Package loci.formats

Class FileStitcher

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.FileStitcher

All Implemented Interfaces:

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

public class FileStitcher
extends ReaderWrapper

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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	FileStitcher.ExternalSeries

Field Summary

Fields

Modifier and Type	Field	Description
private ClassList<IFormatReader>	classList
private ArrayList<CoreMetadata>	core	Core metadata.
private int	coreIndex	The number of the current series.
private boolean	doNotChangePattern
private FileStitcher.ExternalSeries[]	externals
private boolean	group
private int[][]	lenC	Component lengths for each axis type.
private int[][]	lenT	Component lengths for each axis type.
private int[][]	lenZ	Component lengths for each axis type.
private static final org.slf4j.Logger	LOGGER
private static final int	MAX_READERS
private boolean	noStitch
private boolean	patternIds	Whether string ids given should be treated as file patterns rather than single file paths.
private int	series	The number of the current series (non flat).
private int[]	sizeC	Dimensional axis lengths per file.
private int[]	sizeT	Dimensional axis lengths per file.
private int[]	sizeZ	Dimensional axis lengths per file.
private MetadataStore	store

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(IFormatReader r)	Constructs a FileStitcher with the given reader.
FileStitcher(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)	Closes the currently open file.
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)	Returns the series corresponding to the specified core 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()	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	getAdjustedIndex(int no)	Gets the local reader index for use with the given image plane.
FileInfo[]	getAdvancedSeriesUsedFiles(boolean noPixels)	Returns an array of FileInfo objects representing the files needed to open the current series.
FileInfo[]	getAdvancedUsedFiles(boolean noPixels)	Returns an array of FileInfo objects representing the files needed to open this dataset.
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()	Gets the number of valid bits per pixel.
int	getCoreIndex()	Return the index into CoreMetadata of the current resolution/series.
List<CoreMetadata>	getCoreMetadataList()	Obtains the core metadata values for the current file.
String	getDimensionOrder()	Gets a five-character string representing the dimension order in which planes will be returned.
private int	getExternalSeries()
private int	getExternalSeries(int currentSeries)
FilePattern	getFilePattern()	Gets the file pattern object used to build the list of files.
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).
MetadataStore	getMetadataStore()	Retrieves the current metadata store for this reader.
Object	getMetadataStoreRoot()	Retrieves the current metadata store's root object.
int	getPixelType()	Gets the pixel type.
IFormatReader	getReader()	Gets the wrapped reader prototype.
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)	Returns the number of parent directories that are important when processing the given list of files.
int	getResolution()	Get the current resolution level.
int	getSeries()	Gets the currently active series.
int	getSeriesCount()	Gets the number of series in this file.
Hashtable<String,Object>	getSeriesMetadata()	Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
String[]	getSeriesUsedFiles()	Returns an array of filenames needed to open the current series.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
int	getSizeC()	Gets the size of the C dimension.
int	getSizeT()	Gets the size of the T dimension.
int	getSizeX()	Gets the size of the X dimension.
int	getSizeY()	Gets the size of the Y dimension.
int	getSizeZ()	Gets the size of the Z dimension.
int	getThumbSizeX()	Get the size of the X dimension for the thumbnail.
int	getThumbSizeY()	Get the size of the Y dimension for the thumbnail.
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.
IFormatReader[]	getUnderlyingReaders()	Retrieves all underlying readers.
String[]	getUsedFiles()	Returns an array of filenames needed to open this dataset.
String[]	getUsedFiles(boolean noPixels)	Returns an array of filenames needed to open this dataset.
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.
protected void	initFile(String id)	Initializes the given file or file pattern.
protected void	initReader(int sno, int fno)
boolean	isFalseColor()	Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed() is true and the lookup table represents "real" color data.
boolean	isGroupFiles()	Returns true if we should group files in multi-file formats.
boolean	isIndexed()	Gets whether the image planes are indexed color.
boolean	isInterleaved()	Gets whether or not the channels are interleaved.
boolean	isInterleaved(int subC)	Gets whether or not the given sub-channel is interleaved.
boolean	isLittleEndian()	Gets whether the data is in little-endian format.
boolean	isOrderCertain()	Gets whether the dimension order and sizes are known, or merely guesses.
boolean	isRGB()	Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call.
boolean	isThumbnailSeries()	Gets whether the current series is a lower resolution copy of a different series.
boolean	isUsingPatternIds()	Gets whether the reader is using file patterns for IDs.
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.
Object	openPlane(int no, int x, int y, int w, int h)	Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
byte[]	openThumbBytes(int no)	Obtains a thumbnail for the specified image plane from the current file, as a byte array.
void	reopenFile()	Reopen any files that were closed, and which are expected to be open while the reader is open.
int	seriesToCoreIndex(int series)	Returns the first core index corresponding to the specified series.
void	setAxisTypes(int[] axes)	Sets the axis type for each dimensional block.
void	setCanChangePattern(boolean doChange)
void	setCoreIndex(int no)	Set the current resolution/series (ignores subresolutions).
void	setFlattenedResolutions(boolean flatten)	Set whether or not to flatten resolutions into individual series.
void	setGroupFiles(boolean group)	Specifies whether or not to force grouping in multi-file formats.
void	setId(String id)	Sets the current file name.
void	setMetadataOptions(MetadataOptions options)
void	setMetadataStore(MetadataStore store)	Sets the default metadata store for this reader.
void	setNormalized(boolean normalize)	Specifies whether or not to normalize float data.
void	setOriginalMetadataPopulated(boolean populate)	Specifies whether or not to save proprietary metadata in the MetadataStore.
void	setReaderClassList(ClassList<IFormatReader> classList)	Set the ClassList object to use when constructing any helper readers.
void	setResolution(int no)	Set the resolution level.
void	setSeries(int no)	Activates the specified series.
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

