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

Example 61 with Location

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

the class AnalyzeReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    if (!super.isThisType(name, open))
        return false;
    if (!open)
        return false;
    String headerFile = checkSuffix(name, "hdr") ? name : null;
    String extension = name.substring(name.lastIndexOf(".") + 1);
    name = name.substring(0, name.lastIndexOf("."));
    if (extension.equals("img"))
        extension = "hdr";
    else if (extension.equals("IMG"))
        extension = "HDR";
    else if (extension.equals("hdr"))
        extension = "img";
    else if (extension.equals("HDR"))
        extension = "IMG";
    if (extension.equalsIgnoreCase("hdr")) {
        headerFile = name + "." + extension;
    }
    boolean validHeader = false;
    try {
        RandomAccessInputStream headerStream = new RandomAccessInputStream(headerFile);
        validHeader = isThisType(headerStream);
        headerStream.close();
    } catch (IOException e) {
    }
    return new Location(name + "." + extension).exists() && validHeader;
}

Example 62 with Location

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

the class BDReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    Location location = new Location(name);
    String id = location.getAbsolutePath();
    boolean dirCheck = location.isDirectory();
    if (dirCheck)
        return false;
    if (name.endsWith(EXPERIMENT_FILE))
        return true;
    if (!open)
        return false;
    try {
        id = locateExperimentFile(id);
    } catch (FormatException f) {
        return false;
    } catch (IOException f) {
        return false;
    } catch (NullPointerException e) {
        return false;
    }
    if (id.endsWith(EXPERIMENT_FILE)) {
        return true;
    }
    return super.isThisType(name, open);
}

Example 63 with Location

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

the class BDReader method readMetaData.

private IniList readMetaData(String id) throws IOException {
    IniParser parser = new IniParser();
    RandomAccessInputStream idStream = new RandomAccessInputStream(id);
    IniList exp = parser.parseINI(new BufferedReader(new InputStreamReader(idStream, Constants.ENCODING)));
    IniList plate = null;
    IniList xyz = null;
    // Read Plate File
    for (String filename : metadataFiles) {
        if (checkSuffix(filename, "plt")) {
            RandomAccessInputStream stream = new RandomAccessInputStream(filename);
            plate = parser.parseINI(new BufferedReader(new InputStreamReader(stream, Constants.ENCODING)));
            stream.close();
        } else if (checkSuffix(filename, "xyz")) {
            RandomAccessInputStream stream = new RandomAccessInputStream(filename);
            xyz = parser.parseINI(new BufferedReader(new InputStreamReader(stream, Constants.ENCODING)));
            stream.close();
        } else if (filename.endsWith("RoiSummary.txt")) {
            roiFile = filename;
            if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
                RandomAccessInputStream s = new RandomAccessInputStream(filename);
                String line = s.readLine().trim();
                while (!line.endsWith(".adf\"")) {
                    line = s.readLine().trim();
                }
                plateName = line.substring(line.indexOf(':')).trim();
                plateName = plateName.replace('/', File.separatorChar);
                plateName = plateName.replace('\\', File.separatorChar);
                for (int i = 0; i < 3; i++) {
                    plateName = plateName.substring(0, plateName.lastIndexOf(File.separator));
                }
                plateName = plateName.substring(plateName.lastIndexOf(File.separator) + 1);
                s.close();
            }
        }
    }
    if (plate == null)
        throw new IOException("No Plate File");
    IniTable plateType = plate.getTable("PlateType");
    if (plateName == null) {
        plateName = plateType.get("Brand");
    }
    plateDescription = plateType.get("Brand") + " " + plateType.get("Description");
    int nWells = Integer.parseInt(plateType.get("Wells"));
    if (nWells == 96) {
        wellRows = 8;
        wellCols = 12;
    } else if (nWells == 384) {
        wellRows = 16;
        wellCols = 24;
    }
    for (String filename : rootList) {
        String name = new Location(filename).getName();
        if (name.startsWith("Well ")) {
            wellLabels.add(name.split("\\s|\\.")[1]);
        }
    }
    IniTable imageTable = exp.getTable("Image");
    boolean montage = imageTable.get("Montaged").equals("1");
    if (montage) {
        fieldRows = Integer.parseInt(imageTable.get("TilesY"));
        fieldCols = Integer.parseInt(imageTable.get("TilesX"));
    } else {
        fieldRows = 1;
        fieldCols = 1;
    }
    core.clear();
    int coresize = wellLabels.size() * fieldRows * fieldCols;
    CoreMetadata ms0 = new CoreMetadata();
    core.add(ms0);
    for (int i = 1; i < coresize; i++) {
        core.add(new CoreMetadata());
    }
    ms0.sizeC = Integer.parseInt(exp.getTable("General").get("Dyes"));
    ms0.bitsPerPixel = Integer.parseInt(exp.getTable("Camera").get("BitdepthUsed"));
    IniTable dyeTable = exp.getTable("Dyes");
    for (int i = 1; i <= getSizeC(); i++) {
        channelNames.add(dyeTable.get(Integer.toString(i)));
    }
    if (xyz != null) {
        IniTable zTable = xyz.getTable("Z1Axis");
        boolean zEnabled = "1".equals(zTable.get("Z1AxisEnabled")) && "1".equals(zTable.get("Z1AxisMode"));
        if (zEnabled) {
            ms0.sizeZ = (int) Double.parseDouble(zTable.get("Z1AxisValue")) + 1;
        } else {
            ms0.sizeZ = 1;
        }
    } else {
        ms0.sizeZ = 1;
    }
    // Count Images
    ms0.sizeT = 0;
    for (String channelName : channelNames) {
        int images = 0;
        for (String filename : wellList.get(1)) {
            if (filename.startsWith(channelName) && filename.endsWith(".tif")) {
                images++;
            }
        }
        if (images > getImageCount()) {
            ms0.sizeT = images / getSizeZ();
            ms0.imageCount = getSizeZ() * getSizeT() * channelNames.size();
        }
    }
    idStream.close();
    return exp;
}

