io.scif

Interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>

Type Parameters:

M - - Metadata used by this reader for reading images.

P - - Plane return and parameter type for this reader's openPlane(int, long) and readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location>, int, net.imglib2.Interval, P) methods.

All Superinterfaces:

Comparable<org.scijava.Prioritized>, org.scijava.Contextual, Groupable, HasFormat, org.scijava.plugin.HasPluginInfo, HasSource, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.Prioritized, Reader, org.scijava.plugin.RichPlugin, SCIFIOPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Versioned

All Known Implementing Classes:

AbstractReader, APNGFormat.Reader, AVIFormat.Reader, BMPFormat.Reader, BufferedImageReader, ByteArrayReader, DefaultReader, DICOMFormat.Reader, EPSFormat.Reader, FITSFormat.Reader, GIFFormat.Reader, ICSFormat.Reader, ImageIOFormat.Reader, JPEG2000Format.Reader, JPEGFormat.Reader, JPEGTileFormat.Reader, KontronFormat.Reader, LegacyQTFormat.Reader, MicromanagerFormat.Reader, MinimalTIFFFormat.Reader, MNGFormat.Reader, NativeQTFormat.Reader, NRRDFormat.Reader, PCXFormat.Reader, PGMFormat.Reader, PICTFormat.Reader, ScancoISQFormat.Reader, StratecPQCTFormat.Reader, TestImgFormat.Reader, TIFFFormat.Reader, TIFFJAIFormat.Reader

public interface TypedReader<M extends TypedMetadata,P extends DataPlane<?>>
extends Reader

Interface for all Reader implementations that use generic parameters.

Generics are used in Reader concrete implementations to type narrow return types, and to provide parallel methods that can type narrow arguments.

Author:

Mark Hiner

See Also:

openPlane(int, long), readPlane(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location>, int, net.imglib2.Interval, P), setMetadata(M), getMetadata()

Method Summary

Modifier and Type	Method and Description
P	createPlane(net.imglib2.Interval bounds) Creates a blank plane compatible with this reader.
M	getMetadata() Gets the type-specific Metadata for this Reader
Class<P>	getPlaneClass() Returns the class of Planes associated with this Reader.
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, P plane, net.imglib2.Interval bounds, SCIFIOConfig config)
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
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
void	setMetadata(M meta) Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Reader.setMetadata(Metadata).

Methods inherited from interface io.scif.Reader

castToTypedPlane, createPlane, getCurrentLocation, getDomains, getHandle, getImageCount, getOptimalTileHeight, getOptimalTileWidth, getPlaneCount, hasCompanionFiles, isNormalized, openPlane, openPlane, openPlane, openPlane, readPlane, readPlane, setMetadata, setNormalized, setSource, setSource, setSource, setSource

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, close

Methods inherited from interface io.scif.Groupable

fileGroupOption, isSingleFile

Method Detail

openPlane

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

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

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

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

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

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

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long, Plane)

openPlane

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

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

Throws:

FormatException

IOException

See Also:

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

openPlane

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

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

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

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

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

Throws:

FormatException

IOException

See Also:

openPlane(int, long, DataPlane)

openPlane

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

Throws:

FormatException

IOException

See Also:

openPlane(int, long, DataPlane, Interval)

setMetadata

void setMetadata(M meta)
          throws IOException

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

Throws:

IOException

See Also:

Reader.setMetadata(Metadata)

getMetadata

M getMetadata()

Description copied from interface: Reader

Gets the type-specific Metadata for this Reader

Specified by:

getMetadata in interface Reader

readPlane

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

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

Throws:

IOException

See Also:

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

readPlane

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

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

Throws:

IOException

See Also:

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

createPlane

P 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

getPlaneClass

Class<P> getPlaneClass()

Returns the class of Planes associated with this Reader.