io.scif.filters

Class PlaneSeparator

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.PlaneSeparator

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 PlaneSeparator
extends AbstractReaderFilter

Logic to automatically separate the channels in a file.

Constructor Summary

Constructors

Constructor and Description
PlaneSeparator()

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.
long	getOriginalIndex(int imageIndex, long planeIndex) Returns the image number in the original dataset that corresponds to the given image number.
long	getPlaneCount(int imageIndex) Determines the number of planes in the current file.
double	getPriority()
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.
void	separate(net.imagej.axis.AxisType... types) Specify which AxisTypes should be separated.
void	setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source) Sets the source for this reader to read from.
void	setSource(org.scijava.io.location.Location source) Sets the source for this reader to read from.

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, hasCompanionFiles, isCompatible, isNormalized, isSingleFile, metaCheck, openPlaneHelper, planarBounds, readPlane, readPlane, readPlaneHelper, setContext, setMetadata, setNormalized, setParent, setSource, setSource, setSourceHelper, 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

PlaneSeparator

public PlaneSeparator()

Method Detail

separate

public void separate(net.imagej.axis.AxisType... types)

Specify which AxisTypes should be separated.

getOriginalIndex

public long getOriginalIndex(int imageIndex,
                             long planeIndex)

Returns the image number in the original dataset that corresponds to the given image number. For instance, if the original dataset was a single RGB image and the given plane index is 2, the return value will be 0.

Parameters:

planeIndex - is a plane number greater than or equal to 0 and less than getPlaneCount()

Returns:

the corresponding plane number in the original (unseparated) data.

setSource

public void setSource(org.scijava.io.location.Location source)
               throws IOException

Description copied from interface: Reader

Sets the source for this reader to read from.

Specified by:

setSource in interface Reader

Overrides:

setSource in class AbstractReaderFilter

Parameters:

source - the location

Throws:

IOException

setSource

public void setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source)
               throws IOException

Description copied from interface: Reader

Sets the source for this reader to read from.

Specified by:

setSource in interface Reader

Overrides:

setSource in class AbstractReaderFilter

Parameters:

source - - The stream to read from

Throws:

IOException

getPlaneCount

public long getPlaneCount(int imageIndex)

Description copied from interface: Reader

Determines the number of planes in the current file.

Specified by:

getPlaneCount in interface Reader

Overrides:

getPlaneCount in class AbstractReaderFilter

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)

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