Field Details

LOGGER

private static final org.slf4j.Logger LOGGER

MAX_READERS

private static final int MAX_READERS

See Also:

• Constant Field Values

patternIds

private boolean patternIds

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

doNotChangePattern

private boolean doNotChangePattern

sizeZ

private int[] sizeZ

Dimensional axis lengths per file.

sizeC

private int[] sizeC

Dimensional axis lengths per file.

sizeT

private int[] sizeT

Dimensional axis lengths per file.

lenZ

private int[][] lenZ

Component lengths for each axis type.

lenC

private int[][] lenC

Component lengths for each axis type.

lenT

private int[][] lenT

Component lengths for each axis type.

core

private ArrayList<CoreMetadata> core

Core metadata.

coreIndex

private int coreIndex

The number of the current series.

series

private int series

The number of the current series (non flat).

noStitch

private boolean noStitch

group

private boolean group

store

private MetadataStore store

externals

private FileStitcher.ExternalSeries[] externals

classList

private ClassList<IFormatReader> classList

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(IFormatReader r)

Constructs a FileStitcher with the given reader.

Parameters:

r - The reader to use for reading stitched files.

FileStitcher

public FileStitcher(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(ClassList<IFormatReader> classList)

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

getReader

public IFormatReader getReader()

Gets the wrapped reader prototype.

Overrides:

getReader in class 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 IFormatReader getReader(int no)
                        throws FormatException,
IOException

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

Throws:

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 FormatException,
IOException

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

Throws:

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 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:

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 FormatException,
IOException

Description copied from interface: IFormatReader

Returns the number of parent directories that are important when processing the given list of files. The number of directories is relative to the common parent. For example, given a list with these two files: /path/to/file/foo /path/to/file/that/is/related A return value of 0 indicates that "/path/to/file/" is irrelevant. A return value of 1 indicates that "/path/to/" is irrelevant. Return values less than 0 are invalid. All listed files are assumed to belong to datasets of the same format.

