Package loci.formats

Interface IFormatReader

All Superinterfaces:
AutoCloseable, Closeable, ICompressedTileReader, IFormatHandler, IMetadataConfigurable, IPyramidHandler
All Known Implementing Classes:
AFIReader, AIMReader, AliconaReader, AmiraReader, AnalyzeReader, APLReader, APNGReader, ARFReader, AVIReader, BaseTiffReader, BaseZeissReader, BDReader, BDVReader, BIFormatReader, BioRadGelReader, BioRadReader, BioRadSCNReader, BMPReader, BrukerReader, BufferedImageReader, BurleighReader, CanonRawReader, CellH5Reader, CellomicsReader, CellSensReader, CellVoyagerReader, CellWorxReader, ChannelFiller, ChannelMerger, ChannelSeparator, ColumbusReader, CV7000Reader, DCIMGReader, DelegateReader, DeltavisionReader, DicomReader, DimensionSwapper, DNGReader, Ecat7Reader, EPSReader, FakeReader, FEIReader, FEITiffReader, FilePatternReader, FileStitcher, FitsReader, FlexReader, FlowSightReader, FluoviewReader, FormatReader, FujiReader, FV1000Reader, GatanDM2Reader, GatanReader, GelReader, GIFReader, HamamatsuVMSReader, HISReader, HitachiReader, HRDGDFReader, I2IReader, ICSReader, IM3Reader, ImaconReader, ImageIOReader, ImageProcessorReader, ImageReader, ImagicReader, ImarisHDFReader, ImarisReader, ImarisTiffReader, IMODReader, ImprovisionTiffReader, ImspectorReader, InCell3000Reader, InCellReader, INRReader, InveonReader, IonpathMIBITiffReader, IPLabReader, IPWReader, IvisionReader, JDCEReader, JEOLReader, JPEG2000Reader, JPEGReader, JPEGReader.DefaultJPEGReader, JPKReader, JPXReader, KhorosReader, KLBReader, KodakReader, L2DReader, LeicaReader, LeicaSCNReader, LEOReader, LiFlimReader, LIFReader, LIMReader, LMSFileReader, LOFReader, Memoizer, MetamorphReader, MetamorphTiffReader, MetaxpressTiffReader, MIASReader, MicroCTReader, MicromanagerReader, MikroscanTiffReader, MINCReader, MinimalTiffReader, MinMaxCalculator, MNGReader, MolecularImagingReader, MRCReader, MRWReader, MultipleImagesReader, NAFReader, ND2Reader, NDPIReader, NDPISReader, NiftiReader, NikonElementsTiffReader, NikonReader, NikonTiffReader, NRRDReader, OBFReader, OIRReader, OlympusTileReader, OMETiffReader, OMEXMLReader, OpenlabRawReader, OpenlabReader, OperettaReader, OxfordInstrumentsReader, PCIReader, PCORAWReader, PCXReader, PDSReader, PerkinElmerReader, PGMReader, PhotoshopTiffReader, PictReader, PovrayReader, PQBinReader, PrairieReader, PSDReader, PyramidTiffReader, QTReader, QuesantReader, RCPNLReader, ReaderWrapper, RHKReader, SBIGReader, ScanrReader, SDTReader, SeikoReader, SEQReader, SIFReader, SimplePCITiffReader, SISReader, SlideBook7Reader, SlidebookReader, SlidebookTiffReader, SMCameraReader, SPCReader, SPEReader, SpiderReader, SubResolutionFormatReader, SVSReader, TargaReader, TCSReader, TecanReader, TextReader, TiffDelegateReader, TiffJAIReader, TiffReader, TileJPEGReader, TileStitcher, TillVisionReader, TissueFAXSReader, TopometrixReader, TrestleReader, UBMReader, UnisokuReader, VarianFDFReader, VectraReader, VeecoReader, VentanaReader, VGSAMReader, VirtualReader, VisitechReader, VolocityClippingReader, VolocityReader, WATOPReader, WrappedReader, XLEFReader, ZeissCZIReader, ZeissLMSReader, ZeissLSMReader, ZeissTIFFReader, ZeissXRMReader, ZeissZVIReader, ZipReader
public interface IFormatReader extends IFormatHandler, IPyramidHandler, ICompressedTileReader
Interface for all biological file format readers.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    CAN_GROUP
     
