.
get(int) - Method in interface io.scif.Metadata: Returns the ImageMetadata at the specified image within this dataset.
get8BitLookupTable(ColorModel) - Static method in class io.scif.gui.AWTImageTools: Converts an IndexColorModel to a 2D byte array.
getAct() - Method in class io.scif.formats.GIFFormat.Metadata
getActl() - Method in class io.scif.formats.APNGFormat.Metadata
getAdjustedOrder() - Method in class io.scif.AxisGuesser: Gets the adjusted dimension order.
getAdvancedImageUsedLocations(int, boolean) - Method in class io.scif.AbstractParser
getAdvancedImageUsedLocations(int, boolean) - Method in interface io.scif.Parser: Returns an array of LocationInfo objects representing the Locations needed to open the current series.
getAdvancedUsedLocations(boolean) - Method in class io.scif.AbstractParser
getAdvancedUsedLocations(boolean) - Method in interface io.scif.Parser: Returns an array of LocationInfo objects representing the Locations needed to open this dataset.
getAll() - Method in class io.scif.AbstractMetadata
getAll() - Method in interface io.scif.Metadata: Returns the list of ImageMetadata associated with this dataset.
getAllFormats() - Method in class io.scif.services.DefaultFormatService
getAllFormats() - Method in interface io.scif.services.FormatService: Returns a list of all Formats within this context.
getAlpha(int) - Method in class io.scif.gui.Index16ColorModel
getAlpha(int) - Method in class io.scif.gui.SignedColorModel
getAlpha(Object) - Method in class io.scif.gui.SignedColorModel
getAlpha(int) - Method in class io.scif.gui.UnsignedIntColorModel
getAlpha(Object) - Method in class io.scif.gui.UnsignedIntColorModel
getAlphas() - Method in class io.scif.gui.Index16ColorModel: Return the array of alpha color components.
getAltCodec() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getAltPlanes() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getArrayAccess(ImgPlus<?>) - Method in class io.scif.img.DefaultImgUtilityService: Obtains array access instance backing the given img, if any.
getArrayAccess(ImgPlus<?>) - Method in interface io.scif.img.ImgUtilityService: Obtains array access instance backing the given img, if any.
getArrayConverter() - Method in class io.scif.img.converters.DefaultPlaneConverterService
getArrayConverter() - Method in interface io.scif.img.converters.PlaneConverterService
getArtifactId() - Method in class io.scif.app.SCIFIOApp
getAuthorLastName() - Method in class io.scif.formats.ICSFormat.Metadata
getAxes() - Method in class io.scif.AbstractImageMetadata
getAxes() - Method in class io.scif.formats.ICSFormat.Metadata
getAxes() - Method in interface io.scif.ImageMetadata: Returns an array of the types for axes associated with the specified image index.
getAxesLengths() - Method in class io.scif.AbstractImageMetadata
getAxesLengths(List<CalibratedAxis>) - Method in class io.scif.AbstractImageMetadata
getAxesLengths() - Method in interface io.scif.ImageMetadata: Returns an array of the lengths for axes associated with the specified image index.
getAxesLengths(List<CalibratedAxis>) - Method in interface io.scif.ImageMetadata: Returns an array of the lengths for axes in the provided CalibratedAxis list.
getAxesLengthsNonPlanar() - Method in class io.scif.AbstractImageMetadata
getAxesLengthsNonPlanar() - Method in interface io.scif.ImageMetadata: Returns an array of the lengths for the non-planar axes in this image.
getAxesLengthsPlanar() - Method in class io.scif.AbstractImageMetadata
getAxesLengthsPlanar() - Method in interface io.scif.ImageMetadata: Returns an array of the lengths for the planar axes in this image.
getAxesNonPlanar() - Method in class io.scif.AbstractImageMetadata
getAxesNonPlanar() - Method in interface io.scif.ImageMetadata: Returns an array of the CalibratedAxis that define the number of planes in the dataset.
getAxesPlanar() - Method in class io.scif.AbstractImageMetadata
getAxesPlanar() - Method in interface io.scif.ImageMetadata: Returns an array of the CalibratedAxis that, together, define the bounds of a single plane in the dataset.
getAxesSizes() - Method in class io.scif.formats.ICSFormat.Metadata
getAxis(AxisType) - Method in class io.scif.AbstractImageMetadata
getAxis(int) - Method in class io.scif.AbstractImageMetadata
getAxis(AxisType) - Method in interface io.scif.ImageMetadata: Returns the CalibratedAxis associated with the given type.
getAxis(int) - Method in interface io.scif.ImageMetadata: Gets the axis of the (zero-indexed) specified plane.
getAxisCount(int) - Method in class io.scif.AxisGuesser: Gets the number of axes in the pattern of the given type.
getAxisCountC() - Method in class io.scif.AxisGuesser: Gets the number of C axes in the pattern.
getAxisCountS() - Method in class io.scif.AxisGuesser: Gets the number of S axes in the pattern.
getAxisCountT() - Method in class io.scif.AxisGuesser: Gets the number of T axes in the pattern.
getAxisCountZ() - Method in class io.scif.AxisGuesser: Gets the length of the Z axes in the pattern.
getAxisGlobalMaximum(int, AxisType, int) - Method in class io.scif.filters.MinMaxFilter: Retrieves a specified planar axis's global maximum.
getAxisGlobalMinimum(int, AxisType, int) - Method in class io.scif.filters.MinMaxFilter: Retrieves a specified planar axis's global minimum.
getAxisIndex(CalibratedAxis) - Method in class io.scif.AbstractImageMetadata
getAxisIndex(AxisType) - Method in class io.scif.AbstractImageMetadata
getAxisIndex(CalibratedAxis) - Method in interface io.scif.ImageMetadata: Returns the array index for the specified CalibratedAxis.
getAxisIndex(AxisType) - Method in interface io.scif.ImageMetadata: As ImageMetadata.getAxisIndex(CalibratedAxis) but only requires the AxisType of the desired axis.
getAxisKnownMaximum(int, AxisType, int) - Method in class io.scif.filters.MinMaxFilter: Retrieves the specified planar axis's maximum based on the images that have been read.
getAxisKnownMinimum(int, AxisType, int) - Method in class io.scif.filters.MinMaxFilter: Retrieves the specified planar axis's minimum based on the images that have been read.
getAxisLength(int) - Method in class io.scif.AbstractImageMetadata
getAxisLength(CalibratedAxis) - Method in class io.scif.AbstractImageMetadata
getAxisLength(AxisType) - Method in class io.scif.AbstractImageMetadata
getAxisLength(int) - Method in interface io.scif.ImageMetadata: Gets the length of the (zero-indexed) specified plane.
getAxisLength(CalibratedAxis) - Method in interface io.scif.ImageMetadata: A convenience method for looking up the length of an axis based on its type.
getAxisLength(AxisType) - Method in interface io.scif.ImageMetadata: As ImageMetadata.getAxisLength(CalibratedAxis) but only requires the AxisType of the desired axis.
getAxisType(String) - Static method in class io.scif.AxisGuesser: Returns a best guess of the given label's axis type.
getAxisTypes() - Method in class io.scif.AxisGuesser: Gets the guessed axis type for each dimensional block.
getBitDepth() - Method in class io.scif.formats.APNGFormat.IHDRChunk
getBits(int) - Method in class io.scif.codec.BitBuffer: Returns an int value representing the value of the bits read from the byte array, from the current position.
getBitsPerElement() - Method in class io.scif.img.cell.loaders.ByteAccessLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.ByteArrayLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.CharAccessLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.CharArrayLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.DoubleAccessLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.DoubleArrayLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.FloatAccessLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.FloatArrayLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.IntAccessLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.IntArrayLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.LongAccessLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.LongArrayLoader
getBitsPerElement() - Method in interface io.scif.img.cell.loaders.SCIFIOArrayLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.ShortAccessLoader
getBitsPerElement() - Method in class io.scif.img.cell.loaders.ShortArrayLoader
getBitsPerPixel() - Method in class io.scif.AbstractImageMetadata
getBitsPerPixel() - Method in class io.scif.formats.ICSFormat.Metadata
getBitsPerPixel() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getBitsPerPixel() - Method in interface io.scif.ImageMetadata: Returns the number of valid bits per pixel.
getBitsPerPixel(int) - Static method in class io.scif.util.FormatTools: Retrieves how many bytes per pixel the current plane or section has.
getBitsPerSample() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
getBlendOp() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getBlock(int) - Method in class io.scif.FilePattern: Gets the specified numerical block.
getBlock() - Method in class io.scif.FilePatternBlock
getBlocks() - Method in class io.scif.FilePattern: Gets each numerical block.
getBlockSize() - Method in class io.scif.formats.GIFFormat.Metadata
getBlue() - Method in class io.scif.formats.APNGFormat.PLTEChunk
getBlue(int) - Method in class io.scif.gui.Index16ColorModel
getBlue(int) - Method in class io.scif.gui.SignedColorModel
getBlue(Object) - Method in class io.scif.gui.SignedColorModel
getBlue(int) - Method in class io.scif.gui.UnsignedIntColorModel
getBlue(Object) - Method in class io.scif.gui.UnsignedIntColorModel
getBlues() - Method in class io.scif.gui.Index16ColorModel: Return the array of blue color components.
getBmpBitsPerPixel() - Method in class io.scif.formats.AVIFormat.Metadata
getBmpColorsUsed() - Method in class io.scif.formats.AVIFormat.Metadata
getBmpCompression() - Method in class io.scif.formats.AVIFormat.Metadata
getBmpScanLineSize() - Method in class io.scif.formats.AVIFormat.Metadata
getBmpWidth() - Method in class io.scif.formats.AVIFormat.Metadata
getBounds() - Method in class io.scif.AbstractPlane
getBounds() - Method in interface io.scif.Plane
getByteOrder() - Method in class io.scif.formats.ICSFormat.Metadata
getBytes() - Method in class io.scif.BufferedImagePlane: Standardizes this plane's BufferedImage to a byte[].
getBytes() - Method in class io.scif.ByteArrayPlane
getBytes(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(BufferedImage, boolean) - Static method in class io.scif.gui.AWTImageTools: Get the bytes from an image, merging the channels as necessary.
getBytes() - Method in interface io.scif.Plane: Gets this plane's standardized pixel data.
getBytesPerElement() - Method in enum io.scif.formats.tiff.IFDType: Retrieves the number of bytes per element.
getBytesPerLine() - Method in class io.scif.formats.PCXFormat.Metadata
getBytesPerPixel(int) - Static method in class io.scif.util.FormatTools: Retrieves how many bytes per pixel the current plane or section has.
getBytesPerPixel(String) - Static method in class io.scif.util.FormatTools: Retrieves the number of bytes per pixel in the current plane.
getBytesPerPlane() - Method in class io.scif.formats.AVIFormat.Metadata
getBytesPerSample() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
getCalibrationUnit() - Method in class io.scif.formats.TIFFFormat.Metadata
getChannelNames() - Method in class io.scif.formats.ICSFormat.Metadata
getCheckerClass() - Method in class io.scif.AbstractFormat
getCheckerClass() - Method in interface io.scif.Format
getCHUNK_SIGNATURE() - Method in class io.scif.formats.APNGFormat.APNGChunk
getChunkSizes() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getCode() - Method in enum io.scif.codec.CompressionType: Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum io.scif.codec.JPEG2000BoxType: Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum io.scif.codec.JPEG2000SegmentMarker: Implemented as specified by the CodedEnum I/F.
getCode() - Method in interface io.scif.enumeration.CodedEnum: Retrieves the integer "code" for this enumeration.
getCode() - Method in enum io.scif.formats.tiff.FillOrder
getCode() - Method in enum io.scif.formats.tiff.IFDType
getCode() - Method in enum io.scif.formats.tiff.PhotoInterp
getCode() - Method in enum io.scif.formats.tiff.ResolutionUnit
getCode() - Method in enum io.scif.formats.tiff.TiffCompression
getCodec(Class<C>) - Method in interface io.scif.codec.CodecService
getCodec(Class<C>) - Method in class io.scif.codec.DefaultCodecService
getCodec() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getCodecName() - Method in enum io.scif.formats.tiff.TiffCompression: Retrieves the name of the TIFF compression codec.
getCodecOptions() - Method in class io.scif.AbstractWriter
getCodecOptions() - Method in class io.scif.formats.tiff.TiffParser: Retrieves the current set of codec options being used to decompress pixel data.
getCodecOptions() - Method in interface io.scif.Writer
getCodestreamOffset() - Method in class io.scif.formats.JPEG2000Format.Parser: Retrieves the offset to the first contiguous codestream.
getCodestreamPixelType() - Method in class io.scif.formats.JPEG2000Format.Parser: Returns the pixel type as specified in the header.
getCodestreamSizeC() - Method in class io.scif.formats.JPEG2000Format.Parser: Returns the number of channels the image has as specified in the header.
getCodestreamSizeX() - Method in class io.scif.formats.JPEG2000Format.Parser: Returns the width of the image as specified in the header.
getCodestreamSizeY() - Method in class io.scif.formats.JPEG2000Format.Parser: Returns the height of the image as specified in the header.
getColorModel() - Method in class io.scif.AbstractWriter
getColorModel() - Method in interface io.scif.Writer: Gets the color model.
getColorTable() - Method in class io.scif.AbstractPlane
getColorTable(int, long) - Method in class io.scif.formats.AVIFormat.Metadata
getColorTable(int, long) - Method in class io.scif.formats.BMPFormat.Metadata
getColorTable(int, long) - Method in class io.scif.formats.DICOMFormat.Metadata
getColorTable(int, long) - Method in class io.scif.formats.GIFFormat.Metadata
getColorTable(int, long) - Method in class io.scif.formats.JPEG2000Format.Metadata
getColorTable(int, long) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
getColorTable(int, long) - Method in class io.scif.formats.PCXFormat.Metadata
getColorTable(int, long) - Method in class io.scif.formats.qt.PICTFormat.Metadata
getColorTable(int, long) - Method in class io.scif.formats.TestImgFormat.Metadata: Returns the current color table for this dataset
getColorTable(int, long) - Method in class io.scif.formats.TIFFFormat.Metadata
getColorTable(int, long) - Method in interface io.scif.HasColorTable
getColorTable(int, int) - Method in class io.scif.img.cell.SCIFIOCellImg: Returns the ColorTable of the specified image and plane index.
getColorTable(int) - Method in class io.scif.img.SCIFIOImgPlus
getColorTable(int, int) - Method in class io.scif.img.SCIFIOImgPlus
getColorTable() - Method in interface io.scif.Plane: Gets this plane's ColorTable.
getColorTables() - Method in class io.scif.formats.GIFFormat.Metadata
getColourType() - Method in class io.scif.formats.APNGFormat.IHDRChunk
getComment() - Method in class io.scif.formats.tiff.IFD: Convenience method for obtaining the ImageDescription from this IFD.
getComment() - Method in class io.scif.formats.tiff.TiffParser: Convenience method for obtaining a stream's first ImageDescription.
getComments() - Method in class io.scif.formats.JPEG2000Format.Parser: Retrieves the list of comments stored in the file.
getCompanionFile() - Method in class io.scif.formats.TIFFFormat.Metadata
getCompanionFiles() - Method in class io.scif.formats.DICOMFormat.Metadata
getCompression() - Method in class io.scif.AbstractWriter
getCompression() - Method in enum io.scif.codec.CompressionType: Returns the compression.
getCompression() - Method in class io.scif.formats.BMPFormat.Metadata
getCompression() - Method in class io.scif.formats.ICSFormat.Metadata
getCompression() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's compression type (TIFF tag Compression) from this IFD.
getCompression() - Method in interface io.scif.Writer
getCompressionCodecOptions(IFD) - Method in enum io.scif.formats.tiff.TiffCompression: Creates a set of codec options for compression.
getCompressionCodecOptions(IFD, CodecOptions) - Method in enum io.scif.formats.tiff.TiffCompression: Creates a set of codec options for compression.
getCompressionMethod() - Method in class io.scif.formats.APNGFormat.IHDRChunk
getCompressionTypes() - Method in class io.scif.AbstractWriter
getCompressionTypes() - Method in interface io.scif.Writer: Gets the available compression types.
getConstrainedLengths(Metadata, int, SCIFIOConfig) - Method in class io.scif.img.DefaultImgUtilityService
getConstrainedLengths(Metadata, int, SCIFIOConfig) - Method in interface io.scif.img.ImgUtilityService: Returns an N-dimensional list of axis lengths from the given Metadata, constrained by the provided SubRegion (if present)
getContext() - Method in class io.scif.filters.AbstractReaderFilter
getCount() - Method in class io.scif.FilePattern
getCreationDate() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getCreationDate() - Method in class io.scif.formats.TIFFFormat.Metadata
getCurrentLocation() - Method in class io.scif.AbstractReader
getCurrentLocation() - Method in class io.scif.filters.AbstractReaderFilter
getCurrentLocation() - Method in interface io.scif.Reader: Returns the current file.
getData() - Method in class io.scif.AbstractPlane
getData() - Method in interface io.scif.DataPlane: Gets this plane's type-specific pixel data.
getData() - Method in class io.scif.gui.SignedByteBuffer
getData(int) - Method in class io.scif.gui.SignedByteBuffer
getData() - Method in class io.scif.gui.SignedShortBuffer
getData(int) - Method in class io.scif.gui.SignedShortBuffer
getData() - Method in class io.scif.gui.UnsignedIntBuffer
getData(int) - Method in class io.scif.gui.UnsignedIntBuffer
getDataElements(int, Object) - Method in class io.scif.gui.Index16ColorModel
getDataElements(int, Object) - Method in class io.scif.gui.SignedColorModel
getDataElements(int, Object) - Method in class io.scif.gui.UnsignedIntColorModel
getDataFile() - Method in class io.scif.formats.NRRDFormat.Metadata
getDataOffset() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getDataset() - Method in class io.scif.commands.SaveImage
getDatasetInfo() - Method in class io.scif.formats.MNGFormat.Metadata
getDatasetName() - Method in class io.scif.AbstractMetadata
getDatasetName() - Method in interface io.scif.Metadata: Returns a String representation of this Dataset's name
getDatasetSize() - Method in class io.scif.AbstractMetadata
getDatasetSize() - Method in class io.scif.filters.FileStitcherMetadata
getDatasetSize() - Method in interface io.scif.Metadata: Returns the size, in bytes, of the current dataset.
getDataType() - Method in class io.scif.io.DatasetIOPlugin
getDataType() - Method in class io.scif.io.RAIIOPlugin
getDate() - Method in class io.scif.formats.DICOMFormat.Metadata
getDate() - Method in class io.scif.formats.ICSFormat.Metadata
getdBlock() - Method in class io.scif.formats.GIFFormat.Metadata
getDecoder() - Method in class io.scif.formats.JPEGTileFormat.Metadata
getDefaultConfiguration() - Static method in class io.scif.gui.AWTImageTools: Gets the default graphics configuration for the environment.
getDefaultConverter() - Method in class io.scif.img.converters.DefaultPlaneConverterService
getDefaultConverter() - Method in interface io.scif.img.converters.PlaneConverterService
getDefaultOptions() - Static method in class io.scif.codec.CodecOptions: Return CodecOptions with reasonable default values.
getDefaultOptions() - Static method in class io.scif.codec.JPEG2000CodecOptions: Return JPEG2000CodecOptions with reasonable default values.
getDefaultOptions(CodecOptions) - Static method in class io.scif.codec.JPEG2000CodecOptions: Return JPEG2000CodecOptions using the given CodecOptions as the default.
getDelayDen() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getDelayNum() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getDelegateType() - Method in class io.scif.convert.StringToDatasetConverter
getDenominator() - Method in class io.scif.formats.tiff.TiffRational: Gets this number's denominator.
getDescription() - Method in class io.scif.formats.ICSFormat.Metadata
getDescription() - Method in class io.scif.formats.TIFFFormat.Metadata
getDescription() - Method in class io.scif.gui.ComboFileFilter: Returns the filter's description.
getDescription() - Method in class io.scif.gui.FormatFileFilter: Gets the filter's description.
getDestinationLocation() - Method in class io.scif.AbstractMetadata
getDestinationLocation() - Method in interface io.scif.Metadata
getDetectorManufacturer() - Method in class io.scif.formats.ICSFormat.Metadata
getDetectorModel() - Method in class io.scif.formats.ICSFormat.Metadata
getDeviceName() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getDichroicModel() - Method in class io.scif.formats.ICSFormat.Metadata
getDimensionOrder(int) - Method in class io.scif.filters.DimensionSwapper: Returns the (potentially swapped) output order of the AxisTypes.
getDimLengths(Metadata, int, SCIFIOConfig) - Method in class io.scif.img.DefaultImgUtilityService: Compiles an N-dimensional list of axis lengths from the given reader.
getDimLengths(Metadata, int, SCIFIOConfig) - Method in interface io.scif.img.ImgUtilityService: Compiles an N-dimensional list of axis lengths from the given Metadata.
getDispose() - Method in class io.scif.formats.GIFFormat.Metadata
getDisposeOp() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getDomains() - Method in class io.scif.AbstractReader
getDomains() - Method in class io.scif.filters.AbstractReaderFilter
getDomains() - Method in class io.scif.formats.ICSFormat.Reader
getDomains() - Method in interface io.scif.Reader: Returns the list of domains represented by the current file.
getDoubles(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getElem(int) - Method in class io.scif.gui.SignedByteBuffer
getElem(int, int) - Method in class io.scif.gui.SignedByteBuffer
getElem(int, int) - Method in class io.scif.gui.SignedShortBuffer
getElem(int) - Method in class io.scif.gui.UnsignedIntBuffer
getElem(int, int) - Method in class io.scif.gui.UnsignedIntBuffer
getElemDouble(int) - Method in class io.scif.gui.UnsignedIntBuffer
getElemDouble(int, int) - Method in class io.scif.gui.UnsignedIntBuffer
getElementLength() - Method in class io.scif.formats.DICOMFormat.DICOMTag
getElements() - Method in class io.scif.FilePattern
getElements() - Method in class io.scif.FilePatternBlock
getElemFloat(int) - Method in class io.scif.gui.UnsignedIntBuffer
getElemFloat(int, int) - Method in class io.scif.gui.UnsignedIntBuffer
getEmissionModel() - Method in class io.scif.formats.ICSFormat.Metadata
getEMSingleton() - Method in class io.scif.formats.ICSFormat.Metadata
getEMWaves() - Method in class io.scif.formats.ICSFormat.Metadata
getEncoding() - Method in class io.scif.formats.NRRDFormat.Metadata
getEnergy() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getErrorCount() - Method in class io.scif.xml.ValidationErrorHandler
getErrorMessage() - Method in class io.scif.FilePattern: Gets the file pattern error message, if any.
getExcitationModel() - Method in class io.scif.formats.ICSFormat.Metadata
getExifIFDs() - Method in class io.scif.formats.tiff.TiffParser: Returns EXIF IFDs.
getExifTagName(int) - Static method in class io.scif.formats.TIFFFormat.BaseTIFFParser
getExperimenterEmail() - Method in class io.scif.formats.TIFFFormat.Metadata
getExperimenterFirstName() - Method in class io.scif.formats.TIFFFormat.Metadata
getExperimenterLastName() - Method in class io.scif.formats.TIFFFormat.Metadata
getExperimentType() - Method in class io.scif.formats.ICSFormat.Metadata
getExposureTime() - Method in class io.scif.formats.ICSFormat.Metadata
getEXSingleton() - Method in class io.scif.formats.ICSFormat.Metadata
getEXWaves() - Method in class io.scif.formats.ICSFormat.Metadata
getFailureClass() - Method in exception io.scif.DependencyException: Returns the class that was used during a failed instantiation.
getFctl() - Method in class io.scif.formats.APNGFormat.Metadata
getFdatChunks() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getFieldName(int) - Static method in class io.scif.formats.tiff.IFD: Deprecated.
Use DebugUtils.getFieldName(Class, int) instead.
getFileList() - Method in class io.scif.formats.DICOMFormat.Metadata
getFilename(int, int, Reader, String) - Static method in class io.scif.util.FormatTools
getFilenames(String, Reader) - Static method in class io.scif.util.FormatTools
getFilePattern() - Method in class io.scif.AxisGuesser: Gets the file pattern.
getFilePattern() - Method in class io.scif.filters.FileStitcher: Gets the file pattern object used to build the list of files.
getFiles() - Method in class io.scif.FilePattern: Gets a listing of all files matching the given file pattern.
getFillOrder() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's fill order (TIFF tag FillOrder) from this IFD.
getFilterClasses() - Method in interface io.scif.filters.MasterFilter: Returns a list of all filter classes this MasterFilter can enable/disable.
getFilterClasses() - Method in class io.scif.filters.MasterFilterHelper
getFilterClasses() - Method in class io.scif.filters.ReaderFilter
getFilterMethod() - Method in class io.scif.formats.APNGFormat.IHDRChunk
getFilters() - Method in class io.scif.gui.ComboFileFilter: Gets the list of file filters forming this filter combination.
getFilterSetModel() - Method in class io.scif.formats.ICSFormat.Metadata
getFinalCRC() - Method in class io.scif.common.CRC
getFirst() - Method in class io.scif.FilePatternBlock
getFirstIFD() - Method in class io.scif.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 io.scif.formats.tiff.TiffParser: Retrieve a given entry from the first IFD in the stream.
getFirstOffset() - Method in class io.scif.formats.tiff.TiffParser: Gets offset to the first IFD, or -1 if stream is not TIFF.
getFirstSlicePosition() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getFloats(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getFormat() - Method in class io.scif.AbstractHasFormat
getFormat() - Method in class io.scif.DefaultChecker
getFormat() - Method in class io.scif.DefaultMetadata
getFormat() - Method in class io.scif.DefaultParser
getFormat() - Method in class io.scif.DefaultReader
getFormat() - Method in class io.scif.DefaultWriter
getFormat() - Method in class io.scif.filters.AbstractMetadataWrapper
getFormat() - Method in class io.scif.filters.AbstractReaderFilter
getFormat() - Method in class io.scif.gui.FormatFileFilter: Returns the filter's format.
getFormat() - Method in interface io.scif.HasFormat: Provides a link back to the format associated with this component.
getFormat(Location) - Method in class io.scif.services.DefaultFormatService
getFormat(Location, SCIFIOConfig) - Method in class io.scif.services.DefaultFormatService
getFormat(DataHandle<Location>) - Method in class io.scif.services.DefaultFormatService
getFormat(DataHandle<Location>, SCIFIOConfig) - Method in class io.scif.services.DefaultFormatService
getFormat(Location) - Method in interface io.scif.services.FormatService: Returns the first Format known to be compatible with the source provided.
getFormat(Location, SCIFIOConfig) - Method in interface io.scif.services.FormatService: Returns the first Format known to be compatible with the source provided.
getFormat(DataHandle<Location>) - Method in interface io.scif.services.FormatService: As FormatService.getFormat(Location) but takes an initialized DataHandle.
getFormat(DataHandle<Location>, SCIFIOConfig) - Method in interface io.scif.services.FormatService: As FormatService.getFormat(Location, SCIFIOConfig) but takes an initialized DataHandle.
getFormatFromChecker(Class<C>) - Method in class io.scif.services.DefaultFormatService
getFormatFromChecker(Class<C>) - Method in interface io.scif.services.FormatService: Format lookup method using the Checker component.
getFormatFromClass(Class<F>) - Method in class io.scif.services.DefaultFormatService
getFormatFromClass(Class<F>) - Method in interface io.scif.services.FormatService: Lookup method for the Format map.
getFormatFromComponent(Class<?>) - Method in class io.scif.services.DefaultFormatService
getFormatFromComponent(Class<?>) - Method in interface io.scif.services.FormatService: Returns the Format compatible with this component class, or null if no matching Format can be found.
getFormatFromMetadata(Class<M>) - Method in class io.scif.services.DefaultFormatService
getFormatFromMetadata(Class<M>) - Method in interface io.scif.services.FormatService: Format lookup method using the Metadata component.
getFormatFromParser(Class<P>) - Method in class io.scif.services.DefaultFormatService
getFormatFromParser(Class<P>) - Method in interface io.scif.services.FormatService: Format lookup method using the Parser component.
getFormatFromReader(Class<R>) - Method in class io.scif.services.DefaultFormatService
getFormatFromReader(Class<R>) - Method in interface io.scif.services.FormatService: Format lookup method using the Reader component
getFormatFromWriter(Class<W>) - Method in class io.scif.services.DefaultFormatService
getFormatFromWriter(Class<W>) - Method in interface io.scif.services.FormatService: Format lookup method using the Writer component.
getFormatList(Location) - Method in class io.scif.services.DefaultFormatService
getFormatList(Location, SCIFIOConfig, boolean) - Method in class io.scif.services.DefaultFormatService
getFormatList(DataHandle<Location>) - Method in class io.scif.services.DefaultFormatService
getFormatList(DataHandle<Location>, SCIFIOConfig, boolean) - Method in class io.scif.services.DefaultFormatService
getFormatList(Location) - Method in interface io.scif.services.FormatService: Returns a list of all formats that are compatible with the source provided, ordered by their priority.
getFormatList(Location, SCIFIOConfig, boolean) - Method in interface io.scif.services.FormatService: Returns a list of all formats that are compatible with the source provided, ordered by their priority.
getFormatList(DataHandle<Location>) - Method in interface io.scif.services.FormatService: As FormatService.getFormatList(Location) but takes an initialized DataHandle.
getFormatList(DataHandle<Location>, SCIFIOConfig, boolean) - Method in interface io.scif.services.FormatService: As FormatService.getFormatList(Location, SCIFIOConfig, boolean) but takes an initialized DataHandle.
getFormatName() - Method in class io.scif.AbstractFormat
getFormatName() - Method in class io.scif.AbstractHasFormat
getFormatName() - Method in class io.scif.filters.AbstractMetadataWrapper
getFormatName() - Method in class io.scif.filters.AbstractReaderFilter
getFormatName() - Method in interface io.scif.Format: Gets the name of this file format.
getFormatName() - Method in interface io.scif.HasFormat: Helper method for accessing Format.getFormatName().
getFrameCoordinates() - Method in class io.scif.formats.APNGFormat.APNGChunk
getFrameCoordinates() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getFramesPerSecond() - Method in class io.scif.AbstractWriter
getFramesPerSecond() - Method in interface io.scif.Writer
getGains() - Method in class io.scif.formats.ICSFormat.Metadata
getGct() - Method in class io.scif.formats.GIFFormat.Metadata
getGlobal() - Method in class io.scif.formats.BMPFormat.Metadata
getGlobalCRC() - Method in class io.scif.common.CRC
getGreen() - Method in class io.scif.formats.APNGFormat.PLTEChunk
getGreen(int) - Method in class io.scif.gui.Index16ColorModel
getGreen(int) - Method in class io.scif.gui.SignedColorModel
getGreen(Object) - Method in class io.scif.gui.SignedColorModel
getGreen(int) - Method in class io.scif.gui.UnsignedIntColorModel
getGreen(Object) - Method in class io.scif.gui.UnsignedIntColorModel
getGreens() - Method in class io.scif.gui.Index16ColorModel: Return the array of green color components.
getGroupId() - Method in class io.scif.app.SCIFIOApp
getHandle() - Method in class io.scif.AbstractReader
getHandle() - Method in class io.scif.AbstractWriter
getHandle() - Method in class io.scif.filters.AbstractReaderFilter
getHandle() - Method in interface io.scif.Reader: Retrieves the current input stream for this reader.
getHandle() - Method in interface io.scif.Writer: Retrieves a reference to the output source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.
getHeaderPixelType() - Method in class io.scif.formats.JPEG2000Format.Parser: Returns the pixel type as specified in the header.
getHeaderSizeC() - Method in class io.scif.formats.JPEG2000Format.Parser: Returns the number of channels the image has as specified in the header.
getHeaderSizeX() - Method in class io.scif.formats.JPEG2000Format.Parser: Returns the width of the image as specified in the header.
getHeaderSizeY() - Method in class io.scif.formats.JPEG2000Format.Parser: Returns the height of the image as specified in the header.
getHeight() - Method in class io.scif.codec.JPEGTileDecoder
getHeight() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getHeight() - Method in class io.scif.formats.APNGFormat.IHDRChunk
getHeight() - Method in class io.scif.formats.KontronFormat.Metadata
getHeight() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getHeight() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getHeight() - Method in interface io.scif.services.LuraWaveService: Wraps com.luratech.lwf.lwfDecoder#getHeight()
getHelper() - Method in class io.scif.formats.NRRDFormat.Metadata
getHistoryExtents() - Method in class io.scif.formats.ICSFormat.Metadata
getHistoryLabels() - Method in class io.scif.formats.ICSFormat.Metadata
getHistoryUnits() - Method in class io.scif.formats.ICSFormat.Metadata
getIcsLocation() - Method in class io.scif.formats.ICSFormat.Metadata
getIdat() - Method in class io.scif.formats.APNGFormat.Metadata
getIdsLocation() - Method in class io.scif.formats.ICSFormat.Metadata
getIend() - Method in class io.scif.formats.APNGFormat.Metadata
getIFD(long) - Method in class io.scif.formats.tiff.TiffParser: Gets the IFD stored at the given offset.
getIFDIntArray(int) - Method in class io.scif.formats.tiff.IFD: Gets the given directory entry values in int format from this IFD, performing some error checking.
getIFDIntValue(int) - Method in class io.scif.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 io.scif.formats.tiff.IFD: Gets the given directory entry value in int format from this IFD, performing some error checking.
getIFDLongArray(int) - Method in class io.scif.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 io.scif.formats.tiff.IFD: Gets the given directory entry value in long format from this IFD, performing some error checking.
getIFDOffsets() - Method in class io.scif.formats.tiff.TiffParser: Gets the offsets to every IFD in the file.
getIFDRationalValue(int) - Method in class io.scif.formats.tiff.IFD: Gets the given directory entry value in rational format from this IFD, performing some error checking.
getIfds() - Method in class io.scif.formats.EPSFormat.Metadata
getIfds() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
getIFDs() - Method in class io.scif.formats.tiff.TiffParser: Returns all IFDs in the file.
getIFDShortArray(int) - Method in class io.scif.formats.tiff.IFD: Gets the given directory entry values in short format from this IFD, performing some error checking.
getIFDStringValue(int) - Method in class io.scif.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 io.scif.formats.tiff.IFD: Gets the name of the IFD tag encoded by the given number.
getIFDTextValue(int) - Method in class io.scif.formats.tiff.IFD: Gets the given directory entry value as a string (regardless of type).
getIFDValue(int) - Method in class io.scif.formats.tiff.IFD: Gets the given directory entry value from this IFD.
getIFDValue(int, Class<?>) - Method in class io.scif.formats.tiff.IFD: Gets the given directory entry value from this IFD, performing some error checking.
getIFDValue(TiffIFDEntry) - Method in class io.scif.formats.tiff.TiffParser: Retrieve the value corresponding to the given TiffIFDEntry.
getIh() - Method in class io.scif.formats.GIFFormat.Metadata
getIhdr() - Method in class io.scif.formats.APNGFormat.Metadata
getImage() - Method in class io.scif.formats.qt.LegacyQTFormat.Metadata
getImage() - Method in class io.scif.gui.ImageViewer: Gets the currently displayed image.
getImageCount() - Method in class io.scif.AbstractMetadata
getImageCount() - Method in class io.scif.AbstractReader
getImageCount() - Method in class io.scif.filters.AbstractReaderFilter
getImageCount() - Method in class io.scif.filters.FileStitcherMetadata
getImageCount() - Method in class io.scif.formats.JPEG2000Format.Metadata
getImageCount(Location) - Method in class io.scif.img.DefaultImgUtilityService
getImageCount(Location) - Method in interface io.scif.img.ImgUtilityService
getImageCount() - Method in interface io.scif.Metadata: Returns the number of images in this dataset.
getImageCount() - Method in interface io.scif.Reader: Determines the number of images in the current file.
getImageCreationDate(TIFFFormat.Metadata) - Method in class io.scif.formats.TIFFFormat.BaseTIFFParser: Retrieves the image creation date.
getImageDescription() - Method in class io.scif.formats.TIFFFormat.Metadata
getImageIndex() - Method in class io.scif.formats.JPEG2000Format.Index
