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

Example 31 with DataPoint

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

the class BaselineCorrector method correctBasePeakBaselines.

/**
 * Correct the baselines (using base peak chromatograms).
 *
 * @param origDataFile dataFile of concern.
 * @param writer data file writer.
 * @param level the MS level.
 * @param numBins number of m/z bins.
 * @param parameters parameters specific to the actual method for baseline computing.
 * @throws IOException if there are i/o problems.
 * @throws RSessionWrapperException
 * @throws BaselineCorrectionException
 * @throws InterruptedException
 */
private void correctBasePeakBaselines(final RSessionWrapper rSession, final RawDataFile origDataFile, final RawDataFileWriter writer, final int level, final int numBins, final ParameterSet parameters) throws IOException, RSessionWrapperException {
    // Get scan numbers from original file.
    final int[] scanNumbers = origDataFile.getScanNumbers(level);
    final int numScans = scanNumbers.length;
    // Build chromatograms.
    LOG.finest("Building base peak chromatograms.");
    final double[][] baseChrom = buildBasePeakChromatograms(origDataFile, level, numBins);
    // Calculate baselines: done in-place, i.e. overwrite chromatograms to
    // save memory.
    LOG.finest("Calculating baselines.");
    for (int binIndex = 0; !isAborted(origDataFile) && binIndex < numBins; binIndex++) {
        baseChrom[binIndex] = computeBaseline(rSession, origDataFile, baseChrom[binIndex], parameters);
        progressMap.get(origDataFile)[0]++;
    }
    // Subtract baselines.
    LOG.finest("Subtracting baselines.");
    for (int scanIndex = 0; !isAborted(origDataFile) && scanIndex < numScans; scanIndex++) {
        // Get original scan.
        final Scan origScan = origDataFile.getScan(scanNumbers[scanIndex]);
        // Get data points (m/z and intensity pairs) of the original scan
        final DataPoint[] origDataPoints = origScan.getDataPoints();
        // Create and write new corrected scan.
        final SimpleScan newScan = new SimpleScan(origScan);
        newScan.setDataPoints(subtractBasePeakBaselines(origDataFile, origDataPoints, baseChrom, numBins, scanIndex));
        writer.addScan(newScan);
        progressMap.get(origDataFile)[0]++;
    }
}

Example 32 with DataPoint

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

the class BaselineCorrector method subtractBasePeakBaselines.

/**
 * Perform baseline correction in bins (base peak).
 *
 * @param origDataFile dataFile of concern.
 * @param dataPoints input data points to correct.
 * @param baselines the baselines - one per m/z bin.
 * @param numBins the number of m/z bins.
 * @param scanIndex the current scan index that these data points come from.
 * @return the corrected data points.
 */
private DataPoint[] subtractBasePeakBaselines(final RawDataFile origDataFile, final DataPoint[] dataPoints, final double[][] baselines, final int numBins, final int scanIndex) {
    // Create an ArrayList for new data points.
    final DataPoint[] newDataPoints = new DataPoint[dataPoints.length];
    // Determine MZ range.
    final Range<Double> mzRange = origDataFile.getDataMZRange();
    // Loop through all original data points.
    int i = 0;
    for (final DataPoint dp : dataPoints) {
        // Subtract baseline.
        final double mz = dp.getMZ();
        final int bin = RangeUtils.binNumber(mzRange, numBins, mz);
        final double baselineIntenstity = baselines[bin][scanIndex];
        newDataPoints[i++] = baselineIntenstity <= 0.0 ? new SimpleDataPoint(dp) : new SimpleDataPoint(mz, Math.max(0.0, dp.getIntensity() - baselineIntenstity));
    }
    // Return the new data points.
    return newDataPoints;
}

Example 33 with DataPoint

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

the class BaselineCorrector method correctTICBaselines.

