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

Example 71 with DataPoint

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

the class GridMassTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    Format mzFormat = MZmineCore.getConfiguration().getMZFormat();
    Format timeFormat = MZmineCore.getConfiguration().getRTFormat();
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started GRIDMASS v1.0 [Apr-09-2014] on " + dataFile);
    scans = scanSelection.getMatchingScans(dataFile);
    scanNumbers = scanSelection.getMatchingScanNumbers(dataFile);
    totalScans = scans.length;
    // Check if we have any scans
    if (totalScans == 0) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("No scans match the selected criteria");
        return;
    }
    // Check if the scans are properly ordered by RT
    double prevRT = Double.NEGATIVE_INFINITY;
    for (Scan s : scans) {
        if (s.getRetentionTime() < prevRT) {
            setStatus(TaskStatus.ERROR);
            final String msg = "Retention time of scan #" + s.getScanNumber() + " is smaller then the retention time of the previous scan." + " Please make sure you only use scans with increasing retention times." + " You can restrict the scan numbers in the parameters, or you can use the Crop filter module";
            setErrorMessage(msg);
            return;
        }
        prevRT = s.getRetentionTime();
    }
    // Create new feature list
    newPeakList = new SimplePeakList(dataFile + " " + suffix, dataFile);
    int j;
    // minimumTimeSpan
    Scan scan = scans[0];
    double minRT = scan.getRetentionTime();
    double maxRT = scan.getRetentionTime();
    retentiontime = new double[totalScans];
    int i;
    for (i = 0; i < totalScans; i++) {
        scan = scans[i];
        double irt = scan.getRetentionTime();
        if (irt < minRT)
            minRT = irt;
        if (irt > maxRT)
            maxRT = irt;
        retentiontime[i] = irt;
    }
    rtPerScan = (maxRT - minRT) / i;
    // "tolerable" units in scans
    tolScans = Math.max(2, (int) ((minimumTimeSpan / rtPerScan)));
    maxTolScans = Math.max(2, (int) ((maximumTimeSpan / rtPerScan)));
    // Algorithm to find masses:
    // (1) copy masses:intensity > threshold
    // (2) sort intensities descend
    // (3) Find "spot" for each intensity
    // (3.1) if they have not spot ID assigned
    // (3.1.1) Extend mass in mass and time while > 70% pixels > threshold
    // (3.1.2) If extension > mintime ==> mark all pixels with the spot ID
    // (3.1.3) if extension < mintime ==> mark all pixels with spot ID = -1
    // (4) Group spots within a time-tolerance and mass-tolerance
    logger.info("Getting data points on " + dataFile);
    roi = new Datum[totalScans][];
    ArrayList<Datum> roiAL = new ArrayList<Datum>();
    long passed = 0, nopassed = 0;
    minMasa = Double.MAX_VALUE;
    maxMasa = 0;
    int maxJ = 0;
    boolean[] scanOk = new boolean[totalScans];
    Arrays.fill(scanOk, true);
    logger.info("Smoothing data points on " + dataFile + " (Time min=" + smoothTimeSpan + "; Time m/z=" + smoothTimeMZ + ")");
    IndexedDataPoint[][] data = smoothDataPoints(dataFile, smoothTimeSpan, smoothTimeMZ, 0, smoothMZ, 0, minimumHeight);
    logger.info("Determining intensities (mass sum) per scan on " + dataFile);
    for (i = 0; i < totalScans; i++) {
        if (isCanceled())
            return;
        scan = scans[i];
        // scan.getDataPoints();
        IndexedDataPoint[] mzv = data[i];
        double prev = (mzv.length > 0 ? mzv[0].datapoint.getMZ() : 0);
        double massSum = 0;
        for (j = 0; j < mzv.length; j++) {
            if (mzv[j].datapoint.getIntensity() >= minimumHeight)
