Module io.scif

Package io.scif.filters

Class DimensionSwapper

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.DimensionSwapper

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 DimensionSwapper
extends AbstractReaderFilter

Handles swapping the dimension order of an image series. This class is useful for both reassigning ZCT sizes (the input dimension order), and shuffling around the resultant planar order (the output dimension order).

Constructor Summary

Constructors

Constructor	Description
DimensionSwapper()

Method Summary

Modifier and Type	Method	Description
List<net.imagej.axis.AxisType>	getDimensionOrder(int imageIndex)	Returns the (potentially swapped) output order of the AxisTypes.
List<net.imagej.axis.AxisType>	getInputOrder(int imageIndex)	Returns the order for reading AxisTypes from disk.
Metadata	getMetadata()	Gets the type-specific Metadata for this Reader
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, SCIFIOConfig config)	As Reader.openPlane(int, long) 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, SCIFIOConfig config)	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, 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.
void	setOutputOrder(int imageIndex, List<net.imagej.axis.AxisType> outputOrder)	Sets the output dimension order according to the given string (e.g., "XYZCT").
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.
void	swapDimensions(int imageIndex, net.imagej.axis.AxisType... newOrder)	Sets the input dimension order according to the given string (e.g., "XYZCT").

Methods inherited from class io.scif.filters.AbstractReaderFilter

castToTypedPlane, cleanUp, close, close, createPlane, createPlane, fileGroupOption, getContext, getCurrentLocation, getDomains, getFormat, getFormatName, getHandle, getImageCount, getOptimalTileHeight, getOptimalTileWidth, getParentMeta, getPlaneCount, hasCompanionFiles, isCompatible, 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 org.scijava.Contextual

context

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface org.scijava.Prioritized

compareTo, setPriority

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

Methods inherited from interface io.scif.SCIFIOPlugin

getVersion, log

Constructor Detail

DimensionSwapper

public DimensionSwapper()

Method Detail

swapDimensions

public void swapDimensions(int imageIndex,
                           net.imagej.axis.AxisType... newOrder)

Sets the input dimension order according to the given string (e.g., "XYZCT"). This string indicates the planar rasterization order from the source, overriding the detected order. It may result in the dimensional axis sizes changing. If the given order is identical to the file's native order, then nothing happens. Note that this method will throw an exception if X and Y do not appear in positions 0 and 1 (although X and Y can be reversed).

setOutputOrder

public void setOutputOrder(int imageIndex,
                           List<net.imagej.axis.AxisType> outputOrder)

Sets the output dimension order according to the given string (e.g., "XYZCT"). This string indicates the final planar rasterization order—i.e., the mapping from 1D plane number to 3D (Z, C, T) tuple. Changing it will not affect the Z, C or T sizes but will alter the order in which planes are returned when iterating. This method is useful when your application requires a particular output dimension order; e.g., ImageJ virtual stacks must be in XYCZT order.

getInputOrder

public List<net.imagej.axis.AxisType> getInputOrder(int imageIndex)

Returns the order for reading AxisTypes from disk.

getDimensionOrder

public List<net.imagej.axis.AxisType> getDimensionOrder(int imageIndex)

Returns the (potentially swapped) output order of the AxisTypes.

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.

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,
                       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,
                       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,
                       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)

getMetadata

public Metadata getMetadata()

Description copied from interface: Reader

Gets the type-specific Metadata for this Reader

Specified by:

getMetadata in interface Reader

Overrides:

getMetadata in class AbstractReaderFilter

getPriority

public double getPriority()

Specified by:

getPriority in interface org.scijava.Prioritized

Overrides:

getPriority in class org.scijava.plugin.AbstractRichPlugin