Uses of Interface
io.scif.Metadata

Packages that use Metadata

Package	Description
io.scif	Provides the interfaces and default implementations for the components of SCIFIO, and the context for instantiating these components.
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	Provides Format implementations for all file formats that are supported by default in SCIFIO.
io.scif.formats.qt
io.scif.img	Provides SCIFIO-based classes for working with ImgPlus from the imglib2 library.
io.scif.services	Provides a set of Services (singletons within a given context) for working with SCIFIO objects.
io.scif.util	Provides utility classes for common operations on or by SCIFIO components.

Uses of Metadata in io.scif

Classes in io.scif with type parameters of type Metadata

Modifier and Type	Class and Description
class	AbstractTranslator<M extends Metadata,N extends Metadata> Abstract superclass of all SCIFIO Translator components.
class	AbstractTranslator<M extends Metadata,N extends Metadata> Abstract superclass of all SCIFIO Translator components.

Subinterfaces of Metadata in io.scif

Modifier and Type	Interface and Description
interface	TypedMetadata Sub-interface for Metadata to facilitate generic parameterization of SCIFIO components.

Classes in io.scif that implement Metadata

Modifier and Type	Class and Description
class	AbstractMetadata Abstract superclass of all SCIFIO Metadata implementations.
class	DefaultMetadata A dummy Metadata implementation.

Methods in io.scif that return Metadata

Modifier and Type	Method and Description
Metadata	Format.createMetadata() Create an instance of the Metadata associated with this format.
Metadata	AbstractFormat.createMetadata()
Metadata	Parser.getMetadata()
Metadata	Reader.getMetadata() Gets the type-specific Metadata for this Reader
Metadata	Writer.getMetadata() Gets the Metadata that will be used when saving planes.
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream) Creates a Metadata object from the provided image source.
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, Metadata meta) Parses metadata from the provided image source to an existing Metadata object (overwriting may occur).
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, Metadata meta, SCIFIOConfig config) /** As Parser.parse(DataHandle, Metadata) with configuration options.
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config) As Parser.parse(DataHandle) with configuration options.
Metadata	Parser.parse(org.scijava.io.location.Location location) Creates a Metadata object using the provided location of an image source.
Metadata	Parser.parse(org.scijava.io.location.Location location, Metadata meta) Parses metadata using the provided name of an image source, and writes to an existing Metadata object (overwriting may occur).
Metadata	Parser.parse(org.scijava.io.location.Location fileName, Metadata meta, SCIFIOConfig config) As Parser.parse(Location, Metadata) with configuration options.
Metadata	Parser.parse(org.scijava.io.location.Location fileName, SCIFIOConfig config) As Parser.parse(Location) with configuration options.

Methods in io.scif that return types with arguments of type Metadata

Modifier and Type	Method and Description
Class<? extends Metadata>	Translator.dest()
Class<? extends Metadata>	DefaultTranslator.dest()
Class<? extends Metadata>	AbstractFormat.getMetadataClass()
Class<? extends Metadata>	Translator.source()
Class<? extends Metadata>	DefaultTranslator.source()

Methods in io.scif with parameters of type Metadata

Modifier and Type	Method and Description
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, Metadata meta) Parses metadata from the provided image source to an existing Metadata object (overwriting may occur).
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, Metadata meta)
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, Metadata meta, SCIFIOConfig config) /** As Parser.parse(DataHandle, Metadata) with configuration options.
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, Metadata meta, SCIFIOConfig config)
Metadata	Parser.parse(org.scijava.io.location.Location location, Metadata meta) Parses metadata using the provided name of an image source, and writes to an existing Metadata object (overwriting may occur).
M	AbstractParser.parse(org.scijava.io.location.Location loc, Metadata meta)
Metadata	Parser.parse(org.scijava.io.location.Location fileName, Metadata meta, SCIFIOConfig config) As Parser.parse(Location, Metadata) with configuration options.
M	AbstractParser.parse(org.scijava.io.location.Location loc, Metadata meta, SCIFIOConfig config)
void	AbstractWriter.setMetadata(Metadata meta)
void	Reader.setMetadata(Metadata meta) Sets the Metadata for this Reader.
void	AbstractReader.setMetadata(Metadata meta)
void	Writer.setMetadata(Metadata meta) Provides this Writer with a Metadata object to use when interpreting Planes during calls to Writer.savePlane(int, long, io.scif.Plane).
protected void	AbstractParser.setMetaData(Metadata meta) Allows implementations of this class that override AbstractParser.parse(Location, Metadata, SCIFIOConfig) to set the metadata.
void	Translator.translate(Metadata source, List<ImageMetadata> sourceImgMeta, Metadata destination) As Translator.translate(Metadata, Metadata) with the format-specific and image metadata explicitly split out.
void	AbstractTranslator.translate(Metadata source, List<ImageMetadata> sourceImgMeta, Metadata dest)
void	Translator.translate(Metadata source, Metadata destination) Uses the source Metadata to populate the destination Metadata.
void	AbstractTranslator.translate(Metadata source, Metadata dest)
protected void	DefaultTranslator.translateImageMetadata(List<ImageMetadata> source, Metadata dest)

