Package loci.formats

Class FileStitcher

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.FileStitcher

All Implemented Interfaces:

Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler

public class FileStitcher
extends loci.formats.ReaderWrapper

Logic to stitch together files with similar names. Assumes that all files have the same characteristics (e.g., dimensions).

Field Summary

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
FileStitcher()	Constructs a FileStitcher around a new image reader.
FileStitcher(boolean patternIds)	Constructs a FileStitcher around a new image reader.
FileStitcher(loci.formats.IFormatReader r)	Constructs a FileStitcher with the given reader.
FileStitcher(loci.formats.IFormatReader r, boolean patternIds)	Constructs a FileStitcher with the given reader.

Method Summary

Modifier and Type	Method	Description
boolean	canChangePattern()
void	close()
void	close(boolean fileOnly)
protected void	computeAxisLengths()	Computes axis length arrays, and total axis lengths.
protected int[]	computeIndices(int no)	Gets the file index, and image index into that file, corresponding to the given global image index.
int	coreIndexToSeries(int index)
FilePattern	findPattern(String id)
String[]	findPatterns(String id)	Finds the file pattern for the given ID, based on the state of the file stitcher.
short[][]	get16BitLookupTable()
byte[][]	get8BitLookupTable()
int	getAdjustedIndex(int no)	Gets the local reader index for use with the given image plane.
loci.formats.FileInfo[]	getAdvancedSeriesUsedFiles(boolean noPixels)
loci.formats.FileInfo[]	getAdvancedUsedFiles(boolean noPixels)
AxisGuesser	getAxisGuesser()	Gets the axis guesser object used to guess which dimensional axes are which.
int[]	getAxisTypes()	Gets the axis type for each dimensional block.
int	getBitsPerPixel()
int	getCoreIndex()
List<loci.formats.CoreMetadata>	getCoreMetadataList()
String	getDimensionOrder()
FilePattern	getFilePattern()	Gets the file pattern object used to build the list of files.
int	getImageCount()
int	getIndex(int z, int c, int t)
int	getIndex(int z, int c, int t, int moduloZ, int moduloC, int moduloT)
loci.formats.meta.MetadataStore	getMetadataStore()
Object	getMetadataStoreRoot()
int	getPixelType()
loci.formats.IFormatReader	getReader()	Gets the wrapped reader prototype.
loci.formats.IFormatReader	getReader(int no)	Gets the reader appropriate for use with the given image plane.
DimensionSwapper	getReader(int series, int no)	Gets the reader that should be used with the given series and image plane.
int	getRequiredDirectories(String[] files)
int	getResolution()
int	getSeries()
int	getSeriesCount()
Hashtable<String,Object>	getSeriesMetadata()
String[]	getSeriesUsedFiles()
String[]	getSeriesUsedFiles(boolean noPixels)
int	getSizeC()
int	getSizeT()
int	getSizeX()
int	getSizeY()
int	getSizeZ()
int	getThumbSizeX()
int	getThumbSizeY()
loci.formats.codec.Codec	getTileCodec(int no)
loci.formats.codec.CodecOptions	getTileCodecOptions(int no, int x, int y)
loci.formats.IFormatReader[]	getUnderlyingReaders()
String[]	getUsedFiles()
String[]	getUsedFiles(boolean noPixels)
int[]	getZCTCoords(int index)
int[]	getZCTModuloCoords(int index)
protected void	initFile(String id)	Initializes the given file or file pattern.
protected void	initReader(int sno, int fno)
boolean	isFalseColor()
boolean	isGroupFiles()
boolean	isIndexed()
boolean	isInterleaved()
boolean	isInterleaved(int subC)
boolean	isLittleEndian()
boolean	isOrderCertain()
boolean	isRGB()
boolean	isThumbnailSeries()
boolean	isUsingPatternIds()	Gets whether the reader is using file patterns for IDs.
byte[]	openBytes(int no)
byte[]	openBytes(int no, byte[] buf)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	openBytes(int no, int x, int y, int w, int h)
byte[]	openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	openCompressedBytes(int no, int x, int y)
Object	openPlane(int no, int x, int y, int w, int h)
byte[]	openThumbBytes(int no)
void	reopenFile()
int	seriesToCoreIndex(int series)
void	setAxisTypes(int[] axes)	Sets the axis type for each dimensional block.
void	setCanChangePattern(boolean doChange)
void	setCoreIndex(int no)
void	setFlattenedResolutions(boolean flatten)
void	setGroupFiles(boolean group)
void	setId(String id)
void	setMetadataOptions(loci.formats.in.MetadataOptions options)
void	setMetadataStore(loci.formats.meta.MetadataStore store)
void	setNormalized(boolean normalize)
void	setOriginalMetadataPopulated(boolean populate)
void	setReaderClassList(loci.formats.ClassList<loci.formats.IFormatReader> classList)	Set the ClassList object to use when constructing any helper readers.
void	setResolution(int no)
void	setSeries(int no)
void	setUsingPatternIds(boolean patternIds)	Sets whether the reader is using file patterns for IDs.

