Examples with Color ome.xml.model.primitives.Color used on opensource projects

Example 1 with Color

use of ome.xml.model.primitives.Color in project bioformats by openmicroscopy.

the class LeicaReader method parseLUT.

private void parseLUT(int seriesIndex) throws IOException {
    int nChannels = in.readInt();
    if (nChannels > 0)
        core.get(seriesIndex).indexed = true;
    addSeriesMeta("Number of LUT channels", nChannels);
    addSeriesMeta("ID of colored dimension", in.readInt());
    channelColor[seriesIndex] = new Color[nChannels];
    for (int j = 0; j < nChannels; j++) {
        String p = "LUT Channel " + j;
        addSeriesMeta(p + " version", in.readInt());
        addSeriesMeta(p + " inverted?", in.read() == 1);
        addSeriesMeta(p + " description", getString(false));
        addSeriesMeta(p + " filename", getString(false));
        String lut = getString(false);
        addSeriesMeta(p + " name", lut);
        channelColor[seriesIndex][j] = new Color(255, 255, 255, 255);
        if (lut.equalsIgnoreCase("red")) {
            channelColor[seriesIndex][j] = new Color(255, 0, 0, 255);
        } else if (lut.equalsIgnoreCase("green")) {
            channelColor[seriesIndex][j] = new Color(0, 255, 0, 255);
        } else if (lut.equalsIgnoreCase("blue")) {
            channelColor[seriesIndex][j] = new Color(0, 0, 255, 255);
        } else if (lut.equalsIgnoreCase("yellow")) {
            channelColor[seriesIndex][j] = new Color(255, 255, 0, 255);
        } else if (lut.equalsIgnoreCase("cyan")) {
            channelColor[seriesIndex][j] = new Color(0, 255, 255, 255);
        } else if (lut.equalsIgnoreCase("magenta")) {
            channelColor[seriesIndex][j] = new Color(255, 0, 255, 255);
        }
        in.skipBytes(8);
    }
}

Example 2 with Color

use of ome.xml.model.primitives.Color in project bioformats by openmicroscopy.

the class NativeND2Reader method populateMetadataStore.

