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

Example 36 with DataPoint

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

the class RndResampleFilter method filterScan.

public Scan filterScan(Scan scan, ParameterSet parameters) {
    boolean sum_duplicates = parameters.getParameter(RndResampleFilterParameters.SUM_DUPLICATES).getValue();
    boolean remove_zero_intensity = parameters.getParameter(RndResampleFilterParameters.REMOVE_ZERO_INTENSITY).getValue();
    // If CENTROIDED scan, use it as-is
    Scan inputScan;
    if (scan.getSpectrumType() == MassSpectrumType.CENTROIDED)
        inputScan = scan;
    else
        // Otherwise, detect local maxima
        inputScan = new LocMaxCentroidingAlgorithm(scan).centroidScan();
    DataPoint[] dps = inputScan.getDataPoints();
    // Cleanup first: Remove zero intensity data points (if requested)
    // Reuse dps array
    int newNumOfDataPoints = 0;
    for (int i = 0; i < dps.length; ++i) {
        if (!remove_zero_intensity || dps[i].getIntensity() > 0.0) {
            dps[newNumOfDataPoints] = dps[i];
            ++newNumOfDataPoints;
        }
    }
    // Getting started
    SimpleDataPoint[] newDps = new SimpleDataPoint[newNumOfDataPoints];
    for (int i = 0; i < newNumOfDataPoints; ++i) {
        // Set the new m/z value to nearest integer / unit value
        int newMz = (int) Math.round(dps[i].getMZ());
        // Create new DataPoint accordingly (intensity untouched)
        newDps[i] = new SimpleDataPoint(newMz, dps[i].getIntensity());
    }
    // Post-treatments
    // Cleanup: Merge duplicates/overlap
    // ArrayList<SimpleDataPoint> dpsList = new
    // ArrayList<SimpleDataPoint>();
    double prevMz = -1.0, curMz = -1.0;
    double newIntensity = 0.0;
    double divider = 1.0;
    // Reuse dps array
    newNumOfDataPoints = 0;
    for (int i = 0; i < newDps.length; ++i) {
        curMz = newDps[i].getMZ();
        if (i > 0) {
            // Handle duplicates
            if (curMz == prevMz) {
                if (sum_duplicates) {
                    // Use sum
                    newIntensity += newDps[i].getIntensity();
                    dps[newNumOfDataPoints - 1] = new SimpleDataPoint(prevMz, newIntensity);
                } else {
                    // Use average
                    newIntensity += newDps[i].getIntensity();
                    dps[newNumOfDataPoints - 1] = new SimpleDataPoint(prevMz, newIntensity);
                    divider += 1.0;
                }
            } else {
                dps[newNumOfDataPoints - 1] = new SimpleDataPoint(prevMz, newIntensity / divider);
                dps[newNumOfDataPoints] = newDps[i];
                ++newNumOfDataPoints;
                newIntensity = dps[newNumOfDataPoints - 1].getIntensity();
                divider = 1.0;
            }
        } else {
            dps[newNumOfDataPoints] = newDps[i];
            ++newNumOfDataPoints;
        }
        prevMz = newDps[i].getMZ();
    }
    // Create updated scan
    SimpleScan newScan = new SimpleScan(inputScan);
    newScan.setDataPoints(Arrays.copyOfRange(dps, 0, newNumOfDataPoints));
    newScan.setSpectrumType(MassSpectrumType.CENTROIDED);
    return newScan;
}

Example 37 with DataPoint

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

the class SGFilter method filterScan.

@Override
public Scan filterScan(Scan scan, ParameterSet parameters) {
    int numOfDataPoints = parameters.getParameter(SGFilterParameters.datapoints).getValue();
    assert Avalues.containsKey(numOfDataPoints);
    assert Hvalues.containsKey(numOfDataPoints);
    int[] aVals = Avalues.get(numOfDataPoints);
    int h = Hvalues.get(numOfDataPoints).intValue();
    // changed to also allow MS2 if selected in ScanSelection
    int marginSize = (numOfDataPoints + 1) / 2 - 1;
    double sumOfInts;
    DataPoint[] oldDataPoints = scan.getDataPoints();
    int newDataPointsLength = oldDataPoints.length - (marginSize * 2);
    // only process scans with datapoints
    if (newDataPointsLength < 1) {
        return scan;
    }
    DataPoint[] newDataPoints = new DataPoint[newDataPointsLength];
    for (int spectrumInd = marginSize; spectrumInd < (oldDataPoints.length - marginSize); spectrumInd++) {
        // zero intensity data points must be left unchanged
        if (oldDataPoints[spectrumInd].getIntensity() == 0) {
            newDataPoints[spectrumInd - marginSize] = oldDataPoints[spectrumInd];
            continue;
        }
        sumOfInts = aVals[0] * oldDataPoints[spectrumInd].getIntensity();
        for (int windowInd = 1; windowInd <= marginSize; windowInd++) {
            sumOfInts += aVals[windowInd] * (oldDataPoints[spectrumInd + windowInd].getIntensity() + oldDataPoints[spectrumInd - windowInd].getIntensity());
        }
        sumOfInts = sumOfInts / h;
        if (sumOfInts < 0) {
            sumOfInts = 0;
        }
        newDataPoints[spectrumInd - marginSize] = new SimpleDataPoint(oldDataPoints[spectrumInd].getMZ(), sumOfInts);
    }
    SimpleScan newScan = new SimpleScan(scan);
    newScan.setDataPoints(newDataPoints);
    return newScan;
}

