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

Example 21 with TiffCompression

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

the class BaseTiffReader method initStandardMetadata.

/**
 * Parses standard metadata.
 *
 * NOTE: Absolutely <b>no</b> calls to the metadata store should be made in
 * this method or methods that override this method. Data <b>will</b> be
 * overwritten if you do so.
 */
protected void initStandardMetadata() throws FormatException, IOException {
    if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
        return;
    }
    for (int i = 0; i < ifds.size(); i++) {
        put("PageName #" + i, ifds.get(i), IFD.PAGE_NAME);
    }
    IFD firstIFD = ifds.get(0);
    put("ImageWidth", firstIFD, IFD.IMAGE_WIDTH);
    put("ImageLength", firstIFD, IFD.IMAGE_LENGTH);
    put("BitsPerSample", firstIFD, IFD.BITS_PER_SAMPLE);
    if (ifds.get(0).containsKey(IFD.EXIF)) {
        IFDList exifIFDs = tiffParser.getExifIFDs();
        if (exifIFDs.size() > 0) {
            IFD exif = exifIFDs.get(0);
            tiffParser.fillInIFD(exif);
            for (Integer key : exif.keySet()) {
                int k = key.intValue();
                addGlobalMeta(getExifTagName(k), exif.get(key));
            }
        }
    }
    TiffCompression comp = firstIFD.getCompression();
    put("Compression", comp.getCodecName());
    PhotoInterp photo = firstIFD.getPhotometricInterpretation();
    String photoInterp = photo.getName();
    String metaDataPhotoInterp = photo.getMetadataType();
    put("PhotometricInterpretation", photoInterp);
    put("MetaDataPhotometricInterpretation", metaDataPhotoInterp);
    putInt("CellWidth", firstIFD, IFD.CELL_WIDTH);
    putInt("CellLength", firstIFD, IFD.CELL_LENGTH);
    int or = firstIFD.getIFDIntValue(IFD.ORIENTATION);
    // adjust the width and height if necessary
    if (or == 8) {
        put("ImageWidth", firstIFD, IFD.IMAGE_LENGTH);
        put("ImageLength", firstIFD, IFD.IMAGE_WIDTH);
    }
    String orientation = null;
    // there is no case 0
    switch(or) {
        case 1:
            orientation = "1st row -> top; 1st column -> left";
            break;
        case 2:
            orientation = "1st row -> top; 1st column -> right";
            break;
        case 3:
            orientation = "1st row -> bottom; 1st column -> right";
            break;
        case 4:
            orientation = "1st row -> bottom; 1st column -> left";
            break;
        case 5:
            orientation = "1st row -> left; 1st column -> top";
            break;
        case 6:
            orientation = "1st row -> right; 1st column -> top";
            break;
        case 7:
            orientation = "1st row -> right; 1st column -> bottom";
            break;
        case 8:
            orientation = "1st row -> left; 1st column -> bottom";
            break;
    }
    put("Orientation", orientation);
    putInt("SamplesPerPixel", firstIFD, IFD.SAMPLES_PER_PIXEL);
    put("Software", firstIFD, IFD.SOFTWARE);
    put("Instrument Make", firstIFD, IFD.MAKE);
    put("Instrument Model", firstIFD, IFD.MODEL);
    put("Document Name", firstIFD, IFD.DOCUMENT_NAME);
    put("DateTime", getImageCreationDate());
    put("Artist", firstIFD, IFD.ARTIST);
    put("HostComputer", firstIFD, IFD.HOST_COMPUTER);
    put("Copyright", firstIFD, IFD.COPYRIGHT);
    put("NewSubfileType", firstIFD, IFD.NEW_SUBFILE_TYPE);
    int thresh = firstIFD.getIFDIntValue(IFD.THRESHHOLDING);
    String threshholding = null;
    switch(thresh) {
        case 1:
            threshholding = "No dithering or halftoning";
            break;
        case 2:
            threshholding = "Ordered dithering or halftoning";
            break;
        case 3:
            threshholding = "Randomized error diffusion";
            break;
    }
    put("Threshholding", threshholding);
    int fill = firstIFD.getIFDIntValue(IFD.FILL_ORDER);
    String fillOrder = null;
    switch(fill) {
        case 1:
            fillOrder = "Pixels with lower column values are stored " + "in the higher order bits of a byte";
            break;
        case 2:
            fillOrder = "Pixels with lower column values are stored " + "in the lower order bits of a byte";
            break;
    }
    put("FillOrder", fillOrder);
    putInt("Make", firstIFD, IFD.MAKE);
    putInt("Model", firstIFD, IFD.MODEL);
    putInt("MinSampleValue", firstIFD, IFD.MIN_SAMPLE_VALUE);
    putInt("MaxSampleValue", firstIFD, IFD.MAX_SAMPLE_VALUE);
    TiffRational xResolution = firstIFD.getIFDRationalValue(IFD.X_RESOLUTION);
    TiffRational yResolution = firstIFD.getIFDRationalValue(IFD.Y_RESOLUTION);
    if (xResolution != null) {
        put("XResolution", xResolution.doubleValue());
    }
    if (yResolution != null) {
        put("YResolution", yResolution.doubleValue());
    }
    int planar = firstIFD.getIFDIntValue(IFD.PLANAR_CONFIGURATION);