private void populateMetadataStore(ND2Handler handler) throws FormatException {
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    String filename = new Location(getCurrentFile()).getName();
    if (handler != null) {
        ArrayList<String> posNames = handler.getPositionNames();
        int nameWidth = String.valueOf(getSeriesCount()).length();
        for (int i = 0; i < getSeriesCount(); i++) {
            String seriesSuffix = String.format("(series %0" + nameWidth + "d)", i + 1);
            String suffix = (i < posNames.size() && !posNames.get(i).equals("")) ? posNames.get(i) : seriesSuffix;
            String name = filename + " " + suffix;
            store.setImageName(name.trim(), i);
        }
    }
    colors = new int[getEffectiveSizeC()];
    ArrayList<String> channelNames = null;
    if (handler != null) {
        channelNames = handler.getChannelNames();
        if (channelNames.size() < getEffectiveSizeC() && backupHandler != null) {
            channelNames = backupHandler.getChannelNames();
        } else if (channelNames.size() < getEffectiveSizeC()) {
            channelNames = textChannelNames;
        }
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            if (c < channelNames.size()) {
                String channelName = channelNames.get(c);
                Integer channelColor = channelColors.get(channelName);
                colors[c] = channelColor == null ? 0 : channelColor.intValue();
            }
        }
    }
    if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
        return;
    }
    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);
    for (int i = 0; i < getSeriesCount(); i++) {
        // link Instrument and Image
        store.setImageInstrumentRef(instrumentID, i);
        // set the channel color
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            int red = colors[c] & 0xff;
            int green = (colors[c] & 0xff00) >> 8;
            int blue = (colors[c] & 0xff0000) >> 16;
            // doing so can prevent the image from displaying correctly
            if (red != 0 || green != 0 || blue != 0) {
                // always set the alpha to 255, otherwise the colors may not appear
                store.setChannelColor(new Color(red, green, blue, 255), i, c);
            }
        }
    }
    // populate Dimensions data
    if (handler != null) {
        for (int i = 0; i < getSeriesCount(); i++) {
            double sizeX = handler.getPixelSizeX();
            double sizeY = handler.getPixelSizeY();
            double sizeZ = handler.getPixelSizeZ();
            if (trueSizeX > 0) {
                store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(trueSizeX), i);
            } else {
                Length size = FormatTools.getPhysicalSizeX(sizeX);
                if (size != null) {
                    store.setPixelsPhysicalSizeX(size, i);
                }
            }
            if (trueSizeY > 0) {
                store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(trueSizeY), i);
            } else if (trueSizeX > 0) {
                // if the X size is set, assume X and Y are equal
                store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(trueSizeX), i);
            } else {
                Length size = FormatTools.getPhysicalSizeY(sizeY);
                if (size == null) {
                    // if the X size is set, assume X and Y are equal
                    size = FormatTools.getPhysicalSizeY(sizeX);
                }
                if (size != null) {
                    store.setPixelsPhysicalSizeY(size, i);
                }
            }
            if (trueSizeZ != null && trueSizeZ > 0) {
                store.setPixelsPhysicalSizeZ(FormatTools.getPhysicalSizeZ(trueSizeZ), i);
            } else {
                Length size = FormatTools.getPhysicalSizeZ(sizeZ);
                if (size != null) {
                    store.setPixelsPhysicalSizeZ(size, i);
                }
            }
        }
    }
    // populate PlaneTiming and StagePosition data
    if (handler != null && handler.getExposureTimes().size() > 0) {
        exposureTime = handler.getExposureTimes();
    }
    int zcPlanes = getImageCount() / ((split ? getSizeC() : 1) * getSizeT());
    for (int i = 0; i < getSeriesCount(); i++) {
        if (tsT.size() > 0) {
            setSeries(i);
            for (int n = 0; n < getImageCount(); n++) {
                int[] coords = getZCTCoords(n);
                int stampIndex = getIndex(coords[0], split ? 0 : coords[1], 0);
                stampIndex += (coords[2] * getSeriesCount() + i) * zcPlanes;
                if (tsT.size() == getImageCount())
                    stampIndex = n;
                else if (tsT.size() == getSizeZ()) {
                    stampIndex = coords[0];
                }
                if (stampIndex < tsT.size()) {
                    double stamp = tsT.get(stampIndex).doubleValue();
                    store.setPlaneDeltaT(new Time(stamp, UNITS.SECOND), i, n);
                }
                int index = i * getSizeC() + coords[1];
                if (exposureTime.size() == getSizeC()) {
                    index = coords[1];
                }
                if (exposureTime != null && index < exposureTime.size() && exposureTime.get(index) != null) {
                    store.setPlaneExposureTime(new Time(exposureTime.get(index), UNITS.SECOND), i, n);
                }
            }
        }
        if (handler != null) {
            if (posX == null)
                posX = handler.getXPositions();
            if (posY == null)
                posY = handler.getYPositions();
            if (posZ == null)
                posZ = handler.getZPositions();
        }
        String pos = "for position";
        for (int n = 0; n < getImageCount(); n++) {
            int[] coords = getZCTCoords(n);
            int index = coords[0];
            index += (coords[2] * getSeriesCount() + i) * zcPlanes;
            if (posX != null) {
                if (index >= posX.size())