Methods inherited from class loci.formats.ReaderWrapper

duplicate, fileGroupOption, getCurrentFile, getDatasetStructureDescription, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getMetadataOptions, getMetadataValue, getModuloC, getModuloT, getModuloZ, getNativeDataType, getOptimalTileHeight, getOptimalTileWidth, getPossibleDomains, getResolutionCount, getRGBChannelCount, getSeriesMetadataValue, getSuffixes, getSupportedMetadataLevels, getTileColumns, getTileRows, hasCompanionFiles, hasFlattenedResolutions, isMetadataComplete, isMetadataFiltered, isNormalized, isOriginalMetadataPopulated, isSingleFile, isThisType, isThisType, isThisType, isThisType, setFillColor, setMetadataFiltered, unwrap, unwrap, unwrap

Methods inherited from class java.lang.Object

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

Constructor Details

FileStitcher

public FileStitcher()

Constructs a FileStitcher around a new image reader.

FileStitcher

public FileStitcher(boolean patternIds)

Constructs a FileStitcher around a new image reader.

Parameters:

patternIds - Whether string ids given should be treated as file patterns rather than single file paths.

FileStitcher

public FileStitcher(loci.formats.IFormatReader r)

Constructs a FileStitcher with the given reader.

Parameters:

r - The reader to use for reading stitched files.

FileStitcher

public FileStitcher(loci.formats.IFormatReader r,
 boolean patternIds)

Constructs a FileStitcher with the given reader.

Parameters:

r - The reader to use for reading stitched files.

patternIds - Whether string ids given should be treated as file patterns rather than single file paths.

Method Details

setReaderClassList

public void setReaderClassList(loci.formats.ClassList<loci.formats.IFormatReader> classList)

Set the ClassList object to use when constructing any helper readers.

getReader

public loci.formats.IFormatReader getReader()

Gets the wrapped reader prototype.

Overrides:

getReader in class loci.formats.ReaderWrapper

setUsingPatternIds

public void setUsingPatternIds(boolean patternIds)

Sets whether the reader is using file patterns for IDs.

isUsingPatternIds

public boolean isUsingPatternIds()

Gets whether the reader is using file patterns for IDs.

setCanChangePattern

public void setCanChangePattern(boolean doChange)

canChangePattern

public boolean canChangePattern()

getReader

public loci.formats.IFormatReader getReader(int no)
                                     throws loci.formats.FormatException,
IOException

Gets the reader appropriate for use with the given image plane.

Throws:

loci.formats.FormatException

IOException

getReader

public DimensionSwapper getReader(int series,
 int no)

Gets the reader that should be used with the given series and image plane.

getAdjustedIndex

public int getAdjustedIndex(int no)
                     throws loci.formats.FormatException,
IOException

Gets the local reader index for use with the given image plane.

Throws:

loci.formats.FormatException

IOException

getAxisTypes

public int[] getAxisTypes()

Gets the axis type for each dimensional block.

Returns:

An array containing values from the enumeration:

• AxisGuesser.Z_AXIS: focal planes
• AxisGuesser.T_AXIS: time points
• AxisGuesser.C_AXIS: channels
• AxisGuesser.S_AXIS: series

setAxisTypes

public void setAxisTypes(int[] axes)
                  throws loci.formats.FormatException

Sets the axis type for each dimensional block.

Parameters:

axes - An array containing values from the enumeration:

• AxisGuesser.Z_AXIS: focal planes
• AxisGuesser.T_AXIS: time points
• AxisGuesser.C_AXIS: channels
• AxisGuesser.S_AXIS: series

Throws:

loci.formats.FormatException

getFilePattern

public FilePattern getFilePattern()

Gets the file pattern object used to build the list of files.

getAxisGuesser

public AxisGuesser getAxisGuesser()

Gets the axis guesser object used to guess which dimensional axes are which.

findPattern

public FilePattern findPattern(String id)

findPatterns

public String[] findPatterns(String id)

Finds the file pattern for the given ID, based on the state of the file stitcher. Takes both ID map entries and the patternIds flag into account.

