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

Example 1 with PositiveInteger

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

the class Calibrator method computeVariableTimeInterval.

private double computeVariableTimeInterval(IMetadata meta, int series) {
    // collect variable time interval values
    final PositiveInteger sizeT = meta.getPixelsSizeT(series);
    final int tSize = sizeT == null ? 1 : sizeT.getValue();
    final int planeCount = meta.getPlaneCount(series);
    final Time[] deltas = new Time[tSize];
    Arrays.fill(deltas, new Time(Double.NaN, UNITS.SECOND));
    for (int p = 0; p < planeCount; p++) {
        final NonNegativeInteger theZ = meta.getPlaneTheZ(series, p);
        final NonNegativeInteger theC = meta.getPlaneTheC(series, p);
        final NonNegativeInteger theT = meta.getPlaneTheT(series, p);
        if (theZ == null || theC == null || theT == null)
            continue;
        if (theZ.getValue() != 0 || theC.getValue() != 0)
            continue;
        // store delta T value at appropriate index
        final int t = theT.getValue();
        if (t >= tSize)
            continue;
        final Time deltaT = meta.getPlaneDeltaT(series, p);
        if (deltaT == null)
            continue;
        deltas[t] = deltaT;
    }
    // average delta T differences
    double tiTotal = 0;
    int tiCount = 0;
    for (int t = 1; t < tSize; t++) {
        double delta1 = deltas[t - 1].value(UNITS.SECOND).doubleValue();
        ;
        double delta2 = deltas[t].value(UNITS.SECOND).doubleValue();
        ;
        if (Double.isNaN(delta1) || Double.isNaN(delta2))
            continue;
        tiTotal += delta2 - delta1;
        tiCount++;
    }
    if (tiCount == 0)
        return Double.NaN;
    // DeltaT is stored in seconds, and the expected units are seconds
    return (float) (tiTotal / tiCount);
}

Example 2 with PositiveInteger

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

the class MetamorphReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (checkSuffix(id, ND_SUFFIX)) {
        LOGGER.info("Initializing " + id);
        // find an associated STK file
        String stkFile = id.substring(0, id.lastIndexOf("."));
        if (stkFile.indexOf(File.separatorChar) != -1) {
            stkFile = stkFile.substring(stkFile.lastIndexOf(File.separator) + 1);
        }
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        LOGGER.info("Looking for STK file in {}", parent.getAbsolutePath());
        String[] dirList = parent.list(true);
        Arrays.sort(dirList);
        for (String f : dirList) {
            int underscore = f.indexOf('_');
            if (underscore < 0)
                underscore = f.indexOf('.');
            if (underscore < 0)
                underscore = f.length();
            String prefix = f.substring(0, underscore);
            if ((f.equals(stkFile) || stkFile.startsWith(prefix)) && checkSuffix(f, STK_SUFFIX)) {
                stkFile = new Location(parent.getAbsolutePath(), f).getAbsolutePath();
                break;
            }
        }
        if (!checkSuffix(stkFile, STK_SUFFIX)) {
            throw new FormatException("STK file not found in " + parent.getAbsolutePath() + ".");
        }
        super.initFile(stkFile);
    } else
        super.initFile(id);
    Location ndfile = null;
    if (checkSuffix(id, ND_SUFFIX))
        ndfile = new Location(id);
    else if (canLookForND && isGroupFiles()) {
        // an STK file was passed to initFile
        // let's check the parent directory for an .nd file
        Location stk = new Location(id).getAbsoluteFile();
        String stkName = stk.getName();
        String stkPrefix = stkName;
        if (stkPrefix.indexOf('_') >= 0) {
            stkPrefix = stkPrefix.substring(0, stkPrefix.indexOf('_') + 1);
        }
        Location parent = stk.getParentFile();
        String[] list = parent.list(true);
        int matchingChars = 0;
        for (String f : list) {
            if (checkSuffix(f, ND_SUFFIX)) {
                String prefix = f.substring(0, f.lastIndexOf("."));
                if (prefix.indexOf('_') >= 0) {
                    prefix = prefix.substring(0, prefix.indexOf('_') + 1);
                }
                if (stkName.startsWith(prefix) || prefix.equals(stkPrefix)) {
                    int charCount = 0;
                    for (int i = 0; i < f.length(); i++) {
                        if (i >= stkName.length()) {
                            break;
                        }
                        if (f.charAt(i) == stkName.charAt(i)) {
                            charCount++;
                        } else {
                            break;
                        }
                    }
                    if (charCount > matchingChars || (charCount == matchingChars && f.charAt(charCount) == '.')) {
                        ndfile = new Location(parent, f).getAbsoluteFile();
                        matchingChars = charCount;
                    }
                }
            }
        }
    }
    String creationTime = null;
    if (ndfile != null && ndfile.exists() && (fileGroupOption(id) == FormatTools.MUST_GROUP || isGroupFiles())) {
        // parse key/value pairs from .nd file
        int zc = getSizeZ(), cc = getSizeC(), tc = getSizeT();
        int nstages = 0;
        String z = null, c = null, t = null;
        final List<Boolean> hasZ = new ArrayList<Boolean>();
        waveNames = new ArrayList<String>();
        stageNames = new ArrayList<String>();
        boolean useWaveNames = true;
        ndFilename = ndfile.getAbsolutePath();
        String[] lines = DataTools.readFile(ndFilename).split("\n");
        boolean globalDoZ = true;
        boolean doTimelapse = false;
        StringBuilder currentValue = new StringBuilder();
        String key = "";
        for (String line : lines) {
            int comma = line.indexOf(',');
            if (comma <= 0) {
                currentValue.append("\n");
                currentValue.append(line);
                continue;
            }
            String value = currentValue.toString();
            addGlobalMeta(key, value);
            if (key.equals("NZSteps"))
                z = value;
            else if (key.equals("DoTimelapse")) {
                doTimelapse = Boolean.parseBoolean(value);
            } else if (key.equals("NWavelengths"))
                c = value;
            else if (key.equals("NTimePoints"))
                t = value;
            else if (key.startsWith("WaveDoZ")) {
                hasZ.add(Boolean.parseBoolean(value));
            } else if (key.startsWith("WaveName")) {
                String waveName = value.substring(1, value.length() - 1);
                if (waveName.equals("Both lasers") || waveName.startsWith("DUAL")) {
                    bizarreMultichannelAcquisition = true;
                }
