Uses of Package
io.scif

Packages that use io.scif

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.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.formats.tiff	This package contains utility classes for working with a variety of Tiff-based formats.
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.refs	Provides reference management utilities.
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.
io.scif.xml	Provides tools and utility classes for working with XML in SCIFIO.

Classes in io.scif used by io.scif

Class and Description
AbstractChecker Abstract superclass of all SCIFIO Checker implementations.
AbstractGroupable Abstract super-class for all Groupable components.
AbstractHasFormat Abstract superclass for all classes that implement HasFormat.
AbstractHasSource Abstract implementation of the HasSource interface.
AbstractImageMetadata Abstract superclass of all ImageMetadata implementations.
AbstractMetadata Abstract superclass of all SCIFIO Metadata implementations.
AbstractParser Abstract superclass of all SCIFIO Parser implementations.
AbstractPlane Abstract superclass for Plane implementations in SCIFIO.
AbstractReader Abstract superclass of all SCIFIO Reader implementations.
AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
AbstractTranslator Abstract superclass of all SCIFIO Translator components.
AbstractWriter Abstract superclass of all SCIFIO Writer implementations.
ByteArrayPlane A naive Plane implementation that uses byte[] for its underlying data type.
ByteArrayReader Abstract superclass for all Reader implementations that return a ByteArrayPlane when reading datasets.
Checker Interface for all SCIFIO Checker components.
DataPlane Extension of the base Plane interface.
DefaultComponent Marker interface for default class implementations.
DefaultMetadata A dummy Metadata implementation.
FilePattern FilePattern is a collection of methods for handling file patterns, a way of succinctly representing a collection of files meant to be part of the same data series.
Format Interface for all SCIFIO formats.
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
Groupable Interface for components that can group multiple files together (e.g. for Parsing metadata or reading pixels)
HasFormat Super-interface for SCIFIO components that relate back to a Format.
HasMetaTable Interface for components that maintain a MetaTable mapping metadata names to values.
HasSource Interface for components that can be attached to open image sources that should be closed to avoid resource leaks
ImageMetadata ImageMetadata stores the metadata for a single image within a dataset.
LocationInfo Encompasses basic metadata about a Loation.
Metadata Interface for all SCIFIO Metadata objects.
MetadataLevel
MetadataService Interface for services that work with SCIFIO metadata.
MetaTable Marker interface for a String : Object Map.
Parser Interface for all SCIFIO Parsers.
Plane Top-level interface for all Plane representations in SCIFIO.
Reader Interface for all SCIFIO Readers.
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
SCIFIOService Marker interface for all SCIFIO Services.
Translator Interface for all SCIFIO Translators.
TypedMetadata Sub-interface for Metadata to facilitate generic parameterization of SCIFIO components.
TypedParser Interface for all Parser implementations that use generic parameters.
TypedReader Interface for all Reader implementations that use generic parameters.
TypedWriter Interface for all Writer implementations that use generic parameters.
Writer Interface for all SCIFIO writers.

Classes in io.scif used by io.scif.codec

Class and Description
AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
SCIFIOService Marker interface for all SCIFIO Services.

Classes in io.scif used by io.scif.config

Class and Description
MetadataLevel

Classes in io.scif used by io.scif.filters

Class and Description
AbstractHasFormat Abstract superclass for all classes that implement HasFormat.
AbstractHasSource Abstract implementation of the HasSource interface.
AbstractMetadata Abstract superclass of all SCIFIO Metadata implementations.
AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
FilePattern FilePattern is a collection of methods for handling file patterns, a way of succinctly representing a collection of files meant to be part of the same data series.
Format Interface for all SCIFIO formats.
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
Groupable Interface for components that can group multiple files together (e.g. for Parsing metadata or reading pixels)
HasFormat Super-interface for SCIFIO components that relate back to a Format.
HasMetaTable Interface for components that maintain a MetaTable mapping metadata names to values.
HasSource Interface for components that can be attached to open image sources that should be closed to avoid resource leaks
ImageMetadata ImageMetadata stores the metadata for a single image within a dataset.
Metadata Interface for all SCIFIO Metadata objects.
MetaTable Marker interface for a String : Object Map.
Plane Top-level interface for all Plane representations in SCIFIO.
Reader Interface for all SCIFIO Readers.
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
TypedMetadata Sub-interface for Metadata to facilitate generic parameterization of SCIFIO components.