                massSum += mzv[j].datapoint.getMZ() - prev;
            prev = mzv[j].datapoint.getMZ();
            if (mzv[j].datapoint.getMZ() < minMasa)
                minMasa = mzv[j].datapoint.getMZ();
            if (mzv[j].datapoint.getMZ() > maxMasa)
                maxMasa = mzv[j].datapoint.getMZ();
        }
        double dm = 100.0 / (maxMasa - minMasa);
        if (i % 30 == 0 && debug > 0) {
            System.out.println("");
            System.out.print("t=" + Math.round(retentiontime[i] * 100) / 100.0 + ": (in %) ");
        }
        if (scanOk[i]) {
            if (!scanOk[i]) {
                // Disable neighbouring scans, how many ?
                for (j = i; j > 0 && retentiontime[j] + additionTimeMaxPeaksPerScan > retentiontime[i]; j--) {
                    scanOk[j] = false;
                }
                for (j = i; j < totalScans && retentiontime[j] - additionTimeMaxPeaksPerScan < retentiontime[i]; j++) {
                    scanOk[j] = false;
                }
            }
            if (debug > 0)
                System.out.print(((int) (massSum * dm)) + (scanOk[i] ? " " : "*** "));
        } else {
            if (debug > 0)
                System.out.print(((int) (massSum * dm)) + (scanOk[i] ? " " : "* "));
        }
        setProcedure(i, totalScans, 1);
    }
    if (debug > 0)
        System.out.println("");
    String[] it = ignoreTimes.trim().split(", ?");
    for (j = 0; j < it.length; j++) {
        String[] itj = it[j].split("-");
        if (itj.length == 2) {
            Double a = Double.parseDouble(itj[0].trim());
            Double b = Double.parseDouble(itj[1].trim());
            for (i = Math.abs(Arrays.binarySearch(retentiontime, a)); i < totalScans && retentiontime[i] <= b; i++) {
                if (retentiontime[i] >= a) {
                    scanOk[i] = false;
                }
            }
        }
    }
    passed = 0;
    nopassed = 0;
    for (i = 0; i < totalScans; i++) {
        if (i % 100 == 0 && isCanceled())
            return;
        if (scanOk[i]) {
            scan = scans[i];
            IndexedDataPoint[] mzv = data[i];
            DataPoint[] mzvOriginal = scan.getDataPoints();
            ArrayList<Datum> dal = new ArrayList<Datum>();
            for (j = 0; j < mzv.length; j++) {
                if (mzv[j].datapoint.getIntensity() >= minimumHeight) {
                    dal.add(new Datum(mzv[j].datapoint, i, mzvOriginal[mzv[j].index]));
                    passed++;
                } else {
                    nopassed++;
                }
            }
            if (j > maxJ)
                maxJ = j;
            roi[i] = dal.toArray(new Datum[0]);
            roiAL.addAll(dal);
        }
        setProcedure(i, totalScans, 2);
    }
    logger.info(passed + " intensities >= " + minimumHeight + " of " + (passed + nopassed) + " (" + Math.round(passed * 10000.0 / (double) (passed + nopassed)) / 100.0 + "%) on " + dataFile);
    // New "probing" algorithm
    // (1) Generate probes all over chromatograms
    // (2) Move each probe to their closest maximum until it cannot find a
    // new maximum
    // (3) assign spot id to each "center" using all points within region
    // (1) Generate probes all over
    double byMZ = Math.max(mzTol * 2, 1e-6);
    int byScan = Math.max(1, tolScans / 4);
    logger.info("Creating Grid of probes on " + dataFile + " every " + mzFormat.format(byMZ) + " m/z and " + byScan + " scans");
    double m;
    int ndata = (int) Math.round((((double) totalScans / (double) byScan) + 1) * ((maxMasa - minMasa + byMZ) / byMZ));
    Probe[] probes = new Probe[ndata];
    int idata = 0;
    for (i = 0; i < totalScans; i += byScan) {
        if (i % 100 == 0 && isCanceled())
            return;