                waveNames.add(waveName);
            } else if (key.startsWith("Stage")) {
                stageNames.add(value);
            } else if (key.startsWith("StartTime")) {
                creationTime = value;
            } else if (key.equals("ZStepSize")) {
                value = value.replace(',', '.');
                stepSize = Double.parseDouble(value);
            } else if (key.equals("NStagePositions")) {
                nstages = Integer.parseInt(value);
            } else if (key.equals("WaveInFileName")) {
                useWaveNames = Boolean.parseBoolean(value);
            } else if (key.equals("DoZSeries")) {
                globalDoZ = Boolean.parseBoolean(value);
            }
            key = line.substring(1, comma - 1).trim();
            currentValue.delete(0, currentValue.length());
            currentValue.append(line.substring(comma + 1).trim());
        }
        if (!globalDoZ) {
            for (int i = 0; i < hasZ.size(); i++) {
                hasZ.set(i, false);
            }
        }
        if (z != null)
            zc = Integer.parseInt(z);
        if (c != null)
            cc = Integer.parseInt(c);
        if (t != null)
            tc = Integer.parseInt(t);
        else if (!doTimelapse) {
            tc = 1;
        }
        if (cc == 0)
            cc = 1;
        if (cc == 1 && bizarreMultichannelAcquisition) {
            cc = 2;
        }
        if (tc == 0) {
            tc = 1;
        }
        int numFiles = cc * tc;
        if (nstages > 0)
            numFiles *= nstages;
        // determine series count
        int stagesCount = nstages == 0 ? 1 : nstages;
        int seriesCount = stagesCount;
        firstSeriesChannels = new boolean[cc];
        Arrays.fill(firstSeriesChannels, true);
        boolean differentZs = false;
        for (int i = 0; i < cc; i++) {
            boolean hasZ1 = i < hasZ.size() && hasZ.get(i);
            boolean hasZ2 = i != 0 && (i - 1 < hasZ.size()) && hasZ.get(i - 1);
            if (i > 0 && hasZ1 != hasZ2 && globalDoZ) {
                if (!differentZs)
                    seriesCount *= 2;
                differentZs = true;
            }
        }
        int channelsInFirstSeries = cc;
        if (differentZs) {
            channelsInFirstSeries = 0;
            for (int i = 0; i < cc; i++) {
                if ((!hasZ.get(0) && i == 0) || (hasZ.get(0) && hasZ.get(i))) {
                    channelsInFirstSeries++;
                } else
                    firstSeriesChannels[i] = false;
            }
        }
        stks = new String[seriesCount][];
        if (seriesCount == 1)
            stks[0] = new String[numFiles];
        else if (differentZs) {
            for (int i = 0; i < stagesCount; i++) {
                stks[i * 2] = new String[channelsInFirstSeries * tc];
                stks[i * 2 + 1] = new String[(cc - channelsInFirstSeries) * tc];
            }
        } else {
            for (int i = 0; i < stks.length; i++) {
                stks[i] = new String[numFiles / stks.length];
            }
        }
        String prefix = ndfile.getPath();
        prefix = prefix.substring(prefix.lastIndexOf(File.separator) + 1, prefix.lastIndexOf("."));
        // build list of STK files
        boolean anyZ = hasZ.contains(Boolean.TRUE);
        int[] pt = new int[seriesCount];
        for (int i = 0; i < tc; i++) {
            for (int s = 0; s < stagesCount; s++) {
                for (int j = 0; j < cc; j++) {
                    boolean validZ = j >= hasZ.size() || hasZ.get(j);
                    int seriesNdx = s * (seriesCount / stagesCount);
                    if ((seriesCount != 1 && (!validZ || (hasZ.size() > 0 && !hasZ.get(0)))) || (nstages == 0 && ((!validZ && cc > 1) || seriesCount > 1))) {
                        if (anyZ && j > 0 && seriesNdx < seriesCount - 1 && (!validZ || !hasZ.get(0))) {
                            seriesNdx++;
                        }
                    }
                    if (seriesNdx >= stks.length || seriesNdx >= pt.length || pt[seriesNdx] >= stks[seriesNdx].length) {
                        continue;
                    }
                    stks[seriesNdx][pt[seriesNdx]] = prefix;
                    if (j < waveNames.size() && waveNames.get(j) != null) {
                        stks[seriesNdx][pt[seriesNdx]] += "_w" + (j + 1);
                        if (useWaveNames) {
                            String waveName = waveNames.get(j);
                            // If there are underscores in the wavelength name, translate
                            // them to hyphens. (See #558)
                            waveName = waveName.replace('_', '-');
                            // If there are slashes (forward or backward) in the wavelength
                            // name, translate them to hyphens. (See #5922)
                            waveName = waveName.replace('/', '-');
                            waveName = waveName.replace('\\', '-');
                            waveName = waveName.replace('(', '-');
                            waveName = waveName.replace(')', '-');
                            stks[seriesNdx][pt[seriesNdx]] += waveName;
                        }
                    }
                    if (nstages > 0) {
                        stks[seriesNdx][pt[seriesNdx]] += "_s" + (s + 1);
                    }
                    if (tc > 1 || doTimelapse) {
                        stks[seriesNdx][pt[seriesNdx]] += "_t" + (i + 1) + ".STK";
                    } else
                        stks[seriesNdx][pt[seriesNdx]] += ".STK";
                    pt[seriesNdx]++;
                }
            }
        }
        ndfile = ndfile.getAbsoluteFile();
        for (int s = 0; s < stks.length; s++) {
            for (int f = 0; f < stks[s].length; f++) {
                Location l = new Location(ndfile.getParent(), stks[s][f]);
                stks[s][f] = getRealSTKFile(l);
            }
        }
        String file = locateFirstValidFile();
        if (file == null) {
            throw new FormatException("Unable to locate at least one valid STK file!");
        }
        RandomAccessInputStream s = new RandomAccessInputStream(file, 16);
        TiffParser tp = new TiffParser(s);
        IFD ifd = tp.getFirstIFD();
        CoreMetadata ms0 = core.get(0);
        s.close();
        ms0.sizeX = (int) ifd.getImageWidth();
        ms0.sizeY = (int) ifd.getImageLength();
        if (bizarreMultichannelAcquisition) {
            ms0.sizeX /= 2;
        }
        ms0.sizeZ = hasZ.size() > 0 && !hasZ.get(0) ? 1 : zc;
        ms0.sizeC = cc;
        ms0.sizeT = tc;
        ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
        ms0.dimensionOrder = "XYZCT";
        if (stks != null && stks.length > 1) {
            // Note that core can't be replaced with newCore until the end of this block.
