Uses of Interface
io.scif.Reader

Packages that use Reader

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.gui	Provides classes for working with BufferedImage in SCIFIO.
io.scif.img	Provides SCIFIO-based classes for working with ImgPlus from the imglib2 library.
io.scif.img.cell	Provides a Reader backed CachedCellImg implementation and supporting classes.
io.scif.img.cell.loaders	Provides implementations of SCIFIOArrayLoader for each basic ArrayDataAccess type.
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 Reader in io.scif

Subinterfaces of Reader in io.scif

Modifier and Type	Interface and Description
interface	TypedReader<M extends TypedMetadata,P extends DataPlane<?>> Interface for all Reader implementations that use generic parameters.

Classes in io.scif that implement Reader

Modifier and Type	Class and Description
class	AbstractReader<M extends TypedMetadata,P extends DataPlane<?>> Abstract superclass of all SCIFIO Reader implementations.
class	ByteArrayReader<M extends TypedMetadata> Abstract superclass for all Reader implementations that return a ByteArrayPlane when reading datasets.
class	DefaultReader Non-functional default Reader implementation.

Methods in io.scif that return Reader

Modifier and Type	Method and Description
Reader	Format.createReader() Creates an instance of the Reader associated with this format.
Reader	AbstractFormat.createReader()

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

Modifier and Type	Method and Description
Class<? extends Reader>	AbstractFormat.getReaderClass()

Uses of Reader in io.scif.filters

Classes in io.scif.filters that implement Reader

Modifier and Type	Class and Description
class	AbstractReaderFilter Abstract superclass for all Filter that delegate to Reader instances.
class	ChannelFiller For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
class	DimensionSwapper Handles swapping the dimension order of an image series.
class	FileStitcher Logic to stitch together files with similar names.
class	MinMaxFilter Logic to compute minimum and maximum values for each plane.
class	PlaneSeparator Logic to automatically separate the channels in a file.
class	ReaderFilter MasterFilter for wrapping Reader components.

Methods in io.scif.filters that return Reader

Modifier and Type	Method and Description
Reader	ReaderFilter.getParent()
Reader	ReaderFilter.getTail()

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

Constructor and Description
ReaderFilter(Reader r)

Uses of Reader in io.scif.formats

Classes in io.scif.formats that implement Reader

Modifier and Type	Class and Description
static class	APNGFormat.Reader File format SCIFIO Reader for Animated Portable Network Graphics (APNG) images.
static class	AVIFormat.Reader
static class	BMPFormat.Reader
static class	DICOMFormat.Reader
static class	EPSFormat.Reader
static class	FITSFormat.Reader
static class	GIFFormat.Reader
static class	ICSFormat.Reader File format SCIFIO Reader for Image Cytometry Standard (ICS) images.
static class	ImageIOFormat.Reader<M extends ImageIOFormat.Metadata>
static class	JPEG2000Format.Reader
static class	JPEGFormat.Reader
static class	JPEGTileFormat.Reader
static class	KontronFormat.Reader
static class	MicromanagerFormat.Reader
static class	MinimalTIFFFormat.Reader<M extends MinimalTIFFFormat.Metadata>
static class	MNGFormat.Reader
static class	NRRDFormat.Reader
static class	PCXFormat.Reader
static class	PGMFormat.Reader
static class	ScancoISQFormat.Reader
static class	StratecPQCTFormat.Reader
static class	TestImgFormat.Reader Reader for the Fake file format.
static class	TIFFFormat.Reader<M extends TIFFFormat.Metadata> TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.
static class	TIFFJAIFormat.Reader

Methods in io.scif.formats that return Reader

Modifier and Type	Method and Description
Reader	NRRDFormat.Metadata.getHelper()

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

Modifier and Type	Method and Description
void	NRRDFormat.Metadata.setHelper(Reader reader)

Uses of Reader in io.scif.formats.qt

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

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

Uses of Reader in io.scif.gui

Classes in io.scif.gui that implement Reader

Modifier and Type	Class and Description
class	BufferedImageReader<M extends TypedMetadata> BufferedImageReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.

