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Example 36 with VariableType

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

the class MathTestingUtilities method comparePDEResults.

/**
 * Insert the method's description here.
 * Creation date: (8/20/2003 12:58:10 PM)
 */
public static SimulationComparisonSummary comparePDEResults(SimulationSymbolTable testSimSymbolTable, PDEDataManager testDataManager, SimulationSymbolTable refSimSymbolTable, PDEDataManager refDataManager, String[] varsToCompare, double absErrorThreshold, double relErrorThreshold, VCDocument refDocument, DataInfoProvider refDataInfoProvider, VCDocument testDocument, DataInfoProvider testDataInfoProvider) throws DataAccessException, ExpressionException {
    java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
    boolean bTimesEqual = true;
    double[] testTimeArray = testDataManager.getDataSetTimes();
    double[] refTimeArray = refDataManager.getDataSetTimes();
    if (testTimeArray.length != refTimeArray.length) {
        bTimesEqual = false;
    // throw new RuntimeException("Data times for reference and test simulations don't match, cannot compare the two simulations!");
    } else {
        for (int i = 0; i < testTimeArray.length; i++) {
            if (testTimeArray[i] != refTimeArray[i]) {
                bTimesEqual = false;
            }
        }
    }
    // if (!checkSimVars(testSim, refSim)) {
    // //String errorS = "TestVars - ";
    // Variable[] testVars = testSim.getVariables();
    // //for(int i =0;i<vars.length;i+= 1){
    // //errorS+= vars[i].getName()+" ";
    // //}
    // //errorS+=" <<>> RefVars - ";
    // Variable[] refVars = refSim.getVariables();
    // //for(int i =0;i<vars.length;i+= 1){
    // //errorS+= vars[i].getName()+" ";
    // //}
    // throw new RuntimeException(
    // "VarNotMatch testLength="+(testVars != null?testVars.length+"":"null")+" refLength="+(refVars != null?refVars.length+"":"null"));
    // }
    CartesianMesh testMesh = testDataManager.getMesh();
    MathDescription testMathDesc = testSimSymbolTable.getSimulation().getMathDescription();
    // Variable[] refVars = refSim.getVariables();
    MathDescription refMathDesc = refSimSymbolTable.getSimulation().getMathDescription();
    CartesianMesh refMesh = refDataManager.getMesh();
    int[] membraneIndexMapping = null;
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable for testSimulation
    int testNumVol = testMesh.getSizeX() * testMesh.getSizeY() * testMesh.getSizeZ();
    CompartmentSubDomain[] testVolSubDomainLookup = new CompartmentSubDomain[testNumVol];
    for (int i = 0; i < testNumVol; i++) {
        int subVolumeIndex = testMesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = testMathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = testMathDesc.getCompartmentSubDomain(subVolume.getName());
        testVolSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable for testSimulation
    int testNumMem = testMesh.getMembraneElements().length;
    MembraneSubDomain[] testMemSubDomainLookup = new MembraneSubDomain[testNumMem];
    for (int i = 0; i < testNumMem; i++) {
        int insideVolIndex = testMesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = testMesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = testMathDesc.getMembraneSubDomain(testVolSubDomainLookup[insideVolIndex], testVolSubDomainLookup[outsideVolIndex]);
        testMemSubDomainLookup[i] = memSubDomain;
    }
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable for refSimulation
    int refNumVol = refMesh.getSizeX() * refMesh.getSizeY() * refMesh.getSizeZ();
    CompartmentSubDomain[] refVolSubDomainLookup = new CompartmentSubDomain[refNumVol];
    for (int i = 0; i < refNumVol; i++) {
        int subVolumeIndex = refMesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = refMathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = refMathDesc.getCompartmentSubDomain(subVolume.getName());
        refVolSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable for refSimulation
    int refNumMem = refMesh.getMembraneElements().length;
    MembraneSubDomain[] refMemSubDomainLookup = new MembraneSubDomain[refNumMem];
    for (int i = 0; i < refNumMem; i++) {
        int insideVolIndex = refMesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = refMesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = refMathDesc.getMembraneSubDomain(refVolSubDomainLookup[insideVolIndex], refVolSubDomainLookup[outsideVolIndex]);
        refMemSubDomainLookup[i] = memSubDomain;
    }
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    String hashKey = new String("");
    DataErrorSummary tempVar = null;
    DataIdentifier[] refDataIDs = refDataManager.getDataIdentifiers();
    // for each var, do the following :
    for (int i = 0; i < varsToCompare.length; i++) {
        DataIdentifier refDataID = null;
        for (int j = 0; j < refDataIDs.length; j++) {
            if (refDataIDs[j].getName().equals(varsToCompare[i])) {
                refDataID = refDataIDs[j];
                break;
            }
        }
        // 
        // Find REFERENCE variable
        // 
        Variable refVar = getSimVar(refSimSymbolTable, varsToCompare[i]);
        if (refVar == null) {
            // Should only happen if TEST sims were generated 'post-domains' and REFERENCE sims were generated 'pre-domains'
            if (refDataID != null) {
