Package io.scif.filters

Provides wrapping classes for modifying the performance of one or more of a {link io.scif.Format}'s components.

See: Description

Interface Summary

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

Class Summary

Class	Description
AbstractFilter<T>	Abstract superclass for Filter implementations.
AbstractMetadataWrapper	Abstract superclass for concrete implementations of MetadataWrapper.
AbstractReaderFilter	Abstract superclass for all Filter that delegate to Reader instances.
ChannelFiller	For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
ChannelFillerMetadata	MetadataWrapper implementation specifically for use with the ChannelFiller.
DimensionSwapper	Handles swapping the dimension order of an image series.
DimensionSwapperMetadata	MetadataWrapper implementation specifically for use with the DimensionSwapper.
FileStitcher	Logic to stitch together files with similar names.
FileStitcherMetadata
MasterFilterHelper<T extends org.scijava.Contextual>	Helper class for MasterFilter implementations.
MinMaxFilter	Logic to compute minimum and maximum values for each plane.
PlaneSeparator	Logic to automatically separate the channels in a file.
PlaneSeparatorMetadata	MetadataWrapper implementation specifically for use with the PlaneSeparator.
ReaderFilter	MasterFilter for wrapping Reader components.

Package io.scif.filters Description

Provides wrapping classes for modifying the performance of one or more of a {link io.scif.Format}'s components.

Changes since Bio-Formats

• Implemented SCIFIO Filters. Filters are designed to wrap arbitrary classes. An implementation is currently provided for Readers: ReaderFilter.

  Filters are analogous to the ReaderWrappers of Bio-Formats, but function a bit differently. In Bio-Formats, you would create a stack of ReaderWrappers based on what functionality you wanted to add to a given Reader instance.

  In SCIFIO, the Filters are discoverable plugins (via the scijava-common Context). When you create a ReaderFilter (e.g. via InitializeService.initializeReader(org.scijava.io.location.Location)) you get the whole stack of discovered plugins. Each can be individually configured to be enabled by default. This allows dynamic extensibility, as new Filters can be added to the classpath and automatically discovered and enabled.

  The ReaderFilter is then passed around and functions like a normal Reader. But as plugins are enabled and disabled within the Filter, it automatically maintains the stack (based on each Filter's priority), obviating the need for user knowledge of a construction order.

Future plans

• Implement Filters for the remaining component types.

Author:

Mark Hiner