Constructors in io.scif with parameters of type Metadata

Constructor and Description
AbstractMetadata(Metadata copy)
DefaultMetadata(Metadata copy)

Uses of Metadata in io.scif.filters

Subinterfaces of Metadata in io.scif.filters

Modifier and Type	Interface and Description
interface	MetadataWrapper Wrapper for Metadata.

Classes in io.scif.filters that implement Metadata

Modifier and Type	Class and Description
class	AbstractMetadataWrapper Abstract superclass for concrete implementations of MetadataWrapper.
class	ChannelFillerMetadata MetadataWrapper implementation specifically for use with the ChannelFiller.
class	DimensionSwapperMetadata MetadataWrapper implementation specifically for use with the DimensionSwapper.
class	FileStitcherMetadata
class	PlaneSeparatorMetadata MetadataWrapper implementation specifically for use with the PlaneSeparator.

Methods in io.scif.filters that return Metadata

Modifier and Type	Method and Description
Metadata	DimensionSwapper.getMetadata()
Metadata	AbstractReaderFilter.getMetadata()
Metadata	ReaderFilter.getMetadata()
protected Metadata	AbstractReaderFilter.getParentMeta() Convenience accessor for the parent's Metadata
Metadata	MetadataWrapper.unwrap()
Metadata	AbstractMetadataWrapper.unwrap()

Methods in io.scif.filters with parameters of type Metadata

Modifier and Type	Method and Description
void	AbstractReaderFilter.setMetadata(Metadata meta)
void	MetadataWrapper.wrap(Metadata meta) Sets the Metadata this wrapper will delegate to.
void	PlaneSeparatorMetadata.wrap(Metadata meta)
void	AbstractMetadataWrapper.wrap(Metadata meta)

Constructors in io.scif.filters with parameters of type Metadata

Constructor and Description
AbstractMetadataWrapper(Metadata metadata)

Uses of Metadata in io.scif.formats

Classes in io.scif.formats that implement Metadata

Modifier and Type	Class and Description
static class	APNGFormat.Metadata File format SCIFIO Metadata for Animated Portable Network Graphics (APNG) images.
static class	AVIFormat.Metadata
static class	BMPFormat.Metadata
static class	DICOMFormat.Metadata
static class	EPSFormat.Metadata
static class	FITSFormat.Metadata
static class	GIFFormat.Metadata
static class	ICSFormat.Metadata SCIFIO Metadata object for ICS images.
static class	ImageIOFormat.Metadata
static class	JPEG2000Format.Metadata
static class	JPEGFormat.Metadata
static class	JPEGTileFormat.Metadata
static class	KontronFormat.Metadata
static class	MicromanagerFormat.Metadata
static class	MinimalTIFFFormat.Metadata
static class	MNGFormat.Metadata
static class	NRRDFormat.Metadata
static class	PCXFormat.Metadata
static class	PGMFormat.Metadata
static class	ScancoISQFormat.Metadata
static class	StratecPQCTFormat.Metadata
static class	TestImgFormat.Metadata Metadata class for Fake format.
static class	TIFFFormat.Metadata
static class	TIFFJAIFormat.Metadata

Methods in io.scif.formats that return types with arguments of type Metadata

Modifier and Type	Method and Description
Class<? extends Metadata>	ImageIOFormat.ImageIOTranslator.dest()
Class<? extends Metadata>	APNGFormat.APNGTranslator.dest()
Class<? extends Metadata>	TIFFFormat.TIFFTranslator.dest()
Class<? extends Metadata>	EPSFormat.EPSTranslator.dest()
Class<? extends Metadata>	MicromanagerFormat.MicromanagerTranslator.dest()
Class<? extends Metadata>	AVIFormat.Translator.dest()
Class<? extends Metadata>	ICSFormat.ICSTranslator.dest()
Class<? extends Metadata>	TestImgFormat.TestImgTranslator.dest()
Class<? extends Metadata>	ImageIOFormat.ImageIOTranslator.source()
Class<? extends Metadata>	APNGFormat.APNGTranslator.source()
Class<? extends Metadata>	TIFFFormat.TIFFTranslator.source()
Class<? extends Metadata>	EPSFormat.EPSTranslator.source()
Class<? extends Metadata>	MicromanagerFormat.MicromanagerTranslator.source()
Class<? extends Metadata>	AVIFormat.Translator.source()
Class<? extends Metadata>	ICSFormat.ICSTranslator.source()
Class<? extends Metadata>	TestImgFormat.TestImgTranslator.source()