    static final int
    CANNOT_GROUP
     
    static final int
    MUST_GROUP
    File grouping options.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close(boolean fileOnly)
    Closes the currently open file.
    int
    coreIndexToSeries(int index)
    Deprecated.
    This method is no longer required for sub-resolution support.
    int
    fileGroupOption(String id)
    Returns an indication of whether the files in a multi-file dataset can be handled individually.
    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.
    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.
    int
    getBitsPerPixel()
    Gets the number of valid bits per pixel.
    int
    getCoreIndex()
    Deprecated.
    This method is no longer required for sub-resolution support.
    List<CoreMetadata>
    getCoreMetadataList()
    Deprecated.
    Reader internals should not be accessed by reader users
    String
    getCurrentFile()
    Returns the current file.
    String
    getDatasetStructureDescription()
    Returns a short description of the dataset structure.
    String
    getDimensionOrder()
    Gets a five-character string representing the dimension order in which planes will be returned.
    String[]
    getDomains()
    Returns the list of domains represented by the current file.
    int
    getEffectiveSizeC()
    Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
    default Byte
    getFillColor()
    Return the fill value for undefined pixels.
    Hashtable<String,Object>
    getGlobalMetadata()
    Obtains the hashtable containing the metadata field/value pairs from the current file.
    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.
    Object
    getMetadataValue(String field)
    Obtains the specified metadata field's value for the current file.
    Modulo
    getModuloC()
     
    Modulo
    getModuloT()
     
    Modulo
    getModuloZ()
     
    int
    getOptimalTileHeight()
    Returns the optimal sub-image height for use with openBytes.
    int
    getOptimalTileWidth()
    Returns the optimal sub-image width for use with openBytes.
    int
    getPixelType()
    Gets the pixel type.
    String[]
    getPossibleDomains(String id)
    Returns a list of scientific domains in which this format is used.
    int
    getRequiredDirectories(String[] files)
    Returns the number of parent directories that are important when processing the given list of files.
    int
    getRGBChannelCount()
    Gets the number of channels returned with each call to openBytes.
    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.
    Object
    getSeriesMetadataValue(String field)
    Obtains the specified metadata field's value for 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.
    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.
    boolean
    hasCompanionFiles()
    Returns true if this format supports multi-file datasets.
    boolean
    hasFlattenedResolutions()
    Return whether or not resolution flattening is enabled.
    boolean
    isFalseColor()
    Returns false if isIndexed() is false, or if 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
    isMetadataComplete()
    Returns true if this format's metadata is completely parsed.
    boolean
    isMetadataFiltered()
    Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
    boolean
    isNormalized()
    Returns true if we should normalize float data.
    boolean
    isOrderCertain()
    Gets whether the dimension order and sizes are known, or merely guesses.
    boolean
    isOriginalMetadataPopulated()
    Returns true if we should save proprietary metadata in the MetadataStore.
    boolean
    isRGB()
    Checks if the image planes in the file have more than one channel per openBytes(int) call.
    boolean
    isSingleFile(String id)
    Returns true if the named file is expected to be the only file in the dataset.
    boolean
    isThisType(byte[] block)
    Checks if the given block is a valid header for this file format.
    boolean
    isThisType(String name, boolean open)
    Checks if the given file is a valid instance of this file format.
    boolean
    isThisType(loci.common.RandomAccessInputStream stream)
    Checks if the given stream is a valid stream for this file format.
    boolean
    isThumbnailSeries()
    Gets whether the current series is a lower resolution copy of a different series.
    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).
    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)
    Deprecated.
    This method is no longer required for sub-resolution support.
    void
    setCoreIndex(int no)
    Deprecated.
    This method is no longer required for sub-resolution support.
    default void
    setFillColor(Byte color)
    Set the fill value for undefined pixels.
    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
    setMetadataFiltered(boolean filter)
    Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
    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
    setSeries(int no)
    Activates the specified series.

