Examples with NetcdfFileWriter ucar.nc2.NetcdfFileWriter used on opensource projects

Example 1 with NetcdfFileWriter

use of ucar.nc2.NetcdfFileWriter in project mzmine2 by mzmine.

the class MassDetectionTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    // make arrays to contain everything you need
    ArrayList<Integer> pointsInScans = new ArrayList<>();
    ArrayList<Double> allMZ = new ArrayList<>();
    ArrayList<Double> allIntensities = new ArrayList<>();
    // idecies of full mass list where scan starts?
    ArrayList<Integer> startIndex = new ArrayList<>();
    ArrayList<Double> scanAcquisitionTime = new ArrayList<>();
    // XCMS needs this one
    ArrayList<Double> totalIntensity = new ArrayList<>();
    double curTotalIntensity;
    int lastPointCount = 0;
    startIndex.add(0);
    try {
        setStatus(TaskStatus.PROCESSING);
        logger.info("Started mass detector on " + dataFile);
        final Scan[] scans = scanSelection.getMatchingScans(dataFile);
        totalScans = scans.length;
        // Process scans one by one
        for (Scan scan : scans) {
            if (isCanceled())
                return;
            MassDetector detector = massDetector.getModule();
            DataPoint[] mzPeaks = detector.getMassValues(scan, massDetector.getParameterSet());
            SimpleMassList newMassList = new SimpleMassList(name, scan, mzPeaks);
            // Add new mass list to the scan
            scan.addMassList(newMassList);
            if (this.saveToCDF) {
                curTotalIntensity = 0;
                for (int a = 0; a < mzPeaks.length; a++) {
                    DataPoint curMzPeak = mzPeaks[a];
                    allMZ.add(curMzPeak.getMZ());
                    allIntensities.add(curMzPeak.getIntensity());
                    curTotalIntensity += curMzPeak.getIntensity();
                }
                scanAcquisitionTime.add(scan.getRetentionTime());
                pointsInScans.add(0);
                startIndex.add(mzPeaks.length + lastPointCount);
                totalIntensity.add(curTotalIntensity);
                lastPointCount = mzPeaks.length + lastPointCount;
            }
            processedScans++;
        }
        // Update the GUI with all new mass lists
        MZmineProjectImpl project = (MZmineProjectImpl) MZmineCore.getProjectManager().getCurrentProject();
        final RawDataTreeModel treeModel = project.getRawDataTreeModel();
        treeModel.updateGUIWithNewObjects();
        ;
        if (this.saveToCDF) {
            // ************** write mass list *******************************
            final String outFileNamePath = outFilename.getPath();
            logger.info("Saving mass detector results to netCDF file " + outFileNamePath);
            NetcdfFileWriter writer = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFileNamePath, null);
            Dimension dim_massValues = writer.addDimension(null, "mass_values", allMZ.size());
            Dimension dim_intensityValues = writer.addDimension(null, "intensity_values", allIntensities.size());
            Dimension dim_scanIndex = writer.addDimension(null, "scan_index", startIndex.size() - 1);
            Dimension dim_scanAcquisitionTime = writer.addDimension(null, "scan_acquisition_time", scanAcquisitionTime.size());
            Dimension dim_totalIntensity = writer.addDimension(null, "total_intensity", totalIntensity.size());
            Dimension dim_pointsInScans = writer.addDimension(null, "point_count", pointsInScans.size());
            // add dimensions to list
            List<Dimension> dims = new ArrayList<>();
            dims.add(dim_massValues);
            dims.add(dim_intensityValues);
            dims.add(dim_scanIndex);
            dims.add(dim_scanAcquisitionTime);
            dims.add(dim_totalIntensity);
            dims.add(dim_pointsInScans);
            // make the variables that contain the actual data I think.
            Variable var_massValues = writer.addVariable(null, "mass_values", DataType.DOUBLE, "mass_values");
