Uses of Class
io.scif.config.SCIFIOConfig

Packages that use SCIFIOConfig

Package	Description
io.scif	Provides the interfaces and default implementations for the components of SCIFIO, and the context for instantiating these components.
io.scif.config	This package provides configuration options for all SCIFIO 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.img.converters	Provides a PlaneConverterService for populating ImgPlus objects using Reader output.
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 SCIFIOConfig in io.scif

Methods in io.scif with parameters of type SCIFIOConfig

Modifier and Type	Method and Description
protected void	AbstractWriter.checkLocation(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, SCIFIOConfig config) Validate that the given output is consistent with the given configuration.
boolean	AbstractChecker.isFormat(org.scijava.io.location.Location loc, SCIFIOConfig config)
boolean	Checker.isFormat(org.scijava.io.location.Location loc, SCIFIOConfig config) Checks if the provided image source is compatible with this Format.
ByteArrayPlane	DefaultReader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config) Non-functional openPlane implementation.
P	TypedReader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	Reader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config) As Reader.openPlane(int, long, Interval) with configuration options.
P	AbstractReader.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
P	TypedReader.openPlane(int imageIndex, long planeIndex, P plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	Reader.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config) Allows a single Plane object to be reused by reference when opening sub-regions of planes.
Plane	AbstractReader.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	Reader.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config) Allows a single Plane object to be reused by reference when opening complete planes.
Plane	AbstractReader.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
P	TypedReader.openPlane(int imageIndex, long planeIndex, P plane, SCIFIOConfig config)
P	AbstractReader.openPlane(int imageIndex, long planeIndex, P plane, SCIFIOConfig config)
P	TypedReader.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	Reader.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config) As Reader.openPlane(int, long) with configuration options.
P	AbstractReader.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
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)
M	TypedParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, M meta, SCIFIOConfig config) Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta, SCIFIOConfig config)
Metadata	Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config) As Parser.parse(DataHandle) with configuration options.
M	TypedParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config)
M	AbstractParser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, SCIFIOConfig config)
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)
M	TypedParser.parse(org.scijava.io.location.Location fileName, M meta, SCIFIOConfig config) Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(Location, Metadata).
M	AbstractParser.parse(org.scijava.io.location.Location loc, M meta, SCIFIOConfig config)
Metadata	Parser.parse(org.scijava.io.location.Location fileName, SCIFIOConfig config) As Parser.parse(Location) with configuration options.
M	TypedParser.parse(org.scijava.io.location.Location loc, SCIFIOConfig config)
M	AbstractParser.parse(org.scijava.io.location.Location loc, SCIFIOConfig config)
void	AbstractWriter.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config)
void	Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, int imageIndex, SCIFIOConfig config) As Writer.setDest(DataHandle, int), with specification for new configuration options.
void	AbstractWriter.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, SCIFIOConfig config)
void	Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config) As Writer.setDest(DataHandle), with specification for new configuration options.
void	AbstractWriter.setDest(org.scijava.io.location.Location loc, int imageIndex, SCIFIOConfig config)
void	Writer.setDest(org.scijava.io.location.Location location, int imageIndex, SCIFIOConfig config) As Writer.setDest(Location, int) with specification for new configuration options.
void	AbstractWriter.setDest(org.scijava.io.location.Location loc, SCIFIOConfig config)
void	Writer.setDest(org.scijava.io.location.Location location, SCIFIOConfig config) As Writer.setDest(Location) with specification for new configuration options.
void	Reader.setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config) As Reader.setSource(DataHandle) with configuration options.
void	AbstractReader.setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config)
void	Reader.setSource(org.scijava.io.location.Location loc, SCIFIOConfig config) As Reader.setSource(Location) with configuration options.
void	AbstractReader.setSource(org.scijava.io.location.Location loc, SCIFIOConfig config)
protected void	DefaultParser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, DefaultMetadata meta, SCIFIOConfig config)
protected abstract void	AbstractParser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta, SCIFIOConfig config) A helper method, called by AbstractParser.parse(DataHandle, TypedMetadata).

