Examples of loci.formats.tiff.TiffParser

loci.formats.tiff.TiffParser

   * @see loci.formats.FormatReader#isThisType(loci.common.RandomAccessInputStream)
   */
  @Override
  public boolean isThisType(RandomAccessInputStream stream)
      throws IOException {
    TiffParser tiffParser = new TiffParser(stream);
    if (! tiffParser.isValidHeader()) return false;
    IFD ifd = tiffParser.getFirstIFD();
    if (ifd == null) return false;
    tiffParser.fillInIFD(ifd);
    for (int tag: MINIMAL_TAGS)
      try {
        if (ifd.getIFDStringValue(tag) == null) return false;
      } catch (FormatException e) {
        return false;

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   */
  @Override
  protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
      in = new RandomAccessInputStream(id);
      tiffParser = new TiffParser(in);
      tiffParser.setDoCaching(false);
      tiffParser.setUse64BitOffsets(false);
      final Boolean littleEndian = tiffParser.checkHeader();
      if (littleEndian == null) {
        throw new FormatException("Invalid FlowSight file");

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  public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
    throws FormatException, IOException
  {
    IFD ifd = new IFD();
    if (!sequential) {
      TiffParser parser = new TiffParser(currentId);
      try {
        long[] ifdOffsets = parser.getIFDOffsets();
        if (no < ifdOffsets.length) {
          ifd = parser.getIFD(ifdOffsets[no]);
        }
      }
      finally {
        RandomAccessInputStream tiffParserStream = parser.getStream();
        if (tiffParserStream != null) {
          tiffParserStream.close();
        }
      }
    }

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  /* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
  public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    final int blockLen = 4096;
    if (!FormatTools.validStream(stream, blockLen, false)) return false;
    TiffParser parser = new TiffParser(stream);
    if (parser.isValidHeader()) {
      return true;
    }
    stream.seek(4);
    if (stream.readShort() == 0x5374) {
      String check =

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    if (getSeriesCount() > 1) {
      in.close();
      in = new RandomAccessInputStream(getLSMFileFromSeries(getSeries()));
      in.order(!isLittleEndian());
      tiffParser = new TiffParser(in);
    }


    IFDList ifds = ifdsList.get(getSeries());


    if (splitPlanes && getSizeC() > 1 && ifds.size() == getSizeZ() * getSizeT())

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    for (int i=0; i<lsmFilenames.length; i++) {
      RandomAccessInputStream stream =
        new RandomAccessInputStream(lsmFilenames[i]);
      int count = seriesCounts.get(lsmFilenames[i]);


      TiffParser tp = new TiffParser(stream);
      Boolean littleEndian = tp.checkHeader();
      long[] ifdOffsets = tp.getIFDOffsets();
      int ifdsPerSeries = (ifdOffsets.length / 2) / count;


      int offset = 0;
      Object zeissTag = null;
      for (int s=0; s<count; s++, realSeries++) {
        CoreMetadata ms = core.get(realSeries);
        ms.littleEndian = littleEndian;


        IFDList ifds = new IFDList();
        while (ifds.size() < ifdsPerSeries) {
          tp.setDoCaching(offset == 0);
          IFD ifd = tp.getIFD(ifdOffsets[offset]);
          if (offset == 0) zeissTag = ifd.get(ZEISS_ID);
          if (offset > 0 && ifds.size() == 0) {
            ifd.putIFDValue(ZEISS_ID, zeissTag);
          }
          ifds.add(ifd);
          if (zeissTag != null) offset += 2;
          else offset++;
        }


        for (IFD ifd : ifds) {
          tp.fillInIFD(ifd);
        }


        ifdsList.set(realSeries, ifds);
      }
      stream.close();

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    if (in != null) in.close();
    in = new RandomAccessInputStream(file);
    boolean littleEndian = in.read() == TiffConstants.LITTLE;
    in.order(littleEndian);


    tiffParser = new TiffParser(in);
    IFD ifd = tiffParser.getFirstIFD();
    RandomAccessInputStream ras = getCZTag(ifd);
    if (ras == null) return 1;
    ras.order(littleEndian);

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    in.close();
    in = new RandomAccessInputStream(getLSMFileFromSeries(series));
    in.order(isLittleEndian());


    tiffParser = new TiffParser(in);


    PhotoInterp photo = ifd.getPhotometricInterpretation();
    int samples = ifd.getSamplesPerPixel();


    CoreMetadata ms = core.get(series);

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Related Classes of loci.formats.tiff.TiffParser

loci.formats.in.FlowSightReader

loci.formats.in.ZeissLSMReader

loci.formats.out.TiffWriter

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