Examples with ROI cbit.vcell.VirtualMicroscopy.ROI used on opensource projects

Example 56 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class FRAPStudy method createNewSimBioModel.

public static BioModel createNewSimBioModel(FRAPStudy sourceFrapStudy, Parameter[] params, TimeStep tStep, KeyValue simKey, User owner, int startingIndexForRecovery) throws Exception {
    if (owner == null) {
        throw new Exception("Owner is not defined");
    }
    ROI cellROI_2D = sourceFrapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    double df = params[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess();
    double ff = params[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess();
    double bwmRate = params[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess();
    double dc = 0;
    double fc = 0;
    double bs = 0;
    double onRate = 0;
    double offRate = 0;
    if (params.length == FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF) {
        dc = params[FRAPModel.INDEX_SECONDARY_DIFF_RATE].getInitialGuess();
        fc = params[FRAPModel.INDEX_SECONDARY_FRACTION].getInitialGuess();
    } else if (params.length == FRAPModel.NUM_MODEL_PARAMETERS_BINDING) {
        dc = params[FRAPModel.INDEX_SECONDARY_DIFF_RATE].getInitialGuess();
        fc = params[FRAPModel.INDEX_SECONDARY_FRACTION].getInitialGuess();
        bs = params[FRAPModel.INDEX_BINDING_SITE_CONCENTRATION].getInitialGuess();
        onRate = params[FRAPModel.INDEX_ON_RATE].getInitialGuess();
        offRate = params[FRAPModel.INDEX_OFF_RATE].getInitialGuess();
    }
    // immobile fraction
    double fimm = 1 - ff - fc;
    if (fimm < FRAPOptimizationUtils.epsilon && fimm > (0 - FRAPOptimizationUtils.epsilon)) {
        fimm = 0;
    }
    if (fimm < (1 + FRAPOptimizationUtils.epsilon) && fimm > (1 - FRAPOptimizationUtils.epsilon)) {
        fimm = 1;
    }
    Extent extent = sourceFrapStudy.getFrapData().getImageDataset().getExtent();
    double[] timeStamps = sourceFrapStudy.getFrapData().getImageDataset().getImageTimeStamps();
    TimeBounds timeBounds = new TimeBounds(0.0, timeStamps[timeStamps.length - 1] - timeStamps[startingIndexForRecovery]);
    double timeStepVal = timeStamps[startingIndexForRecovery + 1] - timeStamps[startingIndexForRecovery];
    int numX = cellROI_2D.getRoiImages()[0].getNumX();
    int numY = cellROI_2D.getRoiImages()[0].getNumY();
    int numZ = cellROI_2D.getRoiImages().length;
    short[] shortPixels = cellROI_2D.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new Exception("Cell ROI has no ExtraCellular.");
    }
    int subVolume0PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(0).setName((subVolume0PixVal == EXTRACELLULAR_PIXVAL ? EXTRACELLULAR_NAME : CYTOSOL_NAME));
    int subVolume1PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(1).setName((subVolume1PixVal == CYTOSOL_PIXVAL ? CYTOSOL_NAME : EXTRACELLULAR_NAME));
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    model.addFeature(EXTRACELLULAR_NAME);
    Feature extracellular = (Feature) model.getStructure(EXTRACELLULAR_NAME);
    model.addFeature(CYTOSOL_NAME);
    Feature cytosol = (Feature) model.getStructure(CYTOSOL_NAME);
    // Membrane mem = model.addMembrane(EXTRACELLULAR_CYTOSOL_MEM_NAME);
    // model.getStructureTopology().setInsideFeature(mem, cytosol);
    // model.getStructureTopology().setOutsideFeature(mem, extracellular);