    String planarConfig = null;
    switch(planar) {
        case 1:
            planarConfig = "Chunky";
            break;
        case 2:
            planarConfig = "Planar";
            break;
    }
    put("PlanarConfiguration", planarConfig);
    putInt("XPosition", firstIFD, IFD.X_POSITION);
    putInt("YPosition", firstIFD, IFD.Y_POSITION);
    putInt("FreeOffsets", firstIFD, IFD.FREE_OFFSETS);
    putInt("FreeByteCounts", firstIFD, IFD.FREE_BYTE_COUNTS);
    putInt("GrayResponseUnit", firstIFD, IFD.GRAY_RESPONSE_UNIT);
    putInt("GrayResponseCurve", firstIFD, IFD.GRAY_RESPONSE_CURVE);
    putInt("T4Options", firstIFD, IFD.T4_OPTIONS);
    putInt("T6Options", firstIFD, IFD.T6_OPTIONS);
    int res = firstIFD.getIFDIntValue(IFD.RESOLUTION_UNIT);
    String resUnit = null;
    switch(res) {
        case 1:
            resUnit = "None";
            break;
        case 2:
            resUnit = "Inch";
            break;
        case 3:
            resUnit = "Centimeter";
            break;
    }
    put("ResolutionUnit", resUnit);
    putString("PageNumber", firstIFD, IFD.PAGE_NUMBER);
    putInt("TransferFunction", firstIFD, IFD.TRANSFER_FUNCTION);
    int predict = firstIFD.getIFDIntValue(IFD.PREDICTOR);
    String predictor = null;
    switch(predict) {
        case 1:
            predictor = "No prediction scheme";
            break;
        case 2:
            predictor = "Horizontal differencing";
            break;
    }
    put("Predictor", predictor);
    putInt("WhitePoint", firstIFD, IFD.WHITE_POINT);
    putInt("PrimaryChromacities", firstIFD, IFD.PRIMARY_CHROMATICITIES);
    putInt("HalftoneHints", firstIFD, IFD.HALFTONE_HINTS);
    putInt("TileWidth", firstIFD, IFD.TILE_WIDTH);
    putInt("TileLength", firstIFD, IFD.TILE_LENGTH);
    putInt("TileOffsets", firstIFD, IFD.TILE_OFFSETS);
    putInt("TileByteCounts", firstIFD, IFD.TILE_BYTE_COUNTS);
    int ink = firstIFD.getIFDIntValue(IFD.INK_SET);
    String inkSet = null;
    switch(ink) {
        case 1:
            inkSet = "CMYK";
            break;
        case 2:
            inkSet = "Other";
            break;
    }
    put("InkSet", inkSet);
    putInt("InkNames", firstIFD, IFD.INK_NAMES);
    putInt("NumberOfInks", firstIFD, IFD.NUMBER_OF_INKS);
    putInt("DotRange", firstIFD, IFD.DOT_RANGE);
    put("TargetPrinter", firstIFD, IFD.TARGET_PRINTER);
    putInt("ExtraSamples", firstIFD, IFD.EXTRA_SAMPLES);
    int fmt = firstIFD.getIFDIntValue(IFD.SAMPLE_FORMAT);
    String sampleFormat = null;
    switch(fmt) {
        case 1:
            sampleFormat = "unsigned integer";
            break;
        case 2:
            sampleFormat = "two's complement signed integer";
            break;
        case 3:
            sampleFormat = "IEEE floating point";
            break;
        case 4:
            sampleFormat = "undefined";
            break;
    }
    put("SampleFormat", sampleFormat);
    putInt("SMinSampleValue", firstIFD, IFD.S_MIN_SAMPLE_VALUE);
    putInt("SMaxSampleValue", firstIFD, IFD.S_MAX_SAMPLE_VALUE);
    putInt("TransferRange", firstIFD, IFD.TRANSFER_RANGE);
    int jpeg = firstIFD.getIFDIntValue(IFD.JPEG_PROC);
    String jpegProc = null;
    switch(jpeg) {
        case 1:
            jpegProc = "baseline sequential process";
            break;
        case 14:
            jpegProc = "lossless process with Huffman coding";
            break;
    }
    put("JPEGProc", jpegProc);
    putInt("JPEGInterchangeFormat", firstIFD, IFD.JPEG_INTERCHANGE_FORMAT);
    putInt("JPEGRestartInterval", firstIFD, IFD.JPEG_RESTART_INTERVAL);
    putInt("JPEGLosslessPredictors", firstIFD, IFD.JPEG_LOSSLESS_PREDICTORS);
    putInt("JPEGPointTransforms", firstIFD, IFD.JPEG_POINT_TRANSFORMS);
    putInt("JPEGQTables", firstIFD, IFD.JPEG_Q_TABLES);
    putInt("JPEGDCTables", firstIFD, IFD.JPEG_DC_TABLES);
    putInt("JPEGACTables", firstIFD, IFD.JPEG_AC_TABLES);
    putInt("YCbCrCoefficients", firstIFD, IFD.Y_CB_CR_COEFFICIENTS);
    int ycbcr = firstIFD.getIFDIntValue(IFD.Y_CB_CR_SUB_SAMPLING);
    String subSampling = null;
    switch(ycbcr) {
        case 1:
            subSampling = "chroma image dimensions = luma image dimensions";
            break;
        case 2:
            subSampling = "chroma image dimensions are " + "half the luma image dimensions";
            break;
        case 4:
            subSampling = "chroma image dimensions are " + "1/4 the luma image dimensions";
            break;
    }
    put("YCbCrSubSampling", subSampling);
    putInt("YCbCrPositioning", firstIFD, IFD.Y_CB_CR_POSITIONING);
    putInt("ReferenceBlackWhite", firstIFD, IFD.REFERENCE_BLACK_WHITE);
    // bits per sample and number of channels
    int[] q = firstIFD.getBitsPerSample();
    int bps = q[0];
    int numC = q.length;
    if (photo == PhotoInterp.RGB_PALETTE || photo == PhotoInterp.CFA_ARRAY) {
        numC = 3;
    }
    put("BitsPerSample", bps);
    put("NumberOfChannels", numC);
}

