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

Example 11 with SimpleScan

use of net.sf.mzmine.datamodel.impl.SimpleScan 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);
}

Example 12 with SimpleScan

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

the class MeanFilter method filterScan.

@Override
public Scan filterScan(Scan sc, ParameterSet parameters) {
    double windowLength = parameters.getParameter(MeanFilterParameters.oneSidedWindowLength).getValue();
    // changed to also allow MS2 if selected in ScanSelection
    Vector<Double> massWindow = new Vector<Double>();
    Vector<Double> intensityWindow = new Vector<Double>();
    double currentMass;
    double lowLimit;
    double hiLimit;
    double mzVal;
    double elSum;
    DataPoint[] oldDataPoints = sc.getDataPoints();
    DataPoint[] newDataPoints = new DataPoint[oldDataPoints.length];
    int addi = 0;
    for (int i = 0; i < oldDataPoints.length; i++) {
        currentMass = oldDataPoints[i].getMZ();
        lowLimit = currentMass - windowLength;
        hiLimit = currentMass + windowLength;
        // low limit
        if (massWindow.size() > 0) {
            mzVal = massWindow.get(0).doubleValue();
            while ((massWindow.size() > 0) && (mzVal < lowLimit)) {
                massWindow.remove(0);
                intensityWindow.remove(0);
                if (massWindow.size() > 0) {
                    mzVal = massWindow.get(0).doubleValue();
                }
            }
        }
        // limit
        while ((addi < oldDataPoints.length) && (oldDataPoints[addi].getMZ() <= hiLimit)) {
            massWindow.add(oldDataPoints[addi].getMZ());
            intensityWindow.add(oldDataPoints[addi].getIntensity());
            addi++;
        }
        elSum = 0;
        for (int j = 0; j < intensityWindow.size(); j++) {
            elSum += (intensityWindow.get(j)).doubleValue();
        }
        newDataPoints[i] = new SimpleDataPoint(currentMass, elSum / intensityWindow.size());
    }
    // Create filtered scan
    Scan newScan = new SimpleScan(sc.getDataFile(), sc.getScanNumber(), sc.getMSLevel(), sc.getRetentionTime(), sc.getPrecursorMZ(), sc.getPrecursorCharge(), sc.getFragmentScanNumbers(), newDataPoints, MassSpectrumType.CENTROIDED, sc.getPolarity(), sc.getScanDefinition(), sc.getScanningMZRange());
    return newScan;
}

Example 13 with SimpleScan

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

the class ResampleFilter method filterScan.

public Scan filterScan(Scan scan, ParameterSet parameters) {
    double binSize = parameters.getParameter(ResampleFilterParameters.binSize).getValue();
    Range<Double> mzRange = scan.getDataPointMZRange();
    int numberOfBins = (int) Math.round((mzRange.upperEndpoint() - mzRange.lowerEndpoint()) / binSize);
    if (numberOfBins == 0) {
        numberOfBins++;
    }
    // ScanUtils.binValues needs arrays
    DataPoint[] dps = scan.getDataPoints();
    double[] x = new double[dps.length];
    double[] y = new double[dps.length];
    for (int i = 0; i < dps.length; i++) {
        x[i] = dps[i].getMZ();
        y[i] = dps[i].getIntensity();
    }
    // the new intensity values
    double[] newY = ScanUtils.binValues(x, y, mzRange, numberOfBins, scan.getSpectrumType() == MassSpectrumType.PROFILE, ScanUtils.BinningType.AVG);
    SimpleDataPoint[] newPoints = new SimpleDataPoint[newY.length];
    // set the new m/z value in the middle of the bin
    double newX = mzRange.lowerEndpoint() + binSize / 2.0;
    // creates new DataPoints
    for (int i = 0; i < newY.length; i++) {
        newPoints[i] = new SimpleDataPoint(newX, newY[i]);
        newX += binSize;
    }
    // Create updated scan
    SimpleScan newScan = new SimpleScan(scan);
    newScan.setDataPoints(newPoints);
    newScan.setSpectrumType(MassSpectrumType.CENTROIDED);
    return newScan;
}

Example 14 with SimpleScan

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

the class LocMaxCentroidingAlgorithm method centroidScan.