        for (m = minMasa - (i % 2) * byMZ / 2; m <= maxMasa; m += byMZ) {
            probes[idata++] = new Probe(m, i);
        }
        setProcedure(i, totalScans, 3);
    }
    // (2) Move each probe to their closest center
    double mzR = byMZ / 2;
    int scanR = Math.max(byScan - 1, 2);
    logger.info("Finding local maxima for each probe on " + dataFile + " radius: scans=" + scanR + ", m/z=" + mzR);
    int okProbes = 0;
    for (i = 0; i < idata; i++) {
        if (i % 100 == 0 && isCanceled())
            return;
        moveProbeToCenter(probes[i], scanR, mzR);
        if (probes[i].intensityCenter < minimumHeight) {
            probes[i] = null;
        } else {
            okProbes++;
        }
        setProcedure(i, idata, 4);
    }
    if (okProbes > 0) {
        Probe[] pArr = new Probe[okProbes];
        for (okProbes = i = 0; i < idata; i++) {
            if (probes[i] != null) {
                pArr[okProbes++] = probes[i];
            }
        }
        probes = pArr;
        pArr = null;
    }
    // (3) Assign spot id to each "center"
    logger.info("Sorting probes " + dataFile);
    Arrays.sort(probes);
    logger.info("Assigning spot id to local maxima on " + dataFile);
    SpotByProbes sbp = new SpotByProbes();
    ArrayList<SpotByProbes> spots = new ArrayList<SpotByProbes>();
    double mzA = -1;
    int scanA = -1;
    for (i = 0; i < probes.length; i++) {
        if (probes[i] != null && probes[i].intensityCenter >= minimumHeight) {
            if (probes[i].mzCenter != mzA || probes[i].scanCenter != scanA) {
                if (i % 10 == 0 && isCanceled())
                    return;
                if (sbp.size() > 0) {
                    spots.add(sbp);
                    sbp.assignSpotId();
                // System.out.println(sbp.toString());
                }
                sbp = new SpotByProbes();
                mzA = probes[i].mzCenter;
                scanA = probes[i].scanCenter;
            }
            sbp.addProbe(probes[i]);
        }
        setProcedure(i, probes.length, 5);
    }
    if (sbp.size() > 0) {
        spots.add(sbp);
        sbp.assignSpotId();
    // System.out.println(sbp.toString());
    }
    logger.info("Spots:" + spots.size());
    // Assign specific datums to spots to avoid using datums to several
    // spots
    logger.info("Assigning intensities to local maxima on " + dataFile);
    i = 0;
    for (SpotByProbes sx : spots) {
        if (sx.size() > 0) {
            if (i % 100 == 0 && isCanceled())
                return;
            assignSpotIdToDatumsFromScans(sx, scanR, mzR);
        }
        setProcedure(i++, spots.size(), 6);
    }
    // (4) Join Tolerable Centers
    logger.info("Joining tolerable maxima on " + dataFile);
    int criticScans = Math.max(1, tolScans / 2);
    int joins = 0;
    for (i = 0; i < spots.size() - 1; i++) {
        SpotByProbes s1 = spots.get(i);
        if (s1.center != null && s1.size() > 0) {
            if (i % 100 == 0 && isCanceled())
                return;
            for (j = i; j > 0 && j < spots.size() && spots.get(j - 1).center != null && spots.get(j - 1).center.mzCenter + mzTol > s1.center.mzCenter; j--) ;
            for (; j < spots.size(); j++) {
                SpotByProbes s2 = spots.get(j);
                if (i != j && s2.center != null) {
                    if (s2.center.mzCenter - s1.center.mzCenter > mzTol)
                        break;
                    int l = Math.min(Math.abs(s1.minScan - s2.minScan), Math.abs(s1.minScan - s2.maxScan));
                    int r = Math.min(Math.abs(s1.maxScan - s2.minScan), Math.abs(s1.maxScan - s2.maxScan));
                    int d = Math.min(l, r);