            Variable var_intensityValues = writer.addVariable(null, "intensity_values", DataType.DOUBLE, "intensity_values");
            Variable var_scanIndex = writer.addVariable(null, "scan_index", DataType.INT, "scan_index");
            Variable var_scanAcquisitionTime = writer.addVariable(null, "scan_acquisition_time", DataType.DOUBLE, "scan_acquisition_time");
            Variable var_totalIntensity = writer.addVariable(null, "total_intensity", DataType.DOUBLE, "total_intensity");
            Variable var_pointsInScans = writer.addVariable(null, "point_count", DataType.INT, "point_count");
            var_massValues.addAttribute(new Attribute("units", "M/Z"));
            var_intensityValues.addAttribute(new Attribute("units", "Arbitrary Intensity Units"));
            var_scanIndex.addAttribute(new Attribute("units", "index"));
            var_scanAcquisitionTime.addAttribute(new Attribute("units", "seconds"));
            var_totalIntensity.addAttribute(new Attribute("units", "Arbitrary Intensity Units"));
            var_pointsInScans.addAttribute(new Attribute("units", "count"));
            var_massValues.addAttribute(new Attribute("scale_factor", 1.0));
            var_intensityValues.addAttribute(new Attribute("scale_factor", 1.0));
            var_scanIndex.addAttribute(new Attribute("scale_factor", 1.0));
            var_scanAcquisitionTime.addAttribute(new Attribute("scale_factor", 1.0));
            var_totalIntensity.addAttribute(new Attribute("scale_factor", 1.0));
            var_pointsInScans.addAttribute(new Attribute("scale_factor", 1.0));
            // create file
            writer.create();
            ArrayDouble.D1 arr_massValues = new ArrayDouble.D1(dim_massValues.getLength());
            ArrayDouble.D1 arr_intensityValues = new ArrayDouble.D1(dim_intensityValues.getLength());
            ArrayDouble.D1 arr_scanIndex = new ArrayDouble.D1(dim_scanIndex.getLength());
            ArrayDouble.D1 arr_scanAcquisitionTime = new ArrayDouble.D1(dim_scanAcquisitionTime.getLength());
            ArrayDouble.D1 arr_totalIntensity = new ArrayDouble.D1(dim_totalIntensity.getLength());
            ArrayDouble.D1 arr_pointsInScans = new ArrayDouble.D1(dim_pointsInScans.getLength());
            for (int i = 0; i < allMZ.size(); i++) {
                arr_massValues.set(i, allMZ.get(i));
                arr_intensityValues.set(i, allIntensities.get(i));
            }
            int i = 0;
            for (; i < scanAcquisitionTime.size(); i++) {
                arr_scanAcquisitionTime.set(i, scanAcquisitionTime.get(i) * 60);
                arr_pointsInScans.set(i, pointsInScans.get(i));
                arr_scanIndex.set(i, startIndex.get(i));
                arr_totalIntensity.set(i, totalIntensity.get(i));
            }
            // arr_scanIndex.set(i,startIndex.get(i));
            // For tiny test file
            // arr_intensityValues .set(0,200);
            // arr_scanIndex .set(0,0);
            // arr_scanAcquisitionTime .set(0,10);
            // arr_totalIntensity .set(0,200);
            // arr_pointsInScans .set(0,0);
            // arr_intensityValues .set(1,300);
            // arr_scanIndex .set(1,1);
            // arr_scanAcquisitionTime .set(1,20);
            // arr_totalIntensity .set(1,300);
            // arr_pointsInScans .set(1,0);
            writer.write(var_massValues, arr_massValues);
            writer.write(var_intensityValues, arr_intensityValues);
            writer.write(var_scanIndex, arr_scanIndex);
            writer.write(var_scanAcquisitionTime, arr_scanAcquisitionTime);
            writer.write(var_totalIntensity, arr_totalIntensity);
            writer.write(var_pointsInScans, arr_pointsInScans);
            writer.close();
        }
    } catch (Exception e) {
        e.printStackTrace();
        setErrorMessage(e.getMessage());
        setStatus(TaskStatus.ERROR);
    }
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished mass detector on " + dataFile);
}