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

Example 26 with Location

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

the class PrairieReader method initFile.

// -- Internal FormatReader API methods --
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    tiff = new TiffReader();
    if (checkSuffix(id, XML_SUFFIX)) {
        xmlFile = new Location(id);
        findMetadataFiles();
    } else if (checkSuffix(id, CFG_SUFFIX)) {
        cfgFile = new Location(id);
        findMetadataFiles();
    } else if (checkSuffix(id, ENV_SUFFIX)) {
        envFile = new Location(id);
        findMetadataFiles();
    } else {
        // we have been given a TIFF file
        if (isGroupFiles()) {
            findMetadataFiles();
        } else {
            // NB: File grouping is not allowed, so we enter a special mode,
            // which delegates to the TIFF reader for everything.
            singleTiffMode = true;
            tiff.setId(id);
            return;
        }
    }
    currentId = xmlFile.getAbsolutePath();
    parsePrairieMetadata();
    populateCoreMetadata();
    populateOriginalMetadata();
    populateOMEMetadata();
}

Example 27 with Location

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

the class ImagicReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    if (checkSuffix(name, "hed")) {
        return true;
    }
    if (!checkSuffix(name, "img") || !open) {
        return false;
    }
    int lastDot = name.lastIndexOf(".");
    if (lastDot < 0) {
        return false;
    }
    String headerName = name.substring(0, lastDot);
    return new Location(headerName + ".hed").exists();
}

