io.scif.filters

Class AbstractReaderFilter

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.filters.AbstractFilter<Reader>

io.scif.filters.AbstractReaderFilter

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

Direct Known Subclasses:

ChannelFiller, DimensionSwapper, FileStitcher, MinMaxFilter, PlaneSeparator, ReaderFilter

public abstract class AbstractReaderFilter
extends AbstractFilter<Reader>
implements Reader

Abstract superclass for all Filter that delegate to Reader instances.

NB: All concrete implementations of this interface should be annotated as Plugin for automatic discovery.

NB: This class attempts to locate a type-matching MetadataWrapper to protectively wrap the wrapped Reader's Metadata. If none is found, a reference to the Reader's Metadata itself is used.

Author:

Mark Hiner

See Also:

Reader, Filter, AbstractMetadataWrapper

Constructor Summary

Constructors

Constructor and Description
AbstractReaderFilter()
AbstractReaderFilter(Class<? extends MetadataWrapper> metaClass)

Method Summary

Modifier and Type	Method and Description
<P extends Plane> P	castToTypedPlane(Plane plane) Convenience method for casting Plane implementations to the type associated with this Reader.
protected void	cleanUp() Helper method that is always called by the close(boolean) method, if the fileOnly flag is false.
void	close() Closes the image source(s) associated with this component and resets the component to its default state.
void	close(boolean fileOnly) Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
Plane	createPlane(ImageMetadata meta, net.imglib2.Interval bounds) Creates a blank plane compatible with this reader.
Plane	createPlane(net.imglib2.Interval bounds) Creates a blank plane compatible with this reader.
int	fileGroupOption(org.scijava.io.location.Location id) Returns an int indicating that we cannot, must, or might group the files in a given dataset.
org.scijava.Context	getContext()
org.scijava.io.location.Location	getCurrentLocation() Returns the current file.
String[]	getDomains() Returns the list of domains represented by the current file.
Format	getFormat() Provides a link back to the format associated with this component.
String	getFormatName() Helper method for accessing Format.getFormatName().
org.scijava.io.handle.DataHandle<org.scijava.io.location.Location>	getHandle() Retrieves the current input stream for this reader.
int	getImageCount() Determines the number of images in the current file.
Metadata	getMetadata() Gets the type-specific Metadata for this Reader
long	getOptimalTileHeight(int imageIndex) Returns the optimal sub-image height for use with Reader.openPlane(int, long).
long	getOptimalTileWidth(int imageIndex) Returns the optimal sub-image width for use with Reader.openPlane(int, long).
protected Metadata	getParentMeta() Convenience accessor for the parent's Metadata
long	getPlaneCount(int imageIndex) Determines the number of planes in the current file.
boolean	hasCompanionFiles() Returns true if this format supports multi-file datasets.
boolean	isCompatible(Class<?> c) Returns true if this filter is capable of wrapping instances of the provided class.
boolean	isNormalized() Returns true if we should normalize float data.
boolean	isSingleFile(org.scijava.io.location.Location id) Returns true if this is a single-file format.
protected boolean	metaCheck()
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	openPlaneHelper() Allows code to be executed regardless of which openPlane(int, long) signature is called.
protected net.imglib2.Interval	planarBounds(int imageIndex)
Plane	readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> s, int imageIndex, net.imglib2.Interval bounds, int scanlinePad, Plane plane) Reads a raw plane from disk.
Plane	readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> s, int imageIndex, net.imglib2.Interval bounds, Plane plane) Reads a raw plane from disk.
protected void	readPlaneHelper() Allows code to be executed regardless of which readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location>, int, net.imglib2.Interval, io.scif.Plane) signature is called.
void	setContext(org.scijava.Context ctx)
void	setMetadata(Metadata meta) Sets the Metadata for this Reader.
void	setNormalized(boolean normalize) Specifies whether or not to normalize float data.
void	setParent(Object parent) Sets the object which this filter augments.
void	setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle) Sets the source for this reader to read from.
void	setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config) As Reader.setSource(DataHandle) with configuration options.
void	setSource(org.scijava.io.location.Location loc) Sets the source for this reader to read from.
void	setSource(org.scijava.io.location.Location loc, 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 setSource(org.scijava.io.location.Location) signature is called.
Class<?>	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, getPriority, 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, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Constructor Detail

