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

Example 91 with TiffParser

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

the class MIASReader method getChannelColorFromFile.

// -- Helper methods --
/**
 * Get the color associated with the given file's channel.
 * The file must be one of the
 * Well<nnnn>_mode<n>_z<nnn>_t<nnn>_AllModesOverlay.tif
 * files in <experiment>/<plate>/results/
 */
private Color getChannelColorFromFile(String file) throws FormatException, IOException {
    RandomAccessInputStream s = new RandomAccessInputStream(file, 16);
    TiffParser tp = new TiffParser(s);
    IFD ifd = tp.getFirstIFD();
    s.close();
    if (ifd == null)
        return null;
    int[] colorMap = tp.getColorMap(ifd);
    if (colorMap == null)
        return null;
    int nEntries = colorMap.length / 3;
    int max = Integer.MIN_VALUE;
    int maxIndex = -1;
    for (int c = 0; c < 3; c++) {
        int v = (colorMap[c * nEntries] >> 8) & 0xff;
        if (v > max) {
            max = v;
            maxIndex = c;
        } else if (v == max) {
            return new Color(0, 0, 0, 255);
        }
    }
    switch(maxIndex) {
        case // red
        0:
            return new Color(255, 0, 0, 255);
        case // green
        1:
            return new Color(0, 255, 0, 255);
        case // blue
        2:
            return new Color(0, 0, 255, 255);
    }
    return null;
}

Example 92 with TiffParser

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

the class IPWReader method getOptimalTileHeight.

/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
    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.getTileLength();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile height", e);
    } catch (IOException e) {
        LOGGER.debug("Could not retrieve tile length", e);
    }
    return super.getOptimalTileHeight();
}

Example 93 with TiffParser

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

the class IPWReader 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);
    initPOIService();
    imageFiles = new HashMap<Integer, String>();
    Vector<String> fileList = poi.getDocumentList();
    String description = null, creationDate = null;
    CoreMetadata m = core.get(0);
    for (String name : fileList) {
        String relativePath = name.substring(name.lastIndexOf(File.separator) + 1);
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            if (relativePath.equals("CONTENTS")) {
                addGlobalMeta("Version", new String(poi.getDocumentBytes(name), Constants.ENCODING).trim());
            } else if (relativePath.equals("FrameRate")) {
                byte[] b = poi.getDocumentBytes(name, 4);
                addGlobalMeta("Frame Rate", DataTools.bytesToInt(b, true));
            } else if (relativePath.equals("FrameInfo")) {
                RandomAccessInputStream s = poi.getDocumentStream(name);
                s.order(true);
                for (int q = 0; q < s.length() / 2; q++) {
                    addGlobalMetaList("FrameInfo", s.readShort());
                }
                s.close();
            }
        }
        if (relativePath.equals("ImageInfo")) {
            description = new String(poi.getDocumentBytes(name), Constants.ENCODING).trim();
            addGlobalMeta("Image Description", description);
            String timestamp = null;
            // basically the same as in SEQReader
            if (description != null) {
                String[] tokens = description.split("\n");
                for (String token : tokens) {
                    String label = "Timestamp";
                    String data = token.trim();
                    if (token.indexOf('=') != -1) {
                        label = token.substring(0, token.indexOf('=')).trim();
                        data = token.substring(token.indexOf('=') + 1).trim();
                    }
                    addGlobalMeta(label, data);
                    if (label.equals("frames"))
                        m.sizeT = Integer.parseInt(data);
                    else if (label.equals("slices")) {
                        m.sizeZ = Integer.parseInt(data);
                    } else if (label.equals("channels")) {
                        m.sizeC = Integer.parseInt(data);
                    } else if (label.equals("Timestamp"))
                        timestamp = data;
                }
            }
            if (timestamp != null) {
                if (timestamp.length() > 26) {
                    timestamp = timestamp.substring(timestamp.length() - 26);
                }
                creationDate = DateTools.formatDate(timestamp, "MM/dd/yyyy HH:mm:ss aa", ".");
            }
        } else if (relativePath.equals("ImageTIFF")) {
            // pixel data
            String idx = "0";
            if (!name.substring(0, name.lastIndexOf(File.separator)).equals("Root Entry")) {
                idx = name.substring(21, name.indexOf(File.separator, 22));
            }
            imageFiles.put(new Integer(idx), name);
        }
    }
    LOGGER.info("Populating metadata");
    m.imageCount = imageFiles.size();
    RandomAccessInputStream stream = poi.getDocumentStream(imageFiles.get(0));
    TiffParser tp = new TiffParser(stream);
    IFD firstIFD = tp.getFirstIFD();
    stream.close();
    m.rgb = firstIFD.getSamplesPerPixel() > 1;
    if (!isRGB()) {
        m.indexed = firstIFD.getPhotometricInterpretation() == PhotoInterp.RGB_PALETTE;
    }
    if (isIndexed()) {
        m.sizeC = 1;
        m.rgb = false;
    }
    m.littleEndian = firstIFD.isLittleEndian();
    // retrieve axis sizes
    addGlobalMeta("slices", "1");
    addGlobalMeta("channels", "1");
    addGlobalMeta("frames", getImageCount());
    m.sizeX = (int) firstIFD.getImageWidth();
    m.sizeY = (int) firstIFD.getImageLength();
    m.dimensionOrder = isRGB() ? "XYCZT" : "XYZCT";
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    if (getSizeC() == 0)
        m.sizeC = 1;
    if (getSizeT() == 0)
        m.sizeT = 1;
    if (getSizeZ() * getSizeC() * getSizeT() == 1 && getImageCount() != 1) {
        m.sizeZ = getImageCount();
    }
    if (isRGB())
        m.sizeC *= 3;
    int bitsPerSample = firstIFD.getBitsPerSample()[0];
    m.pixelType = firstIFD.getPixelType();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setImageDescription(description, 0);
    if (creationDate != null) {
        store.setImageAcquisitionDate(new Timestamp(creationDate), 0);
    }
}

Example 94 with TiffParser

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

the class ImprovisionTiffReader method getUUID.

// -- Helper methods --
private String getUUID(String path) throws FormatException, IOException {
    RandomAccessInputStream s = new RandomAccessInputStream(path, 16);
    TiffParser parser = new TiffParser(s);
    String comment = parser.getComment();
    s.close();
    comment = comment.replaceAll("\r\n", "\n");
    comment = comment.replaceAll("\r", "\n");
    String[] lines = comment.split("\n");
    for (String line : lines) {
        line = line.trim();
        if (line.startsWith("SampleUUID=")) {
            return line.substring(line.indexOf('=') + 1).trim();
        }
    }
    return "";
}

Example 95 with TiffParser

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

the class SISReader method isThisType.

// -- IFormatReader API methods --
/* @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;
    String software = ifd.getIFDTextValue(IFD.SOFTWARE);
    String make = ifd.getIFDTextValue(IFD.MAKE);
    return (ifd.get(SIS_TAG) != null && (software == null || software.startsWith("analySIS"))) || (ifd.get(SIS_TAG_2) != null && (make != null && make.startsWith("Olympus")));
}