                    boolean overlap = !(s2.maxScan < s1.minScan || s2.minScan > s1.maxScan);
                    if ((d <= criticScans || overlap) && (intensityRatio(s1.center.intensityCenter, s2.center.intensityCenter) > intensitySimilarity)) {
                        if (debug > 2)
                            System.out.println("Joining s1 id " + s1.spotId + "=" + mzFormat.format(s1.center.mzCenter) + " mz [" + mzFormat.format(s1.minMZ) + " ~ " + mzFormat.format(s1.maxMZ) + "] time=" + timeFormat.format(retentiontime[s1.center.scanCenter]) + " int=" + s1.center.intensityCenter + " with s2 id " + s2.spotId + "=" + mzFormat.format(s2.center.mzCenter) + " mz [" + mzFormat.format(s2.minMZ) + " ~ " + mzFormat.format(s2.maxMZ) + "] time=" + timeFormat.format(retentiontime[s2.center.scanCenter]) + " int=" + s2.center.intensityCenter);
                        assignSpotIdToDatumsFromSpotId(s1, s2, scanR, mzR);
                        s1.addProbesFromSpot(s2, true);
                        // restart
                        j = i;
                        joins++;
                    }
                // }
                }
            }
        }
        setProcedure(i, spots.size(), 7);
    }
    logger.info("Joins:" + joins);
    // (5) Remove "Large" spanned masses
    logger.info("Removing long and comparable 'masses' on " + dataFile);
    for (i = 0; i < spots.size() - 1; i++) {
        SpotByProbes s1 = spots.get(i);
        if (s1.center != null && s1.size() > 0) {
            if (i % 100 == 0 && isCanceled())
                return;
            int totalScans = s1.maxScan - s1.minScan + 1;
            int lScan = s1.minScan;
            int rScan = s1.maxScan;
            ArrayList<Integer> toRemove = new ArrayList<Integer>();
            toRemove.add(i);
            for (j = i; j > 0 && j < spots.size() && spots.get(j - 1).center != null && spots.get(j - 1).center.mzCenter + mzTol > s1.center.mzCenter; j--) ;
            for (; j < spots.size(); j++) {
                SpotByProbes s2 = spots.get(j);
                if (i != j && s2.center != null) {
                    if (s2.center.mzCenter - s1.center.mzCenter > mzTol)
                        break;
                    if (intensityRatio(s1.center.intensityCenter, s2.center.intensityCenter) > intensitySimilarity) {
                        int dl = Math.min(Math.abs(lScan - s2.minScan), Math.abs(lScan - s2.maxScan));
                        int dr = Math.min(Math.abs(rScan - s2.minScan), Math.abs(rScan - s2.maxScan));
                        int md = Math.min(dl, dr);
                        if (md <= maxTolScans || !(s2.maxScan < lScan || s2.minScan > rScan)) {
                            // distancia tolerable o intersectan
                            totalScans += s2.maxScan - s2.minScan + 1;
                            toRemove.add(j);
                            lScan = Math.min(lScan, s2.minScan);
                            rScan = Math.max(rScan, s2.maxScan);
                        }
                    }
                }
            }
            if (totalScans * rtPerScan > maximumTimeSpan) {
                if (debug > 2)
                    System.out.println("Removing " + toRemove.size() + " masses around " + mzFormat.format(s1.center.mzCenter) + " m/z (" + s1.spotId + "), time " + timeFormat.format(retentiontime[s1.center.scanCenter]) + ", intensity " + s1.center.intensityCenter + ", Total Scans=" + totalScans + " (" + Math.round(totalScans * rtPerScan * 1000.0) / 1000.0 + " min).");
                for (Integer J : toRemove) {
                    // System.out.println("Removing: "+spots.get(J).spotId);
                    spots.get(J).clear();
                }
            }
        }
        setProcedure(i, spots.size(), 8);
    }
