Uses of Interface
io.scif.SCIFIOPlugin

Packages that use SCIFIOPlugin

Package	Description
io.scif	Provides the interfaces and default implementations for the components of SCIFIO, and the context for instantiating these components.
io.scif.codec	Codecs for encoding and decoding streams of bytes.
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.converters	Provides a PlaneConverterService for populating ImgPlus objects using Reader output.
io.scif.refs	Provides reference management utilities.

Uses of SCIFIOPlugin in io.scif

Subinterfaces of SCIFIOPlugin in io.scif

Modifier and Type	Interface and Description
interface	Checker Interface for all SCIFIO Checker components.
interface	Format Interface for all SCIFIO formats.
interface	HasFormat Super-interface for SCIFIO components that relate back to a Format.
interface	Metadata Interface for all SCIFIO Metadata objects.
interface	Parser Interface for all SCIFIO Parsers.
interface	Reader Interface for all SCIFIO Readers.
interface	Translator Interface for all SCIFIO Translators.
interface	TypedMetadata Sub-interface for Metadata to facilitate generic parameterization of SCIFIO components.
interface	TypedParser<M extends TypedMetadata> Interface for all Parser implementations that use generic parameters.
interface	TypedReader<M extends TypedMetadata,P extends DataPlane<?>> Interface for all Reader implementations that use generic parameters.
interface	TypedWriter<M extends TypedMetadata> Interface for all Writer implementations that use generic parameters.
interface	Writer Interface for all SCIFIO writers.

Classes in io.scif that implement SCIFIOPlugin

Modifier and Type	Class and Description
class	AbstractChecker Abstract superclass of all SCIFIO Checker implementations.
class	AbstractFormat Abstract superclass of all SCIFIO Format implementations.
class	AbstractGroupable Abstract super-class for all Groupable components.
class	AbstractHasFormat Abstract superclass for all classes that implement HasFormat.
class	AbstractHasSource Abstract implementation of the HasSource interface.
class	AbstractMetadata Abstract superclass of all SCIFIO Metadata implementations.
class	AbstractParser<M extends TypedMetadata> Abstract superclass of all SCIFIO Parser implementations.
class	AbstractReader<M extends TypedMetadata,P extends DataPlane<?>> Abstract superclass of all SCIFIO Reader implementations.
class	AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
class	AbstractTranslator<M extends Metadata,N extends Metadata> Abstract superclass of all SCIFIO Translator components.
class	AbstractWriter<M extends TypedMetadata> Abstract superclass of all SCIFIO Writer implementations.
class	ByteArrayReader<M extends TypedMetadata> Abstract superclass for all Reader implementations that return a ByteArrayPlane when reading datasets.
class	DefaultChecker Default Checker implementation.
class	DefaultMetadata A dummy Metadata implementation.
class	DefaultParser Default Parser implementation.
class	DefaultReader Non-functional default Reader implementation.
class	DefaultTranslator Basic Translator implementation.
class	DefaultWriter Non-functional default Writer implementation.

Uses of SCIFIOPlugin in io.scif.codec

Subinterfaces of SCIFIOPlugin in io.scif.codec

Modifier and Type	Interface and Description
interface	Codec This class is an interface for any kind of compression or decompression.

Classes in io.scif.codec that implement SCIFIOPlugin

Modifier and Type	Class and Description
class	AbstractCodec BaseCodec contains default implementation and testing for classes implementing the Codec interface, and acts as a base class for any of the compression classes.
class	Base64Codec Implements encoding (compress) and decoding (decompress) methods for Base64.
class	HuffmanCodec This class implements Huffman decoding.
class	JPEG2000Codec This class implements JPEG 2000 compression and decompression.
class	JPEGCodec This class implements JPEG compression and decompression.
class	LosslessJPEGCodec Decompresses lossless JPEG images.
class	LuraWaveCodec This class provides LuraWave decompression, using LuraWave's Java decoding library.
class	LZWCodec This is an optimized LZW codec for use with TIFF files.
class	MJPBCodec Methods for compressing and decompressing QuickTime Motion JPEG-B data.
class	MSRLECodec Methods for compressing and decompressing data using Microsoft RLE.
class	MSVideoCodec Methods for compressing and decompressing data using Microsoft Video 1.
class	NikonCodec This class implements Nikon decompression.
class	PackbitsCodec This class implements packbits decompression.
class	PassthroughCodec A codec which just returns the exact data it was given, performing no compression or decompression.
class	QTRLECodec Methods for compressing and decompressing data using QuickTime RLE.
class	RPZACodec Implements encoding and decoding methods for Apple RPZA.
class	ZlibCodec This class implements ZLIB decompression.

