Package loci.formats.in

Class SEQReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.SubResolutionFormatReader
loci.formats.in.MinimalTiffReader
loci.formats.in.BaseTiffReader
loci.formats.in.SEQReader
All Implemented Interfaces:
Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler
public class SEQReader extends BaseTiffReader
SEQReader is the file format reader for Image-Pro Sequence files.
Author:
Melissa Linkert melissa at glencoesoftware.com

  • Field Details

    • IMAGE_PRO_TAG_1

      private static final int IMAGE_PRO_TAG_1
      An array of shorts (length 12) with identical values in all of our samples; assuming this is some sort of format identifier.
      See Also:

    • IMAGE_PRO_TAG_2

      private static final int IMAGE_PRO_TAG_2
      Frame rate.
      See Also:

    • IMAGE_PRO_TAG_3

      private static final int IMAGE_PRO_TAG_3
      See Also:

    • files

      private String[] files

  • Constructor Details

    • SEQReader

      public SEQReader()
      Constructs a new Image-Pro SEQ reader.

  • Method Details

    • isThisType

      public boolean isThisType(String name, boolean open)
      Description copied from class: FormatReader
      Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).
      Specified by:
      isThisType in interface IFormatReader
      Overrides:
      isThisType in class FormatReader
      Parameters:
      open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

    • 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

    • 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

    • 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

    • 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
      Overrides:
      openBytes in class MinimalTiffReader
      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:

    • initFile

      protected void initFile(String id) throws FormatException, IOException
      Description copied from class: SubResolutionFormatReader
      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 BaseTiffReader
      Throws:
      FormatException - if a parsing error occurs processing the file.
      IOException - if an I/O error occurs processing the file

    • 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