Package loci.formats.in

Class VarianFDFReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.VarianFDFReader
All Implemented Interfaces:
Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler
public class VarianFDFReader extends FormatReader
VarianFDFReader is the file format reader for Varian FDF files.

  • Field Details

    • files

      private final List<String> files

    • pixelOffsets

      private long[] pixelOffsets

    • pixelSizeX

      private double pixelSizeX

    • pixelSizeY

      private double pixelSizeY

    • pixelSizeZ

      private double pixelSizeZ

    • originX

      private ome.units.quantity.Length originX

    • originY

      private ome.units.quantity.Length originY

    • originZ

      private ome.units.quantity.Length originZ

    • units

      private String[] units

  • Constructor Details

    • VarianFDFReader

      public VarianFDFReader()
      Constructs a new Varian FDF reader.

  • 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 FormatReader
      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

    • getSeriesUsedFiles

      public 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 FormatReader
      See Also:

    • openBytes

      public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException
      Description copied from interface: IFormatReader
      Obtains a sub-image of the specified image plane into a pre-allocated byte array.
      Specified by:
      openBytes in interface IFormatReader
      Specified by:
      openBytes in class FormatReader
      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.
      See Also:

    • 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 FormatReader
      Throws:
      IOException

    • initFile

      protected void initFile(String id) throws FormatException, IOException
      Description copied from class: FormatReader
      Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.
      Overrides:
      initFile in class FormatReader
      Throws:
      FormatException - if a parsing error occurs processing the file.
      IOException - if an I/O error occurs processing the file

    • parseFDF

      private void parseFDF(String file) throws FormatException, IOException
      Throws:
      FormatException
      IOException

    • parseArray

      private String[] parseArray(String value)
      Split a String that represents an array into individual elements.

    • computePhysicalSize

      private double computePhysicalSize(int length, String physicalLength, String unit)
      Return the physical size of a pixel, in microns, along an arbitrary axis based on the supplied physical and pixel lengths of the axis.
      Parameters:
      length - the length, in pixels, of the axis
      physicalLength - the length, in physical units of the axis
      unit - the units for the physical length
      Returns:
      the size, in microns, of a pixel