getImageLength() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
getImageMetadata() - Method in class io.scif.AbstractPlane
getImageMetadata() - Method in class io.scif.img.SCIFIOImgPlus
getImageMetadata() - Method in interface io.scif.Plane: Gets the ImageMetadata associated with this plane.
getImages() - Method in class io.scif.formats.GIFFormat.Metadata
getImagesPerFile() - Method in class io.scif.formats.DICOMFormat.Metadata
getImagesPerFile(String, Reader) - Static method in class io.scif.util.FormatTools
getImageType() - Method in class io.scif.formats.DICOMFormat.Metadata
getImageUsedFiles(int) - Method in class io.scif.AbstractParser
getImageUsedFiles(int, boolean) - Method in class io.scif.AbstractParser
getImageUsedFiles(int, boolean) - Method in class io.scif.formats.DICOMFormat.Parser
getImageUsedFiles(int, boolean) - Method in class io.scif.formats.MicromanagerFormat.Parser
getImageUsedFiles(int, boolean) - Method in class io.scif.formats.NRRDFormat.Parser
getImageUsedFiles(int, boolean) - Method in class io.scif.formats.TIFFFormat.Parser
getImageUsedFiles(int) - Method in interface io.scif.Parser: Returns an array of filenames needed to open the indicated image index.
getImageUsedFiles(int, boolean) - Method in interface io.scif.Parser: Returns an array of filenames needed to open the indicated image.
getImageWidth() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
getImg() - Method in class io.scif.formats.ImageIOFormat.Metadata
getImmersion() - Method in class io.scif.formats.ICSFormat.Metadata
getInputOrder(int) - Method in class io.scif.filters.DimensionSwapper: Returns the order for reading AxisTypes from disk.
getInputType() - Method in class io.scif.convert.FileToDatasetConverter
getInputType() - Method in class io.scif.convert.StringToDatasetConverter
getInstance(int) - Static method in class io.scif.gui.TwoChannelColorSpace
getIntensity() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getInterlaceMethod() - Method in class io.scif.formats.APNGFormat.IHDRChunk
getInterleavedAxisCount() - Method in class io.scif.AbstractImageMetadata
getInterleavedAxisCount() - Method in interface io.scif.ImageMetadata: Returns the number of interleaved axes in this image.
getInts(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of signed integers, one per channel.
getIw() - Method in class io.scif.formats.GIFFormat.Metadata
getIx() - Method in class io.scif.formats.GIFFormat.Metadata
getIy() - Method in class io.scif.formats.GIFFormat.Metadata
getJ2kCodecOptions() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
getJpegOffsets() - Method in class io.scif.formats.qt.PICTFormat.Metadata
getKeyValPairs() - Method in class io.scif.formats.ICSFormat.Metadata
getLaserManufacturer() - Method in class io.scif.formats.ICSFormat.Metadata
getLaserModel() - Method in class io.scif.formats.ICSFormat.Metadata
getLaserPower() - Method in class io.scif.formats.ICSFormat.Metadata
getLaserRepetitionRate() - Method in class io.scif.formats.ICSFormat.Metadata
getLast() - Method in class io.scif.FilePatternBlock
getLastDimensions() - Method in class io.scif.formats.AVIFormat.Metadata
getLastDispose() - Method in class io.scif.formats.GIFFormat.Metadata
getLastIndex() - Method in class io.scif.formats.JPEG2000Format.Metadata
getLastIndexBytes() - Method in class io.scif.formats.JPEG2000Format.Metadata
getLastPlane() - Method in class io.scif.formats.AVIFormat.Metadata
getLastPlane() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
getLastPlaneBytes() - Method in class io.scif.formats.AVIFormat.Metadata
getLastPlaneIndex() - Method in class io.scif.formats.AVIFormat.Metadata
getLeftEdge() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getLength() - Method in class io.scif.formats.APNGFormat.APNGChunk
getLength() - Method in class io.scif.util.SCIFIOMetadataTools.AxisValue
getLengths() - Method in class io.scif.formats.AVIFormat.Metadata
getLengths() - Method in interface io.scif.Plane
getLensNA() - Method in class io.scif.formats.ICSFormat.Metadata
getLicenseCode() - Method in interface io.scif.services.LuraWaveService: Retrieves the current license code as a string.
getLifetime() - Method in class io.scif.formats.ICSFormat.Metadata
getLocation() - Method in class io.scif.formats.DICOMFormat.DICOMTag
getLocation(MicromanagerFormat.Metadata, int, long) - Method in class io.scif.formats.MicromanagerFormat.Position
getLookup() - Method in class io.scif.formats.qt.PICTFormat.Metadata
getLookupTable(ColorModel) - Static method in class io.scif.gui.AWTImageTools: Convers an Index16ColorModel to a 2D short array.
getLut() - Method in class io.scif.formats.JPEG2000Format.Metadata
getLut() - Method in class io.scif.formats.TIFFFormat.Metadata
getLutLength() - Method in class io.scif.filters.ChannelFillerMetadata
getLuts() - Method in class io.scif.formats.TestImgFormat.Metadata: Gets the lookup table attached to this dataset
getMagnification() - Method in class io.scif.formats.ICSFormat.Metadata
getMax() - Method in interface io.scif.Plane
getMaxDataValue() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getMaxPixelValue() - Method in class io.scif.formats.DICOMFormat.Metadata
getMeasurementDate() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getMeasurementIndex() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getMeasurementInfo() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getMetadata() - Method in class io.scif.AbstractParser
getMetadata() - Method in class io.scif.AbstractReader
getMetadata() - Method in class io.scif.AbstractWriter
getMetadata() - Method in class io.scif.filters.AbstractReaderFilter
getMetadata() - Method in class io.scif.filters.DimensionSwapper
getMetadata() - Method in class io.scif.filters.ReaderFilter
getMetadata() - Method in class io.scif.img.SCIFIOImgPlus
getMetadata() - Method in interface io.scif.Parser
getMetadata() - Method in interface io.scif.Reader: Gets the type-specific Metadata for this Reader
getMetadata() - Method in interface io.scif.TypedReader
getMetadata() - Method in interface io.scif.TypedWriter
getMetadata() - Method in interface io.scif.Writer: Gets the Metadata that will be used when saving planes.
getMetadataClass() - Method in class io.scif.AbstractFormat
getMetadataClass() - Method in interface io.scif.Format
getMetadataMap() - Method in class io.scif.io.location.TestImgLocation
getMetadataType() - Method in enum io.scif.formats.tiff.PhotoInterp: Retrieves the metadata type of the photometric interpretation.
getMicroscopeManufacturer() - Method in class io.scif.formats.ICSFormat.Metadata
getMicroscopeModel() - Method in class io.scif.formats.ICSFormat.Metadata
getMillisFromTicks(long, long) - Static method in class io.scif.common.DateTools: Converts from two-word tick representation to milliseconds.
getMin() - Method in interface io.scif.Plane
getMinDataValue() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getMuScaling() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getName() - Method in class io.scif.AbstractImageMetadata
getName() - Method in enum io.scif.codec.JPEG2000BoxType: Returns the name of the box type.
getName() - Method in enum io.scif.codec.JPEG2000SegmentMarker: Returns the name of the segment marker.
getName() - Method in enum io.scif.formats.tiff.FillOrder: Retrieves the given name of the fill order.
getName() - Method in enum io.scif.formats.tiff.PhotoInterp: Retrieves the given name of the photometric interpretation.
getName() - Method in enum io.scif.formats.tiff.ResolutionUnit: Retrieves the given name of the resolution unit.
getName(int) - Method in class io.scif.gui.TwoChannelColorSpace
getName() - Method in class io.scif.io.location.TestImgLocation
getNativeDataType() - Method in class io.scif.filters.MinMaxFilter
getnColorPlanes() - Method in class io.scif.formats.PCXFormat.Metadata
getNonPlanarAxisPosition(Metadata, int, long, AxisType) - Static method in class io.scif.util.FormatTools: Returns the position of the specified AxisType for the given image and plane indices.
getNonThumbnailIFDs() - Method in class io.scif.formats.tiff.TiffParser: Returns non-thumbnail IFDs.
getNumber(String) - Method in class io.scif.NumberFilter: Gets numbers filling the asterisk positions.
getNumComponents() - Method in class io.scif.gui.TwoChannelColorSpace
getNumerator() - Method in class io.scif.formats.tiff.TiffRational: Gets this number's numerator.
getNumFrames() - Method in class io.scif.formats.APNGFormat.ACTLChunk
getNumPages() - Method in class io.scif.formats.TIFFJAIFormat.Metadata
getNumPlays() - Method in class io.scif.formats.APNGFormat.ACTLChunk
getObjectiveModel() - Method in class io.scif.formats.ICSFormat.Metadata
getObjectSize() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getOffset() - Method in class io.scif.formats.APNGFormat.APNGChunk
getOffset() - Method in class io.scif.formats.NRRDFormat.Metadata
getOffset() - Method in class io.scif.formats.PCXFormat.Metadata
getOffset() - Method in class io.scif.formats.PGMFormat.Metadata
getOffsets() - Method in class io.scif.formats.AVIFormat.Metadata
getOffsets() - Method in class io.scif.formats.DICOMFormat.Metadata
getOffsets() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getOnDemandStripOffsets() - Method in class io.scif.formats.tiff.IFD
getOptimalTileHeight(int) - Method in class io.scif.AbstractReader
getOptimalTileHeight(int) - Method in class io.scif.filters.AbstractReaderFilter
getOptimalTileHeight(int) - Method in class io.scif.formats.EPSFormat.Reader
getOptimalTileHeight(int) - Method in class io.scif.formats.ImageIOFormat.Reader
getOptimalTileHeight(int) - Method in class io.scif.formats.MicromanagerFormat.Reader
getOptimalTileHeight(int) - Method in class io.scif.formats.MinimalTIFFFormat.Reader
getOptimalTileHeight(int) - Method in class io.scif.formats.NRRDFormat.Reader
getOptimalTileHeight(int) - Method in interface io.scif.Reader: Returns the optimal sub-image height for use with Reader.openPlane(int, long).
getOptimalTileWidth(int) - Method in class io.scif.AbstractReader
getOptimalTileWidth(int) - Method in class io.scif.filters.AbstractReaderFilter
getOptimalTileWidth(int) - Method in class io.scif.formats.EPSFormat.Reader
getOptimalTileWidth(int) - Method in class io.scif.formats.MicromanagerFormat.Reader
getOptimalTileWidth(int) - Method in class io.scif.formats.MinimalTIFFFormat.Reader
getOptimalTileWidth(int) - Method in interface io.scif.Reader: Returns the optimal sub-image width for use with Reader.openPlane(int, long).
getOriginalDate() - Method in class io.scif.formats.DICOMFormat.Metadata
getOriginalIndex(int, long) - Method in class io.scif.filters.PlaneSeparator: Returns the image number in the original dataset that corresponds to the given image number.
getOriginalInstance() - Method in class io.scif.formats.DICOMFormat.Metadata
getOriginalOrder() - Method in class io.scif.AxisGuesser: Gets the original dimension order.
getOriginalSeries() - Method in class io.scif.formats.DICOMFormat.Metadata
getOriginalTime() - Method in class io.scif.formats.DICOMFormat.Metadata
getOutputFormats() - Method in class io.scif.services.DefaultFormatService
getOutputFormats() - Method in interface io.scif.services.FormatService
getOutputOrder() - Method in class io.scif.filters.DimensionSwapperMetadata: Gets the output order for this dataset.
getOutputType() - Method in class io.scif.convert.FileToDatasetConverter
getOutputType() - Method in class io.scif.convert.StringToDatasetConverter
getParameterLabels() - Method in class io.scif.formats.ICSFormat.Metadata
getParameterScales() - Method in class io.scif.formats.ICSFormat.Metadata
getParameterUnits() - Method in class io.scif.formats.ICSFormat.Metadata
getParent() - Method in class io.scif.filters.AbstractFilter
getParent() - Method in interface io.scif.filters.Filter: Returns the object this filter augments.
getParent() - Method in interface io.scif.filters.MasterFilter: Returns the top of the filter stack.
getParent() - Method in class io.scif.filters.ReaderFilter
getParentMeta() - Method in class io.scif.filters.AbstractReaderFilter: Convenience accessor for the parent's Metadata
getParserClass() - Method in class io.scif.AbstractFormat
getParserClass() - Method in interface io.scif.Format
getPatientAge() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getPatientBirthDate() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getPatientId() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getPatientIndex() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getPatientMeasurementNumber() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getPatientName() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getPatientName() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getPatientNumber() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getPattern() - Method in class io.scif.FilePattern: Gets the file pattern string.
getPhotometricInterpretation() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's photometric interpretation (TIFF tag PhotometricInterpretation) from this IFD.
getPhysicalDepth() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getPhysicalHeight() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getPhysicalWidth() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getPictDimensions(byte[]) - Method in class io.scif.formats.qt.DefaultQTJavaService
getPictDimensions(byte[]) - Method in interface io.scif.formats.qt.QTJavaService: Gets width and height for the given PICT bytes.
getPinholes() - Method in class io.scif.formats.ICSFormat.Metadata
getPixelBytes() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getPixelBytes(BufferedImage, boolean) - Static method in class io.scif.gui.AWTImageTools: Return a 2D array of bytes representing the image.
getPixelBytes(WritableRaster, boolean) - Static method in class io.scif.gui.AWTImageTools: Return a 2D array of bytes representing the image.
getPixelBytes(BufferedImage, boolean, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools: Return a 2D array of bytes representing the image.
getPixelBytes(WritableRaster, boolean, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools: Return a 2D array of bytes representing the image.
getPixelOffset() - Method in class io.scif.formats.FITSFormat.Metadata
getPixelOffset() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getPixels() - Method in class io.scif.formats.GIFFormat.Metadata
getPixels(BufferedImage) - Static method in class io.scif.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 io.scif.gui.AWTImageTools: Gets the image's pixel data as arrays of primitives, one per channel.
getPixels(WritableRaster) - Static method in class io.scif.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 io.scif.gui.AWTImageTools: Gets the raster's pixel data as arrays of primitives, one per channel.
getPixelSizes() - Method in class io.scif.formats.NRRDFormat.Metadata
getPixelSizeX() - Method in class io.scif.formats.DICOMFormat.Metadata
getPixelSizeY() - Method in class io.scif.formats.DICOMFormat.Metadata
getPixelSizeZ() - Method in class io.scif.formats.DICOMFormat.Metadata
getPixelsOffset() - Method in class io.scif.formats.JPEG2000Format.Metadata
getPixelStack() - Method in class io.scif.formats.GIFFormat.Metadata
getPixelType() - Method in class io.scif.AbstractImageMetadata
getPixelType() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's pixel type based on the BitsPerSample tag.
getPixelType(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Gets the pixel type of the given image.
getPixelType(BufferedImage) - Static method in class io.scif.gui.BufferedImageTools: Gets the pixel type of the given image.
getPixelType() - Method in interface io.scif.ImageMetadata: Returns the data type associated with a pixel.
getPixelTypes(String) - Method in class io.scif.AbstractWriter
getPixelTypes(String) - Method in class io.scif.formats.APNGFormat.Writer
getPixelTypes(String) - Method in class io.scif.formats.AVIFormat.Writer
getPixelTypes(String) - Method in class io.scif.formats.EPSFormat.Writer
getPixelTypes(String) - Method in class io.scif.formats.ICSFormat.Writer
getPixelTypes(String) - Method in class io.scif.formats.ImageIOFormat.Writer
getPixelTypes(String) - Method in class io.scif.formats.JPEG2000Format.Writer: Overridden to return the formats supported by the writer.
getPixelTypes(String) - Method in class io.scif.formats.JPEGFormat.Writer
getPixelTypes(String) - Method in class io.scif.formats.qt.NativeQTFormat.Writer
getPixelTypes(String) - Method in class io.scif.formats.TIFFFormat.Writer
getPixelTypes(String) - Method in interface io.scif.Writer: Gets the supported pixel types for the given codec.
getPixelTypeString(int) - Static method in class io.scif.util.FormatTools: Takes a pixel type value and gets a corresponding string representation.
getPlanarAccess(ImgPlus<?>) - Method in class io.scif.img.DefaultImgUtilityService: Obtains planar access instance backing the given img, if any.
getPlanarAccess(ImgPlus<?>) - Method in interface io.scif.img.ImgUtilityService: Obtains planar access instance backing the given img, if any.
getPlanarAxisCount() - Method in class io.scif.AbstractImageMetadata
getPlanarAxisCount() - Method in interface io.scif.ImageMetadata: Returns the number of planar axes in this image.
getPlanarConfiguration() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's planar configuration (TIFF tag PlanarConfiguration) from this IFD.
getPlanarConverter() - Method in class io.scif.img.converters.DefaultPlaneConverterService
getPlanarConverter() - Method in interface io.scif.img.converters.PlaneConverterService
getPlane(BufferedImage) - Method in class io.scif.gui.ImageViewer
getPlaneClass() - Method in class io.scif.AbstractReader
getPlaneClass() - Method in interface io.scif.TypedReader: Returns the class of Planes associated with this Reader.
getPlaneConverter(String) - Method in class io.scif.img.converters.DefaultPlaneConverterService
getPlaneConverter(String) - Method in interface io.scif.img.converters.PlaneConverterService
getPlaneConverterNames() - Method in class io.scif.img.converters.DefaultPlaneConverterService
getPlaneConverterNames() - Method in interface io.scif.img.converters.PlaneConverterService
getPlaneConverters() - Method in class io.scif.img.converters.DefaultPlaneConverterService
getPlaneConverters() - Method in interface io.scif.img.converters.PlaneConverterService
getPlaneCount() - Method in class io.scif.AbstractImageMetadata
getPlaneCount(int) - Method in class io.scif.AbstractReader
getPlaneCount(int) - Method in class io.scif.filters.AbstractReaderFilter
getPlaneCount(int) - Method in class io.scif.filters.FileStitcher
getPlaneCount(int) - Method in class io.scif.filters.MinMaxFilter
getPlaneCount(int) - Method in class io.scif.filters.PlaneSeparator
getPlaneCount() - Method in interface io.scif.ImageMetadata
getPlaneCount(int) - Method in interface io.scif.Reader: Determines the number of planes in the current file.
getPlaneIndex() - Method in class io.scif.formats.JPEG2000Format.Index
getPlaneIndex() - Method in class io.scif.gui.ImageViewer: Gets the index of the currently displayed image.
getPlaneMaximum(int, long) - Method in class io.scif.filters.MinMaxFilter: Retrieves the maximum pixel value for each planar axis of the specified plane.
getPlaneMinimum(int, long) - Method in class io.scif.filters.MinMaxFilter: Retrieves the minimum pixel value for each planar axis of the specified plane.
getPlaneSize() - Method in class io.scif.AbstractImageMetadata
getPlaneSize() - Method in interface io.scif.ImageMetadata: Returns the size, in bytes, of one plane in this image.
getPlaneSize(Reader, int) - Static method in class io.scif.util.FormatTools: Returns the size in bytes of a single plane read by the given Reader.
getPlaneSize(Metadata, int) - Static method in class io.scif.util.FormatTools: Returns the size in bytes of a tile defined by the given Metadata.
getPlaneSize(Metadata, int, int, int) - Static method in class io.scif.util.FormatTools: Returns the size in bytes of a w * h tile.
getPlaneSize(Metadata, Interval, int) - Static method in class io.scif.util.FormatTools: Returns the size in bytes of a plane with the given minima and maxima.
getPlte() - Method in class io.scif.formats.APNGFormat.Metadata
getPluginType() - Method in class io.scif.codec.DefaultCodecService
getPluginType() - Method in class io.scif.img.converters.DefaultPlaneConverterService
getPluginType() - Method in class io.scif.services.DefaultTranslatorService
getPositions() - Method in class io.scif.formats.MicromanagerFormat.Metadata
getPreferredSize() - Method in class io.scif.gui.PreviewPane
getPrefix() - Method in class io.scif.FilePattern: Gets the pattern's text string before any numerical ranges.
getPrefix(int) - Method in class io.scif.FilePattern: Gets the pattern's text string before the given numerical block.
getPrefix() - Method in class io.scif.formats.GIFFormat.Metadata
getPrefixes() - Method in class io.scif.FilePattern: Gets the pattern's text string before each numerical block.
getPrevPixels() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getPrevPlane() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getPriority() - Method in class io.scif.filters.ChannelFiller
getPriority() - Method in class io.scif.filters.DimensionSwapper
getPriority() - Method in class io.scif.filters.FileStitcher
getPriority() - Method in class io.scif.filters.PlaneSeparator
getProjections() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getQTVersion() - Method in class io.scif.formats.qt.DefaultQTJavaService
getQTVersion() - Method in interface io.scif.formats.qt.QTJavaService: Gets the QuickTime for Java version number.
getRange(AxisType) - Method in class io.scif.img.ImageRegion
getRasterLength(long[]) - Static method in class io.scif.util.FormatTools: Computes the number of raster values for a positional array with the given lengths.
getRawSize() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getReaderClass() - Method in class io.scif.AbstractFormat
getReaderClass() - Method in interface io.scif.Format
getReconstructionAlgorithm() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getRed() - Method in class io.scif.formats.APNGFormat.PLTEChunk
getRed(int) - Method in class io.scif.gui.Index16ColorModel
getRed(int) - Method in class io.scif.gui.SignedColorModel
getRed(Object) - Method in class io.scif.gui.SignedColorModel
getRed(int) - Method in class io.scif.gui.UnsignedIntColorModel
getRed(Object) - Method in class io.scif.gui.UnsignedIntColorModel
getReds() - Method in class io.scif.gui.Index16ColorModel: Return the array of red color components.
getReferenceLine() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getRepFormat() - Method in class io.scif.formats.ICSFormat.Metadata
getRescaleIntercept() - Method in class io.scif.formats.DICOMFormat.Metadata
getRescaleSlope() - Method in class io.scif.formats.DICOMFormat.Metadata
getResolution() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getResolutionLevels() - Method in class io.scif.formats.JPEG2000Format.Metadata
getResolutionLevels() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
getResolutionMultiplier() - Method in class io.scif.formats.tiff.IFD: Retrieve the value by which to multiply the X and Y resolution so that the resolutions are in microns per pixel.
getResolutionUnit() - Method in class io.scif.formats.tiff.IFD: Retrieves the image's resolution unit (TIFF tag ResolutionUnit) from this IFD.
getROIs() - Method in class io.scif.AbstractImageMetadata
getROIs() - Method in interface io.scif.ImageMetadata: Retrieves the ROIs associated with this image.
getRowBytes() - Method in class io.scif.formats.qt.PICTFormat.Metadata
getRowsPerStrip() - Method in class io.scif.formats.tiff.IFD: Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip) from this IFD.
getSample(BitBuffer, CodecOptions) - Method in class io.scif.codec.HuffmanCodec
getSamples() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getSamples(IFD, byte[]) - Method in class io.scif.formats.tiff.TiffParser
getSamples(IFD, byte[], int, int, long, long) - Method in class io.scif.formats.tiff.TiffParser
getSamples(IFD, byte[], int, int, long, long, int, int) - Method in class io.scif.formats.tiff.TiffParser
getSamplesPerPixel() - Method in class io.scif.formats.tiff.IFD: Retrieves the number of samples per pixel for the image (TIFF tag SamplesPerPixel) from this IFD.
getSamplingTime() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getScale() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
getScale(Metadata, int, AxisType) - Static method in class io.scif.util.FormatTools: Gets the average scale over the specified axis of the given image metadata.
getScale(ImageMetadata, AxisType) - Static method in class io.scif.util.FormatTools: Gets the average scale over the specified axis of the given image metadata.
getScaleFactor() - Method in class io.scif.formats.TestImgFormat.Metadata
getScanDistance() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getScanline(int) - Method in class io.scif.codec.JPEGTileDecoder
getScannerId() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getScannerType() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getSchemaPath() - Method in class io.scif.xml.ValidationSAXHandler
getSequenceNumber() - Method in class io.scif.formats.APNGFormat.ACTLChunk
getSequenceNumber() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getSequenceNumber() - Method in class io.scif.formats.APNGFormat.FDATChunk
getShorts(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of unsigned shorts, one per channel.
getShorts(WritableRaster) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of unsigned shorts, one per channel.
getShorts(WritableRaster, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools: Extracts pixel data as arrays of unsigned shorts, one per channel.
getSite() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getSize() - Method in class io.scif.AbstractImageMetadata
getSize(Image) - Static method in class io.scif.gui.AWTImageTools: Gets the width and height of the given AWT image, waiting for it to finish loading if necessary.
getSize() - Method in interface io.scif.ImageMetadata: Returns the size, in bytes, of all planes in this image.
getSliceBytes() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getSliceDistance() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getSlices() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getSlices() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getSliceSpacing() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getSliceStart() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getSliceThickness() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getSource() - Method in class io.scif.AbstractMetadata
getSource() - Method in class io.scif.AbstractParser
getSource() - Method in interface io.scif.Metadata: Returns the source used to generate this Metadata object.
getSource() - Method in interface io.scif.Parser
getSourceLocation() - Method in class io.scif.AbstractMetadata
getSourceLocation() - Method in class io.scif.AbstractParser
getSourceLocation() - Method in interface io.scif.Metadata
getSourceLocation() - Method in interface io.scif.Parser
getStagePositions() - Method in class io.scif.formats.ICSFormat.Metadata
getStageX() - Method in class io.scif.formats.ICSFormat.Metadata
getStageY() - Method in class io.scif.formats.ICSFormat.Metadata
getStageZ() - Method in class io.scif.formats.ICSFormat.Metadata
getStart() - Method in class io.scif.formats.EPSFormat.Metadata
getStep() - Method in class io.scif.FilePatternBlock
getStream() - Method in class io.scif.formats.tiff.TiffParser: Gets the stream from which TIFF data is being parsed.
getStream() - Method in class io.scif.formats.tiff.TiffSaver: Gets the stream from which TIFF data is being saved.
getStripByteCounts() - Method in class io.scif.formats.tiff.IFD: Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from this IFD.
getStripOffsets() - Method in class io.scif.formats.tiff.IFD: Retrieves the strip offsets for the image (TIFF tag StripOffsets) from this IFD.
getStrips() - Method in class io.scif.formats.qt.PICTFormat.Metadata
getStylesheet(String, Class<?>) - Method in class io.scif.xml.DefaultXMLService
getStylesheet(String, Class<?>) - Method in interface io.scif.xml.XMLService: Gets an XSLT template from the given resource location.
getSubimage(BufferedImage, boolean, Interval) - Static method in class io.scif.gui.AWTImageTools: Returns a subimage of the specified image.
getSubimage(BufferedImage, boolean, int, int, int, int) - Static method in class io.scif.gui.AWTImageTools: Returns a subimage of the specified image.
getSubimage(byte[], byte[], int, int, int, int, int, int, int, int, boolean) - Static method in class io.scif.util.ImageTools
getSubResolutionIFDs() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
getSuffix() - Method in class io.scif.FilePattern: Gets the pattern's text string after all numerical ranges.
getSuffix() - Method in class io.scif.formats.GIFFormat.Metadata
getSuffixes() - Method in class io.scif.AbstractFormat
getSuffixes() - Method in interface io.scif.Format: Gets the default file suffixes for this file format.
getSuffixes() - Method in class io.scif.services.DefaultFormatService
getSuffixes() - Method in interface io.scif.services.FormatService: Returns a complete list of all suffixes supported within this context.
getSupportedMetadataLevels() - Method in class io.scif.AbstractParser
getSupportedMetadataLevels() - Method in interface io.scif.Parser: Returns a list of MetadataLevel options for determining the granularity of Metadata collection.
getTable() - Method in class io.scif.AbstractImageMetadata
getTable() - Method in class io.scif.AbstractMetadata
getTable(String) - Method in class io.scif.common.IniList: Gets the table with the given name (header).
getTable() - Method in class io.scif.filters.AbstractMetadataWrapper
getTable() - Method in interface io.scif.HasMetaTable
getTables() - Method in class io.scif.AbstractImageMetadata
getTables() - Method in interface io.scif.ImageMetadata: Retrieves the tables associated with this image.
getTag() - Method in class io.scif.formats.tiff.TiffIFDEntry: Retrieves the entry's Tag value.
getTail() - Method in interface io.scif.filters.MasterFilter: Returns the base object (below the filter stack).
getTail() - Method in class io.scif.filters.MasterFilterHelper
getTail() - Method in class io.scif.filters.ReaderFilter
getThumbnailIFDs() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
getThumbnailIFDs() - Method in class io.scif.formats.tiff.TiffParser: Returns thumbnail IFDs.
getThumbSizeX() - Method in class io.scif.AbstractImageMetadata
getThumbSizeX() - Method in interface io.scif.ImageMetadata: Returns the width (in pixels) of the thumbnail planes in this image.
getThumbSizeY() - Method in class io.scif.AbstractImageMetadata
getThumbSizeY() - Method in interface io.scif.ImageMetadata: Returns the height (in pixels) of the thumbnail planes in this image.
getTiffParser() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
getTile(IFD, byte[], int, int) - Method in class io.scif.formats.tiff.TiffParser
getTileLength() - Method in class io.scif.formats.tiff.IFD: Returns the length of an image tile.
getTilesPerColumn() - Method in class io.scif.formats.tiff.IFD: Returns the number of image tiles per column.
getTilesPerRow() - Method in class io.scif.formats.tiff.IFD: Returns the number of image tiles per row.
getTileWidth() - Method in class io.scif.formats.tiff.IFD: Returns the width of an image tile.
getTime(String, String) - Static method in class io.scif.common.DateTools: Converts a string date in the given format to a long timestamp (in Unix format: milliseconds since January 1, 1970).
getTime() - Method in class io.scif.formats.DICOMFormat.Metadata
getTimeIncrement() - Method in class io.scif.formats.TIFFFormat.Metadata
getTimes() - Method in class io.scif.formats.qt.LegacyQTFormat.Metadata
getTimestamps() - Method in class io.scif.formats.ICSFormat.Metadata
getTitle() - Method in class io.scif.app.SCIFIOApp
getTopEdge() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getTransIndex() - Method in class io.scif.formats.GIFFormat.Metadata
getType() - Method in class io.scif.formats.tiff.TiffIFDEntry: Retrieves the entry's Type value.
getType() - Method in class io.scif.gui.TwoChannelColorSpace
getType() - Method in class io.scif.util.SCIFIOMetadataTools.AxisValue
getUniverse() - Method in class io.scif.formats.qt.DefaultQTJavaService
getUniverse() - Method in interface io.scif.formats.qt.QTJavaService: Gets QuickTime for Java reflected universe.
getURI() - Method in class io.scif.io.location.TestImgLocation
getUsedFiles() - Method in class io.scif.AbstractParser
getUsedFiles() - Method in interface io.scif.Parser: Returns an array of filenames needed to open this dataset.
getUsedLocations(boolean) - Method in class io.scif.AbstractParser
getUsedLocations(boolean) - Method in interface io.scif.Parser: Returns an array of filenames needed to open this dataset.
getValidBits() - Method in class io.scif.AbstractWriter
getValidBits() - Method in interface io.scif.Writer
getValueCount() - Method in class io.scif.formats.tiff.TiffIFDEntry: Retrieves the entry's ValueCount value.
getValueOffset() - Method in class io.scif.formats.tiff.TiffIFDEntry: Retrieves the entry's ValueOffset value.
getValueToIndex() - Method in class io.scif.formats.TestImgFormat.Metadata: Gets the pixel value to index maps for this dataset
getVersion() - Method in class io.scif.AbstractSCIFIOPlugin
getVersion() - Method in interface io.scif.SCIFIOPlugin: Gets the version of the SCIFIO software.
getVersion() - Method in class io.scif.services.DefaultFormatService
getVR() - Method in class io.scif.formats.DICOMFormat.DICOMTag
getWavelengths() - Method in class io.scif.formats.ICSFormat.Metadata
getWidth() - Method in class io.scif.codec.JPEGTileDecoder
getWidth() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getWidth() - Method in class io.scif.formats.APNGFormat.IHDRChunk
getWidth() - Method in class io.scif.formats.KontronFormat.Metadata
getWidth() - Method in class io.scif.formats.ScancoISQFormat.Metadata
getWidth() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
getWidth() - Method in interface io.scif.services.LuraWaveService: Wraps com.luratech.lwf.lwfDecoder#getWidth()
getWorkingDistance() - Method in class io.scif.formats.ICSFormat.Metadata
getWriterClass() - Method in class io.scif.AbstractFormat
getWriterClass() - Method in interface io.scif.Format
getWriterForLocation(Location) - Method in class io.scif.services.DefaultFormatService
getWriterForLocation(Location) - Method in interface io.scif.services.FormatService: Writer lookup method using the suffix or other methods to locate a fitting writer.
getXML(Document) - Method in class io.scif.xml.DefaultXMLService
getXML(Document) - Method in interface io.scif.xml.XMLService: Converts the given DOM back to a string.
getxOffset() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getxOrigin() - Method in class io.scif.formats.TIFFFormat.Metadata
getXResolution() - Method in class io.scif.formats.tiff.IFD: Retrieve the X resolution (TIFF tag XResolution) from this IFD.
getyOffset() - Method in class io.scif.formats.APNGFormat.FCTLChunk
getyOrigin() - Method in class io.scif.formats.TIFFFormat.Metadata
getYResolution() - Method in class io.scif.formats.tiff.IFD: Retrieve the Y resolution (TIFF tag YResolution) from this IFD.
GIF_MAGIC_STRING - Static variable in class io.scif.formats.GIFFormat
GIFFormat - Class in io.scif.formats: Handler for the GIF file format.
GIFFormat() - Constructor for class io.scif.formats.GIFFormat
GIFFormat.Checker - Class in io.scif.formats
GIFFormat.Metadata - Class in io.scif.formats
GIFFormat.Parser - Class in io.scif.formats
GIFFormat.Reader - Class in io.scif.formats
GLOBAL_META - Static variable in class io.scif.img.SCIFIOImgPlus
GRAPHICS_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the graphics domain.
GRAY_RESPONSE_CURVE - Static variable in class io.scif.formats.tiff.IFD
GRAY_RESPONSE_UNIT - Static variable in class io.scif.formats.tiff.IFD
Groupable - Interface in io.scif: Interface for components that can group multiple files together (e.g. for Parsing metadata or reading pixels)
groupableIsGroupFiles() - Method in class io.scif.config.SCIFIOConfig
groupableSetGroupFiles(boolean) - Method in class io.scif.config.SCIFIOConfig
guessDimOrder(CalibratedAxis[], long[], long[]) - Method in class io.scif.img.DefaultImgUtilityService
guessDimOrder(CalibratedAxis[], long[], long[]) - Static method in class io.scif.img.ImgSaver: The ImgLib axes structure can contain multiple unknown axes.
guessDimOrder(CalibratedAxis[], long[], long[]) - Method in interface io.scif.img.ImgUtilityService: The ImgLib axes structure can contain multiple unknown axes.
guessInterleavedAxisCount(List<CalibratedAxis>) - Static method in class io.scif.util.SCIFIOMetadataTools: Guesses at a reasonable default interleaved axis count for the given list of dimensional axes.
guessPlanarAxisCount(List<CalibratedAxis>) - Static method in class io.scif.util.SCIFIOMetadataTools: Guesses at a reasonable default planar axis count for the given list of dimensional axes.
gui() - Method in class io.scif.SCIFIO: Gets this application context's GUIService.
GUIService - Interface in io.scif.gui: A Service for working with graphical user interfaces.

