loci.formats

Class DimensionSwapper

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.DimensionSwapper

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

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).

Source code:

Trac, Gitweb

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

Method Summary

Methods

Modifier and Type	Method and Description
int[]	getChannelDimLengths() Gets the lengths of each subdimension of C, in fastest-to-slowest rasterization order.
String[]	getChannelDimTypes() Gets the name of each subdimension of C, in fastest-to-slowest rasterization order.
CoreMetadata[]	getCoreMetadata() Deprecated.
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.
int	getIndex(int z, int c, int t) Gets the rasterized index corresponding to the given Z, C and T coordinates.
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.
int[]	getZCTCoords(int no) Gets the Z, C and T coordinates 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[]	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(String id) Sets the current file name.
void	setOutputOrder(String outputOrder) Sets the output dimension order according to the given string (e.g., "XYZCT").
void	swapDimensions(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, 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, getUnderlyingReaders, getUsedFiles, getUsedFiles, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, 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

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(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(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 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

getChannelDimLengths

public int[] getChannelDimLengths()

Description copied from interface: IFormatReader

Gets the lengths of each subdimension of C, in fastest-to-slowest rasterization order.

Specified by:

getChannelDimLengths in interface IFormatReader

Overrides:

getChannelDimLengths in class ReaderWrapper

getChannelDimTypes

public String[] getChannelDimTypes()

Description copied from interface: IFormatReader

Gets the name of each subdimension of C, in fastest-to-slowest rasterization order. Common subdimensional types are enumerated in FormatTools.

Specified by:

getChannelDimTypes in interface IFormatReader

Overrides:

getChannelDimTypes 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

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,
               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)
                 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,
               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.

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

getZCTCoords

public int[] getZCTCoords(int no)

Description copied from interface: IFormatReader

Gets the Z, C and T coordinates corresponding to the given rasterized index value.

Specified by:

getZCTCoords in interface IFormatReader

Overrides:

getZCTCoords 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.

Specified by:

getIndex in interface IFormatReader

Overrides:

getIndex in class ReaderWrapper

getCoreMetadata

public CoreMetadata[] getCoreMetadata()

Deprecated.

Description copied from interface: IFormatReader

Obtains the core metadata values for the current file.

Specified by:

getCoreMetadata in interface IFormatReader

Overrides:

getCoreMetadata in class ReaderWrapper

See Also:

IFormatReader.getCoreMetadataList()

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

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

reorder

protected int reorder(int no)