loci.formats

Class ChannelFiller

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.ChannelFiller

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class ChannelFiller
extends ReaderWrapper

For indexed color data representing true color, factors out the indices, replacing them with the color table values directly. For all other data (either non-indexed, or indexed with "false color" tables), does nothing.

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.Boolean	filled Whether to fill in the indices.
protected int	lutLength Number of LUT components.

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 and Description
ChannelFiller() Constructs a ChannelFiller around a new image reader.
ChannelFiller(IFormatReader r) Constructs a ChannelFiller with a given reader.

Method Summary

Modifier and Type	Method and Description
short[][]	get16BitLookupTable() Gets the 16-bit color lookup table associated with the most recently opened image.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
int	getBitsPerPixel() Gets the number of valid bits per pixel.
private int	getLookupTableComponentCount() Gets the number of color components in the lookup table.
java.lang.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	getSizeC() Gets the size of the C dimension.
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.
boolean	isFilled() Returns true if the indices are being factored out.
boolean	isIndexed() Gets whether the image planes are indexed color.
boolean	isRGB() Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call.
static ChannelFiller	makeChannelFiller(IFormatReader r) Converts the given reader into a ChannelFiller, 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	setFilled(boolean filled) Toggles whether the indices should be factored out.
void	setId(java.lang.String id) Sets the current file name.

Methods inherited from class loci.formats.ReaderWrapper

close, close, coreIndexToSeries, duplicate, fileGroupOption, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getImageCount, getIndex, getIndex, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isInterleaved, 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 Detail

filled

protected java.lang.Boolean filled

Whether to fill in the indices. By default, indices are filled iff data not false color.

lutLength

protected int lutLength

Number of LUT components.

Constructor Detail

ChannelFiller

public ChannelFiller()

Constructs a ChannelFiller around a new image reader.

ChannelFiller

public ChannelFiller(IFormatReader r)

Constructs a ChannelFiller with a given reader.

Method Detail

makeChannelFiller

public static ChannelFiller makeChannelFiller(IFormatReader r)

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

isFilled

public boolean isFilled()

Returns true if the indices are being factored out.

setFilled

public void setFilled(boolean filled)

Toggles whether the indices should be factored out.

getSizeC

public int getSizeC()

Description copied from interface: IFormatReader

Gets the size of the C dimension.

Specified by:

getSizeC in interface IFormatReader

Overrides:

getSizeC 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

getBitsPerPixel

public int getBitsPerPixel()

Description copied from interface: IFormatReader

Gets the number of valid bits per pixel. The number of valid bits per pixel is always less than or equal to the number of bits per pixel that correspond to IFormatReader.getPixelType().

Specified by:

getBitsPerPixel in interface IFormatReader

Overrides:

getBitsPerPixel in class ReaderWrapper

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   java.io.IOException

Description copied from interface: IFormatReader

Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT8 or FormatTools.UINT8, this method will return null.

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class ReaderWrapper

Throws:

FormatException

java.io.IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.IOException

Description copied from interface: IFormatReader

Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT16 or FormatTools.UINT16, this method will return null.

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class ReaderWrapper

Throws:

FormatException

java.io.IOException

openBytes

public byte[] openBytes(int no)
                 throws FormatException,
                        java.io.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

java.io.IOException

See Also:

IFormatReader.openBytes(int, byte[])

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        java.io.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.

java.io.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,
                        java.io.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

java.io.IOException

openBytes

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

java.io.IOException - if there was a problem reading the file.

openCompressedBytes

public byte[] openCompressedBytes(int no,
                                  int x,
                                  int y)
                           throws FormatException,
                                  java.io.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 frmo 0, @see getTileRows(int))

Returns:

compressed tile bytes

Throws:

FormatException

java.io.IOException

openCompressedBytes

public byte[] openCompressedBytes(int no,
                                  byte[] buf,
                                  int x,
                                  int y)
                           throws FormatException,
                                  java.io.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 frmo 0, @see getTileRows(int))

Returns:

compressed tile bytes

Throws:

FormatException

java.io.IOException

getTileCodec

public Codec getTileCodec(int no)
                   throws FormatException,
                          java.io.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

java.io.IOException

See Also:

ICompressedTileReader.openCompressedBytes(int, int, int)

getTileCodecOptions

public CodecOptions getTileCodecOptions(int no,
                                        int x,
                                        int y)
                                 throws FormatException,
                                        java.io.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 frmo 0, @see getTileRows(int))

Returns:

codec options

Throws:

FormatException

java.io.IOException

See Also:

ICompressedTileReader.getTileCodec(int)

getNativeDataType

public java.lang.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(java.lang.String id)
           throws FormatException,
                  java.io.IOException

Description copied from interface: IFormatHandler

Sets the current file name.

Specified by:

setId in interface IFormatHandler

Overrides:

setId in class ReaderWrapper

Throws:

FormatException

java.io.IOException

getLookupTableComponentCount

private int getLookupTableComponentCount()
                                  throws FormatException,
                                         java.io.IOException

Gets the number of color components in the lookup table.

Throws:

FormatException

java.io.IOException