                throw new RuntimeException("Unexpected reference condition: '" + varsToCompare[i] + "' not found in symboltable but was found in dataidentifiers");
            }
            if (testDocument instanceof BioModel) {
                // Only BioModels need to be checked
                // Look in TEST for a speciescontext with matching species name
                System.out.println("ReferenceVariable: using alternate method to find '" + varsToCompare[i] + "'");
                BioModel refBioModel = (BioModel) refDocument;
                BioModel testBioModel = (BioModel) testDocument;
                SpeciesContext testSpeciesContext = testBioModel.getModel().getSpeciesContext(varsToCompare[i]);
                if (testSpeciesContext != null) {
                    refVar = refSimSymbolTable.getVariable(testSpeciesContext.getSpecies().getCommonName());
                    for (int j = 0; j < refDataIDs.length; j++) {
                        if (refDataIDs[j].getName().equals(testSpeciesContext.getSpecies().getCommonName())) {
                            refDataID = refDataIDs[j];
                            break;
                        }
                    }
                }
            }
            if (refVar == null || refDataID == null) {
                Simulation refSim = refSimSymbolTable.getSimulation();
                throw new RuntimeException("The variable " + varsToCompare[i] + " was not found in Simulation (" + refSim.getName() + " " + refSim.getVersion().getDate() + ")\n");
            }
        }
        // 
        // Find TEST variable (assumed to have sims generated with a software version later than REFERENCE)
        // 
        Variable testVar = getSimVar(testSimSymbolTable, varsToCompare[i]);
        if (testVar == null) {
            // Should only happen if TEST sims were generated 'post-domains' and REFERENCE sims were generated 'pre-domains'
            System.out.println("TestVariable: using alternate method to find '" + varsToCompare[i] + "'");
            BioModel testBioModel = (BioModel) testDocument;
            SpeciesContext[] speciesContexts = testBioModel.getModel().getSpeciesContexts();
            boolean bSkip = false;
            for (int j = 0; j < speciesContexts.length; j++) {
                if (speciesContexts[j].getSpecies().getCommonName().equals(varsToCompare[i])) {
                    testVar = testSimSymbolTable.getVariable(speciesContexts[j].getName());
                    if (testVar == null) {
                        throw new RuntimeException("Speciescontext name '" + speciesContexts[j].getName() + "' not found in testsimsymboltable");
                    }
                    // If we got here it means at least one matching speciescontext was found in TEST with
                    // a species name matching varsToCompare[i].  We can skip because the matching speciesconetext
                    // will be used to do a comparison at some point.
                    bSkip = true;
                    break;
                }
            }
            if (bSkip) {
                // these are tested already using full simcontext names
                System.out.println("Skipping '" + varsToCompare[i] + "' as lookup in testSimSymbolTable");
                continue;
            }
            Simulation refSim = refSimSymbolTable.getSimulation();
            throw new RuntimeException("The variable " + varsToCompare[i] + " was not found in Simulation (" + refSim.getName() + " " + refSim.getVersion().getDate() + ")\n");
        }
        // for each time in timeArray. ('t' is used to index the testTimeArray, for interpolation purposes.)
        int t = 0;
        for (int j = 0; j < refTimeArray.length; j++) {
            // get data block from varName, data from datablock
            SimDataBlock refSimDataBlock = refDataManager.getSimDataBlock(refVar.getName(), refTimeArray[j]);
            double[] refData = refSimDataBlock.getData();
            double[] resampledTestData = null;
            if (bTimesEqual) {
                // If time arrays for both sims are equal, no need to resample/interpolate, just obtain the datablock from dataManager
                SimDataBlock testSimDataBlock = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[j]);
                resampledTestData = testSimDataBlock.getData();
            } else {
                // Time resampling (interpolation) needed.
                while ((t < testTimeArray.length - 2) && (refTimeArray[j] >= testTimeArray[t + 1])) {
                    t++;
                }
                SimDataBlock testSimDataBlock_1 = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[t]);
                double[] testData_1 = testSimDataBlock_1.getData();
                SimDataBlock testSimDataBlock_2 = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[t + 1]);
                double[] testData_2 = testSimDataBlock_2.getData();
                resampledTestData = new double[testData_1.length];
                // 
                for (int m = 0; m < testData_1.length; m++) {
                    resampledTestData[m] = testData_1[m] + (testData_2[m] - testData_1[m]) * (refTimeArray[j] - testTimeArray[t]) / (testTimeArray[t + 1] - testTimeArray[t]);
                }
            }
            // Spatial resampling (interpolation) ...
            double[] spaceResampledData = new double[refData.length];
            if (!testMathDesc.getGeometry().getExtent().compareEqual(refMathDesc.getGeometry().getExtent()) || !testMathDesc.getGeometry().getOrigin().compareEqual(refMathDesc.getGeometry().getOrigin())) {