H

HALFTONE_HINTS - Static variable in class io.scif.formats.tiff.IFD
handles(Object, Object...) - Method in class io.scif.img.ImgPlusCtxCleaningProvider
handles(Object, Object...) - Method in interface io.scif.refs.RefProvider
has(int) - Method in class io.scif.formats.dicom.DICOMDictionary: Checks whether the given code is in the dictionary.
HasColorTable - Interface in io.scif: Interface for SCIFIO components that load ColorTables during parsing.
hasCompanionFiles() - Method in class io.scif.AbstractGroupable
hasCompanionFiles() - Method in class io.scif.AbstractReader
hasCompanionFiles() - Method in class io.scif.filters.AbstractReaderFilter
hasCompanionFiles() - Method in class io.scif.formats.DICOMFormat.Reader
hasCompanionFiles() - Method in class io.scif.formats.MicromanagerFormat.Parser
hasCompanionFiles() - Method in class io.scif.formats.MicromanagerFormat.Reader
hasCompanionFiles() - Method in class io.scif.formats.NRRDFormat.Parser
hasCompanionFiles() - Method in class io.scif.formats.NRRDFormat.Reader
hasCompanionFiles() - Method in interface io.scif.Groupable: Returns true if this format supports multi-file datasets.
hasCompanionFiles() - Method in interface io.scif.Reader: Returns true if this format supports multi-file datasets.
HasFormat - Interface in io.scif: Super-interface for SCIFIO components that relate back to a Format.
hashCode() - Method in class io.scif.formats.tiff.TiffRational: Reasonable hash value for use with hashtables.
hashCode() - Method in class io.scif.io.location.TestImgLocation
hashImg(IterableInterval) - Static method in class io.scif.util.ImageHash
hasInstrumentData() - Method in class io.scif.formats.ICSFormat.Metadata
HasMetaTable - Interface in io.scif: Interface for components that maintain a MetaTable mapping metadata names to values.
hasRange(AxisType) - Method in class io.scif.img.ImageRegion
HasSource - Interface in io.scif: Interface for components that can be attached to open image sources that should be closed to avoid resource leaks
HCS_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the high content screening domain.
head() - Method in class io.scif.img.Range
HEADER_BLOCK - Static variable in class io.scif.formats.ScancoISQFormat.Metadata: Bytes in an ISQ header block
HEADER_BYTES - Static variable in class io.scif.formats.KontronFormat: Length of the header in a Kontron file
HEADER_KEY - Static variable in class io.scif.common.IniTable: Key to use for storing header value (in brackets).
HEADER_SIZE - Static variable in class io.scif.formats.StratecPQCTFormat: Bytes in a for a valid pQCT file
height - Variable in class io.scif.codec.CodecOptions: Height, in pixels, of the image.
HISTOLOGY_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the histology domain.
HOST_COMPUTER - Static variable in class io.scif.formats.tiff.IFD
HuffmanCodec - Class in io.scif.codec: This class implements Huffman decoding.
HuffmanCodec() - Constructor for class io.scif.codec.HuffmanCodec
HuffmanCodecOptions - Class in io.scif.codec: Options for compressing and decompressing Huffman data.
HuffmanCodecOptions() - Constructor for class io.scif.codec.HuffmanCodecOptions

I

ICSFormat - Class in io.scif.formats: SCIFIO Format supporting the ICS image format.
ICSFormat() - Constructor for class io.scif.formats.ICSFormat
ICSFormat.ICSTranslator - Class in io.scif.formats: SCIFIO file format Translator for ICS Metadata objects to the SCIFIO Core metadata type.
ICSFormat.ICSUtils - Class in io.scif.formats: Collection of utility methods and constants for working with ICS images.
ICSFormat.Metadata - Class in io.scif.formats: SCIFIO Metadata object for ICS images.
ICSFormat.Parser - Class in io.scif.formats: SCIFIO file format Parser for ICS images.
ICSFormat.Reader - Class in io.scif.formats: File format SCIFIO Reader for Image Cytometry Standard (ICS) images.
ICSFormat.Writer - Class in io.scif.formats: SCIFIO file format writer for ICS version 1 and 2 files.
ICSTranslator() - Constructor for class io.scif.formats.ICSFormat.ICSTranslator
IDATChunk() - Constructor for class io.scif.formats.APNGFormat.IDATChunk
IENDChunk() - Constructor for class io.scif.formats.APNGFormat.IENDChunk
IFD - Class in io.scif.formats.tiff: Data structure for working with TIFF Image File Directories (IFDs).
IFD(LogService) - Constructor for class io.scif.formats.tiff.IFD
IFD(IFD, LogService) - Constructor for class io.scif.formats.tiff.IFD
IFDList - Class in io.scif.formats.tiff: Data structure for working with a list of TIFF IFDs.
IFDList() - Constructor for class io.scif.formats.tiff.IFDList
IFDType - Enum in io.scif.formats.tiff: An enumeration of IFD types.
IHDRChunk() - Constructor for class io.scif.formats.APNGFormat.IHDRChunk
IMAGE_DESCRIPTION - Static variable in class io.scif.formats.tiff.IFD
IMAGE_LENGTH - Static variable in class io.scif.formats.tiff.IFD
IMAGE_META - Static variable in class io.scif.img.SCIFIOImgPlus
IMAGE_WIDTH - Static variable in class io.scif.formats.tiff.IFD
ImageHash - Class in io.scif.util
ImageHash() - Constructor for class io.scif.util.ImageHash
ImageIOFormat - Class in io.scif.formats: ImageIOReader is the superclass for file format readers that use the javax.imageio package.
ImageIOFormat() - Constructor for class io.scif.formats.ImageIOFormat
ImageIOFormat.ImageIOTranslator - Class in io.scif.formats
ImageIOFormat.Metadata - Class in io.scif.formats
ImageIOFormat.Parser<M extends ImageIOFormat.Metadata> - Class in io.scif.formats
ImageIOFormat.Reader<M extends ImageIOFormat.Metadata> - Class in io.scif.formats
ImageIOFormat.Writer<M extends ImageIOFormat.Metadata> - Class in io.scif.formats
ImageIOTranslator() - Constructor for class io.scif.formats.ImageIOFormat.ImageIOTranslator
IMAGEJ_TAG - Static variable in class io.scif.formats.TIFFFormat.Parser
ImageMetadata - Interface in io.scif: ImageMetadata stores the metadata for a single image within a dataset.
ImageRegion - Class in io.scif.img: A list of dimensional ranges.
ImageRegion(AxisType[], String[]) - Constructor for class io.scif.img.ImageRegion
ImageRegion(AxisType[], Range...) - Constructor for class io.scif.img.ImageRegion
ImageRegion(Map<AxisType, Range>) - Constructor for class io.scif.img.ImageRegion
images(int) - Method in class io.scif.io.location.TestImgLocation.Builder
ImageTools - Class in io.scif.util: A utility class with convenience methods for manipulating images in primitive array form.
ImageViewer - Class in io.scif.gui: A basic renderer for image data.
ImageViewer(Context) - Constructor for class io.scif.gui.ImageViewer: Constructs an image viewer.
ImageViewer(Context, boolean) - Constructor for class io.scif.gui.ImageViewer: Constructs an image viewer.
imgFactory(S) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
ImgFactoryHeuristic - Interface in io.scif.img: Interface for selecting an ImgFactory type based on a list of preferred SCIFIOConfig.ImgModes.
ImgIOException - Exception in io.scif.img: Exception indicating something went wrong during I/O.
ImgIOException(Object, String) - Constructor for exception io.scif.img.ImgIOException
ImgIOException(Throwable) - Constructor for exception io.scif.img.ImgIOException
ImgIOException(String) - Constructor for exception io.scif.img.ImgIOException
ImgOpener - Class in io.scif.img: Reads images from data sources using SCIFIO.
ImgOpener() - Constructor for class io.scif.img.ImgOpener
ImgOpener(Context) - Constructor for class io.scif.img.ImgOpener
imgOpenerGetImgFactoryHeuristic() - Method in class io.scif.config.SCIFIOConfig
imgOpenerGetImgModes() - Method in class io.scif.config.SCIFIOConfig
imgOpenerGetPlaneConverter() - Method in class io.scif.config.SCIFIOConfig
imgOpenerGetRange() - Method in class io.scif.config.SCIFIOConfig
imgOpenerGetRegion() - Method in class io.scif.config.SCIFIOConfig: Returns a ImageRegion specifying dimension constraints.
imgOpenerIsComputeMinMax() - Method in class io.scif.config.SCIFIOConfig
imgOpenerIsOpenAllImages() - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetComputeMinMax(boolean) - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetImgFactoryHeuristic(ImgFactoryHeuristic) - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetImgModes(SCIFIOConfig.ImgMode...) - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetIndex(int) - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetOpenAllImages(boolean) - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetPlaneConverter(PlaneConverter) - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetRange(String) - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetRange(Range) - Method in class io.scif.config.SCIFIOConfig
imgOpenerSetRegion(ImageRegion) - Method in class io.scif.config.SCIFIOConfig
ImgPlusCtxCleaner(Object, ReferenceQueue, Object...) - Constructor for class io.scif.img.ImgPlusCtxCleaningProvider.ImgPlusCtxCleaner
ImgPlusCtxCleaningProvider - Class in io.scif.img: RefProvider plugin for generating ImgPlusCtxCleaningProvider.ImgPlusCtxCleaner instances.
ImgPlusCtxCleaningProvider() - Constructor for class io.scif.img.ImgPlusCtxCleaningProvider
ImgPlusCtxCleaningProvider.ImgPlusCtxCleaner - Class in io.scif.img: PhantomReference implementation used to dispose a Context when all ImgPlus references have been garbage collected.
ImgSaver - Class in io.scif.img: Writes out an ImgPlus using SCIFIO.
ImgSaver() - Constructor for class io.scif.img.ImgSaver
ImgSaver(Context) - Constructor for class io.scif.img.ImgSaver
imgSaverGetWriteRGB() - Method in class io.scif.config.SCIFIOConfig
imgSaverSetWriteRGB(boolean) - Method in class io.scif.config.SCIFIOConfig
imgUtil() - Method in class io.scif.SCIFIO: Gets this application context's ImgUtilityService.
ImgUtilityService - Interface in io.scif.img: Helper methods for converting between SCIFIO and ImgLib2 data structures.
incrementElementLength() - Method in class io.scif.formats.DICOMFormat.DICOMTag
indentXML(String) - Method in class io.scif.xml.DefaultXMLService
indentXML(String, int) - Method in class io.scif.xml.DefaultXMLService
indentXML(String, boolean) - Method in class io.scif.xml.DefaultXMLService
indentXML(String, int, boolean) - Method in class io.scif.xml.DefaultXMLService
indentXML(String) - Method in interface io.scif.xml.XMLService: Indents XML to be more readable.
indentXML(String, int) - Method in interface io.scif.xml.XMLService: Indents XML by the given spacing to be more readable.
indentXML(String, boolean) - Method in interface io.scif.xml.XMLService: Indents XML to be more readable, avoiding any whitespace injection into CDATA if the preserveCData flag is set.
indentXML(String, int, boolean) - Method in interface io.scif.xml.XMLService: Indents XML by the given spacing to be more readable, avoiding any whitespace injection into CDATA if the preserveCData flag is set.
Index() - Constructor for class io.scif.formats.JPEG2000Format.Index
Index(int, long) - Constructor for class io.scif.formats.JPEG2000Format.Index
Index16ColorModel - Class in io.scif.gui: ColorModel that handles 16 bits per channel lookup tables.
Index16ColorModel(int, int, short[][], boolean) - Constructor for class io.scif.gui.Index16ColorModel
indexed(boolean) - Method in class io.scif.io.location.TestImgLocation.Builder
indexedToRGB(BufferedImage, boolean) - Static method in class io.scif.gui.AWTImageTools: Converts an indexed color BufferedImage to an RGB BufferedImage.
indexedToRGB(byte[][], byte[]) - Static method in class io.scif.util.ImageTools: Converts a LUT and an array of indices into an array of RGB tuples.
indexedToRGB(short[][], byte[], boolean) - Static method in class io.scif.util.ImageTools: Converts a LUT and an array of indices into an array of RGB tuples.
INFO_INDICES - Static variable in class io.scif.formats.StratecPQCTFormat.Metadata: Positions of the four measurement info strings in the header
IniList - Class in io.scif.common: A data structure containing a parsed list of INI key/value tables.
IniList() - Constructor for class io.scif.common.IniList
IniParser - Class in io.scif.common: A simple parser for INI configuration files.
IniParser() - Constructor for class io.scif.common.IniParser
IniParser(LogService) - Constructor for class io.scif.common.IniParser
IniTable - Class in io.scif.common: A data structure containing a parsed list of INI key/value tables.
IniTable() - Constructor for class io.scif.common.IniTable
initialiseCRC() - Method in class io.scif.common.CRC
initialize(int, long, Interval) - Method in class io.scif.AbstractWriter: Ensures this writer is prepared to write the given plane of the given image.
initialize(DataHandle<Location>, int) - Method in class io.scif.codec.JPEGTileDecoder
initialize(DataHandle<Location>, int, int) - Method in class io.scif.codec.JPEGTileDecoder
initialize(int, long, Interval) - Method in class io.scif.formats.APNGFormat.Writer
initialize(int, long, Interval) - Method in class io.scif.formats.EPSFormat.Writer
initialize(int, long, Interval) - Method in class io.scif.formats.ICSFormat.Writer
initialize(int, long, Interval) - Method in class io.scif.formats.qt.LegacyQTFormat.Writer
initialize(int, long, Interval) - Method in class io.scif.formats.qt.NativeQTFormat.Writer
initialize(int, long, Interval) - Method in class io.scif.formats.TIFFFormat.Writer
initialize() - Method in class io.scif.refs.DefaultRefManagerService
initialize() - Method in class io.scif.services.DefaultFormatService
initialize(InputStream) - Method in interface io.scif.services.LuraWaveService: Wraps com.luratech.lwf.lwfDecoder#lwfDecoder(InputStream, String, String) .
initializer() - Method in class io.scif.SCIFIO: Gets this application context's InitializeService.
initializeReader(Location) - Method in class io.scif.services.DefaultInitializeService
initializeReader(Location, SCIFIOConfig) - Method in class io.scif.services.DefaultInitializeService
initializeReader(Location) - Method in interface io.scif.services.InitializeService: See InitializeService.initializeReader(Location, SCIFIOConfig).
initializeReader(Location, SCIFIOConfig) - Method in interface io.scif.services.InitializeService: Convenience method for creating a Reader component that is ready to open planes of the provided image source.
InitializeService - Interface in io.scif.services: A collection of methods for initializing the IO components of SCIFIO (Readers and Writers).
initializeWriter(Location, Location) - Method in class io.scif.services.DefaultInitializeService
initializeWriter(Location, Location, SCIFIOConfig) - Method in class io.scif.services.DefaultInitializeService
initializeWriter(Metadata, Location) - Method in class io.scif.services.DefaultInitializeService
initializeWriter(Metadata, Location, SCIFIOConfig) - Method in class io.scif.services.DefaultInitializeService
initializeWriter(Location, Location) - Method in interface io.scif.services.InitializeService: See InitializeService.initializeWriter(Location, Location, SCIFIOConfig).
initializeWriter(Location, Location, SCIFIOConfig) - Method in interface io.scif.services.InitializeService: As InitializeService.initializeWriter(Location, Location) with configuration options.
initializeWriter(Metadata, Location) - Method in interface io.scif.services.InitializeService: See InitializeService.initializeWriter(Location, Location, SCIFIOConfig).
initializeWriter(Metadata, Location, SCIFIOConfig) - Method in interface io.scif.services.InitializeService: As InitializeService.initializeWriter(Metadata, Location) with configuration options.
initMetadata(TIFFFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.TIFFFormat.BaseTIFFParser: Populates the metadata hashtable and metadata store.
initMetadata(TIFFFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.TIFFFormat.Parser
initOutputFile() - Method in class io.scif.commands.SaveAsImage
IniWriter - Class in io.scif.common: A simple writer for INI configuration files.
IniWriter() - Constructor for class io.scif.common.IniWriter
INK_NAMES - Static variable in class io.scif.formats.tiff.IFD
INK_SET - Static variable in class io.scif.formats.tiff.IFD
INT16 - Static variable in class io.scif.util.FormatTools: Identifies the INT16 data type used to store pixel values.
INT32 - Static variable in class io.scif.util.FormatTools: Identifies the INT32 data type used to store pixel values.
INT8 - Static variable in class io.scif.util.FormatTools: Identifies the INT8 data type used to store pixel values.
IntAccessLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for IntArray types.
IntAccessLoader(Reader, ImageRegion, IntFunction<IntAccess>) - Constructor for class io.scif.img.cell.loaders.IntAccessLoader
IntArrayLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for IntArray types.
IntArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.IntArrayLoader
interlaced - Variable in class io.scif.codec.MJPBCodecOptions: Indicates whether or not channels are interlaced.
interleaved - Variable in class io.scif.codec.CodecOptions: Indicates whether or not channels are interleaved.
interleavedDims(int) - Method in class io.scif.io.location.TestImgLocation.Builder
interpolate(short[], byte[], int[], int, int, boolean) - Static method in class io.scif.util.ImageTools
intValue() - Method in class io.scif.formats.tiff.TiffRational: Returns the value of the specified number as an int.
INVALID_LICENSE_MSG - Static variable in interface io.scif.services.LuraWaveService: Message to display if an invalid LuraWave license code is given.
IO - Class in io.scif.img: A static utility class for easy access to ImgSaver and ImgOpener methods.
IO() - Constructor for class io.scif.img.IO
io.scif - package io.scif: Provides the interfaces and default implementations for the components of SCIFIO, and the context for instantiating these components.
io.scif.app - package io.scif.app: Contains the scijava-common app implementation for SCIFIO.
io.scif.codec - package io.scif.codec: Codecs for encoding and decoding streams of bytes.
io.scif.commands - package io.scif.commands
io.scif.common - package io.scif.common: SCIFIO common library.
io.scif.config - package io.scif.config: This package provides configuration options for all SCIFIO components.
io.scif.convert - package io.scif.convert
io.scif.enumeration - package io.scif.enumeration: Contains enums used throughout SCIFIO, and related classes (e.g. exceptions).
io.scif.filters - package io.scif.filters: Provides wrapping classes for modifying the performance of one or more of a {link io.scif.Format}'s components.
io.scif.formats - package io.scif.formats: Provides Format implementations for all file formats that are supported by default in SCIFIO.
io.scif.formats.dicom - package io.scif.formats.dicom
io.scif.formats.qt - package io.scif.formats.qt
io.scif.formats.tiff - package io.scif.formats.tiff: This package contains utility classes for working with a variety of Tiff-based formats.
io.scif.gui - package io.scif.gui: Provides classes for working with BufferedImage in SCIFIO.
io.scif.img - package io.scif.img: Provides SCIFIO-based classes for working with ImgPlus from the imglib2 library.
io.scif.img.axes - package io.scif.img.axes
io.scif.img.cell - package io.scif.img.cell: Provides a Reader backed CachedCellImg implementation and supporting classes.
io.scif.img.cell.loaders - package io.scif.img.cell.loaders: Provides implementations of SCIFIOArrayLoader for each basic ArrayDataAccess type.
io.scif.img.converters - package io.scif.img.converters: Provides a PlaneConverterService for populating ImgPlus objects using Reader output.
io.scif.io - package io.scif.io
io.scif.io.location - package io.scif.io.location
io.scif.refs - package io.scif.refs: Provides reference management utilities.
io.scif.services - package io.scif.services: Provides a set of Services (singletons within a given context) for working with SCIFIO objects.
io.scif.util - package io.scif.util: Provides utility classes for common operations on or by SCIFIO components.
io.scif.xml - package io.scif.xml: Provides tools and utility classes for working with XML in SCIFIO.
isBigTiff() - Method in class io.scif.formats.tiff.IFD: Gets whether this is a BigTIFF IFD.
isBigTiff() - Method in class io.scif.formats.tiff.TiffParser: Returns whether or not the current TIFF file contains BigTIFF data.
isBigTiff() - Method in class io.scif.formats.tiff.TiffSaver: Returns whether or not we are writing BigTIFF data.
isBigTiff() - Method in class io.scif.formats.TIFFFormat.Writer
isBinary() - Method in class io.scif.formats.EPSFormat.Metadata
isCanUsePrevious() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
isCertain() - Method in class io.scif.AxisGuesser: Gets whether the guesser is confident that all axes are correct.
isCompatible(Class<?>) - Method in class io.scif.filters.AbstractFilter
isCompatible(Class<?>) - Method in class io.scif.filters.AbstractReaderFilter
isCompatible(Class<?>) - Method in class io.scif.filters.ChannelFiller
isCompatible(Class<?>) - Method in class io.scif.filters.FileStitcher: FileStitcher is only compatible with ByteArray formats.
isCompatible(Class<?>) - Method in interface io.scif.filters.Filter: Returns true if this filter is capable of wrapping instances of the provided class.
isCompatible() - Method in class io.scif.img.cell.loaders.AbstractArrayLoader
isCompatibleRaster(Raster) - Method in class io.scif.gui.Index16ColorModel
isCompatibleRaster(Raster) - Method in class io.scif.gui.SignedColorModel
isCompatibleRaster(Raster) - Method in class io.scif.gui.UnsignedIntColorModel
isCompressible(Img<T>) - Method in class io.scif.img.DefaultImgUtilityService: see isCompressible(ImgPlus)
isCompressible(ImgPlus<T>) - Method in class io.scif.img.DefaultImgUtilityService: Currently there are limits as to what types of Images can be saved.
isCompressible(Img<T>) - Method in interface io.scif.img.ImgUtilityService: see ImgUtilityService.isCompressible(ImgPlus)
isCompressible(ImgPlus<T>) - Method in interface io.scif.img.ImgUtilityService: Currently there are limits as to what types of Images can be saved.
isCS_sRGB() - Method in class io.scif.gui.TwoChannelColorSpace
isDeflate() - Method in class io.scif.formats.DICOMFormat.Metadata
isEnabled() - Method in class io.scif.AbstractFormat
isEnabled() - Method in interface io.scif.Format
isEqualStrips() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
isFalseColor() - Method in class io.scif.AbstractImageMetadata
isFalseColor() - Method in interface io.scif.ImageMetadata: Returns true if we can ignore the color map (if present).
isFiltered() - Method in class io.scif.AbstractMetadata
isFiltered() - Method in interface io.scif.Metadata: Returns whether or not filterMetadata was set when parsing this Metadata object.
isFixed() - Method in class io.scif.FilePatternBlock
isFlip() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
isFloatingPoint(int) - Static method in class io.scif.util.FormatTools: Determines whether the given pixel type is floating point or integer.
isFormat(Location) - Method in class io.scif.AbstractChecker
isFormat(Location, SCIFIOConfig) - Method in class io.scif.AbstractChecker
isFormat(DataHandle<Location>) - Method in class io.scif.AbstractChecker
isFormat(Location) - Method in interface io.scif.Checker: Checks if the provided image source is compatible with this Format.
isFormat(Location, SCIFIOConfig) - Method in interface io.scif.Checker: Checks if the provided image source is compatible with this Format.
isFormat(DataHandle<Location>) - Method in interface io.scif.Checker: Checks if the given stream is a valid stream for this Format.
isFormat(DataHandle<Location>) - Method in class io.scif.formats.APNGFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.AVIFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.BMPFormat.Checker
isFormat(Location, SCIFIOConfig) - Method in class io.scif.formats.DICOMFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.DICOMFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.GIFFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.JPEG2000Format.Checker
isFormat(Location, SCIFIOConfig) - Method in class io.scif.formats.JPEGFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.JPEGFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.KontronFormat.Checker
isFormat(Location, SCIFIOConfig) - Method in class io.scif.formats.MicromanagerFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.MicromanagerFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.MinimalTIFFFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.MNGFormat.Checker
isFormat(Location, SCIFIOConfig) - Method in class io.scif.formats.NRRDFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.NRRDFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.PCXFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.PGMFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.qt.NativeQTFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.ScancoISQFormat.Checker
isFormat(DataHandle<Location>) - Method in class io.scif.formats.StratecPQCTFormat.Checker
isFormat(Location, SCIFIOConfig) - Method in class io.scif.formats.TestImgFormat.Checker
isFormat(Location) - Method in class io.scif.formats.TestImgFormat.Checker
isIndexed() - Method in class io.scif.AbstractImageMetadata
isIndexed() - Method in interface io.scif.ImageMetadata: Returns true if the planes are stored as indexed color.
isInitialized(int, long) - Method in class io.scif.AbstractWriter
isInitialized(int, long) - Method in interface io.scif.Writer
isInitializeHelper() - Method in class io.scif.formats.NRRDFormat.Metadata
isInSequence() - Method in class io.scif.formats.DICOMFormat.DICOMTag
isInterlace() - Method in class io.scif.formats.GIFFormat.Metadata
isInterlaced() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
isInverted() - Method in class io.scif.formats.DICOMFormat.Metadata
isInvertY() - Method in class io.scif.formats.BMPFormat.Metadata
isJNG() - Method in class io.scif.formats.MNGFormat.Metadata
isJP2K() - Method in class io.scif.formats.DICOMFormat.Metadata
isJPEG() - Method in class io.scif.formats.DICOMFormat.Metadata
isJVM64Bit() - Method in class io.scif.formats.qt.DefaultQTJavaService
isJVM64Bit() - Method in interface io.scif.formats.qt.QTJavaService: Whether this JVM is 64-bit.
isLegacy() - Method in class io.scif.formats.qt.PICTFormat
isLittleEndian() - Method in class io.scif.AbstractImageMetadata
isLittleEndian() - Method in class io.scif.formats.APNGFormat.Metadata
isLittleEndian() - Method in class io.scif.formats.DICOMFormat.DICOMTag
isLittleEndian() - Method in class io.scif.formats.tiff.IFD: Gets whether the TIFF information in this IFD is little-endian.
isLittleEndian() - Method in class io.scif.formats.tiff.TiffSaver: Returns whether or not we are writing little-endian data.
isLittleEndian() - Method in interface io.scif.ImageMetadata: Returns true if each pixel's bytes are in little endian order.
isLookForCompanion() - Method in class io.scif.formats.NRRDFormat.Metadata
isMetadataComplete() - Method in class io.scif.AbstractImageMetadata
isMetadataComplete() - Method in interface io.scif.ImageMetadata: Returns true if we are confident that all of the metadata stored within the image has been parsed.
isMinMaxPopulated(int) - Method in class io.scif.filters.MinMaxFilter: Returns true if the values returned by getAxisGlobalMinimum/Maximum can be trusted.
isMultichannel() - Method in class io.scif.AbstractImageMetadata
isMultichannel() - Method in interface io.scif.ImageMetadata: Returns true if the Axes.CHANNEL axis is a planar axis.
isNormalized() - Method in class io.scif.AbstractReader
isNormalized() - Method in class io.scif.filters.AbstractReaderFilter
isNormalized() - Method in interface io.scif.Reader: Returns true if we should normalize float data.
isNoSubresolutions() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
ISO8601_FORMAT - Static variable in class io.scif.common.DateTools: ISO 8601 date format string.
ISO_SPEED_RATINGS - Static variable in class io.scif.formats.tiff.IFD
isOddLocations() - Method in class io.scif.formats.DICOMFormat.Metadata
isOrderCertain() - Method in class io.scif.AbstractImageMetadata
isOrderCertain() - Method in interface io.scif.ImageMetadata: Returns true if we are confident that the dimension order is correct.
ISQ_ID - Static variable in class io.scif.formats.ScancoISQFormat: The header byte sequence which identifies Scanco ISQ files
isQTExpired() - Method in class io.scif.formats.qt.DefaultQTJavaService
isQTExpired() - Method in interface io.scif.formats.qt.QTJavaService: Whether QuickTime for Java has expired.
isRawBits() - Method in class io.scif.formats.PGMFormat.Metadata
isRawCodestream() - Method in class io.scif.formats.JPEG2000Format.Parser: Whether or not the codestream is raw and not JP2 boxed.
isRegex() - Method in class io.scif.FilePattern: Returns whether or not this pattern is a regular expression.
isRLE() - Method in class io.scif.formats.DICOMFormat.Metadata
isSeparateDefault() - Method in class io.scif.formats.APNGFormat.Metadata
isSigned() - Method in class io.scif.formats.APNGFormat.Metadata
isSigned() - Method in class io.scif.formats.ICSFormat.Metadata
isSigned(int) - Static method in class io.scif.util.FormatTools: Determines whether the given pixel type is signed or unsigned.
isSingleFile(Location) - Method in class io.scif.AbstractGroupable
isSingleFile(Location) - Method in class io.scif.filters.AbstractReaderFilter
isSingleFile(Location) - Method in class io.scif.formats.MicromanagerFormat.Parser
isSingleFile(Location) - Method in class io.scif.formats.NRRDFormat.Parser
isSingleFile(Location) - Method in class io.scif.formats.NRRDFormat.Reader
isSingleFile(Location) - Method in interface io.scif.Groupable: Returns true if this is a single-file format.
isSpork() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
isSupportedCompression(String) - Method in class io.scif.AbstractWriter
isSupportedCompression(String) - Method in interface io.scif.Writer: Checks if the given compression type is supported.
isSupportedType(int, String) - Method in class io.scif.AbstractWriter
isSupportedType(int, String) - Method in interface io.scif.Writer: Checks if the given pixel type is supported.
isThumbnail() - Method in class io.scif.AbstractImageMetadata
isThumbnail() - Method in interface io.scif.ImageMetadata: Determines whether or not this image is a lower-resolution copy of another image.
isTiff() - Method in class io.scif.formats.EPSFormat.Metadata
isTiled() - Method in class io.scif.formats.tiff.IFD
isTransparency() - Method in class io.scif.formats.GIFFormat.Metadata
isUse64Bit() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
isUsingPatternIds() - Method in class io.scif.filters.FileStitcher: Gets whether the reader is using file patterns for IDs.
isValid() - Method in class io.scif.FilePattern: Gets whether the file pattern string is valid.
isValidHeader() - Method in class io.scif.formats.tiff.TiffParser: Tests this stream to see if it represents a TIFF file.
isVersionOne() - Method in class io.scif.formats.qt.PICTFormat.Metadata
isVersionTwo() - Method in class io.scif.formats.ICSFormat.Metadata