Example 28 with Location

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

the class ImprovisionTiffReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    put("Improvision", "yes");
    // parse key/value pairs in the comments
    String[] comments = new String[ifds.size()];
    String tz = null, tc = null, tt = null;
    for (int plane = 0; plane < ifds.size(); plane++) {
        String comment = ifds.get(plane).getComment();
        comments[plane] = comment;
        if (comment != null) {
            String[] lines = comment.split("\n");
            for (String line : lines) {
                int equals = line.indexOf('=');
                if (equals < 0)
                    continue;
                String key = line.substring(0, equals);
                String value = line.substring(equals + 1);
                addGlobalMeta(key, value);
                if (key.equals("TotalZPlanes"))
                    tz = value;
                else if (key.equals("TotalChannels"))
                    tc = value;
                else if (key.equals("TotalTimepoints"))
                    tt = value;
                else if (key.equals("XCalibrationMicrons")) {
                    pixelSizeX = DataTools.parseDouble(value);
                } else if (key.equals("YCalibrationMicrons")) {
                    pixelSizeY = DataTools.parseDouble(value);
                } else if (key.equals("ZCalibrationMicrons")) {
                    pixelSizeZ = DataTools.parseDouble(value);
                } else if (key.equals("WhiteColour")) {
                    String[] rgb = value.split(",");
                    if (rgb.length < 3) {
                        channelColors.add(null);
                        continue;
                    }
                    int red = 255;
                    try {
                        red = Integer.parseInt(rgb[0]);
                    } catch (NumberFormatException e) {
                    }
                    int green = 255;
                    try {
                        green = Integer.parseInt(rgb[1]);
                    } catch (NumberFormatException e) {
                    }
                    int blue = 255;
                    try {
                        blue = Integer.parseInt(rgb[2]);
                    } catch (NumberFormatException e) {
                    }
                    channelColors.add(new Color(red, green, blue, 255));
                }
            }
            metadata.remove("Comment");
        }
    }
    CoreMetadata m = core.get(0);
    m.sizeT = 1;
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    if (getSizeC() == 0)
        m.sizeC = 1;
    if (tz != null)
        m.sizeZ *= Integer.parseInt(tz);
    if (tc != null)
        m.sizeC *= Integer.parseInt(tc);
    if (tt != null)
        m.sizeT *= Integer.parseInt(tt);
    if (getSizeZ() * getSizeC() * getSizeT() < getImageCount()) {
        m.sizeC *= getImageCount();
    } else
        m.imageCount = getSizeZ() * getSizeT() * Integer.parseInt(tc);
    // parse each of the comments to determine axis ordering
    long[] stamps = new long[ifds.size()];
    int[][] coords = new int[ifds.size()][3];
    cNames = new String[getSizeC()];
    boolean multipleFiles = false;
    for (int i = 0; i < ifds.size(); i++) {
        Arrays.fill(coords[i], -1);
        String comment = comments[i];
        // TODO : can use loci.common.IniParser to parse the comments
        comment = comment.replaceAll("\r\n", "\n");
        comment = comment.replaceAll("\r", "\n");
        String channelName = null;
        String[] lines = comment.split("\n");
        for (String line : lines) {