Classes in io.scif used by io.scif.formats

Class and Description
AbstractChecker Abstract superclass of all SCIFIO Checker implementations.
AbstractFormat Abstract superclass of all SCIFIO Format implementations.
AbstractGroupable Abstract super-class for all Groupable components.
AbstractHasFormat Abstract superclass for all classes that implement HasFormat.
AbstractHasSource Abstract implementation of the HasSource interface.
AbstractMetadata Abstract superclass of all SCIFIO Metadata implementations.
AbstractParser Abstract superclass of all SCIFIO Parser implementations.
AbstractReader Abstract superclass of all SCIFIO Reader implementations.
AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
AbstractTranslator Abstract superclass of all SCIFIO Translator components.
AbstractWriter Abstract superclass of all SCIFIO Writer implementations.
BufferedImagePlane A Plane implementation using a BufferedImage for the underlying data representation.
ByteArrayPlane A naive Plane implementation that uses byte[] for its underlying data type.
ByteArrayReader Abstract superclass for all Reader implementations that return a ByteArrayPlane when reading datasets.
Checker Interface for all SCIFIO Checker components.
DefaultTranslator Basic Translator implementation.
Format Interface for all SCIFIO formats.
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
Groupable Interface for components that can group multiple files together (e.g. for Parsing metadata or reading pixels)
HasColorTable Interface for SCIFIO components that load ColorTables during parsing.
HasFormat Super-interface for SCIFIO components that relate back to a Format.
HasMetaTable Interface for components that maintain a MetaTable mapping metadata names to values.
HasSource Interface for components that can be attached to open image sources that should be closed to avoid resource leaks
ImageMetadata ImageMetadata stores the metadata for a single image within a dataset.
Metadata Interface for all SCIFIO Metadata objects.
MetaTable Marker interface for a String : Object Map.
Parser Interface for all SCIFIO Parsers.
Plane Top-level interface for all Plane representations in SCIFIO.
Reader Interface for all SCIFIO Readers.
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
Translator Interface for all SCIFIO Translators.
TypedMetadata Sub-interface for Metadata to facilitate generic parameterization of SCIFIO components.
TypedParser Interface for all Parser implementations that use generic parameters.
TypedReader Interface for all Reader implementations that use generic parameters.
TypedWriter Interface for all Writer implementations that use generic parameters.
Writer Interface for all SCIFIO writers.

Classes in io.scif used by io.scif.formats.qt

Class and Description
AbstractChecker Abstract superclass of all SCIFIO Checker implementations.
AbstractFormat Abstract superclass of all SCIFIO Format implementations.
AbstractGroupable Abstract super-class for all Groupable components.
AbstractHasFormat Abstract superclass for all classes that implement HasFormat.
AbstractHasSource Abstract implementation of the HasSource interface.
AbstractMetadata Abstract superclass of all SCIFIO Metadata implementations.
AbstractParser Abstract superclass of all SCIFIO Parser implementations.
AbstractReader Abstract superclass of all SCIFIO Reader implementations.
AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
AbstractTranslator Abstract superclass of all SCIFIO Translator components.
AbstractWriter Abstract superclass of all SCIFIO Writer implementations.
BufferedImagePlane A Plane implementation using a BufferedImage for the underlying data representation.
ByteArrayPlane A naive Plane implementation that uses byte[] for its underlying data type.
ByteArrayReader Abstract superclass for all Reader implementations that return a ByteArrayPlane when reading datasets.
Checker Interface for all SCIFIO Checker components.
Format Interface for all SCIFIO formats.
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
Groupable Interface for components that can group multiple files together (e.g. for Parsing metadata or reading pixels)
HasColorTable Interface for SCIFIO components that load ColorTables during parsing.
HasFormat Super-interface for SCIFIO components that relate back to a Format.
HasMetaTable Interface for components that maintain a MetaTable mapping metadata names to values.
HasSource Interface for components that can be attached to open image sources that should be closed to avoid resource leaks
ImageMetadata ImageMetadata stores the metadata for a single image within a dataset.
Metadata Interface for all SCIFIO Metadata objects.
MissingLibraryException MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
Parser Interface for all SCIFIO Parsers.
Plane Top-level interface for all Plane representations in SCIFIO.
Reader Interface for all SCIFIO Readers.
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
SCIFIOService Marker interface for all SCIFIO Services.
Translator Interface for all SCIFIO Translators.
TypedMetadata Sub-interface for Metadata to facilitate generic parameterization of SCIFIO components.
TypedParser Interface for all Parser implementations that use generic parameters.
TypedReader Interface for all Reader implementations that use generic parameters.
TypedWriter Interface for all Writer implementations that use generic parameters.
Writer Interface for all SCIFIO writers.

