Examples with DataPoint net.sf.mzmine.datamodel.DataPoint used on opensource projects

Example 56 with DataPoint

use of net.sf.mzmine.datamodel.DataPoint in project mzmine2 by mzmine.

the class MinimumSearchPeakDetector method resolvePeaks.

@Override
public ResolvedPeak[] resolvePeaks(final Feature chromatogram, ParameterSet parameters, RSessionWrapper rSession, CenterFunction mzCenterFunction, double msmsRange, double rTRangeMSMS) {
    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;
    }
    final int lastScan = scanCount - 1;
    assert scanCount > 0;
    final Range<Double> peakDuration = parameters.getParameter(PEAK_DURATION).getValue();
    final double searchRTRange = parameters.getParameter(SEARCH_RT_RANGE).getValue();
    final double minRatio = parameters.getParameter(MIN_RATIO).getValue();
    final double minHeight = Math.max(parameters.getParameter(MIN_ABSOLUTE_HEIGHT).getValue(), parameters.getParameter(MIN_RELATIVE_HEIGHT).getValue() * chromatogram.getHeight());
    final List<ResolvedPeak> resolvedPeaks = new ArrayList<ResolvedPeak>();
    // First, remove all data points below chromatographic threshold.
    final double chromatographicThresholdLevel = MathUtils.calcQuantile(intensities, parameters.getParameter(CHROMATOGRAPHIC_THRESHOLD_LEVEL).getValue());
    for (int i = 0; i < intensities.length; i++) {
        if (intensities[i] < chromatographicThresholdLevel) {
            intensities[i] = 0.0;
        }
    }
    // candidate for a resolved peak.
    startSearch: for (int currentRegionStart = 0; currentRegionStart < lastScan - 2; currentRegionStart++) {
        // Find at least two consecutive non-zero data points
        if (intensities[currentRegionStart] == 0.0 || intensities[currentRegionStart + 1] == 0.0)
            continue;
        double currentRegionHeight = intensities[currentRegionStart];
        endSearch: for (int currentRegionEnd = currentRegionStart + 1; currentRegionEnd < scanCount; currentRegionEnd++) {
            // Update height of current region.
            currentRegionHeight = Math.max(currentRegionHeight, intensities[currentRegionEnd]);
            // have to stop here.
            if (currentRegionEnd == lastScan || intensities[currentRegionEnd + 1] == 0.0) {
                // Find the intensity at the sides (lowest data points).
                final double peakMinLeft = intensities[currentRegionStart];
                final double peakMinRight = intensities[currentRegionEnd];
                // Check the shape of the peak.
                if (currentRegionHeight >= minHeight && currentRegionHeight >= peakMinLeft * minRatio && currentRegionHeight >= peakMinRight * minRatio && peakDuration.contains(retentionTimes[currentRegionEnd] - retentionTimes[currentRegionStart])) {
                    resolvedPeaks.add(new ResolvedPeak(chromatogram, currentRegionStart, currentRegionEnd, mzCenterFunction, msmsRange, rTRangeMSMS));
                }
                // Set the next region start to current region end - 1
                // because it will be immediately
                // increased +1 as we continue the for-cycle.
                currentRegionStart = currentRegionEnd - 1;
                continue startSearch;
            }
            // Minimum duration of peak must be at least searchRTRange.
            if (retentionTimes[currentRegionEnd] - retentionTimes[currentRegionStart] >= searchRTRange) {
                // Set the RT range to check
                final Range<Double> checkRange = Range.closed(retentionTimes[currentRegionEnd] - searchRTRange, retentionTimes[currentRegionEnd] + searchRTRange);
                // current peak i.
                for (int i = currentRegionEnd - 1; i > 0; i--) {
                    if (!checkRange.contains(retentionTimes[i]))
                        break;
                    if (intensities[i] < intensities[currentRegionEnd]) {
                        continue endSearch;
                    }
                }
                // Search on the right from current peak i.
                for (int i = currentRegionEnd + 1; i < scanCount; i++) {
                    if (!checkRange.contains(retentionTimes[i]))
                        break;
                    if (intensities[i] < intensities[currentRegionEnd]) {
                        continue endSearch;
                    }
                }
                // Find the intensity at the sides (lowest data points).
                final double peakMinLeft = intensities[currentRegionStart];
                final double peakMinRight = intensities[currentRegionEnd];
                // ratio condition, continue searching for next minimum.
                if (currentRegionHeight >= peakMinRight * minRatio) {
                    // Check the shape of the peak.
                    if (currentRegionHeight >= minHeight && currentRegionHeight >= peakMinLeft * minRatio && currentRegionHeight >= peakMinRight * minRatio && peakDuration.contains(retentionTimes[currentRegionEnd] - retentionTimes[currentRegionStart])) {
                        resolvedPeaks.add(new ResolvedPeak(chromatogram, currentRegionStart, currentRegionEnd, mzCenterFunction, msmsRange, rTRangeMSMS));
                    }
                    // Set the next region start to current region end-1
                    // because it will be immediately
                    // increased +1 as we continue the for-cycle.
                    currentRegionStart = currentRegionEnd - 1;
                    continue startSearch;
                }
            }
        }
    }
    return resolvedPeaks.toArray(new ResolvedPeak[resolvedPeaks.size()]);
}

