use of cbit.image.VCImage in project vcell by virtualcell.
the class RunRefSimulationFastOp method saveExternalData.
private void saveExternalData(Image image, String varName, ExternalDataIdentifier newROIExtDataID, LocalWorkspace localWorkspace) throws ObjectNotFoundException, ImageException, IOException {
Extent extent = image.getExtent();
Origin origin = image.getOrigin();
ISize isize = image.getISize();
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);
int NumTimePoints = 1;
int NumChannels = 1;
// dimensions: time points, channels, whole image ordered by z slices.
double[][][] pixData = new double[NumTimePoints][NumChannels][];
pixData[0][0] = image.getDoublePixels();
FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
fdos.cartesianMesh = simpleCartesianMesh;
fdos.doubleSpecData = pixData;
fdos.specEDI = newROIExtDataID;
fdos.varNames = new String[] { varName };
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);
}
use of cbit.image.VCImage in project vcell by virtualcell.
the class RunRefSimulationOp method createRefSimBioModel.
private static BioModel createRefSimBioModel(KeyValue simKey, User owner, Origin origin, Extent extent, ROI cellROI_2D, double timeStepVal, TimeBounds timeBounds, String varName, Expression initialConcentration, double baseDiffusionRate) 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);
scs.getDiffusionParameter().setExpression(new Expression(baseDiffusionRate));
// simContext.getMicroscopeMeasurement().addFluorescentSpecies(speciesContexts[0]);
// simContext.getMicroscopeMeasurement().setConvolutionKernel(new MicroscopeMeasurement.ProjectionZKernel());
simContext.setMathDescription(simContext.createNewMathMapping().getMathDescription());
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;
}
use of cbit.image.VCImage in project vcell by virtualcell.
the class DisplayTimeSeries method displayImageTimeSeries.
public static void displayImageTimeSeries(final ImageTimeSeries<Image> imageTimeSeries, String title, WindowListener windowListener) throws ImageException, IOException {
ISize size = imageTimeSeries.getISize();
int dimension = (size.getZ() > 0) ? (3) : (2);
Extent extent = imageTimeSeries.getExtent();
Origin origin = imageTimeSeries.getAllImages()[0].getOrigin();
// don't care ... no surfaces
double filterCutoffFrequency = 0.5;
VCImage vcImage = new VCImageUncompressed(null, new byte[size.getXYZ()], extent, size.getX(), size.getY(), size.getZ());
RegionImage regionImage = new RegionImage(vcImage, dimension, extent, origin, filterCutoffFrequency);
final CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, size, regionImage);
final DataIdentifier dataIdentifier = new DataIdentifier("var", VariableType.VOLUME, new Domain("domain"), false, "var");
final DataSetController dataSetController = new DataSetController() {
@Override
public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
throw new RuntimeException("not yet implemented");
}
@Override
public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
double timePoint = time;
double[] timePoints = getDataSetTimes(vcdataID);
int index = -1;
for (int i = 0; i < timePoints.length; i++) {
if (timePoint == timePoints[i]) {
index = i;
break;
}
}
double[] data = imageTimeSeries.getAllImages()[index].getDoublePixels();
PDEDataInfo pdeDataInfo = new PDEDataInfo(null, null, varName, time, 0);
VariableType varType = VariableType.VOLUME;
return new SimDataBlock(pdeDataInfo, data, varType);
}
@Override
public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
return false;
}
@Override
public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
return null;
}
@Override
public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
return null;
}
@Override
public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
return mesh;
}
@Override
public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
return new AnnotatedFunction[0];
}
@Override
public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
return imageTimeSeries.getImageTimeStamps();
}
@Override
public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
throw new RuntimeException("not yet implemented");
}
@Override
public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
throw new RuntimeException("not yet implemented");
}
@Override
public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
return new DataIdentifier[] { dataIdentifier };
}
@Override
public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
throw new RuntimeException("not yet implemented");
}
@Override
public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public double[] getVtuMeshData(OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws RemoteProxyException, DataAccessException {
// TODO Auto-generated method stub
return null;
}
@Override
public VtuVarInfo[] getVtuVarInfos(OutputContext outputContext, VCDataIdentifier vcDataIdentifier) throws DataAccessException, RemoteProxyException {
// TODO Auto-generated method stub
return null;
}
@Override
public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
// TODO Auto-generated method stub
return null;
}
};
DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {
@Override
public DataSetController getDataSetController() throws DataAccessException {
return dataSetController;
}
};
VCDataManager vcDataManager = new VCDataManager(dataSetControllerProvider);
OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {
public User getOwner() {
return new User("nouser", null);
}
public KeyValue getDataKey() {
return null;
}
public String getID() {
return "mydata";
}
};
PDEDataManager pdeDataManager = new PDEDataManager(outputContext, vcDataManager, vcDataIdentifier);
ClientPDEDataContext myPdeDataContext = new ClientPDEDataContext(pdeDataManager);
PDEDataViewer pdeDataViewer = new PDEDataViewer();
JFrame jframe = new JFrame();
jframe.setTitle(title);
jframe.getContentPane().add(pdeDataViewer);
jframe.setSize(1000, 600);
jframe.setVisible(true);
if (windowListener != null) {
jframe.addWindowListener(windowListener);
}
pdeDataViewer.setPdeDataContext(myPdeDataContext);
}
use of cbit.image.VCImage in project vcell by virtualcell.
the class Generate2DSimBioModelOp method generateBioModel.
public BioModel generateBioModel(Extent extent, ROI cellROI_2D, double[] timeStamps, Integer indexFirstPostbleach, double primaryDiffusionRate, double primaryFraction, double bleachMonitorRate, Double secondaryDiffusionRate, double secondaryFraction, Double bindingSiteConcentration, double bindingOnRate, double bindingOffRate, String extracellularName, String cytosolName, User owner, KeyValue simKey) throws PropertyVetoException, ExpressionException, ModelException, GeometryException, ImageException, MappingException, MathException, MatrixException {
if (owner == null) {
throw new IllegalArgumentException("Owner is not defined");
}
double df = primaryDiffusionRate;
double ff = primaryFraction;
double bwmRate = bleachMonitorRate;
double dc = 0.0;
double fc = 0.0;
if (secondaryDiffusionRate != null) {
dc = secondaryDiffusionRate;
fc = secondaryFraction;
}
double bs = 0.0;
double onRate = 0.0;
double offRate = 0.0;
if (bindingSiteConcentration != null) {
bs = bindingSiteConcentration;
onRate = bindingOnRate;
offRate = bindingOffRate;
}
// immobile fraction
double fimm = 1 - ff - fc;
if (fimm < epsilon && fimm > (0 - epsilon)) {
fimm = 0;
}
if (fimm < (1 + epsilon) && fimm > (1 - epsilon)) {
fimm = 1;
}
int startingIndexForRecovery = indexFirstPostbleach;
TimeBounds timeBounds = new TimeBounds(0.0, timeStamps[timeStamps.length - 1] - timeStamps[startingIndexForRecovery]);
double timeStepVal = timeStamps[startingIndexForRecovery + 1] - timeStamps[startingIndexForRecovery];
ROI cellROI = cellROI_2D;
int numX = cellROI.getISize().getX();
int numY = cellROI.getISize().getY();
int numZ = cellROI.getISize().getZ();
short[] shortPixels = cellROI.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 IllegalArgumentException("Cell ROI has no ExtraCellular.");
}
String EXTRACELLULAR_NAME = extracellularName;
String CYTOSOL_NAME = cytosolName;
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 = 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(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(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(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(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(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);
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);
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(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.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;
}
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