io.scif

Class AbstractReader<M extends TypedMetadata,P extends DataPlane<?>>

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.AbstractHasFormat

io.scif.AbstractHasSource

io.scif.AbstractGroupable

io.scif.AbstractReader<M,P>

All Implemented Interfaces:

Groupable, HasFormat, HasSource, Reader, SCIFIOPlugin, TypedReader<M,P>, 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:

BufferedImageReader, ByteArrayReader

public abstract class AbstractReader<M extends TypedMetadata,P extends DataPlane<?>>
extends AbstractGroupable
implements TypedReader<M,P>

Abstract superclass of all SCIFIO Reader implementations.

Author:

Mark Hiner

See Also:

Reader, HasFormat, Metadata, Plane

Constructor Summary

Constructors

Constructor and Description
AbstractReader(Class<P> planeClass) Constructs a reader and stores a reference to its plane type

Method Summary

Modifier and Type	Method and Description
<T extends Plane> T	castToTypedPlane(Plane plane) Convenience method for casting Plane implementations to the type associated with this Reader.
void	close(boolean fileOnly) Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
protected abstract String[]	createDomainArray() Helper method to lazily create the domain array for this reader instance, to avoid constantly re-creating the array.
org.scijava.io.location.Location	getCurrentLocation() Returns the current file.
String[]	getDomains() Returns the list of domains represented by the current file.
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.
M	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).
Class<P>	getPlaneClass() Returns the class of Planes associated with this Reader.
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	isNormalized() Returns true if we should normalize float data.
P	openPlane(int imageIndex, long planeIndex) Creates a Plane representation of the pixels at the specified indices.
P	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.
P	openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config) As Reader.openPlane(int, long, Interval) with configuration options.
P	openPlane(int imageIndex, long planeIndex, P plane) Generic-parameterized openPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.openPlane(int, long, Plane).
P	openPlane(int imageIndex, long planeIndex, P plane, net.imglib2.Interval bounds) Generic-parameterized openPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.openPlane(int, long, Plane, Interval).
P	openPlane(int imageIndex, long planeIndex, Plane plane) Allows a single Plane object to be reused by reference when opening complete planes.
P	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.
P	openPlane(int imageIndex, long planeIndex, P plane, SCIFIOConfig config)
P	openPlane(int imageIndex, long planeIndex, SCIFIOConfig config) As Reader.openPlane(int, long) with configuration options.
P	readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> s, int imageIndex, net.imglib2.Interval bounds, int scanlinePad, P plane) Generic-parameterized readPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.readPlane(DataHandle, int, Interval, int, Plane) NB Presumes that the source stream s is set to the correct offset, i.e. start of the plane
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.
P	readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> s, int imageIndex, net.imglib2.Interval bounds, P plane) Generic-parameterized readPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.readPlane(DataHandle, int, Interval, Plane) NB Presumes that the source stream s is set to the correct offset, i.e. start of the plane
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.
void	setMetadata(M meta) Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Reader.setMetadata(Metadata).
void	setMetadata(Metadata meta) Sets the Metadata for this Reader.
void	setNormalized(boolean normalize) Specifies whether or not to normalize float data.
void	setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream) 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.

Methods inherited from class io.scif.AbstractGroupable

fileGroupOption, isSingleFile

Methods inherited from class io.scif.AbstractHasSource

close

Methods inherited from class io.scif.AbstractHasFormat

asBrowsableLocation, asBrowsableLocation, getFormat, getFormatName

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, getContext

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.scif.TypedReader

createPlane, openPlane

Methods inherited from interface io.scif.Reader

createPlane

Methods inherited from interface io.scif.HasFormat

getFormat, getFormatName

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, getContext, setContext

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

Methods inherited from interface io.scif.HasSource

close

Methods inherited from interface io.scif.Groupable

fileGroupOption, isSingleFile

Constructor Detail

AbstractReader

public AbstractReader(Class<P> planeClass)

Constructs a reader and stores a reference to its plane type

Method Detail

createDomainArray

protected abstract String[] createDomainArray()

Helper method to lazily create the domain array for this reader instance, to avoid constantly re-creating the array.

openPlane

public P 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

Specified by:

openPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

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 P 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

Specified by:

openPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

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 P 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 P 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 P 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

Specified by:

openPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

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 P 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

Specified by:

openPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

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)

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 M getMetadata()

Description copied from interface: Reader

Gets the type-specific Metadata for this Reader

Specified by:

getMetadata in interface Reader

Specified by:

getMetadata in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

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: Groupable

Returns true if this format supports multi-file datasets.

Specified by:

hasCompanionFiles in interface Groupable

Specified by:

hasCompanionFiles in interface Reader

Overrides:

hasCompanionFiles in class AbstractGroupable

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> stream)
               throws IOException

Description copied from interface: Reader

Sets the source for this reader to read from.

Specified by:

setSource in interface Reader

Parameters:

stream - - 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

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

castToTypedPlane

public <T extends Plane> T 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.

openPlane

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

Description copied from interface: TypedReader

Generic-parameterized openPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.openPlane(int, long, Plane).

Specified by:

openPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long, Plane)

openPlane

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

Specified by:

openPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

Throws:

FormatException

IOException

See Also:

TypedReader.openPlane(int, long, DataPlane)

openPlane

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

Description copied from interface: TypedReader

Generic-parameterized openPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.openPlane(int, long, Plane, Interval).

Specified by:

openPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

Throws:

FormatException

IOException

See Also:

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

setMetadata

public void setMetadata(M meta)
                 throws IOException

Description copied from interface: TypedReader

Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Reader.setMetadata(Metadata).

Specified by:

setMetadata in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

Throws:

IOException

See Also:

Reader.setMetadata(Metadata)

readPlane

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

Description copied from interface: TypedReader

Generic-parameterized readPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.readPlane(DataHandle, int, Interval, Plane)

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

Specified by:

readPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

Throws:

IOException

See Also:

Reader.readPlane(DataHandle, int, Interval, Plane)

readPlane

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

Description copied from interface: TypedReader

Generic-parameterized readPlane method, using TypedMetadata to avoid type erasure conflicts with Reader.readPlane(DataHandle, int, Interval, int, Plane)

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

Specified by:

readPlane in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

Throws:

IOException

See Also:

Reader.readPlane(DataHandle, int, Interval, int, Plane)

getPlaneClass

public Class<P> getPlaneClass()

Description copied from interface: TypedReader

Returns the class of Planes associated with this Reader.

Specified by:

getPlaneClass in interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

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