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

Example 46 with TiffParser

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

the class XMLValidate method main.

public static void main(String[] args) throws Exception {
    CommandLineTools.runUpgradeCheck(args);
    if (args.length == 0) {
        // read from stdin
        process("<stdin>", new BufferedReader(new InputStreamReader(System.in, Constants.ENCODING)));
    } else {
        // read from file(s)
        for (int i = 0; i < args.length; i++) {
            if (args[i].toLowerCase().endsWith("tif") || args[i].toLowerCase().endsWith("tiff")) {
                String comment = new TiffParser(args[i]).getComment();
                process(args[i], new BufferedReader(new StringReader(comment)));
            } else {
                process(args[i], new BufferedReader(new InputStreamReader(new FileInputStream(args[i]), Constants.ENCODING)));
            }
        }
    }
}

Example 47 with TiffParser

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

the class FlowSightReader method isThisType.

/* (non-Javadoc)
   * @see loci.formats.FormatReader#isThisType(loci.common.RandomAccessInputStream)
   */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tiffParser;
    try {
        tiffParser = new TiffParser(stream);
    } catch (java.lang.IllegalArgumentException iae) {
        return false;
    }
    if (!tiffParser.isValidHeader())
        return false;
    IFD ifd = tiffParser.getFirstIFD();
    if (ifd == null)
        return false;
    tiffParser.fillInIFD(ifd);
    for (int tag : MINIMAL_TAGS) {
        try {
            if (ifd.getIFDStringValue(tag) == null)
                return false;
        } catch (FormatException e) {
            return false;
        }
    }
    return true;
}

Example 48 with TiffParser

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

the class OMETiffReader 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 {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    int series = getSeries();
    lastPlane = no;
    int i = info[series][no].ifd;
    if (!info[series][no].exists) {
        Arrays.fill(buf, (byte) 0);
        return buf;
    }
    MinimalTiffReader r = (MinimalTiffReader) info[series][no].reader;
    if (r.getCurrentFile() == null) {
        r.setId(info[series][no].id);
    }
    r.lastPlane = i;
    IFDList ifdList = r.getIFDs();
    if (i >= ifdList.size()) {
        LOGGER.warn("Error untangling IFDs; the OME-TIFF file may be malformed (IFD #{} missing).", i);
        return buf;
    }
    IFD ifd = ifdList.get(i);
    RandomAccessInputStream s = new RandomAccessInputStream(info[series][no].id, 16);
    TiffParser p = new TiffParser(s);
    p.getSamples(ifd, buf, x, y, w, h);
    s.close();
    // lower-right-most tile from a single plane file has been read
    if (r.getImageCount() == 1 && w + x == getSizeX() && h + y == getSizeY()) {
        r.close();
    }
    return buf;
}

Example 49 with TiffParser

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

the class OMETiffReader method isSingleFile.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isSingleFile(String) */
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
    // companion files in a binary-only dataset should always have additional files
    if (checkSuffix(id, "companion.ome")) {
        return false;
    }
    // parse and populate OME-XML metadata
    String fileName = new Location(id).getAbsoluteFile().getAbsolutePath();
    RandomAccessInputStream ras = new RandomAccessInputStream(fileName, 16);
    TiffParser tp = new TiffParser(ras);
    IFD ifd = tp.getFirstIFD();
    long[] ifdOffsets = tp.getIFDOffsets();
    ras.close();
    String xml = ifd.getComment();
    if (service == null)
        setupService();
    OMEXMLMetadata meta;
    try {
        meta = service.createOMEXMLMetadata(xml);
        metaFile = new Location(id).getAbsolutePath();
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    if (meta.getRoot() == null) {
        throw new FormatException("Could not parse OME-XML from TIFF comment");
    }
    int nImages = 0;
    for (int i = 0; i < meta.getImageCount(); i++) {
        int nChannels = meta.getChannelCount(i);
        if (nChannels == 0)
            nChannels = 1;
        int z = meta.getPixelsSizeZ(i).getValue().intValue();
        int t = meta.getPixelsSizeT(i).getValue().intValue();
        nImages += z * t * nChannels;
    }
    return nImages > 0 && nImages <= ifdOffsets.length;
}

Example 50 with TiffParser

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

the class TiffComment method main.

public static void main(String[] args) throws FormatException, IOException {
    CommandLineTools.runUpgradeCheck(args);
    if (args.length == 0) {
        System.out.println("Usage:");
        System.out.println("tiffcomment [-set comment] [-edit] file1 [file2 ...]");
        System.out.println();
        System.out.println("This tool requires an ImageDescription tag to be " + "present in the TIFF file. ");
        System.out.println();
        System.out.println("If using the '-set' option, the new TIFF comment " + "must be specified and may take any of the following forms:");
        System.out.println();
        System.out.println("  * the text of the comment, e.g. 'new comment!'");
        System.out.println("  * the name of the file containing the text of " + "the comment, e.g. 'file.xml'");
        System.out.println("  * '-', to enter the comment using stdin.  " + "Entering a blank line will");
        System.out.println("    terminate reading from stdin.");
        return;
    }
    // parse flags
    boolean edit = false;
    String newComment = null;
    ArrayList<String> files = new ArrayList<String>();
    for (int i = 0; i < args.length; i++) {
        if (!args[i].startsWith("-")) {
            files.add(args[i]);
            continue;
        }
        if (args[i].equals("-edit"))
            edit = true;
        else if (args[i].equals("-set")) {
            newComment = args[++i];
            if (new File(newComment).exists()) {
                newComment = DataTools.readFile(newComment);
            } else if (newComment.equals("-")) {
                newComment = null;
                BufferedReader reader = new BufferedReader(new InputStreamReader(System.in, Constants.ENCODING));
                String line = reader.readLine();
                while (line != null && line.length() > 0) {
                    if (newComment == null)
                        newComment = line;
                    else {
                        newComment += "\n" + line;
                    }
                    line = reader.readLine();
                }
            }
        } else
            System.out.println("Warning: unknown flag: " + args[i]);
    }
    // process files
    for (String file : files) {
        if (edit)
            EditTiffG.openFile(file);
        else if (newComment != null) {
            overwriteComment(file, newComment);
        } else {
            String comment = new TiffParser(file).getComment();
            System.out.println(comment == null ? file + ": no TIFF comment found." : comment);
        }
    }
}