                    index = i;
                if (index < posX.size()) {
                    String key = "X position ";
                    store.setPlanePositionX(posX.get(index), i, n);
                    addSeriesMetaList(key, posX.get(index));
                    addGlobalMetaList(key + pos, posX.get(index));
                }
            }
            if (posY != null) {
                if (index < posY.size()) {
                    String key = "Y position ";
                    store.setPlanePositionY(posY.get(index), i, n);
                    addSeriesMetaList(key, posY.get(index));
                    addGlobalMetaList(key + pos, posY.get(index));
                }
            }
            if (posZ != null) {
                if (index < posZ.size()) {
                    store.setPlanePositionZ(posZ.get(index), i, n);
                    String key = "Z position " + pos + ", plane";
                    addSeriesMetaList(key, posZ.get(index));
                    addGlobalMetaList(key, posZ.get(index));
                }
            }
        }
    }
    if (handler == null) {
        setSeries(0);
        return;
    }
    String detectorID = MetadataTools.createLSID("Detector", 0, 0);
    store.setDetectorID(detectorID, 0, 0);
    store.setDetectorModel(handler.getCameraModel(), 0, 0);
    store.setDetectorType(getDetectorType("Other"), 0, 0);
    ArrayList<String> modality = handler.getModalities();
    ArrayList<String> binning = handler.getBinnings();
    ArrayList<Double> speed = handler.getSpeeds();
    ArrayList<Double> gain = handler.getGains();
    ArrayList<Double> temperature = handler.getTemperatures();
    ArrayList<Double> exWave = handler.getExcitationWavelengths();
    ArrayList<Double> emWave = handler.getEmissionWavelengths();
    ArrayList<Integer> power = handler.getPowers();
    ArrayList<Hashtable<String, String>> rois = handler.getROIs();
    if (backupHandler != null) {
        if (emWave.size() == 0) {
            emWave = backupHandler.getEmissionWavelengths();
        }
        if (exWave.size() == 0) {
            exWave = backupHandler.getExcitationWavelengths();
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            int index = c;
            Double pinholeSize = handler.getPinholeSize();
            if (pinholeSize != null) {
                store.setChannelPinholeSize(new Length(pinholeSize, UNITS.MICROMETER), i, c);
            }
            if (index < channelNames.size()) {
                String channelName = channelNames.get(index);
                store.setChannelName(channelName, i, c);
            } else if (channelNames.size() >= getEffectiveSizeC()) {
                store.setChannelName(channelNames.get(c), i, c);
            }
            if (index < modality.size()) {
                store.setChannelAcquisitionMode(getAcquisitionMode(modality.get(index)), i, c);
            }
            if (index < emWave.size() || index < textEmissionWavelengths.size()) {
                Double value = index < emWave.size() ? emWave.get(index) : textEmissionWavelengths.get(index);
                Length emission = FormatTools.getEmissionWavelength(value);
                if (emission != null) {
                    store.setChannelEmissionWavelength(emission, i, c);
                }
            } else if (emWave.size() > 0 || textEmissionWavelengths.size() > 0) {
                store.setChannelColor(new Color(255, 255, 255, 255), i, c);
            }
            if (index < exWave.size()) {
                Length excitation = FormatTools.getExcitationWavelength(exWave.get(index));
                if (excitation != null) {
                    store.setChannelExcitationWavelength(excitation, i, c);
                }
            }
            if (index < binning.size()) {
                store.setDetectorSettingsBinning(getBinning(binning.get(index)), i, c);
            }
            if (index < gain.size()) {
                store.setDetectorSettingsGain(gain.get(index), i, c);
            }
            if (index < speed.size()) {
                store.setDetectorSettingsReadOutRate(new Frequency(speed.get(index), UNITS.HERTZ), i, c);
            }
            store.setDetectorSettingsID(detectorID, i, c);
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        if (i * getSizeC() < temperature.size()) {
            Double temp = temperature.get(i * getSizeC());
            store.setImagingEnvironmentTemperature(new Temperature(temp, UNITS.CELSIUS), i);
        }
    }
    // populate DetectorSettings
    Double voltage = handler.getVoltage();
    if (voltage != null) {
        store.setDetectorSettingsVoltage(new ElectricPotential(voltage, UNITS.VOLT), 0, 0);
    }
    // populate Objective
    Double na = handler.getNumericalAperture();
    if (na != null) {
        store.setObjectiveLensNA(na, 0, 0);
    }
    Double mag = handler.getMagnification();
    if (mag != null) {
        store.setObjectiveCalibratedMagnification(mag, 0, 0);
    }
    store.setObjectiveModel(handler.getObjectiveModel(), 0, 0);
    String immersion = handler.getImmersion();
    if (immersion == null)
        immersion = "Other";
    store.setObjectiveImmersion(getImmersion(immersion), 0, 0);
    String correction = handler.getCorrection();
    if (correction == null || correction.length() == 0)
        correction = "Other";
    store.setObjectiveCorrection(getCorrection(correction), 0, 0);
    // link Objective to Image
    String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
    store.setObjectiveID(objectiveID, 0, 0);
    if (refractiveIndex == null) {
        refractiveIndex = handler.getRefractiveIndex();
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setObjectiveSettingsID(objectiveID, i);
        if (refractiveIndex != null) {
            store.setObjectiveSettingsRefractiveIndex(refractiveIndex, i);
        }
    }
    setSeries(0);
    if (getMetadataOptions().getMetadataLevel() == MetadataLevel.NO_OVERLAYS) {
        return;
    }
    handler.populateROIs(store);
}