            ArrayList<CoreMetadata> newCore = new ArrayList<CoreMetadata>();
            for (int i = 0; i < stks.length; i++) {
                CoreMetadata ms = new CoreMetadata();
                newCore.add(ms);
                ms.sizeX = getSizeX();
                ms.sizeY = getSizeY();
                ms.sizeZ = getSizeZ();
                ms.sizeC = getSizeC();
                ms.sizeT = getSizeT();
                ms.pixelType = getPixelType();
                ms.imageCount = getImageCount();
                ms.dimensionOrder = getDimensionOrder();
                ms.rgb = isRGB();
                ms.littleEndian = isLittleEndian();
                ms.interleaved = isInterleaved();
                ms.orderCertain = true;
            }
            if (stks.length > nstages) {
                for (int j = 0; j < stagesCount; j++) {
                    int idx = j * 2 + 1;
                    CoreMetadata midx = newCore.get(idx);
                    CoreMetadata pmidx = newCore.get(j * 2);
                    pmidx.sizeC = stks[j * 2].length / getSizeT();
                    midx.sizeC = stks[idx].length / midx.sizeT;
                    midx.sizeZ = hasZ.size() > 1 && hasZ.get(1) && core.get(0).sizeZ == 1 ? zc : 1;
                    pmidx.imageCount = pmidx.sizeC * pmidx.sizeT * pmidx.sizeZ;
                    midx.imageCount = midx.sizeC * midx.sizeT * midx.sizeZ;
                }
            }
            core = newCore;
        }
    }
    if (stks == null) {
        stkReaders = new MetamorphReader[1][1];
        stkReaders[0][0] = new MetamorphReader();
        stkReaders[0][0].setCanLookForND(false);
    } else {
        stkReaders = new MetamorphReader[stks.length][];
        for (int i = 0; i < stks.length; i++) {
            stkReaders[i] = new MetamorphReader[stks[i].length];
            for (int j = 0; j < stkReaders[i].length; j++) {
                stkReaders[i][j] = new MetamorphReader();
                stkReaders[i][j].setCanLookForND(false);
                if (j > 0) {
                    stkReaders[i][j].setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.MINIMUM));
                }
            }
        }
    }
    // check stage labels for plate data
    int rows = 0;
    int cols = 0;
    Map<String, Integer> rowMap = null;
    Map<String, Integer> colMap = null;
    isHCS = true;
    if (null == stageLabels) {
        isHCS = false;
    } else {
        Set<Map.Entry<Integer, Integer>> uniqueWells = new HashSet<Map.Entry<Integer, Integer>>();
        rowMap = new HashMap<String, Integer>();
        colMap = new HashMap<String, Integer>();
        for (String label : stageLabels) {
            if (null == label) {
                isHCS = false;
                break;
            }
            Map.Entry<Integer, Integer> wellCoords = getWellCoords(label);
            if (null == wellCoords) {
                isHCS = false;
                break;
            }
            uniqueWells.add(wellCoords);
            rowMap.put(label, wellCoords.getKey());
            colMap.put(label, wellCoords.getValue());
        }
        if (uniqueWells.size() != stageLabels.length) {
            isHCS = false;
        } else {
            rows = Collections.max(rowMap.values());
            cols = Collections.max(colMap.values());
            CoreMetadata c = core.get(0);
            core.clear();
            c.sizeZ = 1;
            c.sizeT = 1;
            c.imageCount = 1;
            for (int s = 0; s < uniqueWells.size(); s++) {
                CoreMetadata toAdd = new CoreMetadata(c);
                if (s > 0) {
                    toAdd.seriesMetadata.clear();
                }
                core.add(toAdd);
            }
            seriesToIFD = true;
        }
    }
    List<String> timestamps = null;
    MetamorphHandler handler = null;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (isHCS) {
        store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
        store.setPlateRows(new PositiveInteger(rows), 0);
        store.setPlateColumns(new PositiveInteger(cols), 0);
        store.setPlateRowNamingConvention(NamingConvention.LETTER, 0);
        store.setPlateColumnNamingConvention(NamingConvention.NUMBER, 0);
    }
    int nextObjective = 0;
    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    String detectorID = MetadataTools.createLSID("Detector", 0, 0);
    store.setInstrumentID(instrumentID, 0);
    store.setDetectorID(detectorID, 0, 0);
    store.setDetectorType(getDetectorType("Other"), 0, 0);
    for (int i = 0; i < getSeriesCount(); i++) {
        setSeries(i);
        // do not reparse the same XML for every well
        if (i == 0 || !isHCS) {
            handler = new MetamorphHandler(getSeriesMetadata());
        }
        if (isHCS) {
            String label = stageLabels[i];
            String wellID = MetadataTools.createLSID("Well", 0, i);
            store.setWellID(wellID, 0, i);
            store.setWellColumn(new NonNegativeInteger(colMap.get(label)), 0, i);
            store.setWellRow(new NonNegativeInteger(rowMap.get(label)), 0, i);
            store.setWellSampleID(MetadataTools.createLSID("WellSample", 0, i, 0), 0, i, 0);
            store.setWellSampleImageRef(MetadataTools.createLSID("Image", i), 0, i, 0);
            store.setWellSampleIndex(new NonNegativeInteger(i), 0, i, 0);
        }
        store.setImageInstrumentRef(instrumentID, i);
        String comment = getFirstComment(i);
        if (i == 0 || !isHCS) {
            if (comment != null && comment.startsWith("<MetaData>")) {
                try {
                    XMLTools.parseXML(XMLTools.sanitizeXML(comment), handler);
                } catch (IOException e) {
                }
            }
        }
        if (creationTime != null) {
            String date = DateTools.formatDate(creationTime, SHORT_DATE_FORMAT, ".");
            if (date != null) {
                store.setImageAcquisitionDate(new Timestamp(date), 0);
            }
        }
        store.setImageName(makeImageName(i).trim(), i);
        if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
            continue;
        }
