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

Example 51 with IFD

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

the class WritePrecompressedPlanes method main.

public static void main(String[] args) throws FormatException, IOException {
    // print usage if no args specified
    if (args.length == 0) {
        System.out.println("Usage: java WritePrecompressedPlanes " + "[input file 1] ... [input file n] [output file]");
        System.exit(0);
    }
    // first n - 1 args are the input files
    String[] inputFiles = new String[args.length - 1];
    System.arraycopy(args, 0, inputFiles, 0, inputFiles.length);
    // last arg is the output file
    String outputFile = args[args.length - 1];
    // open up one of the input files so that we can read the metadata
    // this assumes that the dimensions of the input files are the same
    ImageReader reader = new ImageReader();
    reader.setId(inputFiles[0]);
    int pixelType = reader.getPixelType();
    // write the pixel data to the output file
    RandomAccessOutputStream out = new RandomAccessOutputStream(outputFile);
    TiffSaver saver = new TiffSaver(out, outputFile);
    saver.setWritingSequentially(true);
    saver.setLittleEndian(reader.isLittleEndian());
    saver.setBigTiff(false);
    saver.writeHeader();
    for (int i = 0; i < inputFiles.length; i++) {
        RandomAccessInputStream in = new RandomAccessInputStream(inputFiles[i]);
        byte[] buf = new byte[(int) in.length()];
        in.readFully(buf);
        in.close();
        IFD ifd = new IFD();
        ifd.put(IFD.IMAGE_WIDTH, reader.getSizeX());
        ifd.put(IFD.IMAGE_LENGTH, reader.getSizeY());
        ifd.put(IFD.LITTLE_ENDIAN, reader.isLittleEndian());
        ifd.put(IFD.SAMPLE_FORMAT, FormatTools.isSigned(pixelType) ? 2 : FormatTools.isFloatingPoint(pixelType) ? 3 : 1);
        ifd.put(IFD.PLANAR_CONFIGURATION, 1);
        ifd.put(IFD.REUSE, out.length());
        out.seek(out.length());
        // this is very important
        // the data is already compressed in a single chunk, so setting the
        // number of rows per strip to something smaller than the full height
        // will require us to re-compress the data
        ifd.put(IFD.ROWS_PER_STRIP, reader.getSizeY());
        saver.writeImage(buf, ifd, i, pixelType, 0, 0, reader.getSizeX(), reader.getSizeY(), i == inputFiles.length - 1, reader.getRGBChannelCount(), true);
    }
    reader.close();
    out.close();
    // reset the TIFF file's compression flag
    // you cannot do this before the pixel data is written, otherwise
    // the pixels will be re-compressed
    saver = new TiffSaver(outputFile);
    for (int i = 0; i < inputFiles.length; i++) {
        RandomAccessInputStream in = new RandomAccessInputStream(outputFile);
        saver.overwriteLastIFDOffset(in);
        saver.overwriteIFDValue(in, i, IFD.COMPRESSION, TiffCompression.JPEG.getCode());
        in.close();
    }
    saver.getStream().close();
}

Example 52 with IFD

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

the class MinimalTiffReader method close.

/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
    super.close(fileOnly);
    if (!fileOnly) {
        if (ifds != null) {
            for (IFD ifd : ifds) {
                try {
                    if (ifd.getOnDemandStripOffsets() != null) {
                        ifd.getOnDemandStripOffsets().close();
                    }
                } catch (FormatException e) {
                    LOGGER.debug("", e);
                }
            }
        }
        ifds = null;
        thumbnailIFDs = null;
        subResolutionIFDs = null;
        lastPlane = 0;
        tiffParser = null;
        resolutionLevels = null;
        j2kCodecOptions = null;
        seriesToIFD = false;
    }
}

Example 53 with IFD

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

the class MinimalTiffReader method get8BitLookupTable.

/* @see loci.formats.IFormatReader#get8BitLookupTable() */
@Override
public byte[][] get8BitLookupTable() 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] <= 8) {
        int[] colorMap = tiffParser.getColorMap(lastIFD);
        if (colorMap == null) {
            // 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)
                    return null;
            } else
                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++) {
                if (colorMap[next] > 255) {
                    table[j][i] = (byte) ((colorMap[next++] >> 8) & 0xff);
                } else {
                    table[j][i] = (byte) (colorMap[next++] & 0xff);
                }
            }
        }
        return table;
    }
    return null;
}

