Examples with PeakInfo dulab.adap.datamodel.PeakInfo used on opensource projects

Example 1 with PeakInfo

use of dulab.adap.datamodel.PeakInfo in project mzmine2 by mzmine.

the class ADAP3DecompositionV1_5Task method getPeaks.

/**
 * Convert MZmine PeakList to a list of ADAP Peaks
 *
 * @param peakList MZmine PeakList object
 * @param edgeToHeightThreshold edge-to-height threshold to determine peaks that can be merged
 * @param deltaToHeightThreshold delta-to-height threshold to determine peaks that can be merged
 * @return list of ADAP Peaks
 */
@Nonnull
public static List<Peak> getPeaks(final PeakList peakList, final double edgeToHeightThreshold, final double deltaToHeightThreshold) {
    RawDataFile dataFile = peakList.getRawDataFile(0);
    List<Peak> peaks = new ArrayList<>();
    for (PeakListRow row : peakList.getRows()) {
        Feature peak = row.getBestPeak();
        int[] scanNumbers = peak.getScanNumbers();
        // Build chromatogram
        NavigableMap<Double, Double> chromatogram = new TreeMap<>();
        for (int scanNumber : scanNumbers) {
            DataPoint dataPoint = peak.getDataPoint(scanNumber);
            if (dataPoint != null)
                chromatogram.put(dataFile.getScan(scanNumber).getRetentionTime(), dataPoint.getIntensity());
        }
        if (chromatogram.size() <= 1)
            continue;
        // Fill out PeakInfo
        PeakInfo info = new PeakInfo();
        try {
            // Note: info.peakID is the index of PeakListRow in PeakList.peakListRows (starts from 0)
            // row.getID is row.myID (starts from 1)
            info.peakID = row.getID() - 1;
            double height = -Double.MIN_VALUE;
            for (int scan : scanNumbers) {
                double intensity = peak.getDataPoint(scan).getIntensity();
                if (intensity > height) {
                    height = intensity;
                    info.peakIndex = scan;
                }
            }
            info.leftApexIndex = scanNumbers[0];
            info.rightApexIndex = scanNumbers[scanNumbers.length - 1];
            info.retTime = peak.getRT();
            info.mzValue = peak.getMZ();
            info.intensity = peak.getHeight();
            info.leftPeakIndex = info.leftApexIndex;
            info.rightPeakIndex = info.rightApexIndex;
        } catch (Exception e) {
            LOG.info("Skipping " + row + ": " + e.getMessage());
            continue;
        }
        peaks.add(new Peak(chromatogram, info));
    }
    FeatureTools.correctPeakBoundaries(peaks, edgeToHeightThreshold, deltaToHeightThreshold);
    return peaks;
}

Example 2 with PeakInfo

use of dulab.adap.datamodel.PeakInfo in project mzmine2 by mzmine.

the class ADAP3AlignerTask method getComponent.

/**
 * Convert a {@link PeakListRow} with one {@link Feature} into {@link Component}.
 *
 * @param row an instance of {@link PeakListRow}. This parameter cannot be null.
 * @return an instance of {@link Component} or null if the row doesn't contain any peaks or isotope patterns.
 */
@Nullable
private Component getComponent(final PeakListRow row) {
    if (row.getNumberOfPeaks() == 0)
        return null;
    // Read Spectrum information
    NavigableMap<Double, Double> spectrum = new TreeMap<>();
    IsotopePattern pattern = row.getBestIsotopePattern();
    if (pattern == null)
        throw new IllegalArgumentException("ADAP Alignment requires mass " + "spectra (or isotopic patterns) of peaks. No spectra found.");
    for (DataPoint dataPoint : pattern.getDataPoints()) spectrum.put(dataPoint.getMZ(), dataPoint.getIntensity());
    // Read Chromatogram
    final Feature peak = row.getBestPeak();
    final RawDataFile dataFile = peak.getDataFile();
    NavigableMap<Double, Double> chromatogram = new TreeMap<>();
    for (final int scan : peak.getScanNumbers()) {
        final DataPoint dataPoint = peak.getDataPoint(scan);
        if (dataPoint != null)
            chromatogram.put(dataFile.getScan(scan).getRetentionTime(), dataPoint.getIntensity());
    }
    return new Component(null, new Peak(chromatogram, new PeakInfo().mzValue(peak.getMZ()).peakID(row.getID())), spectrum, null);
}

Example 3 with PeakInfo

use of dulab.adap.datamodel.PeakInfo in project mzmine2 by mzmine.

the class ADAP3DecompositionV2Utils method getPeaks.