    String roiDataName = FRAPStudy.ROI_EXTDATA_NAME;
    final int SPECIES_COUNT = 4;
    final int FREE_SPECIES_INDEX = 0;
    final int BS_SPECIES_INDEX = 1;
    final int COMPLEX_SPECIES_INDEX = 2;
    final int IMMOBILE_SPECIES_INDEX = 3;
    Expression[] diffusionConstants = null;
    Species[] species = null;
    SpeciesContext[] speciesContexts = null;
    Expression[] initialConditions = null;
    diffusionConstants = new Expression[SPECIES_COUNT];
    species = new Species[SPECIES_COUNT];
    speciesContexts = new SpeciesContext[SPECIES_COUNT];
    initialConditions = new Expression[SPECIES_COUNT];
    // total initial condition
    FieldFunctionArguments postBleach_first = new FieldFunctionArguments(roiDataName, "postbleach_first", new Expression(0), VariableType.VOLUME);
    FieldFunctionArguments prebleach_avg = new FieldFunctionArguments(roiDataName, "prebleach_avg", new Expression(0), VariableType.VOLUME);
    Expression expPostBleach_first = new Expression(postBleach_first.infix());
    Expression expPreBleach_avg = new Expression(prebleach_avg.infix());
    Expression totalIniCondition = Expression.div(expPostBleach_first, expPreBleach_avg);
    // Free Species
    diffusionConstants[FREE_SPECIES_INDEX] = new Expression(df);
    species[FREE_SPECIES_INDEX] = new Species(FRAPStudy.SPECIES_NAME_PREFIX_MOBILE, "Mobile bleachable species");
    speciesContexts[FREE_SPECIES_INDEX] = new SpeciesContext(null, species[FREE_SPECIES_INDEX].getCommonName(), species[FREE_SPECIES_INDEX], cytosol);
    initialConditions[FREE_SPECIES_INDEX] = Expression.mult(new Expression(ff), totalIniCondition);
    // Immobile Species (No diffusion)
    // Set very small diffusion rate on immobile to force evaluation as state variable (instead of FieldData function)
    // If left as a function errors occur because functions involving FieldData require a database connection
    final String IMMOBILE_DIFFUSION_KLUDGE = "1e-14";
    diffusionConstants[IMMOBILE_SPECIES_INDEX] = new Expression(IMMOBILE_DIFFUSION_KLUDGE);
    species[IMMOBILE_SPECIES_INDEX] = new Species(FRAPStudy.SPECIES_NAME_PREFIX_IMMOBILE, "Immobile bleachable species");
    speciesContexts[IMMOBILE_SPECIES_INDEX] = new SpeciesContext(null, species[IMMOBILE_SPECIES_INDEX].getCommonName(), species[IMMOBILE_SPECIES_INDEX], cytosol);
    initialConditions[IMMOBILE_SPECIES_INDEX] = Expression.mult(new Expression(fimm), totalIniCondition);
    // BS Species
    diffusionConstants[BS_SPECIES_INDEX] = new Expression(IMMOBILE_DIFFUSION_KLUDGE);
    species[BS_SPECIES_INDEX] = new Species(FRAPStudy.SPECIES_NAME_PREFIX_BINDING_SITE, "Binding Site species");
    speciesContexts[BS_SPECIES_INDEX] = new SpeciesContext(null, species[BS_SPECIES_INDEX].getCommonName(), species[BS_SPECIES_INDEX], cytosol);
    initialConditions[BS_SPECIES_INDEX] = Expression.mult(new Expression(bs), totalIniCondition);
    // Complex species
    diffusionConstants[COMPLEX_SPECIES_INDEX] = new Expression(dc);
    species[COMPLEX_SPECIES_INDEX] = new Species(FRAPStudy.SPECIES_NAME_PREFIX_SLOW_MOBILE, "Slower mobile bleachable species");
    speciesContexts[COMPLEX_SPECIES_INDEX] = new SpeciesContext(null, species[COMPLEX_SPECIES_INDEX].getCommonName(), species[COMPLEX_SPECIES_INDEX], cytosol);
    initialConditions[COMPLEX_SPECIES_INDEX] = Expression.mult(new Expression(fc), totalIniCondition);
    // add reactions to species if there is bleachWhileMonitoring rate.