Example 54 with IFD

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

the class MinimalTiffReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id, 16);
    initTiffParser();
    Boolean littleEndian = tiffParser.checkHeader();
    if (littleEndian == null) {
        throw new FormatException("Invalid TIFF file: " + id);
    }
    boolean little = littleEndian.booleanValue();
    in.order(little);
    LOGGER.info("Reading IFDs");
    IFDList allIFDs = tiffParser.getIFDs();
    if (allIFDs == null || allIFDs.size() == 0) {
        throw new FormatException("No IFDs found");
    }
    ifds = new IFDList();
    thumbnailIFDs = new IFDList();
    subResolutionIFDs = new ArrayList<IFDList>();
    for (IFD ifd : allIFDs) {
        tiffParser.fillInIFD(ifd);
        Number subfile = (Number) ifd.getIFDValue(IFD.NEW_SUBFILE_TYPE);
        int subfileType = subfile == null ? 0 : subfile.intValue();
        if (subfileType != 1 || allIFDs.size() <= 1) {
            ifds.add(ifd);
        } else if (subfileType == 1) {
            thumbnailIFDs.add(ifd);
        }
    }
    LOGGER.info("Populating metadata");
    CoreMetadata ms0 = core.get(0);
    ms0.imageCount = ifds.size();
    tiffParser.setAssumeEqualStrips(equalStrips);
    for (IFD ifd : ifds) {
        if ((ifd.getCompression() == TiffCompression.JPEG_2000 || ifd.getCompression() == TiffCompression.JPEG_2000_LOSSY) && ifd.getImageWidth() == ifds.get(0).getImageWidth()) {
            LOGGER.debug("Found IFD with JPEG 2000 compression");
            long[] stripOffsets = ifd.getStripOffsets();
            long[] stripByteCounts = ifd.getStripByteCounts();
            if (stripOffsets.length > 0) {
                long stripOffset = stripOffsets[0];
                in.seek(stripOffset);
                JPEG2000MetadataParser metadataParser = new JPEG2000MetadataParser(in, stripOffset + stripByteCounts[0]);
                resolutionLevels = metadataParser.getResolutionLevels();
                if (resolutionLevels != null && !noSubresolutions) {
                    if (LOGGER.isDebugEnabled()) {
                        LOGGER.debug(String.format("Original resolution IFD Levels %d %dx%d Tile %dx%d", resolutionLevels, ifd.getImageWidth(), ifd.getImageLength(), ifd.getTileWidth(), ifd.getTileLength()));
                    }
                    IFDList theseSubResolutionIFDs = new IFDList();
                    subResolutionIFDs.add(theseSubResolutionIFDs);
                    for (int level = 1; level <= resolutionLevels; level++) {
                        IFD newIFD = new IFD(ifd);
                        long imageWidth = ifd.getImageWidth();
                        long imageLength = ifd.getImageLength();
                        long tileWidth = ifd.getTileWidth();
                        long tileLength = ifd.getTileLength();
                        long factor = (long) Math.pow(2, level);
                        long newTileWidth = Math.round((double) tileWidth / factor);
                        newTileWidth = newTileWidth < 1 ? 1 : newTileWidth;
                        long newTileLength = Math.round((double) tileLength / factor);
                        newTileLength = newTileLength < 1 ? 1 : newTileLength;
                        long evenTilesPerRow = imageWidth / tileWidth;
                        long evenTilesPerColumn = imageLength / tileLength;
                        double remainingWidth = ((double) (imageWidth - (evenTilesPerRow * tileWidth))) / factor;
                        remainingWidth = remainingWidth < 1 ? Math.ceil(remainingWidth) : Math.round(remainingWidth);
                        double remainingLength = ((double) (imageLength - (evenTilesPerColumn * tileLength))) / factor;
                        remainingLength = remainingLength < 1 ? Math.ceil(remainingLength) : Math.round(remainingLength);
                        long newImageWidth = (long) ((evenTilesPerRow * newTileWidth) + remainingWidth);
                        long newImageLength = (long) ((evenTilesPerColumn * newTileLength) + remainingLength);
                        int resolutionLevel = Math.abs(level - resolutionLevels);
                        newIFD.put(IFD.IMAGE_WIDTH, newImageWidth);
                        newIFD.put(IFD.IMAGE_LENGTH, newImageLength);
                        newIFD.put(IFD.TILE_WIDTH, newTileWidth);
                        newIFD.put(IFD.TILE_LENGTH, newTileLength);
                        if (LOGGER.isDebugEnabled()) {
                            LOGGER.debug(String.format("Added JPEG 2000 sub-resolution IFD Level %d %dx%d " + "Tile %dx%d", resolutionLevel, newImageWidth, newImageLength, newTileWidth, newTileLength));
                        }
                        theseSubResolutionIFDs.add(newIFD);
                    }
                }
            } else {
                LOGGER.warn("IFD has no strip offsets!");
            }
        }
    }
    IFD firstIFD = ifds.get(0);
    PhotoInterp photo = firstIFD.getPhotometricInterpretation();
    int samples = firstIFD.getSamplesPerPixel();
    ms0.rgb = samples > 1 || photo == PhotoInterp.RGB;
    ms0.interleaved = false;
    ms0.littleEndian = firstIFD.isLittleEndian();
    ms0.sizeX = (int) firstIFD.getImageWidth();
    ms0.sizeY = (int) firstIFD.getImageLength();
    ms0.sizeZ = 1;
    ms0.sizeC = isRGB() ? samples : 1;
    ms0.sizeT = ifds.size();
    ms0.pixelType = firstIFD.getPixelType();
    ms0.metadataComplete = true;
    ms0.indexed = photo == PhotoInterp.RGB_PALETTE && (get8BitLookupTable() != null || get16BitLookupTable() != null);
    if (isIndexed()) {
        ms0.sizeC = 1;
        ms0.rgb = false;
        for (IFD ifd : ifds) {
            ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION, PhotoInterp.RGB_PALETTE);
        }
    }
    if (getSizeC() == 1 && !isIndexed())
        ms0.rgb = false;
    ms0.dimensionOrder = "XYCZT";
    ms0.bitsPerPixel = firstIFD.getBitsPerSample()[0];
    // New core metadata now that we know how many sub-resolutions we have.
    if (resolutionLevels != null && subResolutionIFDs.size() > 0) {
        IFDList ifds = subResolutionIFDs.get(0);
        int seriesCount = ifds.size() + 1;
        if (!hasFlattenedResolutions()) {
            ms0.resolutionCount = seriesCount;
        }
        ms0.sizeT = subResolutionIFDs.size();
        ms0.imageCount = ms0.sizeT;
        if (ms0.sizeT <= 0) {
            ms0.sizeT = 1;
        }
        if (ms0.imageCount <= 0) {
            ms0.imageCount = 1;
        }
        for (IFD ifd : ifds) {
            CoreMetadata ms = new CoreMetadata(this, 0);
            core.add(ms);
            ms.sizeX = (int) ifd.getImageWidth();
            ms.sizeY = (int) ifd.getImageLength();
            ms.sizeT = ms0.sizeT;
            ms.imageCount = ms0.imageCount;
            ms.thumbnail = true;
            ms.resolutionCount = 1;
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 55 with IFD