/**
 * Convert MZmine PeakList to a list of ADAP Peaks
 *
 * @param peakList MZmine PeakList object
 * @return list of ADAP Peaks
 */
@Nonnull
public List<BetterPeak> getPeaks(@Nonnull final PeakList peakList) {
    RawDataFile dataFile = peakList.getRawDataFile(0);
    List<BetterPeak> peaks = new ArrayList<>();
    for (PeakListRow row : peakList.getRows()) {
        Feature peak = row.getBestPeak();
        int[] scanNumbers = peak.getScanNumbers();
        // Build chromatogram
        double[] retTimes = new double[scanNumbers.length];
        double[] intensities = new double[scanNumbers.length];
        for (int i = 0; i < scanNumbers.length; ++i) {
            int scan = scanNumbers[i];
            retTimes[i] = getRetTime(dataFile, scan);
            DataPoint dataPoint = peak.getDataPoint(scan);
            if (dataPoint != null)
                intensities[i] = dataPoint.getIntensity();
        }
        Chromatogram chromatogram = new Chromatogram(retTimes, intensities);
        if (chromatogram.length <= 1)
            continue;
        // Fill out PeakInfo
        PeakInfo info = new PeakInfo();
        try {
            // Note: info.peakID is the index of PeakListRow in PeakList.peakListRows (starts from 0)
            // row.getID is row.myID (starts from 1)
            info.peakID = row.getID() - 1;
            double height = -Double.MIN_VALUE;
            for (int scan : scanNumbers) {
                DataPoint dataPoint = peak.getDataPoint(scan);
                if (dataPoint == null)
                    continue;
                double intensity = dataPoint.getIntensity();
                if (intensity > height) {
                    height = intensity;
                    info.peakIndex = scan;
                }
            }
            info.leftApexIndex = scanNumbers[0];
            info.rightApexIndex = scanNumbers[scanNumbers.length - 1];
            info.retTime = peak.getRT();
            info.mzValue = peak.getMZ();
            info.intensity = peak.getHeight();
            info.leftPeakIndex = info.leftApexIndex;
            info.rightPeakIndex = info.rightApexIndex;
        } catch (Exception e) {
            log.info("Skipping " + row + ": " + e.getMessage());
            continue;
        }
        BetterPeak betterPeak = new BetterPeak(row.getID(), chromatogram, info);
        betterPeak.setParentId(peak.getParentChromatogramRowID());
        peaks.add(betterPeak);
    }
    return peaks;
}

Example 4 with PeakInfo

use of dulab.adap.datamodel.PeakInfo in project mzmine2 by mzmine.

the class ADAPDetector method resolvePeaks.

