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

Example 41 with Function

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

the class GibsonSolver method getStochSolverResultSet.

/**
 * Get data columns and function columns to be ready for plot.
 * Creation date: (8/15/2006 11:36:43 AM)
 * @return cbit.vcell.solver.stoch.StochSolverResultSet
 */
public ODESolverResultSet getStochSolverResultSet() {
    // read .stoch file, this funciton here equals to getODESolverRestultSet()+getStateVariableResultSet()  in ODE.
    ODESolverResultSet stSolverResultSet = new ODESolverResultSet();
    FileInputStream inputStream = null;
    try {
        inputStream = new FileInputStream(getBaseName() + IDA_DATA_EXTENSION);
        InputStreamReader inputStreamReader = new InputStreamReader(inputStream);
        BufferedReader bufferedReader = new BufferedReader(inputStreamReader);
        // Read header
        String line = bufferedReader.readLine();
        if (line == null) {
            // throw exception
            System.out.println("There is no data in output file!");
            return null;
        }
        while (line.indexOf(':') > 0) {
            String name = line.substring(0, line.indexOf(':'));
            stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
            line = line.substring(line.indexOf(':') + 1);
        }
        // Read data
        while ((line = bufferedReader.readLine()) != null) {
            line = line + "\t";
            double[] values = new double[stSolverResultSet.getDataColumnCount()];
            boolean bCompleteRow = true;
            for (int i = 0; i < stSolverResultSet.getDataColumnCount(); i++) {
                if (line.indexOf('\t') == -1) {
                    bCompleteRow = false;
                    break;
                } else {
                    String value = line.substring(0, line.indexOf('\t')).trim();
                    values[i] = Double.valueOf(value).doubleValue();
                    line = line.substring(line.indexOf('\t') + 1);
                }
            }
            if (bCompleteRow) {
                stSolverResultSet.addRow(values);
            } else {
                break;
            }
        }
    // 
    } catch (Exception e) {
        e.printStackTrace(System.out);
        return null;
    } finally {
        try {
            if (inputStream != null) {
                inputStream.close();
            }
        } catch (Exception ex) {
            lg.error(ex.getMessage(), ex);
        }
    }
    /*
	Add appropriate Function columns to result set if the stochastic simulation is to display the trajectory.
	No function columns for the results of multiple stochastic trials
	*/
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    if (simSymbolTable.getSimulation().getSolverTaskDescription().getStochOpt().getNumOfTrials() == 1) {
        Function[] functions = simSymbolTable.getFunctions();
        for (int i = 0; i < functions.length; i++) {
            if (SimulationSymbolTable.isFunctionSaved(functions[i])) {
                Expression exp1 = new Expression(functions[i].getExpression());
                try {
                    exp1 = simSymbolTable.substituteFunctions(exp1);
                } catch (MathException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
                }
                try {
                    FunctionColumnDescription cd = new FunctionColumnDescription(exp1.flatten(), functions[i].getName(), null, functions[i].getName(), false);
                    stSolverResultSet.addFunctionColumn(cd);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                }
            }
        }
    }
    return stSolverResultSet;
}

Example 42 with Function

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

the class HybridSolver method getHybridSolverResultSet.