Example 3 with Color

use of ome.xml.model.primitives.Color in project bioformats by openmicroscopy.

the class OIRReader method parseLUT.

private void parseLUT(Element root, String uid) throws FormatException {
    Element linear = getFirstChild(root, "lut:linear");
    boolean isLinear = false;
    if (linear != null) {
        isLinear = Boolean.valueOf(linear.getTextContent());
    }
    Element data = getFirstChild(root, "lut:data");
    if (data != null) {
        String lutContent = data.getTextContent();
        for (int i = 0; i < channels.size(); i++) {
            if (channels.get(i).lut == null && channels.get(i).id.equals(uid)) {
                if (getPixelType() == FormatTools.UINT8) {
                    channels.get(i).lut = new byte[3][lutContent.length() / 8];
                } else if (getPixelType() == FormatTools.UINT16) {
                    channels.get(i).lut = new short[3][lutContent.length() / 8];
                } else {
                    LOGGER.warn("Skipping LUTs for pixel type {}", getPixelType());
                    return;
                }
                for (int q = 0; q < lutContent.length(); q += 8) {
                    int r = Integer.parseInt(lutContent.substring(q, q + 2), 16);
                    int g = Integer.parseInt(lutContent.substring(q + 2, q + 4), 16);
                    int b = Integer.parseInt(lutContent.substring(q + 4, q + 6), 16);
                    if (channels.get(i).lut instanceof byte[][]) {
                        ((byte[][]) channels.get(i).lut)[0][q / 8] = (byte) (r & 0xff);
                        ((byte[][]) channels.get(i).lut)[1][q / 8] = (byte) (g & 0xff);
                        ((byte[][]) channels.get(i).lut)[2][q / 8] = (byte) (b & 0xff);
                    } else if (channels.get(i).lut instanceof short[][]) {
                        ((short[][]) channels.get(i).lut)[0][q / 8] = (short) ((r & 0xffff) * 256);
                        ((short[][]) channels.get(i).lut)[1][q / 8] = (short) ((g & 0xffff) * 256);
                        ((short[][]) channels.get(i).lut)[2][q / 8] = (short) ((b & 0xffff) * 256);
                    }
                    if (isLinear && q == lutContent.length() - 8) {
                        channels.get(i).color = new Color(r, g, b, 255);
                    }
                }
                break;
            }
        }
    }
}

Example 4 with Color

use of ome.xml.model.primitives.Color in project bioformats by openmicroscopy.