    for (int i = 0; i < initialConditions.length; i++) {
        model.addSpecies(species[i]);
        model.addSpeciesContext(speciesContexts[i]);
        // reaction with BMW rate, which should not be applied to binding site
        if (!(species[i].getCommonName().equals(FRAPStudy.SPECIES_NAME_PREFIX_BINDING_SITE))) {
            SimpleReaction simpleReaction = new SimpleReaction(model, cytosol, speciesContexts[i].getName() + "_bleach", true);
            model.addReactionStep(simpleReaction);
            simpleReaction.addReactant(speciesContexts[i], 1);
            MassActionKinetics massActionKinetics = new MassActionKinetics(simpleReaction);
            simpleReaction.setKinetics(massActionKinetics);
            KineticsParameter kforward = massActionKinetics.getForwardRateParameter();
            simpleReaction.getKinetics().setParameterValue(kforward, new Expression(new Double(bwmRate)));
        }
    }
    // add the binding reaction: F + BS <-> C
    SimpleReaction simpleReaction2 = new SimpleReaction(model, cytosol, "reac_binding", true);
    model.addReactionStep(simpleReaction2);
    simpleReaction2.addReactant(speciesContexts[FREE_SPECIES_INDEX], 1);
    simpleReaction2.addReactant(speciesContexts[BS_SPECIES_INDEX], 1);
    simpleReaction2.addProduct(speciesContexts[COMPLEX_SPECIES_INDEX], 1);
    MassActionKinetics massActionKinetics = new MassActionKinetics(simpleReaction2);
    simpleReaction2.setKinetics(massActionKinetics);
    KineticsParameter kforward = massActionKinetics.getForwardRateParameter();
    KineticsParameter kreverse = massActionKinetics.getReverseRateParameter();
    simpleReaction2.getKinetics().setParameterValue(kforward, new Expression(new Double(onRate)));
    simpleReaction2.getKinetics().setParameterValue(kreverse, new Expression(new Double(offRate)));
    // create simulation context
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    // Membrane plasmaMembrane = model.getStructureTopology().getMembrane(cytosol, extracellular);
    // MembraneMapping plasmaMembraneMapping = (MembraneMapping)simContext.getGeometryContext().getStructureMapping(plasmaMembrane);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    // plasmaMembraneMapping.setGeometryClass(pmSurfaceClass);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i]);
        scs.getInitialConditionParameter().setExpression(initialConditions[i]);
        scs.getDiffusionParameter().setExpression(diffusionConstants[i]);
    }
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    // Add total fluorescence as function of mobile(optional: and slower mobile) and immobile fractions
    mathDesc.addVariable(new Function(FRAPStudy.SPECIES_NAME_PREFIX_COMBINED, new Expression(species[FREE_SPECIES_INDEX].getCommonName() + "+" + species[COMPLEX_SPECIES_INDEX].getCommonName() + "+" + species[IMMOBILE_SPECIES_INDEX].getCommonName()), null));
    simContext.setMathDescription(mathDesc);
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, mathDesc);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
    // newSimulation.getSolverTaskDescription().setTimeStep(timeStep); // Sundials doesn't need time step
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    // use exp time step as output time spec
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    return bioModel;
}

Example 57 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class MicroscopyXmlReader method getFrapData.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
private FRAPData getFrapData(Element param, ClientTaskStatusSupport progressListener) throws XmlParseException {
    Element imageDatasetElement = param.getChild(MicroscopyXMLTags.ImageDatasetTag);
    ImageDataset imageDataset = null;
    if (imageDatasetElement != null) {
        imageDataset = getImageDataset(imageDatasetElement, progressListener);
    }
    @SuppressWarnings("unchecked") List<Element> roiList = param.getChildren(MicroscopyXMLTags.ROITag);
    ROI[] rois = null;
    int numROIs = roiList.size();
    if (numROIs > 0) {
        rois = new ROI[numROIs];
        Iterator<Element> roiIter = roiList.iterator();
        int index = 0;
        while (roiIter.hasNext()) {
            Element roiElement = roiIter.next();
            rois[index++] = getROI(roiElement);
        }
    }
    // reorder ROIs according to the order of FRAPData.VFRAP_ROI_ENUM
    ROI[] reorderedROIs = AnnotatedImageDataset.reorderROIs(rois);
    FRAPData frapData = new FRAPData(imageDataset, reorderedROIs);
    // After loading all the ROI rings, the progress should set to 100.
    if (progressListener != null) {
        progressListener.setProgress(100);
    }
    return frapData;
}

Example 58 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class MicroscopyXmlReader method getROI.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
private ROI getROI(Element param) throws XmlParseException {
    String roiName = param.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag);
    @SuppressWarnings("unchecked") List<Element> ushortImageElementList = param.getChildren(MicroscopyXMLTags.UShortImageTag);
    Iterator<Element> imageElementIter = ushortImageElementList.iterator();
    UShortImage[] images = new UShortImage[ushortImageElementList.size()];
    int imageIndex = 0;
    while (imageElementIter.hasNext()) {
        images[imageIndex++] = getUShortImage(imageElementIter.next());
    }
    ROI roi = new ROI(images, roiName);
    return roi;
}

Example 59 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class MicroscopyXmlproducer method getXML.