Example 38 with DataPoint

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

the class CropFilterTask method run.

/**
 * @see Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started crop filter on " + dataFile);
    scans = scanSelection.getMatchingScans(dataFile);
    totalScans = scans.length;
    // Check if we have any scans
    if (totalScans == 0) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("No scans match the selected criteria");
        return;
    }
    try {
        RawDataFileWriter rawDataFileWriter = MZmineCore.createNewFile(dataFile.getName() + " " + suffix);
        for (Scan scan : scans) {
            SimpleScan scanCopy = new SimpleScan(scan);
            // Check if we have something to crop
            if (!mzRange.encloses(scan.getDataPointMZRange())) {
                DataPoint[] croppedDataPoints = scan.getDataPointsByMass(mzRange);
                scanCopy.setDataPoints(croppedDataPoints);
            }
            rawDataFileWriter.addScan(scanCopy);
            processedScans++;
        }
        RawDataFile filteredRawDataFile = rawDataFileWriter.finishWriting();
        project.addFile(filteredRawDataFile);
        // Remove the original file if requested
        if (removeOriginal) {
            project.removeFile(dataFile);
        }
        setStatus(TaskStatus.FINISHED);
    } catch (Exception e) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage(e.toString());
        e.printStackTrace();
    }
}

Example 39 with DataPoint

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

the class DPPResultsLabelGenerator method generateLabel.

/**
 * @see org.jfree.chart.labels.XYItemLabelGenerator#generateLabel(org.jfree.data.xy.XYDataset,
 *      int, int)
 */
public String generateLabel(XYDataset dataset, int series, int item) {
    // X and Y values of current data point
    double originalX = dataset.getX(series, item).doubleValue();
    double originalY = dataset.getY(series, item).doubleValue();
    // Calculate data size of 1 screen pixel
    double xLength = (double) plot.getXYPlot().getDomainAxis().getRange().getLength();
    double pixelX = xLength / plot.getWidth();
    // Size of data set
    int itemCount = dataset.getItemCount(series);
    // Search for data points higher than this one in the interval
    // from limitLeft to limitRight
    double limitLeft = originalX - ((POINTS_RESERVE_X / 2) * pixelX);
    double limitRight = originalX + ((POINTS_RESERVE_X / 2) * pixelX);
    // Iterate data points to the left and right
    for (int i = 1; (item - i > 0) || (item + i < itemCount); i++) {
        // If we get out of the limit we can stop searching
        if ((item - i > 0) && (dataset.getXValue(series, item - i) < limitLeft) && ((item + i >= itemCount) || (dataset.getXValue(series, item + i) > limitRight)))
            break;
        if ((item + i < itemCount) && (dataset.getXValue(series, item + i) > limitRight) && ((item - i <= 0) || (dataset.getXValue(series, item - i) < limitLeft)))
            break;
        // If we find higher data point, bail out
        if ((item - i > 0) && (originalY <= dataset.getYValue(series, item - i)))
            return null;
        if ((item + i < itemCount) && (originalY <= dataset.getYValue(series, item + i)))
            return null;
    }
    // Create label
    String label = null;
    if (dataset instanceof ScanDataSet) {
        label = ((ScanDataSet) dataset).getAnnotation(item);
    } else if (dataset instanceof DPPResultsDataSet) {
        DataPoint[] dps = ((DPPResultsDataSet) dataset).getDataPoints();
        if (dps[item] instanceof ProcessedDataPoint) {
            ProcessedDataPoint p = (ProcessedDataPoint) dps[item];
            label = createLabel(p);
        }
    }
    if (label == null || label.equals("")) {
        double mzValue = dataset.getXValue(series, item);
        label = mzFormat.format(mzValue);
    }
    return label;
}

Example 40 with DataPoint

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

the class MirrorScanWindow method setScans.