Methods in io.scif.gui with parameters of type Reader

Modifier and Type	Method and Description
protected void	ImageViewer.open(String id, Reader r) Opens from the given data source using the specified reader in a separate thread.
static BufferedImage	AWTImageTools.openImage(Plane plane, byte[] bytes, Reader r, long[] axes, int imageIndex) Creates an image from the given Plane.
static BufferedImage	AWTImageTools.openImage(Plane plane, Reader r, int imageIndex) Creates an image from the given Plane.
static BufferedImage	AWTImageTools.openImage(Plane plane, Reader r, long[] axes, int imageIndex) Creates an image from the given Plane.
static BufferedImage	AWTImageTools.openThumbImage(Plane plane, Reader r, int imageIndex, long[] axes, int thumbSizeX, int thumbSizeY, boolean pad) Creates a thumbnail image from the provided plane, scaling it to the specified thumbnail dimensions.
void	ImageViewer.setImages(Reader reader, BufferedImage[] img) Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.

Uses of Reader in io.scif.img

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

Modifier and Type	Method and Description
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>> 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)
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).
List<SCIFIOImgPlus<?>>	ImgOpener.openImgs(Reader reader) Reads in images using the given Reader.
<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).

Uses of Reader in io.scif.img.cell

Methods in io.scif.img.cell that return Reader

Modifier and Type	Method and Description
Reader	SCIFIOCellImg.reader()
Reader	SCIFIOCellImgFactory.reader()

Methods in io.scif.img.cell with parameters of type Reader

Modifier and Type	Method and Description
void	SCIFIOCellImgFactory.setReader(Reader r, int imageIndex)

Uses of Reader in io.scif.img.cell.loaders

Methods in io.scif.img.cell.loaders that return Reader

Modifier and Type	Method and Description
protected Reader	AbstractArrayLoader.reader()

Constructors in io.scif.img.cell.loaders with parameters of type Reader

Constructor and Description
AbstractArrayLoader(Reader reader, ImageRegion subRegion)
ByteAccessLoader(Reader reader, ImageRegion subRegion, IntFunction<net.imglib2.img.basictypeaccess.ByteAccess> accessFactory)
ByteArrayLoader(Reader reader, ImageRegion subRegion)
CharAccessLoader(Reader reader, ImageRegion subRegion, IntFunction<net.imglib2.img.basictypeaccess.CharAccess> accessFactory)
CharArrayLoader(Reader reader, ImageRegion subRegion)
DoubleAccessLoader(Reader reader, ImageRegion subRegion, IntFunction<net.imglib2.img.basictypeaccess.DoubleAccess> accessFactory)
DoubleArrayLoader(Reader reader, ImageRegion subRegion)
FloatAccessLoader(Reader reader, ImageRegion subRegion, IntFunction<net.imglib2.img.basictypeaccess.FloatAccess> accessFactory)
FloatArrayLoader(Reader reader, ImageRegion subRegion)
IntAccessLoader(Reader reader, ImageRegion subRegion, IntFunction<net.imglib2.img.basictypeaccess.IntAccess> accessFactory)
IntArrayLoader(Reader reader, ImageRegion subRegion)
LongAccessLoader(Reader reader, ImageRegion subRegion, IntFunction<net.imglib2.img.basictypeaccess.LongAccess> accessFactory)
LongArrayLoader(Reader reader, ImageRegion subRegion)
ShortAccessLoader(Reader reader, ImageRegion subRegion, IntFunction<net.imglib2.img.basictypeaccess.ShortAccess> accessFactory)
ShortArrayLoader(Reader reader, ImageRegion subRegion)

Uses of Reader in io.scif.img.converters

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

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 Reader in io.scif.services

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

Modifier and Type	Method and Description
<R extends Reader> Format	DefaultFormatService.getFormatFromReader(Class<R> readerClass)
<R extends Reader> Format	FormatService.getFormatFromReader(Class<R> readerClass) Format lookup method using the Reader component

Uses of Reader in io.scif.util

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

Modifier and Type	Method and Description
static void	FormatTools.convert(Reader input, Writer output, String outputFile) Convenience method for writing all of the images and metadata obtained from the specified Reader into the specified Writer.
static void	FormatTools.convert(Reader input, Writer output, String outputFile, SCIFIOConfig config) As FormatTools.convert(Reader, Writer, String), with configuration options.
static String	FormatTools.getFilename(int imageIndex, int image, Reader r, String pattern)
static String[]	FormatTools.getFilenames(String pattern, Reader r)
static int	FormatTools.getImagesPerFile(String pattern, Reader r)
static long	FormatTools.getPlaneSize(Reader r, int imageIndex) Returns the size in bytes of a single plane read by the given Reader.
static long	FormatTools.nextPlaneIndex(int imageIndex, Reader r, 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, Reader reader, long[] planeIndices) Computes a unique 1-D index corresponding to the given multidimensional position.
static long[]	FormatTools.rasterToPosition(int imageIndex, long planeIndex, Reader reader) Computes a unique N-D position corresponding to the given rasterized index value.