Examples with SimpleDataPoint net.sf.mzmine.datamodel.impl.SimpleDataPoint used on opensource projects

Example 6 with SimpleDataPoint

use of net.sf.mzmine.datamodel.impl.SimpleDataPoint in project mzmine2 by mzmine.

the class IsotopeGrouperTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running isotopic peak grouper on " + peakList);
    // We assume source peakList contains one datafile
    RawDataFile dataFile = peakList.getRawDataFile(0);
    // Create a new deisotoped peakList
    deisotopedPeakList = new SimplePeakList(peakList + " " + suffix, peakList.getRawDataFiles());
    // Collect all selected charge states
    int[] charges = new int[maximumCharge];
    for (int i = 0; i < maximumCharge; i++) charges[i] = i + 1;
    // Sort peaks by descending height
    Feature[] sortedPeaks = peakList.getPeaks(dataFile);
    Arrays.sort(sortedPeaks, new PeakSorter(SortingProperty.Height, SortingDirection.Descending));
    // Loop through all peaks
    totalPeaks = sortedPeaks.length;
    for (int ind = 0; ind < totalPeaks; ind++) {
        if (isCanceled())
            return;
        Feature aPeak = sortedPeaks[ind];
        // Check if peak was already deleted
        if (aPeak == null) {
            processedPeaks++;
            continue;
        }
        // Check which charge state fits best around this peak
        int bestFitCharge = 0;
        int bestFitScore = -1;
        Vector<Feature> bestFitPeaks = null;
        for (int charge : charges) {
            Vector<Feature> fittedPeaks = new Vector<Feature>();
            fittedPeaks.add(aPeak);
            fitPattern(fittedPeaks, aPeak, charge, sortedPeaks);
            int score = fittedPeaks.size();
            if ((score > bestFitScore) || ((score == bestFitScore) && (bestFitCharge > charge))) {
                bestFitScore = score;
                bestFitCharge = charge;
                bestFitPeaks = fittedPeaks;
            }
        }
        PeakListRow oldRow = peakList.getPeakRow(aPeak);
        assert bestFitPeaks != null;
        // isotope, we skip this left the original peak in the feature list.
        if (bestFitPeaks.size() == 1) {
            deisotopedPeakList.addRow(oldRow);
            processedPeaks++;
            continue;
        }
        // Convert the peak pattern to array
        Feature[] originalPeaks = bestFitPeaks.toArray(new Feature[0]);
        // Create a new SimpleIsotopePattern
        DataPoint[] isotopes = new DataPoint[bestFitPeaks.size()];
        for (int i = 0; i < isotopes.length; i++) {
            Feature p = originalPeaks[i];
            isotopes[i] = new SimpleDataPoint(p.getMZ(), p.getHeight());
        }
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(isotopes, IsotopePatternStatus.DETECTED, aPeak.toString());
        // the lowest m/z peak
        if (chooseMostIntense) {
            Arrays.sort(originalPeaks, new PeakSorter(SortingProperty.Height, SortingDirection.Descending));
        } else {
            Arrays.sort(originalPeaks, new PeakSorter(SortingProperty.MZ, SortingDirection.Ascending));
        }
        Feature newPeak = new SimpleFeature(originalPeaks[0]);
        newPeak.setIsotopePattern(newPattern);
        newPeak.setCharge(bestFitCharge);
        // Keep old ID
        int oldID = oldRow.getID();
        SimplePeakListRow newRow = new SimplePeakListRow(oldID);
        PeakUtils.copyPeakListRowProperties(oldRow, newRow);
        newRow.addPeak(dataFile, newPeak);
        deisotopedPeakList.addRow(newRow);
        // Remove all peaks already assigned to isotope pattern
        for (int i = 0; i < sortedPeaks.length; i++) {
            if (bestFitPeaks.contains(sortedPeaks[i]))
                sortedPeaks[i] = null;
        }
        // Update completion rate
        processedPeaks++;
    }
    // Add new peakList to the project
    project.addPeakList(deisotopedPeakList);
    // Load previous applied methods
    for (PeakListAppliedMethod proc : peakList.getAppliedMethods()) {
        deisotopedPeakList.addDescriptionOfAppliedTask(proc);
    }
    // Add task description to peakList
    deisotopedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Isotopic peaks grouper", parameters));
    // Remove the original peakList if requested
    if (removeOriginal)
        project.removePeakList(peakList);
    logger.info("Finished isotopic peak grouper on " + peakList);
    setStatus(TaskStatus.FINISHED);
}

Example 7 with SimpleDataPoint

use of net.sf.mzmine.datamodel.impl.SimpleDataPoint in project mzmine2 by mzmine.