                throw new RuntimeException("Different origins and/or extents for the 2 geometries. Cannot compare the 2 simulations");
            }
            if (testMesh.getSizeX() != refMesh.getSizeX() || testMesh.getSizeY() != refMesh.getSizeY() || testMesh.getSizeZ() != refMesh.getSizeZ()) {
                if (testVar instanceof VolVariable) {
                    if (testMathDesc.getGeometry().getDimension() == 1 && refMathDesc.getGeometry().getDimension() == 1) {
                        spaceResampledData = resample1DSpatial(resampledTestData, testMesh, refMesh);
                    } else if (testMathDesc.getGeometry().getDimension() == 2 && refMathDesc.getGeometry().getDimension() == 2) {
                        spaceResampledData = resample2DSpatial(resampledTestData, testMesh, refMesh);
                    } else if (testMathDesc.getGeometry().getDimension() == 3 && refMathDesc.getGeometry().getDimension() == 3) {
                        spaceResampledData = resample3DSpatial(resampledTestData, testMesh, refMesh);
                    } else {
                        throw new RuntimeException("Comparison of 2 simulations with different geometry dimensions are not handled at this time!");
                    }
                } else {
                    throw new RuntimeException("spatial resampling for variable type: " + testVar.getClass().getName() + " not supported");
                }
            } else {
                // no space resampling required
                if (testVar instanceof MemVariable) {
                    // 
                    if (membraneIndexMapping == null) {
                        membraneIndexMapping = testMesh.getMembraneIndexMapping(refMesh);
                    }
                    spaceResampledData = new double[resampledTestData.length];
                    for (int k = 0; k < resampledTestData.length; k++) {
                        spaceResampledData[k] = resampledTestData[membraneIndexMapping[k]];
                    }
                } else {
                    // 
                    // no reordering needed for other variable types.
                    // 
                    spaceResampledData = resampledTestData;
                }
            }
            // for each point in data block ...
            testDataInfoProvider.getPDEDataContext().setVariableName(testVar.getName());
            for (int k = 0; k < refData.length; k++) {
                if (!testDataInfoProvider.isDefined(k)) {
                    continue;
                }
                // Determine maxRef, minRef, maxAbsErr for variable
                // SubDomain testSubDomain = null;
                String sn = null;
                VariableType refVarType = refDataID.getVariableType();
                if (refVarType.equals(VariableType.VOLUME)) {
                    // testSubDomain = refVolSubDomainLookup[k];
                    sn = refVolSubDomainLookup[k].getName();
                } else if (refVarType.equals(VariableType.MEMBRANE)) {
                    // testSubDomain = refMemSubDomainLookup[k];
                    sn = refMemSubDomainLookup[k].getName();
                } else if (refVarType.equals(VariableType.MEMBRANE_REGION)) {
                    sn = "MRV_" + i;
                } else if (refVarType.equals(VariableType.VOLUME_REGION)) {
                    sn = "VRV_" + i;
                } else {
                    throw new RuntimeException("Var " + refVar.getName() + " not supported yet!");
                }
                // hashKey = refVar.getName()+":"+testSubDomain.getName();
                hashKey = refVar.getName() + ":" + sn;
                tempVar = tempVarHash.get(hashKey);
                if (tempVar == null) {
                    tempVar = new DataErrorSummary(null);
                    tempVarHash.put(hashKey, tempVar);
                }
                tempVar.addDataValues(refData[k], spaceResampledData[k], refTimeArray[j], k, absErrorThreshold, relErrorThreshold);
            }
        // end for (k)
        }
    // end for (j)
    }
    // end for (i)
    Enumeration<String> enumKeys = tempVarHash.keys();
    while (enumKeys.hasMoreElements()) {
        String key = enumKeys.nextElement();
        DataErrorSummary tempVarSummary = tempVarHash.get(key);
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}
Also used : MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) DataIdentifier(cbit.vcell.simdata.DataIdentifier) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) InsideVariable(cbit.vcell.math.InsideVariable) SensVariable(cbit.vcell.solver.ode.SensVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) VolVariable(cbit.vcell.math.VolVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) ReservedVariable(cbit.vcell.math.ReservedVariable) MemVariable(cbit.vcell.math.MemVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) MathDescription(cbit.vcell.math.MathDescription) SpeciesContext(cbit.vcell.model.SpeciesContext) SimDataBlock(cbit.vcell.simdata.SimDataBlock) MemVariable(cbit.vcell.math.MemVariable) SubVolume(cbit.vcell.geometry.SubVolume) AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume) VariableType(cbit.vcell.math.VariableType) VolVariable(cbit.vcell.math.VolVariable) CartesianMesh(cbit.vcell.solvers.CartesianMesh) Simulation(cbit.vcell.solver.Simulation) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) BioModel(cbit.vcell.biomodel.BioModel)

