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

Example 66 with RawDataFile

use of net.sf.mzmine.datamodel.RawDataFile 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 67 with RawDataFile

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

the class QualityParameters method PeakFindRTs.

private static double[] PeakFindRTs(double intensity, double rt, Feature peak) {
    double x1 = 0, x2 = 0, x3 = 0, x4 = 0, y1 = 0, y2 = 0, y3 = 0, y4 = 0, lastDiff1 = intensity, lastDiff2 = intensity, currentDiff, currentRT;
    int[] scanNumbers = peak.getScanNumbers();
    RawDataFile dataFile = peak.getDataFile();
    // peak apex
    for (int i = 1; i < scanNumbers.length - 1; i++) {
        if (peak.getDataPoint(scanNumbers[i]) != null) {
            currentDiff = Math.abs(intensity - peak.getDataPoint(scanNumbers[i]).getIntensity());
            currentRT = dataFile.getScan(scanNumbers[i]).getRetentionTime();
            if (currentDiff < lastDiff1 & currentDiff > 0 & currentRT <= rt & peak.getDataPoint(scanNumbers[i + 1]) != null) {
                x1 = dataFile.getScan(scanNumbers[i]).getRetentionTime();
                y1 = peak.getDataPoint(scanNumbers[i]).getIntensity();
                x2 = dataFile.getScan(scanNumbers[i + 1]).getRetentionTime();
                y2 = peak.getDataPoint(scanNumbers[i + 1]).getIntensity();
                lastDiff1 = currentDiff;
            } else if (currentDiff < lastDiff2 & currentDiff > 0 & currentRT >= rt & peak.getDataPoint(scanNumbers[i - 1]) != null) {
                x3 = dataFile.getScan(scanNumbers[i - 1]).getRetentionTime();
                y3 = peak.getDataPoint(scanNumbers[i - 1]).getIntensity();
                x4 = dataFile.getScan(scanNumbers[i]).getRetentionTime();
                y4 = peak.getDataPoint(scanNumbers[i]).getIntensity();
                lastDiff2 = currentDiff;
            }
        }
    }
    // Calculate RT value for input intensity based on linear regression
    double slope, intercept, rt1, rt2;
    if (y1 > 0) {
        slope = (y2 - y1) / (x2 - x1);
        intercept = y1 - (slope * x1);
        rt1 = (intensity - intercept) / slope;
    } else if (x2 > 0) {
        // Straight drop of peak to 0 intensity
        rt1 = x2;
    } else {
        rt1 = peak.getRawDataPointsRTRange().lowerEndpoint();
    }
    if (y4 > 0) {
        slope = (y4 - y3) / (x4 - x3);
        intercept = y3 - (slope * x3);
        rt2 = (intensity - intercept) / slope;
    } else if (x3 > 0) {
        // Straight drop of peak to 0 intensity
        rt2 = x3;
    } else {
        rt2 = peak.getRawDataPointsRTRange().upperEndpoint();
    }
    return new double[] { rt1, rt2 };
}

Example 68 with RawDataFile

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

the class ScatterPlotAxisSelection method generateOptionsForPeakList.

static ScatterPlotAxisSelection[] generateOptionsForPeakList(PeakList peakList) {
    Vector<ScatterPlotAxisSelection> options = new Vector<ScatterPlotAxisSelection>();
    for (RawDataFile dataFile : peakList.getRawDataFiles()) {
        ScatterPlotAxisSelection newOption = new ScatterPlotAxisSelection(dataFile);
        options.add(newOption);
    }
    for (UserParameter<?, ?> parameter : MZmineCore.getProjectManager().getCurrentProject().getParameters()) {
        if (!(parameter instanceof ComboParameter))
            continue;
        Object[] possibleValues = ((ComboParameter<?>) parameter).getChoices();
        for (Object value : possibleValues) {
            ScatterPlotAxisSelection newOption = new ScatterPlotAxisSelection(parameter, value);
            options.add(newOption);
        }
    }
    return options.toArray(new ScatterPlotAxisSelection[0]);
}