    // Build peaks from assigned datums
    logger.info("Building peak rows on " + dataFile + " (tolereance scans=" + tolScans + ")");
    i = 0;
    for (SpotByProbes sx : spots) {
        if (sx.size() > 0 && sx.maxScan - sx.minScan + 1 >= tolScans) {
            if (i % 100 == 0 && isCanceled())
                return;
            sx.buildMaxDatumFromScans(roi, minimumHeight);
            if (sx.getMaxDatumScans() >= tolScans && (sx.getContigousMaxDatumScans() >= tolScans || sx.getContigousToMaxDatumScansRatio() > 0.5)) {
                Chromatogram peak = new Chromatogram(dataFile, scanNumbers);
                if (addMaxDatumFromScans(sx, peak) > 0) {
                    peak.finishChromatogram();
                    if (peak.getArea() > 1e-6) {
                        newPeakID++;
                        SimplePeakListRow newRow = new SimplePeakListRow(newPeakID);
                        newRow.addPeak(dataFile, peak);
                        newRow.setComment(sx.toString(retentiontime));
                        newPeakList.addRow(newRow);
                        if (debug > 0)
                            System.out.println("Peak added id=" + sx.spotId + " " + mzFormat.format(sx.center.mzCenter) + " mz, time=" + timeFormat.format(retentiontime[sx.center.scanCenter]) + ", intensity=" + sx.center.intensityCenter + ", probes=" + sx.size() + ", data scans=" + sx.getMaxDatumScans() + ", cont scans=" + sx.getContigousMaxDatumScans() + ", cont ratio=" + sx.getContigousToMaxDatumScansRatio() + " area = " + peak.getArea());
                        if (debug > 1) {
                            // Peak info:
                            System.out.println(sx.toString());
                            sx.printDebugInfo();
                        }
                    } else {
                        if (debug > 0)
                            System.out.println("Ignored by area ~ 0 id=" + sx.spotId + " " + mzFormat.format(sx.center.mzCenter) + " mz, time=" + timeFormat.format(retentiontime[sx.center.scanCenter]) + ", intensity=" + sx.center.intensityCenter + ", probes=" + sx.size() + ", data scans=" + sx.getMaxDatumScans() + ", cont scans=" + sx.getContigousMaxDatumScans() + ", cont ratio=" + sx.getContigousToMaxDatumScansRatio() + " area = " + peak.getArea());
                    }
                }
            } else {
                if (debug > 0)
                    System.out.println("Ignored by continous criteria: id=" + sx.spotId + " " + mzFormat.format(sx.center.mzCenter) + " mz, time=" + timeFormat.format(retentiontime[sx.center.scanCenter]) + ", intensity=" + sx.center.intensityCenter + ", probes=" + sx.size() + ", data scans=" + sx.getMaxDatumScans() + ", cont scans=" + sx.getContigousMaxDatumScans() + ", cont ratio=" + sx.getContigousToMaxDatumScansRatio());
            }
        } else {
            if (sx.size() > 0) {
                if (debug > 0)
                    System.out.println("Ignored by time range criteria: id=" + sx.spotId + " " + mzFormat.format(sx.center.mzCenter) + " mz, time=" + timeFormat.format(retentiontime[sx.center.scanCenter]) + ", intensity=" + sx.center.intensityCenter + ", probes=" + sx.size() + ", data scans=" + sx.getMaxDatumScans() + ", cont scans=" + sx.getContigousMaxDatumScans() + ", cont ratio=" + sx.getContigousToMaxDatumScansRatio());
            }
        }
        setProcedure(i++, spots.size(), 9);
    }
    logger.info("Peaks on " + dataFile + " = " + newPeakList.getNumberOfRows());
    // Add new peaklist to the project
    project.addPeakList(newPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(newPeakList);
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished chromatogram builder (RT) on " + dataFile);
}

