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

Example 71 with TiffParser

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

the class EditTiffG method openFile.

public void openFile(File f) {
    try {
        String id = f.getAbsolutePath();
        String xml = new TiffParser(id).getComment();
        setXML(xml);
        file = f;
        setTitle(TITLE + " - " + id);
    } catch (IOException exc) {
        showError(exc);
    }
}

Example 72 with TiffParser

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

the class MinimalTiffReader method initTiffParser.

/**
 * Reinitialize the underlying TiffParser.
 */
protected void initTiffParser() {
    if (in == null) {
        try {
            in = new RandomAccessInputStream(getCurrentFile(), 16);
        } catch (IOException e) {
            LOGGER.error("Could not initialize stream", e);
        }
    }
    tiffParser = new TiffParser(in);
    tiffParser.setDoCaching(false);
    tiffParser.setUse64BitOffsets(use64Bit);
}

Example 73 with TiffParser

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

the class TiffWriter method saveBytes.

// -- IFormatWriter API methods --
/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    IFD ifd = new IFD();
    if (!sequential) {
        TiffParser parser = new TiffParser(currentId);
        try {
            long[] ifdOffsets = parser.getIFDOffsets();
            if (no < ifdOffsets.length) {
                ifd = parser.getIFD(ifdOffsets[no]);
            }
            saveBytes(no, buf, ifd, x, y, w, h);
        } finally {
            RandomAccessInputStream tiffParserStream = parser.getStream();
            if (tiffParserStream != null) {
                tiffParserStream.close();
            }
        }
    } else {
        saveBytes(no, buf, ifd, x, y, w, h);
    }
}

Example 74 with TiffParser

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

the class LeicaReader method findLEIFile.

// -- Helper methods --
/**
 * Find the .lei file that belongs to the same dataset as the given file.
 */
private String findLEIFile(String baseFile) throws FormatException, IOException {
    if (checkSuffix(baseFile, LEI_SUFFIX)) {
        return baseFile;
    } else if (checkSuffix(baseFile, TiffReader.TIFF_SUFFIXES) && isGroupFiles()) {
        // need to find the associated .lei file
        if (ifds == null)
            super.initFile(baseFile);
        in = new RandomAccessInputStream(baseFile, 16);
        TiffParser tp = new TiffParser(in);
        in.order(tp.checkHeader().booleanValue());
        in.seek(0);
        LOGGER.info("Finding companion file name");
        // open the TIFF file and look for the "Image Description" field
        ifds = tp.getIFDs();
        if (ifds == null)
            throw new FormatException("No IFDs found");
        String descr = ifds.get(0).getComment();
        // remove anything of the form "[blah]"
        descr = descr.replaceAll("\\[.*.\\]\n", "");
        // each remaining line in descr is a (key, value) pair,
        // where '=' separates the key from the value
        String lei = baseFile.substring(0, baseFile.lastIndexOf(File.separator) + 1);
        StringBuilder suffix = new StringBuilder();
        StringTokenizer lines = new StringTokenizer(descr, "\n");
        String line = null, key = null, value = null;
        while (lines.hasMoreTokens()) {
            line = lines.nextToken();
            if (line.indexOf('=') == -1)
                continue;
            key = line.substring(0, line.indexOf('=')).trim();
            value = line.substring(line.indexOf('=') + 1).trim();
            addGlobalMeta(key, value);
            if (key.startsWith("Series Name")) {
                suffix.append(value);
            }
        }
        lei += suffix.toString();
        // now open the LEI file
        Location l = new Location(lei).getAbsoluteFile();
        if (l.exists()) {
            return lei;
        } else {
            if (!lei.endsWith("lei") && !lei.endsWith("LEI")) {
                lei = lei.substring(0, lei.lastIndexOf(".") + 1);
                String test = lei + "lei";
                if (new Location(test).exists()) {
                    return test;
                }
                test = lei + "LEI";
                if (new Location(test).exists()) {
                    return test;
                }
            }
            l = l.getParentFile();
            String[] list = l.list();
            for (int i = 0; i < list.length; i++) {
                if (checkSuffix(list[i], LEI_SUFFIX)) {
                    return new Location(l.getAbsolutePath(), list[i]).getAbsolutePath();
                }
            }
        }
    } else if (checkSuffix(baseFile, "raw") && isGroupFiles()) {
        // check for that there is an .lei file in the same directory
        String prefix = baseFile;
        if (prefix.indexOf('.') != -1) {
            prefix = prefix.substring(0, prefix.lastIndexOf("."));
        }
        Location lei = new Location(prefix + ".lei");
        if (!lei.exists()) {
            lei = new Location(prefix + ".LEI");
            while (!lei.exists() && prefix.indexOf('_') != -1) {
                prefix = prefix.substring(0, prefix.lastIndexOf("_"));
                lei = new Location(prefix + ".lei");
                if (!lei.exists())
                    lei = new Location(prefix + ".LEI");
            }
        }
        if (lei.exists())
            return lei.getAbsolutePath();
    }
    return null;
}

Example 75 with TiffParser

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

the class LeicaReader method isThisType.

/* @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;
    return ifd.containsKey(new Integer(LEICA_MAGIC_TAG));
}