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

Example 81 with TiffParser

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

the class MetamorphTiffReader 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 {
    if (getSeriesCount() == 1 && files.length == 1 && !dualCamera) {
        return super.openBytes(no, buf, x, y, w, h);
    }
    int[] lengths = new int[] { getSizeZ(), getEffectiveSizeC(), fieldColumnCount, fieldRowCount, wellCount, getSizeT() };
    int[] zct = getZCTCoords(no);
    Well well = getWell(getSeries());
    int[] position = new int[] { zct[0], zct[1], well.fieldCol, well.fieldRow, well.well, zct[2] };
    if (dualCamera) {
        position[1] = 0;
    }
    int fileIndex = FormatTools.positionToRaster(lengths, position);
    final RandomAccessInputStream s;
    if (fileIndex < files.length) {
        s = new RandomAccessInputStream(files[fileIndex]);
    } else {
        s = new RandomAccessInputStream(files[0]);
    }
    TiffParser parser = new TiffParser(s);
    int ndx = getSeries() * getSizeZ() * getSizeT() + no;
    int[] pos = getZCTCoords(no);
    if (dualCamera) {
        int channel = pos[1];
        pos[1] = 0;
        ndx = getSeries() * getSizeZ() * getSizeT() + FormatTools.positionToRaster(new int[] { getSizeZ(), 1, getSizeT() }, pos);
        pos[1] = channel;
    }
    IFD ifd = files.length == 1 ? ifds.get(ndx) : parser.getFirstIFD();
    int realX = dualCamera ? (pos[1] == 0 ? x : x + pos[1] * getSizeX()) : x;
    parser.getSamples(ifd, buf, realX, y, w, h);
    s.close();
    return buf;
}

Example 82 with TiffParser

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

the class MetamorphTiffReader method parseFile.

private void parseFile(String tiff, MetamorphHandler handler) throws IOException {
    RandomAccessInputStream s = new RandomAccessInputStream(tiff);
    TiffParser parser = new TiffParser(s);
    IFD firstIFD = parser.getFirstIFD();
    String xml = XMLTools.sanitizeXML(firstIFD.getComment());
    XMLTools.parseXML(xml, handler);
    s.close();
}

Example 83 with TiffParser

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

the class MetamorphTiffReader 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;
    comment = comment.trim();
    return comment.startsWith("<MetaData>") && comment.endsWith("</MetaData>");
}

Example 84 with TiffParser

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

the class NDPIReader method isThisType.

// -- IFormatReader API methods --
/* (non-Javadoc)
   * @see loci.formats.FormatReader#isThisType(java.lang.String, boolean)
   */
@Override
public boolean isThisType(String name, boolean open) {
    boolean isThisType = super.isThisType(name, open);
    if (isThisType && open) {
        RandomAccessInputStream stream = null;
        TiffParser parser = null;
        try {
            stream = new RandomAccessInputStream(name);
            parser = new TiffParser(stream);
            parser.setDoCaching(false);
            parser.setUse64BitOffsets(stream.length() >= Math.pow(2, 32));
            if (!parser.isValidHeader()) {
                return false;
            }
            IFD ifd = parser.getFirstIFD();
            if (ifd == null) {
                return false;
            }
            return ifd.containsKey(MARKER_TAG);
        } catch (IOException e) {
            LOGGER.debug("I/O exception during isThisType() evaluation.", e);
            return false;
        } finally {
            try {
                if (stream != null) {
                    stream.close();
                }
                if (parser != null) {
                    parser.getStream().close();
                }
            } catch (IOException e) {
                LOGGER.debug("I/O exception during stream closure.", e);
            }
        }
    }
    return isThisType;
}

Example 85 with TiffParser

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

the class NDPISReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    Location parent = new Location(id).getAbsoluteFile().getParentFile();
    String[] lines = DataTools.readFile(currentId).split("\r\n");
    for (String line : lines) {
        int eq = line.indexOf('=');
        if (eq < 0) {
            continue;
        }
        String key = line.substring(0, eq).trim();
        String value = line.substring(eq + 1).trim();
        if (key.equals("NoImages")) {
            ndpiFiles = new String[Integer.parseInt(value)];
            readers = new ChannelSeparator[ndpiFiles.length];
        } else if (key.startsWith("Image")) {
            int index = Integer.parseInt(key.replaceAll("Image", ""));
            ndpiFiles[index] = new Location(parent, value).getAbsolutePath();
            readers[index] = new ChannelSeparator(new NDPIReader());
            readers[index].setFlattenedResolutions(hasFlattenedResolutions());
        }
    }
    MetadataStore store = makeFilterMetadata();
    readers[0].getReader().setMetadataStore(store);
    readers[0].setId(ndpiFiles[0]);
    core = new ArrayList<CoreMetadata>(readers[0].getCoreMetadataList());
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        ms.sizeC = readers.length;
        ms.rgb = false;
        ms.imageCount = ms.sizeC * ms.sizeZ * ms.sizeT;
    }
    MetadataTools.populatePixels(store, this);
    bandUsed = new int[ndpiFiles.length];
    IFD ifd;
    for (int c = 0; c < readers.length; c++) {
        // populate channel names based on IFD entry
        try (RandomAccessInputStream in = new RandomAccessInputStream(ndpiFiles[c])) {
            TiffParser tp = new TiffParser(in);
            ifd = tp.getIFDs().get(0);
        }
        String channelName = ifd.getIFDStringValue(TAG_CHANNEL);
        Float wavelength = (Float) ifd.getIFDValue(TAG_EMISSION_WAVELENGTH);
        store.setChannelName(channelName, 0, c);
        store.setChannelEmissionWavelength(new Length(wavelength, UNITS.NANOMETER), 0, c);
        bandUsed[c] = 0;
        if (ifd.getSamplesPerPixel() >= 3) {
            // 580 < wavelength <= 780 Red
            if (380 < wavelength && wavelength <= 490)
                bandUsed[c] = 2;
            else if (490 < wavelength && wavelength <= 580)
                bandUsed[c] = 1;
            else if (580 < wavelength && wavelength <= 780)
                bandUsed[c] = 0;
        }
    }
}