Example 37 with VariableType

use of cbit.vcell.math.VariableType 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();
}
Also used : FilamentVariable(cbit.vcell.math.FilamentVariable) VolVariable(cbit.vcell.math.VolVariable) ReservedVariable(cbit.vcell.math.ReservedVariable) ParameterVariable(cbit.vcell.math.ParameterVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) MemVariable(cbit.vcell.math.MemVariable) Variable(cbit.vcell.math.Variable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) MathDescription(cbit.vcell.math.MathDescription) ISize(org.vcell.util.ISize) ArrayList(java.util.ArrayList) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) SubDomain(cbit.vcell.math.SubDomain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) PdeEquation(cbit.vcell.math.PdeEquation) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MemVariable(cbit.vcell.math.MemVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) Vector(java.util.Vector) Enumeration(java.util.Enumeration) VariableType(cbit.vcell.math.VariableType) VolVariable(cbit.vcell.math.VolVariable) SimulationSymbolTable(cbit.vcell.solver.SimulationSymbolTable) MeasureEquation(cbit.vcell.math.MeasureEquation) PdeEquation(cbit.vcell.math.PdeEquation) VolumeRegionEquation(cbit.vcell.math.VolumeRegionEquation) MembraneRegionEquation(cbit.vcell.math.MembraneRegionEquation) Equation(cbit.vcell.math.Equation) MathException(cbit.vcell.math.MathException) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) File(java.io.File)

Example 38 with VariableType

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

the class XmlReader method getOutputFunction.

private AnnotatedFunction getOutputFunction(Element param) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String temp = param.getText();
    Expression exp = unMangleExpression(temp);
    String errStr = unMangle(param.getAttributeValue(XMLTags.ErrorStringTag));
    VariableType funcType = VariableType.UNKNOWN;
    String funcTypeAttr = param.getAttributeValue(XMLTags.FunctionTypeTag);
    if (funcTypeAttr != null) {
        String funcTypeStr = unMangle(funcTypeAttr);
        funcType = VariableType.getVariableTypeFromVariableTypeName(funcTypeStr);
    }
    // -- create new AnnotatedFunction --
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    AnnotatedFunction function = new AnnotatedFunction(name, exp, domain, errStr, funcType, FunctionCategory.OUTPUTFUNCTION);
    return function;
}
Also used : VariableType(cbit.vcell.math.VariableType) Expression(cbit.vcell.parser.Expression) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) Domain(cbit.vcell.math.Variable.Domain) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)