        store.setImageDescription("", i);
        store.setImagingEnvironmentTemperature(new Temperature(handler.getTemperature(), UNITS.CELSIUS), i);
        if (sizeX == null)
            sizeX = handler.getPixelSizeX();
        if (sizeY == null)
            sizeY = handler.getPixelSizeY();
        Length physicalSizeX = FormatTools.getPhysicalSizeX(sizeX);
        Length physicalSizeY = FormatTools.getPhysicalSizeY(sizeY);
        if (physicalSizeX != null) {
            store.setPixelsPhysicalSizeX(physicalSizeX, i);
        }
        if (physicalSizeY != null) {
            store.setPixelsPhysicalSizeY(physicalSizeY, i);
        }
        if (zDistances != null) {
            stepSize = zDistances[0];
        } else {
            List<Double> zPositions = new ArrayList<Double>();
            final List<Double> uniqueZ = new ArrayList<Double>();
            for (IFD ifd : ifds) {
                MetamorphHandler zPlaneHandler = new MetamorphHandler();
                String zComment = ifd.getComment();
                if (zComment != null && zComment.startsWith("<MetaData>")) {
                    try {
                        XMLTools.parseXML(XMLTools.sanitizeXML(zComment), zPlaneHandler);
                    } catch (IOException e) {
                    }
                }
                zPositions = zPlaneHandler.getZPositions();
                for (Double z : zPositions) {
                    if (!uniqueZ.contains(z))
                        uniqueZ.add(z);
                }
            }
            if (uniqueZ.size() > 1 && uniqueZ.size() == getSizeZ()) {
                BigDecimal lastZ = BigDecimal.valueOf(uniqueZ.get(uniqueZ.size() - 1));
                BigDecimal firstZ = BigDecimal.valueOf(uniqueZ.get(0));
                BigDecimal zRange = (lastZ.subtract(firstZ)).abs();
                BigDecimal zSize = BigDecimal.valueOf((double) (getSizeZ() - 1));
                MathContext mc = new MathContext(10, RoundingMode.HALF_UP);
                stepSize = zRange.divide(zSize, mc).doubleValue();
            }
        }
        Length physicalSizeZ = FormatTools.getPhysicalSizeZ(stepSize);
        if (physicalSizeZ != null) {
            store.setPixelsPhysicalSizeZ(physicalSizeZ, i);
        }
        if (handler.getLensNA() != 0 || handler.getLensRI() != 0) {
            String objectiveID = MetadataTools.createLSID("Objective", 0, nextObjective);
            store.setObjectiveID(objectiveID, 0, nextObjective);
            if (handler.getLensNA() != 0) {
                store.setObjectiveLensNA(handler.getLensNA(), 0, nextObjective);
            }
            store.setObjectiveSettingsID(objectiveID, i);
            if (handler.getLensRI() != 0) {
                store.setObjectiveSettingsRefractiveIndex(handler.getLensRI(), i);
            }
            nextObjective++;
        }
        int waveIndex = 0;
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            if (firstSeriesChannels == null || (stageNames != null && stageNames.size() == getSeriesCount())) {
                waveIndex = c;
            } else if (firstSeriesChannels != null) {
                int s = i % 2;
                while (firstSeriesChannels[waveIndex] == (s == 1) && waveIndex < firstSeriesChannels.length) {
                    waveIndex++;
                }
            }
            if (waveNames != null && waveIndex < waveNames.size()) {
                store.setChannelName(waveNames.get(waveIndex).trim(), i, c);
            }
            if (handler.getBinning() != null)
                binning = handler.getBinning();
            if (binning != null) {
                store.setDetectorSettingsBinning(getBinning(binning), i, c);
            }
            if (handler.getReadOutRate() != 0) {
                store.setDetectorSettingsReadOutRate(new Frequency(handler.getReadOutRate(), UNITS.HERTZ), i, c);
            }
            if (gain == null) {
                gain = handler.getGain();
            }
            if (gain != null) {
                store.setDetectorSettingsGain(gain, i, c);
            }
            store.setDetectorSettingsID(detectorID, i, c);
            if (wave != null && waveIndex < wave.length) {
                Length wavelength = FormatTools.getWavelength(wave[waveIndex]);
                if ((int) wave[waveIndex] >= 1) {
                    // link LightSource to Image
                    int laserIndex = i * getEffectiveSizeC() + c;
                    String lightSourceID = MetadataTools.createLSID("LightSource", 0, laserIndex);
                    store.setLaserID(lightSourceID, 0, laserIndex);
                    store.setChannelLightSourceSettingsID(lightSourceID, i, c);
                    store.setLaserType(getLaserType("Other"), 0, laserIndex);
                    store.setLaserLaserMedium(getLaserMedium("Other"), 0, laserIndex);
                    if (wavelength != null) {
                        store.setChannelLightSourceSettingsWavelength(wavelength, i, c);
                    }
                }
            }
            waveIndex++;
        }
        timestamps = handler.getTimestamps();
        for (int t = 0; t < timestamps.size(); t++) {
            String date = DateTools.convertDate(DateTools.getTime(timestamps.get(t), SHORT_DATE_FORMAT, "."), DateTools.UNIX, SHORT_DATE_FORMAT + ".SSS");
            addSeriesMetaList("timestamp", date);
        }
        long startDate = 0;
        if (timestamps.size() > 0) {
            startDate = DateTools.getTime(timestamps.get(0), SHORT_DATE_FORMAT, ".");
        }
        final Length positionX = handler.getStagePositionX();
        final Length positionY = handler.getStagePositionY();
        final List<Double> exposureTimes = handler.getExposures();
        if (exposureTimes.size() == 0) {
            for (int p = 0; p < getImageCount(); p++) {
                exposureTimes.add(exposureTime);
            }
        } else if (exposureTimes.size() == 1 && exposureTimes.size() < getSizeC()) {
            for (int c = 1; c < getSizeC(); c++) {
                MetamorphHandler channelHandler = new MetamorphHandler();
                String channelComment = getComment(i, c);