Uses of SCIFIOPlugin in io.scif.filters

Subinterfaces of SCIFIOPlugin in io.scif.filters

Modifier and Type	Interface and Description
interface	Filter Interface for modifying object behavior.
interface	MasterFilter<T extends org.scijava.Contextual> An entry point for toggling and configuring Filters.
interface	MetadataWrapper Wrapper for Metadata.

Classes in io.scif.filters that implement SCIFIOPlugin

Modifier and Type	Class and Description
class	AbstractFilter<T> Abstract superclass for Filter implementations.
class	AbstractMetadataWrapper Abstract superclass for concrete implementations of MetadataWrapper.
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	ChannelFillerMetadata MetadataWrapper implementation specifically for use with the ChannelFiller.
class	DimensionSwapper Handles swapping the dimension order of an image series.
class	DimensionSwapperMetadata MetadataWrapper implementation specifically for use with the DimensionSwapper.
class	FileStitcher Logic to stitch together files with similar names.
class	FileStitcherMetadata
class	MasterFilterHelper<T extends org.scijava.Contextual> Helper class for MasterFilter implementations.
class	MinMaxFilter Logic to compute minimum and maximum values for each plane.
class	PlaneSeparator Logic to automatically separate the channels in a file.
class	PlaneSeparatorMetadata MetadataWrapper implementation specifically for use with the PlaneSeparator.
class	ReaderFilter MasterFilter for wrapping Reader components.