Example 57 with DataPoint

use of net.sf.mzmine.datamodel.DataPoint in project mzmine2 by mzmine.

the class SavitzkyGolayPeakDetector method resolvePeaks.

@Override
public ResolvedPeak[] resolvePeaks(final Feature chromatogram, ParameterSet parameters, RSessionWrapper rSession, CenterFunction mzCenterFunction, double msmsRange, double rTRangeMSMS) {
    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;
    }
    // Calculate intensity statistics.
    double maxIntensity = 0.0;
    double avgIntensity = 0.0;
    for (final double intensity : intensities) {
        maxIntensity = Math.max(intensity, maxIntensity);
        avgIntensity += intensity;
    }
    avgIntensity /= scanCount;
    final List<Feature> resolvedPeaks = new ArrayList<Feature>(2);
    // noise return an empty array.
    if (avgIntensity <= maxIntensity / 2.0) {
        // Calculate second derivatives of intensity values.
        final double[] secondDerivative = SGDerivative.calculateDerivative(intensities, false, SG_FILTER_LEVEL);
        // Calculate noise threshold.
        final double noiseThreshold = calcDerivativeThreshold(secondDerivative, parameters.getParameter(DERIVATIVE_THRESHOLD_LEVEL).getValue());
        // Search for peaks.
        Arrays.sort(scanNumbers);
        final Feature[] resolvedOriginalPeaks = peaksSearch(chromatogram, scanNumbers, secondDerivative, noiseThreshold, mzCenterFunction, msmsRange, rTRangeMSMS);
        final Range<Double> peakDuration = parameters.getParameter(PEAK_DURATION).getValue();
        final double minimumPeakHeight = parameters.getParameter(MIN_PEAK_HEIGHT).getValue();
        // parameters.
        for (final Feature p : resolvedOriginalPeaks) {
            if (peakDuration.contains(RangeUtils.rangeLength(p.getRawDataPointsRTRange())) && p.getHeight() >= minimumPeakHeight) {
                resolvedPeaks.add(p);
            }
        }
    }
    return resolvedPeaks.toArray(new ResolvedPeak[resolvedPeaks.size()]);
}

Example 58 with DataPoint

use of net.sf.mzmine.datamodel.DataPoint in project mzmine2 by mzmine.

the class ResolvedPeak method getDataPoint.