/**
 * Based on a data base match to a spectral library
 *
 * @param row
 * @param db
 */
public void setScans(SpectralDBPeakIdentity db) {
    Scan scan = db.getQueryScan();
    if (scan == null)
        return;
    // get highest data intensity to calc relative intensity
    double mostIntenseQuery = Arrays.stream(db.getQueryDataPoints(DataPointsTag.ORIGINAL)).mapToDouble(DataPoint::getIntensity).max().orElse(0d);
    double mostIntenseDB = Arrays.stream(db.getLibraryDataPoints(DataPointsTag.ORIGINAL)).mapToDouble(DataPoint::getIntensity).max().orElse(0d);
    if (mostIntenseDB == 0d)
        logger.warning("This data set has no original data points in the library spectrum (development error)");
    if (mostIntenseQuery == 0d)
        logger.warning("This data set has no original data points in the query spectrum (development error)");
    if (mostIntenseDB == 0d || mostIntenseQuery == 0d)
        return;
    // get colors for vision
    Vision vision = MZmineCore.getConfiguration().getColorVision();
    // colors for the different DataPointsTags:
    final Color[] colors = new Color[] { // black = filtered
    Color.black, // unaligned
    ColorPalettes.getNegativeColor(vision), // aligned
    ColorPalettes.getPositiveColor(vision) };
    // scan a
    double precursorMZA = scan.getPrecursorMZ();
    double rtA = scan.getRetentionTime();
    Double precursorMZB = db.getEntry().getPrecursorMZ();
    Double rtB = (Double) db.getEntry().getField(DBEntryField.RT).orElse(0d);
    contentPane.removeAll();
    // create without data
    mirrorSpecrumPlot = SpectrumChartFactory.createMirrorChartPanel("Query: " + scan.getScanDefinition(), precursorMZA, rtA, null, "Library: " + db.getName(), precursorMZB == null ? 0 : precursorMZB, rtB, null, false, true);
    mirrorSpecrumPlot.setMaximumDrawWidth(4200);
    mirrorSpecrumPlot.setMaximumDrawHeight(2500);
    // add data
    DataPoint[][] query = new DataPoint[tags.length][];
    DataPoint[][] library = new DataPoint[tags.length][];
    for (int i = 0; i < tags.length; i++) {
        DataPointsTag tag = tags[i];
        query[i] = db.getQueryDataPoints(tag);
        library[i] = db.getLibraryDataPoints(tag);
    }
    // add datasets and renderer
    // set up renderer
    CombinedDomainXYPlot domainPlot = (CombinedDomainXYPlot) mirrorSpecrumPlot.getChart().getXYPlot();
    NumberAxis axis = (NumberAxis) domainPlot.getDomainAxis();
    axis.setLabel("m/z");
    XYPlot queryPlot = (XYPlot) domainPlot.getSubplots().get(0);
    XYPlot libraryPlot = (XYPlot) domainPlot.getSubplots().get(1);
    // add all datapoints to a dataset that are not present in subsequent masslist
    for (int i = 0; i < tags.length; i++) {
        DataPointsTag tag = tags[i];
        PseudoSpectrumDataSet qdata = new PseudoSpectrumDataSet(true, "Query " + tag.toRemainderString());
        for (DataPoint dp : query[i]) {
            // not contained in other
            if (notInSubsequentMassList(dp, query, i) && mostIntenseQuery > 0)
                qdata.addDP(dp.getMZ(), dp.getIntensity() / mostIntenseQuery * 100d, null);
        }
        PseudoSpectrumDataSet ldata = new PseudoSpectrumDataSet(true, "Library " + tag.toRemainderString());
        for (DataPoint dp : library[i]) {
            if (notInSubsequentMassList(dp, library, i) && mostIntenseDB > 0)
                ldata.addDP(dp.getMZ(), dp.getIntensity() / mostIntenseDB * 100d, null);
        }
        Color color = colors[i];
        PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(color, false);
        PseudoSpectraRenderer renderer2 = new PseudoSpectraRenderer(color, false);
        queryPlot.setDataset(i, qdata);
        queryPlot.setRenderer(i, renderer);
        libraryPlot.setDataset(i, ldata);
        libraryPlot.setRenderer(i, renderer2);
    }
    // add legend
    LegendItem item;
    LegendItemCollection collection = new LegendItemCollection();
    for (int i = 0; i < tags.length; i++) {
        item = new LegendItem(tags[i].toRemainderString(), colors[i]);
        collection.add(item);
    }
    mirrorSpecrumPlot.getChart().removeLegend();
    LegendTitle legend = new LegendTitle(() -> collection);
    legend.setPosition(RectangleEdge.BOTTOM);
    mirrorSpecrumPlot.getChart().addLegend(legend);
    // set y axis title
    queryPlot.getRangeAxis().setLabel("rel. intensity [%] (query)");
    libraryPlot.getRangeAxis().setLabel("rel. intensity [%] (library)");
    contentPane.add(mirrorSpecrumPlot, BorderLayout.CENTER);
    contentPane.revalidate();
    contentPane.repaint();
}