J

JAIIIOService - Interface in io.scif.services: Interface defining methods for reading data using JAI Image I/O.
JAIIIOServiceImpl - Class in io.scif.services: Implementation of JAIIIOService for reading and writing JPEG-2000 data.
JAIIIOServiceImpl() - Constructor for class io.scif.services.JAIIIOServiceImpl
JPEG2000BoxType - Enum in io.scif.codec: An enumeration of JPEG 2000 box types.
JPEG2000Codec - Class in io.scif.codec: This class implements JPEG 2000 compression and decompression.
JPEG2000Codec() - Constructor for class io.scif.codec.JPEG2000Codec
JPEG2000CodecOptions - Class in io.scif.codec: Options for compressing and decompressing JPEG-2000 data.
JPEG2000CodecOptions() - Constructor for class io.scif.codec.JPEG2000CodecOptions: Creates a new instance.
JPEG2000CodecOptions(CodecOptions) - Constructor for class io.scif.codec.JPEG2000CodecOptions: Creates a new instance with options.
JPEG2000Format - Class in io.scif.formats: JPEG2000Reader is the file format reader for JPEG-2000 images.
JPEG2000Format() - Constructor for class io.scif.formats.JPEG2000Format
JPEG2000Format.Checker - Class in io.scif.formats
JPEG2000Format.Index - Class in io.scif.formats
JPEG2000Format.Metadata - Class in io.scif.formats
JPEG2000Format.Parser - Class in io.scif.formats
JPEG2000Format.Reader - Class in io.scif.formats
JPEG2000Format.Writer - Class in io.scif.formats
JPEG2000SegmentMarker - Enum in io.scif.codec: An enumeration of JPEG 2000 segment markers.
JPEG_AC_TABLES - Static variable in class io.scif.formats.tiff.IFD
JPEG_DC_TABLES - Static variable in class io.scif.formats.tiff.IFD
JPEG_INTERCHANGE_FORMAT - Static variable in class io.scif.formats.tiff.IFD
JPEG_INTERCHANGE_FORMAT_LENGTH - Static variable in class io.scif.formats.tiff.IFD
JPEG_LOSSLESS_PREDICTORS - Static variable in class io.scif.formats.tiff.IFD
JPEG_POINT_TRANSFORMS - Static variable in class io.scif.formats.tiff.IFD
JPEG_PROC - Static variable in class io.scif.formats.tiff.IFD
JPEG_Q_TABLES - Static variable in class io.scif.formats.tiff.IFD
JPEG_RESTART_INTERVAL - Static variable in class io.scif.formats.tiff.IFD
JPEG_TABLES - Static variable in class io.scif.formats.tiff.IFD
JPEGCodec - Class in io.scif.codec: This class implements JPEG compression and decompression.
JPEGCodec() - Constructor for class io.scif.codec.JPEGCodec
JPEGFormat - Class in io.scif.formats: JPEGReader is the file format reader for JPEG images.
JPEGFormat() - Constructor for class io.scif.formats.JPEGFormat
JPEGFormat.Checker - Class in io.scif.formats
JPEGFormat.Metadata - Class in io.scif.formats
JPEGFormat.Parser - Class in io.scif.formats
JPEGFormat.Reader - Class in io.scif.formats
JPEGFormat.Writer - Class in io.scif.formats
JPEGTileDecoder - Class in io.scif.codec: TODO
JPEGTileDecoder(Context) - Constructor for class io.scif.codec.JPEGTileDecoder
JPEGTileFormat - Class in io.scif.formats: Reader for decoding JPEG images using java.awt.Toolkit.
JPEGTileFormat() - Constructor for class io.scif.formats.JPEGTileFormat
JPEGTileFormat.Metadata - Class in io.scif.formats
JPEGTileFormat.Parser - Class in io.scif.formats
JPEGTileFormat.Reader - Class in io.scif.formats
JPG - Static variable in class io.scif.codec.LosslessJPEGCodec

K

keyPressed(KeyEvent) - Method in class io.scif.gui.ImageViewer: Handles key presses.
keyReleased(KeyEvent) - Method in class io.scif.gui.ImageViewer
keys - Static variable in class io.scif.formats.ICSFormat.ICSUtils: Metadata field categories.
keys(Hashtable<String, Object>) - Static method in class io.scif.util.SCIFIOMetadataTools: Gets a sorted list of keys from the given hashtable.
keyTyped(KeyEvent) - Method in class io.scif.gui.ImageViewer
KONTRON_ID - Static variable in class io.scif.formats.KontronFormat: Kontron IMGs start with this sequence
KontronFormat - Class in io.scif.formats: The file format reader for Kontron IMG files Kontron IMG files are generated by a Kontron controller computer attached to Alan Boyde's Zeiss DSM 962 scanning electron microscope.
KontronFormat() - Constructor for class io.scif.formats.KontronFormat
KontronFormat.Checker - Class in io.scif.formats
KontronFormat.Metadata - Class in io.scif.formats
KontronFormat.Parser - Class in io.scif.formats
KontronFormat.Reader - Class in io.scif.formats

L

LABEL - Static variable in class io.scif.formats.TIFFFormat.Parser
LEAF - Static variable in class io.scif.formats.ICSFormat.ICSUtils
LegacyQTFormat - Class in io.scif.formats.qt: LegacyQTReader is a file format reader for QuickTime movie files.
LegacyQTFormat() - Constructor for class io.scif.formats.qt.LegacyQTFormat
LegacyQTFormat.LegacyQTTranslator - Class in io.scif.formats.qt
LegacyQTFormat.Metadata - Class in io.scif.formats.qt
LegacyQTFormat.Parser - Class in io.scif.formats.qt
LegacyQTFormat.Reader - Class in io.scif.formats.qt
LegacyQTFormat.Writer - Class in io.scif.formats.qt
LegacyQTTranslator() - Constructor for class io.scif.formats.qt.LegacyQTFormat.LegacyQTTranslator
lengths(long...) - Method in class io.scif.io.location.TestImgLocation.Builder
LICENSE_PROPERTY - Static variable in interface io.scif.services.LuraWaveService: System property to check for the LuraWave license code.
LIFETIME - Static variable in class io.scif.img.axes.SCIFIOAxes: Identifies the Lifetime dimensional type, representing a dimension consisting of a lifetime histogram.
LIGHT_SOURCE - Static variable in class io.scif.formats.tiff.IFD
LITTLE - Static variable in class io.scif.formats.tiff.TiffConstants
little(boolean) - Method in class io.scif.io.location.TestImgLocation.Builder
LITTLE_ENDIAN - Static variable in class io.scif.formats.tiff.IFD
littleEndian - Variable in class io.scif.codec.CodecOptions: Indicates endianness of pixel data.
LM_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the light microscopy domain.
loadArray(Interval) - Method in class io.scif.img.cell.loaders.AbstractArrayLoader
loadArray(Interval, A) - Method in class io.scif.img.cell.loaders.AbstractArrayLoader
loadArray(Interval) - Method in interface io.scif.img.cell.loaders.SCIFIOArrayLoader
loadImage(Image) - Static method in class io.scif.gui.AWTImageTools: Ensures the given AWT image is fully loaded.
loadTable(int, int) - Method in class io.scif.img.cell.loaders.AbstractArrayLoader
loadTable(int, int) - Method in interface io.scif.img.cell.loaders.SCIFIOArrayLoader: Returns the ColorTable for a given set of indices.
LocationInfo - Class in io.scif: Encompasses basic metadata about a Loation.
LocationInfo() - Constructor for class io.scif.LocationInfo
locationMap - Variable in class io.scif.formats.MicromanagerFormat.Position
locationName - Variable in class io.scif.LocationInfo: Absolute path to this file.
log() - Method in class io.scif.AbstractSCIFIOPlugin
log() - Method in interface io.scif.SCIFIOPlugin: Gets a reference to the SciJava context's LogService.
LongAccessLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for LongArray types.
LongAccessLoader(Reader, ImageRegion, IntFunction<LongAccess>) - Constructor for class io.scif.img.cell.loaders.LongAccessLoader
LongArrayLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for LongArray types.
LongArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.LongArrayLoader
longValue() - Method in class io.scif.formats.tiff.TiffRational: Returns the value of the specified number as a long.
lossless - Variable in class io.scif.codec.CodecOptions: Used with codecs allowing lossy and lossless compression.
LosslessJPEGCodec - Class in io.scif.codec: Decompresses lossless JPEG images.
LosslessJPEGCodec() - Constructor for class io.scif.codec.LosslessJPEGCodec
LUMA_BLUE - Static variable in enum io.scif.formats.tiff.PhotoInterp
LUMA_GREEN - Static variable in enum io.scif.formats.tiff.PhotoInterp
LUMA_RED - Static variable in enum io.scif.formats.tiff.PhotoInterp: Default luminance values for YCbCr data.
LuraWaveCodec - Class in io.scif.codec: This class provides LuraWave decompression, using LuraWave's Java decoding library.
LuraWaveCodec() - Constructor for class io.scif.codec.LuraWaveCodec
LuraWaveService - Interface in io.scif.services
lutLength(int) - Method in class io.scif.io.location.TestImgLocation.Builder
LUTS - Static variable in class io.scif.formats.TIFFFormat.Parser
LZWCodec - Class in io.scif.codec: This is an optimized LZW codec for use with TIFF files.
LZWCodec() - Constructor for class io.scif.codec.LZWCodec

M

MAGIC_NUMBER - Static variable in class io.scif.formats.tiff.TiffConstants
MAGIC_NUMBER - Static variable in class io.scif.formats.TIFFFormat.Parser
MAKE - Static variable in class io.scif.formats.tiff.IFD
make24Bits(Object, int, int, boolean, boolean) - Static method in class io.scif.util.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 io.scif.util.ImageTools: Convert an arbitrary primitive type array with 3 samples per pixel to a 3 x (width * height) byte array.
make24Bits(Object, int, int, boolean) - Static method in class io.scif.util.ImageTools: Convert an arbitrary primitive type array with 3 samples per pixel to an int array, i.e.
make24Bits(Object, int, int, boolean, Double, Double) - Static method in class io.scif.util.ImageTools: Convert an arbitrary primitive type array with 3 samples per pixel to an int array, i.e.
makeArray(Object) - Method in class io.scif.img.DefaultImgUtilityService: Wraps raw primitive array in ImgLib2 Array object.
makeArray(Object) - Method in interface io.scif.img.ImgUtilityService: Wraps raw primitive array in ImgLib2 Array object.
makeBuffered(Image) - Static method in class io.scif.gui.AWTImageTools: Creates a buffered image from the given AWT image object.
makeBuffered(Image, ColorModel) - Static method in class io.scif.gui.AWTImageTools: Creates a buffered image possessing the given color model, from the specified AWT image object.
makeColorModel(int, int) - Static method in class io.scif.gui.AWTImageTools: Gets a color model for the given number of color components.
makeColorSpace(int) - Static method in class io.scif.gui.AWTImageTools: Gets a color space for the given number of color components.
makeCompatible(BufferedImage, GraphicsConfiguration) - Static method in class io.scif.gui.AWTImageTools: Creates a buffered image compatible with the given graphics configuration, using the given buffered image as a source.
makeCompressionTypes() - Method in class io.scif.AbstractWriter
makeCompressionTypes() - Method in class io.scif.DefaultWriter
makeCompressionTypes() - Method in class io.scif.formats.APNGFormat.Writer
makeCompressionTypes() - Method in class io.scif.formats.AVIFormat.Writer
makeCompressionTypes() - Method in class io.scif.formats.EPSFormat.Writer
makeCompressionTypes() - Method in class io.scif.formats.ICSFormat.Writer
makeCompressionTypes() - Method in class io.scif.formats.ImageIOFormat.Writer
makeCompressionTypes() - Method in class io.scif.formats.JPEG2000Format.Writer
makeCompressionTypes() - Method in class io.scif.formats.qt.LegacyQTFormat.Writer
makeCompressionTypes() - Method in class io.scif.formats.qt.NativeQTFormat.Writer
makeCompressionTypes() - Method in class io.scif.formats.TIFFFormat.Writer
makeImage(byte[], int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given single-channel byte data.
makeImage(short[], int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given single-channel short data.
makeImage(int[], int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given single-channel int data.
makeImage(float[], int, int) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given single-channel float data.
makeImage(double[], int, int) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given single-channel double data.
makeImage(byte[], int, int, int, boolean, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given byte data.
makeImage(short[], int, int, int, boolean, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given short data.
makeImage(int[], int, int, int, boolean, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given int data.
makeImage(float[], int, int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given float data.
makeImage(double[], int, int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given double data.
makeImage(byte[][], int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given byte data.
makeImage(short[][], int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given short data.
makeImage(int[][], int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given int data.
makeImage(float[][], int, int) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given single-precision floating point data.
makeImage(double[][], int, int) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given double-precision floating point data.
makeImage(byte[], int, int, int, boolean, int, boolean, boolean, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given raw byte array, performing any necessary type conversions.
makeImage(byte[][], int, int, int, boolean, boolean, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given raw byte array, performing any necessary type conversions.
MAKER_NOTE - Static variable in class io.scif.formats.tiff.IFD
makeRef(Object, ReferenceQueue, Object...) - Method in class io.scif.img.ImgPlusCtxCleaningProvider
makeRef(Object, ReferenceQueue, Object...) - Method in interface io.scif.refs.RefProvider
makeRGBImage(byte[], int, int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates an RGB image from the given raw byte array, performing any necessary type conversions.
makeRGBImage(byte[][], int, int) - Static method in class io.scif.gui.AWTImageTools: Creates an RGB image from the given raw byte array
makeSCIFIOImgPlus(Img<T>) - Method in class io.scif.img.DefaultImgUtilityService
makeSCIFIOImgPlus(Img<T>) - Method in interface io.scif.img.ImgUtilityService: Convenience method for wrapping an Img as a SCIFIOImgPlus .
makeSuffixArray() - Method in class io.scif.AbstractFormat: Helper method to cache the suffix array for a format.
makeSuffixArray() - Method in class io.scif.formats.APNGFormat
makeSuffixArray() - Method in class io.scif.formats.AVIFormat
makeSuffixArray() - Method in class io.scif.formats.BMPFormat
makeSuffixArray() - Method in class io.scif.formats.DICOMFormat
makeSuffixArray() - Method in class io.scif.formats.EPSFormat
makeSuffixArray() - Method in class io.scif.formats.FITSFormat
makeSuffixArray() - Method in class io.scif.formats.GIFFormat
makeSuffixArray() - Method in class io.scif.formats.ICSFormat
makeSuffixArray() - Method in class io.scif.formats.JPEG2000Format
makeSuffixArray() - Method in class io.scif.formats.JPEGFormat
makeSuffixArray() - Method in class io.scif.formats.JPEGTileFormat
makeSuffixArray() - Method in class io.scif.formats.KontronFormat
makeSuffixArray() - Method in class io.scif.formats.MicromanagerFormat
makeSuffixArray() - Method in class io.scif.formats.MinimalTIFFFormat
makeSuffixArray() - Method in class io.scif.formats.MNGFormat
makeSuffixArray() - Method in class io.scif.formats.NRRDFormat
makeSuffixArray() - Method in class io.scif.formats.PCXFormat
makeSuffixArray() - Method in class io.scif.formats.PGMFormat
makeSuffixArray() - Method in class io.scif.formats.qt.LegacyQTFormat
makeSuffixArray() - Method in class io.scif.formats.qt.NativeQTFormat
makeSuffixArray() - Method in class io.scif.formats.qt.PICTFormat
makeSuffixArray() - Method in class io.scif.formats.ScancoISQFormat
makeSuffixArray() - Method in class io.scif.formats.StratecPQCTFormat
makeSuffixArray() - Method in class io.scif.formats.TestImgFormat
makeSuffixArray() - Method in class io.scif.formats.TIFFFormat
makeSuffixArray() - Method in class io.scif.formats.TIFFJAIFormat
makeType(int) - Method in class io.scif.img.DefaultImgUtilityService: Converts SCIFIO pixel type to ImgLib2 Type object.
makeType(Object) - Method in class io.scif.img.DefaultImgUtilityService: Converts ImgLib2 Type object to SCIFIO pixel type.
makeType(int) - Method in interface io.scif.img.ImgUtilityService: Converts SCIFIO pixel type to ImgLib2 Type object.
makeType(Object) - Method in interface io.scif.img.ImgUtilityService: Converts ImgLib2 Type object to SCIFIO pixel type.
makeUnsigned(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Converts the given BufferedImage into an image with unsigned pixel data.
manage(Object, Object...) - Method in class io.scif.refs.DefaultRefManagerService
manage(Object, Object...) - Method in interface io.scif.refs.RefManagerService: If there is a corresponding CleaningRef for the given object, it will be created using the given object as its referent and attached to a reference queue.
MasterFilter<T extends org.scijava.Contextual> - Interface in io.scif.filters: An entry point for toggling and configuring Filters.
MasterFilterHelper<T extends org.scijava.Contextual> - Class in io.scif.filters: Helper class for MasterFilter implementations.
MasterFilterHelper(T, Class<? extends T>) - Constructor for class io.scif.filters.MasterFilterHelper
MAX_APERTURE_VALUE - Static variable in class io.scif.formats.tiff.IFD
MAX_SAMPLE_VALUE - Static variable in class io.scif.formats.tiff.IFD
maxBytes - Variable in class io.scif.codec.CodecOptions: If compressing, this is the maximum number of raw bytes to compress.
MEDICAL_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the medical imaging domain.
MemoryTools - Class in io.scif.util: A utility class with convenience methods to obtain information about the heap.
MemoryTools() - Constructor for class io.scif.util.MemoryTools
merge(Map<String, Object>, Map<String, Object>, String) - Static method in class io.scif.util.SCIFIOMetadataTools: Merges the given lists of metadata, prepending the specified prefix for the destination keys.
mergeChannels(BufferedImage[]) - Static method in class io.scif.gui.AWTImageTools: Merges the given images into a single multi-channel image.
META_DATA_BYTE_COUNTS - Static variable in class io.scif.formats.TIFFFormat.Parser
metaCheck() - Method in class io.scif.filters.AbstractReaderFilter
Metadata() - Constructor for class io.scif.formats.APNGFormat.Metadata
Metadata() - Constructor for class io.scif.formats.AVIFormat.Metadata
Metadata() - Constructor for class io.scif.formats.BMPFormat.Metadata
Metadata() - Constructor for class io.scif.formats.DICOMFormat.Metadata
Metadata() - Constructor for class io.scif.formats.EPSFormat.Metadata
Metadata() - Constructor for class io.scif.formats.FITSFormat.Metadata
Metadata() - Constructor for class io.scif.formats.GIFFormat.Metadata
Metadata() - Constructor for class io.scif.formats.ICSFormat.Metadata
Metadata() - Constructor for class io.scif.formats.ImageIOFormat.Metadata
Metadata() - Constructor for class io.scif.formats.JPEG2000Format.Metadata
Metadata() - Constructor for class io.scif.formats.JPEGFormat.Metadata
Metadata() - Constructor for class io.scif.formats.JPEGTileFormat.Metadata
Metadata() - Constructor for class io.scif.formats.KontronFormat.Metadata
Metadata() - Constructor for class io.scif.formats.MicromanagerFormat.Metadata
Metadata() - Constructor for class io.scif.formats.MinimalTIFFFormat.Metadata
Metadata() - Constructor for class io.scif.formats.MNGFormat.Metadata
Metadata() - Constructor for class io.scif.formats.NRRDFormat.Metadata
Metadata() - Constructor for class io.scif.formats.PCXFormat.Metadata
Metadata() - Constructor for class io.scif.formats.PGMFormat.Metadata
Metadata() - Constructor for class io.scif.formats.qt.LegacyQTFormat.Metadata
Metadata() - Constructor for class io.scif.formats.qt.NativeQTFormat.Metadata
Metadata() - Constructor for class io.scif.formats.qt.PICTFormat.Metadata
Metadata() - Constructor for class io.scif.formats.ScancoISQFormat.Metadata
Metadata() - Constructor for class io.scif.formats.StratecPQCTFormat.Metadata
Metadata() - Constructor for class io.scif.formats.TestImgFormat.Metadata
Metadata() - Constructor for class io.scif.formats.TIFFFormat.Metadata
Metadata() - Constructor for class io.scif.formats.TIFFJAIFormat.Metadata
Metadata - Interface in io.scif: Interface for all SCIFIO Metadata objects.
metadata() - Method in class io.scif.SCIFIO: Gets this application context's MetadataService.
metadataComplete(boolean) - Method in class io.scif.io.location.TestImgLocation.Builder
metadataFile - Variable in class io.scif.formats.MicromanagerFormat.Position
MetadataLevel - Enum in io.scif
MetadataService - Interface in io.scif: Interface for services that work with SCIFIO metadata.
MetadataWrapper - Interface in io.scif.filters: Wrapper for Metadata.
MetaTable - Interface in io.scif: Marker interface for a String : Object Map.
METERING_MODE - Static variable in class io.scif.formats.tiff.IFD
MicromanagerFormat - Class in io.scif.formats: MicromanagerReader is the file format reader for Micro-Manager files.
MicromanagerFormat() - Constructor for class io.scif.formats.MicromanagerFormat
MicromanagerFormat.Checker - Class in io.scif.formats
MicromanagerFormat.Metadata - Class in io.scif.formats
MicromanagerFormat.MicromanagerTranslator - Class in io.scif.formats: Necessary dummy translator, so that a Micromanager-OMEXML translator can be used
MicromanagerFormat.Parser - Class in io.scif.formats
MicromanagerFormat.Position - Class in io.scif.formats
MicromanagerFormat.Reader - Class in io.scif.formats
MicromanagerTranslator() - Constructor for class io.scif.formats.MicromanagerFormat.MicromanagerTranslator
MICROSOFT - Static variable in class io.scif.common.DateTools
MICROSOFT_EPOCH - Static variable in class io.scif.common.DateTools
MIN_SAMPLE_VALUE - Static variable in class io.scif.formats.tiff.IFD
MinimalTIFFFormat - Class in io.scif.formats: MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
MinimalTIFFFormat() - Constructor for class io.scif.formats.MinimalTIFFFormat
MinimalTIFFFormat.Checker - Class in io.scif.formats
MinimalTIFFFormat.Metadata - Class in io.scif.formats
MinimalTIFFFormat.Parser<M extends MinimalTIFFFormat.Metadata> - Class in io.scif.formats
MinimalTIFFFormat.Reader<M extends MinimalTIFFFormat.Metadata> - Class in io.scif.formats
MinMaxFilter - Class in io.scif.filters: Logic to compute minimum and maximum values for each plane.
MinMaxFilter() - Constructor for class io.scif.filters.MinMaxFilter
MissingLibraryException - Exception in io.scif: MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
MissingLibraryException() - Constructor for exception io.scif.MissingLibraryException
MissingLibraryException(String) - Constructor for exception io.scif.MissingLibraryException
MissingLibraryException(String, Throwable) - Constructor for exception io.scif.MissingLibraryException
MissingLibraryException(Throwable) - Constructor for exception io.scif.MissingLibraryException
MJPBCodec - Class in io.scif.codec: Methods for compressing and decompressing QuickTime Motion JPEG-B data.
MJPBCodec() - Constructor for class io.scif.codec.MJPBCodec
MJPBCodecOptions - Class in io.scif.codec: Options for compressing and decompressing MJPB data.
MJPBCodecOptions() - Constructor for class io.scif.codec.MJPBCodecOptions
MNG_MAGIC_BYTES - Static variable in class io.scif.formats.MNGFormat.Checker
MNGFormat - Class in io.scif.formats: A handler for the Multiple-image Network Graphics (MNG) file format.
MNGFormat() - Constructor for class io.scif.formats.MNGFormat
MNGFormat.Checker - Class in io.scif.formats
MNGFormat.Metadata - Class in io.scif.formats
MNGFormat.Parser - Class in io.scif.formats
MNGFormat.Reader - Class in io.scif.formats
MODEL - Static variable in class io.scif.formats.tiff.IFD
modifyPlanar(int, Metadata, long...) - Static method in class io.scif.util.SCIFIOMetadataTools: Replaces the first values.length of the provided Metadata's planar axes with the values.
modifyPlanar(int, Metadata, SCIFIOMetadataTools.AxisValue...) - Static method in class io.scif.util.SCIFIOMetadataTools: Iterates over the provided Metadata's planar axes, replacing any instances of axes with the paired values.
mouseDragged(MouseEvent) - Method in class io.scif.gui.ImageViewer: Handles cursor probes.
mouseMoved(MouseEvent) - Method in class io.scif.gui.ImageViewer: Handles cursor probes.
MSRLECodec - Class in io.scif.codec: Methods for compressing and decompressing data using Microsoft RLE.
MSRLECodec() - Constructor for class io.scif.codec.MSRLECodec
MSVideoCodec - Class in io.scif.codec: Methods for compressing and decompressing data using Microsoft Video 1.
MSVideoCodec() - Constructor for class io.scif.codec.MSVideoCodec
MUST_GROUP - Static variable in class io.scif.util.FormatTools: File grouping options.

N

NAME - Static variable in class io.scif.app.SCIFIOApp
name(int) - Method in class io.scif.formats.dicom.DICOMDictionary: Gets the name for the given code.
name(String) - Method in class io.scif.io.location.TestImgLocation.Builder
NAME_FORMAT - Static variable in class io.scif.formats.StratecPQCTFormat.Checker: The regexp for valid pQCT filenames (without extension)
NAME_KEY - Static variable in interface io.scif.MetadataService
NativeQTFormat - Class in io.scif.formats.qt: NativeQTReader is the file format reader for QuickTime movie files.
NativeQTFormat() - Constructor for class io.scif.formats.qt.NativeQTFormat
NativeQTFormat.Checker - Class in io.scif.formats.qt
NativeQTFormat.Metadata - Class in io.scif.formats.qt
NativeQTFormat.NativeQTTranslator - Class in io.scif.formats.qt
NativeQTFormat.Parser - Class in io.scif.formats.qt
NativeQTFormat.Reader - Class in io.scif.formats.qt
NativeQTFormat.Writer - Class in io.scif.formats.qt
NativeQTTranslator() - Constructor for class io.scif.formats.qt.NativeQTFormat.NativeQTTranslator
NEW_SUBFILE_TYPE - Static variable in class io.scif.formats.tiff.IFD
nextPlaneIndex(int, Reader, long[], long[], long[]) - Static method in class io.scif.util.FormatTools: Computes the next plane index for a given position, using the current min and max planar values.
nextPlaneIndex(int, Metadata, long[], long[], long[]) - Static method in class io.scif.util.FormatTools: Computes the next plane index for a given position, using the current min and max planar values.
nextPlaneIndex(long[], long[], long[], long[]) - Static method in class io.scif.util.FormatTools: Computes the next plane index for a given position, using the current min and max planar values.
NikonCodec - Class in io.scif.codec: This class implements Nikon decompression.
NikonCodec() - Constructor for class io.scif.codec.NikonCodec
NikonCodecOptions - Class in io.scif.codec: Options for compressing and decompressing Nikon NEF data.
NikonCodecOptions() - Constructor for class io.scif.codec.NikonCodecOptions
nio() - Method in class io.scif.SCIFIO: Gets this application context's NIOService.
NO_LICENSE_MSG - Static variable in interface io.scif.services.LuraWaveService: Message to display if no LuraWave license code is given.
NO_LURAWAVE_MSG - Static variable in interface io.scif.services.LuraWaveService: Message displayed if the LuraWave LWF decoder library is not found.
NON_GRAPHICS_DOMAINS - Static variable in class io.scif.util.FormatTools: List of non-graphics domains.
NON_HCS_DOMAINS - Static variable in class io.scif.util.FormatTools: List of non-HCS domains.
NON_SPECIAL_DOMAINS - Static variable in class io.scif.util.FormatTools: List of domains that do not require special handling.
NRRD_MAGIC_STRING - Static variable in class io.scif.formats.NRRDFormat.Checker
NRRDFormat - Class in io.scif.formats: File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
NRRDFormat() - Constructor for class io.scif.formats.NRRDFormat
NRRDFormat.Checker - Class in io.scif.formats
NRRDFormat.Metadata - Class in io.scif.formats
NRRDFormat.Parser - Class in io.scif.formats
NRRDFormat.Reader - Class in io.scif.formats
NUMBER_OF_INKS - Static variable in class io.scif.formats.tiff.IFD
NumberFilter - Class in io.scif: NumberFilter is a helper filter for FilePattern.findPattern().
NumberFilter(String, String) - Constructor for class io.scif.NumberFilter: Creates a filter for files containing a numerical block, sandwiched between the given strings.
numDecompositionLevels - Variable in class io.scif.codec.JPEG2000CodecOptions: The number of decomposition levels as would be provided to: J2KImageWriteParam#setNumDecompositionLevels(int) (WRITE).