Uses of SCIFIOPlugin in io.scif.formats

Classes in io.scif.formats that implement SCIFIOPlugin

Modifier and Type	Class and Description
class	APNGFormat SCIFIO Format supporting the PNG and APNG image formats.
static class	APNGFormat.APNGTranslator This class can be used for translating any io.scif.Metadata to Metadata for writing Animated Portable Network Graphics (APNG) files.
static class	APNGFormat.Checker File format SCIFIO Checker for Animated Portable Network Graphics (APNG) images.
static class	APNGFormat.Metadata File format SCIFIO Metadata for Animated Portable Network Graphics (APNG) images.
static class	APNGFormat.Parser File format SCIFIO Parser for Animated Portable Network Graphics (APNG) images.
static class	APNGFormat.Reader File format SCIFIO Reader for Animated Portable Network Graphics (APNG) images.
static class	APNGFormat.Writer The SCIFIO file format writer for PNG and APNG files.
class	AVIFormat AVIReader is the file format reader for AVI files.
static class	AVIFormat.Checker
static class	AVIFormat.Metadata
static class	AVIFormat.Parser
static class	AVIFormat.Reader
static class	AVIFormat.Translator
static class	AVIFormat.Writer
class	BMPFormat BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
static class	BMPFormat.Checker
static class	BMPFormat.Metadata
static class	BMPFormat.Parser
static class	BMPFormat.Reader
class	DICOMFormat DICOMReader is the file format reader for DICOM files.
static class	DICOMFormat.Checker
static class	DICOMFormat.Metadata
static class	DICOMFormat.Parser
static class	DICOMFormat.Reader
class	EPSFormat Reader is the file format reader for Encapsulated PostScript (EPS) files.
static class	EPSFormat.EPSTranslator Necessary dummy translator, so that an EPS-OMEXML translator can be used.
static class	EPSFormat.Metadata
static class	EPSFormat.Parser
static class	EPSFormat.Reader
static class	EPSFormat.Writer
class	FITSFormat FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
static class	FITSFormat.Metadata
static class	FITSFormat.Parser
static class	FITSFormat.Reader
class	GIFFormat Handler for the GIF file format.
static class	GIFFormat.Checker
static class	GIFFormat.Metadata
static class	GIFFormat.Parser
static class	GIFFormat.Reader
class	ICSFormat SCIFIO Format supporting the ICS image format.
static class	ICSFormat.ICSTranslator SCIFIO file format Translator for ICS Metadata objects to the SCIFIO Core metadata type.
static class	ICSFormat.Metadata SCIFIO Metadata object for ICS images.
static class	ICSFormat.Parser SCIFIO file format Parser for ICS images.
static class	ICSFormat.Reader File format SCIFIO Reader for Image Cytometry Standard (ICS) images.
static class	ICSFormat.Writer SCIFIO file format writer for ICS version 1 and 2 files.
class	ImageIOFormat ImageIOReader is the superclass for file format readers that use the javax.imageio package.
static class	ImageIOFormat.ImageIOTranslator
static class	ImageIOFormat.Metadata
static class	ImageIOFormat.Parser<M extends ImageIOFormat.Metadata>
static class	ImageIOFormat.Reader<M extends ImageIOFormat.Metadata>
static class	ImageIOFormat.Writer<M extends ImageIOFormat.Metadata>
class	JPEG2000Format JPEG2000Reader is the file format reader for JPEG-2000 images.
static class	JPEG2000Format.Checker
static class	JPEG2000Format.Metadata
static class	JPEG2000Format.Parser
static class	JPEG2000Format.Reader
static class	JPEG2000Format.Writer
class	JPEGFormat JPEGReader is the file format reader for JPEG images.
static class	JPEGFormat.Checker
static class	JPEGFormat.Metadata
static class	JPEGFormat.Parser
static class	JPEGFormat.Reader
static class	JPEGFormat.Writer
class	JPEGTileFormat Reader for decoding JPEG images using java.awt.Toolkit.
static class	JPEGTileFormat.Metadata
static class	JPEGTileFormat.Parser
static class	JPEGTileFormat.Reader
class	KontronFormat 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.
static class	KontronFormat.Checker
static class	KontronFormat.Metadata
static class	KontronFormat.Parser
static class	KontronFormat.Reader
class	MicromanagerFormat MicromanagerReader is the file format reader for Micro-Manager files.
static class	MicromanagerFormat.Checker
static class	MicromanagerFormat.Metadata
static class	MicromanagerFormat.MicromanagerTranslator Necessary dummy translator, so that a Micromanager-OMEXML translator can be used
static class	MicromanagerFormat.Parser
static class	MicromanagerFormat.Reader
class	MinimalTIFFFormat MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
static class	MinimalTIFFFormat.Checker
static class	MinimalTIFFFormat.Metadata
static class	MinimalTIFFFormat.Parser<M extends MinimalTIFFFormat.Metadata>
static class	MinimalTIFFFormat.Reader<M extends MinimalTIFFFormat.Metadata>
class	MNGFormat A handler for the Multiple-image Network Graphics (MNG) file format.
static class	MNGFormat.Checker
static class	MNGFormat.Metadata
static class	MNGFormat.Parser
static class	MNGFormat.Reader
class	NRRDFormat File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
static class	NRRDFormat.Checker
static class	NRRDFormat.Metadata
static class	NRRDFormat.Parser
static class	NRRDFormat.Reader
class	PCXFormat PCXReader is the file format reader for PCX files (originally used by PC Paintbrush; now used in Zeiss' LSM Image Browser).
static class	PCXFormat.Checker
static class	PCXFormat.Metadata
static class	PCXFormat.Parser
static class	PCXFormat.Reader
class	PGMFormat Handler plugin for the PGM file format.
static class	PGMFormat.Checker
static class	PGMFormat.Metadata
static class	PGMFormat.Parser
static class	PGMFormat.Reader
class	ScancoISQFormat 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
static class	ScancoISQFormat.Checker
static class	ScancoISQFormat.Metadata
static class	ScancoISQFormat.Parser
static class	ScancoISQFormat.Reader
class	StratecPQCTFormat The file format reader for Stratec pQCT files.
static class	StratecPQCTFormat.Checker
static class	StratecPQCTFormat.Metadata
static class	StratecPQCTFormat.Parser
static class	StratecPQCTFormat.Reader
class	TestImgFormat TestImgFormat is the file format reader for creatign test input data.
static class	TestImgFormat.Checker
static class	TestImgFormat.Metadata Metadata class for Fake format.
static class	TestImgFormat.Parser Parser for Fake file format.
static class	TestImgFormat.Reader Reader for the Fake file format.
static class	TestImgFormat.TestImgTranslator Translator from Metadata to TestImgFormat$Metadata .
class	TIFFFormat Handler for the TIFF file format.
static class	TIFFFormat.BaseTIFFParser BaseTiffParser is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
static class	TIFFFormat.Metadata
static class	TIFFFormat.Parser
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	TIFFFormat.TIFFTranslator This class can be used for translating any io.scif.Metadata to Metadata for writing TIFF. files.
static class	TIFFFormat.Writer<M extends TIFFFormat.Metadata> TiffWriter is the file format writer for TIFF files.
class	TIFFJAIFormat TiffJAIReader is a file format reader for TIFF images.
static class	TIFFJAIFormat.Metadata
static class	TIFFJAIFormat.Parser
static class	TIFFJAIFormat.Reader