getRequiredDirectories

public int getRequiredDirectories(String[] files)
                           throws loci.formats.FormatException,
IOException

Specified by:

getRequiredDirectories in interface loci.formats.IFormatReader

Overrides:

getRequiredDirectories in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

getImageCount

public int getImageCount()

Specified by:

getImageCount in interface loci.formats.IFormatReader

Overrides:

getImageCount in class loci.formats.ReaderWrapper

isRGB

public boolean isRGB()

Specified by:

isRGB in interface loci.formats.IFormatReader

Overrides:

isRGB in class loci.formats.ReaderWrapper

getSizeX

public int getSizeX()

Specified by:

getSizeX in interface loci.formats.IFormatReader

Overrides:

getSizeX in class loci.formats.ReaderWrapper

getSizeY

public int getSizeY()

Specified by:

getSizeY in interface loci.formats.IFormatReader

Overrides:

getSizeY in class loci.formats.ReaderWrapper

getSizeZ

public int getSizeZ()

Specified by:

getSizeZ in interface loci.formats.IFormatReader

Overrides:

getSizeZ in class loci.formats.ReaderWrapper

getSizeC

public int getSizeC()

Specified by:

getSizeC in interface loci.formats.IFormatReader

Overrides:

getSizeC in class loci.formats.ReaderWrapper

getSizeT

public int getSizeT()

Specified by:

getSizeT in interface loci.formats.IFormatReader

Overrides:

getSizeT in class loci.formats.ReaderWrapper

getPixelType

public int getPixelType()

Specified by:

getPixelType in interface loci.formats.IFormatReader

Overrides:

getPixelType in class loci.formats.ReaderWrapper

getBitsPerPixel

public int getBitsPerPixel()

Specified by:

getBitsPerPixel in interface loci.formats.IFormatReader

Overrides:

getBitsPerPixel in class loci.formats.ReaderWrapper

isIndexed

public boolean isIndexed()

Specified by:

isIndexed in interface loci.formats.IFormatReader

Overrides:

isIndexed in class loci.formats.ReaderWrapper

isFalseColor

public boolean isFalseColor()

Specified by:

isFalseColor in interface loci.formats.IFormatReader

Overrides:

isFalseColor in class loci.formats.ReaderWrapper

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws loci.formats.FormatException,
IOException

Specified by:

get8BitLookupTable in interface loci.formats.IFormatReader

Overrides:

get8BitLookupTable in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws loci.formats.FormatException,
IOException

Specified by:

get16BitLookupTable in interface loci.formats.IFormatReader

Overrides:

get16BitLookupTable in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

getThumbSizeX

public int getThumbSizeX()

Specified by:

getThumbSizeX in interface loci.formats.IFormatReader

Overrides:

getThumbSizeX in class loci.formats.ReaderWrapper

getThumbSizeY

public int getThumbSizeY()

Specified by:

getThumbSizeY in interface loci.formats.IFormatReader

Overrides:

getThumbSizeY in class loci.formats.ReaderWrapper

isLittleEndian

public boolean isLittleEndian()

Specified by:

isLittleEndian in interface loci.formats.IFormatReader

Overrides:

isLittleEndian in class loci.formats.ReaderWrapper

getDimensionOrder

public String getDimensionOrder()

Specified by:

getDimensionOrder in interface loci.formats.IFormatReader

Overrides:

getDimensionOrder in class loci.formats.ReaderWrapper

isOrderCertain

public boolean isOrderCertain()

Specified by:

isOrderCertain in interface loci.formats.IFormatReader

Overrides:

isOrderCertain in class loci.formats.ReaderWrapper

isThumbnailSeries

public boolean isThumbnailSeries()

Specified by:

isThumbnailSeries in interface loci.formats.IFormatReader

Overrides:

isThumbnailSeries in class loci.formats.ReaderWrapper

isInterleaved

public boolean isInterleaved()

Specified by:

isInterleaved in interface loci.formats.IFormatReader

Overrides:

isInterleaved in class loci.formats.ReaderWrapper

isInterleaved

public boolean isInterleaved(int subC)

Specified by:

isInterleaved in interface loci.formats.IFormatReader

Overrides:

isInterleaved in class loci.formats.ReaderWrapper

openBytes

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

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

openBytes

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

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

openBytes

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

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

openBytes

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

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

openPlane

public Object openPlane(int no,
 int x,
 int y,
 int w,
 int h)
                 throws loci.formats.FormatException,
IOException