                if (channelComment != null && channelComment.startsWith("<MetaData>")) {
                    try {
                        XMLTools.parseXML(XMLTools.sanitizeXML(channelComment), channelHandler);
                    } catch (IOException e) {
                    }
                }
                final List<Double> channelExpTime = channelHandler.getExposures();
                exposureTimes.add(channelExpTime.get(0));
            }
        }
        int lastFile = -1;
        IFDList lastIFDs = null;
        IFD lastIFD = null;
        double distance = zStart;
        TiffParser tp = null;
        RandomAccessInputStream stream = null;
        for (int p = 0; p < getImageCount(); p++) {
            int[] coords = getZCTCoords(p);
            Double deltaT = 0d;
            Double expTime = exposureTime;
            Double xmlZPosition = null;
            int fileIndex = getIndex(0, coords[1], coords[2]) / getSizeZ();
            if (fileIndex >= 0) {
                String file = stks == null ? currentId : stks[i][fileIndex];
                if (file != null) {
                    if (fileIndex != lastFile) {
                        if (stream != null) {
                            stream.close();
                        }
                        stream = new RandomAccessInputStream(file, 16);
                        tp = new TiffParser(stream);
                        tp.checkHeader();
                        IFDList f = tp.getIFDs();
                        if (f.size() > 0) {
                            lastFile = fileIndex;
                            lastIFDs = f;
                        } else {
                            file = null;
                            stks[i][fileIndex] = null;
                        }
                    }
                }
                if (file != null) {
                    lastIFD = lastIFDs.get(p % lastIFDs.size());
                    Object commentEntry = lastIFD.get(IFD.IMAGE_DESCRIPTION);
                    if (commentEntry != null) {
                        if (commentEntry instanceof String) {
                            comment = (String) commentEntry;
                        } else if (commentEntry instanceof TiffIFDEntry) {
                            comment = tp.getIFDValue((TiffIFDEntry) commentEntry).toString();
                        }
                    }
                    if (comment != null)
                        comment = comment.trim();
                    if (comment != null && comment.startsWith("<MetaData>")) {
                        String[] lines = comment.split("\n");
                        timestamps = new ArrayList<String>();
                        for (String line : lines) {
                            line = line.trim();
                            if (line.startsWith("<prop")) {
                                int firstQuote = line.indexOf("\"") + 1;
                                int lastQuote = line.lastIndexOf("\"");
                                String key = line.substring(firstQuote, line.indexOf("\"", firstQuote));
                                String value = line.substring(line.lastIndexOf("\"", lastQuote - 1) + 1, lastQuote);
                                if (key.equals("z-position")) {
                                    xmlZPosition = new Double(value);
                                } else if (key.equals("acquisition-time-local")) {
                                    timestamps.add(value);
                                }
                            }
                        }
                    }
                }
            }
            int index = 0;
            if (timestamps.size() > 0) {
                if (coords[2] < timestamps.size())
                    index = coords[2];
                String stamp = timestamps.get(index);
                long ms = DateTools.getTime(stamp, SHORT_DATE_FORMAT, ".");
                deltaT = (ms - startDate) / 1000.0;
            } else if (internalStamps != null && p < internalStamps.length) {
                long delta = internalStamps[p] - internalStamps[0];
                deltaT = delta / 1000.0;
                if (coords[2] < exposureTimes.size())
                    index = coords[2];
            }
            if (index == 0 && p > 0 && exposureTimes.size() > 0) {
                index = coords[1] % exposureTimes.size();
            }
            if (index < exposureTimes.size()) {
                expTime = exposureTimes.get(index);
            }
            if (deltaT != null) {
                store.setPlaneDeltaT(new Time(deltaT, UNITS.SECOND), i, p);
            }
            if (expTime != null) {
                store.setPlaneExposureTime(new Time(expTime, UNITS.SECOND), i, p);
            }
            if (stageX != null && p < stageX.length) {
                store.setPlanePositionX(stageX[p], i, p);
            } else if (positionX != null) {
                store.setPlanePositionX(positionX, i, p);
            }
            if (stageY != null && p < stageY.length) {
                store.setPlanePositionY(stageY[p], i, p);
            } else if (positionY != null) {
                store.setPlanePositionY(positionY, i, p);
            }
            if (zDistances != null && p < zDistances.length) {
                if (p > 0) {
                    if (zDistances[p] != 0d)
                        distance += zDistances[p];
                    else
                        distance += zDistances[0];
                }
                final Length zPos = new Length(distance, UNITS.REFERENCEFRAME);
                store.setPlanePositionZ(zPos, i, p);
            } else if (xmlZPosition != null) {
                final Length zPos = new Length(xmlZPosition, UNITS.REFERENCEFRAME);
                store.setPlanePositionZ(zPos, i, p);
            }
        }
        if (stream != null) {
            stream.close();
        }
    }
    setSeries(0);
}

Example 3 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger 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 4 with PositiveInteger

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

the class FlexReader method populateMetadataStore.