Example 72 with DataPoint

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

the class GridMassTask method smoothDataPoints.

public IndexedDataPoint[][] smoothDataPoints(RawDataFile dataFile, double timeSpan, double timeMZSpan, int scanSpan, double mzTol, int mzPoints, double minimumHeight) {
    int[] scanNumbers = dataFile.getScanNumbers(1);
    int totalScans = scanNumbers.length;
    // [relative scan][j value]
    DataPoint[][] mzValues = null;
    DataPoint[] mzValuesJ = null;
    int[] mzValuesScan = null;
    int[] mzValuesMZidx = null;
    IndexedDataPoint[][] newMZValues = null;
    IndexedDataPoint[] tmpDP = new IndexedDataPoint[0];
    newMZValues = new IndexedDataPoint[totalScans][];
    int i, j, si, sj, ii, k, ssi, ssj, m;
    double timeSmoothingMZtol = Math.max(timeMZSpan, 1e-6);
    int modts = Math.max(1, totalScans / 10);
    for (i = 0; i < totalScans; i++) {
        if (i % 100 == 0 && isCanceled())
            return null;
        // Smoothing in TIME space
        Scan scan = dataFile.getScan(scanNumbers[i]);
        double rt = retentiontime[i];
        DataPoint[] xDP = null;
        IndexedDataPoint[] iDP = null;
        sj = si = i;
        ssi = ssj = i;
        int t = 0;
        if (timeSpan > 0 || scanSpan > 0) {
            if (scan != null) {
                for (si = i; si > 1; si--) {
                    if (retentiontime[si - 1] < rt - timeSpan / 2) {
                        break;
                    }
                }
                for (sj = i; sj < totalScans - 1; sj++) {
                    if (retentiontime[sj + 1] >= 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;
                }
            }
            if (scan != null && sj > si) {
                // Allocate
                if (mzValues == null || mzValues.length < sj - si + 1) {
                    mzValues = new DataPoint[sj - si + 1][];
                    mzValuesScan = new int[sj - si + 1];
                    mzValuesMZidx = new int[sj - si + 1];
                }
                // Load Data Points
                for (j = si; j <= sj; j++) {
                    int jsi = j - si;
                    if (mzValues[jsi] == null || jsi >= mzValuesScan.length - 1 || mzValuesScan[jsi + 1] != scanNumbers[j]) {
                        Scan xscan = dataFile.getScan(scanNumbers[j]);
                        mzValues[jsi] = xscan.getDataPoints();
                        mzValuesScan[jsi] = scanNumbers[j];
                    } else {
                        mzValues[jsi] = mzValues[jsi + 1];
                        mzValuesScan[jsi] = mzValuesScan[jsi + 1];
                    }
                    mzValuesMZidx[jsi] = 0;
                }
                // Estimate Averages
                ii = i - si;
                if (tmpDP.length < mzValues[ii].length)
                    tmpDP = new IndexedDataPoint[mzValues[ii].length * 3 / 2];
                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 <= sj - si; j++) {
                            for (mzValuesJ = mzValues[j]; mzValuesMZidx[j] < mzValuesJ.length - 1 && mzValuesJ[mzValuesMZidx[j] + 1].getMZ() < mz - timeSmoothingMZtol; mzValuesMZidx[j]++) ;
                            f = mzValuesMZidx[j];
                            for (m = mzValuesMZidx[j] + 1; m < mzValuesJ.length && mzValuesJ[m].getMZ() < mz + timeSmoothingMZtol; m++) {
                                if (Math.abs(mzValuesJ[m].getMZ() - mz) < Math.abs(mzValuesJ[f].getMZ() - mz)) {
                                    f = m;
                                } else {
                                    // parar la búsqueda
                                    break;
                                }
                            }
                            if (f > 0 && f < mzValuesJ.length && Math.abs(mzValuesJ[f].getMZ() - mz) <= timeSmoothingMZtol && mzValuesJ[f].getIntensity() > 0) {
                                // >=
                                // minimumHeight
                                // ?
                                // System.out.println("mz="+mz+"; Closer="+mzValuesJ[f].getMZ()+", f="+f+",
                                // Intensity="+mzValuesJ[f].getIntensity());
                                a += mzValuesJ[f].getIntensity();
                                c++;
                            }
                        }
                        intensidad = c > 0 ? a / c : 0;
                        if (intensidad >= minimumHeight) {
                            tmpDP[t++] = new IndexedDataPoint(k, new SimpleDataPoint(mz, intensidad));
                        }
                    }
                }
            }
        } else if (scan != null) {
            xDP = scan.getDataPoints();
            if (tmpDP.length < xDP.length)
                tmpDP = new IndexedDataPoint[xDP.length];
            for (k = 0; k < xDP.length; k++) {
                if (xDP[k].getIntensity() >= minimumHeight) {
                    tmpDP[t++] = new IndexedDataPoint(k, xDP[k]);
                }
            }
        }
        iDP = new IndexedDataPoint[t];
        for (k = 0; k < t; k++) {
            iDP[k] = tmpDP[k];
        }
        newMZValues[i] = iDP;
        setProcedure(i, totalScans, 0);
        if (i % modts == 0) {
            logger.info("Smoothing/Caching " + dataFile + "..." + (i / modts) * 10 + "%");
        }
    }
    return newMZValues;
}

Example 73 with DataPoint

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

the class GridMassTask method massCenter.

double[] massCenter(int l, int r, double min, double max) {
    double x = 0;
    double y = 0;
    double sum = 0;
    double maxValue = 0;
    for (int i = l; i <= r; i++) {
        DataPoint[] mzs = getCachedDataPoints(scans[i].getScanNumber());
        if (mzs != null) {
            for (int j = findFirstMass(min, mzs); j < mzs.length; j++) {
                double mass = mzs[j].getMZ();
                if (mass >= min) {
                    if (mass <= max) {
                        double intensity = mzs[j].getIntensity();
                        if (intensity >= minimumHeight) {
                            x += i * intensity;
                            y += mass * intensity;
                            sum += intensity;
                            if (intensity > maxValue) {
                                maxValue = intensity;
                            }
                        }
                    } else {
                        break;
                    }
                }
            }
        }
    }
    if (sum > 0.0) {
        x /= sum;
        y /= sum;
    }
    return new double[] { x, y, maxValue };
}