            int equals = line.indexOf('=');
            if (equals < 0)
                continue;
            String key = line.substring(0, equals);
            String value = line.substring(equals + 1);
            if (key.equals("TimeStampMicroSeconds")) {
                stamps[i] = Long.parseLong(value);
            } else if (key.equals("ZPlane"))
                coords[i][0] = Integer.parseInt(value);
            else if (key.equals("ChannelNo")) {
                coords[i][1] = Integer.parseInt(value);
                int ndx = Integer.parseInt(value) - 1;
                if (cNames[ndx] == null)
                    cNames[ndx] = channelName;
            } else if (key.equals("TimepointName")) {
                coords[i][2] = Integer.parseInt(value);
            } else if (key.equals("ChannelName")) {
                channelName = value;
            } else if (key.equals("MultiFileTIFF")) {
                multipleFiles = value.equalsIgnoreCase("yes");
            }
            if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM && coords[i][0] >= 0 && coords[i][1] >= 0 && coords[i][2] >= 0) {
                break;
            }
        }
    }
    if (multipleFiles) {
        // look for other TIFF files that belong to this dataset
        String currentUUID = getUUID(currentId);
        Location parent = new Location(currentId).getAbsoluteFile().getParentFile();
        String[] list = parent.list(true);
        Arrays.sort(list);
        ArrayList<String> matchingFiles = new ArrayList<String>();
        for (String f : list) {
            String path = new Location(parent, f).getAbsolutePath();
            if (isThisType(path) && getUUID(path).equals(currentUUID)) {
                matchingFiles.add(path);
            }
        }
        files = matchingFiles.toArray(new String[matchingFiles.size()]);
    } else {
        files = new String[] { currentId };
    }
    if (files.length * ifds.size() < getImageCount()) {
        files = new String[] { currentId };
        m.imageCount = ifds.size();
        m.sizeZ = ifds.size();
        m.sizeT = 1;
        if (!isRGB()) {
            m.sizeC = 1;
        }
    }
    readers = new MinimalTiffReader[files.length];
    for (int i = 0; i < readers.length; i++) {
        readers[i] = new MinimalTiffReader();
        readers[i].setId(files[i]);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // determine average time per plane
        long sum = 0;
        for (int i = 1; i < stamps.length; i++) {
            long diff = stamps[i] - stamps[i - 1];
            if (diff > 0)
                sum += diff;
        }
        pixelSizeT = (int) (sum / getSizeT());
    }
    // determine dimension order
    m.dimensionOrder = "XY";
    if (isRGB())
        m.dimensionOrder += 'C';
    for (int i = 1; i < coords.length; i++) {
        int zDiff = coords[i][0] - coords[i - 1][0];
        int cDiff = coords[i][1] - coords[i - 1][1];
        int tDiff = coords[i][2] - coords[i - 1][2];
        if (zDiff > 0 && getDimensionOrder().indexOf('Z') < 0) {
            m.dimensionOrder += 'Z';
        }
        if (cDiff > 0 && getDimensionOrder().indexOf('C') < 0) {
            m.dimensionOrder += 'C';
        }
        if (tDiff > 0 && getDimensionOrder().indexOf('T') < 0) {
            m.dimensionOrder += 'T';
        }
        if (m.dimensionOrder.length() == 5)
            break;
    }
    if (getDimensionOrder().indexOf('Z') < 0)
        m.dimensionOrder += 'Z';
    if (getDimensionOrder().indexOf('C') < 0)
        m.dimensionOrder += 'C';
    if (getDimensionOrder().indexOf('T') < 0)
        m.dimensionOrder += 'T';
}