Specified by:

openPlane in interface loci.formats.IFormatReader

Overrides:

openPlane in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

openThumbBytes

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

Specified by:

openThumbBytes in interface loci.formats.IFormatReader

Overrides:

openThumbBytes in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Overrides:

close in class loci.formats.ReaderWrapper

Throws:

IOException

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface loci.formats.IFormatReader

Overrides:

close in class loci.formats.ReaderWrapper

Throws:

IOException

getSeriesCount

public int getSeriesCount()

Specified by:

getSeriesCount in interface loci.formats.IFormatReader

Overrides:

getSeriesCount in class loci.formats.ReaderWrapper

setSeries

public void setSeries(int no)

Specified by:

setSeries in interface loci.formats.IFormatReader

Overrides:

setSeries in class loci.formats.ReaderWrapper

getSeries

public int getSeries()

Specified by:

getSeries in interface loci.formats.IFormatReader

Overrides:

getSeries in class loci.formats.ReaderWrapper

setResolution

public void setResolution(int no)

Specified by:

setResolution in interface loci.formats.IPyramidHandler

Overrides:

setResolution in class loci.formats.ReaderWrapper

getResolution

public int getResolution()

Specified by:

getResolution in interface loci.formats.IPyramidHandler

Overrides:

getResolution in class loci.formats.ReaderWrapper

seriesToCoreIndex

public int seriesToCoreIndex(int series)

Specified by:

seriesToCoreIndex in interface loci.formats.IFormatReader

Overrides:

seriesToCoreIndex in class loci.formats.ReaderWrapper

coreIndexToSeries

public int coreIndexToSeries(int index)

Specified by:

coreIndexToSeries in interface loci.formats.IFormatReader

Overrides:

coreIndexToSeries in class loci.formats.ReaderWrapper

setCoreIndex

public void setCoreIndex(int no)

Specified by:

setCoreIndex in interface loci.formats.IFormatReader

Overrides:

setCoreIndex in class loci.formats.ReaderWrapper

getCoreIndex

public int getCoreIndex()

Specified by:

getCoreIndex in interface loci.formats.IFormatReader

Overrides:

getCoreIndex in class loci.formats.ReaderWrapper

setFlattenedResolutions

public void setFlattenedResolutions(boolean flatten)

Specified by:

setFlattenedResolutions in interface loci.formats.IFormatReader

Overrides:

setFlattenedResolutions in class loci.formats.ReaderWrapper

setGroupFiles

public void setGroupFiles(boolean group)

Specified by:

setGroupFiles in interface loci.formats.IFormatReader

Overrides:

setGroupFiles in class loci.formats.ReaderWrapper

isGroupFiles

public boolean isGroupFiles()

Specified by:

isGroupFiles in interface loci.formats.IFormatReader

Overrides:

isGroupFiles in class loci.formats.ReaderWrapper

setMetadataOptions

public void setMetadataOptions(loci.formats.in.MetadataOptions options)

Specified by:

setMetadataOptions in interface loci.formats.IMetadataConfigurable

Overrides:

setMetadataOptions in class loci.formats.ReaderWrapper

setNormalized

public void setNormalized(boolean normalize)

Specified by:

setNormalized in interface loci.formats.IFormatReader

Overrides:

setNormalized in class loci.formats.ReaderWrapper

setOriginalMetadataPopulated

public void setOriginalMetadataPopulated(boolean populate)

Specified by:

setOriginalMetadataPopulated in interface loci.formats.IFormatReader

Overrides:

setOriginalMetadataPopulated in class loci.formats.ReaderWrapper

getUsedFiles

public String[] getUsedFiles()

Specified by:

getUsedFiles in interface loci.formats.IFormatReader

Overrides:

getUsedFiles in class loci.formats.ReaderWrapper

getUsedFiles

public String[] getUsedFiles(boolean noPixels)

Specified by:

getUsedFiles in interface loci.formats.IFormatReader

Overrides:

getUsedFiles in class loci.formats.ReaderWrapper

getSeriesUsedFiles

public String[] getSeriesUsedFiles()

Specified by:

getSeriesUsedFiles in interface loci.formats.IFormatReader

Overrides:

getSeriesUsedFiles in class loci.formats.ReaderWrapper

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface loci.formats.IFormatReader

Overrides:

getSeriesUsedFiles in class loci.formats.ReaderWrapper

getAdvancedUsedFiles

public loci.formats.FileInfo[] getAdvancedUsedFiles(boolean noPixels)

Specified by:

getAdvancedUsedFiles in interface loci.formats.IFormatReader

Overrides:

getAdvancedUsedFiles in class loci.formats.ReaderWrapper

getAdvancedSeriesUsedFiles

public loci.formats.FileInfo[] getAdvancedSeriesUsedFiles(boolean noPixels)

