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

Example 1 with SimpleScan

use of net.sf.mzmine.datamodel.impl.SimpleScan 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 2 with SimpleScan

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

the class ScanSmoothingTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started Scan Smoothing on " + dataFile);
    scanNumbers = dataFile.getScanNumbers(1);
    totalScans = scanNumbers.length;
    RawDataFileWriter newRDFW = null;
    int timepassed = 0;
    int mzpassed = 0;
    try {
        newRDFW = MZmineCore.createNewFile(dataFile.getName() + ' ' + suffix);
        // [relative scan][j value]
        DataPoint[][] mzValues = null;
        int i, j, si, sj, ii, k, ssi, ssj;
        for (i = 0; i < totalScans; i++) {
            if (isCanceled())
                return;
            // Smoothing in TIME space
            Scan scan = dataFile.getScan(scanNumbers[i]);
            if (scan != null) {
                double rt = scan.getRetentionTime();
                final SimpleScan newScan = new SimpleScan(scan);
                DataPoint[] newDP = null;
                sj = si = i;
                ssi = ssj = i;
                if (timeSpan > 0 || scanSpan > 0) {
                    double timeMZtol = Math.max(mzTol, 1e-5);
                    for (si = i; si > 1; si--) {
                        Scan scanS = dataFile.getScan(scanNumbers[si - 1]);
                        if (scanS == null || scanS.getRetentionTime() < rt - timeSpan / 2) {
                            break;
                        }
                    }
                    for (sj = i; sj < totalScans - 1; sj++) {
                        Scan scanS = dataFile.getScan(scanNumbers[sj + 1]);
                        if (scanS == null || scanS.getRetentionTime() >= rt + timeSpan / 2) {
                            break;
                        }
                    }
                    ssi = i - (scanSpan - 1) / 2;
                    ssj = i + (scanSpan - 1) / 2;
                    if (ssi < 0) {
                        ssj += -ssi;
                        ssi = 0;
                    }
                    if (ssj >= totalScans) {
                        ssi -= (ssj - totalScans + 1);
                        ssj = totalScans - 1;
                    }
                    if (sj - si + 1 < scanSpan) {
                        si = ssi;
                        sj = ssj;
                    // si = Math.min(si, ssi);
                    // sj = Math.max(sj, ssj);
                    }
                    if (sj > si) {
                        timepassed++;
                        // 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 Averages
                        ii = i - si;
                        newDP = new DataPoint[mzValues[ii].length];
                        for (k = 0; k < mzValues[ii].length; k++) {
                            DataPoint dp = mzValues[ii][k];
                            double mz = dp.getMZ();
                            double intensidad = 0;
                            if (dp.getIntensity() > 0) {
                                // only process
                                // those > 0
                                double a = 0;
                                short c = 0;
                                int f = 0;
                                for (j = 0; j < mzValues.length; j++) {
                                    // System.out.println(j);
                                    if (mzValues[j].length > k && Math.abs(mzValues[j][k].getMZ() - mz) < timeMZtol) {
                                        f = k;
                                    } else {
                                        f = findFirstMass(mz, mzValues[j]);
                                        if (Math.abs(mzValues[j][f].getMZ() - mz) > timeMZtol) {
                                            f = -f;
                                        }
                                    }
                                    if (f >= 0 && mzValues[j][f].getIntensity() >= minimumHeight) {
                                        a += mzValues[j][f].getIntensity();
                                        c++;
                                    } else {
                                        c = (short) (c + 0);
                                    }
                                }
                                intensidad = c > 0 ? a / c : 0;
                            }
                            newDP[k] = new SimpleDataPoint(mz, intensidad);
                        }
                    }
                } else if (scan != null) {
                    newDP = scan.getDataPoints();
                }
                if ((mzTol > 0 || mzPoints > 0)) {
                    mzpassed++;
                    DataPoint[] updatedDP = new DataPoint[newDP.length];
                    for (k = 0; k < newDP.length; k++) {
                        double mz = newDP[k].getMZ();
                        double intensidad = 0;
                        if (newDP[k].getIntensity() > 0) {
                            for (si = k; si > 0 && (newDP[si].getMZ() + mzTol >= mz || k - si <= mzPoints); si--) ;
                            for (sj = k; sj < newDP.length - 1 && (newDP[sj].getMZ() - mzTol <= mz || sj - k <= mzPoints); sj++) ;
                            double sum = 0;
                            for (j = si; j <= sj; j++) {
                                sum += newDP[j].getIntensity();
                            }
                            intensidad = sum / (sj - si + 1);
                        }
                        updatedDP[k] = new SimpleDataPoint(mz, intensidad);
                    }
                    newDP = updatedDP;
                }
                // Register new smoothing data
                if (scan != null && newDP != null) {
                    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);
            if (mzpassed + timepassed < totalScans / 2) {
                logger.warning("It seems that parameters were not properly set. Scans processed : time=" + timepassed + ", mz=" + mzpassed);
            }
            logger.info("Finished Scan Smoothing on " + dataFile);
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 3 with SimpleScan

use of net.sf.mzmine.datamodel.impl.SimpleScan 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 4 with SimpleScan

use of net.sf.mzmine.datamodel.impl.SimpleScan 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 5 with SimpleScan

use of net.sf.mzmine.datamodel.impl.SimpleScan 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]++;
    }
}