the class RawDataFileImpl method readDataPoints.

public synchronized DataPoint[] readDataPoints(int ID) throws IOException {
    final Long currentOffset = dataPointsOffsets.get(ID);
    final Integer numOfDataPoints = dataPointsLengths.get(ID);
    if ((currentOffset == null) || (numOfDataPoints == null)) {
        throw new IllegalArgumentException("Unknown storage ID " + ID);
    }
    final int numOfBytes = numOfDataPoints * 2 * 4;
    if (buffer.capacity() < numOfBytes) {
        buffer = ByteBuffer.allocate(numOfBytes * 2);
    } else {
        // JDK 9 breaks compatibility with JRE8: need to cast
        // https://stackoverflow.com/questions/48693695/java-nio-buffer-not-loading-clear-method-on-runtime
        ((Buffer) buffer).clear();
    }
    dataPointsFile.seek(currentOffset);
    dataPointsFile.read(buffer.array(), 0, numOfBytes);
    FloatBuffer floatBuffer = buffer.asFloatBuffer();
    DataPoint[] dataPoints = new DataPoint[numOfDataPoints];
    for (int i = 0; i < numOfDataPoints; i++) {
        float mz = floatBuffer.get();
        float intensity = floatBuffer.get();
        dataPoints[i] = new SimpleDataPoint(mz, intensity);
    }
    return dataPoints;
}

Example 8 with SimpleDataPoint

use of net.sf.mzmine.datamodel.impl.SimpleDataPoint in project mzmine2 by mzmine.

the class ManualPickerTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.finest("Starting manual peak picker, RT: " + rtRange + ", m/z: " + mzRange);
    // Calculate total number of scans to process
    for (RawDataFile dataFile : dataFiles) {
        int[] scanNumbers = dataFile.getScanNumbers(1, rtRange);
        totalScans += scanNumbers.length;
    }
    // Find peak in each data file
    for (RawDataFile dataFile : dataFiles) {
        ManualPeak newPeak = new ManualPeak(dataFile);
        boolean dataPointFound = false;
        int[] scanNumbers = dataFile.getScanNumbers(1, rtRange);
        for (int scanNumber : scanNumbers) {
            if (isCanceled())
                return;
            // Get next scan
            Scan scan = dataFile.getScan(scanNumber);
            // Find most intense m/z peak
            DataPoint basePeak = ScanUtils.findBasePeak(scan, mzRange);
            if (basePeak != null) {
                if (basePeak.getIntensity() > 0)
                    dataPointFound = true;
                newPeak.addDatapoint(scan.getScanNumber(), basePeak);
            } else {
                final double mzCenter = (mzRange.lowerEndpoint() + mzRange.upperEndpoint()) / 2.0;
                DataPoint fakeDataPoint = new SimpleDataPoint(mzCenter, 0);
                newPeak.addDatapoint(scan.getScanNumber(), fakeDataPoint);
            }
            processedScans++;
        }
        if (dataPointFound) {
            newPeak.finalizePeak();
            if (newPeak.getArea() > 0)
                peakListRow.addPeak(dataFile, newPeak);
        } else {
            peakListRow.removePeak(dataFile);
        }
    }
    // Notify the GUI that peaklist contents have changed
    if (peakList != null) {
        // Check if the feature list row has been added to the feature list, and
        // if it has not, add it
        List<PeakListRow> rows = Arrays.asList(peakList.getRows());
        if (!rows.contains(peakListRow)) {
            peakList.addRow(peakListRow);
        }
        // Add quality parameters to peaks
        QualityParameters.calculateQualityParameters(peakList);
        project.notifyObjectChanged(peakList, true);
    }
    if (table != null) {
        ((AbstractTableModel) table.getModel()).fireTableDataChanged();
    }
    logger.finest("Finished manual peak picker, " + processedScans + " scans processed");
    setStatus(TaskStatus.FINISHED);
}

Example 9 with SimpleDataPoint

use of net.sf.mzmine.datamodel.impl.SimpleDataPoint in project mzmine2 by mzmine.