Example 64 with Location

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

the class BDReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    // make sure we have the experiment file
    id = locateExperimentFile(id);
    super.initFile(id);
    Location dir = new Location(id).getAbsoluteFile().getParentFile();
    rootList = dir.list(true);
    Arrays.sort(rootList);
    for (int i = 0; i < rootList.length; i++) {
        String file = rootList[i];
        Location f = new Location(dir, file);
        rootList[i] = f.getAbsolutePath();
        if (!f.isDirectory()) {
            if (checkSuffix(file, META_EXT) && !f.isDirectory()) {
                metadataFiles.add(f.getAbsolutePath());
            }
        } else {
            String[] wells = f.list(true);
            Arrays.sort(wells);
            wellList.add(wells);
            for (String well : wells) {
                Location wellFile = new Location(f, well);
                if (!wellFile.isDirectory()) {
                    if (checkSuffix(well, META_EXT)) {
                        metadataFiles.add(wellFile.getAbsolutePath());
                    }
                }
            }
        }
    }
    // parse Experiment metadata
    IniList experiment = readMetaData(id);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        objective = experiment.getTable("Geometry").get("Name");
        IniTable camera = experiment.getTable("Camera");
        binning = camera.get("BinX") + "x" + camera.get("BinY");
        parseChannelData(dir);
        addGlobalMeta("Objective", objective);
        addGlobalMeta("Camera binning", binning);
    }
    final List<String> uniqueRows = new ArrayList<String>();
    final List<String> uniqueColumns = new ArrayList<String>();
    for (String well : wellLabels) {
        String row = well.substring(0, 1).trim();
        String column = well.substring(1).trim();
        if (!uniqueRows.contains(row) && row.length() > 0)
            uniqueRows.add(row);
        if (!uniqueColumns.contains(column) && column.length() > 0) {
            uniqueColumns.add(column);
        }
    }
    int nSlices = getSizeZ() == 0 ? 1 : getSizeZ();
    int nTimepoints = getSizeT();
    int nWells = wellLabels.size();
    int nChannels = getSizeC() == 0 ? channelNames.size() : getSizeC();
    if (nChannels == 0)
        nChannels = 1;
    tiffs = getTiffs();
    reader = new MinimalTiffReader();
    reader.setId(tiffs[0][0]);
    int sizeX = reader.getSizeX();
    int sizeY = reader.getSizeY();
    int pixelType = reader.getPixelType();
    boolean rgb = reader.isRGB();
    boolean interleaved = reader.isInterleaved();
    boolean indexed = reader.isIndexed();
    boolean littleEndian = reader.isLittleEndian();
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        IniParser parser = new IniParser();
        for (String metadataFile : metadataFiles) {
            String filename = new Location(metadataFile).getName();
            if (!checkSuffix(metadataFile, new String[] { "txt", "bmp", "adf", "roi" })) {
                String data = DataTools.readFile(metadataFile);
                IniList ini = parser.parseINI(new BufferedReader(new StringReader(data)));
                HashMap<String, String> h = ini.flattenIntoHashMap();
                for (String key : h.keySet()) {
                    addGlobalMeta(filename + " " + key, h.get(key));
                }
            }
        }
    }
    int coresize = core.size();
    core.clear();
    for (int i = 0; i < coresize; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeC = nChannels;
        ms.sizeZ = nSlices;
        ms.sizeT = nTimepoints;
        ms.sizeX = sizeX / fieldCols;
        ms.sizeY = sizeY / fieldRows;
        ms.pixelType = pixelType;
        ms.rgb = rgb;
        ms.interleaved = interleaved;
        ms.indexed = indexed;
        ms.littleEndian = littleEndian;
        ms.dimensionOrder = "XYZTC";
        ms.imageCount = nSlices * nTimepoints * nChannels;
    }
    MetadataStore store = makeFilterMetadata();
    boolean populatePlanes = getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM;
    MetadataTools.populatePixels(store, this, populatePlanes);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(fieldRows * fieldCols);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    for (int row = 0; row < wellRows; row++) {
        for (int col = 0; col < wellCols; col++) {
            int index = row * wellCols + col;
            store.setWellID(MetadataTools.createLSID("Well", 0, index), 0, index);
            store.setWellRow(new NonNegativeInteger(row), 0, index);
            store.setWellColumn(new NonNegativeInteger(col), 0, index);
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        int well = i / (fieldRows * fieldCols);