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

the class MinimalTiffReader method openBytes.

/**
 * @see loci.formats.FormatReader#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);
    IFD firstIFD = ifds.get(0);
    lastPlane = no;
    IFD ifd;
    if (seriesToIFD) {
        ifd = ifds.get(getSeries());
    } else {
        ifd = ifds.get(no);
    }
    if ((firstIFD.getCompression() == TiffCompression.JPEG_2000 || firstIFD.getCompression() == TiffCompression.JPEG_2000_LOSSY) && resolutionLevels != null) {
        if (getCoreIndex() > 0) {
            ifd = subResolutionIFDs.get(no).get(getCoreIndex() - 1);
        }
        setResolutionLevel(ifd);
    }
    if (tiffParser == null) {
        initTiffParser();
    }
    tiffParser.getSamples(ifd, buf, x, y, w, h);
    boolean float16 = getPixelType() == FormatTools.FLOAT && firstIFD.getBitsPerSample()[0] == 16;
    boolean float24 = getPixelType() == FormatTools.FLOAT && firstIFD.getBitsPerSample()[0] == 24;
    if (float16 || float24) {
        int nPixels = w * h * getRGBChannelCount();
        int nBytes = float16 ? 2 : 3;
        int mantissaBits = float16 ? 10 : 16;
        int exponentBits = float16 ? 5 : 7;
        int maxExponent = (int) Math.pow(2, exponentBits) - 1;
        int bits = (nBytes * 8) - 1;
        byte[] newBuf = new byte[buf.length];
        for (int i = 0; i < nPixels; i++) {
            int v = DataTools.bytesToInt(buf, i * nBytes, nBytes, isLittleEndian());
            int sign = v >> bits;
            int exponent = (v >> mantissaBits) & (int) (Math.pow(2, exponentBits) - 1);
            int mantissa = v & (int) (Math.pow(2, mantissaBits) - 1);
            if (exponent == 0) {
                if (mantissa != 0) {
                    while ((mantissa & (int) Math.pow(2, mantissaBits)) == 0) {
                        mantissa <<= 1;
                        exponent--;
                    }
                    exponent++;
                    mantissa &= (int) (Math.pow(2, mantissaBits) - 1);
                    exponent += 127 - (Math.pow(2, exponentBits - 1) - 1);
                }
            } else if (exponent == maxExponent) {
                exponent = 255;
            } else {
                exponent += 127 - (Math.pow(2, exponentBits - 1) - 1);
            }
            mantissa <<= (23 - mantissaBits);
            int value = (sign << 31) | (exponent << 23) | mantissa;
            DataTools.unpackBytes(value, newBuf, i * 4, 4, isLittleEndian());
        }
        System.arraycopy(newBuf, 0, buf, 0, newBuf.length);
    }
    return buf;
}