loci.formats

Class DimensionSwapper

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.DimensionSwapper

All Implemented Interfaces:

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

public class DimensionSwapper
extends ReaderWrapper

Handles swapping the dimension order of an image series. This class is useful for both reassigning ZCT sizes (the input dimension order), and shuffling around the resultant planar order (the output dimension order).

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.List<CoreMetadata>	core Core metadata associated with this dimension swapper.

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

Method Summary

Modifier and Type	Method and Description
java.util.List<CoreMetadata>	getCoreMetadataList() Obtains the core metadata values for the current file.
java.lang.String	getDimensionOrder() Gets a five-character string representing the dimension order in which planes will be returned.
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).
java.lang.String	getInputOrder()
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.
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[]	getZCTCoords(int no) 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.
static DimensionSwapper	makeDimensionSwapper(IFormatReader r) Converts the given reader into a DimensionSwapper, 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.
byte[]	openThumbBytes(int no) Obtains a thumbnail for the specified image plane from the current file, as a byte array.
protected int	reorder(int no)
void	setId(java.lang.String id) Sets the current file name.
void	setOutputOrder(java.lang.String outputOrder) Sets the output dimension order according to the given string (e.g., "XYZCT").
void	swapDimensions(java.lang.String order) Sets the input dimension order according to the given string (e.g., "XYZCT").

Methods inherited from class loci.formats.ReaderWrapper

close, close, coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCurrentFile, getDatasetStructureDescription, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getImageCount, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getNativeDataType, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, 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

core

private java.util.List<CoreMetadata> core

Core metadata associated with this dimension swapper.

Constructor Detail

DimensionSwapper

public DimensionSwapper()

Constructs a DimensionSwapper around a new image reader.

DimensionSwapper

public DimensionSwapper(IFormatReader r)

Constructs a DimensionSwapper with the given reader.

Method Detail

makeDimensionSwapper

public static DimensionSwapper makeDimensionSwapper(IFormatReader r)

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

swapDimensions

public void swapDimensions(java.lang.String order)

Sets the input dimension order according to the given string (e.g., "XYZCT"). This string indicates the planar rasterization order from the source, overriding the detected order. It may result in the dimensional axis sizes changing. If the given order is identical to the file's native order, then nothing happens. Note that this method will throw an exception if X and Y do not appear in positions 0 and 1 (although X and Y can be reversed).

setOutputOrder

public void setOutputOrder(java.lang.String outputOrder)

Sets the output dimension order according to the given string (e.g., "XYZCT"). This string indicates the final planar rasterization order—i.e., the mapping from 1D plane number to 3D (Z, C, T) tuple. Changing it will not affect the Z, C or T sizes but will alter the order in which planes are returned when iterating. This method is useful when your application requires a particular output dimension order; e.g., ImageJ virtual stacks must be in XYCZT order.

getInputOrder

public java.lang.String getInputOrder()

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

getDimensionOrder

public java.lang.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

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,
                        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)
                 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,
                        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.

openThumbBytes

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

java.io.IOException

getZCTCoords

public int[] getZCTCoords(int no)

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

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

getCoreMetadataList

public java.util.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

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

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)

reorder

protected int reorder(int no)