public Scan centroidScan() {
    // Copy all scan properties
    this.newScan = new SimpleScan(inputScan);
    // Load data points
    for (int i = 0; i < dataPoints.length; ++i) {
        mzBuffer[i] = dataPoints[i].getMZ();
        intensityBuffer[i] = dataPoints[i].getIntensity();
    }
    final int numOfDataPoints = inputScan.getNumberOfDataPoints();
    int newNumOfDataPoints = 0;
    // If there are no data points, just return the scan
    ArrayList<DataPoint> newDataPoints = new ArrayList<DataPoint>();
    if (numOfDataPoints == 0) {
        for (int i = 0; i < numOfDataPoints; ++i) {
            newDataPoints.add(new SimpleDataPoint(mzBuffer[i], intensityBuffer[i]));
        }
        newScan.setDataPoints(newDataPoints.toArray(new SimpleDataPoint[newDataPoints.size()]));
        newScan.setSpectrumType(MassSpectrumType.CENTROIDED);
        return newScan;
    }
    int localMaximumIndex = 0;
    int rangeBeginning = 0, rangeEnd;
    boolean ascending = true;
    // Iterate through all data points
    for (int i = 0; i < numOfDataPoints - 1; i++) {
        final boolean nextIsBigger = intensityBuffer[i + 1] > intensityBuffer[i];
        final boolean nextIsZero = intensityBuffer[i + 1] == 0f;
        final boolean currentIsZero = intensityBuffer[i] == 0f;
        // Ignore zero intensity regions
        if (currentIsZero) {
            continue;
        }
        // Add current (non-zero) data point to the current m/z peak
        rangeEnd = i;
        // Check for local maximum
        if (ascending && (!nextIsBigger)) {
            localMaximumIndex = i;
            ascending = false;
            continue;
        }
        // Check for the end of the peak
        if ((!ascending) && (nextIsBigger || nextIsZero)) {
            final int numOfPeakDataPoints = rangeEnd - rangeBeginning;
            // Add the m/z peak if it has at least 4 data points
            if (numOfPeakDataPoints >= 4) {
                // Add the new data point
                mzBuffer[newNumOfDataPoints] = mzBuffer[localMaximumIndex];
                intensityBuffer[newNumOfDataPoints] = intensityBuffer[localMaximumIndex];
                newNumOfDataPoints++;
            }
            // Reset and start with new peak
            ascending = true;
            rangeBeginning = i;
        }
    }
    // Store the new data points
    for (int i = 0; i < newNumOfDataPoints; ++i) {
        newDataPoints.add(new SimpleDataPoint(mzBuffer[i], intensityBuffer[i]));
    }
    newScan.setDataPoints(newDataPoints.toArray(new SimpleDataPoint[newDataPoints.size()]));
    newScan.setSpectrumType(MassSpectrumType.CENTROIDED);
    return newScan;
}

Example 15 with SimpleScan

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

the class RawFileMergeTask method run.

@Override
public void run() {
    try {
        setStatus(TaskStatus.PROCESSING);
        // total number of scans
        StringBuilder s = new StringBuilder();
        s.append("Merge files: ");
        for (RawDataFile r : raw) {
            s.append(r.getName());
            s.append(", ");
        }
        LOG.info(s.toString());
        // put all in a list and sort by rt
        List<Scan> scans = new ArrayList<>();
        for (RawDataFile r : raw) {
            // some files are only for MS2
            boolean isMS2Only = useMS2Marker && r.getName().contains(ms2Marker);
            int[] snarray = r.getScanNumbers();
            for (int sn : snarray) {
                if (isCanceled())
                    return;
                Scan scan = r.getScan(sn);
                if (!isMS2Only || scan.getMSLevel() > 1) {
                    scans.add(scan);
                }
            }
        }
        // sort by rt
        scans.sort(new Comparator<Scan>() {

            @Override
            public int compare(Scan a, Scan b) {
                return Double.compare(a.getRetentionTime(), b.getRetentionTime());
            }
        });
        // create new file
        RawDataFileWriter rawDataFileWriter = MZmineCore.createNewFile(raw[0].getName() + " " + suffix);
        int i = 0;
        for (Scan scan : scans) {
            if (isCanceled())
                return;
            // copy, reset scan number
            SimpleScan scanCopy = new SimpleScan(scan);
            scanCopy.setScanNumber(i);
            rawDataFileWriter.addScan(scanCopy);
            i++;
        }
        RawDataFile filteredRawDataFile = rawDataFileWriter.finishWriting();
        project.addFile(filteredRawDataFile);
        if (getStatus() == TaskStatus.PROCESSING)
            setStatus(TaskStatus.FINISHED);
    } catch (IOException e) {
        throw new MSDKRuntimeException(e);
    }
}