private void populateMetadataStore(MetadataStore store) throws FormatException {
    LOGGER.info("Populating MetadataStore");
    MetadataTools.populatePixels(store, this, true);
    Location currentFile = new Location(getCurrentFile()).getAbsoluteFile();
    int[] lengths = new int[] { fieldCount, wellCount, plateCount };
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    PositiveInteger maxFieldCount = FormatTools.getMaxFieldCount(fieldCount);
    if (maxFieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(maxFieldCount, 0, 0);
    }
    plateAcqStartTime = DateTools.formatDate(plateAcqStartTime, "dd.MM.yyyy  HH:mm:ss");
    if (plateAcqStartTime != null) {
        store.setPlateAcquisitionStartTime(new Timestamp(plateAcqStartTime), 0, 0);
    }
    for (int row = 0; row < wellRows; row++) {
        for (int col = 0; col < wellColumns; col++) {
            int well = row * wellColumns + col;
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellRow(new NonNegativeInteger(row), 0, well);
            store.setWellColumn(new NonNegativeInteger(col), 0, well);
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        int[] pos = FormatTools.rasterToPosition(lengths, i);
        String imageID = MetadataTools.createLSID("Image", i);
        store.setImageID(imageID, i);
        int well = wellNumber[pos[1]][0] * wellColumns + wellNumber[pos[1]][1];
        char wellRow = (char) ('A' + wellNumber[pos[1]][0]);
        store.setImageName("Well " + wellRow + "-" + (wellNumber[pos[1]][1] + 1) + "; Field #" + (pos[0] + 1), i);
        if (acquisitionDates.get(i) != null) {
            store.setImageAcquisitionDate(acquisitionDates.get(i), i);
        }
        if (wellRows == 0 && wellColumns == 0) {
            well = pos[1];
            NonNegativeInteger row = new NonNegativeInteger(wellNumber[pos[1]][0]);
            NonNegativeInteger col = new NonNegativeInteger(wellNumber[pos[1]][1]);
            String wellID = MetadataTools.createLSID("Well", pos[2], well);
            store.setWellID(wellID, pos[2], well);
            store.setWellRow(row, pos[2], pos[1]);
            store.setWellColumn(col, pos[2], pos[1]);
        }
        String wellSample = MetadataTools.createLSID("WellSample", pos[2], well, pos[0]);
        store.setWellSampleID(wellSample, pos[2], well, pos[0]);
        store.setWellSampleIndex(new NonNegativeInteger(i), pos[2], well, pos[0]);
        store.setWellSampleImageRef(imageID, pos[2], well, pos[0]);
        store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        if (plateName == null)
            plateName = currentFile.getParentFile().getName();
        if (plateBarcode != null)
            plateName = plateBarcode + " " + plateName;
        store.setPlateName(plateName, 0);
        store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
        store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
        for (int i = 0; i < getSeriesCount(); i++) {
            int[] pos = FormatTools.rasterToPosition(lengths, i);
            store.setImageInstrumentRef(instrumentID, i);
            int seriesIndex = i * getImageCount();
            if (seriesIndex < objectiveRefs.size()) {
                store.setObjectiveSettingsID(objectiveRefs.get(seriesIndex), i);
            }
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                int channelIndex = seriesIndex + c;
                if (seriesIndex > 0 && channelNames.length == getEffectiveSizeC() * getSeriesCount()) {
                    channelIndex = i * getEffectiveSizeC() + c;
                }
                if (channelNames != null && channelIndex >= channelNames.length) {
                    channelIndex = c;
                }
                if (channelNames != null && channelIndex < channelNames.length) {
                    store.setChannelName(channelNames[channelIndex], i, c);
                }
            }
            if (seriesIndex < lightSourceCombinationRefs.size()) {
                String lightSourceCombo = lightSourceCombinationRefs.get(seriesIndex);
                List<String> lightSources = lightSourceCombinationIDs.get(lightSourceCombo);
                for (int c = 0; c < getEffectiveSizeC(); c++) {
                    int index = seriesIndex + c;
                    if (index < cameraRefs.size()) {
                        store.setDetectorSettingsID(cameraRefs.get(index), i, c);
                        if (index < binnings.size()) {
                            store.setDetectorSettingsBinning(getBinning(binnings.get(index)), i, c);
                        }
                    }
                    if (lightSources != null && c < lightSources.size()) {
                        store.setChannelLightSourceSettingsID(lightSources.get(c), i, c);
                    } else if (c > 0 && lightSources != null && lightSources.size() == 1) {
                        lightSourceCombo = lightSourceCombinationRefs.get(seriesIndex + c);
                        lightSources = lightSourceCombinationIDs.get(lightSourceCombo);
                        store.setChannelLightSourceSettingsID(lightSources.get(0), i, c);
                    }
                    if (index < filterSets.size()) {
                        FilterGroup group = filterSetMap.get(filterSets.get(index));
                        if (group != null) {
                            if (group.emission != null) {
                                store.setLightPathEmissionFilterRef(group.emission, i, c, 0);
                            }
                            if (group.excitation != null) {
                                store.setLightPathExcitationFilterRef(group.excitation, i, c, 0);
                            }
                            if (group.dichroic != null) {
                                store.setLightPathDichroicRef(group.dichroic, i, c);
                            }
                        }
                    }
                }
            }
            if (seriesIndex < xSizes.size()) {
                Length size = FormatTools.getPhysicalSizeX(xSizes.get(seriesIndex));
                if (size != null) {
                    store.setPixelsPhysicalSizeX(size, i);
                }
            }
            if (seriesIndex < ySizes.size()) {
                Length size = FormatTools.getPhysicalSizeY(ySizes.get(seriesIndex));
                if (size != null) {
                    store.setPixelsPhysicalSizeY(size, i);
                }
            }
            int well = wellNumber[pos[1]][0] * wellColumns + wellNumber[pos[1]][1];
            if (wellRows == 0 && wellColumns == 0) {
                well = pos[1];
            }
            if (pos[0] < xPositions.size()) {
                Length l = new Length(xPositions.get(pos[0]), UNITS.REFERENCEFRAME);
                store.setWellSamplePositionX(l, pos[2], well, pos[0]);
            }
            if (pos[0] < yPositions.size()) {
                Length l = new Length(yPositions.get(pos[0]), UNITS.REFERENCEFRAME);