the class MIASReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    if (checkSuffix(id, "txt")) {
        // first need to find a relevant TIFF file
        Location base = new Location(id).getAbsoluteFile();
        Location plate = null;
        if (base.getParentFile().getName().equals("Batchresults")) {
            Location experiment = base.getParentFile().getParentFile();
            String[] plates = experiment.list(true);
            Arrays.sort(plates);
            plate = new Location(experiment, plates[0]);
        } else {
            plate = base.getParentFile();
            if (plate.getName().equals("results"))
                plate = plate.getParentFile();
        }
        String[] list = plate.list(true);
        for (String f : list) {
            if (f.startsWith("Well")) {
                Location well = new Location(plate, f);
                String[] wellList = well.list(true);
                for (String file : wellList) {
                    String path = new Location(well, file).getAbsolutePath();
                    if (isThisType(path) && checkSuffix(path, new String[] { "tif", "tiff" })) {
                        initFile(path);
                        return;
                    }
                }
            }
        }
        throw new FormatException("Could not locate an appropriate TIFF file.");
    }
    if (!isGroupFiles()) {
        tiffs = new String[][] { { id } };
        readers = new MinimalTiffReader[1][1];
        readers[0][0] = new MinimalTiffReader();
        TiffReader r = new TiffReader();
        r.setMetadataStore(getMetadataStore());
        r.setId(tiffs[0][0]);
        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();
        tileRows = 1;
        tileCols = 1;
        return;
    }
    analysisFiles = new ArrayList<AnalysisFile>();
    // MIAS is a high content screening format which supports multiple plates,
    // wells and fields.
    // Most of the metadata comes from the directory hierarchy, as very little
    // metadata is present in the actual files.
    // 
    // The directory hierarchy is either:
    // 
    // <experiment name>                        top level experiment directory
    // Batchresults                           analysis results for experiment
    // <plate number>_<plate barcode>         one directory for each plate
    // results                              analysis results for plate
    // Well<xxxx>                           one directory for each well
    // mode<x>_z<xxx>_t<xxx>_im<x>_<x>.tif
    // 
    // or:
    // 
    // <experiment name>                        top level experiment directory
    // <plate number>                         plate directory (3 digits)
    // <well number>                        well directory (4 digits)
    // <channel number>                   channel directory (1 digit)
    // <tile row>_<tile col>_<Z>_<T>.tif
    // 
    // Each TIFF file contains a single grayscale plane.  The "mode" block
    // refers to the channel number; the "z" and "t" blocks refer to the
    // Z section and timepoint, respectively.  The "im<x>_<x>" block gives
    // the row and column coordinates of the image within a mosaic.
    // 
    // We are initially given one of these TIFF files; from there, we need
    // to find the top level experiment directory and work our way down to
    // determine how many plates and wells are present.
    LOGGER.info("Building list of TIFF files");
    Location baseFile = new Location(id).getAbsoluteFile();
    Location plate = baseFile.getParentFile().getParentFile();
    String plateName = plate.getName();
    if (!(plateName.length() == 3 || (plateName.length() > 3 && plateName.replaceAll("\\d", "").startsWith("-")))) {
        plate = plate.getParentFile();
        plateName = plate.getName();
    }
    int plateNumber = Integer.parseInt(plateName.substring(0, 3));
    Location experiment = plate.getParentFile();
    String[] directories = experiment.list(true);
    Arrays.sort(directories);
    for (String dir : directories) {
        Location f = new Location(experiment, dir);
        if (dir.equals("Batchresults")) {
            String[] results = f.list(true);
            for (String result : results) {
                Location file = new Location(f, result);
                if (result.startsWith("NEO_Results")) {
                    resultFile = file.getAbsolutePath();
                    AnalysisFile af = new AnalysisFile();
                    af.filename = resultFile;
                    analysisFiles.add(af);
                } else if (result.startsWith("NEO_PlateOutput_")) {
                    int plateIndex = Integer.parseInt(result.substring(16, 19));
                    if (plateIndex == plateNumber) {
                        AnalysisFile af = new AnalysisFile();
                        af.filename = file.getAbsolutePath();
                        af.plate = 0;
                        analysisFiles.add(af);
                    }
                }
            }
        }
    }
    String[] list = plate.list(true);
    Arrays.sort(list);
    final List<String> wellDirectories = new ArrayList<String>();
    for (String dir : list) {
        Location f = new Location(plate, dir);
        if (f.getName().startsWith("Well") || f.getName().length() == 4) {
            // directory name is valid, but we need to make sure that the
            // directory contains a TIFF or a subdirectory
            String[] wellList = f.list(true);
            if (wellList != null) {
                boolean validWell = false;
                for (String potentialTIFF : wellList) {
                    if (potentialTIFF.toLowerCase().endsWith(".tif") || new Location(f, potentialTIFF).isDirectory()) {
                        validWell = true;
                        break;
                    }
                }
                if (validWell)
                    wellDirectories.add(f.getAbsolutePath());
            }
        } else if (f.getName().equals("results")) {
            String[] resultsList = f.list(true);
            for (String result : resultsList) {
                // exclude proprietary program state files
                if (!result.endsWith(".sav") && !result.endsWith(".dsv") && !result.endsWith(".dat")) {
                    Location r = new Location(f, result);
                    AnalysisFile af = new AnalysisFile();
                    af.filename = r.getAbsolutePath();
                    af.plate = 0;
                    if (result.toLowerCase().startsWith("well")) {
                        af.well = Integer.parseInt(result.substring(4, 8)) - 1;