Example 29 with Location

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

the class InveonReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "hdr")) {
        id += ".hdr";
    }
    super.initFile(id);
    String headerData = DataTools.readFile(id);
    String[] lines = headerData.split("\n");
    String date = null;
    String institution = null, investigator = null;
    String model = null;
    String description = null;
    Double pixelSizeX = null;
    Double pixelSizeY = null;
    Double pixelSizeZ = null;
    int frames = 0;
    for (String line : lines) {
        line = line.trim();
        if (!line.startsWith("#")) {
            int space = line.indexOf(' ');
            if (space < 0) {
                continue;
            }
            String key = line.substring(0, space);
            String value = line.substring(space + 1);
            if (key.equals("institution")) {
                institution = value;
            } else if (key.equals("investigator")) {
                investigator = value;
            } else if (key.equals("study")) {
                description = value;
            } else if (key.equals("model")) {
                value = transformModel(value);
                model = value;
            } else if (key.equals("modality")) {
                value = transformModality(value);
            } else if (key.equals("modality_configuration")) {
                value = transformModalityConfiguration(value);
            } else if (key.equals("file_type")) {
                value = transformFileType(value);
            } else if (key.equals("acquisition_mode")) {
                value = transformAcquisitionMode(value);
            } else if (key.equals("bed_control")) {
                value = transformBedControl(value);
            } else if (key.equals("bed_motion")) {
                value = transformBedMotion(value);
            } else if (key.equals("registration_available")) {
                value = transformRegistrationAvailable(value);
            } else if (key.equals("normalization_applied")) {
                value = transformNormalizationApplied(value);
            } else if (key.equals("recon_algorithm")) {
                value = transformReconAlgorithm(value);
            } else if (key.equals("x_filter")) {
                value = transformFilter(value);
            } else if (key.equals("y_filter")) {
                value = transformFilter(value);
            } else if (key.equals("z_filter")) {
                value = transformFilter(value);
            } else if (key.equals("subject_orientation")) {
                value = transformSubjectOrientation(value);
            } else if (key.equals("subject_length_units")) {
                value = transformSubjectLengthUnits(value);
            } else if (key.equals("subject_weight_units")) {
                value = transformSubjectWeightUnits(value);
            } else if (key.equals("gantry_rotation")) {
                value = transformGantryRotation(value);
            } else if (key.equals("rotation_direction")) {
                value = transformRotationDirection(value);
            } else if (key.equals("ct_warping")) {
                value = transformCTWarping(value);
            } else if (key.equals("ct_projection_interpolation")) {
                value = transformCTProjectionInterpolation(value);
            } else if (key.equals("event_type")) {
                value = transformEventType(value);
            } else if (key.equals("projection") || key.equals("ct_projection_center_offset") || key.equals("ct_projection_horizontal_bed_offset")) {
                space = value.indexOf(' ');
                int index = Integer.parseInt(value.substring(0, space));
                value = value.substring(space + 1);
                key += " " + index;
            } else if (key.equals("user")) {
                space = value.indexOf(' ');
                key = value.substring(0, space);
                value = value.substring(space + 1);
            } else if (key.equals("file_name")) {
                // remove path from stored file name, if present
                value = value.replace('/', File.separatorChar);
                value = value.replace('\\', File.separatorChar);
                value = value.substring(value.lastIndexOf(File.separator) + 1);
                Location header = new Location(currentId).getAbsoluteFile();
                datFile = new Location(header.getParent(), value).getAbsolutePath();
            } else if (key.equals("time_frames")) {
                int sizeT = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeT = sizeT;
                }
            } else if (key.equals("total_frames")) {
                frames = Integer.parseInt(value);
            } else if (key.equals("number_of_bed_positions")) {
                int nPos = (int) Math.min(frames, Integer.parseInt(value));
                if (nPos > 1) {
                    CoreMetadata original = core.get(0);
                    core.clear();
                    for (int i = 0; i < nPos; i++) {
                        core.add(original);
                    }
                }
            } else if (key.equals("data_type")) {
                setDataType(value);
            } else if (key.equals("x_dimension")) {
                int sizeX = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeX = sizeX;
                }
            } else if (key.equals("y_dimension")) {
                int sizeY = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeY = sizeY;
                }
            } else if (key.equals("z_dimension")) {
                int sizeZ = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeZ = sizeZ;
                }
            } else if (key.equals("scan_time")) {
                date = value;
            } else if (key.equals("data_file_pointer")) {
                String[] values = value.split(" ");
                int[] ints = new int[values.length];
                for (int i = 0; i < ints.length; i++) {
                    ints[i] = Integer.parseInt(values[i]);
                }
                byte[] b = DataTools.intsToBytes(ints, false);
                dataPointers.add(DataTools.bytesToLong(b, false));
            } else // pixel sizes stored in mm
            if (key.equals("pixel_size_x")) {
                pixelSizeX = new Double(value) * 1000;
            } else if (key.equals("pixel_size_y")) {
                pixelSizeY = new Double(value) * 1000;
            } else if (key.equals("pixel_size_z")) {
                pixelSizeZ = new Double(value) * 1000;
            }
            addGlobalMeta(key, value);
        }
    }
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        if (ms.sizeZ == 0) {
            ms.sizeZ = 1;
        }
        if (ms.sizeT == 0) {
            ms.sizeT = 1;
        }
        ms.sizeC = 1;
        ms.rgb = false;
        ms.interleaved = false;
        ms.indexed = false;
        ms.dimensionOrder = "XYZCT";
        ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String experimenter = null, instrument = null;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        experimenter = MetadataTools.createLSID("Experimenter", 0);
        store.setExperimenterID(experimenter, 0);
        store.setExperimenterUserName(investigator, 0);
        store.setExperimenterInstitution(institution, 0);
        instrument = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrument, 0);
        store.setMicroscopeModel(model, 0);
    }
    for (int i = 0; i < core.size(); i++) {
        if (date != null) {
            String newDate = DateTools.formatDate(date, "EEE MMM dd HH:mm:ss yyyy");
            if (newDate != null) {
                store.setImageAcquisitionDate(new Timestamp(newDate), i);
            }
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            if (experimenter != null) {
                store.setImageExperimenterRef(experimenter, i);
            }
            if (instrument != null) {
                store.setImageInstrumentRef(instrument, i);
            }
            store.setImageDescription(description, i);
            Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
            Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
            Length sizeZ = FormatTools.getPhysicalSizeZ(pixelSizeZ);
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, i);
            }
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, i);
            }
            if (sizeZ != null) {
                store.setPixelsPhysicalSizeZ(sizeZ, i);
            }
        }
    }
}

