loci.formats.in

## Class TiffDelegateReader

- java.lang.Object
- - loci.formats.FormatHandler
  - - loci.formats.FormatReader
    - - loci.formats.DelegateReader
      - - loci.formats.in.TiffDelegateReader

- All Implemented Interfaces:
    java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

      public class TiffDelegateReader
      extends DelegateReader

  TiffDelegateReader is a file format reader for TIFF files. It does not read files directly, but chooses which TIFF reader is more appropriate.
  See Also:
    `TiffReader`, `TiffJAIReader`

- - ### Field Summary

    - ### Fields inherited from class loci.formats.DelegateReader

      `legacyReader, legacyReaderInitialized, nativeReader, nativeReaderInitialized, useLegacy`

    - ### Fields inherited from class loci.formats.FormatReader

      `core, coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION`

    - ### Fields inherited from class loci.formats.FormatHandler

      `COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes`

    - ### Fields inherited from interface loci.formats.IFormatReader

      `CAN_GROUP, CANNOT_GROUP, MUST_GROUP`

  - ### Constructor Summary

    Constructors
    Constructor and Description
    `TiffDelegateReader()` Constructs a new TIFF reader.

  - ### Method Summary

    All Methods Instance Methods Concrete Methods
    Modifier and Type | Method and Description
    --- | ---
    `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.
    `void` | `setId(java.lang.String id)` Initialize a reader from the input file name.

    - ### Methods inherited from class loci.formats.DelegateReader

      `close, get16BitLookupTable, get8BitLookupTable, getMetadataOptions, getOptimalTileHeight, getOptimalTileWidth, getSeriesUsedFiles, getSupportedMetadataLevels, isLegacy, isThisType, isThisType, reopenFile, setCoreIndex, setFlattenedResolutions, setGroupFiles, setLegacy, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries`

    - ### Methods inherited from class loci.formats.FormatReader

      `addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, initFile, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, seriesToCoreIndex, setFillColor, updateMetadataLists`

    - ### Methods inherited from class loci.formats.FormatHandler

      `checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes`

    - ### Methods inherited from class java.lang.Object

      `clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

    - ### Methods inherited from interface loci.formats.IFormatHandler

      `getFormat, getNativeDataType, getSuffixes`

    - ### Methods inherited from interface loci.formats.ICompressedTileReader

      `getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes`

- - ### Constructor Detail

    - #### TiffDelegateReader

          public TiffDelegateReader()

      Constructs a new TIFF reader.

  - ### Method Detail

    - #### 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 `DelegateReader`
      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.

    - #### setId

          public void setId(java.lang.String id)
                     throws FormatException,
                            java.io.IOException

      Description copied from class: `FormatReader`
      Initialize a reader from the input file name. Call `FormatReader.initFile(String id)` to initialize the input file, read all of the metadata and set the reader up for reading planes. The performance of this method depends on the format and can be up to several minutes for large file sets.
      Specified by:
        `setId` in interface `IFormatHandler`
      Overrides:
        `setId` in class `DelegateReader`
      Parameters:
        `id` - a `String` specifying the path to the file
      Throws:
        `FormatException`
        `java.io.IOException`

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