AbstractReaderFilter

public AbstractReaderFilter()

AbstractReaderFilter

public AbstractReaderFilter(Class<? extends MetadataWrapper> metaClass)

Method Detail

setSourceHelper

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

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

Parameters:

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

Throws:

IOException

openPlaneHelper

protected void openPlaneHelper()

Allows code to be executed regardless of which openPlane(int, long) signature is called.

readPlaneHelper

protected void readPlaneHelper()

Allows code to be executed regardless of which readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location>, int, net.imglib2.Interval, io.scif.Plane) signature is called.

getParentMeta

protected Metadata getParentMeta()

Convenience accessor for the parent's Metadata

target

public Class<?> target()

Specified by:

target in interface Filter

Returns:

The target type operated on by this filter

setParent

public void setParent(Object parent)

Description copied from interface: Filter

Sets the object which this filter augments.

Specified by:

setParent in interface Filter

Overrides:

setParent in class AbstractFilter<Reader>

Parameters:

parent - - The object wrapped by this filter

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 AbstractFilter<Reader>

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

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,
                       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

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)
                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

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long)

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

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

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

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

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

Throws:

FormatException

IOException

See Also:

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

fileGroupOption

public int fileGroupOption(org.scijava.io.location.Location id)
                    throws FormatException,
                           IOException

Description copied from interface: Groupable

Returns an int indicating that we cannot, must, or might group the files in a given dataset.

Specified by:

fileGroupOption in interface Groupable

Throws:

FormatException

IOException

getCurrentLocation

public org.scijava.io.location.Location getCurrentLocation()

Description copied from interface: Reader

Returns the current file.

Specified by:

getCurrentLocation in interface Reader

getDomains

public String[] getDomains()

Description copied from interface: Reader

Returns the list of domains represented by the current file.

Specified by:

getDomains in interface Reader

getHandle

public org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> getHandle()

Description copied from interface: Reader

Retrieves the current input stream for this reader.

Specified by:

getHandle in interface Reader

Returns:

A RandomAccessInputStream

getOptimalTileWidth

public long getOptimalTileWidth(int imageIndex)

Description copied from interface: Reader

Returns the optimal sub-image width for use with Reader.openPlane(int, long).

Specified by:

getOptimalTileWidth in interface Reader

getOptimalTileHeight

public long getOptimalTileHeight(int imageIndex)

Description copied from interface: Reader

Returns the optimal sub-image height for use with Reader.openPlane(int, long).

Specified by:

getOptimalTileHeight in interface Reader

setMetadata

public void setMetadata(Metadata meta)
                 throws IOException

Description copied from interface: Reader

Sets the Metadata for this Reader.

NB: This method has accepts a general Metadata so that this signature can appear in the base interface for all Readers, but behavior if provided with a Metadata instance not associated with this Reader is undefined and should throw an exception.

Specified by:

setMetadata in interface Reader

Throws:

IOException

getMetadata

public Metadata getMetadata()

Description copied from interface: Reader

Gets the type-specific Metadata for this Reader

Specified by:

getMetadata in interface Reader

setNormalized

public void setNormalized(boolean normalize)

Description copied from interface: Reader

Specifies whether or not to normalize float data.

Specified by:

setNormalized in interface Reader

isNormalized

public boolean isNormalized()

Description copied from interface: Reader

Returns true if we should normalize float data.

Specified by:

isNormalized in interface Reader

hasCompanionFiles

public boolean hasCompanionFiles()

Description copied from interface: Reader

Returns true if this format supports multi-file datasets.

Specified by:

hasCompanionFiles in interface Groupable

Specified by:

hasCompanionFiles in interface Reader

setSource

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

Description copied from interface: Reader

Sets the source for this reader to read from.

Specified by:

setSource in interface Reader

Parameters:

loc - the location

Throws:

IOException

setSource

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

Description copied from interface: Reader

Sets the source for this reader to read from.