Methods in io.scif.formats with parameters of type Metadata

Modifier and Type	Method and Description
void	MicromanagerFormat.Parser.populateMetadata(String[] jsonData, MicromanagerFormat.Metadata source, Metadata dest)

Uses of Metadata in io.scif.formats.qt

Classes in io.scif.formats.qt that implement Metadata

Modifier and Type	Class and Description
static class	LegacyQTFormat.Metadata
static class	NativeQTFormat.Metadata
static class	PICTFormat.Metadata

Methods in io.scif.formats.qt that return types with arguments of type Metadata

Modifier and Type	Method and Description
Class<? extends Metadata>	NativeQTFormat.NativeQTTranslator.dest()
Class<? extends Metadata>	LegacyQTFormat.LegacyQTTranslator.dest()
Class<? extends Metadata>	NativeQTFormat.NativeQTTranslator.source()
Class<? extends Metadata>	LegacyQTFormat.LegacyQTTranslator.source()

Uses of Metadata in io.scif.img

Methods in io.scif.img that return Metadata

Modifier and Type	Method and Description
Metadata	SCIFIOImgPlus.getMetadata()
Metadata	ImgSaver.saveImg(org.scijava.io.location.Location id, net.imglib2.img.Img<?> img) Entry point for saving an ImgPlus.
Metadata	ImgSaver.saveImg(org.scijava.io.location.Location id, net.imglib2.img.Img<?> img, SCIFIOConfig config) As ImgSaver.saveImg(Location, Img) with configuration options.
Metadata	ImgSaver.saveImg(org.scijava.io.location.Location id, SCIFIOImgPlus<?> img, int imageIndex) Location id provided.
Metadata	ImgSaver.saveImg(org.scijava.io.location.Location id, SCIFIOImgPlus<?> img, int imageIndex, SCIFIOConfig config) As ImgSaver.saveImg(Location, SCIFIOImgPlus, int) with configuration options.
Metadata	ImgSaver.saveImg(String destination, net.imglib2.img.Img<?> img) Entry point for saving an ImgPlus.
Metadata	ImgSaver.saveImg(String destination, net.imglib2.img.Img<?> img, SCIFIOConfig config) As ImgSaver.saveImg(Location, Img) with configuration options.
Metadata	ImgSaver.saveImg(String destination, SCIFIOImgPlus<?> img, int imageIndex) Location id provided.
Metadata	ImgSaver.saveImg(String destination, SCIFIOImgPlus<?> img, int imageIndex, SCIFIOConfig config) As ImgSaver.saveImg(Location, SCIFIOImgPlus, int) with configuration options.

Methods in io.scif.img with parameters of type Metadata

Modifier and Type	Method and Description
<T> net.imglib2.img.ImgFactory<T>	ImgFactoryHeuristic.createFactory(Metadata m, SCIFIOConfig.ImgMode[] imgModes, T t)
<T> net.imglib2.img.ImgFactory<T>	DefaultImgFactoryHeuristic.createFactory(Metadata m, SCIFIOConfig.ImgMode[] imgModes, T type)
long[]	ImgUtilityService.getConstrainedLengths(Metadata m, int imageIndex, SCIFIOConfig config) Returns an N-dimensional list of axis lengths from the given Metadata, constrained by the provided SubRegion (if present)
long[]	DefaultImgUtilityService.getConstrainedLengths(Metadata m, int imageIndex, SCIFIOConfig config)
long[]	ImgUtilityService.getDimLengths(Metadata m, int imageIndex, SCIFIOConfig config) Compiles an N-dimensional list of axis lengths from the given Metadata.
long[]	DefaultImgUtilityService.getDimLengths(Metadata m, int imageIndex, SCIFIOConfig config) Compiles an N-dimensional list of axis lengths from the given reader.
void	SCIFIOImgPlus.setMetadata(Metadata meta) Sets the Metadata object for this ImgPlus.

