io.scif.filters

Class FileStitcher

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.FileStitcher

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 FileStitcher
extends AbstractReaderFilter

Logic to stitch together files with similar names. Assumes that all files have the same characteristics (e.g., dimensions).

Constructor Summary

Constructors

Constructor and Description
FileStitcher() Constructs a FileStitcher around a new image reader.
FileStitcher(boolean patternIds) Constructs a FileStitcher with the given reader.

Method Summary

Modifier and Type	Method and Description
boolean	canChangePattern()
protected void	cleanUp() Helper method that is always called by the AbstractReaderFilter.close(boolean) method, if the fileOnly flag is false.
FilePattern	findPattern(org.scijava.io.location.BrowsableLocation id) Constructs a new FilePattern around the pattern extracted from the given id.
String[]	findPatterns(org.scijava.io.location.BrowsableLocation id) Finds the file pattern for the given ID, based on the state of the file stitcher.
FilePattern	getFilePattern() Gets the file pattern object used to build the list of files.
long	getPlaneCount(int imageIndex) Determines the number of planes in the current file.
double	getPriority()
boolean	isCompatible(Class<?> c) FileStitcher is only compatible with ByteArray formats.
boolean	isUsingPatternIds() Gets whether the reader is using file patterns for IDs.
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, net.imglib2.Interval bounds, SCIFIOConfig config) Allows a single Plane object to be reused by reference when opening sub-regions of planes.
void	setCanChangePattern(boolean doChange)
void	setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> source, SCIFIOConfig config) As Reader.setSource(DataHandle) with configuration options.
void	setSource(org.scijava.io.location.Location source, SCIFIOConfig config) As Reader.setSource(Location) 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.
void	setUsingPatternIds(boolean patternIds) Sets whether the reader is using file patterns for IDs.

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, isNormalized, isSingleFile, metaCheck, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlaneHelper, planarBounds, readPlane, readPlane, readPlaneHelper, setContext, setMetadata, setNormalized, setParent, 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

FileStitcher

public FileStitcher()

Constructs a FileStitcher around a new image reader.

FileStitcher

public FileStitcher(boolean patternIds)

Constructs a FileStitcher with the given reader.

Parameters:

patternIds - Whether string ids given should be treated as file patterns rather than single file paths.

Method Detail

setUsingPatternIds

public void setUsingPatternIds(boolean patternIds)

Sets whether the reader is using file patterns for IDs.

isUsingPatternIds

public boolean isUsingPatternIds()

Gets whether the reader is using file patterns for IDs.

setCanChangePattern

public void setCanChangePattern(boolean doChange)

canChangePattern

public boolean canChangePattern()

getFilePattern

public FilePattern getFilePattern()

Gets the file pattern object used to build the list of files.

findPattern

public FilePattern findPattern(org.scijava.io.location.BrowsableLocation id)
                        throws IOException

Constructs a new FilePattern around the pattern extracted from the given id.

Throws:

IOException

findPatterns

public String[] findPatterns(org.scijava.io.location.BrowsableLocation id)
                      throws IOException

Finds the file pattern for the given ID, based on the state of the file stitcher. Takes both ID map entries and the patternIds flag into account.

Throws:

IOException

setSource

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

Description copied from interface: Reader

As Reader.setSource(Location) with configuration options.

Specified by:

setSource in interface Reader

Overrides:

setSource in class AbstractReaderFilter

Parameters:

source - the Location

config - Configuration information to use for this read.

Throws:

IOException

setSource

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

Description copied from interface: Reader

As Reader.setSource(DataHandle) with configuration options.

Specified by:

setSource in interface Reader

Overrides:

setSource in class AbstractReaderFilter

Parameters:

source - - The handle to read from

config - Configuration information to use for this read.

Throws:

IOException

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.

isCompatible

public boolean isCompatible(Class<?> c)

FileStitcher is only compatible with ByteArray formats.

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

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,
                       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