Examples with MDBService loci.formats.services.MDBService used on opensource projects

Example 1 with MDBService

use of loci.formats.services.MDBService in project bioformats by openmicroscopy.

the class APLReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    LOGGER.debug("Initializing {}", id);
    // find the corresponding .mtb file
    if (!checkSuffix(id, "mtb")) {
        if (checkSuffix(id, METADATA_SUFFIXES)) {
            int separator = id.lastIndexOf(File.separator);
            if (separator < 0)
                separator = 0;
            int underscore = id.lastIndexOf("_");
            if (underscore < separator || checkSuffix(id, "apl")) {
                underscore = id.lastIndexOf(".");
            }
            String mtbFile = id.substring(0, underscore) + "_d.mtb";
            if (!new Location(mtbFile).exists()) {
                throw new FormatException(".mtb file not found");
            }
            currentId = new Location(mtbFile).getAbsolutePath();
        } else {
            Location parent = new Location(id).getAbsoluteFile().getParentFile();
            parent = parent.getParentFile();
            String[] list = parent.list(true);
            for (String f : list) {
                if (checkSuffix(f, "mtb")) {
                    currentId = new Location(parent, f).getAbsolutePath();
                    break;
                }
            }
            if (!checkSuffix(currentId, "mtb")) {
                throw new FormatException(".mtb file not found");
            }
        }
    }
    String mtb = new Location(currentId).getAbsolutePath();
    LOGGER.debug("Reading .mtb file '{}'", mtb);
    MDBService mdb = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        mdb = factory.getInstance(MDBService.class);
    } catch (DependencyException de) {
        throw new FormatException("MDB Tools Java library not found", de);
    }
    String[] columnNames = null;
    List<String[]> rows = null;
    try {
        mdb.initialize(mtb);
        rows = mdb.parseDatabase().get(0);
        columnNames = rows.get(0);
        String[] tmpNames = columnNames;
        columnNames = new String[tmpNames.length - 1];
        System.arraycopy(tmpNames, 1, columnNames, 0, columnNames.length);
    } finally {
        mdb.close();
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 1; i < rows.size(); i++) {
            String[] row = rows.get(i);
            for (int q = 0; q < row.length; q++) {
                addGlobalMetaList(columnNames[q], row[q]);
            }
        }
    }
    used = new ArrayList<String>();
    used.add(mtb);
    String tnb = mtb.substring(0, mtb.lastIndexOf("."));
    if (tnb.lastIndexOf("_") > tnb.lastIndexOf(File.separator)) {
        tnb = tnb.substring(0, tnb.lastIndexOf("_"));
    }
    used.add(tnb + "_1.tnb");
    used.add(tnb + ".apl");
    String idPath = new Location(id).getAbsolutePath();
    if (!used.contains(idPath) && checkSuffix(idPath, METADATA_SUFFIXES)) {
        used.add(idPath);
    }
    // calculate indexes to relevant metadata
    int calibrationUnit = DataTools.indexOf(columnNames, "Calibration Unit");
    int colorChannels = DataTools.indexOf(columnNames, "Color Channels");
    int frames = DataTools.indexOf(columnNames, "Frames");
    int calibratedHeight = DataTools.indexOf(columnNames, "Height");
    int calibratedWidth = DataTools.indexOf(columnNames, "Width");
    int path = DataTools.indexOf(columnNames, "Image Path");
    if (path == -1) {
        path = DataTools.indexOf(columnNames, "Path");
    }
    int filename = DataTools.indexOf(columnNames, "File Name");
    int magnification = DataTools.indexOf(columnNames, "Magnification");
    int width = DataTools.indexOf(columnNames, "X-Resolution");
    int height = DataTools.indexOf(columnNames, "Y-Resolution");
    int imageType = DataTools.indexOf(columnNames, "Image Type");
    int imageName = DataTools.indexOf(columnNames, "Image Name");
    int zLayers = DataTools.indexOf(columnNames, "Z-Layers");
    String parentDirectory = mtb.substring(0, mtb.lastIndexOf(File.separator));
    // look for the directory that contains TIFF and XML files
    LOGGER.debug("Searching {} for a directory with TIFFs", parentDirectory);
    Location dir = new Location(parentDirectory);
    String topDirectory = null;
    int index = 2;
    String pathName = rows.get(index++)[path].trim();
    while (pathName.equals("") && index < rows.size()) {
        pathName = rows.get(index++)[path].trim();
    }
    pathName = pathName.replace('\\', File.separatorChar);
    pathName = pathName.replaceAll("/", File.separator);
    String[] dirs = pathName.split(File.separatorChar == '\\' ? "\\\\" : File.separator);
    for (int i = dirs.length - 1; i >= 0; i--) {