Uses of Metadata in io.scif.services

Methods in io.scif.services with type parameters of type Metadata

Modifier and Type	Method and Description
<M extends Metadata> boolean	FormatService.addFormat(Format format) Makes the provided Format available for image IO operations in this context.
<M extends Metadata> Format	DefaultFormatService.getFormatFromMetadata(Class<M> metadataClass)
<M extends Metadata> Format	FormatService.getFormatFromMetadata(Class<M> metadataClass) Format lookup method using the Metadata component.

Methods in io.scif.services that return Metadata

Modifier and Type	Method and Description
Metadata	InitializeService.parseMetadata(org.scijava.io.location.Location id) Convenience method to parse Metadata without reading the underlying pixels.
Metadata	DefaultInitializeService.parseMetadata(org.scijava.io.location.Location id)
Metadata	InitializeService.parseMetadata(org.scijava.io.location.Location id, SCIFIOConfig config) As InitializeService.parseMetadata(Location) with a flag to open the underlying dataset when parsing, if desired.
Metadata	DefaultInitializeService.parseMetadata(org.scijava.io.location.Location id, SCIFIOConfig config)
Metadata	DatasetIOService.save(net.imagej.Dataset dataset, org.scijava.io.location.Location destination) Saves a dataset to a destination (such as a file on disk).
Metadata	DefaultDatasetIOService.save(net.imagej.Dataset dataset, org.scijava.io.location.Location destination)
Metadata	DatasetIOService.save(net.imagej.Dataset dataset, org.scijava.io.location.Location destination, SCIFIOConfig config) Saves a dataset to a destination (such as a file on disk).
Metadata	DefaultDatasetIOService.save(net.imagej.Dataset dataset, org.scijava.io.location.Location destination, SCIFIOConfig config)
Metadata	DatasetIOService.save(net.imagej.Dataset dataset, String destination) Saves a dataset to a destination (such as a file on disk).
Metadata	DefaultDatasetIOService.save(net.imagej.Dataset dataset, String destination)
Metadata	DatasetIOService.save(net.imagej.Dataset dataset, String destination, SCIFIOConfig config) Saves a dataset to a destination (such as a file on disk).
Metadata	DefaultDatasetIOService.save(net.imagej.Dataset dataset, String destination, SCIFIOConfig config)

Methods in io.scif.services with parameters of type Metadata

Modifier and Type	Method and Description
Translator	DefaultTranslatorService.findTranslator(Metadata source, Metadata dest, boolean exact)
Translator	TranslatorService.findTranslator(Metadata source, Metadata dest, boolean exact) Returns a translator capable of translating from the source Metadata to the dest Metadata type, or null if no such Translator exists.
Writer	InitializeService.initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination) See InitializeService.initializeWriter(Location, Location, SCIFIOConfig).
Writer	DefaultInitializeService.initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination)
Writer	InitializeService.initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination, SCIFIOConfig config) As InitializeService.initializeWriter(Metadata, Location) with configuration options.
Writer	DefaultInitializeService.initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination, SCIFIOConfig config)
boolean	DefaultTranslatorService.translate(Metadata source, Metadata dest, boolean exact)
boolean	TranslatorService.translate(Metadata source, Metadata dest, boolean exact) Convenience method to immediately translate from the source Metadata to the dest Metadata type, assuming an appropriate Translator is found.

Method parameters in io.scif.services with type arguments of type Metadata

Modifier and Type	Method and Description
Translator	DefaultTranslatorService.findTranslator(Class<? extends Metadata> source, Class<? extends Metadata> dest, boolean exact)
Translator	DefaultTranslatorService.findTranslator(Class<? extends Metadata> source, Class<? extends Metadata> dest, boolean exact)
Translator	TranslatorService.findTranslator(Class<? extends Metadata> source, Class<? extends Metadata> dest, boolean exact) Returns a translator capable of translating from the source Metadata to the dest Metadata type, or null if no such Translator exists.
Translator	TranslatorService.findTranslator(Class<? extends Metadata> source, Class<? extends Metadata> dest, boolean exact) Returns a translator capable of translating from the source Metadata to the dest Metadata type, or null if no such Translator exists.

Uses of Metadata in io.scif.util

Methods in io.scif.util with type parameters of type Metadata

Modifier and Type	Method and Description
static <M extends Metadata> M	SCIFIOMetadataTools.castMeta(Metadata meta) Casts the provided Metadata object to the generic type of this method.

Methods in io.scif.util that return Metadata

Modifier and Type	Method and Description
static Metadata	SCIFIOMetadataTools.unwrapMetadata(Metadata meta) Unwraps the provided Metadata class if it has been wrapped in MetadataWrapper(s).