                    }
                    analysisFiles.add(af);
                }
            }
        } else if (f.getName().equals("Nugenesistemplate.txt")) {
            templateFile = f.getAbsolutePath();
        }
    }
    int nWells = wellDirectories.size();
    LOGGER.debug("Found {} wells.", nWells);
    readers = new MinimalTiffReader[nWells][];
    tiffs = new String[nWells][];
    int[] zCount = new int[nWells];
    int[] cCount = new int[nWells];
    int[] tCount = new int[nWells];
    String[] order = new String[nWells];
    wellNumber = new int[nWells];
    String[] wells = wellDirectories.toArray(new String[nWells]);
    Arrays.sort(wells);
    for (int j = 0; j < nWells; j++) {
        Location well = new Location(wells[j]);
        String wellName = well.getName().replaceAll("Well", "");
        wellNumber[j] = Integer.parseInt(wellName) - 1;
        String[] tiffFiles = well.list(true);
        final List<String> tmpFiles = new ArrayList<String>();
        for (String tiff : tiffFiles) {
            String name = tiff.toLowerCase();
            if (name.endsWith(".tif") || name.endsWith(".tiff")) {
                tmpFiles.add(new Location(well, tiff).getAbsolutePath());
            }
        }
        if (tmpFiles.size() == 0) {
            LOGGER.debug("No TIFFs in well directory {}", wells[j]);
            // directories which contain the TIFFs
            for (String dir : tiffFiles) {
                Location file = new Location(well, dir);
                if (dir.length() == 1 && file.isDirectory()) {
                    cCount[j]++;
                    String[] tiffs = file.list(true);
                    for (String tiff : tiffs) {
                        String name = tiff.toLowerCase();
                        if (name.endsWith(".tif") || name.endsWith(".tiff")) {
                            tmpFiles.add(new Location(file, tiff).getAbsolutePath());
                        }
                    }
                }
            }
        }
        tiffFiles = tmpFiles.toArray(new String[0]);
        if (ArrayUtils.isEmpty(tiffFiles)) {
            throw new FormatException("Empty dataset - No tiff files were found.");
        }
        Location firstTiff = new Location(tiffFiles[0]);
        List<String> names = new ArrayList<String>();
        for (Location f : firstTiff.getParentFile().listFiles()) {
            names.add(f.getName());
        }
        FilePattern fp = new FilePattern(FilePattern.findPattern(firstTiff.getName(), null, names.toArray(new String[names.size()])));
        String[] blocks = fp.getPrefixes();
        order[j] = "XY";
        int[] count = fp.getCount();
        for (int block = blocks.length - 1; block >= 0; block--) {
            blocks[block] = blocks[block].toLowerCase();
            blocks[block] = blocks[block].substring(blocks[block].lastIndexOf("_") + 1);
            if (blocks[block].equals("z")) {
                zCount[j] = count[block];
                order[j] += 'Z';
            } else if (blocks[block].equals("t")) {
                tCount[j] = count[block];
                order[j] += 'T';
            } else if (blocks[block].equals("mode")) {
                cCount[j] = count[block];
                order[j] += 'C';
            } else if (blocks[block].equals("im"))
                tileRows = count[block];
            else if (blocks[block].equals(""))
                tileCols = count[block];
            else if (blocks[block].replaceAll("\\d", "").length() == 0) {
                if (block == 3)
                    tileRows = count[block];
                else if (block == 2)
                    tileCols = count[block];
                else if (block == 0) {
                    zCount[j] = count[block];
                    order[j] += 'Z';
                } else if (block == 1) {
                    tCount[j] = count[block];
                    order[j] += 'T';
                }
            } else {
                throw new FormatException("Unsupported block '" + blocks[block]);
            }
        }
        Arrays.sort(tiffFiles);
        tiffs[j] = tiffFiles;
        LOGGER.debug("Well {} has {} files.", j, tiffFiles.length);
        readers[j] = new MinimalTiffReader[tiffFiles.length];
        for (int k = 0; k < tiffFiles.length; k++) {
            readers[j][k] = new MinimalTiffReader();
        }
    }
    // Populate core metadata
    LOGGER.info("Populating core metadata");
    int nSeries = tiffs.length;
    bpp = new int[nSeries];
    if (readers.length == 0) {
        throw new FormatException("No wells were found.");
    }
    // assume that all wells have the same width, height, and pixel type
    readers[0][0].setId(tiffs[0][0]);
    tileWidth = readers[0][0].getSizeX();
    tileHeight = readers[0][0].getSizeY();
    if (tileCols == 0)
        tileCols = 1;
    if (tileRows == 0)
        tileRows = 1;
    core.clear();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeZ = zCount[i];
        ms.sizeC = cCount[i];
        ms.sizeT = tCount[i];
        if (ms.sizeZ == 0)
            ms.sizeZ = 1;
        if (ms.sizeC == 0)
            ms.sizeC = 1;
        if (ms.sizeT == 0)
            ms.sizeT = 1;
        ms.sizeX = tileWidth * tileCols;
        ms.sizeY = tileHeight * tileRows;
        ms.pixelType = readers[0][0].getPixelType();
        ms.sizeC *= readers[0][0].getSizeC();
        ms.rgb = readers[0][0].isRGB();
        ms.littleEndian = readers[0][0].isLittleEndian();
        ms.interleaved = readers[0][0].isInterleaved();
        ms.indexed = readers[0][0].isIndexed();
        ms.falseColor = readers[0][0].isFalseColor();
        ms.dimensionOrder = order[i];
        if (ms.dimensionOrder.indexOf('Z') == -1) {
            ms.dimensionOrder += 'Z';
        }
        if (ms.dimensionOrder.indexOf('C') == -1) {
            ms.dimensionOrder += 'C';
        }
        if (ms.dimensionOrder.indexOf('T') == -1) {
            ms.dimensionOrder += 'T';
        }
        ms.imageCount = ms.sizeZ * ms.sizeT * cCount[i];
        if (ms.imageCount == 0) {
            ms.imageCount = 1;
        }
        bpp[i] = FormatTools.getBytesPerPixel(ms.pixelType);
    }
    // Populate metadata hashtable
    LOGGER.info("Populating metadata hashtable");
    if (resultFile != null && getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String[] cols = null;
        final List<String> rows = new ArrayList<String>();
        boolean doKeyValue = true;
        int nStarLines = 0;
        String analysisResults = DataTools.readFile(resultFile);
        String[] lines = analysisResults.split("\n");
        for (String line : lines) {
