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

Example 86 with IFD

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

the class CompressDecompressTest method assertCompression.

/**
 * Tests the writing of the tiles.
 * @param compression The compression to use.
 * @param lossy whether or not this is a lossy compression type
 */
private void assertCompression(TiffCompression compression, boolean lossy) throws Exception {
    IFD ifd = new IFD();
    int w = 64;
    int h = 64;
    int bpp = 8;
    ifd.put(IFD.IMAGE_WIDTH, w);
    ifd.put(IFD.IMAGE_LENGTH, h);
    ifd.put(IFD.BITS_PER_SAMPLE, new int[] { bpp });
    ifd.put(IFD.SAMPLES_PER_PIXEL, 1);
    ifd.put(IFD.LITTLE_ENDIAN, Boolean.TRUE);
    byte[] plane = new byte[w * h * (bpp / 8)];
    for (int i = 0; i < plane.length; i++) {
        plane[i] = (byte) i;
    }
    String beforeCompression, afterCompression, afterDecompression;
    CodecOptions options = compression.getCompressionCodecOptions(ifd);
    byte[] compressed;
    beforeCompression = Hashing.md5().hashBytes(plane).toString();
    compressed = compression.compress(plane, options);
    afterCompression = Hashing.md5().hashBytes(compressed).toString();
    if (compression.equals(TiffCompression.UNCOMPRESSED)) {
        if (!beforeCompression.equals(afterCompression)) {
            fail("Compression: " + compression.getCodecName() + " " + String.format("Compression MD5 %s != %s", beforeCompression, afterCompression));
        }
        afterDecompression = Hashing.md5().hashBytes(compression.decompress(compressed, options)).toString();
        if (!beforeCompression.equals(afterDecompression)) {
            fail("Compression: " + compression.getCodecName() + " " + String.format("Decompression MD5 %s != %s", beforeCompression, afterDecompression));
        }
    } else {
        if (beforeCompression.equals(afterCompression)) {
            fail("Compression: " + compression.getCodecName() + " " + String.format("Compression MD5 %s != %s", beforeCompression, afterCompression));
        }
        afterDecompression = Hashing.md5().hashBytes(compression.decompress(compressed, options)).toString();
        if (!lossy && !beforeCompression.equals(afterDecompression)) {
            fail("Compression: " + compression.getCodecName() + " " + String.format("Decompression MD5 %s != %s", beforeCompression, afterDecompression));
        }
    }
}

Example 87 with IFD

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

the class MinimalTiffReader method get16BitLookupTable.

/* @see loci.formats.IFormatReader#get16BitLookupTable() */
@Override
public short[][] get16BitLookupTable() throws FormatException, IOException {
    FormatTools.assertId(currentId, true, 1);
    if (ifds == null || lastPlane < 0 || lastPlane >= ifds.size())
        return null;
    IFD lastIFD = ifds.get(lastPlane);
    int[] bits = lastIFD.getBitsPerSample();
    if (bits[0] <= 16 && bits[0] > 8) {
        int[] colorMap = tiffParser.getColorMap(lastIFD);
        if (colorMap == null || colorMap.length < 65536 * 3) {
            // it's possible that the LUT is only present in the first IFD
            if (lastPlane != 0) {
                lastIFD = ifds.get(0);
                colorMap = tiffParser.getColorMap(lastIFD);
                if (colorMap == null || colorMap.length < 65536 * 3)
                    return null;
            } else
                return null;
        }
        short[][] table = new short[3][colorMap.length / 3];
        int next = 0;
        for (int i = 0; i < table.length; i++) {
            for (int j = 0; j < table[0].length; j++) {
                table[i][j] = (short) (colorMap[next++] & 0xffff);
            }
        }
        return table;
    }
    return null;
}

Example 88 with IFD

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

the class TiffWriter method saveBytes.

