io.scif

Interface Reader

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, org.scijava.plugin.RichPlugin, SCIFIOPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Versioned

All Known Subinterfaces:

TypedReader<M,P>

All Known Implementing Classes:

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

public interface Reader
extends HasFormat, HasSource, Groupable

Interface for all SCIFIO Readers.

Reader components generate Plane representations of images via the openPlane(int, long) methods. These planes can then be used by calling software (e.g. for display) or passed to another method for writing to an output source (e.g. via the Writer.savePlane(int, long, io.scif.Plane) methods).

Before a Reader can be used, it must be initialized via setSource(org.scijava.io.location.Location) and setMetadata(io.scif.Metadata) calls.

Author:

Mark Hiner

See Also:

Plane, Metadata, Writer.savePlane(int, long, io.scif.Plane)

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.
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.
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.
Metadata	getMetadata() Gets the type-specific Metadata for this Reader
long	getOptimalTileHeight(int imageIndex) Returns the optimal sub-image height for use with openPlane(int, long).
long	getOptimalTileWidth(int imageIndex) Returns the optimal sub-image width for use with openPlane(int, long).
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.
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 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 openPlane(int, long) with configuration options.
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.
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 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 setSource(Location) with configuration options.

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

Plane openPlane(int imageIndex,
                long planeIndex)
         throws FormatException,
                IOException

Creates a Plane representation of the pixels at the specified indices.

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

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

Creates a Plane representation of a desired sub-region from the pixels at the specified indices.

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

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

Allows a single Plane object to be reused by reference when opening complete planes.

Throws:

IllegalArgumentException - If the provided Plane type is not compatible with this Reader.

FormatException

IOException

See Also:

openPlane(int, long)

openPlane

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

Allows a single Plane object to be reused by reference when opening sub-regions of planes.

Throws:

IllegalArgumentException - If the provided Plane type is not compatible with this Reader.

FormatException

IOException

See Also:

openPlane(int, long, Interval)

openPlane

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

As openPlane(int, long) with configuration options.

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

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

As openPlane(int, long, Interval) with configuration options.

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

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

Allows a single Plane object to be reused by reference when opening complete planes.

Throws:

IllegalArgumentException - If the provided Plane type is not compatible with this Reader.

FormatException

IOException

See Also:

openPlane(int, long, SCIFIOConfig)

openPlane

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

Allows a single Plane object to be reused by reference when opening sub-regions of planes.

Throws:

IllegalArgumentException - If the provided Plane type is not compatible with this Reader.

FormatException

IOException

See Also:

openPlane(int, long, Interval, SCIFIOConfig)

getCurrentLocation

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

Returns the current file.

getDomains

String[] getDomains()

Returns the list of domains represented by the current file.

getHandle

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

Retrieves the current input stream for this reader.

Returns:

A RandomAccessInputStream

getOptimalTileWidth

long getOptimalTileWidth(int imageIndex)

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

getOptimalTileHeight

long getOptimalTileHeight(int imageIndex)

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

setMetadata

void setMetadata(Metadata meta)
          throws IOException

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.

Throws:

IllegalArgumentException - If the provided Metadata type is not compatible with this Reader.

IOException

getMetadata

Metadata getMetadata()

Gets the type-specific Metadata for this Reader

setNormalized

void setNormalized(boolean normalize)

Specifies whether or not to normalize float data.

isNormalized

boolean isNormalized()

Returns true if we should normalize float data.

hasCompanionFiles

boolean hasCompanionFiles()

Returns true if this format supports multi-file datasets.

Specified by:

hasCompanionFiles in interface Groupable

setSource

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

Sets the source for this reader to read from.

Parameters:

loc - the location

Throws:

IOException

setSource

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

Sets the source for this reader to read from.

Parameters:

stream - - The stream to read from

Throws:

IOException

setSource

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

As setSource(Location) with configuration options.

Parameters:

loc - the Location

config - Configuration information to use for this read.

Throws:

IOException

setSource

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

As setSource(DataHandle) with configuration options.

Parameters:

handle - - The handle to read from

config - Configuration information to use for this read.

Throws:

IOException

readPlane

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

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

Throws:

IllegalArgumentException - If the provided Plane type is not compatible with this Reader.

IOException

readPlane

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

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

Throws:

IllegalArgumentException - If the provided Plane type is not compatible with this Reader.

IOException

getPlaneCount

long getPlaneCount(int imageIndex)

Determines the number of planes in the current file.

getImageCount

int getImageCount()

Determines the number of images in the current file.

createPlane

Plane createPlane(net.imglib2.Interval bounds)

Creates a blank plane compatible with this reader.

Parameters:

bounds - bounds of the planar axes.

Returns:

The created plane

createPlane

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

Creates a blank plane compatible with this reader.

Parameters:

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

bounds - bounds of the planar axes.

Returns:

The created plane

castToTypedPlane

<P extends Plane> P castToTypedPlane(Plane plane)

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.

Parameters:

plane - - The base Plane to cast.

Returns:

The Plane argument cast to P.

Throws:

IllegalArgumentException - If the provided Plane type is not compatible with this Reader.