            line = line.trim();
            if (line.length() == 0)
                continue;
            if (line.startsWith("******") && line.endsWith("******"))
                nStarLines++;
            if (doKeyValue) {
                String[] n = line.split("\t");
                if (n[0].endsWith(":"))
                    n[0] = n[0].substring(0, n[0].length() - 1);
                if (n.length >= 2)
                    addGlobalMeta(n[0], n[1]);
            } else {
                if (cols == null)
                    cols = line.split("\t");
                else
                    rows.add(line);
            }
            if (nStarLines == 2)
                doKeyValue = false;
        }
        for (String row : rows) {
            String[] d = row.split("\t");
            for (int col = 3; col < cols.length; col++) {
                addGlobalMeta("Plate " + d[0] + ", Well " + d[2] + " " + cols[col], d[col]);
                if (cols[col].equals("AreaCode")) {
                    String wellID = d[col].replaceAll("\\D", "");
                    wellColumns = Integer.parseInt(wellID);
                }
            }
        }
    }
    // Populate MetadataStore
    LOGGER.info("Populating MetadataStore");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    // assume that a 96 well plate is 8x12, and a 384 well plate is 16x24
    if (wellColumns == 0) {
        if (nWells == 96) {
            wellColumns = 12;
        } else if (nWells == 384) {
            wellColumns = 24;
        } else {
            LOGGER.warn("Could not determine the plate dimensions.");
            wellColumns = 24;
        }
    }
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    String plateAcqId = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqId, 0, 0);
    store.setPlateAcquisitionMaximumFieldCount(new PositiveInteger(1), 0, 0);
    for (int well = 0; well < nWells; well++) {
        int wellIndex = wellNumber[well];
        int row = wellIndex / wellColumns;
        int wellCol = (wellIndex % wellColumns) + 1;
        char wellRow = (char) ('A' + row);
        store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
        store.setWellRow(new NonNegativeInteger(row), 0, well);
        store.setWellColumn(new NonNegativeInteger(wellCol - 1), 0, well);
        String imageID = MetadataTools.createLSID("Image", well);
        String wellSampleID = MetadataTools.createLSID("WellSample", 0, well, 0);
        store.setWellSampleID(wellSampleID, 0, well, 0);
        store.setWellSampleIndex(new NonNegativeInteger(well), 0, well, 0);
        store.setImageID(imageID, well);
        store.setImageName("Well " + wellRow + wellCol, well);
        store.setWellSampleImageRef(imageID, 0, well, 0);
        store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, well);
    }
    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    if (level != MetadataLevel.MINIMUM) {
        String experimentID = MetadataTools.createLSID("Experiment", 0);
        store.setExperimentID(experimentID, 0);
        store.setExperimentType(getExperimentType("Other"), 0);
        store.setExperimentDescription(experiment.getName(), 0);
        // populate SPW metadata
        store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
        store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
        parseTemplateFile(store);
        plateName = plateName.substring(plateName.indexOf('-') + 1);
        store.setPlateName(plateName, 0);
        store.setPlateExternalIdentifier(plateName, 0);
        for (int well = 0; well < nWells; well++) {
            // populate Image/Pixels metadata
            store.setImageExperimentRef(experimentID, well);
            String instrumentID = MetadataTools.createLSID("Instrument", 0);
            store.setInstrumentID(instrumentID, 0);
            store.setImageInstrumentRef(instrumentID, well);
        }
        roiFiles = new ArrayList<AnalysisFile>();
        for (AnalysisFile af : analysisFiles) {
            String file = af.filename;
            String name = new Location(file).getName();
            if (!name.startsWith("Well"))
                continue;
            if (name.endsWith("AllModesOverlay.tif")) {
                roiFiles.add(af);
            } else if (name.endsWith("overlay.tif")) {
                roiFiles.add(af);
            }
        }
        if (level != MetadataLevel.NO_OVERLAYS) {
            // populate image-level ROIs
            Color[] colors = new Color[getSizeC()];
            int nextROI = 0;
            for (AnalysisFile af : analysisFiles) {
                String file = af.filename;
                String name = new Location(file).getName();
                if (!name.startsWith("Well"))
                    continue;
                int[] position = getPositionFromFile(file);
                int well = position[0];
                if (name.endsWith("detail.txt")) {
                    String data = DataTools.readFile(file);
                    String[] lines = data.split("\n");
                    int start = 0;
                    while (start < lines.length && !lines[start].startsWith("Label")) {
                        start++;
                    }
                    if (start >= lines.length)
                        continue;
                    String[] columns = lines[start].split("\t");
                    List<String> columnNames = Arrays.asList(columns);
                    for (int j = start + 1; j < lines.length; j++) {
                        populateROI(columnNames, lines[j].split("\t"), well, nextROI++, position[1], position[2], store);
                    }
                } else if (name.endsWith("AllModesOverlay.tif")) {
                    // results/Well<nnnn>_mode<n>_z<nnn>_t<nnn>_AllModesOverlay.tif
                    if (colors[position[3]] != null)
                        continue;
                    try {
                        colors[position[3]] = getChannelColorFromFile(file);
                    } catch (IOException e) {
                    }
                    if (colors[position[3]] == null)
                        continue;
                    for (int s = 0; s < getSeriesCount(); s++) {
                        store.setChannelColor(colors[position[3]], s, position[3]);
                    }
                    if (position[3] == 0) {
                        nextROI += parseMasks(store, well, nextROI, file);
                    }
                } else if (name.endsWith("overlay.tif")) {
                    nextROI += parseMasks(store, well, nextROI, file);
                }
            }
        }
    }
}