Example 30 with Location

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

the class L2DReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "l2d") && isGroupFiles()) {
        // find the corresponding .l2d file
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        parent = parent.getParentFile();
        String[] list = parent.list();
        for (String file : list) {
            if (checkSuffix(file, "l2d")) {
                initFile(new Location(parent, file).getAbsolutePath());
                return;
            }
        }
        throw new FormatException("Could not find .l2d file");
    } else if (!isGroupFiles()) {
        super.initFile(id);
        tiffs = new String[][] { { id } };
        TiffReader r = new TiffReader();
        r.setMetadataStore(getMetadataStore());
        r.setId(id);
        core = new ArrayList<CoreMetadata>(r.getCoreMetadataList());
        metadataStore = r.getMetadataStore();
        final Map<String, Object> globalMetadata = r.getGlobalMetadata();
        for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
            addGlobalMeta(entry.getKey(), entry.getValue());
        }
        r.close();
        reader = new MinimalTiffReader();
        return;
    }
    super.initFile(id);
    String[] scans = getScanNames();
    Location parent = new Location(id).getAbsoluteFile().getParentFile();
    // remove scan names that do not correspond to existing directories
    final List<String> validScans = new ArrayList<String>();
    for (String s : scans) {
        Location scanDir = new Location(parent, s);
        if (scanDir.exists() && scanDir.isDirectory())
            validScans.add(s);
    }
    scans = validScans.toArray(new String[validScans.size()]);
    // read metadata from each scan
    tiffs = new String[scans.length][];
    metadataFiles = new List[scans.length];
    core = new ArrayList<CoreMetadata>(scans.length);
    String[] comments = new String[scans.length];
    String[] wavelengths = new String[scans.length];
    String[] dates = new String[scans.length];
    String model = null;
    tileWidth = new int[scans.length];
    tileHeight = new int[scans.length];
    core.clear();
    for (int i = 0; i < scans.length; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        setSeries(i);
        metadataFiles[i] = new ArrayList<String>();
        String scanName = scans[i] + ".scn";
        Location scanDir = new Location(parent, scans[i]);
        // read .scn file from each scan
        String scanPath = new Location(scanDir, scanName).getAbsolutePath();
        addDirectory(scanDir.getAbsolutePath(), i);
        String scanData = DataTools.readFile(scanPath);
        String[] lines = scanData.split("\n");
        for (String line : lines) {
            if (!line.startsWith("#")) {
                String key = line.substring(0, line.indexOf('='));
                String value = line.substring(line.indexOf('=') + 1);
                addSeriesMeta(key, value);
                if (key.equals("ExperimentNames")) {
                // TODO : parse experiment metadata - this is typically a list of
                // overlay shapes, or analysis data
                } else if (key.equals("ImageNames")) {
                    tiffs[i] = value.split(",");
                    for (int t = 0; t < tiffs[i].length; t++) {
                        tiffs[i][t] = new Location(scanDir, tiffs[i][t].trim()).getAbsolutePath();
                    }
                } else if (key.equals("Comments")) {
                    comments[i] = value;
                } else if (key.equals("ScanDate")) {
                    dates[i] = value;
                } else if (key.equals("ScannerName")) {
                    model = value;
                } else if (key.equals("ScanChannels")) {
                    wavelengths[i] = value;
                }
            }
        }
    }
    setSeries(0);
    reader = new MinimalTiffReader();
    MetadataStore store = makeFilterMetadata();
    for (int i = 0; i < getSeriesCount(); i++) {
        CoreMetadata ms = core.get(i);
        ms.imageCount = tiffs[i].length;
        ms.sizeC = tiffs[i].length;
        ms.sizeT = 1;
        ms.sizeZ = 1;
        ms.dimensionOrder = "XYCZT";
        reader.setId(tiffs[i][0]);
        ms.sizeX = reader.getSizeX();
        ms.sizeY = reader.getSizeY();
        ms.sizeC *= reader.getSizeC();
        ms.rgb = reader.isRGB();
        ms.indexed = reader.isIndexed();
        ms.littleEndian = reader.isLittleEndian();
        ms.pixelType = reader.getPixelType();
        tileWidth[i] = reader.getOptimalTileWidth();
        tileHeight[i] = reader.getOptimalTileHeight();
    }
    MetadataTools.populatePixels(store, this);
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName(scans[i], i);
        if (dates[i] != null) {
            dates[i] = DateTools.formatDate(dates[i], DATE_FORMAT);
            if (dates[i] != null) {
                store.setImageAcquisitionDate(new Timestamp(dates[i]), i);
            }
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        for (int i = 0; i < getSeriesCount(); i++) {
            store.setImageInstrumentRef(instrumentID, i);
            store.setImageDescription(comments[i], i);
            if (wavelengths[i] != null) {
                String[] waves = wavelengths[i].split("[, ]");
                if (waves.length < getEffectiveSizeC()) {
                    LOGGER.debug("Expected {} wavelengths; got {} wavelengths.", getEffectiveSizeC(), waves.length);
                }
                for (int q = 0; q < waves.length; q++) {
                    String laser = MetadataTools.createLSID("LightSource", 0, q);
                    store.setLaserID(laser, 0, q);
                    Double wave = new Double(waves[q].trim());
                    Length wavelength = FormatTools.getWavelength(wave);
                    if (wavelength != null) {
                        store.setLaserWavelength(wavelength, 0, q);
                    }
                    store.setLaserType(getLaserType("Other"), 0, q);
                    store.setLaserLaserMedium(getLaserMedium("Other"), 0, q);
                    store.setChannelLightSourceSettingsID(laser, i, q);
                }
            }
        }
        store.setMicroscopeModel(model, 0);
        store.setMicroscopeType(getMicroscopeType("Other"), 0);
    }
}