Classes in io.scif used by io.scif.formats.tiff

Class and Description
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
SCIFIOService Marker interface for all SCIFIO Services.

Classes in io.scif used by io.scif.gui

Class and Description
AbstractGroupable Abstract super-class for all Groupable components.
AbstractHasFormat Abstract superclass for all classes that implement HasFormat.
AbstractHasSource Abstract implementation of the HasSource interface.
AbstractReader Abstract superclass of all SCIFIO Reader implementations.
AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
BufferedImagePlane A Plane implementation using a BufferedImage for the underlying data representation.
Format Interface for all SCIFIO formats.
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
Groupable Interface for components that can group multiple files together (e.g. for Parsing metadata or reading pixels)
HasFormat Super-interface for SCIFIO components that relate back to a Format.
HasSource Interface for components that can be attached to open image sources that should be closed to avoid resource leaks
ImageMetadata ImageMetadata stores the metadata for a single image within a dataset.
Plane Top-level interface for all Plane representations in SCIFIO.
Reader Interface for all SCIFIO Readers.
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
SCIFIOService Marker interface for all SCIFIO Services.
TypedMetadata Sub-interface for Metadata to facilitate generic parameterization of SCIFIO components.
TypedReader Interface for all Reader implementations that use generic parameters.
Writer Interface for all SCIFIO writers.

Classes in io.scif used by io.scif.img

Class and Description
AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
ImageMetadata ImageMetadata stores the metadata for a single image within a dataset.
Metadata Interface for all SCIFIO Metadata objects.
Reader Interface for all SCIFIO Readers.
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
SCIFIOService Marker interface for all SCIFIO Services.
Writer Interface for all SCIFIO writers.

Classes in io.scif used by io.scif.img.cell

Class and Description
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
Reader Interface for all SCIFIO Readers.

Classes in io.scif used by io.scif.img.cell.loaders

Class and Description
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
Reader Interface for all SCIFIO Readers.

Classes in io.scif used by io.scif.img.converters

Class and Description
AbstractSCIFIOPlugin Abstract superclass of all SCIFIOPlugin implementations.
Reader Interface for all SCIFIO Readers.
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
SCIFIOService Marker interface for all SCIFIO Services.

Classes in io.scif used by io.scif.refs

Class and Description
SCIFIOPlugin Marker interface for org.scijava.plugin.SciJavaPlugin implementations in the io.scif package.
SCIFIOService Marker interface for all SCIFIO Services.

Classes in io.scif used by io.scif.services

Class and Description
Checker Interface for all SCIFIO Checker components.
DependencyException Exception thrown when there is an object instantiation error or error processing dependencies.
Format Interface for all SCIFIO formats.
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
Metadata Interface for all SCIFIO Metadata objects.
Parser Interface for all SCIFIO Parsers.
Reader Interface for all SCIFIO Readers.
SCIFIOService Marker interface for all SCIFIO Services.
Translator Interface for all SCIFIO Translators.
Writer Interface for all SCIFIO writers.

Classes in io.scif used by io.scif.util

Class and Description
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
ImageMetadata ImageMetadata stores the metadata for a single image within a dataset.
Metadata Interface for all SCIFIO Metadata objects.
Reader Interface for all SCIFIO Readers.
Writer Interface for all SCIFIO writers.

Classes in io.scif used by io.scif.xml

Class and Description
SCIFIOService Marker interface for all SCIFIO Services.