loci.formats

Class TileStitcher

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.TileStitcher

All Implemented Interfaces:

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

public class TileStitcher
extends ReaderWrapper

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	TileStitcher.TileCoordinate

Field Summary

Fields

Modifier and Type	Field and Description
private static org.slf4j.Logger	LOGGER
private java.lang.Integer[][]	tileMap
private int	tileX
private int	tileY

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

Method Summary

Modifier and Type	Method and Description
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	getSeriesCount() Gets the number of series in this file.
int	getSizeX() Gets the size of the X dimension.
int	getSizeY() Gets the size of the Y 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.
int	getTileColumns(int no) Get the number of columns of tiles in the specified plane in the current series.
int	getTileRows(int no) Get the number of rows of tiles in the specified plane in the current series.
static TileStitcher	makeTileStitcher(IFormatReader r) Converts the given reader into a TileStitcher, 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(java.lang.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, 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, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeZ, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, 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

LOGGER

private static final org.slf4j.Logger LOGGER

tileX

private int tileX

tileY

private int tileY

tileMap

private java.lang.Integer[][] tileMap

Constructor Detail

TileStitcher

public TileStitcher()

Constructs a TileStitcher around a new image reader.

TileStitcher

public TileStitcher(IFormatReader r)

Constructs a TileStitcher with the given reader.

Method Detail

makeTileStitcher

public static TileStitcher makeTileStitcher(IFormatReader r)

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

getSizeX

public int getSizeX()

Description copied from interface: IFormatReader

Gets the size of the X dimension.

Specified by:

getSizeX in interface IFormatReader

Overrides:

getSizeX in class ReaderWrapper

getSizeY

public int getSizeY()

Description copied from interface: IFormatReader

Gets the size of the Y dimension.

Specified by:

getSizeY in interface IFormatReader

Overrides:

getSizeY in class ReaderWrapper

getSeriesCount

public int getSeriesCount()

Description copied from interface: IFormatReader

Gets the number of series in this file.

Specified by:

getSeriesCount in interface IFormatReader

Overrides:

getSeriesCount in class ReaderWrapper

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.

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

getTileRows

public int getTileRows(int no)

Description copied from interface: ICompressedTileReader

Get the number of rows of tiles in the specified plane in the current series.

Specified by:

getTileRows in interface ICompressedTileReader

Overrides:

getTileRows in class ReaderWrapper

Parameters:

no - plane index

Returns:

tile row count

getTileColumns

public int getTileColumns(int no)

Description copied from interface: ICompressedTileReader

Get the number of columns of tiles in the specified plane in the current series.

Specified by:

getTileColumns in interface ICompressedTileReader

Overrides:

getTileColumns in class ReaderWrapper

Parameters:

no - plane index

Returns:

tile column count

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