Methods in io.scif.util with parameters of type Metadata

Modifier and Type	Method and Description
static void	FormatTools.calibrate(Metadata m, int imageIndex, double[] scale) Applies the given scale value, and an origin of 0.0, to each LinearAxis in the provided Metadata.
static void	FormatTools.calibrate(Metadata m, int imageIndex, double[] scale, double[] origin) Applies the given scale and origin values to each LinearAxis in the provided Metadata.
static <M extends Metadata> M	SCIFIOMetadataTools.castMeta(Metadata meta) Casts the provided Metadata object to the generic type of this method.
static void	FormatTools.checkBufferSize(int imageIndex, Metadata m, int len) Checks that the given buffer length is long enough to hold planes of the specified image index, using the provided Reader.
static void	FormatTools.checkBufferSize(Metadata m, int len, net.imglib2.Interval bounds, int imageIndex) Checks that the given buffer size is large enough to hold an image with the given planar lengths.
static void	FormatTools.checkPlaneForReading(Metadata m, int imageIndex, long planeIndex, int bufLength, net.imglib2.Interval bounds) As FormatTools.checkPlaneForWriting(io.scif.Metadata, int, long, int, net.imglib2.Interval) but also asserts that the Metadata has a non-null source attached.
static void	FormatTools.checkPlaneForWriting(Metadata m, int imageIndex, long planeIndex, int bufLength, net.imglib2.Interval bounds) Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given Metadata.
static void	FormatTools.checkPlaneNumber(Metadata m, int imageIndex, long planeIndex) Checks that the given plane number is valid for the given reader.
static void	FormatTools.checkTileSize(Metadata m, net.imglib2.Interval bounds, int imageIndex) Checks that the given tile size is valid for the given reader.
static long	FormatTools.getNonPlanarAxisPosition(Metadata m, int imageIndex, long planeIndex, net.imagej.axis.AxisType type) Returns the position of the specified AxisType for the given image and plane indices.
static long	FormatTools.getPlaneSize(Metadata m, int imageIndex) Returns the size in bytes of a tile defined by the given Metadata.
static long	FormatTools.getPlaneSize(Metadata m, net.imglib2.Interval bounds, int imageIndex) Returns the size in bytes of a plane with the given minima and maxima.
static long	FormatTools.getPlaneSize(Metadata m, int width, int height, int imageIndex) Returns the size in bytes of a w * h tile.
static double	FormatTools.getScale(Metadata m, int imageIndex, net.imagej.axis.AxisType axisType) Gets the average scale over the specified axis of the given image metadata.
static long[]	SCIFIOMetadataTools.modifyPlanar(int imageIndex, Metadata meta, long... values) Replaces the first values.length of the provided Metadata's planar axes with the values.
static long[]	SCIFIOMetadataTools.modifyPlanar(int imageIndex, Metadata meta, SCIFIOMetadataTools.AxisValue... axes) Iterates over the provided Metadata's planar axes, replacing any instances of axes with the paired values.
static long	FormatTools.nextPlaneIndex(int imageIndex, Metadata m, long[] pos, long[] offsets, long[] cropLengths) Computes the next plane index for a given position, using the current min and max planar values.
static long	FormatTools.positionToRaster(int imageIndex, Metadata m, long[] planeIndices) Computes a unique 1-D index corresponding to the given multidimensional position.
static long[]	FormatTools.rasterToPosition(int imageIndex, long planeIndex, Metadata m) Computes a unique N-D position corresponding to the given rasterized index value.
static long[]	FormatTools.rasterToPosition(int imageIndex, long planeIndex, Metadata m, List<net.imagej.axis.CalibratedAxis> expectedAxis) Computes a unique N-D position corresponding to the given rasterized index value.
static Metadata	SCIFIOMetadataTools.unwrapMetadata(Metadata meta) Unwraps the provided Metadata class if it has been wrapped in MetadataWrapper(s).
static void	SCIFIOMetadataTools.verifyMinimumPopulated(Metadata src, org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out) Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
static void	SCIFIOMetadataTools.verifyMinimumPopulated(Metadata src, org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex) Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.
static void	SCIFIOMetadataTools.verifyMinimumPopulated(Metadata src, org.scijava.io.location.Location loc)
static void	SCIFIOMetadataTools.verifyMinimumPopulated(Metadata src, org.scijava.io.location.Location loc, int imageIndex)
static boolean	SCIFIOMetadataTools.wholePlane(int imageIndex, Metadata meta, net.imglib2.Interval bounds) Returns true if the provided axes correspond to a complete image plane
static boolean	SCIFIOMetadataTools.wholeRow(int imageIndex, Metadata meta, net.imglib2.Interval bounds) Returns true if the provided axes correspond to a complete image row