/**
 * This method returns a representative datapoint of this peak in a given scan
 */
@Override
public DataPoint getDataPoint(int scanNumber) {
    int index = Arrays.binarySearch(scanNumbers, scanNumber);
    if (index < 0)
        return null;
    SimpleDataPoint dp = new SimpleDataPoint(dataPointMZValues[index], dataPointIntensityValues[index]);
    return dp;
}

Example 59 with DataPoint

use of net.sf.mzmine.datamodel.DataPoint in project mzmine2 by mzmine.

the class SpectraVisualizerWindow method loadRawData.

public void loadRawData(Scan scan) {
    logger.finest("Loading scan #" + scan.getScanNumber() + " from " + dataFile + " for spectra visualizer");
    spectrumDataSet = new ScanDataSet(scan);
    this.currentScan = scan;
    // If the plot mode has not been set yet, set it accordingly
    if (spectrumPlot.getPlotMode() == null) {
        spectrumPlot.setPlotMode(currentScan.getSpectrumType());
        toolBar.setCentroidButton(currentScan.getSpectrumType());
    }
    // Clean up the MS/MS selector combo
    final JComboBox<String> msmsSelector = bottomPanel.getMSMSSelector();
    // We disable the MSMS selector first and then enable it again later
    // after updating the items. If we skip this, the size of the
    // selector may not be adjusted properly (timing issues?)
    msmsSelector.setEnabled(false);
    msmsSelector.removeAllItems();
    boolean msmsVisible = false;
    // Add parent scan to MS/MS selector combo
    NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
    NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
    NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();
    // Add all fragment scans to MS/MS selector combo
    int[] fragmentScans = currentScan.getFragmentScanNumbers();
    if (fragmentScans != null) {
        for (int fragment : fragmentScans) {
            Scan fragmentScan = dataFile.getScan(fragment);
            if (fragmentScan == null)
                continue;
            final String itemText = "Fragment scan #" + fragment + ", RT: " + rtFormat.format(fragmentScan.getRetentionTime()) + ", precursor m/z: " + mzFormat.format(fragmentScan.getPrecursorMZ());
            // Updating the combo in other than Swing thread may cause
            // exception
            SwingUtilities.invokeLater(new Runnable() {

                @Override
                public void run() {
                    msmsSelector.addItem(itemText);
                }
            });
            msmsVisible = true;
        }
    }
    msmsSelector.setEnabled(true);
    // Update the visibility of MS/MS selection combo
    bottomPanel.setMSMSSelectorVisible(msmsVisible);
    // Set window and plot titles
    String windowTitle = "Spectrum: [" + dataFile.getName() + "; scan #" + currentScan.getScanNumber() + "]";
    String spectrumTitle = ScanUtils.scanToString(currentScan, true);
    DataPoint basePeak = currentScan.getHighestDataPoint();
    if (basePeak != null) {
        spectrumTitle += ", base peak: " + mzFormat.format(basePeak.getMZ()) + " m/z (" + intensityFormat.format(basePeak.getIntensity()) + ")";
    }
    String spectrumSubtitle = null;
    if (!Strings.isNullOrEmpty(currentScan.getScanDefinition())) {
        spectrumSubtitle = "Scan definition: " + currentScan.getScanDefinition();
    }
    setTitle(windowTitle);
    spectrumPlot.setTitle(spectrumTitle, spectrumSubtitle);
    // Set plot data set
    spectrumPlot.removeAllDataSets();
    spectrumPlot.addDataSet(spectrumDataSet, scanColor, false);
    // Reload feature list
    bottomPanel.rebuildPeakListSelector();
}

Example 60 with DataPoint

use of net.sf.mzmine.datamodel.DataPoint in project mzmine2 by mzmine.

the class SpectrumChartFactory method createMSMSDataSet.

public static PseudoSpectrumDataSet createMSMSDataSet(double precursorMZ, double rt, DataPoint[] dps, String label) {
    NumberFormat mzForm = MZmineCore.getConfiguration().getMZFormat();
    NumberFormat rtForm = MZmineCore.getConfiguration().getRTFormat();
    if (label == null)
        label = "";
    else if (!label.isEmpty())
        label = " (" + label + ")";
    // data
    PseudoSpectrumDataSet series = new PseudoSpectrumDataSet(true, MessageFormat.format("MSMS for m/z={0} RT={1}{2}", mzForm.format(precursorMZ), rtForm.format(rt), label));
    // for each row
    for (DataPoint dp : dps) {
        series.addDP(dp.getMZ(), dp.getIntensity(), null);
    }
    return series;
}