Examples with TiffParser loci.formats.tiff.TiffParser used on opensource projects

Example 21 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class IPWReader method getOptimalTileWidth.

/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
    FormatTools.assertId(currentId, true, 1);
    try {
        RandomAccessInputStream stream = poi.getDocumentStream(imageFiles.get(0));
        TiffParser tp = new TiffParser(stream);
        IFD ifd = tp.getFirstIFD();
        stream.close();
        return (int) ifd.getTileWidth();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile width", e);
    } catch (IOException e) {
        LOGGER.debug("Could not retrieve tile height", e);
    }
    return super.getOptimalTileWidth();
}

Example 22 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class IPWReader method get8BitLookupTable.

/* @see loci.formats.IFormatReader#get8BitLookupTable() */
@Override
public byte[][] get8BitLookupTable() throws FormatException, IOException {
    FormatTools.assertId(currentId, true, 1);
    RandomAccessInputStream stream = poi.getDocumentStream(imageFiles.get(0));
    TiffParser tp = new TiffParser(stream);
    IFD firstIFD = tp.getFirstIFD();
    int[] bits = firstIFD.getBitsPerSample();
    if (bits[0] <= 8) {
        int[] colorMap = tp.getColorMap(firstIFD);
        if (colorMap == null) {
            return null;
        }
        byte[][] table = new byte[3][colorMap.length / 3];
        int next = 0;
        for (int j = 0; j < table.length; j++) {
            for (int i = 0; i < table[0].length; i++) {
                table[j][i] = (byte) (colorMap[next++] >> 8);
            }
        }
        return table;
    }
    return null;
}

Example 23 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class IPWReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    if (poi == null) {
        initPOIService();
    }
    RandomAccessInputStream stream = poi.getDocumentStream(imageFiles.get(no));
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    tp.getSamples(ifd, buf, x, y, w, h);
    stream.close();
    return buf;
}

Example 24 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class ImprovisionTiffReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tp = new TiffParser(stream);
    String comment = tp.getComment();
    if (comment == null)
        return false;
    return comment.indexOf(IMPROVISION_MAGIC_STRING) >= 0;
}

Example 25 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class SEQReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser parser = new TiffParser(stream);
    parser.setDoCaching(false);
    IFD ifd = parser.getFirstIFD();
    if (ifd == null)
        return false;
    parser.fillInIFD(ifd);
    Object tag1 = ifd.get(IMAGE_PRO_TAG_1);
    Object tag3 = ifd.get(IMAGE_PRO_TAG_3);
    return (tag1 != null && (tag1 instanceof short[])) || (tag3 != null && (tag3 instanceof int[]));
}