/**
 * This method returns a XML representation for a Biomodel object.
 * Creation date: (2/14/2001 3:41:13 PM)
 * @param param cbit.vcell.biomodel.BioModel
 * @return Element
 * @throws XmlParseException
 * @throws cbit.vcell.parser.ExpressionException
 */
private static Element getXML(FRAPData param, Xmlproducer vcellXMLProducer, ClientTaskStatusSupport progressListener, boolean bSaveCompressed) throws XmlParseException, cbit.vcell.parser.ExpressionException {
    Element frapDataNode = new Element(MicroscopyXMLTags.FRAPDataTag);
    // Get ImageDataset
    if (param.getImageDataset() != null) {
        frapDataNode.addContent(getXML(param.getImageDataset(), vcellXMLProducer, progressListener, bSaveCompressed));
    }
    // Get ROIs
    ROI[] rois = param.getRois();
    for (int i = 0; i < rois.length; i++) {
        frapDataNode.addContent(getXML(rois[i], vcellXMLProducer, bSaveCompressed));
    }
    // We assume saving ROI rings takes 5% of the total progress
    if (progressListener != null) {
        progressListener.setProgress(100);
    }
    return frapDataNode;
}

Example 60 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class NonGUIFRAPTest method runSolver.

/**
 * @param args
 */
public static void runSolver(String[] args) throws Exception {
    String startingIndexForRecovery = args[0];
    String freeDiffusionRateStr = args[1];
    String freeMobileFractionStr = args[2];
    String complexDiffusionRateStr = args[3];
    String complexMobileFractionStr = args[4];
    String bleachWhileMonitoringRateString = args[5];
    String immobileFractionStr = args[6];
    String bindingSiteConcentrationStr = args[7];
    String reacOnRateStr = args[8];
    String reacOffRateStr = args[9];
    String workingDirectoryPath = args[10];
    String inputFRAPDataFileName = args[11];
    String inputCellROIFileName = args[12];
    String inputBleachROIFileName = args[13];
    String inputBackgroundROIFileName = args[14];
    String outputXMLFileName = args[15];
    String commaSepTimeStamps = args[16];
    String commaSepExtentXYZ = args[17];
    LocalWorkspace localWorkspace = new LocalWorkspace(new File(workingDirectoryPath));
    ExternalDataFileContents extDataFileContents = readExternalDataContents(inputFRAPDataFileName, inputCellROIFileName, inputBleachROIFileName, inputBackgroundROIFileName);
    ROI cellROI = new ROI(extDataFileContents.cellROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    ROI bleachROI = new ROI(extDataFileContents.bleachROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    ROI backgroundROI = new ROI(extDataFileContents.backgroundROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
    // Insert Time information
    double[] timeStamps = new double[extDataFileContents.imageData.getAllImages().length];
    StringTokenizer commaStringTokenizer = new StringTokenizer(commaSepTimeStamps, ",");
    int timeCount = 0;
    while (commaStringTokenizer.hasMoreTokens()) {
        timeStamps[timeCount] = Double.parseDouble(commaStringTokenizer.nextToken());
        timeCount++;
    }
    ImageDataset frapDataImageDataSet = new ImageDataset(extDataFileContents.imageData.getAllImages(), timeStamps, 1);
    // Insert Extent information
    commaStringTokenizer = new StringTokenizer(commaSepExtentXYZ, ",");
    Extent extent = new Extent(Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()));
    frapDataImageDataSet.setExtent(extent);
    bleachROI.getRoiImages()[0].setExtent(extent);
    cellROI.getRoiImages()[0].setExtent(extent);
    backgroundROI.getRoiImages()[0].setExtent(extent);
    FRAPData frapData = FrapDataUtils.importFRAPDataFromImageDataSet(frapDataImageDataSet);
    frapData.addReplaceRoi(bleachROI);
    frapData.addReplaceRoi(cellROI);
    frapData.addReplaceRoi(backgroundROI);
    FRAPStudy frapStudy = new FRAPStudy();
