use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class FRAPStudy method getCartesianMesh.
public CartesianMesh getCartesianMesh() throws Exception {
CartesianMesh cartesianMesh = null;
ImageDataset imgDataSet = getFrapData().getImageDataset();
Extent extent = imgDataSet.getExtent();
ISize isize = imgDataSet.getISize();
Origin origin = new Origin(0, 0, 0);
if (getBioModel() == null) {
cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
} else {
RegionImage regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
if (regionImage == null) {
getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().updateAll();
regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
}
cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
}
return cartesianMesh;
}
use of cbit.image.VCImageUncompressed 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;
}
use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class SimulationData method createPostProcessingMesh.
private CartesianMesh createPostProcessingMesh(String varName, OutputContext outputContext) throws DataAccessException {
try {
refreshDataProcessingOutputInfo(outputContext);
// create mesh here because we know the variablename
ISize varISize = dataProcessingOutputInfo.getVariableISize(varName);
Extent varExtent = dataProcessingOutputInfo.getVariableExtent(varName);
Origin varOrigin = dataProcessingOutputInfo.getVariableOrigin(varName);
VCImage vcImage = new VCImageUncompressed(null, new byte[varISize.getXYZ()], varExtent, varISize.getX(), varISize.getY(), varISize.getZ());
RegionImage regionImage = new RegionImage(vcImage, 1 + (varISize.getY() > 0 ? 1 : 0) + (varISize.getZ() > 0 ? 1 : 0), varExtent, varOrigin, RegionImage.NO_SMOOTHING);
return CartesianMesh.createSimpleCartesianMesh(dataProcessingOutputInfo.getVariableOrigin(varName), varExtent, varISize, regionImage);
} catch (DataAccessException dae) {
throw dae;
} catch (Exception e) {
throw new DataAccessException(e.getMessage(), (e.getCause() == null ? e : e.getCause()));
}
}
use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class RunRefSimulationFastOp method getROIDataGenerator.
private ROIDataGenerator getROIDataGenerator(LocalContext localWorkspace, ROI[] rois) throws ImageException, IOException {
// create ROI image
short[] roiFieldData = null;
if (rois.length > 0) {
Origin origin = new Origin(0, 0, 0);
Extent extent = rois[0].getRoiImages()[0].getExtent();
ISize isize = rois[0].getISize();
int numROIX = rois[0].getISize().getX();
int numROIY = rois[0].getISize().getY();
roiFieldData = new short[numROIX * numROIY];
short regionCounter = 1;
for (int roiIdx = 0; roiIdx < rois.length; roiIdx++) {
short[] roiImg = rois[roiIdx].getPixelsXYZ();
for (int pixelIdx = 0; pixelIdx < (numROIX * numROIY); pixelIdx++) {
if (roiImg[pixelIdx] > 0) {
roiFieldData[pixelIdx] = regionCounter;
}
}
regionCounter++;
}
// create field data
int NumTimePoints = 1;
// 8 rois integrated into 1 image
int NumChannels = 1;
short[][][] pixData = new short[NumTimePoints][NumChannels][];
pixData[0][0] = roiFieldData;
// get extental data id
VCImage vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ());
RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
CartesianMesh simpleCartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
ExternalDataIdentifier newROIExtDataID = createNewExternalDataInfo(localWorkspace, ROI_SUMDATA_NAME).getExternalDataIdentifier();
try {
FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
fdos.cartesianMesh = simpleCartesianMesh;
fdos.shortSpecData = pixData;
fdos.specEDI = newROIExtDataID;
fdos.varNames = new String[] { "roiSumDataVar" };
fdos.owner = LocalWorkspace.getDefaultOwner();
fdos.times = new double[] { 0.0 };
fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
fdos.origin = origin;
fdos.extent = extent;
fdos.isize = isize;
localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return new ROIDataGenerator(ROI_EXTDATA_NAME, /*name*/
new int[] { 0 }, /* volumePoints*/
new int[0], /* membranePoints*/
regionCounter, /*numRegions*/
0, /*zSlice*/
newROIExtDataID.getKey(), /* fieldDataKey, sample image*/
new FieldFunctionArguments(ROI_SUMDATA_NAME, ROI_SUMDATA_VARNAME, new Expression(0), VariableType.VOLUME), /*FieldFunctionArguments, sample image*/
false);
}
return null;
}
use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class RunRefSimulationFastOp method createRefSimBioModel.
private BioModel createRefSimBioModel(KeyValue simKey, User owner, Origin origin, Extent extent, ROI cellROI_2D, double timeStepVal, TimeBounds timeBounds, String varName, Expression initialConcentration, FieldFunctionArguments psfFFA, Expression chirpedDiffusionRate) throws Exception {
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);
geometry.getGeometrySpec().setOrigin(origin);
if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
throw new Exception("Cell ROI has no ExtraCellular.");
}
String EXTRACELLULAR_NAME = "ec";
String CYTOSOL_NAME = "cyt";
String PLASMAMEMBRANE_NAME = "pm";
ImageSubVolume subVolume0 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0);
ImageSubVolume subVolume1 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1);
if (subVolume0.getPixelValue() == EXTRACELLULAR_PIXVAL) {
subVolume0.setName(EXTRACELLULAR_NAME);
subVolume1.setName(CYTOSOL_NAME);
} else {
subVolume0.setName(CYTOSOL_NAME);
subVolume1.setName(EXTRACELLULAR_NAME);
}
geometry.getGeometrySurfaceDescription().updateAll();
BioModel bioModel = new BioModel(null);
bioModel.setName("unnamed");
Model model = new Model("model");
bioModel.setModel(model);
Feature extracellular = model.addFeature(EXTRACELLULAR_NAME);
Feature cytosol = model.addFeature(CYTOSOL_NAME);
Membrane plasmaMembrane = model.addMembrane(PLASMAMEMBRANE_NAME);
SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
bioModel.addSimulationContext(simContext);
FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(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));
plasmaMembraneMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
// Mobile Species
Species diffusingSpecies = model.addSpecies(new Species("species", "Mobile bleachable species"));
SpeciesContext diffusingSpeciesContext = model.addSpeciesContext(diffusingSpecies, cytosol);
diffusingSpeciesContext.setName(varName);
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(diffusingSpeciesContext);
scs.getInitialConditionParameter().setExpression(initialConcentration);
chirpedDiffusionRate.bindExpression(scs);
scs.getDiffusionParameter().setExpression(chirpedDiffusionRate);
// simContext.getMicroscopeMeasurement().addFluorescentSpecies(speciesContexts[0]);
// simContext.getMicroscopeMeasurement().setConvolutionKernel(new MicroscopeMeasurement.ProjectionZKernel());
MathDescription mathDescription = simContext.createNewMathMapping().getMathDescription();
// maybe there is a way that works for simContext.getMicroscopeMeasurement().... but this is needed now.
mathDescription.addVariable(new Function(Simulation.PSF_FUNCTION_NAME, new Expression(psfFFA.infix()), null));
simContext.setMathDescription(mathDescription);
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, simContext.getMathDescription());
newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
simContext.addSimulation(newSimulation);
newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
newSimulation.getSolverTaskDescription().setTimeStep(new TimeStep(timeStepVal, timeStepVal, timeStepVal));
return bioModel;
}
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