Examples with FilamentVariable cbit.vcell.math.FilamentVariable used on opensource projects

Example 6 with FilamentVariable

use of cbit.vcell.math.FilamentVariable in project vcell by virtualcell.

the class ModelOptimizationSpec method removeUncoupledParameters.

public void removeUncoupledParameters() {
    try {
        localIssueList.clear();
        MathMapping mathMapping = getSimulationContext().createNewMathMapping();
        MathDescription mathDesc = mathMapping.getMathDescription();
        MathSystemHash mathSystemHash = fromMath(mathDesc);
        Graph graph = mathSystemHash.getDependencyGraph(mathSystemHash.getSymbols());
        Tree[] spanningTrees = graph.getSpanningForest();
        // 
        for (int i = 0; i < spanningTrees.length; i++) {
            Node[] treeNodes = spanningTrees[i].getNodes();
            boolean bHasStateVariables = false;
            for (int j = 0; j < treeNodes.length; j++) {
                Node node = treeNodes[j];
                Variable var = mathDesc.getVariable(node.getName());
                if (var instanceof VolVariable || var instanceof MemVariable || var instanceof FilamentVariable || var instanceof VolumeRegionVariable || var instanceof MembraneRegionVariable || var instanceof FilamentRegionVariable) {
                    bHasStateVariables = true;
                    break;
                }
            }
            if (!bHasStateVariables) {
                spanningTrees = (Tree[]) BeanUtils.removeElement(spanningTrees, spanningTrees[i]);
                i--;
            }
        }
        // 
        // remove parameters not mapped to a surviving tree (not coupled to any state variables
        // 
        ArrayList<ParameterMappingSpec> paramMappingSpecsList = new ArrayList<ParameterMappingSpec>();
        paramMappingSpecsList.addAll(Arrays.asList(fieldParameterMappingSpecs));
        for (int i = 0; i < paramMappingSpecsList.size(); i++) {
            Parameter parameter = paramMappingSpecsList.get(i).getModelParameter();
            String mathName = mathMapping.getMathSymbolMapping().getVariable(parameter).getName();
            boolean bFoundInTree = false;
            for (int j = 0; j < spanningTrees.length; j++) {
                Node node = spanningTrees[j].getNode(mathName);
                if (node != null) {
                    bFoundInTree = true;
                }
            }
            if (!bFoundInTree) {
                paramMappingSpecsList.remove(i);
                i--;
            }
        }
        ParameterMappingSpec[] parameterMappingSpecs = new ParameterMappingSpec[paramMappingSpecsList.size()];
        paramMappingSpecsList.toArray(parameterMappingSpecs);
        setParameterMappingSpecs(parameterMappingSpecs);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        localIssueList.add(new Issue(this, localIssueContext, IssueCategory.ParameterEstimationGeneralWarning, e.getMessage(), Issue.SEVERITY_WARNING));
    // throw new RuntimeException(e.getMessage());
    }
}

Example 7 with FilamentVariable

use of cbit.vcell.math.FilamentVariable in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writeVariables.