                store.setWellSamplePositionY(l, pos[2], well, pos[0]);
            }
            for (int image = 0; image < getImageCount(); image++) {
                int plane = i * getImageCount() + image;
                int c = getZCTCoords(image)[1];
                if (plane < planePositionX.size()) {
                    store.setPlanePositionX(planePositionX.get(plane), i, image);
                }
                if (plane < planePositionY.size()) {
                    store.setPlanePositionY(planePositionY.get(plane), i, image);
                }
                if (plane < planePositionZ.size()) {
                    store.setPlanePositionZ(planePositionZ.get(plane), i, image);
                }
                if (plane - image + c < planeExposureTime.size()) {
                    if (planeExposureTime.get(plane - image + c) != null) {
                        store.setPlaneExposureTime(new Time(planeExposureTime.get(plane - image + c), UNITS.SECOND), i, image);
                    }
                }
                if (plane < planeDeltaT.size() && planeDeltaT.get(plane) != null) {
                    store.setPlaneDeltaT(new Time(planeDeltaT.get(plane), UNITS.SECOND), i, image);
                }
            }
        }
    }
}

Example 5 with PositiveInteger

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

the class ScanrReader 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 (metadataFiles.size() > 0) {
        // this dataset has already been initialized
        return;
    }
    // make sure we have the .xml file
    if (!checkSuffix(id, "xml") && isGroupFiles()) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        if (checkSuffix(id, "tif") && parent.getName().equalsIgnoreCase("Data")) {
            parent = parent.getParentFile();
        }
        String[] list = parent.list();
        for (String file : list) {
            if (file.equals(XML_FILE)) {
                id = new Location(parent, file).getAbsolutePath();
                super.initFile(id);
                break;
            }
        }
        if (!checkSuffix(id, "xml")) {
            throw new FormatException("Could not find " + XML_FILE + " in " + parent.getAbsolutePath());
        }
    } else if (!isGroupFiles() && checkSuffix(id, "tif")) {
        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();
        tiffs = new String[] { id };
        reader = new MinimalTiffReader();
        return;
    }
    Location dir = new Location(id).getAbsoluteFile().getParentFile();
    String[] list = dir.list(true);
    for (String file : list) {
        Location f = new Location(dir, file);
        if (checkSuffix(file, METADATA_SUFFIXES) && !f.isDirectory()) {
            metadataFiles.add(f.getAbsolutePath());
        }
    }
    // parse XML metadata
    String xml = DataTools.readFile(id).trim();
    if (xml.startsWith("<?")) {
        xml = xml.substring(xml.indexOf("?>") + 2);
    }
    xml = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" + xml;
    XMLTools.parseXML(xml, new ScanrHandler());
    final List<String> uniqueRows = new ArrayList<String>();
    final List<String> uniqueColumns = new ArrayList<String>();
    if (wellRows == 0 || wellColumns == 0) {
        for (String well : wellLabels.keySet()) {
            if (!Character.isLetter(well.charAt(0)))
                continue;
            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);
            }
        }
        wellRows = uniqueRows.size();
        wellColumns = uniqueColumns.size();
        if (wellRows * wellColumns != wellCount) {
            adjustWellDimensions();
        }
    }
    int nChannels = getSizeC() == 0 ? channelNames.size() : (int) Math.min(channelNames.size(), getSizeC());
    if (nChannels == 0)
        nChannels = 1;
    int nSlices = getSizeZ() == 0 ? 1 : getSizeZ();
    int nTimepoints = getSizeT();
    int nWells = wellCount;
    int nPos = 0;
    if (foundPositions)
        nPos = fieldPositionX.length;
    else
        nPos = fieldRows * fieldColumns;
    if (nPos == 0)
        nPos = 1;
    // get list of TIFF files
    Location dataDir = new Location(dir, "data");
    list = dataDir.list(true);
    if (list == null) {
        // try to find the TIFFs in the current directory
        list = dir.list(true);
    } else
        dir = dataDir;
    if (nTimepoints == 0 || list.length < nTimepoints * nChannels * nSlices * nWells * nPos) {
        nTimepoints = list.length / (nChannels * nWells * nPos * nSlices);
        if (nTimepoints == 0)
            nTimepoints = 1;
    }
    tiffs = new String[nChannels * nWells * nPos * nTimepoints * nSlices];
    Arrays.sort(list, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            int lastSeparator1 = s1.lastIndexOf(File.separator) + 1;
            int lastSeparator2 = s2.lastIndexOf(File.separator) + 1;
            String dir1 = s1.substring(0, lastSeparator1);
            String dir2 = s2.substring(0, lastSeparator2);
            if (!dir1.equals(dir2)) {
                return dir1.compareTo(dir2);
            }
            int dash1 = s1.indexOf("-", lastSeparator1);
            int dash2 = s2.indexOf("-", lastSeparator2);
            String label1 = dash1 < 0 ? "" : s1.substring(lastSeparator1, dash1);
            String label2 = dash2 < 0 ? "" : s2.substring(lastSeparator2, dash2);
            if (label1.equals(label2)) {
                String remainder1 = dash1 < 0 ? s1 : s1.substring(dash1);
                String remainder2 = dash2 < 0 ? s2 : s2.substring(dash2);
                return remainder1.compareTo(remainder2);
            }
            Integer index1 = wellLabels.get(label1);
            Integer index2 = wellLabels.get(label2);
            if (index1 == null && index2 != null) {
                return 1;
            } else if (index1 != null && index2 == null) {
                return -1;
            }
            return index1.compareTo(index2);
        }
    });
    int lastListIndex = 0;
    int next = 0;
    String[] keys = wellLabels.keySet().toArray(new String[wellLabels.size()]);
    Arrays.sort(keys, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            char row1 = s1.charAt(0);
            char row2 = s2.charAt(0);
            final Integer col1 = new Integer(s1.substring(1));
            final Integer col2 = new Integer(s2.substring(1));
            if (row1 < row2) {
                return -1;
            } else if (row1 > row2) {
                return 1;
            }
            return col1.compareTo(col2);
        }
    });
    int realPosCount = 0;
    for (int well = 0; well < nWells; well++) {
        int missingWellFiles = 0;
        int wellIndex = wellNumbers.get(well);
        String wellPos = getBlock(wellIndex, "W");
        int originalIndex = next;
        for (int pos = 0; pos < nPos; pos++) {
            String posPos = getBlock(pos + 1, "P");
            int posIndex = next;
            for (int z = 0; z < nSlices; z++) {
                String zPos = getBlock(z, "Z");