/**
 * Get data columns and function columns to be ready for plot.
 * Creation date: (8/15/2006 11:36:43 AM)
 * @return cbit.vcell.solver.stoch.StochSolverResultSet
 */
private ODESolverResultSet getHybridSolverResultSet() {
    // read .stoch file, this funciton here equals to getODESolverRestultSet()+getStateVariableResultSet()  in ODE.
    ODESolverResultSet stSolverResultSet = new ODESolverResultSet();
    try {
        String filename = getBaseName() + NETCDF_DATA_EXTENSION;
        NetCDFEvaluator ncEva = new NetCDFEvaluator();
        NetCDFReader ncReader = null;
        try {
            ncEva.setNetCDFTarget(filename);
            ncReader = ncEva.getNetCDFReader();
        } catch (Exception e) {
            e.printStackTrace(System.err);
            throw new RuntimeException("Cannot open simulation result file: " + filename + "!");
        }
        // Read result according to trial number
        if (ncReader.getNumTrials() == 1) {
            // Read header
            String[] varNames = ncReader.getSpeciesNames_val();
            // first column will be time t.
            stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
            // following columns are stoch variables
            for (int i = 0; i < varNames.length; i++) {
                stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(varNames[i]));
            }
            // Read data
            // data only, no time points
            ArrayDouble data = (ArrayDouble) ncEva.getTimeSeriesData(1);
            double[] timePoints = ncReader.getTimePoints();
            System.out.println("time points length is " + timePoints.length);
            // shape[0]:num of timepoints, shape[1]: num of species
            int[] shape = data.getShape();
            if (// one species
            shape.length == 1) {
                ArrayDouble.D1 temData = (ArrayDouble.D1) data;
                System.out.println("one species in time series data and size is " + temData.getSize());
                for (// rows
                int k = 0; // rows
                k < timePoints.length; // rows
                k++) {
                    double[] values = new double[stSolverResultSet.getDataColumnCount()];
                    values[0] = timePoints[k];
                    for (int i = 1; i < stSolverResultSet.getDataColumnCount(); i++) {
                        values[i] = temData.get(k);
                    }
                    stSolverResultSet.addRow(values);
                }
            }
            if (// more than one species
            shape.length == 2) {
                ArrayDouble.D2 temData = (ArrayDouble.D2) data;
                System.out.println("multiple species in time series, the length of time series is :" + data.getShape()[0] + ", and the total number of speceis is: " + data.getShape()[1]);
                for (// rows
                int k = 0; // rows
                k < timePoints.length; // rows
                k++) {
                    double[] values = new double[stSolverResultSet.getDataColumnCount()];
                    values[0] = timePoints[k];
                    for (int i = 1; i < stSolverResultSet.getDataColumnCount(); i++) {
                        values[i] = temData.get(k, i - 1);
                    }
                    stSolverResultSet.addRow(values);
                }
            }
        } else if (ncReader.getNumTrials() > 1) {
            // Read header
            String[] varNames = ncReader.getSpeciesNames_val();
            // first column will be time t.
            stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("TrialNo"));
            // following columns are stoch variables
            for (int i = 0; i < varNames.length; i++) {
                stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(varNames[i]));
            }
            // Read data
            // data only, no trial numbers
            ArrayDouble data = (ArrayDouble) ncEva.getDataOverTrials(ncReader.getTimePoints().length - 1);
            int[] trialNum = ncEva.getNetCDFReader().getTrialNumbers();
            // System.out.println("total trials are "+trialNum.length);
            // shape[0]:number of trials, shape[1]: num of species
            int[] shape = data.getShape();
            if (// one species
            shape.length == 1) {
                ArrayDouble.D1 temData = (ArrayDouble.D1) data;
                // System.out.println("one species over trials, size is: "+temData.getSize());
                for (// rows
                int k = 0; // rows
                k < trialNum.length; // rows
                k++) {
                    double[] values = new double[stSolverResultSet.getDataColumnCount()];
                    values[0] = trialNum[k];
                    for (int i = 1; i < stSolverResultSet.getDataColumnCount(); i++) {
                        values[i] = temData.get(k);
                    }
                    stSolverResultSet.addRow(values);
                }
            }
            if (// more than one species
            shape.length == 2) {
                ArrayDouble.D2 temData = (ArrayDouble.D2) data;
                // System.out.println("multiple species in multiple trials, the length of trials is :"+data.getShape()[0]+", and the total number of speceis is: "+data.getShape()[1]);
                for (// rows
                int k = 0; // rows
                k < trialNum.length; // rows
                k++) {
                    double[] values = new double[stSolverResultSet.getDataColumnCount()];
                    values[0] = trialNum[k];
                    for (int i = 1; i < stSolverResultSet.getDataColumnCount(); i++) {
                        values[i] = temData.get(k, i - 1);
                    }
                    stSolverResultSet.addRow(values);
                }
            }
        } else {
            throw new RuntimeException("Number of trials should be a countable positive value, from 1 to N.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.err);
        throw new RuntimeException("Problem encountered in parsing hybrid simulation results.\n" + e.getMessage());
    }
    /*
	 *Add appropriate Function columns to result set if the stochastic simulation is to display the trajectory.
	 *No function columns for the results of multiple stochastic trials.
	 *In stochastic simulation the functions include probability functions and clamped variable.
	 */
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    if (simSymbolTable.getSimulation().getSolverTaskDescription().getStochOpt().getNumOfTrials() == 1) {
        Function[] functions = simSymbolTable.getFunctions();
        for (int i = 0; i < functions.length; i++) {
            if (SimulationSymbolTable.isFunctionSaved(functions[i])) {
                Expression exp1 = new Expression(functions[i].getExpression());
                try {
                    exp1 = simSymbolTable.substituteFunctions(exp1);
                } catch (MathException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
                }
                try {
                    FunctionColumnDescription cd = new FunctionColumnDescription(exp1.flatten(), functions[i].getName(), null, functions[i].getName(), false);
                    stSolverResultSet.addFunctionColumn(cd);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                }
            }
        }
    }
    return stSolverResultSet;
}