    Methods inherited from interface java.io.Closeable

    close

    Methods inherited from interface loci.formats.ICompressedTileReader

    getTileCodec, getTileCodecOptions, getTileColumns, getTileRows, openCompressedBytes, openCompressedBytes

    Methods inherited from interface loci.formats.IFormatHandler

    getFormat, getNativeDataType, getSuffixes, isThisType, setId

    Methods inherited from interface loci.formats.IMetadataConfigurable

    getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

    Methods inherited from interface loci.formats.IPyramidHandler

    getResolution, getResolutionCount, setResolution

  • Field Details

  • Method Details

    • isThisType

      boolean isThisType(String name, boolean open)
      Checks if the given file is a valid instance of this file format.
      Parameters:
      open - If true, and the file extension is insufficient to determine the file type, the file may be opened for further analysis, or other relatively expensive file system operations (such as file existence tests and directory listings) may be performed. If false, file system access is not allowed.

    • isThisType

      boolean isThisType(byte[] block)
      Checks if the given block is a valid header for this file format.
      See Also:

    • isThisType

      boolean isThisType(loci.common.RandomAccessInputStream stream) throws IOException
      Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.
      Parameters:
      stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.
      Returns:
      true if the file represented by the stream can be read by this reader; false otherwise.
      Throws:
      IOException

    • getImageCount

      int getImageCount()
      Determines the number of image planes in the current file.

    • isRGB

      boolean isRGB()
      Checks if the image planes in the file have more than one channel per openBytes(int) call. This method returns true if and only if getRGBChannelCount() returns a value greater than 1.

    • getSizeX

      int getSizeX()
      Gets the size of the X dimension.

    • getSizeY

      int getSizeY()
      Gets the size of the Y dimension.

    • getSizeZ

      int getSizeZ()
      Gets the size of the Z dimension.

    • getSizeC

      int getSizeC()
      Gets the size of the C dimension.

    • getSizeT

      int getSizeT()
      Gets the size of the T dimension.

    • getPixelType

      int getPixelType()
      Gets the pixel type.
      Returns:
      the pixel type as an enumeration from FormatTools static pixel types such as FormatTools.INT8.

    • getBitsPerPixel

      int getBitsPerPixel()
      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 getPixelType().

    • getEffectiveSizeC

      int getEffectiveSizeC()
      Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().

    • getRGBChannelCount

      int getRGBChannelCount()
      Gets the number of channels returned with each call to openBytes. The most common case where this value is greater than 1 is for interleaved RGB data, such as a 24-bit color image plane. However, it is possible for this value to be greater than 1 for non-interleaved data, such as an RGB TIFF with Planar rather than Chunky configuration.

    • isIndexed

      boolean isIndexed()
      Gets whether the image planes are indexed color. This value has no impact on getSizeC(), getEffectiveSizeC() or getRGBChannelCount().

    • isFalseColor

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

    • get8BitLookupTable

      byte[][] get8BitLookupTable() throws FormatException, IOException
      Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if isIndexed() returns false, then this may return null. Also, if getPixelType() returns anything other than FormatTools.INT8 or FormatTools.UINT8, this method will return null.
      Throws:
      FormatException
      IOException

    • get16BitLookupTable

      short[][] get16BitLookupTable() throws FormatException, IOException
      Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if isIndexed() returns false, then this may return null. Also, if getPixelType() returns anything other than FormatTools.INT16 or FormatTools.UINT16, this method will return null.
      Throws:
      FormatException
      IOException

    • getModuloZ

      Modulo getModuloZ()

    • getModuloC

      Modulo getModuloC()

    • getModuloT

      Modulo getModuloT()

    • getThumbSizeX

      int getThumbSizeX()
      Get the size of the X dimension for the thumbnail.

    • getThumbSizeY

      int getThumbSizeY()
      Get the size of the Y dimension for the thumbnail.

    • isLittleEndian

      boolean isLittleEndian()
      Gets whether the data is in little-endian format.

    • getDimensionOrder

      String getDimensionOrder()
      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 isInterleaved() method will return true.

    • isOrderCertain

      boolean isOrderCertain()
      Gets whether the dimension order and sizes are known, or merely guesses.