/**
 * Correct the baselines (using TIC chromatograms).
 *
 * @param origDataFile dataFile of concern.
 * @param writer data file writer.
 * @param level the MS level.
 * @param numBins number of m/z bins.
 * @param parameters parameters specific to the actual method for baseline computing.
 * @throws IOException if there are i/o problems.
 * @throws RSessionWrapperException
 * @throws BaselineCorrectionException
 */
private void correctTICBaselines(final RSessionWrapper rSession, final RawDataFile origDataFile, final RawDataFileWriter writer, final int level, final int numBins, final ParameterSet parameters) throws IOException, RSessionWrapperException {
    // Get scan numbers from original file.
    final int[] scanNumbers = origDataFile.getScanNumbers(level);
    final int numScans = scanNumbers.length;
    // Build chromatograms.
    LOG.finest("Building TIC chromatograms.");
    final double[][] baseChrom = buildTICChromatograms(origDataFile, level, numBins);
    // Calculate baselines: done in-place, i.e. overwrite chromatograms to
    // save memory.
    LOG.finest("Calculating baselines.");
    for (int binIndex = 0; !isAborted(origDataFile) && binIndex < numBins; binIndex++) {
        // Calculate baseline.
        // final double[] baseline = asymBaseline(baseChrom[binIndex]);
        final double[] baseline = computeBaseline(rSession, origDataFile, baseChrom[binIndex], parameters);
        // Normalize the baseline w.r.t. chromatogram (TIC).
        for (int scanIndex = 0; !isAborted(origDataFile) && scanIndex < numScans; scanIndex++) {
            final double bc = baseChrom[binIndex][scanIndex];
            if (bc != 0.0) {
                baseChrom[binIndex][scanIndex] = baseline[scanIndex] / bc;
            }
        }
        progressMap.get(origDataFile)[0]++;
    }
    // Subtract baselines.
    LOG.finest("Subtracting baselines.");
    for (int scanIndex = 0; !isAborted(origDataFile) && scanIndex < numScans; scanIndex++) {
        // Get original scan.
        final Scan origScan = origDataFile.getScan(scanNumbers[scanIndex]);
        // Get data points (m/z and intensity pairs) of the original scan
        final DataPoint[] origDataPoints = origScan.getDataPoints();
        // Create and write new corrected scan.
        final SimpleScan newScan = new SimpleScan(origScan);
        newScan.setDataPoints(subtractTICBaselines(origDataFile, origDataPoints, baseChrom, numBins, scanIndex));
        writer.addScan(newScan);
        progressMap.get(origDataFile)[0]++;
    }
}

Example 34 with DataPoint

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

the class BaselineCorrector method copyScansToWriter.

/**
 * Copy scans to RawDataFileWriter.
 *
 * @param origDataFile dataFile of concern.
 * @param writer writer to copy scans to.
 * @param level MS-level of scans to copy.
 * @throws IOException if there are i/o problems.
 */
private void copyScansToWriter(final RawDataFile origDataFile, final RawDataFileWriter writer, final int level) throws IOException {
    LOG.finest("Copy scans");
    // Get scan numbers for MS-level.
    final int[] scanNumbers = origDataFile.getScanNumbers(level);
    final int numScans = scanNumbers.length;
    // Create copy of scans.
    for (int scanIndex = 0; !isAborted(origDataFile) && scanIndex < numScans; scanIndex++) {
        // Get original scan.
        final Scan origScan = origDataFile.getScan(scanNumbers[scanIndex]);
        // Get data points (m/z and intensity pairs) of the original scan
        final DataPoint[] origDataPoints = origScan.getDataPoints();
        final DataPoint[] newDataPoints = new DataPoint[origDataPoints.length];
        // Copy original data points.
        int i = 0;
        for (final DataPoint dp : origDataPoints) {
            newDataPoints[i++] = new SimpleDataPoint(dp);
        }
        // Create new copied scan.
        final SimpleScan newScan = new SimpleScan(origScan);
        newScan.setDataPoints(newDataPoints);
        writer.addScan(newScan);
        progressMap.get(origDataFile)[0]++;
    }
}

Example 35 with DataPoint

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

the class BaselineCorrector method buildBasePeakChromatograms.

/**
 * Constructs base peak (max) chromatograms - one for each m/z bin.
 *
 * @param origDataFile dataFile of concern.
 * @param level the MS level.
 * @param numBins number of m/z bins.
 * @return the chromatograms as double[number of bins][number of scans].
 */
private double[][] buildBasePeakChromatograms(final RawDataFile origDataFile, final int level, final int numBins) {
    // Get scan numbers from original file.
    final int[] scanNumbers = origDataFile.getScanNumbers(level);
    final int numScans = scanNumbers.length;
    // Determine MZ range.
    final Range<Double> mzRange = origDataFile.getDataMZRange();
    // Create chromatograms.
    final double[][] chromatograms = new double[numBins][numScans];
    for (int scanIndex = 0; !isAborted(origDataFile) && scanIndex < numScans; scanIndex++) {
        // Get original scan.
        final Scan scan = origDataFile.getScan(scanNumbers[scanIndex]);
        // Process data points.
        for (final DataPoint dataPoint : scan.getDataPoints()) {
            final int bin = RangeUtils.binNumber(mzRange, numBins, dataPoint.getMZ());
            final double value = chromatograms[bin][scanIndex];
            chromatograms[bin][scanIndex] = Math.max(value, dataPoint.getIntensity());
        }
        progressMap.get(origDataFile)[0]++;
    }
    return chromatograms;
}