the class PearsonCorrelation method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started Scan Alignment on " + dataFile);
    scanNumbers = dataFile.getScanNumbers(1);
    totalScans = scanNumbers.length;
    RawDataFileWriter newRDFW = null;
    try {
        newRDFW = MZmineCore.createNewFile(dataFile.getName() + ' ' + suffix);
        // [relative scan][j value]
        DataPoint[][] mzValues = null;
        int i, j, si, sj, ii, k, shift, ks;
        int[] shiftedScans = new int[mzSpan * 2 + 1];
        for (i = 0; i < totalScans; i++) {
            if (isCanceled())
                return;
            Scan scan = dataFile.getScan(scanNumbers[i]);
            si = (int) Math.max(0, i - scanSpan);
            sj = (int) (si + 2 * scanSpan);
            if (sj >= totalScans) {
                si = (int) Math.max(0, si - (sj - totalScans + 1));
                sj = (int) (si + 2 * scanSpan);
            }
            if (scan != null) {
                // Allocate
                if (mzValues == null || mzValues.length < sj - si + 1)
                    mzValues = new DataPoint[sj - si + 1][];
                // Load Data Points
                for (j = si; j <= sj; j++) {
                    Scan xscan = dataFile.getScan(scanNumbers[j]);
                    mzValues[j - si] = xscan.getDataPoints();
                }
                // Estimate Correlations
                ii = i - si;
                final SimpleScan newScan = new SimpleScan(scan);
                DataPoint[] newDP = new DataPoint[mzValues[ii].length];
                int maxShift = 0;
                double maxCorrelation = 0;
                int ndp = mzValues[ii].length;
                // System.out.print("Scan="+i);
                for (shift = -mzSpan; shift <= mzSpan; shift++) {
                    PearsonCorrelation thisShift = new PearsonCorrelation();
                    for (k = 0; k < ndp; k++) {
                        ks = k + shift;
                        if (ks >= 0 && ks < ndp && mzValues[ii][ks].getIntensity() >= minimumHeight) {
                            DataPoint dp = mzValues[ii][k];
                            double mz = dp.getMZ();
                            int f = 0;
                            for (j = 0; j < mzValues.length; j++) {
                                // System.out.println(j);
                                if (j != ii) {
                                    if (mzValues[j].length > k && Math.abs(mzValues[j][k].getMZ() - mz) < 1e-10) {
                                        f = k;
                                    } else {
                                        f = findFirstMass(mz, mzValues[j]);
                                        if (Math.abs(mzValues[j][f].getMZ() - mz) > 1e-10) {
                                            f = -f;
                                        }
                                    }
                                    if (f >= 0) {
                                        if (logScale) {
                                            thisShift.enter(Math.log(mzValues[j][f].getIntensity()), Math.log(mzValues[ii][ks].getIntensity()));
                                        } else {
                                            thisShift.enter(mzValues[j][f].getIntensity(), mzValues[ii][ks].getIntensity());
                                        }
                                    }
                                }
                            }
                        }
                    }
                    // correlation="+Math.round(thisShift.correlation()*1000)/1000.0);
                    if (thisShift.correlation() > maxCorrelation) {
                        maxShift = shift;
                        maxCorrelation = thisShift.correlation();
                    }
                // newDP[k] = new SimpleDataPoint(mz, c > 0 ? a/c : 0);
                }
                // Copy DataPoints with maxShift as the shift
                shift = maxShift;
                // System.out.println("\nScan="+i+", Shift="+maxShift+", Correlation="+maxCorrelation);
                shiftedScans[maxShift + mzSpan]++;
                for (k = 0; k < ndp; k++) {
                    ks = k + shift;
                    if (ks >= 0 && ks < ndp) {
                        newDP[k] = new SimpleDataPoint(mzValues[ii][k].getMZ(), mzValues[ii][ks].getIntensity());
                    } else {
                        newDP[k] = new SimpleDataPoint(mzValues[ii][k].getMZ(), 0);
                    }
                }
                newScan.setDataPoints(newDP);
                newRDFW.addScan(newScan);
            }
            processedScans++;
        }
        if (!isCanceled()) {
            // Finalize writing
            newRDF = newRDFW.finishWriting();
            // Add the newly created file to the project
            project.addFile(newRDF);
            // Remove the original data file if requested
            if (removeOriginal) {
                project.removeFile(dataFile);
            }
            setStatus(TaskStatus.FINISHED);
            String shifts = "";
            for (i = -mzSpan; i <= mzSpan; i++) {
                shifts = shifts + i + ":" + shiftedScans[i + mzSpan] + " | ";
            }
            logger.info("Finished Scan Alignment on " + dataFile + ". Scans per shift = " + shifts);
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 10 with SimpleDataPoint

use of net.sf.mzmine.datamodel.impl.SimpleDataPoint in project mzmine2 by mzmine.

the class BaselineCorrector method subtractTICBaselines.

/**
 * Perform baseline correction in bins (TIC).
 *
 * @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[] subtractTICBaselines(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() * (1.0 - baselineIntenstity)));
    }
    // Return the new data points.
    return newDataPoints;
}