Specified by:

getRequiredDirectories in interface IFormatReader

Overrides:

getRequiredDirectories in class ReaderWrapper

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

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

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

getSizeZ

public int getSizeZ()

Description copied from interface: IFormatReader

Gets the size of the Z dimension.

Specified by:

getSizeZ in interface IFormatReader

Overrides:

getSizeZ in class ReaderWrapper

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

getSizeT

public int getSizeT()

Description copied from interface: IFormatReader

Gets the size of the T dimension.

Specified by:

getSizeT in interface IFormatReader

Overrides:

getSizeT in class ReaderWrapper

getPixelType

public int getPixelType()

Description copied from interface: IFormatReader

Gets the pixel type.

Specified by:

getPixelType in interface IFormatReader

Overrides:

getPixelType in class ReaderWrapper

Returns:

the pixel type as an enumeration from FormatTools static pixel types such as FormatTools.INT8.

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

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

isFalseColor

public boolean isFalseColor()

Description copied from interface: IFormatReader

Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed() is true and the lookup table represents "real" color data. Returns true if IFormatReader.isIndexed() is true and the lookup table is only present to aid in visualization.

Specified by:

isFalseColor in interface IFormatReader

Overrides:

isFalseColor in class ReaderWrapper

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
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

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
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

IOException

getThumbSizeX

public int getThumbSizeX()

Description copied from interface: IFormatReader

Get the size of the X dimension for the thumbnail.

Specified by:

getThumbSizeX in interface IFormatReader

Overrides:

getThumbSizeX in class ReaderWrapper

getThumbSizeY

public int getThumbSizeY()

Description copied from interface: IFormatReader

Get the size of the Y dimension for the thumbnail.

Specified by:

getThumbSizeY in interface IFormatReader

Overrides:

getThumbSizeY in class ReaderWrapper

isLittleEndian

public boolean isLittleEndian()

Description copied from interface: IFormatReader

Gets whether the data is in little-endian format.

Specified by:

isLittleEndian in interface IFormatReader

Overrides:

isLittleEndian 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

isOrderCertain

public boolean isOrderCertain()

Description copied from interface: IFormatReader

Gets whether the dimension order and sizes are known, or merely guesses.

Specified by:

isOrderCertain in interface IFormatReader

Overrides:

isOrderCertain in class ReaderWrapper

isThumbnailSeries

public boolean isThumbnailSeries()

Description copied from interface: IFormatReader

Gets whether the current series is a lower resolution copy of a different series.

Specified by:

isThumbnailSeries in interface IFormatReader

Overrides:

isThumbnailSeries 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

isInterleaved

public boolean isInterleaved(int subC)

Description copied from interface: IFormatReader

Gets whether or not the given sub-channel is interleaved. This method exists because some data with multiple rasterized sub-dimensions within C have one sub-dimension interleaved, and the other not—e.g., SDTReader handles spectral-lifetime data with interleaved lifetime bins and non-interleaved spectral channels.

Specified by:

isInterleaved in interface IFormatReader

Overrides:

isInterleaved 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.

openPlane

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

Description copied from interface: IFormatReader

Obtains the specified image plane (or sub-image thereof) in the reader's native data structure. For most readers this is a byte array; however, some readers call external APIs that work with other types such as BufferedImage. The openPlane method exists to maintain generality and efficiency while avoiding pollution of the API with AWT-specific logic.

Specified by:

openPlane in interface IFormatReader

Overrides:

openPlane in class ReaderWrapper

Throws:

FormatException

IOException

See Also:

• FormatReader
• BufferedImageReader

openThumbBytes

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

Description copied from interface: IFormatReader

Obtains a thumbnail for the specified image plane from the current file, as a byte array.