Uses of SCIFIOPlugin in io.scif.formats.qt

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

Modifier and Type	Class and Description
class	LegacyQTFormat LegacyQTReader is a file format reader for QuickTime movie files.
static class	LegacyQTFormat.LegacyQTTranslator
static class	LegacyQTFormat.Metadata
static class	LegacyQTFormat.Parser
static class	LegacyQTFormat.Reader
static class	LegacyQTFormat.Writer
class	NativeQTFormat NativeQTReader is the file format reader for QuickTime movie files.
static class	NativeQTFormat.Checker
static class	NativeQTFormat.Metadata
static class	NativeQTFormat.NativeQTTranslator
static class	NativeQTFormat.Parser
static class	NativeQTFormat.Reader
static class	NativeQTFormat.Writer
class	PICTFormat PictReader is the file format reader for Apple PICT files.
static class	PICTFormat.Metadata
static class	PICTFormat.Parser
static class	PICTFormat.Reader

Uses of SCIFIOPlugin in io.scif.gui

Classes in io.scif.gui that implement SCIFIOPlugin

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.

Uses of SCIFIOPlugin in io.scif.img

Classes in io.scif.img that implement SCIFIOPlugin

Modifier and Type	Class and Description
class	AbstractImgIOComponent Abstract superclass for ImgIOComponents (such as ImgOpener or ImgSaver).
class	ImgOpener Reads images from data sources using SCIFIO.
class	ImgPlusCtxCleaningProvider RefProvider plugin for generating ImgPlusCtxCleaningProvider.ImgPlusCtxCleaner instances.
class	ImgSaver Writes out an ImgPlus using SCIFIO.

Uses of SCIFIOPlugin in io.scif.img.converters

Subinterfaces of SCIFIOPlugin in io.scif.img.converters

Modifier and Type	Interface and Description
interface	PlaneConverter Interface for using planes read by SCIFIO Readers to populate ImgPlus instances.

Classes in io.scif.img.converters that implement SCIFIOPlugin

Modifier and Type	Class and Description
class	AbstractPlaneConverter Abstract superclass for PlaneConverter implementations.
class	ArrayDataAccessConverter PlaneConverter implementation specialized for populating ArrayImg instances.
class	PlanarAccessConverter PlaneConverter implementation specialized for populating PlanarAccess instances.
class	RandomAccessConverter Generalized PlaneConverter implementation.

Uses of SCIFIOPlugin in io.scif.refs

Subinterfaces of SCIFIOPlugin in io.scif.refs

Modifier and Type	Interface and Description
interface	RefProvider Interface for plugins that create references for a given referent.