    • isThumbnailSeries

      boolean isThumbnailSeries()
      Gets whether the current series is a lower resolution copy of a different series.

    • isInterleaved

      boolean isInterleaved()
      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, getDimensionOrder() returns XYCTZ or XYCZT, and this method returns true. Note that this flag returns whether or not the data returned by 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.

    • isInterleaved

      boolean isInterleaved(int subC)
      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.

    • openBytes

      byte[] openBytes(int no) throws FormatException, IOException
      Obtains the specified image plane from the current file as a byte array.
      Throws:
      FormatException
      IOException
      See Also:

    • openBytes

      byte[] openBytes(int no, int x, int y, int w, int h) throws FormatException, IOException
      Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
      Throws:
      FormatException
      IOException

    • openBytes

      byte[] openBytes(int no, byte[] buf) throws FormatException, IOException
      Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
      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

      byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException
      Obtains a sub-image of the specified image plane into a pre-allocated byte array.
      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

      Object openPlane(int no, int x, int y, int w, int h) throws FormatException, IOException
      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.
      Throws:
      FormatException
      IOException
      See Also:

    • openThumbBytes

      byte[] openThumbBytes(int no) throws FormatException, IOException
      Obtains a thumbnail for the specified image plane from the current file, as a byte array.
      Throws:
      FormatException
      IOException

    • close

      void close(boolean fileOnly) throws IOException
      Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().
      Throws:
      IOException

    • getSeriesCount

      int getSeriesCount()
      Gets the number of series in this file.

    • setSeries

      void setSeries(int no)
      Activates the specified series. This also resets the resolution to 0.

    • getSeries

      int getSeries()
      Gets the currently active series.

    • setNormalized

      void setNormalized(boolean normalize)
      Specifies whether or not to normalize float data.

    • isNormalized

      boolean isNormalized()
      Returns true if we should normalize float data.

    • setOriginalMetadataPopulated

      void setOriginalMetadataPopulated(boolean populate)
      Specifies whether or not to save proprietary metadata in the MetadataStore.

    • isOriginalMetadataPopulated

      boolean isOriginalMetadataPopulated()
      Returns true if we should save proprietary metadata in the MetadataStore.

    • setGroupFiles

      void setGroupFiles(boolean group)
      Specifies whether or not to force grouping in multi-file formats.
      See Also:

    • isGroupFiles

      boolean isGroupFiles()
      Returns true if we should group files in multi-file formats.
      See Also:

    • setFillColor

      default void setFillColor(Byte color)
      Set the fill value for undefined pixels. This can be used to override the default fill value defined in a reader. The default implementation in IFormatReader is a no-op.
      Parameters:
      color - value that will be used to fill pixel byte arrays

    • getFillColor

      default Byte getFillColor()
      Return the fill value for undefined pixels. The default implementation in IFormatReader always returns 0.
      See Also:

    • isMetadataComplete

      boolean isMetadataComplete()
      Returns true if this format's metadata is completely parsed.

    • fileGroupOption

      int fileGroupOption(String id) throws FormatException, IOException
      Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.
      Parameters:
      id - a file in the multi-file dataset
      Returns:
      an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).
      Throws:
      FormatException
      IOException
      See Also:

    • getUsedFiles

      String[] getUsedFiles()
      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.

    • getUsedFiles

      String[] getUsedFiles(boolean noPixels)
      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.

    • getSeriesUsedFiles

      String[] getSeriesUsedFiles()
      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.

    • getSeriesUsedFiles

      String[] getSeriesUsedFiles(boolean noPixels)
      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.

    • getAdvancedUsedFiles

      FileInfo[] getAdvancedUsedFiles(boolean noPixels)
      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.

    • getAdvancedSeriesUsedFiles

      FileInfo[] getAdvancedSeriesUsedFiles(boolean noPixels)
      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.

    • getCurrentFile

      String getCurrentFile()
      Returns the current file.

    • getDomains

      String[] getDomains()
      Returns the list of domains represented by the current file.

    • getIndex

      int getIndex(int z, int c, int t)
      Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).

    • getIndex

      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). 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.

    • getZCTCoords

      int[] getZCTCoords(int index)
      Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.

