FileStitcher (Bio-Formats API)

java.lang.Object
- loci.formats.ReaderWrapper
- - loci.formats.FileStitcher

All Implemented Interfaces:

java.io.Closeable, java.lang.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 and Description

(package private) class FileStitcher.ExternalSeries

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

Field Summary

Fields
Modifier and Type	Field and Description
`private ClassList<IFormatReader>`	`classList`
`private java.util.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 org.slf4j.Logger`	`LOGGER`
`private static 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 and 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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(java.lang.String id)`
`java.lang.String[]`	`findPatterns(java.lang.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.
`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.
`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.
`java.lang.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(java.lang.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.
`java.util.Hashtable<java.lang.String,java.lang.Object>`	`getSeriesMetadata()` Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
`java.lang.String[]`	`getSeriesUsedFiles()` Returns an array of filenames needed to open the current series.
`java.lang.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.
`java.lang.String[]`	`getUsedFiles()` Returns an array of filenames needed to open this dataset.
`java.lang.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(java.lang.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.
`java.lang.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(java.lang.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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - 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 java.util.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 Detail
  - 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 Detail
  - 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,
                               java.io.IOException
```
    Gets the reader appropriate for use with the given image plane.
    
    Throws:
    
    FormatException
    
    java.io.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,
                            java.io.IOException
```
    Gets the local reader index for use with the given image plane.
    
    Throws:
    
    FormatException
    
    java.io.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(java.lang.String id)
```
  - findPatterns
```
public java.lang.String[] findPatterns(java.lang.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(java.lang.String[] files)
                           throws FormatException,
                                  java.io.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
    
    java.io.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,
                                   java.io.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
    
    java.io.IOException
  - get16BitLookupTable
```
public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.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
    
    java.io.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 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
  - 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,
                        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,
                        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,
                        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,
                        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.
  - openPlane
```
public java.lang.Object openPlane(int no,
                                  int x,
                                  int y,
                                  int w,
                                  int h)
                           throws FormatException,
                                  java.io.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
    
    java.io.IOException
    
    See Also:
    
    FormatReader, BufferedImageReader
  - 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
  - close
```
public void close()
           throws java.io.IOException
```
    Specified by:
    
    close in interface java.io.Closeable
    
    Specified by:
    
    close in interface java.lang.AutoCloseable
    
    Overrides:
    
    close in class ReaderWrapper
    
    Throws:
    
    java.io.IOException
  - close
```
public void close(boolean fileOnly)
           throws java.io.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:
    
    java.io.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.util.Hashtable<java.lang.String,java.lang.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 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
  - 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 java.lang.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 java.io.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:
    
    java.io.IOException
  - 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 from 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 from 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 from 0, @see getTileRows(int))
    
    Returns:
    
    codec options
    
    Throws:
    
    FormatException
    
    java.io.IOException
    
    See Also:
    
    ICompressedTileReader.getTileCodec(int)
  - initFile
```
protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.IOException
```
    Initializes the given file or file pattern.
    
    Throws:
    
    FormatException
    
    java.io.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,
                               java.io.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
    
    java.io.IOException
  - initReader
```
protected void initReader(int sno,
                          int fno)
```

Class FileStitcher

Nested Class Summary

Field Summary

Fields inherited from class loci.formats.ReaderWrapper

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.ReaderWrapper

Methods inherited from class java.lang.Object

Field Detail

LOGGER

MAX_READERS

patternIds

doNotChangePattern

sizeZ

sizeC

sizeT

lenZ

lenC

lenT

core

coreIndex

series

noStitch

group

store

externals

classList

Constructor Detail

FileStitcher

FileStitcher

FileStitcher

FileStitcher

Method Detail

setReaderClassList

getReader

setUsingPatternIds

isUsingPatternIds

setCanChangePattern

canChangePattern

getReader

getReader

getAdjustedIndex

getAxisTypes

setAxisTypes

getFilePattern

getAxisGuesser

findPattern

findPatterns

getRequiredDirectories

getImageCount

isRGB

getSizeX

getSizeY

getSizeZ

getSizeC

getSizeT

getPixelType

getBitsPerPixel

isIndexed

isFalseColor

get8BitLookupTable

get16BitLookupTable

getThumbSizeX

getThumbSizeY

isLittleEndian

getDimensionOrder

isOrderCertain

isThumbnailSeries

isInterleaved

isInterleaved

openBytes

openBytes

openBytes

openBytes

openPlane

openThumbBytes

close

close

getSeriesCount