Package loci.formats

Class ChannelSeparator

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.ChannelSeparator

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class ChannelSeparator
extends ReaderWrapper

Logic to automatically separate the channels in a file.

Field Summary

Fields

Modifier and Type	Field	Description
private byte[]	lastImage	Last image opened.
private int	lastImageHeight	Height of last image opened.
private int	lastImageIndex	Index of last image opened.
private int	lastImageSeries	Series of last image opened.
private int	lastImageWidth	Width of last image opened.
private int	lastImageX	X index of last image opened.
private int	lastImageY	Y index of last image opened.

Fields inherited from class loci.formats.ReaderWrapper

reader

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
ChannelSeparator()	Constructs a ChannelSeparator around a new image reader.
ChannelSeparator(IFormatReader r)	Constructs a ChannelSeparator with the given reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
String	getDimensionOrder()	Gets a five-character string representing the dimension order in which planes will be returned.
int	getImageCount()	Determines the number of image planes in the current file.
int	getIndex(int z, int c, int t)	Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
int	getIndex(int z, int c, int t, int moduloZ, int moduloC, int moduloT)	Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes).
Class<?>	getNativeDataType()	Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object).
int	getOriginalIndex(int no)	Returns the image number in the original dataset that corresponds to the given image number.
Codec	getTileCodec(int no)	Retrieve a codec that can be used to decompress compressed tiles.
CodecOptions	getTileCodecOptions(int no, int x, int y)	Retrieve codec options that can be used to decompressed the specified tile.
int[]	getZCTCoords(int index)	Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.
int[]	getZCTModuloCoords(int index)	Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value.
boolean	isRGB()	Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call.
static ChannelSeparator	makeChannelSeparator(IFormatReader r)	Converts the given reader into a ChannelSeparator, wrapping if needed.
byte[]	openBytes(int no)	Obtains the specified image plane from the current file as a byte array.
byte[]	openBytes(int no, byte[] buf)	Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)	Obtains a sub-image of the specified image plane into a pre-allocated byte array.
byte[]	openBytes(int no, int x, int y, int w, int h)	Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
byte[]	openCompressedBytes(int no, byte[] buf, int x, int y)	Retrieve the specified tile without performing any decompression.
byte[]	openCompressedBytes(int no, int x, int y)	Retrieve the specified tile without performing any decompression.
byte[]	openThumbBytes(int no)	Obtains a thumbnail for the specified image plane from the current file, as a byte array.
void	setId(String id)	Sets the current file name.

Methods inherited from class loci.formats.ReaderWrapper

close, coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, unwrap, unwrap, unwrap

Methods inherited from class java.lang.Object

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

Field Details

lastImage

private byte[] lastImage

Last image opened.

lastImageIndex

private int lastImageIndex

Index of last image opened.

lastImageSeries

private int lastImageSeries

Series of last image opened.

lastImageX

private int lastImageX

X index of last image opened.

lastImageY

private int lastImageY

Y index of last image opened.

lastImageWidth

private int lastImageWidth

Width of last image opened.

lastImageHeight

private int lastImageHeight

Height of last image opened.

Constructor Details

ChannelSeparator

public ChannelSeparator()

Constructs a ChannelSeparator around a new image reader.

ChannelSeparator

public ChannelSeparator(IFormatReader r)

Constructs a ChannelSeparator with the given reader.

Method Details

makeChannelSeparator

public static ChannelSeparator makeChannelSeparator(IFormatReader r)

Converts the given reader into a ChannelSeparator, wrapping if needed.

getOriginalIndex

public int getOriginalIndex(int no)

Returns the image number in the original dataset that corresponds to the given image number. For instance, if the original dataset was a single RGB image and the given image number is 2, the return value will be 0.

Parameters:

no - is an image number greater than or equal to 0 and less than getImageCount()

Returns:

the corresponding image number in the original (unseparated) data.

getImageCount

public int getImageCount()

Description copied from interface: IFormatReader

Determines the number of image planes in the current file.

Specified by:

getImageCount in interface IFormatReader

Overrides:

getImageCount in class ReaderWrapper

getDimensionOrder

public String getDimensionOrder()

Description copied from interface: IFormatReader

Gets a five-character string representing the dimension order in which planes will be returned. Valid orders are:

• XYCTZ
• XYCZT
• XYTCZ
• XYTZC
• XYZCT
• XYZTC

In cases where the channels are interleaved (e.g., CXYTZ), C will be the first dimension after X and Y (e.g., XYCTZ) and the IFormatReader.isInterleaved() method will return true.