Example 22 with TiffCompression

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

the class TiffCompressionDecompressTest method testGROUP_4_FAX.

@Test(expectedExceptions = { FormatException.class })
public void testGROUP_4_FAX() throws FormatException, IOException {
    TiffCompression compression = TiffCompression.GROUP_3_FAX;
    assertNotNull(compression.decompress(DATA, OPTIONS));
}

Example 23 with TiffCompression

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

the class TiffCompressionDecompressTest method testTHUNDERSCAN.

@Test(expectedExceptions = { FormatException.class })
public void testTHUNDERSCAN() throws FormatException, IOException {
    TiffCompression compression = TiffCompression.THUNDERSCAN;
    assertNotNull(compression.decompress(DATA, OPTIONS));
}

Example 24 with TiffCompression

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

the class TiffCompressionDecompressTest method testGROUP_3_FAX.

@Test(expectedExceptions = { FormatException.class })
public void testGROUP_3_FAX() throws FormatException, IOException {
    TiffCompression compression = TiffCompression.GROUP_3_FAX;
    assertNotNull(compression.decompress(DATA, OPTIONS));
}

Example 25 with TiffCompression

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

the class TiffCompressionDecompressTest method testPACK_BITS.

@Test
public void testPACK_BITS() throws FormatException, IOException {
    TiffCompression compression = TiffCompression.PACK_BITS;
    assertNotNull(compression.decompress(DATA, OPTIONS));
}