Example 69 with RawDataFile

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

the class ScatterPlotAxisSelection method getValue.

public double getValue(PeakListRow row) {
    if (file != null) {
        Feature peak = row.getPeak(file);
        if (peak == null)
            return 0;
        else
            return peak.getArea();
    }
    double totalArea = 0;
    int numOfFiles = 0;
    for (RawDataFile dataFile : row.getRawDataFiles()) {
        Object fileValue = MZmineCore.getProjectManager().getCurrentProject().getParameterValue(parameter, dataFile);
        if (fileValue == null)
            continue;
        if (fileValue.toString().equals(parameterValue.toString())) {
            Feature peak = row.getPeak(dataFile);
            if ((peak != null) && (peak.getArea() > 0)) {
                totalArea += peak.getArea();
                numOfFiles++;
            }
        }
    }
    if (numOfFiles == 0)
        return 0;
    totalArea /= numOfFiles;
    return totalArea;
}

Example 70 with RawDataFile

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

the class PeakFinderTask method fillList.

public void fillList(boolean masterList) {
    for (int i = 0; i < peakList.getNumberOfRawDataFiles(); i++) {
        if (i != masterSample) {
            RawDataFile datafile1;
            RawDataFile datafile2;
            if (masterList) {
                datafile1 = peakList.getRawDataFile(masterSample);
                datafile2 = peakList.getRawDataFile(i);
            } else {
                datafile1 = peakList.getRawDataFile(i);
                datafile2 = peakList.getRawDataFile(masterSample);
            }
            RegressionInfo info = new RegressionInfo();
            for (PeakListRow row : peakList.getRows()) {
                Feature peaki = row.getPeak(datafile1);
                Feature peake = row.getPeak(datafile2);
                if (peaki != null && peake != null) {
                    info.addData(peake.getRT(), peaki.getRT());
                }
            }
            info.setFunction();
            // Canceled?
            if (isCanceled()) {
                return;
            }
            Vector<Gap> gaps = new Vector<Gap>();
            // if necessary
            for (int row = 0; row < peakList.getNumberOfRows(); row++) {
                PeakListRow sourceRow = peakList.getRow(row);
                PeakListRow newRow = processedPeakList.getRow(row);
                Feature sourcePeak = sourceRow.getPeak(datafile1);
                if (sourcePeak == null) {
                    // Create a new gap
                    double mz = sourceRow.getAverageMZ();
                    double rt2 = -1;
                    if (!masterList) {
                        if (processedPeakList.getRow(row).getPeak(datafile2) != null) {
                            rt2 = processedPeakList.getRow(row).getPeak(datafile2).getRT();
                        }
                    } else {
                        if (peakList.getRow(row).getPeak(datafile2) != null) {
                            rt2 = peakList.getRow(row).getPeak(datafile2).getRT();
                        }
                    }
                    if (rt2 > -1) {
                        double rt = info.predict(rt2);
                        if (rt != -1) {
                            Range<Double> mzRange = mzTolerance.getToleranceRange(mz);
                            Range<Double> rtRange = rtTolerance.getToleranceRange(rt);
                            Gap newGap = new Gap(newRow, datafile1, mzRange, rtRange, intTolerance);
                            gaps.add(newGap);
                        }
                    }
                } else {
                    newRow.addPeak(datafile1, sourcePeak);
                }
            }
            // Stop processing this file if there are no gaps
            if (gaps.size() == 0) {
                processedScans.addAndGet(datafile1.getNumOfScans());
                continue;
            }
            // Get all scans of this data file
            int[] scanNumbers = datafile1.getScanNumbers(1);
            // Process each scan
            for (int scanNumber : scanNumbers) {
                // Canceled?
                if (isCanceled()) {
                    return;
                }
                // Get the scan
                Scan scan = datafile1.getScan(scanNumber);
                // Feed this scan to all gaps
                for (Gap gap : gaps) {
                    gap.offerNextScan(scan);
                }
                processedScans.incrementAndGet();
            }
            // Finalize gaps
            for (Gap gap : gaps) {
                gap.noMoreOffers();
            }
        }
    }
}