Example 39 with VariableType

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

the class OutputFunctionsListTableModel method setValueAt.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2004 2:01:23 PM)
 * @param aValue java.lang.Object
 * @param rowIndex int
 * @param columnIndex int
 */
public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    AnnotatedFunction outputFunction = getValueAt(rowIndex);
    switch(columnIndex) {
        case COLUMN_OUTPUTFN_EXPRESSION:
            {
                try {
                    Expression exp = new Expression((String) aValue);
                    if (exp.compareEqual(outputFunction.getExpression())) {
                        return;
                    }
                    exp.bindExpression(outputFunctionContext);
                    VariableType vt = outputFunctionContext.computeFunctionTypeWRTExpression(outputFunction, exp);
                    if (!vt.compareEqual(outputFunction.getFunctionType())) {
                    }
                    outputFunction.setExpression(exp);
                    fireTableRowsUpdated(rowIndex, rowIndex);
                    outputFunctionContext.firePropertyChange("outputFunctions", null, outputFunctionContext.getOutputFunctionsList());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
                } catch (InconsistentDomainException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
                }
                break;
            }
    }
}
Also used : VariableType(cbit.vcell.math.VariableType) ScopedExpression(cbit.gui.ScopedExpression) Expression(cbit.vcell.parser.Expression) InconsistentDomainException(cbit.vcell.math.InconsistentDomainException) ExpressionException(cbit.vcell.parser.ExpressionException) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)

Example 40 with VariableType

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

the class OutputFunctionsPanel method addFunction.

private void addFunction() throws Exception {
    String funcName = getFunctionNameTextField().getText();
    Expression funcExp = null;
    funcExp = new Expression(getFunctionExpressionTextField().getText());
    Domain domain = null;
    VariableType newFunctionVariableType = null;
    boolean bSpatial = simulationWorkspace.getSimulationOwner().getGeometry().getDimension() > 0;
    if (bSpatial) {
        Object selectedItem = getSubdomainComboBox().getSelectedItem();
        if (selectedItem instanceof GeometryClass) {
            GeometryClass geoClass = (GeometryClass) selectedItem;
            domain = new Domain(geoClass);
            if (selectedItem instanceof SubVolume) {
                newFunctionVariableType = VariableType.VOLUME;
            } else if (selectedItem instanceof SurfaceClass) {
                newFunctionVariableType = VariableType.MEMBRANE;
            }
        } else if (selectedItem instanceof VariableType) {
            newFunctionVariableType = (VariableType) selectedItem;
        } else {
            newFunctionVariableType = VariableType.UNKNOWN;
        }
    } else {
        newFunctionVariableType = VariableType.NONSPATIAL;
    }
    AnnotatedFunction tempFunction = new AnnotatedFunction(funcName, funcExp, domain, null, newFunctionVariableType, FunctionCategory.OUTPUTFUNCTION);
    VariableType vt = outputFunctionContext.computeFunctionTypeWRTExpression(tempFunction, funcExp);
    FunctionCategory category = FunctionCategory.OUTPUTFUNCTION;
    if (vt.equals(VariableType.POSTPROCESSING)) {
        category = FunctionCategory.POSTPROCESSFUNCTION;
    }
    AnnotatedFunction newFunction = new AnnotatedFunction(funcName, funcExp, domain, null, vt, category);
    outputFunctionContext.addOutputFunction(newFunction);
    setSelectedObjects(new Object[] { newFunction });
    enableDeleteFnButton();
}
Also used : GeometryClass(cbit.vcell.geometry.GeometryClass) VariableType(cbit.vcell.math.VariableType) Expression(cbit.vcell.parser.Expression) SurfaceClass(cbit.vcell.geometry.SurfaceClass) SubVolume(cbit.vcell.geometry.SubVolume) Domain(cbit.vcell.math.Variable.Domain) FunctionCategory(cbit.vcell.solver.AnnotatedFunction.FunctionCategory) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)

Aggregations

VariableType (cbit.vcell.math.VariableType)54 CartesianMesh (cbit.vcell.solvers.CartesianMesh)17 DataAccessException (org.vcell.util.DataAccessException)15 File (java.io.File)13 ISize (org.vcell.util.ISize)12 Expression (cbit.vcell.parser.Expression)11 ExternalDataIdentifier (org.vcell.util.document.ExternalDataIdentifier)11 SinglePoint (cbit.vcell.geometry.SinglePoint)10 VCDataIdentifier (org.vcell.util.document.VCDataIdentifier)10 Domain (cbit.vcell.math.Variable.Domain)9 ExpressionException (cbit.vcell.parser.ExpressionException)9 DataIdentifier (cbit.vcell.simdata.DataIdentifier)9 ArrayList (java.util.ArrayList)9 AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)8 ReservedVariable (cbit.vcell.math.ReservedVariable)8 Variable (cbit.vcell.math.Variable)8 SimDataBlock (cbit.vcell.simdata.SimDataBlock)8 VCSimulationDataIdentifier (cbit.vcell.solver.VCSimulationDataIdentifier)8 Hashtable (java.util.Hashtable)8 MathException (cbit.vcell.math.MathException)7