Example 74 with DataPoint

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

the class GridMassTask method findFirstMass.

static int findFirstMass(double mass, DataPoint[] mzValues) {
    int l = 0;
    int r = mzValues.length - 1;
    int mid = 0;
    while (l < r) {
        mid = (r + l) / 2;
        if (mzValues[mid].getMZ() > mass) {
            r = mid - 1;
        } else if (mzValues[mid].getMZ() < mass) {
            l = mid + 1;
        } else {
            return mid;
        }
    }
    while (l > 0 && mzValues[l].getMZ() > mass) l--;
    return l;
}

Example 75 with DataPoint

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

the class CsvReadTask method run.

@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    Scanner scanner;
    logger.setLevel(Level.ALL);
    try {
        scanner = new Scanner(file);
        dataSource = getFileName(scanner);
        if (dataSource == null) {
            setErrorMessage("Could not open data file " + file.getAbsolutePath());
            setStatus(TaskStatus.ERROR);
            return;
        }
        logger.info("opening raw file " + dataSource);
        String acquisitionDate = getAcqusitionDate(scanner);
        if (acquisitionDate == null) {
            setErrorMessage("Could not find acquisition date in file " + file.getAbsolutePath());
            setStatus(TaskStatus.ERROR);
            return;
        }
        logger.info("Date of acquisition " + acquisitionDate);
        // scanner.useDelimiter(",");
        List<String> mzsList = new ArrayList<String>();
        String mstype = "";
        String ions = "";
        while (scanner.hasNextLine()) {
            String line = scanner.nextLine();
            logger.fine("checking line: " + line + " for 'Time'...");
            if (line.startsWith("Time")) {
                String[] axes = line.split(",");
                logger.fine("Found axes" + Arrays.toString(axes));
                for (int i = 1; i < axes.length; i++) {
                    String axis = axes[i];
                    ions += axis + ", ";
                    if (axis.contains("->")) {
                        mstype = "MS/MS";
                        logger.fine("axis " + axis + " is an ms^2 scan");
                        String mz = axis.substring(axis.indexOf("-> ") + 3);
                        mz.trim();
                        logger.fine("Axis " + axis + " was scanned at m/z = '" + mz + "'");
                        mzsList.add(mz);
                    } else {
                        String mz = axis.replaceAll("[^0-9]", "");
                        logger.fine("axis " + axis + " was scanned at " + mz);
                        mzsList.add(mz);
                    }
                }
                break;
            }
        }
        int[] mzs = new int[mzsList.size()];
        for (int i = 0; i < mzsList.size(); i++) mzs[i] = Integer.valueOf(mzsList.get(i));
        Range<Double> mzRange = Range.closed((double) mzs[0] - 10, (double) mzs[1] + 10);
        int scanNumber = 1;
        while (scanner.hasNextLine()) {
            String line = scanner.nextLine();
            if (line == null || line.trim().equals(""))
                continue;
            String[] columns = line.split(",");
            if (columns == null || columns.length != mzs.length + 1)
                continue;
            double rt = Double.valueOf(columns[0]) / 60;
            DataPoint[] dataPoints = new SimpleDataPoint[mzs.length];
            for (int i = 0; i < dataPoints.length; i++) {
                String intensity = columns[i + 1];
                dataPoints[i] = new SimpleDataPoint(mzs[i], Double.valueOf(intensity));
            }
            Scan scan = new SimpleScan(null, scanNumber, 1, rt, 0.0, 1, null, dataPoints, MassSpectrumType.CENTROIDED, PolarityType.POSITIVE, "ICP-" + mstype + " " + ions.substring(0, ions.length() - 2), mzRange);
            newMZmineFile.addScan(scan);
            scanNumber++;
        }
        finalRawDataFile = newMZmineFile.finishWriting();
        project.addFile(finalRawDataFile);
    } catch (Exception e) {
        setErrorMessage(e.getMessage());
        setStatus(TaskStatus.ERROR);
        return;
    }
    this.setStatus(TaskStatus.FINISHED);
}