@Override
public ResolvedPeak[] resolvePeaks(final Feature chromatogram, final ParameterSet parameters, RSessionWrapper rSession, CenterFunction mzCenterFunction, double msmsRange, double rTRangeMSMS) throws RSessionWrapperException {
    int[] scanNumbers = chromatogram.getScanNumbers();
    final int scanCount = scanNumbers.length;
    double[] retentionTimes = new double[scanCount];
    double[] intensities = new double[scanCount];
    RawDataFile dataFile = chromatogram.getDataFile();
    for (int i = 0; i < scanCount; i++) {
        final int scanNum = scanNumbers[i];
        retentionTimes[i] = dataFile.getScan(scanNum).getRetentionTime();
        DataPoint dp = chromatogram.getDataPoint(scanNum);
        if (dp != null)
            intensities[i] = dp.getIntensity();
        else
            intensities[i] = 0.0;
    }
    // List<PeakInfo> ADAPPeaks = new ArrayList<PeakInfo>();
    List<PeakInfo> ADAPPeaks = null;
    Range<Double> peakDuration = parameters.getParameter(PEAK_DURATION).getValue();
    final MZmineProcessingStep<SNEstimatorChoice> signalNoiseEstimator = parameters.getParameter(SN_ESTIMATORS).getValue();
    String SNCode = signalNoiseEstimator.getModule().getSNCode();
    double signalNoiseWindowMult = -1.0;
    boolean absWavCoeffs = false;
    Map<String, Object> informationSN = new HashMap<String, Object>();
    if (SNCode == "Wavelet Coefficient Estimator") {
        informationSN.put("code", "Wavelet Coefficient Estimator");
        signalNoiseWindowMult = signalNoiseEstimator.getParameterSet().getParameter(HALF_WAVELET_WINDOW).getValue();
        absWavCoeffs = signalNoiseEstimator.getParameterSet().getParameter(ABS_WAV_COEFFS).getValue();
        informationSN.put("multiplier", signalNoiseWindowMult);
        informationSN.put("absolutewavecoeffs", absWavCoeffs);
    }
    if (SNCode == "Intensity Window Estimator") {
        informationSN.put("code", "Intensity Window Estimator");
    }
    // get the average rt spacing
    double rtSum = 0.0;
    for (int i = 0; i < retentionTimes.length - 1; i++) {
        rtSum += retentionTimes[i + 1] - retentionTimes[i];
    }
    double avgRTInterval = rtSum / (retentionTimes.length - 1);
    // Change the lower and uper bounds for the wavelet scales from retention times to number of
    // scans.
    Range<Double> rtRangeForCWTScales = parameters.getParameter(RT_FOR_CWT_SCALES_DURATION).getValue();
    double rtLow = rtRangeForCWTScales.lowerEndpoint();
    double rtHigh = rtRangeForCWTScales.upperEndpoint();
    int numScansRTLow = (int) Math.round(rtLow / avgRTInterval);
    int numScansRTHigh = (int) Math.round(rtHigh / avgRTInterval);
    if (numScansRTLow < 1) {
        numScansRTLow = 1;
    }
    if (numScansRTHigh >= retentionTimes.length) {
        numScansRTHigh = retentionTimes.length;
    }
    ADAPPeaks = DeconvoluteSignal(retentionTimes, intensities, chromatogram.getMZ(), parameters.getParameter(SN_THRESHOLD).getValue(), parameters.getParameter(MIN_FEAT_HEIGHT).getValue(), peakDuration, parameters.getParameter(COEF_AREA_THRESHOLD).getValue(), numScansRTLow, numScansRTHigh, informationSN);
    final List<ResolvedPeak> resolvedPeaks;
    if (ADAPPeaks == null) {
        resolvedPeaks = new ArrayList<ResolvedPeak>(0);
    } else {
        // Process peak matrix.
        resolvedPeaks = new ArrayList<ResolvedPeak>(ADAPPeaks.size());
        // for (final double[] peakRow : peakMatrix) {
        for (int i = 0; i < ADAPPeaks.size(); i++) {
            PeakInfo curPeak = ADAPPeaks.get(i);
            SimplePeakInformation information = new SimplePeakInformation();
            information.addProperty("Signal-to-Noise", Double.toString(curPeak.signalToNoiseRatio));
            information.addProperty("Coefficient-over-area", Double.toString(curPeak.coeffOverArea));
            // information.addProperty("index",
            // //Integer.toString(scans[(int) peakIndex[j] - 1])); // Substract one because r-indices
            // start from 1
            // Integer.toString((int) curPeak.peakIndex));
            // information.addProperty("sharpness",
            // Double.toString(curPeak.sharpness));
            // information.addProperty("signalToNoiseRatio",
            // Double.toString(curPeak.signalToNoiseRatio));
            // information.addProperty("isShared",
            // Boolean.toString(curPeak.isShared));
            // //Boolean.toString(1.0 == curPeak.isShared));
            // information.addProperty("offset",
            // Integer.toString((int) curPeak.offset));
            ResolvedPeak peak = new ResolvedPeak(chromatogram, curPeak.leftApexIndex, curPeak.rightApexIndex, mzCenterFunction, msmsRange, rTRangeMSMS);
            peak.setPeakInformation(information);
            resolvedPeaks.add(peak);
        // resolvedPeaks.add(new ResolvedPeak(chromatogram,curPeak.leftApexIndex,
        // curPeak.rightApexIndex));
        }
    }
    return resolvedPeaks.toArray(new ResolvedPeak[resolvedPeaks.size()]);
}

Example 5 with PeakInfo

use of dulab.adap.datamodel.PeakInfo in project mzmine2 by mzmine.

the class ADAPInterface method getComponent.

public static Component getComponent(final PeakListRow row) {
    if (row.getNumberOfPeaks() == 0)
        throw new IllegalArgumentException("No peaks found");
    NavigableMap<Double, Double> spectrum = new TreeMap<>();
    // Read Spectrum information
    IsotopePattern ip = row.getBestIsotopePattern();
    if (ip != null) {
        for (DataPoint dataPoint : ip.getDataPoints()) spectrum.put(dataPoint.getMZ(), dataPoint.getIntensity());
    }
    // Read Chromatogram
    final Feature peak = row.getBestPeak();
    final RawDataFile dataFile = peak.getDataFile();
    NavigableMap<Double, Double> chromatogram = new TreeMap<>();
    for (final int scan : peak.getScanNumbers()) {
        final DataPoint dataPoint = peak.getDataPoint(scan);
        if (dataPoint != null)
            chromatogram.put(dataFile.getScan(scan).getRetentionTime(), dataPoint.getIntensity());
    }
    return new Component(null, new Peak(chromatogram, new PeakInfo().mzValue(peak.getMZ()).peakID(row.getID())), spectrum, null);
}