Examples with Range org.vcell.util.Range used on opensource projects

Example 26 with Range

use of org.vcell.util.Range in project vcell by virtualcell.

the class EstParams_TwoDiffComponentPanel method setData.

public void setData(final FRAPOptData frapOptData, final FRAPData fData, Parameter[] modelParams, final double[] frapDataTimeStamps, int startIndexForRecovery, boolean[] selectedROIs) throws Exception {
    this.frapOptData = frapOptData;
    double[] prebleachAverage = FrapDataUtils.calculatePreBleachAverageXYZ(fData, startIndexForRecovery);
    spatialAnalysisResults = FRAPStudy.spatialAnalysis(null, startIndexForRecovery, frapDataTimeStamps[startIndexForRecovery], modelParams, fData, prebleachAverage);
    // allDataHash use AnalysisParameters as key, the value is dataSource[] which should have length as 2: expDataSource & simDataSouce
    allDataHash = spatialAnalysisResults.createSummaryReportSourceData(frapDataTimeStamps, startIndexForRecovery, selectedROIs, false);
    final SpatialAnalysisResults finalSpatialAnalysisResults = spatialAnalysisResults;
    try {
        getPureDiffusionPanel().setData(frapOptData, modelParams);
        multisourcePlotPane.forceXYRange(new Range(frapDataTimeStamps[0], frapDataTimeStamps[frapDataTimeStamps.length - 1]), new Range(0, 1.5));
        plotDerivedSimulationResults(finalSpatialAnalysisResults.getAnalysisParameters());
    } catch (Exception e) {
        throw new RuntimeException("Error setting data to result panel for diffusion with one diffusing component.");
    }
}

Example 27 with Range

use of org.vcell.util.Range in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method calcMinMaxPixelValueRange.

private Range calcMinMaxPixelValueRange(ImageDataset argImageDataset) {
    UShortImage[] allImages = argImageDataset.getAllImages();
    double min = 0;
    double max = min;
    for (int i = 0; i < allImages.length; i++) {
        ImageStatistics imageStats = allImages[i].getImageStatistics();
        if (i == 0 || imageStats.minValue < min) {
            min = imageStats.minValue;
        }
        if (i == 0 || imageStats.maxValue > max) {
            max = imageStats.maxValue;
        }
    }
    if (max < SHORT_TO_BYTE_FACTOR) {
        return new Range(min, max);
    }
    return new Range(min / SHORT_TO_BYTE_FACTOR, max / SHORT_TO_BYTE_FACTOR);
}

Example 28 with Range

use of org.vcell.util.Range in project vcell by virtualcell.

the class OutputOptionsPanel method actionOutputOptionButtonState.

private void actionOutputOptionButtonState(java.awt.event.ActionEvent actionEvent) {
    try {
        if (solverTaskDescription == null) {
            return;
        }
        OutputTimeSpec outputTimeSpec = solverTaskDescription.getOutputTimeSpec();
        if (actionEvent.getSource() == getDefaultOutputRadioButton() && !outputTimeSpec.isDefault()) {
            solverTaskDescription.setOutputTimeSpec(new DefaultOutputTimeSpec());
        } else if (actionEvent.getSource() == getUniformOutputRadioButton() && !outputTimeSpec.isUniform()) {
            double outputTime = 0.0;
            if (solverTaskDescription.getSolverDescription().isSemiImplicitPdeSolver()) {
                String floatStr = "" + (float) (((DefaultOutputTimeSpec) outputTimeSpec).getKeepEvery() * solverTaskDescription.getTimeStep().getDefaultTimeStep());
                outputTime = Double.parseDouble(floatStr);
            } else {
                TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
                Range outputTimeRange = NumberUtils.getDecimalRange(timeBounds.getStartingTime(), timeBounds.getEndingTime() / 100, true, true);
                outputTime = outputTimeRange.getMax();
            }
            solverTaskDescription.setOutputTimeSpec(new UniformOutputTimeSpec(outputTime));
        } else if (actionEvent.getSource() == getExplicitOutputRadioButton() && !outputTimeSpec.isExplicit()) {
            TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
            solverTaskDescription.setOutputTimeSpec(new ExplicitOutputTimeSpec(new double[] { timeBounds.getStartingTime(), timeBounds.getEndingTime() }));
        }
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 29 with Range

use of org.vcell.util.Range in project vcell by virtualcell.