                for (int t = 0; t < nTimepoints; t++) {
                    String tPos = getBlock(t, "T");
                    for (int c = 0; c < nChannels; c++) {
                        for (int i = lastListIndex; i < list.length; i++) {
                            String file = list[i];
                            if (file.indexOf(wellPos) != -1 && file.indexOf(zPos) != -1 && file.indexOf(posPos) != -1 && file.indexOf(tPos) != -1 && file.indexOf(channelNames.get(c)) != -1) {
                                tiffs[next++] = new Location(dir, file).getAbsolutePath();
                                if (c == nChannels - 1) {
                                    lastListIndex = i;
                                }
                                break;
                            }
                        }
                        if (next == originalIndex) {
                            missingWellFiles++;
                        }
                    }
                }
            }
            if (posIndex != next)
                realPosCount++;
        }
        if (next == originalIndex && well < keys.length) {
            wellLabels.remove(keys[well]);
        }
        if (next == originalIndex && missingWellFiles == nSlices * nTimepoints * nChannels * nPos) {
            wellNumbers.remove(well);
        }
    }
    nWells = wellNumbers.size();
    if (wellLabels.size() > 0 && wellLabels.size() != nWells) {
        uniqueRows.clear();
        uniqueColumns.clear();
        for (String well : wellLabels.keySet()) {
            if (!Character.isLetter(well.charAt(0)))
                continue;
            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);
            }
        }
        nWells = uniqueRows.size() * uniqueColumns.size();
        adjustWellDimensions();
    }
    if (realPosCount < nPos) {
        nPos = realPosCount;
    }
    reader = new MinimalTiffReader();
    reader.setId(tiffs[0]);
    int sizeX = reader.getSizeX();
    int sizeY = reader.getSizeY();
    int pixelType = reader.getPixelType();
    tileWidth = reader.getOptimalTileWidth();
    tileHeight = reader.getOptimalTileHeight();
    switch(pixelType) {
        case FormatTools.INT8:
            pixelType = FormatTools.UINT8;
            break;
        case FormatTools.INT16:
            pixelType = FormatTools.UINT16;
            break;
    }
    boolean rgb = reader.isRGB();
    boolean interleaved = reader.isInterleaved();
    boolean indexed = reader.isIndexed();
    boolean littleEndian = reader.isLittleEndian();
    reader.close();
    int seriesCount = nWells * nPos;
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeC = nChannels;
        ms.sizeZ = nSlices;
        ms.sizeT = nTimepoints;
        ms.sizeX = sizeX;
        ms.sizeY = sizeY;
        ms.pixelType = pixelType;
        ms.rgb = rgb;
        ms.interleaved = interleaved;
        ms.indexed = indexed;
        ms.littleEndian = littleEndian;
        ms.dimensionOrder = "XYCTZ";
        ms.imageCount = nSlices * nTimepoints * nChannels;
        ms.bitsPerPixel = 12;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    store.setPlateColumns(new PositiveInteger(wellColumns), 0);
    store.setPlateRows(new PositiveInteger(wellRows), 0);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    int nFields = 0;
    if (foundPositions) {
        nFields = fieldPositionX.length;
    } else {
        nFields = fieldRows * fieldColumns;
    }
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(nFields);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        int field = i % nFields;
        int well = i / nFields;
        int index = well;
        while (wellNumbers.get(index) == null && index < wellNumbers.size()) {
            index++;
        }
        int wellIndex = wellNumbers.get(index) == null ? index : wellNumbers.get(index) - 1;
        int wellRow = wellIndex / wellColumns;
        int wellCol = wellIndex % wellColumns;
        if (field == 0) {
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellColumn(new NonNegativeInteger(wellCol), 0, well);
            store.setWellRow(new NonNegativeInteger(wellRow), 0, well);
        }
        String wellSample = MetadataTools.createLSID("WellSample", 0, well, field);
        store.setWellSampleID(wellSample, 0, well, field);
        store.setWellSampleIndex(new NonNegativeInteger(i), 0, well, field);
        String imageID = MetadataTools.createLSID("Image", i);
        store.setWellSampleImageRef(imageID, 0, well, field);
        store.setImageID(imageID, i);
        String name = "Well " + (well + 1) + ", Field " + (field + 1) + " (Spot " + (i + 1) + ")";
        store.setImageName(name, i);
        store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 0; i < getSeriesCount(); i++) {
            for (int c = 0; c < getSizeC(); c++) {
                store.setChannelName(channelNames.get(c), i, c);
            }
            Length x = FormatTools.getPhysicalSizeX(pixelSize);
            Length y = FormatTools.getPhysicalSizeY(pixelSize);
            if (x != null) {
                store.setPixelsPhysicalSizeX(x, i);
            }
            if (y != null) {
                store.setPixelsPhysicalSizeY(y, i);
            }
            if (fieldPositionX != null && fieldPositionY != null) {
                int field = i % nFields;
                int well = i / nFields;
                final Length posX = fieldPositionX[field];
                final Length posY = fieldPositionY[field];
                store.setWellSamplePositionX(posX, 0, well, field);
                store.setWellSamplePositionY(posY, 0, well, field);
                for (int c = 0; c < getSizeC(); c++) {
                    int image = getIndex(0, c, 0);
                    store.setPlaneTheZ(new NonNegativeInteger(0), i, image);
                    store.setPlaneTheC(new NonNegativeInteger(c), i, image);
                    store.setPlaneTheT(new NonNegativeInteger(0), i, image);
                    store.setPlanePositionX(fieldPositionX[field], i, image);
                    store.setPlanePositionY(fieldPositionY[field], i, image);
                    // exposure time is stored in milliseconds
                    // convert to seconds before populating MetadataStore
                    Double time = exposures.get(c);
                    if (time != null) {
                        time /= 1000;
                        store.setPlaneExposureTime(new Time(time, UNITS.SECOND), i, image);
                    }
                    if (deltaT != null) {
                        store.setPlaneDeltaT(new Time(deltaT, UNITS.SECOND), i, image);
                    }
                }
            }
        }
        String row = wellRows > 26 ? "Number" : "Letter";
        String col = wellRows > 26 ? "Letter" : "Number";
        store.setPlateRowNamingConvention(getNamingConvention(row), 0);
        store.setPlateColumnNamingConvention(getNamingConvention(col), 0);
        store.setPlateName(plateName, 0);
    }
}