Example 5 with Color

use of ome.xml.model.primitives.Color in project bioformats by openmicroscopy.

the class MIASReader method parseMasks.

/**
 * Parse Mask ROIs from the given TIFF and place them in the given
 * MetadataStore.
 * @return the number of masks parsed
 */
private int parseMasks(MetadataStore store, int series, int roi, String overlayTiff) throws FormatException, IOException {
    if (!parseMasks || series >= getSeriesCount())
        return 0;
    int nOverlays = 0;
    for (int i = 0; i < 3; i++) {
        String roiId = MetadataTools.createLSID("ROI", series, roi + nOverlays);
        String maskId = MetadataTools.createLSID("Mask", series, roi + nOverlays, 0);
        overlayFiles.put(maskId, overlayTiff);
        overlayPlanes.put(maskId, i);
        boolean validMask = populateMaskPixels(series, roi + nOverlays, 0, store);
        if (validMask) {
            store.setROIID(roiId, roi + nOverlays);
            String maskID = MetadataTools.createLSID("Shape", roi + nOverlays, 0);
            store.setMaskID(maskID, roi + nOverlays, 0);
            store.setMaskX(0d, roi + nOverlays, 0);
            store.setMaskY(0d, roi + nOverlays, 0);
            store.setMaskWidth((double) getSizeX(), roi + nOverlays, 0);
            store.setMaskHeight((double) getSizeY(), roi + nOverlays, 0);
            int color = 0xff000000 | (0xff << (8 * (2 - i)));
            store.setMaskStrokeColor(new Color(color), roi + nOverlays, 0);
            store.setMaskFillColor(new Color(color), roi + nOverlays, 0);
            store.setImageROIRef(roiId, series, roi + nOverlays);
            nOverlays++;
        }
    }
    return nOverlays;
}