O

OECF - Static variable in class io.scif.formats.tiff.IFD
offset() - Method in class io.scif.filters.PlaneSeparatorMetadata: Returns the number of axes being separated.
ok() - Method in class io.scif.xml.ValidationErrorHandler
OnDemandLongArray - Class in io.scif.formats.tiff
OnDemandLongArray(DataHandle<Location>) - Constructor for class io.scif.formats.tiff.OnDemandLongArray
open(String) - Method in class io.scif.gui.ImageViewer: Convenience overload of ImageViewer.open(Location) for backwards compatibility.
open(Location) - Method in class io.scif.gui.ImageViewer: Opens the given data source using the current format reader.
open(String, Reader) - Method in class io.scif.gui.ImageViewer: Opens from the given data source using the specified reader in a separate thread.
open(Location) - Static method in class io.scif.img.IO
open(String) - Static method in class io.scif.img.IO
open(Location, T) - Static method in class io.scif.img.IO
open(String, T) - Static method in class io.scif.img.IO
open(String, SCIFIOConfig) - Static method in class io.scif.img.IO
open(Location, SCIFIOConfig) - Static method in class io.scif.img.IO
open(Location, T, SCIFIOConfig) - Static method in class io.scif.img.IO
open(String, T, SCIFIOConfig) - Static method in class io.scif.img.IO
open(String, ImgFactory<T>) - Static method in class io.scif.img.IO
open(Location, ImgFactory<T>) - Static method in class io.scif.img.IO
open(String, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO
open(Location, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO
open(Reader, SCIFIOConfig) - Static method in class io.scif.img.IO
open(Reader, T, SCIFIOConfig) - Static method in class io.scif.img.IO
open(Reader, T, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO
open(String, ImgFactory<T>, T) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(String, ImgFactory).
open(Location, ImgFactory<T>, T) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(Location, ImgFactory).
open(String) - Method in class io.scif.io.DatasetIOPlugin
open(Location) - Method in class io.scif.io.DatasetIOPlugin
open(Location) - Method in interface io.scif.services.DatasetIOService: Loads a dataset from a source (such as a file on disk).
open(String) - Method in interface io.scif.services.DatasetIOService
open(Location, SCIFIOConfig) - Method in interface io.scif.services.DatasetIOService: As DatasetIOService.open(Location), with the given io.scif.config.SCIFIOConfig.
open(String, SCIFIOConfig) - Method in interface io.scif.services.DatasetIOService: Loads a dataset from a source (such as a file on disk).
open(Location) - Method in class io.scif.services.DefaultDatasetIOService
open(String) - Method in class io.scif.services.DefaultDatasetIOService
open(Location, SCIFIOConfig) - Method in class io.scif.services.DefaultDatasetIOService
open(String, SCIFIOConfig) - Method in class io.scif.services.DefaultDatasetIOService
openAll(Location) - Static method in class io.scif.img.IO
openAll(String) - Static method in class io.scif.img.IO
openAll(Location, T) - Static method in class io.scif.img.IO
openAll(String, T) - Static method in class io.scif.img.IO
openAll(String, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(Location, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(String, T, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(Location, T, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(String, ImgFactory<T>) - Static method in class io.scif.img.IO
openAll(Location, ImgFactory<T>) - Static method in class io.scif.img.IO
openAll(String, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(Location, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(Reader, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(Reader, T, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(Reader, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(Reader, T, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO
openAll(String, ImgFactory<T>, T) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(String, ImgFactory).
openAll(Location, ImgFactory<T>, T) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(Location, ImgFactory).
openAll(Location) - Method in interface io.scif.services.DatasetIOService: Load all the datasets from a given source.
openAll(String) - Method in interface io.scif.services.DatasetIOService
openAll(Location, SCIFIOConfig) - Method in interface io.scif.services.DatasetIOService: As DatasetIOService.openAll(Location), with a given io.scif.config.SCIFIOConfig.
openAll(String, SCIFIOConfig) - Method in interface io.scif.services.DatasetIOService
openAll(Location) - Method in class io.scif.services.DefaultDatasetIOService
openAll(String) - Method in class io.scif.services.DefaultDatasetIOService
openAll(String, SCIFIOConfig) - Method in class io.scif.services.DefaultDatasetIOService
openAll(Location, SCIFIOConfig) - Method in class io.scif.services.DefaultDatasetIOService
openAllDouble(Location) - Static method in class io.scif.img.IO: As ImgOpener.openImgs(Location) with a guaranteed DoubleType.
openAllDouble(String) - Static method in class io.scif.img.IO
openAllFloat(Location) - Static method in class io.scif.img.IO: As ImgOpener.openImgs(Location) with a guaranteed FloatType .
openAllFloat(String) - Static method in class io.scif.img.IO
openAllUnsignedByte(Location) - Static method in class io.scif.img.IO: As ImgOpener.openImgs(Location) with a guaranteed UnsignedByteType.
openAllUnsignedByte(String) - Static method in class io.scif.img.IO
openBufferedImage(TIFFJAIFormat.Metadata, long) - Static method in class io.scif.formats.TIFFJAIFormat: Obtains a BufferedImage from the given data source using JAI.
OpenDataset - Class in io.scif.commands: Command for opening a given File as a Dataset.
OpenDataset() - Constructor for class io.scif.commands.OpenDataset
openDouble(Location) - Static method in class io.scif.img.IO: As ImgOpener.openImgs(Location) with a guaranteed DoubleType.
openDouble(String) - Static method in class io.scif.img.IO
openDoubleImgs(String) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAllDouble(String).
opener() - Static method in class io.scif.img.IO: Creates a new ImgOpener.
openFloat(Location) - Static method in class io.scif.img.IO: As ImgOpener.openImgs(Location) with a guaranteed FloatType .
openFloat(String) - Static method in class io.scif.img.IO
openFloatImgs(String) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAllFloat(String).
openImage(Plane, Reader, int) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given Plane.
openImage(Plane, Reader, long[], int) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given Plane.
openImage(Plane, byte[], Reader, long[], int) - Static method in class io.scif.gui.AWTImageTools: Creates an image from the given Plane.
openImg(String) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(String).
openImg(String, T) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(String, RealType).
openImg(String, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(String, SCIFIOConfig).
openImg(String, T, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(String, RealType, SCIFIOConfig).
openImg(String, ImgFactory<T>) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(String, ImgFactory).
openImg(String, ImgFactory<T>, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(String, ImgFactory, SCIFIOConfig).
openImg(String, ImgFactory<T>, T) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(String, ImgFactory) or ImgOpener.openImgs(String, RealType).
openImg(Reader, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(Reader, SCIFIOConfig).
openImg(Reader, T, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(Reader, Object, SCIFIOConfig).
openImg(Reader, T, ImgFactory<T>, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(Reader, Object, SCIFIOConfig) or ImgOpener.openImgs(Reader, ImgFactory, SCIFIOConfig).
openImg(String, T) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(String, RealType).
openImg(String, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(String, SCIFIOConfig).
openImg(String, T, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(String, RealType, SCIFIOConfig).
openImg(String, ImgFactory<T>) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(String, ImgFactory).
openImg(String, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(String, ImgFactory, SCIFIOConfig).
openImg(String, ImgFactory<T>, T) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(String, ImgFactory).
openImg(Reader, T, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(Reader, RealType, SCIFIOConfig).
openImg(Reader, T, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.open(Reader, RealType, ImgFactory, SCIFIOConfig).
openImgs(String) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(String, T) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(String, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(String, T, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(String, ImgFactory<T>) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(String, ImgFactory<T>, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(Location) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(Location, T) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(Location, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(Location, T, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(Location, ImgFactory<T>) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(Location, ImgFactory<T>, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images from the given source.
openImgs(Reader) - Method in class io.scif.img.ImgOpener: Reads in images using the given Reader.
openImgs(Reader, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images using the given Reader.
openImgs(Reader, T, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images using the given Reader.
openImgs(Reader, ImgFactory<T>, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Reads in images using the given Reader.
openImgs(String, ImgFactory<T>, T) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(String, ImgFactory).
openImgs(Reader, T, ImgFactory<T>, SCIFIOConfig) - Method in class io.scif.img.ImgOpener: Deprecated.
Use ImgOpener.openImgs(Reader, ImgFactory, SCIFIOConfig).
openImgs(String) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(String).
openImgs(String, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(String, SCIFIOConfig).
openImgs(String, ImgFactory<T>) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(String, ImgFactory).
openImgs(String, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(String, ImgFactory, SCIFIOConfig).
openImgs(String, ImgFactory<T>, T) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(String, ImgFactory).
openImgs(String, T, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(String, RealType, SCIFIOConfig).
openImgs(String, T) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(String, RealType).
openImgs(Reader, T, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(Reader, RealType, SCIFIOConfig).
openImgs(Reader, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(Reader, ImgFactory, SCIFIOConfig).
openImgs(Reader, T, ImgFactory<T>, SCIFIOConfig) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAll(Reader, RealType, ImgFactory, SCIFIOConfig).
openPlane(int, long) - Method in class io.scif.AbstractReader
openPlane(int, long, Interval) - Method in class io.scif.AbstractReader
openPlane(int, long, Plane) - Method in class io.scif.AbstractReader
openPlane(int, long, Plane, Interval) - Method in class io.scif.AbstractReader
openPlane(int, long, SCIFIOConfig) - Method in class io.scif.AbstractReader
openPlane(int, long, Interval, SCIFIOConfig) - Method in class io.scif.AbstractReader
openPlane(int, long, Plane, SCIFIOConfig) - Method in class io.scif.AbstractReader
openPlane(int, long, Plane, Interval, SCIFIOConfig) - Method in class io.scif.AbstractReader
openPlane(int, long, P) - Method in class io.scif.AbstractReader
openPlane(int, long, P, SCIFIOConfig) - Method in class io.scif.AbstractReader
openPlane(int, long, P, Interval) - Method in class io.scif.AbstractReader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.DefaultReader: Non-functional openPlane implementation.
openPlane(int, long) - Method in class io.scif.filters.AbstractReaderFilter
openPlane(int, long, Interval) - Method in class io.scif.filters.AbstractReaderFilter
openPlane(int, long, Plane) - Method in class io.scif.filters.AbstractReaderFilter
openPlane(int, long, Plane, Interval) - Method in class io.scif.filters.AbstractReaderFilter
openPlane(int, long, SCIFIOConfig) - Method in class io.scif.filters.AbstractReaderFilter
openPlane(int, long, Interval, SCIFIOConfig) - Method in class io.scif.filters.AbstractReaderFilter
openPlane(int, long, Plane, SCIFIOConfig) - Method in class io.scif.filters.AbstractReaderFilter
openPlane(int, long, Plane, Interval, SCIFIOConfig) - Method in class io.scif.filters.AbstractReaderFilter
openPlane(int, long) - Method in class io.scif.filters.ChannelFiller
openPlane(int, long, Plane) - Method in class io.scif.filters.ChannelFiller
openPlane(int, long, Interval) - Method in class io.scif.filters.ChannelFiller
openPlane(int, long, Plane, Interval) - Method in class io.scif.filters.ChannelFiller
openPlane(int, long, SCIFIOConfig) - Method in class io.scif.filters.ChannelFiller
openPlane(int, long, Plane, SCIFIOConfig) - Method in class io.scif.filters.ChannelFiller
openPlane(int, long, Interval, SCIFIOConfig) - Method in class io.scif.filters.ChannelFiller
openPlane(int, long, Plane, Interval, SCIFIOConfig) - Method in class io.scif.filters.ChannelFiller
openPlane(int, long) - Method in class io.scif.filters.DimensionSwapper
openPlane(int, long, Plane) - Method in class io.scif.filters.DimensionSwapper
openPlane(int, long, Interval) - Method in class io.scif.filters.DimensionSwapper
openPlane(int, long, Plane, Interval) - Method in class io.scif.filters.DimensionSwapper
openPlane(int, long, SCIFIOConfig) - Method in class io.scif.filters.DimensionSwapper
openPlane(int, long, Interval, SCIFIOConfig) - Method in class io.scif.filters.DimensionSwapper
openPlane(int, long, Plane, SCIFIOConfig) - Method in class io.scif.filters.DimensionSwapper
openPlane(int, long, Plane, Interval, SCIFIOConfig) - Method in class io.scif.filters.DimensionSwapper
openPlane(int, long, Interval, SCIFIOConfig) - Method in class io.scif.filters.FileStitcher
openPlane(int, long, Plane, Interval, SCIFIOConfig) - Method in class io.scif.filters.FileStitcher
openPlane(int, long) - Method in class io.scif.filters.MinMaxFilter
openPlane(int, long, Plane) - Method in class io.scif.filters.MinMaxFilter
openPlane(int, long, Interval) - Method in class io.scif.filters.MinMaxFilter
openPlane(int, long, Plane, Interval) - Method in class io.scif.filters.MinMaxFilter
openPlane(int, long, SCIFIOConfig) - Method in class io.scif.filters.MinMaxFilter
openPlane(int, long, Plane, SCIFIOConfig) - Method in class io.scif.filters.MinMaxFilter
openPlane(int, long, Interval, SCIFIOConfig) - Method in class io.scif.filters.MinMaxFilter
openPlane(int, long, Plane, Interval, SCIFIOConfig) - Method in class io.scif.filters.MinMaxFilter
openPlane(int, long) - Method in class io.scif.filters.PlaneSeparator
openPlane(int, long, Plane) - Method in class io.scif.filters.PlaneSeparator
openPlane(int, long, Interval) - Method in class io.scif.filters.PlaneSeparator
openPlane(int, long, Plane, Interval) - Method in class io.scif.filters.PlaneSeparator
openPlane(int, long, SCIFIOConfig) - Method in class io.scif.filters.PlaneSeparator
openPlane(int, long, Plane, SCIFIOConfig) - Method in class io.scif.filters.PlaneSeparator
openPlane(int, long, Interval, SCIFIOConfig) - Method in class io.scif.filters.PlaneSeparator
openPlane(int, long, Plane, Interval, SCIFIOConfig) - Method in class io.scif.filters.PlaneSeparator
openPlane(int, long, BufferedImagePlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.APNGFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.AVIFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.BMPFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.DICOMFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.EPSFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.FITSFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.GIFFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.ICSFormat.Reader
openPlane(int, long, BufferedImagePlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.ImageIOFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.JPEG2000Format.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.JPEGTileFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.KontronFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.MicromanagerFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.MinimalTIFFFormat.Reader
openPlane(int, long, BufferedImagePlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.MNGFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.NRRDFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.PCXFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.PGMFormat.Reader
openPlane(int, long, BufferedImagePlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.qt.LegacyQTFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.qt.NativeQTFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.qt.PICTFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.ScancoISQFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.StratecPQCTFormat.Reader
openPlane(int, long, ByteArrayPlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.TestImgFormat.Reader
openPlane(int, long, BufferedImagePlane, Interval, SCIFIOConfig) - Method in class io.scif.formats.TIFFJAIFormat.Reader
openPlane(int, long) - Method in interface io.scif.Reader: Creates a Plane representation of the pixels at the specified indices.
openPlane(int, long, Interval) - Method in interface io.scif.Reader: Creates a Plane representation of a desired sub-region from the pixels at the specified indices.
openPlane(int, long, Plane) - Method in interface io.scif.Reader: Allows a single Plane object to be reused by reference when opening complete planes.
openPlane(int, long, Plane, Interval) - Method in interface io.scif.Reader: Allows a single Plane object to be reused by reference when opening sub-regions of planes.
openPlane(int, long, SCIFIOConfig) - Method in interface io.scif.Reader: As Reader.openPlane(int, long) with configuration options.
openPlane(int, long, Interval, SCIFIOConfig) - Method in interface io.scif.Reader: As Reader.openPlane(int, long, Interval) with configuration options.
openPlane(int, long, Plane, SCIFIOConfig) - Method in interface io.scif.Reader: Allows a single Plane object to be reused by reference when opening complete planes.
openPlane(int, long, Plane, Interval, SCIFIOConfig) - Method in interface io.scif.Reader: Allows a single Plane object to be reused by reference when opening sub-regions of planes.
openPlane(int, long) - Method in interface io.scif.TypedReader
openPlane(int, long, Interval) - Method in interface io.scif.TypedReader
openPlane(int, long, P) - Method in interface io.scif.TypedReader: Generic-parameterized openPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.openPlane(int, long, Plane).
openPlane(int, long, P, Interval) - Method in interface io.scif.TypedReader: Generic-parameterized openPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.openPlane(int, long, Plane, Interval).
openPlane(int, long, SCIFIOConfig) - Method in interface io.scif.TypedReader
openPlane(int, long, Interval, SCIFIOConfig) - Method in interface io.scif.TypedReader
openPlane(int, long, P, SCIFIOConfig) - Method in interface io.scif.TypedReader
openPlane(int, long, P, Interval, SCIFIOConfig) - Method in interface io.scif.TypedReader
openPlaneHelper() - Method in class io.scif.filters.AbstractReaderFilter: Allows code to be executed regardless of which AbstractReaderFilter.openPlane(int, long) signature is called.
openThumbImage(Plane, Reader, int, long[], int, int, boolean) - Static method in class io.scif.gui.AWTImageTools: Creates a thumbnail image from the provided plane, scaling it to the specified thumbnail dimensions.
openUnsignedByte(Location) - Static method in class io.scif.img.IO: As ImgOpener.openImgs(Location) with a guaranteed UnsignedByteType.
openUnsignedByte(String) - Static method in class io.scif.img.IO
openUnsignedByteImgs(String) - Static method in class io.scif.img.IO: Deprecated.
Use IO.openAllUnsignedByte(String).
orderCertain(boolean) - Method in class io.scif.io.location.TestImgLocation.Builder
ORIENTATION - Static variable in class io.scif.formats.tiff.IFD
OTHER_KEYS - Static variable in class io.scif.formats.ICSFormat.ICSUtils
outputClass() - Method in class io.scif.img.cell.loaders.AbstractArrayLoader
outputClass() - Method in class io.scif.img.cell.loaders.ByteAccessLoader
outputClass() - Method in class io.scif.img.cell.loaders.ByteArrayLoader
outputClass() - Method in class io.scif.img.cell.loaders.CharAccessLoader
outputClass() - Method in class io.scif.img.cell.loaders.CharArrayLoader
outputClass() - Method in class io.scif.img.cell.loaders.DoubleAccessLoader
outputClass() - Method in class io.scif.img.cell.loaders.DoubleArrayLoader
outputClass() - Method in class io.scif.img.cell.loaders.FloatAccessLoader
outputClass() - Method in class io.scif.img.cell.loaders.FloatArrayLoader
outputClass() - Method in class io.scif.img.cell.loaders.IntAccessLoader
outputClass() - Method in class io.scif.img.cell.loaders.IntArrayLoader
outputClass() - Method in class io.scif.img.cell.loaders.LongAccessLoader
outputClass() - Method in class io.scif.img.cell.loaders.LongArrayLoader
outputClass() - Method in class io.scif.img.cell.loaders.ShortAccessLoader
outputClass() - Method in class io.scif.img.cell.loaders.ShortArrayLoader
overwriteComment(DataHandle<Location>, Object) - Method in class io.scif.formats.tiff.TiffSaver: Convenience method for overwriting a file's first ImageDescription.
overwriteIFDValue(DataHandle<Location>, int, int, Object) - Method in class io.scif.formats.tiff.TiffSaver: Surgically overwrites an existing IFD value with the given one.
overwriteLastIFDOffset(DataHandle<Location>) - Method in class io.scif.formats.tiff.TiffSaver
ownsLocationType(Location) - Method in interface io.scif.Format: This is only needed by Format that depend on their own Location types (e.g.

P

PackbitsCodec - Class in io.scif.codec: This class implements packbits decompression.
PackbitsCodec() - Constructor for class io.scif.codec.PackbitsCodec
padImage(BufferedImage, int, int) - Static method in class io.scif.gui.AWTImageTools: Pads (or crops) the image to the given width and height.
padImage(byte[], boolean, int, int, int, int) - Static method in class io.scif.util.ImageTools: Pads (or crops) the byte array to the given width and height.
padImage(short[], boolean, int, int, int, int) - Static method in class io.scif.util.ImageTools: Pads (or crops) the short array to the given width and height.
padImage(int[], boolean, int, int, int, int) - Static method in class io.scif.util.ImageTools: Pads (or crops) the int array to the given width and height.
padImage(float[], boolean, int, int, int, int) - Static method in class io.scif.util.ImageTools: Pads (or crops) the float array to the given width and height.
padImage(double[], boolean, int, int, int, int) - Static method in class io.scif.util.ImageTools: Pads (or crops) the double array to the given width and height.
PAGE_NAME - Static variable in class io.scif.formats.tiff.IFD
PAGE_NUMBER - Static variable in class io.scif.formats.tiff.IFD
parse(Location) - Method in class io.scif.AbstractParser
parse(DataHandle<Location>) - Method in class io.scif.AbstractParser
parse(Location, Metadata) - Method in class io.scif.AbstractParser
parse(DataHandle<Location>, Metadata) - Method in class io.scif.AbstractParser
parse(DataHandle<Location>, M) - Method in class io.scif.AbstractParser
parse(Location, M, SCIFIOConfig) - Method in class io.scif.AbstractParser
parse(DataHandle<Location>, M, SCIFIOConfig) - Method in class io.scif.AbstractParser
parse(Location, SCIFIOConfig) - Method in class io.scif.AbstractParser
parse(DataHandle<Location>, SCIFIOConfig) - Method in class io.scif.AbstractParser
parse(Location, Metadata, SCIFIOConfig) - Method in class io.scif.AbstractParser
parse(DataHandle<Location>, Metadata, SCIFIOConfig) - Method in class io.scif.AbstractParser
parse(String) - Method in class io.scif.DefaultMetadataService
parse(String, String) - Method in class io.scif.DefaultMetadataService
parse(DataHandle<Location>, JPEG2000Format.Metadata, long) - Method in class io.scif.formats.JPEG2000Format.Parser
parse(DataHandle<Location>, NRRDFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.NRRDFormat.Parser
parse(String) - Method in interface io.scif.MetadataService: Parses key/value pairs from the given string, using the default separator regex of "[&\n]" (i.e., ampersand or newline).
parse(String, String) - Method in interface io.scif.MetadataService: Parses key/value pairs from the given string, using the specified separator regex.
parse(Location) - Method in interface io.scif.Parser: Creates a Metadata object using the provided location of an image source.
parse(DataHandle<Location>) - Method in interface io.scif.Parser: Creates a Metadata object from the provided image source.
parse(Location, Metadata) - Method in interface io.scif.Parser: Parses metadata using the provided name of an image source, and writes to an existing Metadata object (overwriting may occur).
parse(DataHandle<Location>, Metadata) - Method in interface io.scif.Parser: Parses metadata from the provided image source to an existing Metadata object (overwriting may occur).
parse(Location, SCIFIOConfig) - Method in interface io.scif.Parser: As Parser.parse(Location) with configuration options.
parse(DataHandle<Location>, SCIFIOConfig) - Method in interface io.scif.Parser: As Parser.parse(DataHandle) with configuration options.
parse(Location, Metadata, SCIFIOConfig) - Method in interface io.scif.Parser: As Parser.parse(Location, Metadata) with configuration options.
parse(DataHandle<Location>, Metadata, SCIFIOConfig) - Method in interface io.scif.Parser: /** As Parser.parse(DataHandle, Metadata) with configuration options.
parse(Location) - Method in interface io.scif.TypedParser
parse(DataHandle<Location>) - Method in interface io.scif.TypedParser
parse(Location, SCIFIOConfig) - Method in interface io.scif.TypedParser
parse(DataHandle<Location>, SCIFIOConfig) - Method in interface io.scif.TypedParser
parse(DataHandle<Location>, M) - Method in interface io.scif.TypedParser: Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).
parse(Location, M, SCIFIOConfig) - Method in interface io.scif.TypedParser: Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(Location, Metadata).
parse(DataHandle<Location>, M, SCIFIOConfig) - Method in interface io.scif.TypedParser: Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).
parseDOM(File) - Method in class io.scif.xml.DefaultXMLService
parseDOM(String) - Method in class io.scif.xml.DefaultXMLService
parseDOM(InputStream) - Method in class io.scif.xml.DefaultXMLService
parseDOM(File) - Method in interface io.scif.xml.XMLService: Parses a DOM from the given XML file on disk.
parseDOM(String) - Method in interface io.scif.xml.XMLService: Parses a DOM from the given XML string.
parseDOM(InputStream) - Method in interface io.scif.xml.XMLService: Parses a DOM from the given XML input stream.
parseINI(String) - Method in class io.scif.common.IniParser: Parses the INI-style configuration data from the given resource.
parseINI(String, Class<?>) - Method in class io.scif.common.IniParser: Parses the INI-style configuration data from the given resource, using the given class to find the resource.
parseINI(BufferedReader) - Method in class io.scif.common.IniParser: Parses the INI-style configuration data from the given input stream.
parseMetadata(Location) - Method in class io.scif.services.DefaultInitializeService
parseMetadata(Location, SCIFIOConfig) - Method in class io.scif.services.DefaultInitializeService
parseMetadata(Location) - Method in interface io.scif.services.InitializeService: Convenience method to parse Metadata without reading the underlying pixels.
parseMetadata(Location, SCIFIOConfig) - Method in interface io.scif.services.InitializeService: As InitializeService.parseMetadata(Location) with a flag to open the underlying dataset when parsing, if desired.
Parser() - Constructor for class io.scif.formats.APNGFormat.Parser
Parser() - Constructor for class io.scif.formats.AVIFormat.Parser
Parser() - Constructor for class io.scif.formats.BMPFormat.Parser
Parser() - Constructor for class io.scif.formats.DICOMFormat.Parser
Parser() - Constructor for class io.scif.formats.EPSFormat.Parser
Parser() - Constructor for class io.scif.formats.FITSFormat.Parser
Parser() - Constructor for class io.scif.formats.GIFFormat.Parser
Parser() - Constructor for class io.scif.formats.ICSFormat.Parser
Parser() - Constructor for class io.scif.formats.ImageIOFormat.Parser
Parser() - Constructor for class io.scif.formats.JPEG2000Format.Parser
Parser() - Constructor for class io.scif.formats.JPEGFormat.Parser
Parser() - Constructor for class io.scif.formats.JPEGTileFormat.Parser
Parser() - Constructor for class io.scif.formats.KontronFormat.Parser
Parser() - Constructor for class io.scif.formats.MicromanagerFormat.Parser
Parser() - Constructor for class io.scif.formats.MinimalTIFFFormat.Parser
Parser() - Constructor for class io.scif.formats.MNGFormat.Parser
Parser() - Constructor for class io.scif.formats.NRRDFormat.Parser
Parser() - Constructor for class io.scif.formats.PCXFormat.Parser
Parser() - Constructor for class io.scif.formats.PGMFormat.Parser
Parser() - Constructor for class io.scif.formats.qt.LegacyQTFormat.Parser
Parser() - Constructor for class io.scif.formats.qt.NativeQTFormat.Parser
Parser() - Constructor for class io.scif.formats.qt.PICTFormat.Parser
Parser() - Constructor for class io.scif.formats.ScancoISQFormat.Parser
Parser() - Constructor for class io.scif.formats.StratecPQCTFormat.Parser
Parser() - Constructor for class io.scif.formats.TestImgFormat.Parser
Parser() - Constructor for class io.scif.formats.TIFFFormat.Parser
Parser() - Constructor for class io.scif.formats.TIFFJAIFormat.Parser
Parser - Interface in io.scif: Interface for all SCIFIO Parsers.
ParserErrorHandler - Class in io.scif.xml: Used by various XMLTools methods to handle XML parsing errors.
ParserErrorHandler(LogService) - Constructor for class io.scif.xml.ParserErrorHandler
parserGetLevel() - Method in class io.scif.config.SCIFIOConfig
parserIsFiltered() - Method in class io.scif.config.SCIFIOConfig
parserIsSaveOriginalMetadata() - Method in class io.scif.config.SCIFIOConfig
parserSetFiltered(boolean) - Method in class io.scif.config.SCIFIOConfig
parserSetLevel(MetadataLevel) - Method in class io.scif.config.SCIFIOConfig
parserSetSaveOriginalMetadata(boolean) - Method in class io.scif.config.SCIFIOConfig
parseXML(String) - Method in class io.scif.xml.DefaultXMLService
parseXML(String, DefaultHandler) - Method in class io.scif.xml.DefaultXMLService
parseXML(DataHandle<Location>, DefaultHandler) - Method in class io.scif.xml.DefaultXMLService
parseXML(byte[], DefaultHandler) - Method in class io.scif.xml.DefaultXMLService
parseXML(InputStream, DefaultHandler) - Method in class io.scif.xml.DefaultXMLService
parseXML(String) - Method in interface io.scif.xml.XMLService: Parses the given XML string into a list of key/value pairs.
parseXML(String, DefaultHandler) - Method in interface io.scif.xml.XMLService: Parses the given XML string using the specified XML handler.
parseXML(DataHandle<Location>, DefaultHandler) - Method in interface io.scif.xml.XMLService: Parses the XML contained in the given data handle into using the specified XML handler.
parseXML(byte[], DefaultHandler) - Method in interface io.scif.xml.XMLService: Parses the XML contained in the given byte array into using the specified XML handler.
parseXML(InputStream, DefaultHandler) - Method in interface io.scif.xml.XMLService: Parses the XML contained in the given InputStream using the specified XML handler.
PassthroughCodec - Class in io.scif.codec: A codec which just returns the exact data it was given, performing no compression or decompression.
PassthroughCodec() - Constructor for class io.scif.codec.PassthroughCodec
PCX_MAGIC_BYTE - Static variable in class io.scif.formats.PCXFormat.Checker
PCXFormat - Class in io.scif.formats: PCXReader is the file format reader for PCX files (originally used by PC Paintbrush; now used in Zeiss' LSM Image Browser).
PCXFormat() - Constructor for class io.scif.formats.PCXFormat
PCXFormat.Checker - Class in io.scif.formats
PCXFormat.Metadata - Class in io.scif.formats
PCXFormat.Parser - Class in io.scif.formats
PCXFormat.Reader - Class in io.scif.formats
PGM_MAGIC_CHAR - Static variable in class io.scif.formats.PGMFormat.Checker
PGMFormat - Class in io.scif.formats: Handler plugin for the PGM file format.
PGMFormat() - Constructor for class io.scif.formats.PGMFormat
PGMFormat.Checker - Class in io.scif.formats
PGMFormat.Metadata - Class in io.scif.formats
PGMFormat.Parser - Class in io.scif.formats
PGMFormat.Reader - Class in io.scif.formats
PHASE - Static variable in class io.scif.img.axes.SCIFIOAxes: Identifies the Phase dimensional type, representing a dimension consisting of phases.
PhotoInterp - Enum in io.scif.formats.tiff: Utility class for working with TIFF photometric interpretations.
PHOTOMETRIC_INTERPRETATION - Static variable in class io.scif.formats.tiff.IFD
PICTFormat - Class in io.scif.formats.qt: PictReader is the file format reader for Apple PICT files.
PICTFormat() - Constructor for class io.scif.formats.qt.PICTFormat
PICTFormat.Metadata - Class in io.scif.formats.qt
PICTFormat.Parser - Class in io.scif.formats.qt
PICTFormat.Reader - Class in io.scif.formats.qt
pictToImage(byte[]) - Method in class io.scif.formats.qt.DefaultQTJavaService
pictToImage(byte[]) - Method in interface io.scif.formats.qt.QTJavaService: Converts the given byte array in PICT format to a Java image.
PIXEL_X_DIMENSION - Static variable in class io.scif.formats.tiff.IFD
PIXEL_Y_DIMENSION - Static variable in class io.scif.formats.tiff.IFD
pixelSize - Variable in class io.scif.formats.MicromanagerFormat.Position
pixelType(String) - Method in class io.scif.io.location.TestImgLocation.Builder
pixelTypeFromBytes(int, boolean, boolean) - Static method in class io.scif.util.FormatTools: Returns an appropriate pixel type given the number of bytes per pixel.
pixelTypeFromString(String) - Static method in class io.scif.util.FormatTools: Takes a string value and maps it to one of the pixel type enumerations.
PLANAR_CONFIGURATION - Static variable in class io.scif.formats.tiff.IFD
PlanarAccessConverter - Class in io.scif.img.converters: PlaneConverter implementation specialized for populating PlanarAccess instances.
PlanarAccessConverter() - Constructor for class io.scif.img.converters.PlanarAccessConverter
planarBounds(int) - Method in class io.scif.filters.AbstractReaderFilter
planarDims(int) - Method in class io.scif.io.location.TestImgLocation.Builder
Plane - Interface in io.scif: Top-level interface for all Plane representations in SCIFIO.
PlaneConverter - Interface in io.scif.img.converters: Interface for using planes read by SCIFIO Readers to populate ImgPlus instances.
planeConverter() - Method in class io.scif.SCIFIO: Gets this application context's PlaneConverterService.
PlaneConverterService - Interface in io.scif.img.converters: Interface for requesting PlaneConverters to convert planes read by SCIFIO Readers to ImgPlus instances.
PlaneSeparator - Class in io.scif.filters: Logic to automatically separate the channels in a file.
PlaneSeparator() - Constructor for class io.scif.filters.PlaneSeparator
PlaneSeparatorMetadata - Class in io.scif.filters: MetadataWrapper implementation specifically for use with the PlaneSeparator.
PlaneSeparatorMetadata() - Constructor for class io.scif.filters.PlaneSeparatorMetadata
PLTEChunk() - Constructor for class io.scif.formats.APNGFormat.PLTEChunk
PNG_SIGNATURE - Static variable in class io.scif.formats.APNGFormat
POLARIZATION - Static variable in class io.scif.img.axes.SCIFIOAxes: Identifies the Polarization dimensional type, representing a dimension consisting of polarization states.
populate(String, List<CalibratedAxis>, long[], int, boolean, boolean, boolean, boolean, boolean) - Method in class io.scif.AbstractImageMetadata
populate(String, List<CalibratedAxis>, long[], int, int, boolean, boolean, boolean, boolean, boolean) - Method in class io.scif.AbstractImageMetadata
populate(Plane) - Method in class io.scif.AbstractPlane
populate(DataPlane<T>) - Method in class io.scif.AbstractPlane
populate(ImageMetadata, Interval) - Method in class io.scif.AbstractPlane
populate(T, Interval) - Method in class io.scif.AbstractPlane
populate(ImageMetadata, T, Interval) - Method in class io.scif.AbstractPlane
populate(DataPlane<T>) - Method in interface io.scif.DataPlane: Populate this plane by copying the provided plane.
populate(T, Interval) - Method in interface io.scif.DataPlane: Populate this plane using the specified lengths and offsets, with the provided data representation of the pixels in that region.
populate(ImageMetadata, T, Interval) - Method in interface io.scif.DataPlane: As DataPlane.populate(Object, Interval), but also sets the ImageMetadata of the source from which this Plane was read.
populate(Object, Map<String, Object>) - Method in class io.scif.DefaultMetadataService
populate(String, List<CalibratedAxis>, long[], int, boolean, boolean, boolean, boolean, boolean) - Method in interface io.scif.ImageMetadata: As ImageMetadata.populate(String, List, long[], int, boolean, boolean, boolean, boolean, boolean) but automatically determines bits per pixel.
populate(String, List<CalibratedAxis>, long[], int, int, boolean, boolean, boolean, boolean, boolean) - Method in interface io.scif.ImageMetadata: Convenience method for manually populating an ImageMetadata.
populate(Object, Map<String, Object>) - Method in interface io.scif.MetadataService: Populates fields of the given metadata object with information from the given map.
populate(ImageMetadata, Interval) - Method in interface io.scif.Plane: Populates this planes offsets, dimensions and Metadata.
populate(Plane) - Method in interface io.scif.Plane: Populates this plane by copying the fields of the provided plane
populateImageMetadata() - Method in class io.scif.DefaultMetadata
populateImageMetadata() - Method in class io.scif.filters.AbstractMetadataWrapper
populateImageMetadata() - Method in class io.scif.filters.ChannelFillerMetadata
populateImageMetadata() - Method in class io.scif.filters.PlaneSeparatorMetadata
populateImageMetadata() - Method in class io.scif.formats.APNGFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.AVIFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.BMPFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.DICOMFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.EPSFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.FITSFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.GIFFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.ICSFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.ImageIOFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.JPEG2000Format.Metadata
populateImageMetadata() - Method in class io.scif.formats.JPEGTileFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.KontronFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.MicromanagerFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.MNGFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.NRRDFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.PCXFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.PGMFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.qt.LegacyQTFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.qt.PICTFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.ScancoISQFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.StratecPQCTFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.TestImgFormat.Metadata: Generates ImageMetadata based on the id of this dataset.
populateImageMetadata() - Method in class io.scif.formats.TIFFFormat.Metadata
populateImageMetadata() - Method in class io.scif.formats.TIFFJAIFormat.Metadata
populateImageMetadata() - Method in interface io.scif.Metadata: Generates format-agnostic image metadata structures based on this instance's format-specific metadata.
populateMetadata(String[], MicromanagerFormat.Metadata, Metadata) - Method in class io.scif.formats.MicromanagerFormat.Parser
populatePlane(Reader, int, int, byte[], ImgPlus<T>, SCIFIOConfig) - Method in class io.scif.img.converters.ArrayDataAccessConverter
populatePlane(Reader, int, int, byte[], ImgPlus<T>, SCIFIOConfig) - Method in class io.scif.img.converters.PlanarAccessConverter: Populates plane by reference using PlanarAccess interface.
populatePlane(Reader, int, int, byte[], ImgPlus<T>, SCIFIOConfig) - Method in interface io.scif.img.converters.PlaneConverter
populatePlane(Reader, int, int, byte[], ImgPlus<T>, SCIFIOConfig) - Method in class io.scif.img.converters.RandomAccessConverter: Uses a cursor to populate the plane.
Position() - Constructor for class io.scif.formats.MicromanagerFormat.Position
positionToRaster(int, Reader, long[]) - Static method in class io.scif.util.FormatTools: Computes a unique 1-D index corresponding to the given multidimensional position.
positionToRaster(int, Metadata, long[]) - Static method in class io.scif.util.FormatTools: Computes a unique 1-D index corresponding to the given multidimensional position.
positionToRaster(long[], long[]) - Static method in class io.scif.util.FormatTools: Computes a unique 1-D index corresponding to the given multidimensional position.
PREDICTOR - Static variable in class io.scif.formats.tiff.IFD
PreviewPane - Class in io.scif.gui: PreviewPane is a panel for use as a JFileChooser accessory, displaying a thumbnail for the selected image, loaded in a separate thread.
PreviewPane(Context, JFileChooser) - Constructor for class io.scif.gui.PreviewPane: Constructs a preview pane for the given file chooser.
previousImage - Variable in class io.scif.codec.CodecOptions: Pixels for preceding image (READ/WRITE).
PRIMARY_CHROMATICITIES - Static variable in class io.scif.formats.tiff.IFD
printIFD() - Method in class io.scif.formats.tiff.IFD: Prints the contents of this IFD.
PRIORITY - Static variable in class io.scif.formats.MinimalTIFFFormat
PRIORITY - Static variable in class io.scif.formats.TIFFFormat
PRIORITY - Static variable in interface io.scif.services.FormatService
propertyChange(PropertyChangeEvent) - Method in class io.scif.gui.PreviewPane: Property change event, to listen for when a new file is selected, or the file chooser closes.
put(String, Object) - Method in class io.scif.DefaultMetaTable
put(String, String) - Method in class io.scif.formats.ICSFormat.Metadata
put(MetaTable, String, IFD, int) - Method in class io.scif.formats.TIFFFormat.BaseTIFFParser
putAuthorLastName(String) - Method in class io.scif.formats.ICSFormat.Metadata
putAxes(String[]) - Method in class io.scif.formats.ICSFormat.Metadata
putAxesSizes(double[]) - Method in class io.scif.formats.ICSFormat.Metadata
putBitsPerPixel(Integer) - Method in class io.scif.formats.ICSFormat.Metadata
putByteOrder(String) - Method in class io.scif.formats.ICSFormat.Metadata
putChannelNames(Map<Integer, String>) - Method in class io.scif.formats.ICSFormat.Metadata
putCompression(String) - Method in class io.scif.formats.ICSFormat.Metadata
putDate(String) - Method in class io.scif.formats.ICSFormat.Metadata
putDescription(String) - Method in class io.scif.formats.ICSFormat.Metadata
putDetectorManufacturer(String) - Method in class io.scif.formats.ICSFormat.Metadata
putDetectorModel(String) - Method in class io.scif.formats.ICSFormat.Metadata
putDichroicModel(String) - Method in class io.scif.formats.ICSFormat.Metadata
putEmissionModel(String) - Method in class io.scif.formats.ICSFormat.Metadata
putEMSingleton(Integer[]) - Method in class io.scif.formats.ICSFormat.Metadata
putEMWaves(Integer[]) - Method in class io.scif.formats.ICSFormat.Metadata
putExcitationModel(String) - Method in class io.scif.formats.ICSFormat.Metadata
putExperimentType(String) - Method in class io.scif.formats.ICSFormat.Metadata
putExposureTime(Double) - Method in class io.scif.formats.ICSFormat.Metadata
putEXSingleton(Integer[]) - Method in class io.scif.formats.ICSFormat.Metadata
putEXWaves(Integer[]) - Method in class io.scif.formats.ICSFormat.Metadata
putFilterSetModel(String) - Method in class io.scif.formats.ICSFormat.Metadata
putGains(Map<Integer, Double>) - Method in class io.scif.formats.ICSFormat.Metadata
putIFDValue(int, Object) - Method in class io.scif.formats.tiff.IFD: Adds a directory entry to this IFD.
putIFDValue(int, short) - Method in class io.scif.formats.tiff.IFD: Adds a directory entry of type BYTE to this IFD.
putIFDValue(int, int) - Method in class io.scif.formats.tiff.IFD: Adds a directory entry of type SHORT to this IFD.
putIFDValue(int, long) - Method in class io.scif.formats.tiff.IFD: Adds a directory entry of type LONG to this IFD.
putImmersion(String) - Method in class io.scif.formats.ICSFormat.Metadata
putInt(MetaTable, String, IFD, int) - Method in class io.scif.formats.TIFFFormat.BaseTIFFParser
putLaserManufacturer(String) - Method in class io.scif.formats.ICSFormat.Metadata
putLaserModel(String) - Method in class io.scif.formats.ICSFormat.Metadata
putLaserPower(Double) - Method in class io.scif.formats.ICSFormat.Metadata
putLaserRepetitionRate(Double) - Method in class io.scif.formats.ICSFormat.Metadata
putLensNA(Double) - Method in class io.scif.formats.ICSFormat.Metadata
putLifetime(boolean) - Method in class io.scif.formats.ICSFormat.Metadata
putList(String, Object) - Method in class io.scif.DefaultMetaTable
putList(String, Object) - Method in interface io.scif.MetaTable: Special Map.put(Object, Object) implementation.
putMagnification(Double) - Method in class io.scif.formats.ICSFormat.Metadata
putMicroscopeManufacturer(String) - Method in class io.scif.formats.ICSFormat.Metadata
putMicroscopeModel(String) - Method in class io.scif.formats.ICSFormat.Metadata
putObjectiveModel(String) - Method in class io.scif.formats.ICSFormat.Metadata
putPhysicalPixelSizes(double[]) - Method in class io.scif.formats.ICSFormat.Metadata
putPinholes(Map<Integer, Double>) - Method in class io.scif.formats.ICSFormat.Metadata
putPixelSizes(Double[]) - Method in class io.scif.formats.ICSFormat.Metadata
putRepFormat(String) - Method in class io.scif.formats.ICSFormat.Metadata
putSigned(boolean) - Method in class io.scif.formats.ICSFormat.Metadata
putStagePositions(Double[]) - Method in class io.scif.formats.ICSFormat.Metadata
putStageX(Double) - Method in class io.scif.formats.ICSFormat.Metadata
putStageY(Double) - Method in class io.scif.formats.ICSFormat.Metadata
putStageZ(Double) - Method in class io.scif.formats.ICSFormat.Metadata
putTimestamps(Double[]) - Method in class io.scif.formats.ICSFormat.Metadata
putUnits(String[]) - Method in class io.scif.formats.ICSFormat.Metadata
putWavelengths(Map<Integer, Integer>) - Method in class io.scif.formats.ICSFormat.Metadata
putWorkingDistance(Double) - Method in class io.scif.formats.ICSFormat.Metadata

Q

qtJava() - Method in class io.scif.SCIFIO: Gets this application context's QTJavaService.
QTJavaService - Interface in io.scif.formats.qt: Interface for services that work with QuickTime for Java.
QTRLECodec - Class in io.scif.codec: Methods for compressing and decompressing data using QuickTime RLE.
QTRLECodec() - Constructor for class io.scif.codec.QTRLECodec
quality - Variable in class io.scif.codec.CodecOptions: Compression quality level as it would be provided to: javax.imageio.ImageWriteParam#compressionQuality (WRITE).
QUALITY_HIGH - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating High quality.
QUALITY_LOW - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Low quality.
QUALITY_MAXIMUM - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Maximum quality.
QUALITY_NORMAL - Static variable in class io.scif.formats.qt.NativeQTFormat.Writer: Value indicating Normal quality.