Uses of SCIFIOConfig in io.scif.config

Methods in io.scif.config that return SCIFIOConfig

Modifier and Type	Method and Description
SCIFIOConfig	SCIFIOConfig.checkerSetOpen(boolean open)
SCIFIOConfig	SCIFIOConfig.clone()
SCIFIOConfig	SCIFIOConfig.enableBufferedReading(boolean enabled)
SCIFIOConfig	SCIFIOConfig.groupableSetGroupFiles(boolean groupFiles)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetComputeMinMax(boolean computeMinMax)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetImgFactoryHeuristic(ImgFactoryHeuristic imgFactoryHeuristic)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetImgModes(SCIFIOConfig.ImgMode... imgModes)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetIndex(int index)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetOpenAllImages(boolean openAll)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetPlaneConverter(PlaneConverter planeConverter)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetRange(Range range)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetRange(String range)
SCIFIOConfig	SCIFIOConfig.imgOpenerSetRegion(ImageRegion region)
SCIFIOConfig	SCIFIOConfig.imgSaverSetWriteRGB(boolean rgb)
SCIFIOConfig	SCIFIOConfig.parserSetFiltered(boolean filterMetadata)
SCIFIOConfig	SCIFIOConfig.parserSetLevel(MetadataLevel level)
SCIFIOConfig	SCIFIOConfig.parserSetSaveOriginalMetadata(boolean saveOriginalMetadata)
SCIFIOConfig	SCIFIOConfig.writerSetCodecOptions(CodecOptions options)
SCIFIOConfig	SCIFIOConfig.writerSetColorModel(ColorModel cm)
SCIFIOConfig	SCIFIOConfig.writerSetCompression(CompressionType compressType)
SCIFIOConfig	SCIFIOConfig.writerSetCompression(String compress)
SCIFIOConfig	SCIFIOConfig.writerSetFailIfOverwriting(boolean failIfOverwriting) Warning: "overwriting" behavior is format-specific and not guaranteed to result in a valid image.
SCIFIOConfig	SCIFIOConfig.writerSetFramesPerSecond(int rate)
SCIFIOConfig	SCIFIOConfig.writerSetSequential(boolean sequential) Sets whether or not we know that planes will be written sequentially.

Constructors in io.scif.config with parameters of type SCIFIOConfig

Constructor and Description
SCIFIOConfig(SCIFIOConfig config) Copying constructor.

Uses of SCIFIOConfig in io.scif.filters

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

Modifier and Type	Method and Description
Plane	FileStitcher.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	FileStitcher.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config)
Plane	ChannelFiller.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	PlaneSeparator.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	MinMaxFilter.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	DimensionSwapper.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
Plane	AbstractReaderFilter.openPlane(int imageIndex, long planeIndex, SCIFIOConfig config)
void	FileStitcher.setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config)
void	AbstractReaderFilter.setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config)
void	FileStitcher.setSource(org.scijava.io.location.Location source, SCIFIOConfig config)
void	AbstractReaderFilter.setSource(org.scijava.io.location.Location loc, SCIFIOConfig config)
protected void	FileStitcher.setSourceHelper(org.scijava.io.location.Location source, SCIFIOConfig config)
protected void	ChannelFiller.setSourceHelper(org.scijava.io.location.Location source, SCIFIOConfig config)
protected void	DimensionSwapper.setSourceHelper(org.scijava.io.location.Location source, SCIFIOConfig config)
protected void	AbstractReaderFilter.setSourceHelper(org.scijava.io.location.Location source, SCIFIOConfig config) Allows code to be executed regardless of which AbstractReaderFilter.setSource(org.scijava.io.location.Location) signature is called.

