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

Example 81 with Location

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

the class MicromanagerReader method buildTIFFList.

/**
 * Populate the list of TIFF files using the given file name as a pattern.
 */
private void buildTIFFList(int posIndex, String baseTiff) {
    LOGGER.info("Building list of TIFFs");
    Position p = positions.get(posIndex);
    if ((p.tiffs.size() > 0 && p.tiffs.size() == p.fileNameMap.size()) || baseTiff == null) {
        return;
    }
    p.tiffs.clear();
    String prefix = "";
    if (baseTiff.indexOf(File.separator) != -1) {
        prefix = baseTiff.substring(0, baseTiff.lastIndexOf(File.separator) + 1);
        baseTiff = baseTiff.substring(baseTiff.lastIndexOf(File.separator) + 1);
    }
    String[] blocks = baseTiff.split("_");
    StringBuilder filename = new StringBuilder();
    for (int t = 0; t < getSizeT(); t++) {
        for (int c = 0; c < getSizeC(); c++) {
            for (int z = 0; z < getSizeZ(); z++) {
                // file names are of format:
                // img_<T>_<channel name>_<T>.tif
                filename.append(prefix);
                if (!prefix.endsWith(File.separator) && !blocks[0].startsWith(File.separator)) {
                    filename.append(File.separator);
                }
                filename.append(blocks[0]);
                filename.append("_");
                int zeros = blocks[1].length() - String.valueOf(t).length();
                for (int q = 0; q < zeros; q++) {
                    filename.append("0");
                }
                filename.append(t);
                filename.append("_");
                String prechannel = filename.toString();
                if (blocks[2].length() > 0) {
                    String channel = p.channels[c];
                    if (channel.indexOf('-') != -1) {
                        channel = channel.substring(0, channel.indexOf('-'));
                    }
                    filename.append(channel);
                }
                filename.append("_");
                zeros = blocks[3].length() - String.valueOf(z).length() - 4;
                for (int q = 0; q < zeros; q++) {
                    filename.append("0");
                }
                filename.append(z);
                filename.append(".tif");
                if (!new Location(filename.toString()).exists() && blocks[2].length() > 0) {
                    // rewind and try using the full channel name
                    filename = new StringBuilder(prechannel);
                    String channel = p.channels[c];
                    filename.append(channel);
                    filename.append("_");
                    zeros = blocks[3].length() - String.valueOf(z).length() - 4;
                    for (int q = 0; q < zeros; q++) {
                        filename.append("0");
                    }
                    filename.append(z);
                    filename.append(".tif");
                }
                p.tiffs.add(filename.toString());
                filename.delete(0, filename.length());
            }
        }
    }
    // adjust timepoint count, if needed
    // acquisitions can be stopped part-way through, but this isn't always
    // noted in the metadata
    int firstEmptyTimepoint = -1;
    int nextFile = 0;
    for (int t = 0; t < getSizeT(); t++) {
        boolean emptyTimepoint = true;
        for (int c = 0; c < getSizeC(); c++) {
            for (int z = 0; z < getSizeZ(); z++) {
                String file = p.tiffs.get(nextFile++);
                if (new Location(file).exists()) {
                    emptyTimepoint = false;
                    break;
                }
            }
            if (!emptyTimepoint) {
                break;
            }
        }
        if (emptyTimepoint && firstEmptyTimepoint < 0) {
            firstEmptyTimepoint = t;
        } else if (!emptyTimepoint && firstEmptyTimepoint >= 0) {
            firstEmptyTimepoint = -1;
        }
    }
    if (firstEmptyTimepoint >= 0) {
        int imageCount = getImageCount() / getSizeT();
        core.get(posIndex).sizeT = firstEmptyTimepoint;
        core.get(posIndex).imageCount = imageCount * getSizeT();
    }
}

