io.scif.filters

Class ChannelFiller

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.filters.AbstractFilter<Reader>

io.scif.filters.AbstractReaderFilter

io.scif.filters.ChannelFiller

All Implemented Interfaces:

Filter, Groupable, HasFormat, HasSource, Reader, SCIFIOPlugin, Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.Versioned

public class ChannelFiller
extends AbstractReaderFilter

For indexed color data representing true color, factors out the indices, replacing them with the color table values directly. For all other data (either non-indexed, or indexed with "false color" tables), does nothing. NB: lut length is not guaranteed to be accurate until a plane has been read

Constructor Summary

Constructors

Constructor and Description
ChannelFiller()

Method Summary

Modifier and Type	Method and Description
protected void	cleanUp() Helper method that is always called by the AbstractReaderFilter.close(boolean) method, if the fileOnly flag is false.
double	getPriority()
boolean	isCompatible(Class<?> c) Returns true if this filter is capable of wrapping instances of the provided class.
Plane	openPlane(int imageIndex, long planeIndex) Creates a Plane representation of the pixels at the specified indices.
Plane	openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds) Creates a Plane representation of a desired sub-region from the pixels at the specified indices.
Plane	openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config) As Reader.openPlane(int, long, Interval) with configuration options.
Plane	openPlane(int imageIndex, long planeIndex, Plane plane) Allows a single Plane object to be reused by reference when opening complete planes.
Plane	openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Allows a single Plane object to be reused by reference when opening sub-regions of planes.
Plane	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	openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config) Allows a single Plane object to be reused by reference when opening complete planes.
Plane	openPlane(int imageIndex, long planeIndex, SCIFIOConfig config) As Reader.openPlane(int, long) with configuration options.
protected void	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.

Methods inherited from class io.scif.filters.AbstractReaderFilter

castToTypedPlane, close, close, createPlane, createPlane, fileGroupOption, getContext, getCurrentLocation, getDomains, getFormat, getFormatName, getHandle, getImageCount, getMetadata, getOptimalTileHeight, getOptimalTileWidth, getParentMeta, getPlaneCount, hasCompanionFiles, isNormalized, isSingleFile, metaCheck, openPlaneHelper, planarBounds, readPlane, readPlane, readPlaneHelper, setContext, setMetadata, setNormalized, setParent, setSource, setSource, setSource, setSource, target

Methods inherited from class io.scif.filters.AbstractFilter

enabledDefault, getParent, reset

Methods inherited from class io.scif.AbstractSCIFIOPlugin

getVersion, log

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, setInfo, setPriority, toString

Methods inherited from class org.scijava.AbstractContextual

context

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface io.scif.SCIFIOPlugin

getVersion, log

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

Methods inherited from interface org.scijava.Contextual

context

Methods inherited from interface org.scijava.Prioritized

compareTo, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Constructor Detail

ChannelFiller

public ChannelFiller()

Method Detail

isCompatible

public boolean isCompatible(Class<?> c)

Description copied from interface: Filter

Returns true if this filter is capable of wrapping instances of the provided class.

Specified by:

isCompatible in interface Filter

Overrides:

isCompatible in class AbstractReaderFilter

Parameters:

c - - Class to check compatibility

Returns:

True if this filter can call setParent on instances of c

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Creates a Plane representation of the pixels at the specified indices.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

Returns:

The complete Plane at the specified indices.

Throws:

FormatException

IOException

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       Plane plane)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Allows a single Plane object to be reused by reference when opening complete planes.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long)

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       net.imglib2.Interval bounds)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Creates a Plane representation of a desired sub-region from the pixels at the specified indices.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

bounds - bounds of the planar axes.

Returns:

The desired sub-region at the specified indices.

Throws:

FormatException

IOException

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       Plane plane,
                       net.imglib2.Interval bounds)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Allows a single Plane object to be reused by reference when opening sub-regions of planes.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long, Interval)

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

Description copied from interface: Reader

As Reader.openPlane(int, long) with configuration options.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

config - Configuration information to use for this read.

Returns:

The complete Plane at the specified indices.

Throws:

FormatException

IOException

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       Plane plane,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Allows a single Plane object to be reused by reference when opening complete planes.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long, SCIFIOConfig)

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       net.imglib2.Interval bounds,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

Description copied from interface: Reader

As Reader.openPlane(int, long, Interval) with configuration options.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

bounds - bounds of the planar axes.

config - Configuration information to use for this read.

Returns:

The desired sub-region at the specified indices.

Throws:

FormatException

IOException

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       Plane plane,
                       net.imglib2.Interval bounds,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Allows a single Plane object to be reused by reference when opening sub-regions of planes.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long, Interval, SCIFIOConfig)

setSourceHelper

protected void setSourceHelper(org.scijava.io.location.Location source,
                               SCIFIOConfig config)

Description copied from class: AbstractReaderFilter

Allows code to be executed regardless of which AbstractReaderFilter.setSource(org.scijava.io.location.Location) signature is called.

Overrides:

setSourceHelper in class AbstractReaderFilter

Parameters:

source - - Lowest common denominator of arguments in the setSource series.

getPriority

public double getPriority()

Specified by:

getPriority in interface org.scijava.Prioritized

Overrides:

getPriority in class org.scijava.plugin.AbstractRichPlugin

cleanUp

protected void cleanUp()
                throws IOException

Description copied from class: AbstractReaderFilter

Helper method that is always called by the AbstractReaderFilter.close(boolean) method, if the fileOnly flag is false.

Overrides:

cleanUp in class AbstractReaderFilter

Throws:

IOException