        if (dirs[i].indexOf("_DocumentFiles") > 0) {
            Location file = new Location(dir, dirs[i]);
            if (file.exists()) {
                topDirectory = file.getAbsolutePath();
                break;
            }
        }
    }
    if (topDirectory == null) {
        String[] list = dir.list();
        for (String f : list) {
            LOGGER.debug("  '{}'", f);
            Location file = new Location(dir, f);
            if (file.isDirectory() && f.indexOf("_DocumentFiles") > 0) {
                topDirectory = file.getAbsolutePath();
                LOGGER.debug("Found {}", topDirectory);
                break;
            }
        }
    }
    if (topDirectory == null) {
        throw new FormatException("Could not find a directory with TIFF files.");
    }
    final List<Integer> seriesIndexes = new ArrayList<Integer>();
    for (int i = 1; i < rows.size(); i++) {
        String file = parseFilename(rows.get(i), filename, path);
        if (file.equals(""))
            continue;
        file = topDirectory + File.separator + file;
        if (new Location(file).exists() && checkSuffix(file, "tif")) {
            seriesIndexes.add(i);
        }
    }
    int seriesCount = seriesIndexes.size();
    core.clear();
    tiffFiles = new String[seriesCount];
    xmlFiles = new String[seriesCount];
    parser = new TiffParser[seriesCount];
    ifds = new IFDList[seriesCount];
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        int secondRow = seriesIndexes.get(i);
        int firstRow = secondRow - 1;
        String[] row2 = rows.get(firstRow);
        String[] row3 = rows.get(secondRow);
        if (frames > -1) {
            ms.sizeT = parseDimension(row3[frames]);
        }
        if (zLayers > -1) {
            ms.sizeZ = parseDimension(row3[zLayers]);
        }
        if (colorChannels > -1) {
            ms.sizeC = parseDimension(row3[colorChannels]);
        } else if (imageType > -1) {
            if (row3[imageType] != null && row3[imageType].equals("RGB")) {
                ms.sizeC = 3;
            }
        }
        ms.dimensionOrder = "XYCZT";
        if (ms.sizeZ == 0)
            ms.sizeZ = 1;
        if (ms.sizeC == 0)
            ms.sizeC = 1;
        if (ms.sizeT == 0)
            ms.sizeT = 1;
        xmlFiles[i] = topDirectory + File.separator + parseFilename(row2, filename, path);
        tiffFiles[i] = topDirectory + File.separator + parseFilename(row3, filename, path);
        parser[i] = new TiffParser(tiffFiles[i]);
        parser[i].setDoCaching(false);
        ifds[i] = parser[i].getIFDs();
        for (IFD ifd : ifds[i]) {
            parser[i].fillInIFD(ifd);
        }
        // get core metadata from TIFF file
        IFD ifd = ifds[i].get(0);
        PhotoInterp photo = ifd.getPhotometricInterpretation();
        int samples = ifd.getSamplesPerPixel();
        ms.sizeX = (int) ifd.getImageWidth();
        ms.sizeY = (int) ifd.getImageLength();
        ms.rgb = samples > 1 || photo == PhotoInterp.RGB;
        ms.pixelType = ifd.getPixelType();
        ms.littleEndian = ifd.isLittleEndian();
        ms.indexed = photo == PhotoInterp.RGB_PALETTE && ifd.containsKey(IFD.COLOR_MAP);
        ms.imageCount = ifds[i].size();
        if (ms.sizeZ * ms.sizeT * (ms.rgb ? 1 : ms.sizeC) != ms.imageCount) {
            ms.sizeT = ms.imageCount / (ms.rgb ? 1 : ms.sizeC);
            ms.sizeZ = 1;
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    for (int i = 0; i < seriesCount; i++) {
        String[] row = rows.get(seriesIndexes.get(i));
        // populate Image data
        MetadataTools.setDefaultCreationDate(store, mtb, i);
        store.setImageName(row[imageName].trim(), i);
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            // populate Dimensions data
            // calculate physical X and Y sizes
            double realWidth = Double.parseDouble(row[calibratedWidth]);
            double realHeight = Double.parseDouble(row[calibratedHeight]);
            String units = row[calibrationUnit];
            CoreMetadata ms = core.get(i);
            double px = realWidth / ms.sizeX;
            double py = realHeight / ms.sizeY;
            Length physicalSizeX = FormatTools.getPhysicalSizeX(px, units);
            Length physicalSizeY = FormatTools.getPhysicalSizeY(py, units);
            if (physicalSizeX != null) {
                store.setPixelsPhysicalSizeX(physicalSizeX, i);
            }
            if (physicalSizeY != null) {
                store.setPixelsPhysicalSizeY(physicalSizeY, i);
            }
        }
    }
    setSeries(0);
}

Example 2 with MDBService

use of loci.formats.services.MDBService in project bioformats by openmicroscopy.

the class ZeissLSMReader method parseMDB.