    • getZCTModuloCoords

      int[] getZCTModuloCoords(int index)
      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.

    • getMetadataValue

      Object getMetadataValue(String field)
      Obtains the specified metadata field's value for the current file.
      Parameters:
      field - the name associated with the metadata field
      Returns:
      the value, or null if the field doesn't exist

    • getSeriesMetadataValue

      Object getSeriesMetadataValue(String field)
      Obtains the specified metadata field's value for the current series in the current file.
      Parameters:
      field - the name associated with the metadata field
      Returns:
      the value, or null if the field doesn't exist

    • getGlobalMetadata

      Hashtable<String,Object> getGlobalMetadata()
      Obtains the hashtable containing the metadata field/value pairs from the current file.
      Returns:
      the hashtable containing all non-series-specific metadata from the file

    • getSeriesMetadata

      Hashtable<String,Object> getSeriesMetadata()
      Obtains the hashtable containing metadata field/value pairs from the current series in the current file.

    • getCoreMetadataList

      @Deprecated List<CoreMetadata> getCoreMetadataList()
      Deprecated.
      Reader internals should not be accessed by reader users
      Obtains the core metadata values for the current file.

    • setMetadataFiltered

      void setMetadataFiltered(boolean filter)
      Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.

    • isMetadataFiltered

      boolean isMetadataFiltered()
      Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.

    • setMetadataStore

      void setMetadataStore(MetadataStore store)
      Sets the default metadata store for this reader.
      Parameters:
      store - a metadata store implementation.

    • getMetadataStore

      MetadataStore getMetadataStore()
      Retrieves the current metadata store for this reader. You can be assured that this method will never return a null metadata store.
      Returns:
      A metadata store implementation.

    • getMetadataStoreRoot

      Object getMetadataStoreRoot()
      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.
      Returns:
      Current metadata store's root object fully populated.

    • getUnderlyingReaders

      IFormatReader[] getUnderlyingReaders()
      Retrieves all underlying readers. Returns null if there are no underlying readers.

    • isSingleFile

      boolean isSingleFile(String id) throws FormatException, IOException
      Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.
      Throws:
      FormatException
      IOException

    • getRequiredDirectories

      int getRequiredDirectories(String[] files) throws FormatException, IOException
      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.
      Throws:
      FormatException
      IOException

    • getDatasetStructureDescription

      String getDatasetStructureDescription()
      Returns a short description of the dataset structure.

    • getPossibleDomains

      String[] getPossibleDomains(String id) throws FormatException, IOException
      Returns a list of scientific domains in which this format is used.
      Throws:
      FormatException
      IOException

    • hasCompanionFiles

      boolean hasCompanionFiles()
      Returns true if this format supports multi-file datasets.

    • getOptimalTileWidth

      int getOptimalTileWidth()
      Returns the optimal sub-image width for use with openBytes.

    • getOptimalTileHeight

      int getOptimalTileHeight()
      Returns the optimal sub-image height for use with openBytes.

    • seriesToCoreIndex

      @Deprecated int seriesToCoreIndex(int series)
      Deprecated.
      This method is no longer required for sub-resolution support.
      Returns the first core index corresponding to the specified series.

    • coreIndexToSeries

      @Deprecated int coreIndexToSeries(int index)
      Deprecated.
      This method is no longer required for sub-resolution support.
      Returns the series corresponding to the specified core index.

    • getCoreIndex

      @Deprecated int getCoreIndex()
      Deprecated.
      This method is no longer required for sub-resolution support.
      Return the index into CoreMetadata of the current resolution/series.

    • setCoreIndex

      @Deprecated void setCoreIndex(int no)
      Deprecated.
      This method is no longer required for sub-resolution support.
      Set the current resolution/series (ignores subresolutions). Equivalent to setSeries, but with flattened resolutions always set to false.

    • hasFlattenedResolutions

      boolean hasFlattenedResolutions()
      Return whether or not resolution flattening is enabled.

    • setFlattenedResolutions

      void setFlattenedResolutions(boolean flatten)
      Set whether or not to flatten resolutions into individual series.

    • reopenFile

      void reopenFile() throws IOException
      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.
      Throws:
      IOException