Package loci.formats.in

Class NikonTiffReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.SubResolutionFormatReader
loci.formats.in.MinimalTiffReader
loci.formats.in.BaseTiffReader
loci.formats.in.NikonTiffReader
All Implemented Interfaces:
Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler
public class NikonTiffReader extends BaseTiffReader
NikonTiffReader is the file format reader for Nikon TIFF files.

  • Field Details

    • TOP_LEVEL_KEYS

      private static final String[] TOP_LEVEL_KEYS

    • physicalSizeX

      private double physicalSizeX

    • physicalSizeY

      private double physicalSizeY

    • physicalSizeZ

      private double physicalSizeZ

    • filterModels

      private List<String> filterModels

    • dichroicModels

      private List<String> dichroicModels

    • laserIDs

      private List<String> laserIDs

    • magnification

      private Double magnification

    • lensNA

      private double lensNA

    • workingDistance

      private double workingDistance

    • pinholeSize

      private double pinholeSize

    • correction

      private String correction

    • immersion

      private String immersion

    • gain

      private List<Double> gain

    • wavelength

      private List<Double> wavelength

    • emWave

      private List<Double> emWave

    • exWave

      private List<Double> exWave

  • Constructor Details

    • NikonTiffReader

      public NikonTiffReader()

  • Method Details

    • isThisType

      public boolean isThisType(loci.common.RandomAccessInputStream stream) throws IOException
      Description copied from interface: IFormatReader
      Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.
      Specified by:
      isThisType in interface IFormatReader
      Overrides:
      isThisType in class MinimalTiffReader
      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

    • close

      public void close(boolean fileOnly) throws 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 MinimalTiffReader
      Throws:
      IOException

    • initStandardMetadata

      protected void initStandardMetadata() throws FormatException, IOException
      Description copied from class: BaseTiffReader
      Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.
      Overrides:
      initStandardMetadata in class BaseTiffReader
      Throws:
      FormatException
      IOException

    • initMetadataStore

      protected void initMetadataStore() throws FormatException
      Description copied from class: BaseTiffReader
      Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself. All calls to the active MetadataStore should be made in this method and only in this method. This is especially important for sub-classes that override the getters for pixel set array size, etc.
      Overrides:
      initMetadataStore in class BaseTiffReader
      Throws:
      FormatException

    • parseDimensionSizes

      private void parseDimensionSizes(String[] labels, String[] sizes)