Examples with CDA jmprojection.CDA used on opensource projects

Example 1 with CDA

use of jmprojection.CDA in project mzmine2 by mzmine.

the class CDADataset method run.

@Override
public void run() {
    status = TaskStatus.PROCESSING;
    if (selectedRows.length == 0) {
        this.status = TaskStatus.ERROR;
        errorMessage = "No peaks selected for CDA plot";
        return;
    }
    if (selectedRawDataFiles.length == 0) {
        this.status = TaskStatus.ERROR;
        errorMessage = "No raw data files selected for CDA plot";
        return;
    }
    logger.info("Computing projection plot");
    // Generate matrix of raw data (input to CDA)
    boolean useArea = false;
    if (parameters.getParameter(ProjectionPlotParameters.peakMeasurementType).getValue() == PeakMeasurementType.AREA)
        useArea = true;
    double[][] rawData = new double[selectedRawDataFiles.length][selectedRows.length];
    for (int rowIndex = 0; rowIndex < selectedRows.length; rowIndex++) {
        PeakListRow peakListRow = selectedRows[rowIndex];
        for (int fileIndex = 0; fileIndex < selectedRawDataFiles.length; fileIndex++) {
            RawDataFile rawDataFile = selectedRawDataFiles[fileIndex];
            Feature p = peakListRow.getPeak(rawDataFile);
            if (p != null) {
                if (useArea)
                    rawData[fileIndex][rowIndex] = p.getArea();
                else
                    rawData[fileIndex][rowIndex] = p.getHeight();
            }
        }
    }
    int numComponents = xAxisDimension;
    if (yAxisDimension > numComponents)
        numComponents = yAxisDimension;
    // Scale data and do CDA
    Preprocess.scaleToUnityVariance(rawData);
    CDA cdaProj = new CDA(rawData);
    cdaProj.iterate(100);
    if (status == TaskStatus.CANCELED)
        return;
    double[][] result = cdaProj.getState();
    if (status == TaskStatus.CANCELED)
        return;
    component1Coords = result[xAxisDimension - 1];
    component2Coords = result[yAxisDimension - 1];
    ProjectionPlotWindow newFrame = new ProjectionPlotWindow(peakList, this, parameters);
    newFrame.setVisible(true);
    status = TaskStatus.FINISHED;
    logger.info("Finished computing projection plot.");
}