R

RAIIOPlugin<T extends net.imglib2.type.Type<T>> - Class in io.scif.io: I/O plugin for RandomAccessibleIntervals.
RAIIOPlugin() - Constructor for class io.scif.io.RAIIOPlugin
RandomAccessConverter - Class in io.scif.img.converters: Generalized PlaneConverter implementation.
RandomAccessConverter() - Constructor for class io.scif.img.converters.RandomAccessConverter
Range - Class in io.scif.img: A list of Long values with extra convenience functionality.
Range(String) - Constructor for class io.scif.img.Range
Range(Long) - Constructor for class io.scif.img.Range: Creates a singleton DimRange.
Range(Long, Long) - Constructor for class io.scif.img.Range: Creates the DimRange: [start, end]
Range(long[]) - Constructor for class io.scif.img.Range: Constructs a DimRange that includes only the values contained in the provided array.
rasterToPosition(int, long, Metadata, List<CalibratedAxis>) - Static method in class io.scif.util.FormatTools: Computes a unique N-D position corresponding to the given rasterized index value.
rasterToPosition(int, long, Reader) - Static method in class io.scif.util.FormatTools: Computes a unique N-D position corresponding to the given rasterized index value.
rasterToPosition(int, long, Metadata) - Static method in class io.scif.util.FormatTools: Computes a unique N-D position corresponding to the given rasterized index value.
rasterToPosition(long[], long) - Static method in class io.scif.util.FormatTools: Computes a unique N-D position corresponding to the given rasterized index value.
rasterToPosition(long[], long, long[]) - Static method in class io.scif.util.FormatTools: Computes a unique N-D position corresponding to the given rasterized index value.
Reader() - Constructor for class io.scif.formats.APNGFormat.Reader
Reader() - Constructor for class io.scif.formats.AVIFormat.Reader
Reader() - Constructor for class io.scif.formats.BMPFormat.Reader
Reader() - Constructor for class io.scif.formats.DICOMFormat.Reader
Reader() - Constructor for class io.scif.formats.EPSFormat.Reader
Reader() - Constructor for class io.scif.formats.FITSFormat.Reader
Reader() - Constructor for class io.scif.formats.GIFFormat.Reader
Reader() - Constructor for class io.scif.formats.ICSFormat.Reader
Reader() - Constructor for class io.scif.formats.ImageIOFormat.Reader
Reader() - Constructor for class io.scif.formats.JPEG2000Format.Reader
Reader() - Constructor for class io.scif.formats.JPEGFormat.Reader
Reader() - Constructor for class io.scif.formats.JPEGTileFormat.Reader
Reader() - Constructor for class io.scif.formats.KontronFormat.Reader
Reader() - Constructor for class io.scif.formats.MicromanagerFormat.Reader
Reader() - Constructor for class io.scif.formats.MinimalTIFFFormat.Reader
Reader() - Constructor for class io.scif.formats.MNGFormat.Reader
Reader() - Constructor for class io.scif.formats.NRRDFormat.Reader
Reader() - Constructor for class io.scif.formats.PCXFormat.Reader
Reader() - Constructor for class io.scif.formats.PGMFormat.Reader
Reader() - Constructor for class io.scif.formats.qt.LegacyQTFormat.Reader
Reader() - Constructor for class io.scif.formats.qt.NativeQTFormat.Reader
Reader() - Constructor for class io.scif.formats.qt.PICTFormat.Reader
Reader() - Constructor for class io.scif.formats.ScancoISQFormat.Reader
Reader() - Constructor for class io.scif.formats.StratecPQCTFormat.Reader
Reader() - Constructor for class io.scif.formats.TestImgFormat.Reader
Reader() - Constructor for class io.scif.formats.TIFFFormat.Reader
Reader() - Constructor for class io.scif.formats.TIFFJAIFormat.Reader
reader() - Method in class io.scif.img.cell.loaders.AbstractArrayLoader
reader() - Method in class io.scif.img.cell.SCIFIOCellImg
reader() - Method in class io.scif.img.cell.SCIFIOCellImgFactory
reader - Variable in class io.scif.LocationInfo: io.scif.Reader implementation that would be used to read this file.
Reader - Interface in io.scif: Interface for all SCIFIO Readers.
ReaderFilter - Class in io.scif.filters: MasterFilter for wrapping Reader components.
ReaderFilter(Reader) - Constructor for class io.scif.filters.ReaderFilter
readImage(InputStream, JPEG2000CodecOptions) - Method in interface io.scif.services.JAIIIOService: Reads an image using JAI Image I/O using the JPEG 2000 codec.
readImage(InputStream) - Method in interface io.scif.services.JAIIIOService: Reads an image using JAI Image I/O using the JPEG 2000 codec.
readImage(InputStream, JPEG2000CodecOptions) - Method in class io.scif.services.JAIIIOServiceImpl
readImage(InputStream) - Method in class io.scif.services.JAIIIOServiceImpl
readPlane(DataHandle<Location>, int, Interval, Plane) - Method in class io.scif.AbstractReader
readPlane(DataHandle<Location>, int, Interval, int, Plane) - Method in class io.scif.AbstractReader
readPlane(DataHandle<Location>, int, Interval, P) - Method in class io.scif.AbstractReader
readPlane(DataHandle<Location>, int, Interval, int, P) - Method in class io.scif.AbstractReader
readPlane(DataHandle<Location>, int, Interval, Plane) - Method in class io.scif.filters.AbstractReaderFilter
readPlane(DataHandle<Location>, int, Interval, int, Plane) - Method in class io.scif.filters.AbstractReaderFilter
readPlane(DataHandle<Location>, int, Interval, Plane) - Method in interface io.scif.Reader: Reads a raw plane from disk.
readPlane(DataHandle<Location>, int, Interval, int, Plane) - Method in interface io.scif.Reader: Reads a raw plane from disk.
readPlane(DataHandle<Location>, int, Interval, P) - Method in interface io.scif.TypedReader: Generic-parameterized readPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.readPlane(DataHandle, int, Interval, Plane) NB Presumes that the source stream s is set to the correct offset, i.e. start of the plane
readPlane(DataHandle<Location>, int, Interval, int, P) - Method in interface io.scif.TypedReader: Generic-parameterized readPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.readPlane(DataHandle, int, Interval, int, Plane) NB Presumes that the source stream s is set to the correct offset, i.e. start of the plane
readPlaneHelper() - Method in class io.scif.filters.AbstractReaderFilter: Allows code to be executed regardless of which AbstractReaderFilter.readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location>, int, net.imglib2.Interval, io.scif.Plane) signature is called.
readRaster(InputStream, JPEG2000CodecOptions) - Method in interface io.scif.services.JAIIIOService: Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
readRaster(InputStream) - Method in interface io.scif.services.JAIIIOService: Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
readRaster(InputStream, JPEG2000CodecOptions) - Method in class io.scif.services.JAIIIOServiceImpl
readRaster(InputStream) - Method in class io.scif.services.JAIIIOServiceImpl
readTiffIFDEntry() - Method in class io.scif.formats.tiff.TiffParser
reduce() - Method in class io.scif.formats.tiff.TiffRational: Reduces this rational's fraction to lowest terms.
REFERENCE_BLACK_WHITE - Static variable in class io.scif.formats.tiff.IFD
RefManagerService - Interface in io.scif.refs: A Service implementation for helping with Reference management.
RefProvider - Interface in io.scif.refs: Interface for plugins that create references for a given referent.
RELATED_SOUND_FILE - Static variable in class io.scif.formats.tiff.IFD
removeComponents(Format) - Method in class io.scif.services.DefaultFormatService
removeComponents(Format) - Method in interface io.scif.services.FormatService: Removes any mappings involving this Format's components.
removeFormat(Format) - Method in class io.scif.services.DefaultFormatService
removeFormat(Format) - Method in interface io.scif.services.FormatService: Removes the provided Format from this context, if it was previously available.
reset() - Method in class io.scif.filters.AbstractFilter
reset() - Method in interface io.scif.filters.Filter: Clears any configuration performed on this filter.
reset() - Method in interface io.scif.filters.MasterFilter: Disables all enabled filters maintained by this MasterFilter.
reset() - Method in class io.scif.filters.MasterFilterHelper
reset() - Method in class io.scif.filters.ReaderFilter
resolution - Variable in class io.scif.codec.JPEG2000CodecOptions: The resolution level as would be provided to: J2KImageWriteParam#setResolution(int) (READ).
RESOLUTION_UNIT - Static variable in class io.scif.formats.tiff.IFD
ResolutionUnit - Enum in io.scif.formats.tiff: Utility class for working with TIFF resolution units.
resolve(URI) - Method in class io.scif.io.location.TestImgLocationResolver
resolveEntity(String, String) - Method in class io.scif.xml.BaseHandler
REUSE - Static variable in class io.scif.formats.tiff.IFD
ROWS_PER_STRIP - Static variable in class io.scif.formats.tiff.IFD
RPZACodec - Class in io.scif.codec: Implements encoding and decoding methods for Apple RPZA.
RPZACodec() - Constructor for class io.scif.codec.RPZACodec
RST_0 - Static variable in class io.scif.codec.LosslessJPEGCodec
RST_1 - Static variable in class io.scif.codec.LosslessJPEGCodec
RST_2 - Static variable in class io.scif.codec.LosslessJPEGCodec
RST_3 - Static variable in class io.scif.codec.LosslessJPEGCodec
RST_4 - Static variable in class io.scif.codec.LosslessJPEGCodec
RST_5 - Static variable in class io.scif.codec.LosslessJPEGCodec
RST_6 - Static variable in class io.scif.codec.LosslessJPEGCodec
RST_7 - Static variable in class io.scif.codec.LosslessJPEGCodec
run() - Method in class io.scif.commands.OpenDataset
run() - Method in class io.scif.commands.SaveAsImage
run() - Method in class io.scif.commands.SaveImage
run() - Method in class io.scif.gui.ImageViewer: Handles animation.
run() - Method in class io.scif.gui.PreviewPane: Thumbnail loading routine.

