Examples with RandomAccessInputStream loci.common.RandomAccessInputStream used on opensource projects

Example 71 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class ExtractFlexMetadata method main.

public static void main(String[] args) throws Exception {
    File dir;
    if (args.length != 1 || !(dir = new File(args[0])).canRead()) {
        System.out.println("Usage: java ExtractFlexMetadata dir");
        return;
    }
    for (File file : dir.listFiles()) {
        if (file.getName().endsWith(".flex")) {
            String id = file.getPath();
            int dot = id.lastIndexOf(".");
            String outId = (dot >= 0 ? id.substring(0, dot) : id) + ".xml";
            RandomAccessInputStream in = new RandomAccessInputStream(id);
            TiffParser parser = new TiffParser(in);
            IFD firstIFD = parser.getIFDs().get(0);
            String xml = firstIFD.getIFDTextValue(FlexReader.FLEX);
            in.close();
            FileWriter writer = new FileWriter(new File(outId));
            writer.write(xml);
            writer.close();
            System.out.println("Writing header of: " + id);
        }
    }
    System.out.println("Done");
}

Example 72 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class CellVoyagerReader method initFile.

@Override
protected void initFile(final String id) throws FormatException, IOException {
    super.initFile(id);
    measurementFolder = new Location(id).getAbsoluteFile();
    if (!measurementFolder.exists()) {
        throw new IOException("File " + id + " does not exist.");
    }
    if (!measurementFolder.isDirectory()) {
        measurementFolder = measurementFolder.getParentFile();
        if (measurementFolder.getName().equals("Image")) {
            measurementFolder = measurementFolder.getParentFile();
        }
    }
    imageFolder = new Location(measurementFolder, "Image");
    measurementResultFile = new Location(measurementFolder, "MeasurementResult.xml");
    if (!measurementResultFile.exists()) {
        throw new IOException("Could not find " + measurementResultFile + " in folder.");
    }
    omeMeasurementFile = new Location(measurementFolder, "MeasurementResult.ome.xml");
    if (!omeMeasurementFile.exists()) {
        throw new IOException("Could not find " + omeMeasurementFile + " in folder.");
    }
    /*
     * Open MeasurementSettings file
     */
    RandomAccessInputStream result = new RandomAccessInputStream(measurementResultFile.getAbsolutePath());
    Document msDocument = null;
    try {
        msDocument = XMLTools.parseDOM(result);
    } catch (ParserConfigurationException e) {
        throw new IOException(e);
    } catch (SAXException e) {
        throw new IOException(e);
    } finally {
        result.close();
    }
    msDocument.getDocumentElement().normalize();
    /*
     * Check file version
     */
    final String fileVersionMajor = getChildText(msDocument.getDocumentElement(), new String[] { "FileVersion", "Major" });
    // Note the typo here.
    final String fileVersionMinor = getChildText(msDocument.getDocumentElement(), new String[] { "FileVersion", "Miner" });
    if (!fileVersionMajor.equals("1") || !fileVersionMinor.equals("0")) {
        LOGGER.warn("Detected a file version " + fileVersionMajor + "." + fileVersionMinor + ". This reader was built by reverse-engineering v1.0 files only. Errors might occur.");
    }
    /*
     * Open OME metadata file
     */
    RandomAccessInputStream measurement = new RandomAccessInputStream(omeMeasurementFile.getAbsolutePath());
    Document omeDocument = null;
    try {
        omeDocument = XMLTools.parseDOM(measurement);
    } catch (ParserConfigurationException e) {
        throw new IOException(e);
    } catch (SAXException e) {
        throw new IOException(e);
    } finally {
        measurement.close();
    }
    omeDocument.getDocumentElement().normalize();
    /*
     * Extract metadata from MeasurementSetting.xml & OME xml file. This is
     * where the core of parsing and fetching useful info happens
     */
    readInfo(msDocument, omeDocument);
}

Example 73 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class CellomicsReader 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[] zct = getZCTCoords(no);
    String file = files[getSeries() * getSizeC() + zct[1]];
    RandomAccessInputStream s = getDecompressedStream(file);
    int planeSize = FormatTools.getPlaneSize(this);
    s.seek(52 + zct[0] * planeSize);
    readPlane(s, x, y, w, h, buf);
    s.close();
    return buf;
}

Example 74 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class CellomicsReader method getDecompressedStream.

private RandomAccessInputStream getDecompressedStream(String filename) throws FormatException, IOException {
    RandomAccessInputStream s = new RandomAccessInputStream(filename);
    if (checkSuffix(filename, "c01")) {
        LOGGER.info("Decompressing file");
        s.seek(4);
        ZlibCodec codec = new ZlibCodec();
        byte[] file = codec.decompress(s, null);
        s.close();
        return new RandomAccessInputStream(file);
    }
    return s;
}

Example 75 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class DeltavisionReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "dv")) {
        if (checkSuffix(id, "dv.log") || checkSuffix(id, "r3d.log")) {
            id = id.substring(0, id.lastIndexOf("."));
        } else if (id.endsWith("_log.txt")) {
            id = id.substring(0, id.lastIndexOf("_")) + ".dv";
        }
        Location file = new Location(id).getAbsoluteFile();
        if (!file.exists()) {
            Location dir = file.getParentFile();
            String[] list = dir.list(true);
            String name = file.getName();
            name = name.substring(0, name.lastIndexOf("."));
            for (String f : list) {
                if (checkSuffix(f, "dv") && f.startsWith(name)) {
                    id = new Location(dir, f).getAbsolutePath();
                    break;
                }
            }
        }
    }
    super.initFile(id);
    findLogFiles();
    in = new RandomAccessInputStream(currentId);
    initPixels();
    MetadataLevel metadataLevel = metadataOptions.getMetadataLevel();
    if (metadataLevel != MetadataLevel.MINIMUM) {
        initExtraMetadata();
    }
}