        int field = i % (fieldRows * fieldCols);
        MetadataTools.setDefaultCreationDate(store, tiffs[well][0], i);
        String name = wellLabels.get(well);
        String row = name.substring(0, 1);
        Integer col = Integer.parseInt(name.substring(1));
        int index = (row.charAt(0) - 'A') * wellCols + col - 1;
        String wellSampleID = MetadataTools.createLSID("WellSample", 0, index, field);
        store.setWellSampleID(wellSampleID, 0, index, field);
        store.setWellSampleIndex(new NonNegativeInteger(i), 0, index, field);
        String imageID = MetadataTools.createLSID("Image", i);
        store.setWellSampleImageRef(imageID, 0, index, field);
        store.setImageID(imageID, i);
        store.setImageName(name + " Field #" + (field + 1), i);
        store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, i);
    }
    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    if (level != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        if (objective != null) {
            String[] tokens = objective.split(" ");
            String mag = tokens[0].replaceAll("[xX]", "");
            String na = null;
            int naIndex = 0;
            for (int i = 0; i < tokens.length; i++) {
                if (tokens[i].equals("NA")) {
                    naIndex = i + 1;
                    na = tokens[naIndex];
                    break;
                }
            }
            Double magnification = new Double(mag);
            store.setObjectiveNominalMagnification(magnification, 0, 0);
            if (na != null) {
                na = na.substring(0, 1) + "." + na.substring(1);
                store.setObjectiveLensNA(new Double(na), 0, 0);
            }
            if (naIndex + 1 < tokens.length) {
                store.setObjectiveManufacturer(tokens[naIndex + 1], 0, 0);
            }
        }
        // populate LogicalChannel data
        for (int i = 0; i < getSeriesCount(); i++) {
            store.setImageInstrumentRef(instrumentID, i);
            store.setObjectiveSettingsID(objectiveID, i);
            for (int c = 0; c < getSizeC(); c++) {
                store.setChannelName(channelNames.get(c), i, c);
                Length emission = FormatTools.getEmissionWavelength(emWave[c]);
                Length excitation = FormatTools.getExcitationWavelength(exWave[c]);
                if (emission != null) {
                    store.setChannelEmissionWavelength(emission, i, c);
                }
                if (excitation != null) {
                    store.setChannelExcitationWavelength(excitation, i, c);
                }
                String detectorID = MetadataTools.createLSID("Detector", 0, c);
                store.setDetectorID(detectorID, 0, c);
                store.setDetectorSettingsID(detectorID, i, c);
                store.setDetectorSettingsGain(gain[c], i, c);
                store.setDetectorSettingsOffset(offset[c], i, c);
                store.setDetectorSettingsBinning(getBinning(binning), i, c);
            }
            long firstPlane = 0;
            for (int p = 0; p < getImageCount(); p++) {
                int[] zct = getZCTCoords(p);
                store.setPlaneExposureTime(new Time(exposure[zct[1]], UNITS.SECOND), i, p);
                String file = getFilename(i, p);
                if (file != null) {
                    long plane = getTimestamp(file);
                    if (p == 0) {
                        firstPlane = plane;
                    }
                    double timestamp = (plane - firstPlane) / 1000.0;
                    store.setPlaneDeltaT(new Time(timestamp, UNITS.SECOND), i, p);
                }
            }
        }
        store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
        store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
        store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
        store.setPlateName(plateName, 0);
        store.setPlateDescription(plateDescription, 0);
        if (level != MetadataLevel.NO_OVERLAYS) {
            parseROIs(store);
        }
    }
}

Example 65 with Location

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

the class BDReader method locateExperimentFile.

// -- Helper methods --
/* Locate the experiment file given any file in set */
private String locateExperimentFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "exp")) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        if (checkSuffix(id, "tif"))
            parent = parent.getParentFile();
        Location expFile = new Location(parent, EXPERIMENT_FILE);
        if (expFile.exists()) {
            return expFile.getAbsolutePath();
        }
        throw new FormatException("Could not find " + EXPERIMENT_FILE + " in " + parent.getAbsolutePath());
    }
    return id;
}