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

Example 46 with Location

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

the class TCSReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    // not allowed to touch the file system
    if (!open)
        return false;
    // check that there is no LEI file
    String prefix = name;
    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 false;
    try {
        RandomAccessInputStream s = new RandomAccessInputStream(name);
        boolean isThisType = isThisType(s);
        s.close();
        return isThisType;
    } catch (IOException e) {
        LOGGER.debug("", e);
        return false;
    }
}

Example 47 with Location

use of loci.common.Location 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 48 with Location

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

the class CellVoyagerReader method isThisType.

@Override
public boolean isThisType(final String name, final boolean open) {
    /*
     * We want to be pointed to any file in the directory that contains
     * 'MeasurementResult.xml'.
     */
    final String localName = new Location(name).getName();
    if (localName.equals("MeasurementResult.xml")) {
        return true;
    }
    final Location parent = new Location(name).getAbsoluteFile().getParentFile();
    Location xml = new Location(parent, "MeasurementResult.xml");
    if (!xml.exists() && parent != null) {
        if (parent.getParent() == null) {
            return false;
        }
        xml = new Location(parent.getParentFile(), "MeasurementResult.xml");
        if (!xml.exists()) {
            return false;
        }
    }
    return super.isThisType(name, open);
}

Example 49 with Location

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

the class CellWorxReader method getSeriesUsedFiles.

/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
    FormatTools.assertId(currentId, true, 1);
    final List<String> files = new ArrayList<String>();
    files.add(currentId);
    if (plateLogFile != null && new Location(plateLogFile).exists()) {
        files.add(plateLogFile);
    }
    if (zMapFile != null)
        files.add(zMapFile);
    int row = getWellRow(getSeries());
    int col = getWellColumn(getSeries());
    if (new Location(logFiles[row][col]).exists()) {
        files.add(logFiles[row][col]);
    }
    if (!noPixels) {
        if (checkSuffix(wellFiles[row][col][0], "pnl")) {
            if (new Location(wellFiles[row][col][0]).exists()) {
                files.add(wellFiles[row][col][0]);
            }
        } else {
            for (String f : wellFiles[row][col]) {
                if (new Location(f).exists()) {
                    files.add(f);
                }
            }
        }
    }
    return files.toArray(new String[files.size()]);
}

Example 50 with Location

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

the class CellWorxReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    if (checkSuffix(name, "pnl") || checkSuffix(name, "htd")) {
        return super.isThisType(name, open);
    }
    if (!open)
        return false;
    Location current = new Location(name).getAbsoluteFile();
    Location parent = current.getParentFile();
    String htdName = current.getName();
    while (htdName.indexOf('_') > 0) {
        htdName = htdName.substring(0, htdName.lastIndexOf("_"));
        if (new Location(parent, htdName + ".htd").exists() || new Location(parent, htdName + ".HTD").exists()) {
            return checkSuffix(name, "log") || isGroupFiles();
        }
    }
    return false;
}