    frapStudy.setFrapData(frapData);
    // old model parameters, need to rewrite
    // FRAPStudy.FRAPModelParameters frapModelParameters = new FRAPStudy.FRAPModelParameters(
    // new FRAPStudy.InitialModelParameters(freeDiffusionRateStr, freeMobileFractionStr, bleachWhileMonitoringRateString, startingIndexForRecovery),
    // null,
    // null);
    // frapStudy.setFrapModelParameters(frapModelParameters);
    frapStudy.refreshDependentROIs();
    ExternalDataInfo imageDatasetExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.IMAGE_EXTDATA_NAME);
    ExternalDataInfo roiExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_EXTDATA_NAME);
    frapStudy.setFrapDataExternalDataInfo(imageDatasetExternalDataInfo);
    frapStudy.setRoiExternalDataInfo(roiExternalDataInfo);
    frapStudy.saveImageDatasetAsExternalData(localWorkspace, frapStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    frapStudy.saveROIsAsExternalData(localWorkspace, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    // Double bleachWhileMonitoringRate =
    // (!bleachWhileMonitoringRateString.equals("-")
    // ?Double.parseDouble(bleachWhileMonitoringRateString)
    // :null);
    double fd, ff, bwmr, cd, cf, imf, bs, on, off;
    try {
        fd = Double.parseDouble(freeDiffusionRateStr);
        ff = Double.parseDouble(freeMobileFractionStr);
        bwmr = Double.parseDouble(bleachWhileMonitoringRateString);
        cd = Double.parseDouble(complexDiffusionRateStr);
        cf = Double.parseDouble(complexMobileFractionStr);
        imf = Double.parseDouble(immobileFractionStr);
        bs = Double.parseDouble(bindingSiteConcentrationStr);
        on = Double.parseDouble(reacOnRateStr);
        off = Double.parseDouble(reacOffRateStr);
    } catch (NumberFormatException e) {
        throw new Exception("Input parameters are not all valid. Check if they are empty or in illegal forms.");
    }
    BioModel bioModel = FRAPStudy.createNewSimBioModel(frapStudy, createParameterArray(fd, ff, bwmr, cd, cf, imf, bs, on, off), null, LocalWorkspace.createNewKeyValue(), LocalWorkspace.getDefaultOwner(), new Integer(frapStudy.getStartingIndexForRecovery()));
    frapStudy.setBioModel(bioModel);
    // no progress listener, need to change
    MicroscopyXmlproducer.writeXMLFile(frapStudy, new File(outputXMLFileName), true, null, false);
    FRAPStudy.runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), imageDatasetExternalDataInfo.getExternalDataIdentifier(), roiExternalDataInfo.getExternalDataIdentifier(), null);
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(bioModel.getSimulations()[0].getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), FieldDataFileOperationSpec.JOBINDEX_DEFAULT);
    PDEDataManager simulationDataManager = new PDEDataManager(null, localWorkspace.getVCDataManager(), vcSimulationDataIdentifier);
    double[] frapDataTimeStamps = frapData.getImageDataset().getImageTimeStamps();
    VCDataManager testVCDataManager = localWorkspace.getVCDataManager();
    double[] prebleachAverage = testVCDataManager.getSimDataBlock(null, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), "prebleach_avg", 0).getData();
    // TODO: need to create parameters here.
    Parameter[] parameters = null;
    SpatialAnalysisResults spatialAnalysisResults = FRAPStudy.spatialAnalysis(simulationDataManager, new Integer(frapStudy.getStartingIndexForRecovery()), frapDataTimeStamps[new Integer(frapStudy.getStartingIndexForRecovery())], parameters, frapData, prebleachAverage);
    dumpSummaryReport(spatialAnalysisResults, frapDataTimeStamps, new Integer(startingIndexForRecovery).intValue(), new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
    dumpSpatialResults(spatialAnalysisResults, frapDataTimeStamps, new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
}