S

S_AXIS - Static variable in class io.scif.AxisGuesser: Axis type for series.
S_MAX_SAMPLE_VALUE - Static variable in class io.scif.formats.tiff.IFD
S_MIN_SAMPLE_VALUE - Static variable in class io.scif.formats.tiff.IFD
SAMPLE_FORMAT - Static variable in class io.scif.formats.tiff.IFD
SAMPLES_PER_PIXEL - Static variable in class io.scif.formats.tiff.IFD
sanitizeXML(String) - Method in class io.scif.xml.DefaultXMLService
sanitizeXML(String) - Method in interface io.scif.xml.XMLService: Remove invalid characters from an XML string.
SATURATION - Static variable in class io.scif.formats.tiff.IFD
save(String) - Method in class io.scif.gui.ImageViewer: Convenience overload of ImageViewer.save(java.lang.String), saves the current image to the given local file destination.
save(Location) - Method in class io.scif.gui.ImageViewer: Saves the current images to the given destination using the current format writer.
save(String, Writer) - Method in class io.scif.gui.ImageViewer: Saves to the given data destination using the specified writer in a separate thread.
save(String, Img<?>) - Static method in class io.scif.img.IO
save(Location, Img<?>) - Static method in class io.scif.img.IO
save(String, SCIFIOImgPlus<?>, int) - Static method in class io.scif.img.IO
save(Location, SCIFIOImgPlus<?>, int) - Static method in class io.scif.img.IO
save(Writer, Img<?>) - Static method in class io.scif.img.IO
save(Writer, SCIFIOImgPlus<?>, int) - Static method in class io.scif.img.IO
save(Dataset, String) - Method in class io.scif.io.DatasetIOPlugin
save(Dataset, Location) - Method in class io.scif.io.DatasetIOPlugin
save(RandomAccessibleInterval<T>, String) - Method in class io.scif.io.RAIIOPlugin
save(RandomAccessibleInterval<T>, Location) - Method in class io.scif.io.RAIIOPlugin
save(Dataset, Location) - Method in interface io.scif.services.DatasetIOService: Saves a dataset to a destination (such as a file on disk).
save(Dataset, Location, SCIFIOConfig) - Method in interface io.scif.services.DatasetIOService: Saves a dataset to a destination (such as a file on disk).
save(Dataset, String, SCIFIOConfig) - Method in interface io.scif.services.DatasetIOService: Saves a dataset to a destination (such as a file on disk).
save(Dataset, String) - Method in interface io.scif.services.DatasetIOService: Saves a dataset to a destination (such as a file on disk).
save(Dataset, String) - Method in class io.scif.services.DefaultDatasetIOService
save(Dataset, Location) - Method in class io.scif.services.DefaultDatasetIOService
save(Dataset, String, SCIFIOConfig) - Method in class io.scif.services.DefaultDatasetIOService
save(Dataset, Location, SCIFIOConfig) - Method in class io.scif.services.DefaultDatasetIOService
SaveAsImage - Class in io.scif.commands: Saves the current Dataset to disk using a user-specified file name.
SaveAsImage() - Constructor for class io.scif.commands.SaveAsImage
SaveDataset - Class in io.scif.commands: Command for saving a Dataset to a given destination.
SaveDataset() - Constructor for class io.scif.commands.SaveDataset
SaveImage - Class in io.scif.commands: Saves the current Dataset to disk.
SaveImage() - Constructor for class io.scif.commands.SaveImage
saveImg(String, Img<?>) - Method in class io.scif.img.ImgSaver: Entry point for saving an ImgPlus.
saveImg(String, SCIFIOImgPlus<?>, int) - Method in class io.scif.img.ImgSaver: Location id provided.
saveImg(String, Img<?>, SCIFIOConfig) - Method in class io.scif.img.ImgSaver: As ImgSaver.saveImg(Location, Img) with configuration options.
saveImg(String, SCIFIOImgPlus<?>, int, SCIFIOConfig) - Method in class io.scif.img.ImgSaver: As ImgSaver.saveImg(Location, SCIFIOImgPlus, int) with configuration options.
saveImg(Location, Img<?>) - Method in class io.scif.img.ImgSaver: Entry point for saving an ImgPlus.
saveImg(Location, SCIFIOImgPlus<?>, int) - Method in class io.scif.img.ImgSaver: Location id provided.
saveImg(Location, Img<?>, SCIFIOConfig) - Method in class io.scif.img.ImgSaver: As ImgSaver.saveImg(Location, Img) with configuration options.
saveImg(Location, SCIFIOImgPlus<?>, int, SCIFIOConfig) - Method in class io.scif.img.ImgSaver: As ImgSaver.saveImg(Location, SCIFIOImgPlus, int) with configuration options.
saveImg(Writer, Img<?>) - Method in class io.scif.img.ImgSaver: Writer and Img provided
saveImg(Writer, SCIFIOImgPlus<?>, int) - Method in class io.scif.img.ImgSaver: Writer provided.
saveImg(Writer, Img<?>, SCIFIOConfig) - Method in class io.scif.img.ImgSaver: As ImgSaver.saveImg(Writer, Img), with configuration options.
saveImg(Writer, SCIFIOImgPlus<?>, int, SCIFIOConfig) - Method in class io.scif.img.ImgSaver: As ImgSaver.saveImg(Writer, SCIFIOImgPlus, int), with configuration options.
saveImg(String, Img<?>) - Static method in class io.scif.img.IO: Deprecated.
Use IO.save(String, Img).
saveImg(String, SCIFIOImgPlus<?>, int) - Static method in class io.scif.img.IO: Deprecated.
Use IO.save(String, SCIFIOImgPlus, int).
saveImg(Writer, Img<?>) - Static method in class io.scif.img.IO: Deprecated.
Use IO.save(Writer, Img).
saveImg(Writer, SCIFIOImgPlus<?>, int) - Static method in class io.scif.img.IO: Deprecated.
Use IO.save(Writer, SCIFIOImgPlus, int).
saveINI(IniList, String) - Method in class io.scif.common.IniWriter: Saves the given IniList to the given file.
saveINI(IniList, String, boolean) - Method in class io.scif.common.IniWriter: Saves the given IniList to the given file.
savePlane(int, long, Plane) - Method in class io.scif.AbstractWriter
savePlane(int, long, Plane, Interval) - Method in class io.scif.AbstractWriter
savePlane(int, long, Plane, IFD, Interval) - Method in class io.scif.formats.TIFFFormat.Writer: Saves the given image to the specified series in the current file.
savePlane(int, long, Plane) - Method in interface io.scif.Writer: Saves the provided plane to the specified image and plane index of this Writer's destination image.
savePlane(int, long, Plane, Interval) - Method in interface io.scif.Writer: Saves the specified tile (sub-region) of the provided plane to the specified image and plane index of this Writer's destination image.
scale(BufferedImage, int, int, boolean) - Static method in class io.scif.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 io.scif.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 io.scif.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 io.scif.gui.AWTImageTools: Scales the image using the AWT Image API.
scaleFactor(int) - Method in class io.scif.io.location.TestImgLocation.Builder
scales(double...) - Method in class io.scif.io.location.TestImgLocation.Builder
ScancoISQFormat - Class in io.scif.formats: The file format reader for Scanco ISQ files ISQ images are generated by Scanco X-ray microtomography scanners Scanco ISQ Header Information: Scanco uses OpenVMS on Alpha workstations Little endian byte order (the least significant bit occupies the lowest memory position) BYTE 00 char check[16]; // CTDATA-HEADER_V1 16 int data_type; 20 int nr_of_bytes; 24 int nr_of_blocks; 28 int patient_index; 32 int scanner_id; 36 int creation_date[2]; 44 int dimx_p; 48 int dimy_p; 52 int dimz_p; 56 int dimx_µm; 60 int dimy_µm; 64 int dimz_µm; 68 int slice_thickness_µm; 72 int slice_increment_µm; 76 int slice_1_pos_µm; 80 int min_data_value; 84 int max_data_value; 88 int mu_scaling; 92 int nr_of_samples; 96 int nr_of_projections; 100 int scandist_µm; 104 int scanner_type; 108 int sampletime_µs; 112 int index_measurement; 116 int site; 120 int reference_line_µm; 124 int recon_alg; 128 char name[40]; 168 int energy; // V 172 int intensity; // µA ... 508 int data_offset; // Number of optional header blocks
ScancoISQFormat() - Constructor for class io.scif.formats.ScancoISQFormat
ScancoISQFormat.Checker - Class in io.scif.formats
ScancoISQFormat.Metadata - Class in io.scif.formats
ScancoISQFormat.Parser - Class in io.scif.formats
ScancoISQFormat.Reader - Class in io.scif.formats
scanData(byte[], int, boolean) - Static method in class io.scif.util.ImageTools: Scan a plane for the channel min and max values.
SCENE_CAPTURE_TYPE - Static variable in class io.scif.formats.tiff.IFD
SCENE_TYPE - Static variable in class io.scif.formats.tiff.IFD
SCIFIO - Class in io.scif: Convenience Context wrapper.
SCIFIO() - Constructor for class io.scif.SCIFIO: Creates a new SCIFIO application context with all SCIFIO and SciJava services.
SCIFIO(Context) - Constructor for class io.scif.SCIFIO: Creates a new SCIFIO application context which wraps the given existing SciJava context.
SCIFIOApp - Class in io.scif.app: Provides version information for SCIFIO, accessible to the scijava-common context.
SCIFIOApp() - Constructor for class io.scif.app.SCIFIOApp
SCIFIOArrayLoader<A> - Interface in io.scif.img.cell.loaders: Interface for requesting arrays from SCIFIO Readers by SCIFIOCellImgs.
SCIFIOAxes - Class in io.scif.img.axes: A collection of AxisTypes useful to scientific image formats.
SCIFIOCellImg<T extends net.imglib2.type.NativeType<T>,A extends net.imglib2.img.basictypeaccess.DataAccess> - Class in io.scif.img.cell: CachedCellImg implementation backed by a SCIFIO Reader.
SCIFIOCellImg(SCIFIOCellImgFactory<T>, CellGrid, Fraction, Cache<Long, Cell<A>>, A, IoSync) - Constructor for class io.scif.img.cell.SCIFIOCellImg
SCIFIOCellImgFactory<T extends net.imglib2.type.NativeType<T>> - Class in io.scif.img.cell: Factory for creating SCIFIOCellImgs.
SCIFIOCellImgFactory(T) - Constructor for class io.scif.img.cell.SCIFIOCellImgFactory: Create a new SCIFIOCellImgFactory with default configuration.
SCIFIOCellImgFactory(T, DiskCachedCellImgOptions) - Constructor for class io.scif.img.cell.SCIFIOCellImgFactory: Create a new SCIFIOCellImgFactory with the specified configuration.
SCIFIOCellImgFactory() - Constructor for class io.scif.img.cell.SCIFIOCellImgFactory: Deprecated.
SCIFIOCellImgFactory(int...) - Constructor for class io.scif.img.cell.SCIFIOCellImgFactory: Deprecated.
SCIFIOConfig - Class in io.scif.config: Configuration class for all SCIFIO components.
SCIFIOConfig() - Constructor for class io.scif.config.SCIFIOConfig: Zero-param constructor.
SCIFIOConfig(Context) - Constructor for class io.scif.config.SCIFIOConfig: Context-injecting constructor.
SCIFIOConfig(SCIFIOConfig) - Constructor for class io.scif.config.SCIFIOConfig: Copying constructor.
SCIFIOConfig.ImgMode - Enum in io.scif.config: Access type options for opening datasets.
SCIFIOImgPlus<T> - Class in io.scif.img: SCIFIO extension of ImgPlus that adds SCIFIOImgPlus.getColorTable(int, int) API for specifying both the plane and image index.
SCIFIOImgPlus(Img<T>) - Constructor for class io.scif.img.SCIFIOImgPlus
SCIFIOImgPlus(Img<T>, String) - Constructor for class io.scif.img.SCIFIOImgPlus
SCIFIOImgPlus(Img<T>, String, AxisType[]) - Constructor for class io.scif.img.SCIFIOImgPlus
SCIFIOImgPlus(Img<T>, ImgPlusMetadata) - Constructor for class io.scif.img.SCIFIOImgPlus
SCIFIOImgPlus(Img<T>, String, AxisType[], double[]) - Constructor for class io.scif.img.SCIFIOImgPlus
SCIFIOImgPlus(ImgPlus<T>) - Constructor for class io.scif.img.SCIFIOImgPlus
SCIFIOMetadataTools - Class in io.scif.util: A utility class for working with Metadata objects.
SCIFIOMetadataTools.AxisValue - Class in io.scif.util: Helper class that pairs an AxisType with a length.
SCIFIOPlugin - Interface in io.scif: Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
SCIFIOService - Interface in io.scif: Marker interface for all SCIFIO Services.
SEM_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the scanning electron microscopy domain.
SENSING_METHOD - Static variable in class io.scif.formats.tiff.IFD
separate(AxisType...) - Method in class io.scif.filters.PlaneSeparator: Specify which AxisTypes should be separated.
separate(AxisType...) - Method in class io.scif.filters.PlaneSeparatorMetadata: Specify which AxisTypes should be separated.
serialVersionUID - Static variable in exception io.scif.DependencyException: Serial for this version.
SERIES_NAME - Static variable in class io.scif.util.FormatTools
SERIES_NUM - Static variable in class io.scif.util.FormatTools: Patterns to be used when constructing a pattern for output filenames.
ServiceException - Exception in io.scif.services: Exception thrown when there is an error within a given service.
ServiceException(String) - Constructor for exception io.scif.services.ServiceException: Default constructor.
ServiceException(String, Throwable) - Constructor for exception io.scif.services.ServiceException: Default constructor.
ServiceException(Throwable) - Constructor for exception io.scif.services.ServiceException: Default constructor.
setAct(int[]) - Method in class io.scif.formats.GIFFormat.Metadata: Sets the active color table
setActl(APNGFormat.ACTLChunk) - Method in class io.scif.formats.APNGFormat.Metadata
setAltCodec(String) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setAltPlanes(int) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setAssumeEqualStrips(boolean) - Method in class io.scif.formats.tiff.TiffParser: Sets whether or not to assume that strips are of equal size.
setAxes(CalibratedAxis[], long[]) - Method in class io.scif.AbstractImageMetadata
setAxes(CalibratedAxis...) - Method in class io.scif.AbstractImageMetadata
setAxes(CalibratedAxis[], long[]) - Method in interface io.scif.ImageMetadata: Convenience method to set both the axis types and lengths for this ImageMetadata.
setAxes(CalibratedAxis...) - Method in interface io.scif.ImageMetadata: Sets the Axes types for this image.
setAxis(int, CalibratedAxis) - Method in class io.scif.AbstractImageMetadata
setAxis(int, CalibratedAxis) - Method in interface io.scif.ImageMetadata: Sets the axis at the specified index, if an axis with a matching type is not already defined.
setAxisLength(CalibratedAxis, long) - Method in class io.scif.AbstractImageMetadata
setAxisLength(AxisType, long) - Method in class io.scif.AbstractImageMetadata
setAxisLength(CalibratedAxis, long) - Method in interface io.scif.ImageMetadata: Sets the length for the specified axis.
setAxisLength(AxisType, long) - Method in interface io.scif.ImageMetadata: As ImageMetadata.setAxisLength(CalibratedAxis, long) but requires only the AxisType.
setAxisLengths(long[]) - Method in class io.scif.AbstractImageMetadata
setAxisLengths(long[]) - Method in interface io.scif.ImageMetadata: Sets the lengths of each axis.
setAxisType(int, AxisType) - Method in class io.scif.AbstractImageMetadata
setAxisType(int, AxisType) - Method in interface io.scif.ImageMetadata: As ImageMetadata.setAxis(int, CalibratedAxis) but using the default calibration values, per FormatTools.createAxis(AxisType).
setAxisTypes(AxisType...) - Method in class io.scif.AbstractImageMetadata
setAxisTypes(int[]) - Method in class io.scif.AxisGuesser: Sets the axis type for each dimensional block.
setAxisTypes(AxisType...) - Method in interface io.scif.ImageMetadata: Sets the Axes types for this image.
setBackslashContinuesLine(boolean) - Method in class io.scif.common.IniParser: Set whether or not a '\' at the end of a line signifies that the line continues on the following line.
setBigTiff(boolean) - Method in class io.scif.formats.tiff.TiffSaver: Sets whether or not BigTIFF data should be written.
setBigTiff(boolean) - Method in class io.scif.formats.TIFFFormat.Writer: Sets whether or not BigTIFF files should be written.
setBinary(boolean) - Method in class io.scif.formats.EPSFormat.Metadata
setBitDepth(byte) - Method in class io.scif.formats.APNGFormat.IHDRChunk
setBitsPerPixel(int) - Method in class io.scif.AbstractImageMetadata
setBitsPerPixel(int) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setBitsPerPixel(int) - Method in interface io.scif.ImageMetadata: Sets the number of valid bits per pixel.
setBlendOp(byte) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setBlockSize(int) - Method in class io.scif.formats.GIFFormat.Metadata
setBlue(byte[]) - Method in class io.scif.formats.APNGFormat.PLTEChunk
setBmpBitsPerPixel(short) - Method in class io.scif.formats.AVIFormat.Metadata
setBmpColorsUsed(int) - Method in class io.scif.formats.AVIFormat.Metadata
setBmpCompression(int) - Method in class io.scif.formats.AVIFormat.Metadata
setBmpScanLineSize(int) - Method in class io.scif.formats.AVIFormat.Metadata
setBmpWidth(int) - Method in class io.scif.formats.AVIFormat.Metadata
setBounds(Interval) - Method in class io.scif.AbstractPlane
setBounds(Interval) - Method in interface io.scif.Plane: Sets this plane's bounds relative to the underlying image.
setBytesPerLine(int) - Method in class io.scif.formats.PCXFormat.Metadata
setBytesPerPlane(int) - Method in class io.scif.formats.AVIFormat.Metadata
setCalibrationUnit(String) - Method in class io.scif.formats.TIFFFormat.Metadata
setCanChangePattern(boolean) - Method in class io.scif.filters.FileStitcher
setCanUsePrevious(boolean) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setChunkSizes(List<Integer>) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setCodec(int) - Method in class io.scif.formats.qt.LegacyQTFormat.Writer: Sets the encoded movie's codec.
setCodec(String) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setCodec(int) - Method in class io.scif.formats.qt.NativeQTFormat.Writer: Sets the encoded movie's codec.
setCodecOptions(CodecOptions) - Method in class io.scif.formats.tiff.TiffParser: Sets the codec options to be used when decompressing pixel data.
setCodecOptions(CodecOptions) - Method in class io.scif.formats.tiff.TiffSaver: Sets the codec options.
setColorModel(ColorModel) - Method in class io.scif.AbstractWriter
setColorModel(ColorModel) - Method in interface io.scif.Writer: Sets the color model.
setColorTable(ColorTable) - Method in class io.scif.AbstractPlane
setColorTable(ColorTable) - Method in interface io.scif.Plane: Sets the ColorTable for this plane.
setColorTables(Vector<int[]>) - Method in class io.scif.formats.GIFFormat.Metadata
setColourType(byte) - Method in class io.scif.formats.APNGFormat.IHDRChunk
setCommentDelimiter(String) - Method in class io.scif.common.IniParser: Set the String that identifies a comment.
setCompanionFile(Location) - Method in class io.scif.formats.TIFFFormat.Metadata
setCompanionFiles(List<BrowsableLocation>) - Method in class io.scif.formats.DICOMFormat.Metadata
setCompression(int) - Method in class io.scif.formats.BMPFormat.Metadata
setCompressionMethod(byte) - Method in class io.scif.formats.APNGFormat.IHDRChunk
setContext(Context) - Method in class io.scif.filters.AbstractReaderFilter
setCreationDate(long) - Method in class io.scif.formats.ScancoISQFormat.Metadata: Converts the given timestamp to a creation date Timestamp starts from byte 36 of the file
setCreationDate(String) - Method in class io.scif.formats.TIFFFormat.Metadata
setData(T) - Method in class io.scif.AbstractPlane
setData(BufferedImage) - Method in class io.scif.BufferedImagePlane
setData(T) - Method in interface io.scif.DataPlane: Sets the native pixel data for this plane.
setDataFile(Location) - Method in class io.scif.formats.NRRDFormat.Metadata
setDataOffset(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata: Sets the starting point of image date in the file The 16-bit optional header number is found at byte 508 in the file.
setDataset(Dataset) - Method in class io.scif.commands.SaveImage
setDatasetInfo(MNGFormat.MNGDatasetInfo) - Method in class io.scif.formats.MNGFormat.Metadata
setDatasetName(String) - Method in class io.scif.AbstractMetadata
setDatasetName(String) - Method in interface io.scif.Metadata: Sets the name for this dataset.
setDate(String) - Method in class io.scif.formats.DICOMFormat.Metadata
setdBlock(byte[]) - Method in class io.scif.formats.GIFFormat.Metadata
setDecoder(JPEGTileDecoder) - Method in class io.scif.formats.JPEGTileFormat.Metadata
setDeflate(boolean) - Method in class io.scif.formats.DICOMFormat.Metadata
setDelayDen(short) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setDelayNum(short) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setDescription(String) - Method in class io.scif.formats.TIFFFormat.Metadata
setDest(Location) - Method in class io.scif.AbstractWriter
setDest(DataHandle<Location>) - Method in class io.scif.AbstractWriter
setDest(Location, int) - Method in class io.scif.AbstractWriter
setDest(DataHandle<Location>, int) - Method in class io.scif.AbstractWriter
setDest(Location, SCIFIOConfig) - Method in class io.scif.AbstractWriter
setDest(DataHandle<Location>, SCIFIOConfig) - Method in class io.scif.AbstractWriter
setDest(Location, int, SCIFIOConfig) - Method in class io.scif.AbstractWriter
setDest(DataHandle<Location>, int, SCIFIOConfig) - Method in class io.scif.AbstractWriter
setDest(DataHandle<Location>, int, SCIFIOConfig) - Method in class io.scif.formats.APNGFormat.Writer
setDest(DataHandle<Location>, int, SCIFIOConfig) - Method in class io.scif.formats.AVIFormat.Writer
setDest(DataHandle<Location>, int, SCIFIOConfig) - Method in class io.scif.formats.ICSFormat.Writer
setDest(DataHandle<Location>, int, SCIFIOConfig) - Method in class io.scif.formats.qt.NativeQTFormat.Writer
setDest(DataHandle<Location>, int, SCIFIOConfig) - Method in class io.scif.formats.TIFFFormat.Writer
setDest(Location) - Method in interface io.scif.Writer: Sets the source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.
setDest(DataHandle<Location>) - Method in interface io.scif.Writer: Sets the source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.
setDest(Location, int) - Method in interface io.scif.Writer: As Writer.setDest(Location) with specification for source image index.
setDest(DataHandle<Location>, int) - Method in interface io.scif.Writer: As Writer.setDest(DataHandle), with specification for source image index.
setDest(Location, SCIFIOConfig) - Method in interface io.scif.Writer: As Writer.setDest(Location) with specification for new configuration options.
setDest(DataHandle<Location>, SCIFIOConfig) - Method in interface io.scif.Writer: As Writer.setDest(DataHandle), with specification for new configuration options.
setDest(Location, int, SCIFIOConfig) - Method in interface io.scif.Writer: As Writer.setDest(Location, int) with specification for new configuration options.
setDest(DataHandle<Location>, int, SCIFIOConfig) - Method in interface io.scif.Writer: As Writer.setDest(DataHandle, int), with specification for new configuration options.
setDestinationLocation(Location) - Method in class io.scif.AbstractMetadata
setDestinationLocation(Location) - Method in interface io.scif.Metadata: Sets the output location.
setDeviceName(String) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setDispose(int) - Method in class io.scif.formats.GIFFormat.Metadata
setDisposeOp(byte) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setDoCaching(boolean) - Method in class io.scif.formats.tiff.TiffParser: Sets whether or not IFD entries should be cached.
setElem(int, int) - Method in class io.scif.gui.SignedByteBuffer
setElem(int, int, int) - Method in class io.scif.gui.SignedByteBuffer
setElem(int, int, int) - Method in class io.scif.gui.SignedShortBuffer
setElem(int, int) - Method in class io.scif.gui.UnsignedIntBuffer
setElem(int, int, int) - Method in class io.scif.gui.UnsignedIntBuffer
setElemDouble(int, double) - Method in class io.scif.gui.UnsignedIntBuffer
setElemDouble(int, int, double) - Method in class io.scif.gui.UnsignedIntBuffer
setElementLength(int) - Method in class io.scif.formats.DICOMFormat.DICOMTag
setElemFloat(int, float) - Method in class io.scif.gui.UnsignedIntBuffer
setElemFloat(int, int, float) - Method in class io.scif.gui.UnsignedIntBuffer
setEnabled(boolean) - Method in class io.scif.AbstractFormat
setEnabled(boolean) - Method in interface io.scif.Format: Toggle whether this Format should be used when checking image compatibility.
setEncoding(String) - Method in class io.scif.formats.NRRDFormat.Metadata
setEnergy(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setEqualStrips(boolean) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setExperimenterEmail(String) - Method in class io.scif.formats.TIFFFormat.Metadata
setExperimenterFirstName(String) - Method in class io.scif.formats.TIFFFormat.Metadata
setExperimenterLastName(String) - Method in class io.scif.formats.TIFFFormat.Metadata
setFalseColor(boolean) - Method in class io.scif.AbstractImageMetadata
setFalseColor(boolean) - Method in interface io.scif.ImageMetadata: Sets whether or not we can ignore the color map (if present).
setFctl(List<APNGFormat.FCTLChunk>) - Method in class io.scif.formats.APNGFormat.Metadata
setFileList(Map<Integer, List<BrowsableLocation>>) - Method in class io.scif.formats.DICOMFormat.Metadata
setFiltered(boolean) - Method in class io.scif.AbstractMetadata
setFiltered(boolean) - Method in interface io.scif.Metadata: Sets whether this metadata was filtered when parsed.
setFilterMethod(byte) - Method in class io.scif.formats.APNGFormat.IHDRChunk
setFirstSlicePosition(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setFlip(boolean) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setGct(int[]) - Method in class io.scif.formats.GIFFormat.Metadata: Sets the global color table (raw values) for this dataset
setGlobal(long) - Method in class io.scif.formats.BMPFormat.Metadata
setGlobalCRC(int) - Method in class io.scif.common.CRC
setGreen(byte[]) - Method in class io.scif.formats.APNGFormat.PLTEChunk
setHasInstrumentData(boolean) - Method in class io.scif.formats.ICSFormat.Metadata
setHeight(int) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setHeight(int) - Method in class io.scif.formats.APNGFormat.IHDRChunk
setHeight(long) - Method in class io.scif.formats.KontronFormat.Metadata
setHeight(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setHeight(short) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setHelper(Reader) - Method in class io.scif.formats.NRRDFormat.Metadata
setIcsLocation(Location) - Method in class io.scif.formats.ICSFormat.Metadata
setIdat(List<APNGFormat.IDATChunk>) - Method in class io.scif.formats.APNGFormat.Metadata
setIdsLocation(Location) - Method in class io.scif.formats.ICSFormat.Metadata
setIend(APNGFormat.IENDChunk) - Method in class io.scif.formats.APNGFormat.Metadata
setIfds(IFDList) - Method in class io.scif.formats.EPSFormat.Metadata
setIfds(IFDList) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setIh(int) - Method in class io.scif.formats.GIFFormat.Metadata
setIhdr(APNGFormat.IHDRChunk) - Method in class io.scif.formats.APNGFormat.Metadata
setImage(Image) - Method in class io.scif.formats.qt.LegacyQTFormat.Metadata
setImageDescription(String) - Method in class io.scif.formats.TIFFFormat.Metadata
setImageIndex(int) - Method in class io.scif.formats.JPEG2000Format.Index
setImageMetadata(ImageMetadata) - Method in class io.scif.AbstractPlane
setImageMetadata(ImageMetadata) - Method in class io.scif.img.SCIFIOImgPlus: Sets the ImageMetadata object for this ImgPlus.
setImageMetadata(ImageMetadata) - Method in interface io.scif.Plane: Sets the ImageMetadata representation of the underlying image.
setImages(Vector<byte[]>) - Method in class io.scif.formats.GIFFormat.Metadata
setImages(BufferedImage[]) - Method in class io.scif.gui.ImageViewer: Sets the viewer to display the given images.
setImages(Reader, BufferedImage[]) - Method in class io.scif.gui.ImageViewer: Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.
setImagesPerFile(int) - Method in class io.scif.formats.DICOMFormat.Metadata
setImageType(String) - Method in class io.scif.formats.DICOMFormat.Metadata
setImg(BufferedImage) - Method in class io.scif.formats.ImageIOFormat.Metadata
setImgMeta(ImageMetadata) - Method in class io.scif.filters.FileStitcherMetadata
setIndex(int) - Method in class io.scif.img.cell.loaders.AbstractArrayLoader
setIndex(int) - Method in interface io.scif.img.cell.loaders.SCIFIOArrayLoader
setIndexed(boolean) - Method in class io.scif.AbstractImageMetadata
setIndexed(boolean) - Method in interface io.scif.ImageMetadata: Sets whether or not the planes are stored as indexed color.
setInitializeHelper(boolean) - Method in class io.scif.formats.NRRDFormat.Metadata
setInSequence(boolean) - Method in class io.scif.formats.DICOMFormat.DICOMTag
setIntensity(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setInterlace(boolean) - Method in class io.scif.formats.GIFFormat.Metadata
setInterlaced(boolean) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setInterlaceMethod(byte) - Method in class io.scif.formats.APNGFormat.IHDRChunk
setInterleavedAxisCount(int) - Method in class io.scif.AbstractImageMetadata
setInterleavedAxisCount(int) - Method in interface io.scif.ImageMetadata: Sets the number of interleaved axes in this image.
setInverted(boolean) - Method in class io.scif.formats.DICOMFormat.Metadata
setInvertY(boolean) - Method in class io.scif.formats.BMPFormat.Metadata
setIw(int) - Method in class io.scif.formats.GIFFormat.Metadata
setIx(int) - Method in class io.scif.formats.GIFFormat.Metadata
setIy(int) - Method in class io.scif.formats.GIFFormat.Metadata
setJ2kCodecOptions(JPEG2000CodecOptions) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setJNG(boolean) - Method in class io.scif.formats.MNGFormat.Metadata
setJP2K(boolean) - Method in class io.scif.formats.DICOMFormat.Metadata
setJPEG(boolean) - Method in class io.scif.formats.DICOMFormat.Metadata
setJpegOffsets(List<Long>) - Method in class io.scif.formats.qt.PICTFormat.Metadata
setKeyValPairs(Map<String, String>) - Method in class io.scif.formats.ICSFormat.Metadata
setLastDimensions(int[]) - Method in class io.scif.formats.AVIFormat.Metadata
setLastDispose(int) - Method in class io.scif.formats.GIFFormat.Metadata
setLastIndex(int, long) - Method in class io.scif.formats.JPEG2000Format.Metadata
setLastIndexBytes(byte[]) - Method in class io.scif.formats.JPEG2000Format.Metadata
setLastPlane(ByteArrayPlane) - Method in class io.scif.formats.AVIFormat.Metadata
setLastPlane(long) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setLastPlaneIndex(long) - Method in class io.scif.formats.AVIFormat.Metadata
setLeftEdge(short) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setLegacy(boolean) - Method in class io.scif.formats.qt.PICTFormat
setLength(int) - Method in class io.scif.formats.APNGFormat.APNGChunk
setLength(long) - Method in class io.scif.util.SCIFIOMetadataTools.AxisValue
setLengths(List<Long>) - Method in class io.scif.formats.AVIFormat.Metadata
setLicenseCode(String) - Method in interface io.scif.services.LuraWaveService: Overrides the license code to use when initializing the LuraWave decoder.
setLittleEndian(boolean) - Method in class io.scif.AbstractImageMetadata
setLittleEndian(boolean) - Method in class io.scif.formats.APNGFormat.Metadata: Sets the littleEndian flag on this metadata.
setLittleEndian(boolean) - Method in class io.scif.formats.DICOMFormat.DICOMTag
setLittleEndian(boolean) - Method in class io.scif.formats.tiff.TiffSaver: Sets whether or not little-endian data should be written.
setLittleEndian(boolean) - Method in interface io.scif.ImageMetadata: Sets whether or not each pixel's bytes are in little endian order.
setLoader(SCIFIOArrayLoader<?>) - Method in class io.scif.img.cell.SCIFIOCellImg
setLocation(int) - Method in class io.scif.formats.DICOMFormat.DICOMTag
setLookForCompanion(boolean) - Method in class io.scif.formats.NRRDFormat.Metadata
setLookup(byte[][]) - Method in class io.scif.formats.qt.PICTFormat.Metadata
setLut(int[][]) - Method in class io.scif.formats.JPEG2000Format.Metadata
setLut(byte[][]) - Method in class io.scif.formats.TIFFFormat.Metadata
setLuts(ColorTable[][]) - Method in class io.scif.formats.TestImgFormat.Metadata: Sets the lookup table for this dataset.
setMaxDataValue(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setMaxPixelValue(int) - Method in class io.scif.formats.DICOMFormat.Metadata
setMeasurementDate(int) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setMeasurementIndex(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setMeasurementInfo(DataHandle<Location>) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setMetaData(Metadata) - Method in class io.scif.AbstractParser: Allows implementations of this class that override AbstractParser.parse(Location, Metadata, SCIFIOConfig) to set the metadata.
setMetadata(Metadata) - Method in class io.scif.AbstractReader
setMetadata(M) - Method in class io.scif.AbstractReader
setMetadata(Metadata) - Method in class io.scif.AbstractWriter
setMetadata(M) - Method in class io.scif.AbstractWriter
setMetadata(Metadata) - Method in class io.scif.filters.AbstractReaderFilter
setMetadata(APNGFormat.Metadata) - Method in class io.scif.formats.APNGFormat.Reader
setMetadata(ICSFormat.Metadata) - Method in class io.scif.formats.ICSFormat.Reader
setMetadata(MicromanagerFormat.Metadata) - Method in class io.scif.formats.MicromanagerFormat.Reader
setMetadata(Metadata) - Method in class io.scif.img.SCIFIOImgPlus: Sets the Metadata object for this ImgPlus.
setMetadata(Metadata) - Method in interface io.scif.Reader: Sets the Metadata for this Reader.
setMetadata(M) - Method in interface io.scif.TypedReader: Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Reader.setMetadata(Metadata).
setMetadata(M) - Method in interface io.scif.TypedWriter: Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Writer.setMetadata(Metadata).
setMetadata(Metadata) - Method in interface io.scif.Writer: Provides this Writer with a Metadata object to use when interpreting Planes during calls to Writer.savePlane(int, long, io.scif.Plane).
setMetadataComplete(boolean) - Method in class io.scif.AbstractImageMetadata
setMetadataComplete(boolean) - Method in interface io.scif.ImageMetadata: Sets whether or not we are confident that all of the metadata stored within the image has been parsed.
setMinDataValue(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setMuScaling(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setName(String) - Method in class io.scif.AbstractImageMetadata
setnColorPlanes(int) - Method in class io.scif.formats.PCXFormat.Metadata
setNormalized(boolean) - Method in class io.scif.AbstractReader
setNormalized(boolean) - Method in class io.scif.filters.AbstractReaderFilter
setNormalized(boolean) - Method in interface io.scif.Reader: Specifies whether or not to normalize float data.
setNoSubresolutions(boolean) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setNumFrames(int) - Method in class io.scif.formats.APNGFormat.ACTLChunk
setNumPages(int) - Method in class io.scif.formats.TIFFJAIFormat.Metadata
setNumPlays(int) - Method in class io.scif.formats.APNGFormat.ACTLChunk
setObjectSize(double) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setOddLocations(boolean) - Method in class io.scif.formats.DICOMFormat.Metadata
setOffset(long) - Method in class io.scif.formats.APNGFormat.APNGChunk
setOffset(long) - Method in class io.scif.formats.NRRDFormat.Metadata
setOffset(long) - Method in class io.scif.formats.PCXFormat.Metadata
setOffset(long) - Method in class io.scif.formats.PGMFormat.Metadata
setOffsets(List<Long>) - Method in class io.scif.formats.AVIFormat.Metadata
setOffsets(long[]) - Method in class io.scif.formats.DICOMFormat.Metadata
setOffsets(List<Integer>) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setOrderCertain(boolean) - Method in class io.scif.AbstractImageMetadata
setOrderCertain(boolean) - Method in interface io.scif.ImageMetadata: Sets whether or not we are confident that the dimension order is correct.
setOriginalDate(String) - Method in class io.scif.formats.DICOMFormat.Metadata
setOriginalInstance(String) - Method in class io.scif.formats.DICOMFormat.Metadata
setOriginalSeries(int) - Method in class io.scif.formats.DICOMFormat.Metadata
setOriginalTime(String) - Method in class io.scif.formats.DICOMFormat.Metadata
setOutputOrder(int, List<AxisType>) - Method in class io.scif.filters.DimensionSwapper: Sets the output dimension order according to the given string (e.g., "XYZCT").
setOutputOrder(List<AxisType>[]) - Method in class io.scif.filters.DimensionSwapperMetadata: Sets the output order for this dataset.
setParent(Object) - Method in class io.scif.filters.AbstractFilter
setParent(Object) - Method in class io.scif.filters.AbstractReaderFilter
setParent(Object) - Method in interface io.scif.filters.Filter: Sets the object which this filter augments.
setParent(Object) - Method in interface io.scif.filters.MasterFilter: Sets the wrapped object.
setParent(Object) - Method in class io.scif.filters.ReaderFilter
setPatientAge(int) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setPatientBirthDate(int) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setPatientId(String) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setPatientIndex(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setPatientMeasurementNumber(short) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setPatientName(String) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setPatientName(String) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setPatientNumber(int) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setPhysicalDepth(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setPhysicalHeight(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setPhysicalWidth(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setPixelBytes(long) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setPixelOffset(long) - Method in class io.scif.formats.FITSFormat.Metadata
setPixelOffset(long) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setPixels(byte[]) - Method in class io.scif.formats.GIFFormat.Metadata
setPixelSizes(String[]) - Method in class io.scif.formats.NRRDFormat.Metadata
setPixelSizeX(String) - Method in class io.scif.formats.DICOMFormat.Metadata
setPixelSizeY(String) - Method in class io.scif.formats.DICOMFormat.Metadata
setPixelSizeZ(Double) - Method in class io.scif.formats.DICOMFormat.Metadata
setPixelsOffset(long) - Method in class io.scif.formats.JPEG2000Format.Metadata
setPixelStack(byte[]) - Method in class io.scif.formats.GIFFormat.Metadata
setPixelType(int) - Method in class io.scif.AbstractImageMetadata
setPixelType(int) - Method in interface io.scif.ImageMetadata: Sets the data type associated with a pixel.
setPlanarAxisCount(int) - Method in class io.scif.AbstractImageMetadata
setPlanarAxisCount(int) - Method in interface io.scif.ImageMetadata: Sets the number of planar axes in this image.
setPlaneIndex(long) - Method in class io.scif.formats.JPEG2000Format.Index
setPlte(APNGFormat.PLTEChunk) - Method in class io.scif.formats.APNGFormat.Metadata
setPositions(List<MicromanagerFormat.Position>) - Method in class io.scif.formats.MicromanagerFormat.Metadata
setPrefix(short[]) - Method in class io.scif.formats.GIFFormat.Metadata
setPrevPixels(byte[]) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setPrevPlane(long) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setProjections(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setQuality(int) - Method in class io.scif.formats.qt.LegacyQTFormat.Writer: Sets the quality of the encoded movie.
setQuality(int) - Method in class io.scif.formats.qt.NativeQTFormat.Writer: Sets the quality of the encoded movie.
setRawBits(boolean) - Method in class io.scif.formats.PGMFormat.Metadata
setRawSize(int) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setReader(Reader, int) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
setReconstructionAlgorithm(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setRed(byte[]) - Method in class io.scif.formats.APNGFormat.PLTEChunk
setReferenceLine(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setRescaleIntercept(double) - Method in class io.scif.formats.DICOMFormat.Metadata
setRescaleSlope(double) - Method in class io.scif.formats.DICOMFormat.Metadata
setResolution(double) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setResolutionLevel(IFD) - Method in class io.scif.formats.MinimalTIFFFormat.Reader: Sets the resolution level when we have JPEG 2000 compressed data.
setResolutionLevels(Integer) - Method in class io.scif.formats.JPEG2000Format.Metadata
setResolutionLevels(Integer) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setRLE(boolean) - Method in class io.scif.formats.DICOMFormat.Metadata
setROIs(Object) - Method in class io.scif.AbstractImageMetadata
setROIs(Object) - Method in interface io.scif.ImageMetadata: Sets the ROIs associated with this image.
setRowBytes(int) - Method in class io.scif.formats.qt.PICTFormat.Metadata
setSamples(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setSamplingTime(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setScale(int) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setScanDistance(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setScannerId(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setScannerType(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setSeparateDefault(boolean) - Method in class io.scif.formats.APNGFormat.Metadata: Sets whether or not the first (default) frame is part of the animation or not.
setSequenceNumber(int) - Method in class io.scif.formats.APNGFormat.ACTLChunk
setSequenceNumber(int) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setSequenceNumber(int) - Method in class io.scif.formats.APNGFormat.FDATChunk
setSigned(boolean) - Method in class io.scif.formats.APNGFormat.Metadata: Sets whether this dataset's pixel type is signed or not.
setSite(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setSize(int) - Method in class io.scif.formats.tiff.OnDemandLongArray
setSliceDistance(double) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setSlices(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setSlices(short) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setSliceSpacing(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setSliceStart(double) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setSliceThickness(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setSource(DataHandle<Location>) - Method in class io.scif.AbstractMetadata
setSource(Location) - Method in class io.scif.AbstractReader
setSource(DataHandle<Location>) - Method in class io.scif.AbstractReader
setSource(Location, SCIFIOConfig) - Method in class io.scif.AbstractReader
setSource(DataHandle<Location>, SCIFIOConfig) - Method in class io.scif.AbstractReader
setSource(DataHandle<Location>) - Method in class io.scif.filters.AbstractMetadataWrapper
setSource(Location) - Method in class io.scif.filters.AbstractReaderFilter
setSource(DataHandle<Location>) - Method in class io.scif.filters.AbstractReaderFilter
setSource(Location, SCIFIOConfig) - Method in class io.scif.filters.AbstractReaderFilter
setSource(DataHandle<Location>, SCIFIOConfig) - Method in class io.scif.filters.AbstractReaderFilter
setSource(Location, SCIFIOConfig) - Method in class io.scif.filters.FileStitcher
setSource(DataHandle<Location>, SCIFIOConfig) - Method in class io.scif.filters.FileStitcher
setSource(Location) - Method in class io.scif.filters.PlaneSeparator
setSource(DataHandle<Location>) - Method in class io.scif.filters.PlaneSeparator
setSource(DataHandle<Location>, SCIFIOConfig) - Method in class io.scif.formats.ICSFormat.Reader
setSource(DataHandle<Location>) - Method in interface io.scif.Metadata: Sets the input source attached to this Metadata object.
setSource(Location) - Method in interface io.scif.Reader: Sets the source for this reader to read from.
setSource(DataHandle<Location>) - Method in interface io.scif.Reader: Sets the source for this reader to read from.
setSource(Location, SCIFIOConfig) - Method in interface io.scif.Reader: As Reader.setSource(Location) with configuration options.
setSource(DataHandle<Location>, SCIFIOConfig) - Method in interface io.scif.Reader: As Reader.setSource(DataHandle) with configuration options.
setSourceHelper(Location, SCIFIOConfig) - Method in class io.scif.filters.AbstractReaderFilter: Allows code to be executed regardless of which AbstractReaderFilter.setSource(org.scijava.io.location.Location) signature is called.
setSourceHelper(Location, SCIFIOConfig) - Method in class io.scif.filters.ChannelFiller
setSourceHelper(Location, SCIFIOConfig) - Method in class io.scif.filters.DimensionSwapper
setSourceHelper(Location, SCIFIOConfig) - Method in class io.scif.filters.FileStitcher
setSourceLocation(Location) - Method in class io.scif.AbstractMetadata
setSourceLocation(Location) - Method in class io.scif.filters.AbstractMetadataWrapper
setSourceLocation(Location) - Method in interface io.scif.Metadata: Sets the input source location.
setSpork(boolean) - Method in class io.scif.formats.qt.NativeQTFormat.Metadata
setStart(int) - Method in class io.scif.formats.EPSFormat.Metadata
setStoredRGB(boolean) - Method in class io.scif.formats.ICSFormat.Metadata
setStrips(List<Object>) - Method in class io.scif.formats.qt.PICTFormat.Metadata
setSubRegion(ImageRegion) - Method in class io.scif.img.cell.SCIFIOCellImgFactory
setSubResolutionIFDs(List<IFDList>) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setSuffix(byte[]) - Method in class io.scif.formats.GIFFormat.Metadata
setTable(MetaTable) - Method in class io.scif.AbstractImageMetadata
setTable(MetaTable) - Method in class io.scif.AbstractMetadata
setTable(MetaTable, boolean) - Method in class io.scif.filters.AbstractMetadataWrapper
setTable(MetaTable, boolean) - Method in interface io.scif.filters.MetadataWrapper
setTable(MetaTable) - Method in interface io.scif.HasMetaTable: Sets the table for this component
setTables(Object) - Method in class io.scif.AbstractImageMetadata
setTables(Object) - Method in interface io.scif.ImageMetadata: Sets the tables associated with this image.
setTagValue(int) - Method in class io.scif.formats.DICOMFormat.DICOMTag
setThumbnail(boolean) - Method in class io.scif.AbstractImageMetadata
setThumbnail(boolean) - Method in interface io.scif.ImageMetadata: Sets whether or not this image is a lower-resolution copy of another image.
setThumbnailIFDs(IFDList) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setThumbSizeX(long) - Method in class io.scif.AbstractImageMetadata
setThumbSizeX(long) - Method in interface io.scif.ImageMetadata: Sets width (in pixels) of thumbnail planes in this image.
setThumbSizeY(long) - Method in class io.scif.AbstractImageMetadata
setThumbSizeY(long) - Method in interface io.scif.ImageMetadata: Sets height (in pixels) of thumbnail planes in this image.
setTiff(boolean) - Method in class io.scif.formats.EPSFormat.Metadata
setTiffParser(TiffParser) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setTime(String) - Method in class io.scif.formats.DICOMFormat.Metadata
setTimeIncrement(Double) - Method in class io.scif.formats.TIFFFormat.Metadata
setTimes(int[]) - Method in class io.scif.formats.qt.LegacyQTFormat.Metadata
setTopEdge(short) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setTransIndex(int) - Method in class io.scif.formats.GIFFormat.Metadata
setTransparency(boolean) - Method in class io.scif.formats.GIFFormat.Metadata
setType(CalibratedAxis) - Method in class io.scif.util.SCIFIOMetadataTools.AxisValue
setUniverse(ReflectedUniverse) - Method in class io.scif.formats.TIFFJAIFormat.Metadata
setUse64Bit(boolean) - Method in class io.scif.formats.MinimalTIFFFormat.Metadata
setUse64BitOffsets(boolean) - Method in class io.scif.formats.tiff.TiffParser: Sets whether or not 64-bit offsets are used for non-BigTIFF files.
setUsingPatternIds(boolean) - Method in class io.scif.filters.FileStitcher: Sets whether the reader is using file patterns for IDs.
setValueToIndex(int[][]) - Method in class io.scif.formats.TestImgFormat.Metadata: Sets the pixel value to index maps for this dataset
setVersionOne(boolean) - Method in class io.scif.formats.qt.PICTFormat.Metadata
setVersionTwo(boolean) - Method in class io.scif.formats.ICSFormat.Metadata
setVisible(boolean) - Method in class io.scif.gui.ImageViewer
setVR(int) - Method in class io.scif.formats.DICOMFormat.DICOMTag
setWidth(int) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setWidth(int) - Method in class io.scif.formats.APNGFormat.IHDRChunk
setWidth(long) - Method in class io.scif.formats.KontronFormat.Metadata
setWidth(int) - Method in class io.scif.formats.ScancoISQFormat.Metadata
setWidth(short) - Method in class io.scif.formats.StratecPQCTFormat.Metadata
setWritingSequentially(boolean) - Method in class io.scif.formats.tiff.TiffSaver: Sets whether or not we know that the planes will be written sequentially.
setxOffset(int) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setxOrigin(Integer) - Method in class io.scif.formats.TIFFFormat.Metadata
setYCbCrCorrection(boolean) - Method in class io.scif.formats.tiff.TiffParser: Sets whether or not YCbCr color correction is allowed.
setyOffset(int) - Method in class io.scif.formats.APNGFormat.FCTLChunk
setyOrigin(Integer) - Method in class io.scif.formats.TIFFFormat.Metadata
SHARPNESS - Static variable in class io.scif.formats.tiff.IFD
ShortAccessLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for ShortArray types.
ShortAccessLoader(Reader, ImageRegion, IntFunction<ShortAccess>) - Constructor for class io.scif.img.cell.loaders.ShortAccessLoader
ShortArrayLoader - Class in io.scif.img.cell.loaders: SCIFIOArrayLoader implementation for ShortArray types.
ShortArrayLoader(Reader, ImageRegion) - Constructor for class io.scif.img.cell.loaders.ShortArrayLoader
shortValue() - Method in class io.scif.formats.tiff.TiffRational: Returns the value of the specified number as a short.
shuffle(int, int[]) - Static method in class io.scif.formats.TestImgFormat.TestImgUtils: Fisher-Yates shuffle with constant seeds to ensure reproducibility.
SHUTTER_SPEED_VALUE - Static variable in class io.scif.formats.tiff.IFD
signed - Variable in class io.scif.codec.CodecOptions: Indicates whether or not the pixel data is signed.
SignedByteBuffer - Class in io.scif.gui: DataBuffer that stores signed bytes.
SignedByteBuffer(byte[], int) - Constructor for class io.scif.gui.SignedByteBuffer: Construct a new buffer of signed bytes using the given byte array.
SignedByteBuffer(byte[][], int) - Constructor for class io.scif.gui.SignedByteBuffer: Construct a new buffer of signed bytes using the given 2D byte array.
SignedColorModel - Class in io.scif.gui: ColorModel that handles 8, 16 and 32 bits per channel signed data.
SignedColorModel(int, int, int) - Constructor for class io.scif.gui.SignedColorModel
SignedShortBuffer - Class in io.scif.gui: DataBuffer that stores signed shorts.
SignedShortBuffer(int) - Constructor for class io.scif.gui.SignedShortBuffer
SignedShortBuffer(int, int) - Constructor for class io.scif.gui.SignedShortBuffer
SignedShortBuffer(short[], int) - Constructor for class io.scif.gui.SignedShortBuffer
SignedShortBuffer(short[], int, int) - Constructor for class io.scif.gui.SignedShortBuffer
SignedShortBuffer(short[][], int) - Constructor for class io.scif.gui.SignedShortBuffer
SignedShortBuffer(short[][], int, int[]) - Constructor for class io.scif.gui.SignedShortBuffer
size() - Method in class io.scif.codec.ByteVector
size() - Method in class io.scif.formats.tiff.OnDemandLongArray
size() - Method in class io.scif.img.ImageRegion
skipBits(long) - Method in class io.scif.codec.BitBuffer: Skips a number of bits in the BitBuffer.
sliceThickness - Variable in class io.scif.formats.MicromanagerFormat.Position
SOF0 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF1 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF10 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF11 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF13 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF14 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF15 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF2 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF3 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF5 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF6 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF7 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOF9 - Static variable in class io.scif.codec.LosslessJPEGCodec
SOFTWARE - Static variable in class io.scif.formats.tiff.IFD
SOI - Static variable in class io.scif.codec.LosslessJPEGCodec
sortFilters(FileFilter[]) - Static method in class io.scif.gui.ComboFileFilter: Sorts the given list of file filters, and combines filters with identical descriptions into a combination filter that accepts anything any of its constituant filters do.
sortFilters(Vector) - Static method in class io.scif.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.
SOS - Static variable in class io.scif.codec.LosslessJPEGCodec
source() - Method in class io.scif.DefaultTranslator
source() - Method in class io.scif.formats.APNGFormat.APNGTranslator
source() - Method in class io.scif.formats.AVIFormat.Translator
source() - Method in class io.scif.formats.EPSFormat.EPSTranslator
source() - Method in class io.scif.formats.ICSFormat.ICSTranslator
source() - Method in class io.scif.formats.ImageIOFormat.ImageIOTranslator
source() - Method in class io.scif.formats.MicromanagerFormat.MicromanagerTranslator
source() - Method in class io.scif.formats.qt.LegacyQTFormat.LegacyQTTranslator
source() - Method in class io.scif.formats.qt.NativeQTFormat.NativeQTTranslator
source() - Method in class io.scif.formats.TestImgFormat.TestImgTranslator
source() - Method in class io.scif.formats.TIFFFormat.TIFFTranslator
source() - Method in interface io.scif.Translator
SPATIAL_FREQUENCY_RESPONSE - Static variable in class io.scif.formats.tiff.IFD
SPECTRA - Static variable in class io.scif.img.axes.SCIFIOAxes: Identifies the Spectra dimensional type, representing a dimension consisting of spectral channels.
SPECTRAL_SENSITIVITY - Static variable in class io.scif.formats.tiff.IFD
split - Variable in class io.scif.codec.NikonCodecOptions
splitChannels(BufferedImage) - Static method in class io.scif.gui.AWTImageTools: Splits the given multi-channel image into single-channel images.
splitChannels(byte[], long[], long[], int, boolean, boolean) - Static method in class io.scif.util.ImageTools: Splits the given multi-channel array into a 2D array.
splitChannels(byte[], byte[], long[], long[], int, boolean, boolean, long) - Static method in class io.scif.util.ImageTools: Splits the given multi-channel array into a 2D array.
splitting(AxisType) - Method in class io.scif.filters.PlaneSeparatorMetadata
SPM_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies the scanning probe microscopy domain.
startDocument() - Method in class io.scif.xml.ValidationSAXHandler
startElement(String, String, String, Attributes) - Method in class io.scif.xml.ValidationSAXHandler
stateChanged(ChangeEvent) - Method in class io.scif.gui.ImageViewer: Handles slider events.
storedRGB() - Method in class io.scif.formats.ICSFormat.Metadata
StratecPQCTFormat - Class in io.scif.formats: The file format reader for Stratec pQCT files.
StratecPQCTFormat() - Constructor for class io.scif.formats.StratecPQCTFormat
StratecPQCTFormat.Checker - Class in io.scif.formats
StratecPQCTFormat.Metadata - Class in io.scif.formats
StratecPQCTFormat.Parser - Class in io.scif.formats
StratecPQCTFormat.Reader - Class in io.scif.formats
StringToDatasetConverter - Class in io.scif.convert: Converter for loading Datasets from Strings.
StringToDatasetConverter() - Constructor for class io.scif.convert.StringToDatasetConverter
STRIP_BYTE_COUNTS - Static variable in class io.scif.formats.tiff.IFD
STRIP_OFFSETS - Static variable in class io.scif.formats.tiff.IFD
STUB_FIELD - Static variable in interface io.scif.services.LuraWaveService: Identifying field in stub class.
SUB_IFD - Static variable in class io.scif.formats.tiff.IFD
SUB_SEC_TIME - Static variable in class io.scif.formats.tiff.IFD
SUB_SEC_TIME_DIGITIZED - Static variable in class io.scif.formats.tiff.IFD
SUB_SEC_TIME_ORIGINAL - Static variable in class io.scif.formats.tiff.IFD
SUBFILE_TYPE - Static variable in class io.scif.formats.tiff.IFD
SUBJECT_DISTANCE - Static variable in class io.scif.formats.tiff.IFD
SUBJECT_DISTANCE_RANGE - Static variable in class io.scif.formats.tiff.IFD
SUBJECT_LOCATION - Static variable in class io.scif.formats.tiff.IFD
suffixNecessary() - Method in class io.scif.AbstractChecker
suffixNecessary() - Method in interface io.scif.Checker: Whether the file extension matching one of the format's suffixes is necessary to identify the file as a source compatible with this format.
suffixNecessary() - Method in class io.scif.formats.APNGFormat.Checker
suffixNecessary() - Method in class io.scif.formats.AVIFormat.Checker
suffixNecessary() - Method in class io.scif.formats.DICOMFormat.Checker
suffixNecessary() - Method in class io.scif.formats.JPEG2000Format.Checker
suffixNecessary() - Method in class io.scif.formats.JPEGFormat.Checker
suffixNecessary() - Method in class io.scif.formats.KontronFormat.Checker
suffixNecessary() - Method in class io.scif.formats.MinimalTIFFFormat.Checker
suffixNecessary() - Method in class io.scif.formats.PGMFormat.Checker
suffixNecessary() - Method in class io.scif.formats.qt.NativeQTFormat.Checker
suffixNecessary() - Method in class io.scif.formats.TestImgFormat.Checker
suffixSufficient() - Method in class io.scif.AbstractChecker
suffixSufficient() - Method in interface io.scif.Checker: Whether the file extension matching one of the format's suffixes is sufficient to identify the file as a source compatible with this format.
suffixSufficient() - Method in class io.scif.formats.DICOMFormat.Checker
suffixSufficient() - Method in class io.scif.formats.JPEG2000Format.Checker
suffixSufficient() - Method in class io.scif.formats.JPEGFormat.Checker
suffixSufficient() - Method in class io.scif.formats.KontronFormat.Checker
suffixSufficient() - Method in class io.scif.formats.ScancoISQFormat.Checker
suffixSufficient() - Method in class io.scif.formats.StratecPQCTFormat.Checker
suffixSufficient() - Method in class io.scif.formats.TestImgFormat.Checker
supports(URI) - Method in class io.scif.io.location.TestImgLocationResolver
supportsOpen(String) - Method in class io.scif.io.DatasetIOPlugin
supportsOpen(Location) - Method in class io.scif.io.DatasetIOPlugin
supportsSave(String) - Method in class io.scif.io.DatasetIOPlugin
supportsSave(Location) - Method in class io.scif.io.DatasetIOPlugin
supportsSave(String) - Method in class io.scif.io.RAIIOPlugin
supportsSave(Location) - Method in class io.scif.io.RAIIOPlugin
swapDimensions(int, AxisType...) - Method in class io.scif.filters.DimensionSwapper: Sets the input dimension order according to the given string (e.g., "XYZCT").