the class IMGExporter method main.

public static void main(String[] args) throws Exception {
    if (args.length < 7) {
        System.out.println("Usage: IMGExporter username userkey simulationkey userdatadir beginTimeIndex endTimeIndex {varName1 varName2 ...}");
        System.exit(0);
    }
    String userName = args[0];
    String userKey = args[1];
    String SimulationKey = args[2];
    String primaryDirStr = args[3];
    int beginTimeIndex = Integer.valueOf(args[4]);
    int endTimeIndex = Integer.valueOf(args[5]);
    String[] varNames = new String[args.length - 6];
    if (args.length > 6) {
        for (int i = 6; i < args.length; i++) {
            varNames[i - 6] = args[i];
        }
    }
    PropertyLoader.loadProperties();
    User user = new User(userName, new KeyValue(userKey));
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(new KeyValue(SimulationKey), user);
    VCSimulationDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, 0);
    class PrintingExportServiceImpl extends ExportServiceImpl {

        public PrintingExportServiceImpl() {
            super();
        }

        @Override
        protected void fireExportEvent(ExportEvent event) {
            super.fireExportEvent(event);
            System.out.println("Event type=" + event.getEventTypeID() + " JobID=" + event.getJobID() + " progress=" + event.getProgress());
        }
    }
    ExportServiceImpl exportServiceImpl = new PrintingExportServiceImpl();
    Cachetable cachetable = new Cachetable(10 * Cachetable.minute);
    File primaryDir = new File(primaryDirStr);
    DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cachetable, primaryDir, null);
    DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
    double[] allTimes = dataSetControllerImpl.getDataSetTimes(vcdID);
    TimeSpecs timeSpecs = new TimeSpecs(beginTimeIndex, endTimeIndex, allTimes, ExportConstants.TIME_RANGE);
    VariableSpecs variableSpecs = new VariableSpecs(varNames, ExportConstants.VARIABLE_MULTI);
    GeometrySpecs geometrySpecs = new GeometrySpecs(null, 0, 0, ExportConstants.GEOMETRY_SLICE);
    DisplayPreferences displayPreferences = new DisplayPreferences(DisplayAdapterService.BLUERED, new Range(0, 1), DisplayAdapterService.createBlueRedSpecialColors());
    MovieSpecs movieSpecs = new MovieSpecs(// /
    1000.0, // /
    false, // /
    new DisplayPreferences[] { displayPreferences }, // /
    ExportFormat.FORMAT_JPEG, // /
    0, // /
    1, // /
    1, // /
    1, ImagePaneModel.MESH_MODE, FormatSpecificSpecs.CODEC_JPEG, 1.0f, false, FormatSpecificSpecs.PARTICLE_SELECT);
    ExportSpecs exportSpecs = new ExportSpecs(vcdID, ExportFormat.QUICKTIME, variableSpecs, timeSpecs, geometrySpecs, movieSpecs, "IMGExporterTest", null);
    exportServiceImpl.makeRemoteFile(null, user, dataServerImpl, exportSpecs);
}

Example 30 with Range

use of org.vcell.util.Range in project vcell by virtualcell.

the class Plot2D method getXDataRange.

/**
 * Insert the method's description here.
 * Creation date: (2/8/2001 1:32:46 PM)
 * @return cbit.image.Range
 */
public Range getXDataRange() {
    double xmin = 0;
    double xmax = 0;
    for (int i = 0; i < plotDatas.length; i++) {
        if (isVisiblePlot(i)) {
            xmin = Math.min(xmin, plotDatas[i].getIndependentMin());
            xmax = Math.max(xmax, plotDatas[i].getIndependentMax());
        }
    }
    xDataRange = new Range(xmin, xmax);
    return xDataRange;
}