loci.formats

Class TileStitcher

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.TileStitcher

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

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 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
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.
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).
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, getDimensionOrder, getDomains, getEffectiveSizeC, 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, 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 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,
                        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 image index within the file.

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 image index within the file.

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.

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

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