Specified by:

getDimensionOrder in interface IFormatReader

Overrides:

getDimensionOrder in class ReaderWrapper

isRGB

public boolean isRGB()

Description copied from interface: IFormatReader

Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call. This method returns true if and only if IFormatReader.getRGBChannelCount() returns a value greater than 1.

Specified by:

isRGB in interface IFormatReader

Overrides:

isRGB in class ReaderWrapper

openBytes

public byte[] openBytes(int no)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains the specified image plane from the current file as a byte array.

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class ReaderWrapper

Throws:

FormatException

IOException

See Also:

• IFormatReader.openBytes(int, byte[])

openBytes

public byte[] openBytes(int no,
 byte[] buf)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class ReaderWrapper

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

Returns:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

IOException - if there was a problem reading the file.

openBytes

public byte[] openBytes(int no,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class ReaderWrapper

Throws:

FormatException

IOException

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class ReaderWrapper

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

Returns:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

IOException - if there was a problem reading the file.

openThumbBytes

public byte[] openThumbBytes(int no)
                      throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a thumbnail for the specified image plane from the current file, as a byte array.

Specified by:

openThumbBytes in interface IFormatReader

Overrides:

openThumbBytes in class ReaderWrapper

Throws:

FormatException

IOException

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class ReaderWrapper

Throws:

IOException

getIndex

public int getIndex(int z,
 int c,
 int t)

Description copied from interface: IFormatReader

Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).

Specified by:

getIndex in interface IFormatReader

Overrides:

getIndex in class ReaderWrapper

getIndex

public int getIndex(int z,
 int c,
 int t,
 int moduloZ,
 int moduloC,
 int moduloT)

Description copied from interface: IFormatReader

Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes). Note that the Z, C and T coordinates take the modulo dimension sizes into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.

Specified by:

getIndex in interface IFormatReader

Overrides:

getIndex in class ReaderWrapper

getZCTCoords

public int[] getZCTCoords(int index)

Description copied from interface: IFormatReader

Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.

Specified by:

getZCTCoords in interface IFormatReader

Overrides:

getZCTCoords in class ReaderWrapper

getZCTModuloCoords

public int[] getZCTModuloCoords(int index)

Description copied from interface: IFormatReader

Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value. Note that the Z, C and T coordinates are not the same as those returned by getZCTCoords(int) because the size of the modulo dimensions is taken into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.

Specified by:

getZCTModuloCoords in interface IFormatReader

Overrides:

getZCTModuloCoords in class ReaderWrapper

openCompressedBytes

public byte[] openCompressedBytes(int no,
 int x,
 int y)
                           throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve the specified tile without performing any decompression.

Specified by:

openCompressedBytes in interface ICompressedTileReader

Overrides:

openCompressedBytes in class ReaderWrapper

Parameters:

no - plane index

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

compressed tile bytes

Throws:

FormatException

IOException

openCompressedBytes

public byte[] openCompressedBytes(int no,
 byte[] buf,
 int x,
 int y)
                           throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve the specified tile without performing any decompression.

Specified by:

openCompressedBytes in interface ICompressedTileReader

Overrides:

openCompressedBytes in class ReaderWrapper

Parameters:

no - plane index

buf - pre-allocated buffer in which to store compressed bytes

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

compressed tile bytes

Throws:

FormatException

IOException

getTileCodec

public Codec getTileCodec(int no)
                   throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve a codec that can be used to decompress compressed tiles.

Specified by:

getTileCodec in interface ICompressedTileReader

Overrides:

getTileCodec in class ReaderWrapper

Parameters:

no - plane index

Returns:

codec that can be used for compressed tiles in the specified plane

Throws:

FormatException

IOException

See Also:

• ICompressedTileReader.openCompressedBytes(int,int,int)

getTileCodecOptions

public CodecOptions getTileCodecOptions(int no,
 int x,
 int y)
                                 throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve codec options that can be used to decompressed the specified tile.

Specified by:

getTileCodecOptions in interface ICompressedTileReader

Overrides:

getTileCodecOptions in class ReaderWrapper

Parameters:

no - plane index

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

codec options

Throws:

FormatException

IOException

See Also:

• ICompressedTileReader.getTileCodec(int)

getNativeDataType

public Class<?> getNativeDataType()

Description copied from interface: IFormatHandler

Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object). For most readers this type will be a byte array; however, some readers call external APIs that work with other types such as BufferedImage.

Specified by:

getNativeDataType in interface IFormatHandler

Overrides:

getNativeDataType in class ReaderWrapper

setId

public void setId(String id)
           throws FormatException,
IOException

Description copied from interface: IFormatHandler

Sets the current file name.

Specified by:

setId in interface IFormatHandler

Overrides:

setId in class ReaderWrapper

Throws:

FormatException

IOException