Example 43 with Function

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

the class CellQuanVCTranslator method addRateFunction.

private Function addRateFunction(Element varRef, String compName, String mangledName) {
    Element role;
    String stoich = null, roleAtt = null;
    // can only imply the delta function if the stoichiometry attribute is present also
    // not sure if there can be more than one, if not, could just pass in the 'role' element itself.
    @SuppressWarnings("unchecked") Iterator<Element> i = varRef.getChildren(CELLMLTags.ROLE, sNamespace).iterator();
    while (i.hasNext()) {
        role = i.next();
        stoich = role.getAttributeValue(CELLMLTags.stoichiometry, sAttNamespace);
        roleAtt = role.getAttributeValue(CELLMLTags.role, sAttNamespace);
        if (stoich != null)
            break;
    }
    if (stoich != null) {
        // Can only imply the function if a variable_ref with a role of "rate" exists
        JDOMTreeWalker reactionWalker = new JDOMTreeWalker((Element) varRef.getParent(), new ElementFilter(CELLMLTags.ROLE));
        Element rateRole = reactionWalker.getMatchingElement(CELLMLTags.role, sAttNamespace, CELLMLTags.rateRole);
        if (rateRole != null) {
            String rateVarName = ((Element) rateRole.getParent()).getAttributeValue(CELLMLTags.variable, sAttNamespace);
            StringBuffer formula = new StringBuffer("(");
            if (roleAtt.equals(CELLMLTags.productRole))
                formula.append("-(");
            formula.append(stoich + "*" + nm.getMangledName(compName, rateVarName));
            if (roleAtt.equals(CELLMLTags.productRole))
                formula.append(")");
            formula.append(")");
            try {
                Domain domain = null;
                return new Function(mangledName, new Expression(formula.toString()), domain);
            // fnsVector.add(function);
            // mathDescription.addVariable(function);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Error adding function (" + mangledName + ") to mathDexcription : " + e.getMessage());
            }
        }
    }
    return null;
}

Example 44 with Function

use of cbit.vcell.math.Function 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;
}

Example 45 with Function

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

the class OutputFunctionContext method propertyChange.

public void propertyChange(java.beans.PropertyChangeEvent event) {
    if (event.getSource() == simulationOwner && event.getPropertyName().equals("mathDescription")) {
        rebindAll();
    }
    if (event.getPropertyName().equals("geometry")) {
        Geometry oldGeometry = (Geometry) event.getOldValue();
        Geometry newGeometry = (Geometry) event.getNewValue();
        // changing from ode to pde
        if (oldGeometry != null && oldGeometry.getDimension() == 0 && newGeometry.getDimension() > 0) {
            ArrayList<AnnotatedFunction> newFuncList = new ArrayList<AnnotatedFunction>();
            for (AnnotatedFunction function : outputFunctionsList) {
                try {
                    Expression newexp = new Expression(function.getExpression());
                    // making sure that output function is not direct function of constant.
                    newexp.bindExpression(this);
                    // here use math description as symbol table because we allow
                    // new expression itself to be function of constant.
                    MathDescription mathDescription = getSimulationOwner().getMathDescription();
                    newexp = MathUtilities.substituteFunctions(newexp, mathDescription).flatten();
                    VariableType newFuncType = VariableType.VOLUME;
                    String[] symbols = newexp.getSymbols();
                    if (symbols != null) {
                        // figure out the function type
                        VariableType[] varTypes = new VariableType[symbols.length];
                        for (int i = 0; i < symbols.length; i++) {
                            Variable var = mathDescription.getVariable(symbols[i]);
                            varTypes[i] = VariableType.getVariableType(var);
                        }
                        // check with flattened expression to find out the variable type of the new expression
                        Function flattenedFunction = new Function(function.getName(), newexp, function.getDomain());
                        newFuncType = SimulationSymbolTable.getFunctionVariableType(flattenedFunction, getSimulationOwner().getMathDescription(), symbols, varTypes, true);
                    }
                    AnnotatedFunction newFunc = new AnnotatedFunction(function.getName(), function.getExpression(), function.getDomain(), "", newFuncType, FunctionCategory.OUTPUTFUNCTION);
                    newFuncList.add(newFunc);
                    newFunc.bind(this);
                } catch (ExpressionException ex) {
                    ex.printStackTrace();
                    throw new RuntimeException(ex.getMessage());
                } catch (InconsistentDomainException ex) {
                    ex.printStackTrace();
                    throw new RuntimeException(ex.getMessage());
                }
            }
            try {
                setOutputFunctions0(newFuncList);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
                throw new RuntimeException(e.getMessage());
            }
        }
    }
}