Specified by:

getAdvancedSeriesUsedFiles in interface loci.formats.IFormatReader

Overrides:

getAdvancedSeriesUsedFiles in class loci.formats.ReaderWrapper

getIndex

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

Specified by:

getIndex in interface loci.formats.IFormatReader

Overrides:

getIndex in class loci.formats.ReaderWrapper

getIndex

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

Specified by:

getIndex in interface loci.formats.IFormatReader

Overrides:

getIndex in class loci.formats.ReaderWrapper

getZCTCoords

public int[] getZCTCoords(int index)

Specified by:

getZCTCoords in interface loci.formats.IFormatReader

Overrides:

getZCTCoords in class loci.formats.ReaderWrapper

getZCTModuloCoords

public int[] getZCTModuloCoords(int index)

Specified by:

getZCTModuloCoords in interface loci.formats.IFormatReader

Overrides:

getZCTModuloCoords in class loci.formats.ReaderWrapper

getSeriesMetadata

public Hashtable<String,Object> getSeriesMetadata()

Specified by:

getSeriesMetadata in interface loci.formats.IFormatReader

Overrides:

getSeriesMetadata in class loci.formats.ReaderWrapper

getCoreMetadataList

public List<loci.formats.CoreMetadata> getCoreMetadataList()

Specified by:

getCoreMetadataList in interface loci.formats.IFormatReader

Overrides:

getCoreMetadataList in class loci.formats.ReaderWrapper

setMetadataStore

public void setMetadataStore(loci.formats.meta.MetadataStore store)

Specified by:

setMetadataStore in interface loci.formats.IFormatReader

Overrides:

setMetadataStore in class loci.formats.ReaderWrapper

getMetadataStore

public loci.formats.meta.MetadataStore getMetadataStore()

Specified by:

getMetadataStore in interface loci.formats.IFormatReader

Overrides:

getMetadataStore in class loci.formats.ReaderWrapper

getMetadataStoreRoot

public Object getMetadataStoreRoot()

Specified by:

getMetadataStoreRoot in interface loci.formats.IFormatReader

Overrides:

getMetadataStoreRoot in class loci.formats.ReaderWrapper

getUnderlyingReaders

public loci.formats.IFormatReader[] getUnderlyingReaders()

Specified by:

getUnderlyingReaders in interface loci.formats.IFormatReader

Overrides:

getUnderlyingReaders in class loci.formats.ReaderWrapper

reopenFile

public void reopenFile()
                throws IOException

Specified by:

reopenFile in interface loci.formats.IFormatReader

Overrides:

reopenFile in class loci.formats.ReaderWrapper

Throws:

IOException

setId

public void setId(String id)
           throws loci.formats.FormatException,
IOException

Specified by:

setId in interface loci.formats.IFormatHandler

Overrides:

setId in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

openCompressedBytes

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

Specified by:

openCompressedBytes in interface loci.formats.ICompressedTileReader

Overrides:

openCompressedBytes in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

openCompressedBytes

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

Specified by:

openCompressedBytes in interface loci.formats.ICompressedTileReader

Overrides:

openCompressedBytes in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

getTileCodec

public loci.formats.codec.Codec getTileCodec(int no)
                                      throws loci.formats.FormatException,
IOException

Specified by:

getTileCodec in interface loci.formats.ICompressedTileReader

Overrides:

getTileCodec in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

getTileCodecOptions

public loci.formats.codec.CodecOptions getTileCodecOptions(int no,
 int x,
 int y)
                                                    throws loci.formats.FormatException,
IOException

Specified by:

getTileCodecOptions in interface loci.formats.ICompressedTileReader

Overrides:

getTileCodecOptions in class loci.formats.ReaderWrapper

Throws:

loci.formats.FormatException

IOException

initFile

protected void initFile(String id)
                 throws loci.formats.FormatException,
IOException

Initializes the given file or file pattern.

Throws:

loci.formats.FormatException

IOException

computeAxisLengths

protected void computeAxisLengths()
                           throws loci.formats.FormatException

Computes axis length arrays, and total axis lengths.

Throws:

loci.formats.FormatException

computeIndices

protected int[] computeIndices(int no)
                        throws loci.formats.FormatException,
IOException

Gets the file index, and image index into that file, corresponding to the given global image index.

Returns:

An array of size 2, dimensioned {file index, image index}.

Throws:

loci.formats.FormatException

IOException

initReader

protected void initReader(int sno,
 int fno)