/**
 *# Variables : type name unit time_dependent_flag advection_flag solve_whole_mesh_flag solve_regions
 *VARIABLE_BEGIN
 *VOLUME_ODE rB uM
 *VOLUME_PDE rf uM false false
 *VOLUME_PDE r uM false false
 *VOLUME_ODE rfB uM
 *VARIABLE_END
 * @throws MathException
 * @throws ExpressionException
 * @throws IOException
 */
private void writeVariables() throws MathException, ExpressionException, IOException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    printWriter.println("# Variables : type name domain time_dependent_flag advection_flag grad_flag solve_whole_mesh_flag solve_regions");
    printWriter.println(FVInputFileKeyword.VARIABLE_BEGIN);
    MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
    Variable[] vars = simSymbolTable.getVariables();
    ArrayList<RandomVariable> rvList = new ArrayList<RandomVariable>();
    for (int i = 0; i < vars.length; i++) {
        String varName = vars[i].getName();
        String domainName = vars[i].getDomain() == null ? null : vars[i].getDomain().getName();
        if (vars[i] instanceof VolumeRandomVariable || vars[i] instanceof MembraneRandomVariable) {
            rvList.add((RandomVariable) vars[i]);
        } else if (vars[i] instanceof VolVariable) {
            if (bChomboSolver && domainName == null) {
                throw new MathException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " requires that every variable is defined in a single domain");
            }
            VolVariable volVar = (VolVariable) vars[i];
            if (mathDesc.isPDE(volVar)) {
                boolean hasTimeVaryingDiffusionOrAdvection = simSymbolTable.hasTimeVaryingDiffusionOrAdvection(volVar);
                final boolean hasVelocity = mathDesc.hasVelocity(volVar);
                final boolean hasGradient = mathDesc.hasGradient(volVar);
                if (mathDesc.isPdeSteady(volVar)) {
                    printWriter.print("VOLUME_PDE_STEADY ");
                } else {
                    printWriter.print("VOLUME_PDE ");
                }
                printWriter.print(varName + " " + domainName + " " + hasTimeVaryingDiffusionOrAdvection + " " + hasVelocity + " " + hasGradient);
            } else {
                printWriter.print("VOLUME_ODE " + varName + " " + domainName);
            }
            if (domainName == null) {
                Vector<SubDomain> listOfSubDomains = new Vector<SubDomain>();
                int totalNumCompartments = 0;
                Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
                while (subDomainEnum.hasMoreElements()) {
                    SubDomain subDomain = subDomainEnum.nextElement();
                    if (subDomain instanceof CompartmentSubDomain) {
                        CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) subDomain;
                        totalNumCompartments++;
                        Equation varEquation = subDomain.getEquation(vars[i]);
                        if (varEquation != null) {
                            if (!(varEquation instanceof PdeEquation) || !((PdeEquation) varEquation).isDummy(simSymbolTable, compartmentSubDomain)) {
                                listOfSubDomains.add(compartmentSubDomain);
                            }
                        }
                    }
                }
                if ((totalNumCompartments == listOfSubDomains.size()) || (listOfSubDomains.size() == 0 && simTask.getSimulation().getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE))) {
                    printWriter.print(" true");
                } else {
                    printWriter.print(" false");
                    for (int j = 0; j < listOfSubDomains.size(); j++) {
                        CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) listOfSubDomains.elementAt(j);
                        printWriter.print(" " + compartmentSubDomain.getName());
                    }
                }
                printWriter.println();
            } else {
                printWriter.println(" false " + domainName);
            }
        } else if (vars[i] instanceof VolumeParticleVariable) {
            printWriter.println(FVInputFileKeyword.VOLUME_PARTICLE + " " + varName + " " + domainName);
        } else if (vars[i] instanceof MembraneParticleVariable) {
            printWriter.println(FVInputFileKeyword.MEMBRANE_PARTICLE + " " + varName + " " + domainName);
        } else if (vars[i] instanceof VolumeRegionVariable) {
            printWriter.println("VOLUME_REGION " + varName + " " + domainName);
        } else if (vars[i] instanceof MemVariable) {
            if (bChomboSolver && domainName == null) {
                throw new MathException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " requires that every variable is defined in a single domain");
            }
            MemVariable memVar = (MemVariable) vars[i];
            if (mathDesc.isPDE(memVar)) {
                printWriter.println("MEMBRANE_PDE " + varName + " " + domainName + " " + simSymbolTable.hasTimeVaryingDiffusionOrAdvection(memVar));
            } else {
                printWriter.println("MEMBRANE_ODE " + varName + " " + domainName);
            }
        } else if (vars[i] instanceof MembraneRegionVariable) {
            printWriter.println("MEMBRANE_REGION " + varName + " " + domainName);
        } else if (vars[i] instanceof FilamentVariable) {
            throw new RuntimeException("Filament application not supported yet");
        }
    }
    int numRandomVariables = rvList.size();
    if (numRandomVariables > 0) {
        ISize samplingSize = simTask.getSimulation().getMeshSpecification().getSamplingSize();
        String[] varNameArr = new String[numRandomVariables];
        VariableType[] varTypeArr = new VariableType[numRandomVariables];
        double[][] dataArr = new double[numRandomVariables][];
        for (int i = 0; i < numRandomVariables; i++) {
            RandomVariable rv = rvList.get(i);
            varNameArr[i] = rv.getName();
            int numRandomNumbers = 0;
            if (rv instanceof VolumeRandomVariable) {
                printWriter.print("VOLUME_RANDOM");
                varTypeArr[i] = VariableType.VOLUME;
                numRandomNumbers = samplingSize.getXYZ();
            } else if (rv instanceof MembraneRandomVariable) {
                printWriter.print("MEMBRANE_RANDOM");
                varTypeArr[i] = VariableType.MEMBRANE;
                numRandomNumbers = resampledGeometry.getGeometrySurfaceDescription().getSurfaceCollection().getTotalPolygonCount();
            } else {
                throw new RuntimeException("Unknown RandomVariable type");
            }
            printWriter.println(" " + varNameArr[i]);
            dataArr[i] = generateRandomNumbers(rv, numRandomNumbers);
        }
        File rvFile = new File(workingDirectory, simTask.getSimulationJobID() + RANDOM_VARIABLE_FILE_EXTENSION);
        DataSet.writeNew(rvFile, varNameArr, varTypeArr, samplingSize, dataArr);
    }
    printWriter.println(FVInputFileKeyword.VARIABLE_END);
    printWriter.println();
}