Specified by:

setSource in interface Reader

Parameters:

handle - - The stream to read from

Throws:

IOException

setSource

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

Description copied from interface: Reader

As Reader.setSource(Location) with configuration options.

Specified by:

setSource in interface Reader

Parameters:

loc - 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> handle,
                      SCIFIOConfig config)
               throws IOException

Description copied from interface: Reader

As Reader.setSource(DataHandle) with configuration options.

Specified by:

setSource in interface Reader

Parameters:

handle - - The handle to read from

config - Configuration information to use for this read.

Throws:

IOException

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: HasSource

Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.

Specified by:

close in interface HasSource

Parameters:

fileOnly - - If true, only the associated source(s) are closed.

Throws:

IOException

close

public void close()
           throws IOException

Description copied from interface: HasSource

Closes the image source(s) associated with this component and resets the component to its default state.

Equivalent to calling close(false).

Specified by:

close in interface HasSource

Throws:

IOException

readPlane

public Plane readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> s,
                       int imageIndex,
                       net.imglib2.Interval bounds,
                       Plane plane)
                throws IOException

Description copied from interface: Reader

Reads a raw plane from disk.

NB Presumes that the source stream s is set to the correct offset, i.e. start of the plane

Specified by:

readPlane in interface Reader

Throws:

IOException

readPlane

public Plane readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> s,
                       int imageIndex,
                       net.imglib2.Interval bounds,
                       int scanlinePad,
                       Plane plane)
                throws IOException

Description copied from interface: Reader

Reads a raw plane from disk.

NB Presumes that the source stream s is set to the correct offset, i.e. start of the plane

Specified by:

readPlane in interface Reader

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

getImageCount

public int getImageCount()

Description copied from interface: Reader

Determines the number of images in the current file.

Specified by:

getImageCount in interface Reader

createPlane

public Plane createPlane(net.imglib2.Interval bounds)

Description copied from interface: Reader

Creates a blank plane compatible with this reader.

Specified by:

createPlane in interface Reader

Parameters:

bounds - bounds of the planar axes.

Returns:

The created plane

createPlane

public Plane createPlane(ImageMetadata meta,
                         net.imglib2.Interval bounds)

Description copied from interface: Reader

Creates a blank plane compatible with this reader.

Specified by:

createPlane in interface Reader

Parameters:

meta - - ImageMetadata to use to populate the new plane.

bounds - bounds of the planar axes.

Returns:

The created plane

castToTypedPlane

public <P extends Plane> P castToTypedPlane(Plane plane)

Description copied from interface: Reader

Convenience method for casting Plane implementations to the type associated with this Reader.

NB: this method will fail if the provided Plane is not compatible with this Reader.

Specified by:

castToTypedPlane in interface Reader

Parameters:

plane - - The base Plane to cast.

Returns:

The Plane argument cast to P.

isSingleFile

public boolean isSingleFile(org.scijava.io.location.Location id)
                     throws FormatException,
                            IOException

Description copied from interface: Groupable

Returns true if this is a single-file format.

Specified by:

isSingleFile in interface Groupable

Throws:

FormatException

IOException

getFormat

public Format getFormat()

Description copied from interface: HasFormat

Provides a link back to the format associated with this component.

Specified by:

getFormat in interface HasFormat

Returns:

the associated Format

getFormatName

public String getFormatName()

Description copied from interface: HasFormat

Helper method for accessing Format.getFormatName(). Some Formats may be polymorphic and wish to provide additional name information based on the specific dataset open - this method allows overriding of that behavior.

Specified by:

getFormatName in interface HasFormat

Returns:

the name of the associated Format

getContext

public org.scijava.Context getContext()

Specified by:

getContext in interface org.scijava.Contextual

Overrides:

getContext in class org.scijava.AbstractContextual

setContext

public void setContext(org.scijava.Context ctx)

Specified by:

setContext in interface org.scijava.Contextual

metaCheck

protected boolean metaCheck()

cleanUp

protected void cleanUp()
                throws IOException

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

Throws:

IOException

planarBounds

protected net.imglib2.Interval planarBounds(int imageIndex)