Uses of SCIFIOConfig in io.scif.formats

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

Modifier and Type	Method and Description
protected void	TIFFFormat.Parser.initMetadata(TIFFFormat.Metadata meta, SCIFIOConfig config)
protected void	TIFFFormat.BaseTIFFParser.initMetadata(TIFFFormat.Metadata meta, SCIFIOConfig config) Populates the metadata hashtable and metadata store.
boolean	NRRDFormat.Checker.isFormat(org.scijava.io.location.Location loc, SCIFIOConfig config)
boolean	MicromanagerFormat.Checker.isFormat(org.scijava.io.location.Location location, SCIFIOConfig config)
boolean	DICOMFormat.Checker.isFormat(org.scijava.io.location.Location location, SCIFIOConfig config)
boolean	JPEGFormat.Checker.isFormat(org.scijava.io.location.Location name, SCIFIOConfig config)
boolean	TestImgFormat.Checker.isFormat(org.scijava.io.location.Location loc, SCIFIOConfig config)
BufferedImagePlane	ImageIOFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
BufferedImagePlane	MNGFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
BufferedImagePlane	TIFFJAIFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
BufferedImagePlane	APNGFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	NRRDFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	FITSFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	MinimalTIFFFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	PGMFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	JPEGTileFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	JPEG2000Format.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	BMPFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	KontronFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	PCXFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	EPSFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	MicromanagerFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	GIFFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	ScancoISQFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	StratecPQCTFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	DICOMFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	AVIFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	ICSFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	TestImgFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
NRRDFormat.Metadata	NRRDFormat.Parser.parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, NRRDFormat.Metadata meta, SCIFIOConfig config)
void	APNGFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config)
void	TIFFFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> dest, int imageIndex, SCIFIOConfig config)
void	AVIFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config)
void	ICSFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config)
void	ICSFormat.Reader.setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, SCIFIOConfig config)
protected void	APNGFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, APNGFormat.Metadata meta, SCIFIOConfig config)
protected void	AVIFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, AVIFormat.Metadata meta, SCIFIOConfig config)
protected void	BMPFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, BMPFormat.Metadata meta, SCIFIOConfig config)
protected void	DICOMFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, DICOMFormat.Metadata meta, SCIFIOConfig config)
protected void	EPSFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, EPSFormat.Metadata meta, SCIFIOConfig config)
protected void	FITSFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, FITSFormat.Metadata meta, SCIFIOConfig config)
protected void	GIFFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, GIFFormat.Metadata meta, SCIFIOConfig config)
protected void	ICSFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, ICSFormat.Metadata meta, SCIFIOConfig config)
protected void	JPEG2000Format.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, JPEG2000Format.Metadata meta, SCIFIOConfig config)
void	JPEGFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, JPEGFormat.Metadata meta, SCIFIOConfig config)
protected void	JPEGTileFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, JPEGTileFormat.Metadata meta, SCIFIOConfig config)
void	KontronFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, KontronFormat.Metadata meta, SCIFIOConfig config)
protected void	MicromanagerFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, MicromanagerFormat.Metadata meta, SCIFIOConfig config)
protected void	MNGFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, MNGFormat.Metadata meta, SCIFIOConfig config)
protected void	MinimalTIFFFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, M meta, SCIFIOConfig config)
protected void	ImageIOFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta, SCIFIOConfig config)
protected void	NRRDFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, NRRDFormat.Metadata meta, SCIFIOConfig config)
protected void	PCXFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, PCXFormat.Metadata meta, SCIFIOConfig config)
protected void	PGMFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, PGMFormat.Metadata meta, SCIFIOConfig config)
protected void	ScancoISQFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, ScancoISQFormat.Metadata meta, SCIFIOConfig config)
void	StratecPQCTFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, StratecPQCTFormat.Metadata meta, SCIFIOConfig config)
protected void	TestImgFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, TestImgFormat.Metadata meta, SCIFIOConfig config)
protected void	TIFFFormat.BaseTIFFParser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, TIFFFormat.Metadata meta, SCIFIOConfig config)
protected void	TIFFJAIFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, TIFFJAIFormat.Metadata meta, SCIFIOConfig config)

Uses of SCIFIOConfig in io.scif.formats.qt

Methods in io.scif.formats.qt with parameters of type SCIFIOConfig

Modifier and Type	Method and Description
BufferedImagePlane	LegacyQTFormat.Reader.openPlane(int imageIndex, long planeIndex, BufferedImagePlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	PICTFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
ByteArrayPlane	NativeQTFormat.Reader.openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
void	NativeQTFormat.Writer.setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, int imageIndex, SCIFIOConfig config)
protected void	LegacyQTFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, LegacyQTFormat.Metadata meta, SCIFIOConfig config)
protected void	NativeQTFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, NativeQTFormat.Metadata meta, SCIFIOConfig config)
protected void	PICTFormat.Parser.typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, PICTFormat.Metadata meta, SCIFIOConfig config)

