use of cbit.vcell.solver.TimeStep in project vcell by virtualcell.
the class MatcheableTest method null2.
@Test
public void null2() {
TimeStep t = null;
SequenceLocation sl = null;
assertTrue(Matchable.areEqual(t, t));
assertTrue(Matchable.areEqual(t, sl));
assertTrue(Matchable.areEqual(t, null));
}
use of cbit.vcell.solver.TimeStep 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;
}
use of cbit.vcell.solver.TimeStep 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;
}
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