Package loci.formats

Class ChannelMerger

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.ChannelMerger

All Implemented Interfaces:

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

public class ChannelMerger
extends ReaderWrapper

Logic to automatically merge channels in a file.

Field Summary

Fields

Modifier and Type	Field	Description
private static final org.slf4j.Logger	LOGGER

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
ChannelMerger()	Constructs a ChannelMerger around a new image reader.
ChannelMerger(IFormatReader r)	Constructs a ChannelMerger with the given reader.

Method Summary

Modifier and Type	Method	Description
boolean	canMerge()	Determines whether the channels in the file can be merged.
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	isIndexed()	Gets whether the image planes are indexed color.
boolean	isInterleaved()	Gets whether or not the channels are interleaved.
boolean	isRGB()	Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call.
static ChannelMerger	makeChannelMerger(IFormatReader r)	Converts the given reader into a ChannelMerger, 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.
void	setId(String id)	Sets the current file name.

Methods inherited from class loci.formats.ReaderWrapper

close, 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, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, openThumbBytes, 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

LOGGER

private static final org.slf4j.Logger LOGGER

Constructor Details

ChannelMerger

public ChannelMerger()

Constructs a ChannelMerger around a new image reader.

ChannelMerger

public ChannelMerger(IFormatReader r)

Constructs a ChannelMerger with the given reader.

Method Details

makeChannelMerger

public static ChannelMerger makeChannelMerger(IFormatReader r)

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

canMerge

public boolean canMerge()

Determines whether the channels in the file can be merged.

getOriginalIndex

public int getOriginalIndex(int no)
                     throws FormatException,
IOException

Returns the image number in the original dataset that corresponds to the given image number.

Parameters:

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

Returns:

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

Throws:

FormatException

IOException

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

isInterleaved

public boolean isInterleaved()

Description copied from interface: IFormatReader

Gets whether or not the channels are interleaved. This method exists because X and Y must appear first in the dimension order. For interleaved data, IFormatReader.getDimensionOrder() returns XYCTZ or XYCZT, and this method returns true. Note that this flag returns whether or not the data returned by IFormatReader.openBytes(int) is interleaved. In most cases, this will match the interleaving in the original file, but for some formats (e.g. TIFF) channel re-ordering is done internally and the return value of this method will not match what is in the original file.

Specified by:

isInterleaved in interface IFormatReader

Overrides:

isInterleaved 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

isIndexed

public boolean isIndexed()

Description copied from interface: IFormatReader

Gets whether the image planes are indexed color. This value has no impact on IFormatReader.getSizeC(), IFormatReader.getEffectiveSizeC() or IFormatReader.getRGBChannelCount().

Specified by:

isIndexed in interface IFormatReader

Overrides:

isIndexed 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.

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

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

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