/**
 * Saves the given image to the specified series in the current file.
 * The IFD hashtable allows specification of TIFF parameters such as bit
 * depth, compression and units.
 */
public void saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h) throws IOException, FormatException {
    if (checkParams)
        checkParams(no, buf, x, y, w, h);
    if (ifd == null)
        ifd = new IFD();
    MetadataRetrieve retrieve = getMetadataRetrieve();
    int type = FormatTools.pixelTypeFromString(retrieve.getPixelsType(series).toString());
    int index = no;
    int imageWidth = retrieve.getPixelsSizeX(series).getValue().intValue();
    int imageHeight = retrieve.getPixelsSizeY(series).getValue().intValue();
    int currentTileSizeX = getTileSizeX();
    int currentTileSizeY = getTileSizeY();
    if (currentTileSizeX != imageWidth || currentTileSizeY != imageHeight) {
        ifd.put(new Integer(IFD.TILE_WIDTH), new Long(currentTileSizeX));
        ifd.put(new Integer(IFD.TILE_LENGTH), new Long(currentTileSizeY));
    }
    if (currentTileSizeX < w || currentTileSizeY < h) {
        int numTilesX = (w + (x % currentTileSizeX) + currentTileSizeX - 1) / currentTileSizeX;
        int numTilesY = (h + (y % currentTileSizeY) + currentTileSizeY - 1) / currentTileSizeY;
        for (int yTileIndex = 0; yTileIndex < numTilesY; yTileIndex++) {
            for (int xTileIndex = 0; xTileIndex < numTilesX; xTileIndex++) {
                Region tileParams = new Region();
                tileParams.width = xTileIndex < numTilesX - 1 ? currentTileSizeX - (x % currentTileSizeX) : w - (currentTileSizeX * xTileIndex);
                tileParams.height = yTileIndex < numTilesY - 1 ? currentTileSizeY - (y % currentTileSizeY) : h - (currentTileSizeY * yTileIndex);
                tileParams.x = x + (xTileIndex * currentTileSizeX) - (xTileIndex > 0 ? (x % currentTileSizeX) : 0);
                tileParams.y = y + (yTileIndex * currentTileSizeY) - (yTileIndex > 0 ? (y % currentTileSizeY) : 0);
                byte[] tileBuf = getTile(buf, tileParams, new Region(x, y, w, h));
                // This operation is synchronized
                synchronized (this) {
                    // This operation is synchronized against the TIFF saver.
                    synchronized (tiffSaver) {
                        index = prepareToWriteImage(no, tileBuf, ifd, tileParams.x, tileParams.y, tileParams.width, tileParams.height);
                        if (index == -1) {
                            return;
                        }
                    }
                }
                tiffSaver.writeImage(tileBuf, ifd, index, type, tileParams.x, tileParams.y, tileParams.width, tileParams.height, no == getPlaneCount() - 1 && getSeries() == retrieve.getImageCount() - 1);
            }
        }
    } else {
        // This operation is synchronized
        synchronized (this) {
            // This operation is synchronized against the TIFF saver.
            synchronized (tiffSaver) {
                index = prepareToWriteImage(no, buf, ifd, x, y, w, h);
                if (index == -1) {
                    return;
                }
            }
        }
        tiffSaver.writeImage(buf, ifd, index, type, x, y, w, h, no == getPlaneCount() - 1 && getSeries() == retrieve.getImageCount() - 1);
    }
}

Example 89 with IFD

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

the class TiffWriter method saveBytes.

// -- IFormatWriter API methods --
/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
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]);
            }
            saveBytes(no, buf, ifd, x, y, w, h);
        } finally {
            RandomAccessInputStream tiffParserStream = parser.getStream();
            if (tiffParserStream != null) {
                tiffParserStream.close();
            }
        }
    } else {
        saveBytes(no, buf, ifd, x, y, w, h);
    }
}

Example 90 with IFD

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

the class LeicaReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    if (ifd == null)
        return false;
    return ifd.containsKey(new Integer(LEICA_MAGIC_TAG));
}