Uses of SCIFIOConfig in io.scif.img

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

Modifier and Type	Method and Description
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.
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.open(org.scijava.io.location.Location source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)
static SCIFIOImgPlus<?>	IO.open(org.scijava.io.location.Location source, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.open(org.scijava.io.location.Location source, T type, SCIFIOConfig config)
static SCIFIOImgPlus<?>	IO.open(Reader reader, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T>> SCIFIOImgPlus<T>	IO.open(Reader reader, T type, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.open(Reader reader, T type, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.open(String source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)
static SCIFIOImgPlus<?>	IO.open(String source, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.open(String source, T type, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openAll(org.scijava.io.location.Location source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)
static List<SCIFIOImgPlus<?>>	IO.openAll(org.scijava.io.location.Location source, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openAll(org.scijava.io.location.Location source, T type, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T>> List<SCIFIOImgPlus<T>>	IO.openAll(Reader reader, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)
static List<SCIFIOImgPlus<?>>	IO.openAll(Reader reader, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T>> List<SCIFIOImgPlus<T>>	IO.openAll(Reader reader, T type, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openAll(Reader reader, T type, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openAll(String source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)
static List<SCIFIOImgPlus<?>>	IO.openAll(String source, SCIFIOConfig config)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openAll(String source, T type, SCIFIOConfig config)
SCIFIOImgPlus<?>	ImgOpener.openImg(Reader reader, SCIFIOConfig config) Deprecated. Use ImgOpener.openImgs(Reader, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T>> SCIFIOImgPlus<T>	ImgOpener.openImg(Reader reader, T type, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Deprecated. Use ImgOpener.openImgs(Reader, Object, SCIFIOConfig) or ImgOpener.openImgs(Reader, ImgFactory, SCIFIOConfig).
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.openImg(Reader reader, T type, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Deprecated. Use IO.open(Reader, RealType, ImgFactory, SCIFIOConfig).
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.openImg(Reader reader, T type, SCIFIOConfig config) Deprecated. Use IO.open(Reader, RealType, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	ImgOpener.openImg(Reader reader, T type, SCIFIOConfig config) Deprecated. Use ImgOpener.openImgs(Reader, Object, SCIFIOConfig).
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.openImg(String source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Deprecated. Use IO.open(String, ImgFactory, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	ImgOpener.openImg(String source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Deprecated. Use ImgOpener.openImgs(String, ImgFactory, SCIFIOConfig).
static SCIFIOImgPlus<?>	IO.openImg(String source, SCIFIOConfig config) Deprecated. Use IO.open(String, SCIFIOConfig).
SCIFIOImgPlus<?>	ImgOpener.openImg(String source, SCIFIOConfig config) Deprecated. Use ImgOpener.openImgs(String, SCIFIOConfig).
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	IO.openImg(String source, T type, SCIFIOConfig config) Deprecated. Use IO.open(String, RealType, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	ImgOpener.openImg(String source, T type, SCIFIOConfig config) Deprecated. Use ImgOpener.openImgs(String, RealType, SCIFIOConfig).
<T> List<SCIFIOImgPlus<T>>	ImgOpener.openImgs(org.scijava.io.location.Location source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Reads in images from the given source.
List<SCIFIOImgPlus<?>>	ImgOpener.openImgs(org.scijava.io.location.Location source, SCIFIOConfig config) Reads in images from the given source.
<T> List<SCIFIOImgPlus<T>>	ImgOpener.openImgs(org.scijava.io.location.Location source, T type, SCIFIOConfig config) Reads in images from the given source.
<T> List<SCIFIOImgPlus<T>>	ImgOpener.openImgs(Reader reader, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Reads in images using the given Reader.
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openImgs(Reader reader, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Deprecated. Use IO.openAll(Reader, ImgFactory, SCIFIOConfig).
List<SCIFIOImgPlus<?>>	ImgOpener.openImgs(Reader reader, SCIFIOConfig config) Reads in images using the given Reader.
<T extends net.imglib2.type.numeric.RealType<T>> List<SCIFIOImgPlus<T>>	ImgOpener.openImgs(Reader reader, T type, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Deprecated. Use ImgOpener.openImgs(Reader, ImgFactory, SCIFIOConfig).
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openImgs(Reader reader, T type, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Deprecated. Use IO.openAll(Reader, RealType, ImgFactory, SCIFIOConfig).
<T> List<SCIFIOImgPlus<T>>	ImgOpener.openImgs(Reader reader, T type, SCIFIOConfig config) Reads in images using the given Reader.
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openImgs(Reader reader, T type, SCIFIOConfig config) Deprecated. Use IO.openAll(Reader, RealType, SCIFIOConfig).
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openImgs(String source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Deprecated. Use IO.openAll(String, ImgFactory, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	ImgOpener.openImgs(String source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config) Reads in images from the given source.
static List<SCIFIOImgPlus<?>>	IO.openImgs(String source, SCIFIOConfig config) Deprecated. Use IO.openAll(String, SCIFIOConfig).
List<SCIFIOImgPlus<?>>	ImgOpener.openImgs(String source, SCIFIOConfig config) Reads in images from the given source.
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	IO.openImgs(String source, T type, SCIFIOConfig config) Deprecated. Use IO.openAll(String, RealType, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	ImgOpener.openImgs(String source, T type, SCIFIOConfig config) Reads in images from the given source.
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, SCIFIOConfig config) As ImgSaver.saveImg(Location, SCIFIOImgPlus, int) with configuration options.
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, SCIFIOConfig config) As ImgSaver.saveImg(Location, SCIFIOImgPlus, int) with configuration options.
void	ImgSaver.saveImg(Writer w, net.imglib2.img.Img<?> img, SCIFIOConfig config) As ImgSaver.saveImg(Writer, Img), with configuration options.
void	ImgSaver.saveImg(Writer w, SCIFIOImgPlus<?> img, int imageIndex, SCIFIOConfig config) As ImgSaver.saveImg(Writer, SCIFIOImgPlus, int), with configuration options.