Specified by:

openThumbBytes in interface IFormatReader

Overrides:

openThumbBytes in class ReaderWrapper

Throws:

FormatException

IOException

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Overrides:

close in class ReaderWrapper

Throws:

IOException

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class ReaderWrapper

Throws:

IOException

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

setSeries

public void setSeries(int no)

Description copied from interface: IFormatReader

Activates the specified series. This also resets the resolution to 0.

Specified by:

setSeries in interface IFormatReader

Overrides:

setSeries in class ReaderWrapper

getSeries

public int getSeries()

Description copied from interface: IFormatReader

Gets the currently active series.

Specified by:

getSeries in interface IFormatReader

Overrides:

getSeries in class ReaderWrapper

setResolution

public void setResolution(int no)

Description copied from interface: IPyramidHandler

Set the resolution level.

Specified by:

setResolution in interface IPyramidHandler

Overrides:

setResolution in class ReaderWrapper

See Also:

• IPyramidHandler.getResolutionCount()

getResolution

public int getResolution()

Description copied from interface: IPyramidHandler

Get the current resolution level.

Specified by:

getResolution in interface IPyramidHandler

Overrides:

getResolution in class ReaderWrapper

See Also:

• IPyramidHandler.getResolutionCount()

seriesToCoreIndex

public int seriesToCoreIndex(int series)

Description copied from interface: IFormatReader

Returns the first core index corresponding to the specified series.

Specified by:

seriesToCoreIndex in interface IFormatReader

Overrides:

seriesToCoreIndex in class ReaderWrapper

coreIndexToSeries

public int coreIndexToSeries(int index)

Description copied from interface: IFormatReader

Returns the series corresponding to the specified core index.

Specified by:

coreIndexToSeries in interface IFormatReader

Overrides:

coreIndexToSeries in class ReaderWrapper

setCoreIndex

public void setCoreIndex(int no)

Description copied from interface: IFormatReader

Set the current resolution/series (ignores subresolutions). Equivalent to setSeries, but with flattened resolutions always set to false.

Specified by:

setCoreIndex in interface IFormatReader

Overrides:

setCoreIndex in class ReaderWrapper

getCoreIndex

public int getCoreIndex()

Description copied from interface: IFormatReader

Return the index into CoreMetadata of the current resolution/series.

Specified by:

getCoreIndex in interface IFormatReader

Overrides:

getCoreIndex in class ReaderWrapper

setFlattenedResolutions

public void setFlattenedResolutions(boolean flatten)

Description copied from interface: IFormatReader

Set whether or not to flatten resolutions into individual series.

Specified by:

setFlattenedResolutions in interface IFormatReader

Overrides:

setFlattenedResolutions in class ReaderWrapper

setGroupFiles

public void setGroupFiles(boolean group)

Description copied from interface: IFormatReader

Specifies whether or not to force grouping in multi-file formats.

Specified by:

setGroupFiles in interface IFormatReader

Overrides:

setGroupFiles in class ReaderWrapper

See Also:

• IFormatReader.fileGroupOption(String)
• IFormatReader.isGroupFiles()

isGroupFiles

public boolean isGroupFiles()

Description copied from interface: IFormatReader

Returns true if we should group files in multi-file formats.

Specified by:

isGroupFiles in interface IFormatReader

Overrides:

isGroupFiles in class ReaderWrapper

See Also:

• IFormatReader.setGroupFiles(boolean)
• IFormatReader.fileGroupOption(String)

setMetadataOptions

public void setMetadataOptions(MetadataOptions options)

Specified by:

setMetadataOptions in interface IMetadataConfigurable

Overrides:

setMetadataOptions in class ReaderWrapper

setNormalized

public void setNormalized(boolean normalize)

Description copied from interface: IFormatReader

Specifies whether or not to normalize float data.

Specified by:

setNormalized in interface IFormatReader

Overrides:

setNormalized in class ReaderWrapper

setOriginalMetadataPopulated

public void setOriginalMetadataPopulated(boolean populate)

Description copied from interface: IFormatReader

Specifies whether or not to save proprietary metadata in the MetadataStore.