/**
 * Parse a .mdb file and return a list of referenced .lsm files.
 */
private String[] parseMDB(String mdbFile) throws FormatException, IOException {
    Location mdb = new Location(mdbFile).getAbsoluteFile();
    Location parent = mdb.getParentFile();
    MDBService mdbService = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        mdbService = factory.getInstance(MDBService.class);
    } catch (DependencyException de) {
        throw new FormatException("MDB Tools Java library not found", de);
    }
    try {
        mdbService.initialize(mdbFile);
    } catch (Exception e) {
        return null;
    }
    Vector<Vector<String[]>> tables = mdbService.parseDatabase();
    mdbService.close();
    final List<String> referencedLSMs = new ArrayList<String>();
    int referenceCount = 0;
    for (Vector<String[]> table : tables) {
        String[] columnNames = table.get(0);
        String tableName = columnNames[0];
        for (int row = 1; row < table.size(); row++) {
            String[] tableRow = table.get(row);
            for (int col = 0; col < tableRow.length; col++) {
                String key = tableName + " " + columnNames[col + 1];
                if (currentId != null) {
                    addGlobalMetaList(key, tableRow[col]);
                }
                if (tableName.equals("Recordings") && columnNames[col + 1] != null && columnNames[col + 1].equals("SampleData")) {
                    String filename = tableRow[col].trim();
                    filename = filename.replace('\\', File.separatorChar);
                    filename = filename.replace('/', File.separatorChar);
                    filename = filename.substring(filename.lastIndexOf(File.separator) + 1);
                    if (filename.length() > 0) {
                        Location file = new Location(parent, filename);
                        if (file.exists()) {
                            referencedLSMs.add(file.getAbsolutePath());
                        }
                    }
                    referenceCount++;
                }
            }
        }
    }
    if (referencedLSMs.size() == referenceCount) {
        return referencedLSMs.toArray(new String[0]);
    }
    String[] fileList = parent.list(true);
    Arrays.sort(fileList);
    for (int i = 0; i < fileList.length; i++) {
        Location f = new Location(fileList[i]);
        if (!f.exists()) {
            f = new Location(parent, fileList[i]);
        }
        String absolutePath = f.getAbsolutePath();
        if (checkSuffix(fileList[i], "mdb") && (!absolutePath.equals(mdbFile) && !fileList[i].equals(mdbFile) && !absolutePath.equals(new Location(mdbFile).getAbsolutePath()))) {
            if (referencedLSMs.size() > 0) {
                return referencedLSMs.toArray(new String[0]);
            }
            break;
        }
    }
    referencedLSMs.clear();
    int mdbCount = 0;
    for (int i = 0; i < fileList.length; i++) {
        String absolutePath = new Location(parent, fileList[i]).getAbsolutePath();
        if (checkSuffix(fileList[i], "lsm")) {
            referencedLSMs.add(absolutePath);
        } else if (checkSuffix(fileList[i], "mdb")) {
            mdbCount++;
        }
    }
    if (mdbCount > 1 || ((referencedLSMs.size() > referenceCount) && mdbCount > 1)) {
        for (int i = 0; i < fileList.length; i++) {
            String absolutePath = new Location(parent, fileList[i]).getAbsolutePath();
            if (checkSuffix(fileList[i], "mdb") && !absolutePath.endsWith(mdbFile)) {
                String[] files = parseMDB(absolutePath);
                for (String f : files) {
                    referencedLSMs.remove(f);
                }
            }
        }
    }
    return referencedLSMs.toArray(new String[0]);
}

Example 3 with MDBService

use of loci.formats.services.MDBService in project bioformats by openmicroscopy.

the class MissingMDBServiceTest method testInstantiate.

@Test(expectedExceptions = { DependencyException.class })
public void testInstantiate() throws DependencyException {
    MDBService service = sf.getInstance(MDBService.class);
    assertNotNull(service);
}