Uses of SCIFIOConfig in io.scif.img.converters

Methods in io.scif.img.converters with parameters of type SCIFIOConfig

Modifier and Type	Method and Description
<T extends net.imglib2.type.numeric.RealType<T>> void	RandomAccessConverter.populatePlane(Reader reader, int imageIndex, int planeIndex, byte[] plane, net.imagej.ImgPlus<T> img, SCIFIOConfig config) Uses a cursor to populate the plane.
<T extends net.imglib2.type.numeric.RealType<T>> void	ArrayDataAccessConverter.populatePlane(Reader reader, int imageIndex, int planeIndex, byte[] source, net.imagej.ImgPlus<T> dest, SCIFIOConfig config)
<T extends net.imglib2.type.numeric.RealType<T>> void	PlaneConverter.populatePlane(Reader reader, int imageIndex, int planeIndex, byte[] source, net.imagej.ImgPlus<T> dest, SCIFIOConfig config)
<T extends net.imglib2.type.numeric.RealType<T>> void	PlanarAccessConverter.populatePlane(Reader reader, int imageIndex, int planeIndex, byte[] plane, net.imagej.ImgPlus<T> planarImg, SCIFIOConfig config) Populates plane by reference using PlanarAccess interface.

Uses of SCIFIOConfig in io.scif.services

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

Modifier and Type	Method and Description
Format	DefaultFormatService.getFormat(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config)
Format	FormatService.getFormat(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config) As FormatService.getFormat(Location, SCIFIOConfig) but takes an initialized DataHandle.
Format	DefaultFormatService.getFormat(org.scijava.io.location.Location id, SCIFIOConfig config)
Format	FormatService.getFormat(org.scijava.io.location.Location id, SCIFIOConfig config) Returns the first Format known to be compatible with the source provided.
List<Format>	DefaultFormatService.getFormatList(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config, boolean greedy)
List<Format>	FormatService.getFormatList(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config, boolean greedy) As FormatService.getFormatList(Location, SCIFIOConfig, boolean) but takes an initialized DataHandle.
List<Format>	DefaultFormatService.getFormatList(org.scijava.io.location.Location id, SCIFIOConfig config, boolean greedy)
List<Format>	FormatService.getFormatList(org.scijava.io.location.Location id, SCIFIOConfig config, boolean greedy) Returns a list of all formats that are compatible with the source provided, ordered by their priority.
ReaderFilter	InitializeService.initializeReader(org.scijava.io.location.Location id, SCIFIOConfig config) Convenience method for creating a Reader component that is ready to open planes of the provided image source.
ReaderFilter	DefaultInitializeService.initializeReader(org.scijava.io.location.Location id, SCIFIOConfig config)
Writer	InitializeService.initializeWriter(org.scijava.io.location.Location source, org.scijava.io.location.Location destination, SCIFIOConfig config) As InitializeService.initializeWriter(Location, Location) with configuration options.
Writer	DefaultInitializeService.initializeWriter(org.scijava.io.location.Location source, org.scijava.io.location.Location destination, SCIFIOConfig config)
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)
net.imagej.Dataset	DatasetIOService.open(org.scijava.io.location.Location source, SCIFIOConfig config) As DatasetIOService.open(Location), with the given io.scif.config.SCIFIOConfig.
net.imagej.Dataset	DefaultDatasetIOService.open(org.scijava.io.location.Location source, SCIFIOConfig config)
net.imagej.Dataset	DatasetIOService.open(String source, SCIFIOConfig config) Loads a dataset from a source (such as a file on disk).
net.imagej.Dataset	DefaultDatasetIOService.open(String source, SCIFIOConfig config)
List<net.imagej.Dataset>	DatasetIOService.openAll(org.scijava.io.location.Location source, SCIFIOConfig config) As DatasetIOService.openAll(Location), with a given io.scif.config.SCIFIOConfig.
List<net.imagej.Dataset>	DefaultDatasetIOService.openAll(org.scijava.io.location.Location source, SCIFIOConfig config)
List<net.imagej.Dataset>	DatasetIOService.openAll(String source, SCIFIOConfig config)
List<net.imagej.Dataset>	DefaultDatasetIOService.openAll(String source, SCIFIOConfig config)
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, 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, 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)

Uses of SCIFIOConfig in io.scif.util

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

Modifier and Type	Method and Description
static void	FormatTools.convert(Reader input, Writer output, String outputFile, SCIFIOConfig config) As FormatTools.convert(Reader, Writer, String), with configuration options.