Specified by:

setOriginalMetadataPopulated in interface IFormatReader

Overrides:

setOriginalMetadataPopulated in class ReaderWrapper

getUsedFiles

public String[] getUsedFiles()

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. The first element in the array is expected to be the path passed to IFormatHandler.setId(String). The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getUsedFiles in interface IFormatReader

Overrides:

getUsedFiles in class ReaderWrapper

getUsedFiles

public String[] getUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getUsedFiles in interface IFormatReader

Overrides:

getUsedFiles in class ReaderWrapper

getSeriesUsedFiles

public String[] getSeriesUsedFiles()

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. The first element in the array is expected to be the path passed to IFormatHandler.setId(String). The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class ReaderWrapper

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class ReaderWrapper

getAdvancedUsedFiles

public FileInfo[] getAdvancedUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of FileInfo objects representing the files needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

Specified by:

getAdvancedUsedFiles in interface IFormatReader

Overrides:

getAdvancedUsedFiles in class ReaderWrapper

getAdvancedSeriesUsedFiles

public FileInfo[] getAdvancedSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of FileInfo objects representing the files needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

Specified by:

getAdvancedSeriesUsedFiles in interface IFormatReader

Overrides:

getAdvancedSeriesUsedFiles 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

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

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

getSeriesMetadata

public Hashtable<String,Object> getSeriesMetadata()

Description copied from interface: IFormatReader

Obtains the hashtable containing metadata field/value pairs from the current series in the current file.

Specified by:

getSeriesMetadata in interface IFormatReader

Overrides:

getSeriesMetadata in class ReaderWrapper

getCoreMetadataList

public List<CoreMetadata> getCoreMetadataList()

Description copied from interface: IFormatReader

Obtains the core metadata values for the current file.

Specified by:

getCoreMetadataList in interface IFormatReader

Overrides:

getCoreMetadataList in class ReaderWrapper

setMetadataStore

public void setMetadataStore(MetadataStore store)

Description copied from interface: IFormatReader

Sets the default metadata store for this reader.

Specified by:

setMetadataStore in interface IFormatReader

Overrides:

setMetadataStore in class ReaderWrapper

Parameters:

store - a metadata store implementation.

getMetadataStore

public MetadataStore getMetadataStore()

Description copied from interface: IFormatReader

Retrieves the current metadata store for this reader. You can be assured that this method will never return a null metadata store.

Specified by:

getMetadataStore in interface IFormatReader

Overrides:

getMetadataStore in class ReaderWrapper

Returns:

A metadata store implementation.

getMetadataStoreRoot

public Object getMetadataStoreRoot()

Description copied from interface: IFormatReader

Retrieves the current metadata store's root object. It is guaranteed that all file parsing has been performed by the reader prior to retrieval. Requests for a full populated root object should be made using this method.

Specified by:

getMetadataStoreRoot in interface IFormatReader

Overrides:

getMetadataStoreRoot in class ReaderWrapper

Returns:

Current metadata store's root object fully populated.

getUnderlyingReaders

public IFormatReader[] getUnderlyingReaders()

Description copied from interface: IFormatReader

Retrieves all underlying readers. Returns null if there are no underlying readers.

Specified by:

getUnderlyingReaders in interface IFormatReader

Overrides:

getUnderlyingReaders in class ReaderWrapper

reopenFile

public void reopenFile()
                throws IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class ReaderWrapper

Throws:

IOException

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

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)

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Initializes the given file or file pattern.

Throws:

FormatException

IOException

getExternalSeries

private int getExternalSeries()

getExternalSeries

private int getExternalSeries(int currentSeries)

computeAxisLengths

protected void computeAxisLengths()
                           throws FormatException

Computes axis length arrays, and total axis lengths.

Throws:

FormatException

computeIndices

protected int[] computeIndices(int no)
                        throws 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:

FormatException

IOException

initReader

protected void initReader(int sno,
 int fno)