T

T4_OPTIONS - Static variable in class io.scif.formats.tiff.IFD
T6_OPTIONS - Static variable in class io.scif.formats.tiff.IFD
T_AXIS - Static variable in class io.scif.AxisGuesser: Axis type for time points.
T_NUM - Static variable in class io.scif.util.FormatTools
table - Variable in class io.scif.codec.HuffmanCodecOptions
tail() - Method in class io.scif.img.Range
target() - Method in class io.scif.filters.AbstractReaderFilter
target() - Method in interface io.scif.filters.Filter
target() - Method in class io.scif.filters.MasterFilterHelper
TARGET_PRINTER - Static variable in class io.scif.formats.tiff.IFD
temperature - Variable in class io.scif.formats.MicromanagerFormat.Position
test() - Method in class io.scif.codec.AbstractCodec: Main testing method default implementation.
TestImgFormat - Class in io.scif.formats: TestImgFormat is the file format reader for creatign test input data.
TestImgFormat() - Constructor for class io.scif.formats.TestImgFormat
TestImgFormat.Checker - Class in io.scif.formats
TestImgFormat.Metadata - Class in io.scif.formats: Metadata class for Fake format.
TestImgFormat.Parser - Class in io.scif.formats: Parser for Fake file format.
TestImgFormat.Reader - Class in io.scif.formats: Reader for the Fake file format.
TestImgFormat.TestImgTranslator - Class in io.scif.formats: Translator from Metadata to TestImgFormat$Metadata .
TestImgFormat.TestImgUtils - Class in io.scif.formats: Helper methods for the test img file format.
TestImgLocation - Class in io.scif.io.location: A Location for specifying virtual test images, to be used in combination with TestImgFormat.
TestImgLocation.Builder - Class in io.scif.io.location
TestImgLocationResolver - Class in io.scif.io.location: Implementation of LocationResolver for TestImgLocation.
TestImgLocationResolver() - Constructor for class io.scif.io.location.TestImgLocationResolver
TestImgTranslator() - Constructor for class io.scif.formats.TestImgFormat.TestImgTranslator
TestImgUtils() - Constructor for class io.scif.formats.TestImgFormat.TestImgUtils
THRESHHOLDING - Static variable in class io.scif.formats.tiff.IFD
thumbnail(boolean) - Method in class io.scif.io.location.TestImgLocation.Builder
THUMBNAIL_DIMENSION - Static variable in class io.scif.AbstractImageMetadata: Default thumbnail width and height.
THUMBNAIL_DIMENSION - Static variable in class io.scif.util.FormatTools: Default height and width for thumbnails.
thumbSizeX(int) - Method in class io.scif.io.location.TestImgLocation.Builder
thumbSizeY(int) - Method in class io.scif.io.location.TestImgLocation.Builder
tiff() - Method in class io.scif.SCIFIO: Gets this application context's TiffService.
TIFF_SUFFIXES - Static variable in class io.scif.formats.TIFFFormat
TiffCompression - Enum in io.scif.formats.tiff: Utility class for performing compression operations with a TIFF file.
TiffConstants - Class in io.scif.formats.tiff: Generally useful TIFF-related constants.
TIFFFormat - Class in io.scif.formats: Handler for the TIFF file format.
TIFFFormat() - Constructor for class io.scif.formats.TIFFFormat
TIFFFormat.BaseTIFFParser - Class in io.scif.formats: BaseTiffParser is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
TIFFFormat.Metadata - Class in io.scif.formats
TIFFFormat.Parser - Class in io.scif.formats
TIFFFormat.Reader<M extends TIFFFormat.Metadata> - Class in io.scif.formats: TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.
TIFFFormat.TIFFTranslator - Class in io.scif.formats: This class can be used for translating any io.scif.Metadata to Metadata for writing TIFF. files.
TIFFFormat.Writer<M extends TIFFFormat.Metadata> - Class in io.scif.formats: TiffWriter is the file format writer for TIFF files.
TiffIFDEntry - Class in io.scif.formats.tiff: This class represents a single raw TIFF IFD entry.
TiffIFDEntry(int, IFDType, int, long) - Constructor for class io.scif.formats.tiff.TiffIFDEntry
TIFFJAIFormat - Class in io.scif.formats: TiffJAIReader is a file format reader for TIFF images.
TIFFJAIFormat() - Constructor for class io.scif.formats.TIFFJAIFormat
TIFFJAIFormat.Metadata - Class in io.scif.formats
TIFFJAIFormat.Parser - Class in io.scif.formats
TIFFJAIFormat.Reader - Class in io.scif.formats
TiffParser - Class in io.scif.formats.tiff: Parses TIFF data from an input source.
TiffParser(Context, Location) - Constructor for class io.scif.formats.tiff.TiffParser: Constructs a new TIFF parser from the given file name.
TiffParser(Context, DataHandle<Location>) - Constructor for class io.scif.formats.tiff.TiffParser: Constructs a new TIFF parser from the given input source.
TiffRational - Class in io.scif.formats.tiff: A rational number (numerator over denominator).
TiffRational(long, long) - Constructor for class io.scif.formats.tiff.TiffRational: Constructs a rational number.
tiffs - Variable in class io.scif.formats.MicromanagerFormat.Position
TiffSaver - Class in io.scif.formats.tiff: Writes TIFF data to an output location.
TiffSaver(Context, String) - Constructor for class io.scif.formats.tiff.TiffSaver: Constructs a new TIFF saver from the given filename.
TiffSaver(Context, Location) - Constructor for class io.scif.formats.tiff.TiffSaver
TiffSaver(Context, DataHandle<Location>) - Constructor for class io.scif.formats.tiff.TiffSaver: Constructs a new TIFF saver from the given output source.
TiffSaver(DataHandle<Location>, BytesLocation) - Constructor for class io.scif.formats.tiff.TiffSaver: Constructs a new TIFF saver from the given output source.
TiffService - Interface in io.scif.formats.tiff: Interface for services that work with TIFF files.
TIFFTranslator() - Constructor for class io.scif.formats.TIFFFormat.TIFFTranslator
TILE_BYTE_COUNTS - Static variable in class io.scif.formats.tiff.IFD
TILE_LENGTH - Static variable in class io.scif.formats.tiff.IFD
TILE_OFFSETS - Static variable in class io.scif.formats.tiff.IFD
TILE_WIDTH - Static variable in class io.scif.formats.tiff.IFD
tileGridXOffset - Variable in class io.scif.codec.CodecOptions: Horizontal offset of the tile grid as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileGridYOffset - Variable in class io.scif.codec.CodecOptions: Vertical offset of the tile grid as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileHeight - Variable in class io.scif.codec.CodecOptions: Tile height as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileWidth - Variable in class io.scif.codec.CodecOptions: Tile width as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
time - Variable in class io.scif.formats.MicromanagerFormat.Position
TIMESTAMP - Static variable in class io.scif.util.FormatTools
timestamps - Variable in class io.scif.formats.MicromanagerFormat.Position
toByteArray() - Method in class io.scif.codec.BitWriter: Gets an array containing all bits written thus far.
toByteArray() - Method in class io.scif.codec.ByteVector
toCIEXYZ(float[]) - Method in class io.scif.gui.TwoChannelColorSpace
toRGB(float[]) - Method in class io.scif.gui.TwoChannelColorSpace
toString() - Method in class io.scif.AbstractImageMetadata
toString() - Method in exception io.scif.DependencyException
toString() - Method in class io.scif.FieldPrinter
toString() - Method in class io.scif.formats.APNGFormat.APNGChunk
toString() - Method in class io.scif.formats.tiff.TiffIFDEntry
toString() - Method in class io.scif.formats.tiff.TiffRational: Returns a string representation of the object.
toString() - Method in class io.scif.gui.ComboFileFilter: Gets a string representation of this file filter.
toString() - Method in class io.scif.gui.FormatFileFilter: Gets a string representation of this file filter.
toString() - Method in class io.scif.io.location.TestImgLocation
toString() - Method in class io.scif.LocationInfo
totalAvailableMemory() - Static method in class io.scif.util.MemoryTools: Returns the total amount of remaining memory.
TRANSFER_FUNCTION - Static variable in class io.scif.formats.tiff.IFD
TRANSFER_RANGE - Static variable in class io.scif.formats.tiff.IFD
transformXML(String, Templates) - Method in class io.scif.xml.DefaultXMLService
transformXML(Source, Templates) - Method in class io.scif.xml.DefaultXMLService
transformXML(String, Templates) - Method in interface io.scif.xml.XMLService: Transforms the given XML string using the specified XSLT stylesheet.
transformXML(Source, Templates) - Method in interface io.scif.xml.XMLService: Transforms the given XML data using the specified XSLT stylesheet.
translate(Metadata, Metadata) - Method in class io.scif.AbstractTranslator
translate(Metadata, List<ImageMetadata>, Metadata) - Method in class io.scif.AbstractTranslator
translate(Metadata, Metadata, boolean) - Method in class io.scif.services.DefaultTranslatorService
translate(Metadata, Metadata, boolean) - Method in interface io.scif.services.TranslatorService: Convenience method to immediately translate from the source Metadata to the dest Metadata type, assuming an appropriate Translator is found.
translate(Metadata, Metadata) - Method in interface io.scif.Translator: Uses the source Metadata to populate the destination Metadata.
translate(Metadata, List<ImageMetadata>, Metadata) - Method in interface io.scif.Translator: As Translator.translate(Metadata, Metadata) with the format-specific and image metadata explicitly split out.
translateFormatMetadata(M, N) - Method in class io.scif.AbstractTranslator: Use format-specific metadata from the source to populate the destination's format-specific metadata.
translateImageMetadata(List<ImageMetadata>, N) - Method in class io.scif.AbstractTranslator: Use format-agnostic metadata (ImageMetadata to populate the destination's format-specific metadata.
translateImageMetadata(List<ImageMetadata>, Metadata) - Method in class io.scif.DefaultTranslator
translateImageMetadata(List<ImageMetadata>, APNGFormat.Metadata) - Method in class io.scif.formats.APNGFormat.APNGTranslator
translateImageMetadata(List<ImageMetadata>, AVIFormat.Metadata) - Method in class io.scif.formats.AVIFormat.Translator
translateImageMetadata(List<ImageMetadata>, ICSFormat.Metadata) - Method in class io.scif.formats.ICSFormat.ICSTranslator
translateImageMetadata(List<ImageMetadata>, ImageIOFormat.Metadata) - Method in class io.scif.formats.ImageIOFormat.ImageIOTranslator
translateImageMetadata(List<ImageMetadata>, LegacyQTFormat.Metadata) - Method in class io.scif.formats.qt.LegacyQTFormat.LegacyQTTranslator
translateImageMetadata(List<ImageMetadata>, NativeQTFormat.Metadata) - Method in class io.scif.formats.qt.NativeQTFormat.NativeQTTranslator
translateImageMetadata(List<ImageMetadata>, TestImgFormat.Metadata) - Method in class io.scif.formats.TestImgFormat.TestImgTranslator
translateImageMetadata(List<ImageMetadata>, TIFFFormat.Metadata) - Method in class io.scif.formats.TIFFFormat.TIFFTranslator
Translator() - Constructor for class io.scif.formats.AVIFormat.Translator
translator() - Method in class io.scif.SCIFIO: Gets this application context's TranslatorService.
Translator - Interface in io.scif: Interface for all SCIFIO Translators.
TranslatorService - Interface in io.scif.services: Collection of methods for creating and using appropriate Translators to convert between Metadata types.
TwoChannelColorSpace - Class in io.scif.gui: ColorSpace for 2-channel images.
TwoChannelColorSpace(int, int) - Constructor for class io.scif.gui.TwoChannelColorSpace
TypedMetadata - Interface in io.scif: Sub-interface for Metadata to facilitate generic parameterization of SCIFIO components.
typedParse(DataHandle<Location>, M, SCIFIOConfig) - Method in class io.scif.AbstractParser: A helper method, called by AbstractParser.parse(DataHandle, TypedMetadata).
typedParse(DataHandle<Location>, DefaultMetadata, SCIFIOConfig) - Method in class io.scif.DefaultParser
typedParse(DataHandle<Location>, APNGFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.APNGFormat.Parser
typedParse(DataHandle<Location>, AVIFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.AVIFormat.Parser
typedParse(DataHandle<Location>, BMPFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.BMPFormat.Parser
typedParse(DataHandle<Location>, DICOMFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.DICOMFormat.Parser
typedParse(DataHandle<Location>, EPSFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.EPSFormat.Parser
typedParse(DataHandle<Location>, FITSFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.FITSFormat.Parser
typedParse(DataHandle<Location>, GIFFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.GIFFormat.Parser
typedParse(DataHandle<Location>, ICSFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.ICSFormat.Parser
typedParse(DataHandle<Location>, M, SCIFIOConfig) - Method in class io.scif.formats.ImageIOFormat.Parser
typedParse(DataHandle<Location>, JPEG2000Format.Metadata, SCIFIOConfig) - Method in class io.scif.formats.JPEG2000Format.Parser
typedParse(DataHandle<Location>, JPEGFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.JPEGFormat.Parser
typedParse(DataHandle<Location>, JPEGTileFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.JPEGTileFormat.Parser
typedParse(DataHandle<Location>, KontronFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.KontronFormat.Parser
typedParse(DataHandle<Location>, MicromanagerFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.MicromanagerFormat.Parser
typedParse(DataHandle<Location>, M, SCIFIOConfig) - Method in class io.scif.formats.MinimalTIFFFormat.Parser
typedParse(DataHandle<Location>, MNGFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.MNGFormat.Parser
typedParse(DataHandle<Location>, NRRDFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.NRRDFormat.Parser
typedParse(DataHandle<Location>, PCXFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.PCXFormat.Parser
typedParse(DataHandle<Location>, PGMFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.PGMFormat.Parser
typedParse(DataHandle<Location>, LegacyQTFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.qt.LegacyQTFormat.Parser
typedParse(DataHandle<Location>, NativeQTFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.qt.NativeQTFormat.Parser
typedParse(DataHandle<Location>, PICTFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.qt.PICTFormat.Parser
typedParse(DataHandle<Location>, ScancoISQFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.ScancoISQFormat.Parser
typedParse(DataHandle<Location>, StratecPQCTFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.StratecPQCTFormat.Parser
typedParse(DataHandle<Location>, TestImgFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.TestImgFormat.Parser
typedParse(DataHandle<Location>, TIFFFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.TIFFFormat.BaseTIFFParser
typedParse(DataHandle<Location>, TIFFJAIFormat.Metadata, SCIFIOConfig) - Method in class io.scif.formats.TIFFJAIFormat.Parser
TypedParser<M extends TypedMetadata> - Interface in io.scif: Interface for all Parser implementations that use generic parameters.
TypedReader<M extends TypedMetadata,P extends DataPlane<?>> - Interface in io.scif: Interface for all Reader implementations that use generic parameters.
typedTranslate(M, List<ImageMetadata>, N) - Method in class io.scif.AbstractTranslator: This method provides a hook for subclasses that need access to both the Metadata and ImageMetadata.
TypedWriter<M extends TypedMetadata> - Interface in io.scif: Interface for all Writer implementations that use generic parameters.

U

UINT16 - Static variable in class io.scif.util.FormatTools: Identifies the UINT16 data type used to store pixel values.
UINT32 - Static variable in class io.scif.util.FormatTools: Identifies the UINT32 data type used to store pixel values.
UINT8 - Static variable in class io.scif.util.FormatTools: Identifies the UINT8 data type used to store pixel values.
undifference(byte[], IFD) - Method in class io.scif.formats.tiff.DefaultTiffService
undifference(byte[], IFD) - Method in interface io.scif.formats.tiff.TiffService: Undoes in-place differencing according to the given predictor value.
UNIT - Static variable in class io.scif.formats.ScancoISQFormat.Metadata: The unit of the spatial calibration, e.g.
UNIT - Static variable in class io.scif.formats.StratecPQCTFormat.Metadata: Unit used in spatial calibration
units(String...) - Method in class io.scif.io.location.TestImgLocation.Builder
universe() - Method in class io.scif.formats.TIFFJAIFormat.Metadata
UNIX - Static variable in class io.scif.common.DateTools: Timestamp formats.
UNIX_EPOCH - Static variable in class io.scif.common.DateTools: Milliseconds until UNIX epoch.
UNIX_EPOCH - Static variable in class io.scif.formats.ScancoISQFormat.Metadata: January 1 1970 as a VMS timestamp, i.e. in 100 nanosecond ticks from November 17, 1858
UNKNOWN_AXIS - Static variable in class io.scif.AxisGuesser: Axis type for unclassified axes.
UNKNOWN_DOMAIN - Static variable in class io.scif.util.FormatTools: Identifies an unknown domain.
UnsignedIntBuffer - Class in io.scif.gui: DataBuffer that stores unsigned ints.
UnsignedIntBuffer(int[], int) - Constructor for class io.scif.gui.UnsignedIntBuffer: Construct a new buffer of unsigned ints using the given int array.
UnsignedIntBuffer(int[][], int) - Constructor for class io.scif.gui.UnsignedIntBuffer: Construct a new buffer of unsigned ints using the given 2D int array.
UnsignedIntColorModel - Class in io.scif.gui: ColorModel that handles unsigned 32 bit data.
UnsignedIntColorModel(int, int, int) - Constructor for class io.scif.gui.UnsignedIntColorModel
UnsupportedCompressionException - Exception in io.scif: UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.
UnsupportedCompressionException() - Constructor for exception io.scif.UnsupportedCompressionException
UnsupportedCompressionException(String) - Constructor for exception io.scif.UnsupportedCompressionException
UnsupportedCompressionException(String, Throwable) - Constructor for exception io.scif.UnsupportedCompressionException
UnsupportedCompressionException(Throwable) - Constructor for exception io.scif.UnsupportedCompressionException
unwrap() - Method in class io.scif.filters.AbstractMetadataWrapper
unwrap() - Method in interface io.scif.filters.MetadataWrapper
unwrapMetadata(Metadata) - Static method in class io.scif.util.SCIFIOMetadataTools: Unwraps the provided Metadata class if it has been wrapped in MetadataWrapper(s).
updateCRC(int) - Method in class io.scif.common.CRC
updateLabel(int, int) - Method in class io.scif.gui.ImageViewer: Updates cursor probe label.
updateSource(Location) - Method in class io.scif.AbstractParser
updateSource(Location) - Method in interface io.scif.Parser: Updates the source being operated on by this parser (e.g. in multi-file formats).
usedToInitialize - Variable in class io.scif.LocationInfo: Whether or not this file can be passed to the appropriate reader's setId(String) method.
USER_COMMENT - Static variable in class io.scif.formats.tiff.IFD
utils() - Method in class io.scif.img.AbstractImgIOComponent
utils() - Method in class io.scif.img.cell.loaders.AbstractArrayLoader

V

validateXML(String) - Method in class io.scif.xml.DefaultXMLService
validateXML(String, String) - Method in class io.scif.xml.DefaultXMLService
validateXML(String) - Method in interface io.scif.xml.XMLService: Attempts to validate the given XML string using Java's XML validation facility.
validateXML(String, String) - Method in interface io.scif.xml.XMLService: Attempts to validate the given XML string using Java's XML validation facility.
ValidationErrorHandler - Class in io.scif.xml: Used by validateXML to handle XML validation errors.
ValidationErrorHandler(LogService) - Constructor for class io.scif.xml.ValidationErrorHandler
ValidationSAXHandler - Class in io.scif.xml
ValidationSAXHandler(LogService) - Constructor for class io.scif.xml.ValidationSAXHandler
validStream(DataHandle<Location>, int, boolean) - Static method in class io.scif.util.FormatTools: Returns true if the given DataHandle contains at least 'len' bytes.
validStream(DataHandle<Location>, int, DataHandle.ByteOrder) - Static method in class io.scif.util.FormatTools: Returns true if the given DataHandle contains at least 'len' bytes.
valueOf(String) - Static method in enum io.scif.codec.CompressionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.codec.JPEG2000BoxType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.codec.JPEG2000SegmentMarker: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.config.SCIFIOConfig.ImgMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.formats.tiff.FillOrder: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.formats.tiff.IFDType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.formats.tiff.PhotoInterp: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.formats.tiff.ResolutionUnit: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.formats.tiff.TiffCompression: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.scif.MetadataLevel: Returns the enum constant of this type with the specified name.
values() - Static method in enum io.scif.codec.CompressionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.codec.JPEG2000BoxType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.codec.JPEG2000SegmentMarker: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.config.SCIFIOConfig.ImgMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.formats.tiff.FillOrder: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.formats.tiff.IFDType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.formats.tiff.PhotoInterp: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.formats.tiff.ResolutionUnit: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.formats.tiff.TiffCompression: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.scif.MetadataLevel: Returns an array containing the constants of this enum type, in the order they are declared.
verifyMinimumPopulated(Metadata, DataHandle<Location>) - Static method in class io.scif.util.SCIFIOMetadataTools: Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
verifyMinimumPopulated(Metadata, DataHandle<Location>, int) - Static method in class io.scif.util.SCIFIOMetadataTools: Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.
verifyMinimumPopulated(Metadata, Location) - Static method in class io.scif.util.SCIFIOMetadataTools
verifyMinimumPopulated(Metadata, Location, int) - Static method in class io.scif.util.SCIFIOMetadataTools
voltage - Variable in class io.scif.formats.MicromanagerFormat.Position
vPredictor - Variable in class io.scif.codec.NikonCodecOptions
vr(int) - Method in class io.scif.formats.dicom.DICOMDictionary: Gets the VR for the given code.

W

wait(boolean) - Method in class io.scif.gui.ImageViewer: Toggles wait cursor.
warning(SAXParseException) - Method in class io.scif.xml.ParserErrorHandler
warning(SAXParseException) - Method in class io.scif.xml.ValidationErrorHandler
WHITE_BALANCE - Static variable in class io.scif.formats.tiff.IFD
WHITE_POINT - Static variable in class io.scif.formats.tiff.IFD
wholePlane(int, Metadata, Interval) - Static method in class io.scif.util.SCIFIOMetadataTools: Returns true if the provided axes correspond to a complete image plane
wholeRow(int, Metadata, Interval) - Static method in class io.scif.util.SCIFIOMetadataTools: Returns true if the provided axes correspond to a complete image row
width - Variable in class io.scif.codec.CodecOptions: Width, in pixels, of the image.
windowActivated(WindowEvent) - Method in class io.scif.gui.ImageViewer
windowClosed(WindowEvent) - Method in class io.scif.gui.ImageViewer
windowClosing(WindowEvent) - Method in class io.scif.gui.ImageViewer
windowDeactivated(WindowEvent) - Method in class io.scif.gui.ImageViewer
windowDeiconified(WindowEvent) - Method in class io.scif.gui.ImageViewer
windowIconified(WindowEvent) - Method in class io.scif.gui.ImageViewer
windowOpened(WindowEvent) - Method in class io.scif.gui.ImageViewer
wrap(Metadata) - Method in class io.scif.filters.AbstractMetadataWrapper
wrap(Metadata) - Method in interface io.scif.filters.MetadataWrapper: Sets the Metadata this wrapper will delegate to.
wrap(Metadata) - Method in class io.scif.filters.PlaneSeparatorMetadata
write(int, int) - Method in class io.scif.codec.BitWriter: Writes the given value using the given number of bits.
write(String) - Method in class io.scif.codec.BitWriter: Writes the bits represented by a bit string to the buffer.
writeHeader() - Method in class io.scif.formats.tiff.TiffSaver: Writes the TIFF file header.
writeIFD(IFD, long) - Method in class io.scif.formats.tiff.TiffSaver
writeIFDValue(DataHandle<Location>, long, int, Object) - Method in class io.scif.formats.tiff.TiffSaver: Writes the given IFD value to the given output object.
writeImage(byte[][], IFDList, int) - Method in class io.scif.formats.tiff.TiffSaver
writeImage(byte[], IFD, int, int, boolean) - Method in class io.scif.formats.tiff.TiffSaver
writeImage(byte[], IFD, long, int, int, int, int, int, boolean) - Method in class io.scif.formats.tiff.TiffSaver: Writes to any rectangle from the passed block.
writeImage(byte[], IFD, long, int, int, int, int, int, boolean, Integer, boolean) - Method in class io.scif.formats.tiff.TiffSaver
writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in interface io.scif.services.JAIIIOService: Writes an image using JAI Image I/O using the JPEG 2000 codec.
writeImage(OutputStream, BufferedImage, boolean, int[], double) - Method in interface io.scif.services.JAIIIOService: Deprecated.
Replaced by JAIIIOService.writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) .
writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in class io.scif.services.JAIIIOServiceImpl
writeImage(OutputStream, BufferedImage, boolean, int[], double) - Method in class io.scif.services.JAIIIOServiceImpl: Deprecated.
use JAIIIOService#writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions)
writePlane(int, long, Plane, Interval) - Method in class io.scif.AbstractWriter: Helper method invoked by AbstractWriter.savePlane(int, long, io.scif.Plane) to perform actual format- specific output.
writePlane(int, long, Plane, Interval) - Method in class io.scif.DefaultWriter: Non-functional savePlane implementation.
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.APNGFormat.Writer
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.AVIFormat.Writer
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.EPSFormat.Writer
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.ICSFormat.Writer
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.ImageIOFormat.Writer
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.JPEG2000Format.Writer
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.qt.LegacyQTFormat.Writer
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.qt.NativeQTFormat.Writer
writePlane(int, long, Plane, Interval) - Method in class io.scif.formats.TIFFFormat.Writer
Writer() - Constructor for class io.scif.formats.APNGFormat.Writer
Writer() - Constructor for class io.scif.formats.AVIFormat.Writer
Writer() - Constructor for class io.scif.formats.EPSFormat.Writer
Writer() - Constructor for class io.scif.formats.ICSFormat.Writer
Writer(String) - Constructor for class io.scif.formats.ImageIOFormat.Writer
Writer() - Constructor for class io.scif.formats.JPEG2000Format.Writer
Writer() - Constructor for class io.scif.formats.JPEGFormat.Writer
Writer() - Constructor for class io.scif.formats.qt.LegacyQTFormat.Writer
Writer() - Constructor for class io.scif.formats.qt.NativeQTFormat.Writer
Writer() - Constructor for class io.scif.formats.TIFFFormat.Writer
Writer - Interface in io.scif: Interface for all SCIFIO writers.
writerGetCodecOptions() - Method in class io.scif.config.SCIFIOConfig
writerGetColorModel() - Method in class io.scif.config.SCIFIOConfig
writerGetCompression() - Method in class io.scif.config.SCIFIOConfig
writerGetFailIfOverwriting() - Method in class io.scif.config.SCIFIOConfig
writerGetFramesPerSecond() - Method in class io.scif.config.SCIFIOConfig
writerIsSequential() - Method in class io.scif.config.SCIFIOConfig
writerSetCodecOptions(CodecOptions) - Method in class io.scif.config.SCIFIOConfig
writerSetColorModel(ColorModel) - Method in class io.scif.config.SCIFIOConfig
writerSetCompression(String) - Method in class io.scif.config.SCIFIOConfig
writerSetCompression(CompressionType) - Method in class io.scif.config.SCIFIOConfig
writerSetFailIfOverwriting(boolean) - Method in class io.scif.config.SCIFIOConfig: Warning: "overwriting" behavior is format-specific and not guaranteed to result in a valid image.
writerSetFramesPerSecond(int) - Method in class io.scif.config.SCIFIOConfig
writerSetSequential(boolean) - Method in class io.scif.config.SCIFIOConfig: Sets whether or not we know that planes will be written sequentially.
writeSequential() - Method in class io.scif.AbstractWriter
writeSequential() - Method in interface io.scif.Writer

X

x() - Method in class io.scif.gui.XYCTuple
X_POSITION - Static variable in class io.scif.formats.tiff.IFD
X_RESOLUTION - Static variable in class io.scif.formats.tiff.IFD
xml() - Method in class io.scif.SCIFIO: Gets this application context's XMLService.
xmlFile - Variable in class io.scif.formats.MicromanagerFormat.Position
XMLService - Interface in io.scif.xml: Interface for services that work with XML.
XYCTuple - Class in io.scif.gui: Helper class for converting N-D Metadata to x,y,c values for use in AWT classes.
XYCTuple(ImageMetadata, long[]) - Constructor for class io.scif.gui.XYCTuple
XYCTuple(long, long, long) - Constructor for class io.scif.gui.XYCTuple

Y

y() - Method in class io.scif.gui.XYCTuple
Y_CB_CR_COEFFICIENTS - Static variable in class io.scif.formats.tiff.IFD
Y_CB_CR_POSITIONING - Static variable in class io.scif.formats.tiff.IFD
Y_CB_CR_SUB_SAMPLING - Static variable in class io.scif.formats.tiff.IFD
Y_POSITION - Static variable in class io.scif.formats.tiff.IFD
Y_RESOLUTION - Static variable in class io.scif.formats.tiff.IFD
ycbcr - Variable in class io.scif.codec.CodecOptions: Whether or not the decompressed data will be stored as YCbCr.

Z

Z_AXIS - Static variable in class io.scif.AxisGuesser: Axis type for focal planes.
Z_NUM - Static variable in class io.scif.util.FormatTools
ZlibCodec - Class in io.scif.codec: This class implements ZLIB decompression.
ZlibCodec() - Constructor for class io.scif.codec.ZlibCodec
ZVI - Static variable in class io.scif.common.DateTools
ZVI_EPOCH - Static variable in class io.scif.common.DateTools

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