Example 8 with FilamentVariable

use of cbit.vcell.math.FilamentVariable in project vcell by virtualcell.

the class MathTestingUtilities method substituteWithExactSolution.

/**
 * Insert the method's description here.
 * Creation date: (1/24/2003 10:18:14 AM)
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param subDomain cbit.vcell.math.SubDomain
 */
private static Expression substituteWithExactSolution(Expression origExp, MembraneSubDomain subDomain, MathDescription exactMathDesc) throws ExpressionException {
    Expression substitutedExp = new Expression(origExp);
    substitutedExp.bindExpression(exactMathDesc);
    substitutedExp = MathUtilities.substituteFunctions(substitutedExp, exactMathDesc);
    substitutedExp.bindExpression(null);
    substitutedExp = substitutedExp.flatten();
    substitutedExp.bindExpression(exactMathDesc);
    String[] symbols = substitutedExp.getSymbols();
    for (int i = 0; symbols != null && i < symbols.length; i++) {
        Variable var = (Variable) substitutedExp.getSymbolBinding(symbols[i]);
        if (var instanceof MemVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof InsideVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getInsideCompartment().getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof OutsideVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getOutsideCompartment().getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof VolumeRegionVariable || var instanceof MemVariable || var instanceof MembraneRegionVariable || var instanceof FilamentVariable || var instanceof FilamentRegionVariable) {
            throw new RuntimeException("variable substitution not yet implemented for Variable type " + var.getClass().getName() + "(" + var.getName() + ")");
        }
    }
    substitutedExp.bindExpression(null);
    return substitutedExp;
}

Example 9 with FilamentVariable

use of cbit.vcell.math.FilamentVariable in project vcell by virtualcell.

the class MathTestingUtilities method substituteWithExactSolution.

/**
 * Insert the method's description here.
 * Creation date: (1/24/2003 10:18:14 AM)
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param subDomain cbit.vcell.math.SubDomain
 */
private static Expression substituteWithExactSolution(Expression origExp, CompartmentSubDomain subDomain, MathDescription exactMathDesc) throws ExpressionException {
    Expression substitutedExp = new Expression(origExp);
    substitutedExp.bindExpression(exactMathDesc);
    substitutedExp = MathUtilities.substituteFunctions(substitutedExp, exactMathDesc);
    substitutedExp.bindExpression(null);
    substitutedExp = substitutedExp.flatten();
    substitutedExp.bindExpression(exactMathDesc);
    String[] symbols = substitutedExp.getSymbols();
    for (int i = 0; i < symbols.length; i++) {
        Variable var = (Variable) substitutedExp.getSymbolBinding(symbols[i]);
        if (var instanceof VolVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof VolumeRegionVariable || var instanceof MemVariable || var instanceof MembraneRegionVariable || var instanceof FilamentVariable || var instanceof FilamentRegionVariable) {
            throw new RuntimeException("variable substitution not yet implemented for Variable type " + var.getClass().getName() + "(" + var.getName() + ")");
        }
    }
    substitutedExp.bindExpression(null);
    return substitutedExp;
}