Example 82 with Location

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

the class MicromanagerReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
public void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    tiffReader = new MinimalTiffReader();
    positions = new Vector<Position>();
    LOGGER.info("Reading metadata file");
    // find metadata.txt
    Location file = new Location(currentId).getAbsoluteFile();
    Location parentFile = file.getParentFile();
    if (file.exists()) {
        if (parentFile.getName().indexOf("Pos_") >= 0) {
            parentFile = parentFile.getParentFile();
            String[] dirs = parentFile.list(true);
            Arrays.sort(dirs);
            for (String dir : dirs) {
                if (dir.indexOf("Pos_") >= 0) {
                    Position pos = new Position();
                    Location posDir = new Location(parentFile, dir);
                    pos.metadataFile = new Location(posDir, METADATA).getAbsolutePath();
                    positions.add(pos);
                }
            }
        } else {
            Position pos = new Position();
            Location metadata = new Location(parentFile, METADATA);
            if (!metadata.exists()) {
                if (file.getName().endsWith(METADATA)) {
                    metadata = file;
                } else {
                    metadata = new Location(parentFile, getPrefixMetadataName(file.getName()));
                }
            }
            pos.metadataFile = metadata.getAbsolutePath();
            positions.add(pos);
        }
    }
    int seriesCount = positions.size();
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        core.add(new CoreMetadata());
        setSeries(i);
        parsePosition(i);
    }
    setSeries(0);
    populateMetadata();
}

Example 83 with Location

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

the class MicromanagerReader method buildTIFFList.

private void buildTIFFList(int posIndex) throws FormatException {
    Position p = positions.get(posIndex);
    CoreMetadata ms = core.get(posIndex);
    String parent = new Location(p.metadataFile).getParent();
    LOGGER.info("Finding image file names");
    // find the name of a TIFF file
    if (p.tiffs == null) {
        p.tiffs = new Vector<String>();
    }
    if (p.baseTiff != null) {
        buildTIFFList(posIndex, parent + File.separator + p.baseTiff);
    }
    if (p.tiffs.size() == 0) {
        Vector<String> uniqueZ = new Vector<String>();
        Vector<String> uniqueC = new Vector<String>();
        Vector<String> uniqueT = new Vector<String>();
        Location dir = new Location(p.metadataFile).getAbsoluteFile().getParentFile();
        String[] files = dir.list(true);
        Arrays.sort(files);
        for (String f : files) {
            if (checkSuffix(f, "tif") || checkSuffix(f, "tiff")) {
                String[] blocks = f.split("_");
                if (!uniqueT.contains(blocks[1]))
                    uniqueT.add(blocks[1]);
                if (!uniqueC.contains(blocks[2]))
                    uniqueC.add(blocks[2]);
                if (!uniqueZ.contains(blocks[3]))
                    uniqueZ.add(blocks[3]);
                String path = new Location(dir, f).getAbsolutePath();
                p.tiffs.add(path);
            }
        }
        if (getSizeZ() * getSizeC() * getSizeT() != uniqueZ.size() * uniqueC.size() * uniqueT.size()) {
            ms.sizeZ = uniqueZ.size();
            ms.sizeC = uniqueC.size();
            ms.sizeT = uniqueT.size();
        }
        if (p.tiffs.size() == 0) {
            throw new FormatException("Could not find TIFF files.");
        }
    }
}

Example 84 with Location

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

the class MicromanagerReader 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;
    if (name.equals(METADATA) || name.endsWith(File.separator + METADATA) || name.equals(XML) || name.endsWith(File.separator + XML) || name.endsWith("_" + METADATA)) {
        final int blockSize = 1048576;
        try {
            RandomAccessInputStream stream = new RandomAccessInputStream(name);
            long length = stream.length();
            String data = stream.readString((int) Math.min(blockSize, length));
            data = data.toLowerCase();
            stream.close();
            return length > 0 && (data.indexOf("micro-manager") >= 0 || data.indexOf("micromanager") >= 0);
        } catch (IOException e) {
            return false;
        }
    } else if (!isGroupFiles()) {
        // is chosen
        return false;
    }
    try {
        Location thisFile = new Location(name).getAbsoluteFile();
        Location parent = thisFile.getParentFile();
        Location metaFile = new Location(parent, METADATA);
        if (!metaFile.exists()) {
            metaFile = new Location(parent, getPrefixMetadataName(thisFile.getName()));
        }
        RandomAccessInputStream s = new RandomAccessInputStream(name);
        boolean validTIFF = isThisType(s);
        s.close();
        return validTIFF && isThisType(metaFile.getAbsolutePath(), open);
    } catch (NullPointerException e) {
    } catch (IOException e) {
    }
    return false;
}

Example 85 with Location

use of loci.common.Location 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;
}