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

Example 1 with ParameterVariable

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

the class FiniteVolumeFileWriter method write.

/**
 * Insert the method's description here.
 * Creation date: (5/9/2005 2:52:48 PM)
 * @throws MathException
 * @throws ExpressionException
 * @throws DataAccessException
 * @throws IOException
 */
public void write(String[] parameterNames) throws Exception {
    Variable[] originalVars = null;
    Simulation simulation = simTask.getSimulation();
    MathDescription mathDesc = simulation.getMathDescription();
    if (bChomboSolver) {
        writeJMSParamters();
        writeSimulationParamters();
        writeModelDescription();
        writeChomboSpec();
        writeVariables();
        writePostProcessingBlock();
        writeCompartments();
        writeMembranes();
    } else {
        if (simTask.getSimulation().isSerialParameterScan()) {
            originalVars = (Variable[]) BeanUtils.getArray(mathDesc.getVariables(), Variable.class);
            Variable[] allVars = (Variable[]) BeanUtils.getArray(mathDesc.getVariables(), Variable.class);
            MathOverrides mathOverrides = simulation.getMathOverrides();
            String[] scanParameters = mathOverrides.getOverridenConstantNames();
            for (int i = 0; i < scanParameters.length; i++) {
                String scanParameter = scanParameters[i];
                Variable mathVariable = mathDesc.getVariable(scanParameter);
                // 
                if (mathVariable instanceof Constant) {
                    Constant origConstant = (Constant) mathVariable;
                    for (int j = 0; j < allVars.length; j++) {
                        if (allVars[j].equals(origConstant)) {
                            allVars[j] = new ParameterVariable(origConstant.getName());
                            break;
                        }
                    }
                }
            }
            mathDesc.setAllVariables(allVars);
        }
        writeJMSParamters();
        writeSimulationParamters();
        writeModelDescription();
        writeMeshFile();
        writeVariables();
        if (mathDesc.isSpatialHybrid()) {
            writeSmoldyn();
        }
        writeParameters(parameterNames);
        writeSerialParameterScans();
        writeFieldData();
        writePostProcessingBlock();
        writeCompartments();
        writeMembranes();
        if (originalVars != null) {
            mathDesc.setAllVariables(originalVars);
        }
    }
}

Example 2 with ParameterVariable

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

the class OdeFileWriter method createSymbolTable.

/**
 * OdeFileCoder constructor comment.
 * @throws Exception
 */
private void createSymbolTable() throws Exception {
    // 
    // Create symbol table for binding sensitivity variable expressions. (Cannot bind to simulation,
    // since it does not have the sensitivity variables corresponding to the volume variables).
    // 
    varsSymbolTable = new VariableSymbolTable();
    // SymbolTableEntry.index doesn't matter ... just code generating binding by var names not index.
    varsSymbolTable.addVar(ReservedVariable.TIME);
    int count = 0;
    Variable[] variables = simTask.getSimulationJob().getSimulationSymbolTable().getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof VolVariable) {
            VolVariable vVar = (VolVariable) variables[i];
            vVar.setIndex(count);
            varsSymbolTable.addVar(vVar);
            count++;
        } else if (variables[i] instanceof Function) {
            Function func = (Function) variables[i];
            func.setIndex(count);
            varsSymbolTable.addVar(func);
            count++;
        } else if (variables[i] instanceof Constant) {
            Constant constant = (Constant) variables[i];
            constant.setIndex(count);
            varsSymbolTable.addVar(constant);
            count++;
        } else if (variables[i] instanceof ParameterVariable) {
            ParameterVariable param = (ParameterVariable) variables[i];
            param.setIndex(count);
            varsSymbolTable.addVar(param);
            count++;
        }
    }
    // Get the vector of sensVariables, needed for creating SensStateVariables
    Vector<SensStateVariable> sensVars = new Vector<SensStateVariable>();
    for (int i = 0; i < getStateVariableCount(); i++) {
        if (simTask.getSimulation().getSolverTaskDescription().getSensitivityParameter() != null) {
            if (getStateVariable(i) instanceof SensStateVariable) {
                sensVars.addElement((SensStateVariable) getStateVariable(i));
            }
        }
    }
    for (int j = count; j < (count + sensVars.size()); j++) {
        SensVariable sVar = (SensVariable) (sensVars.elementAt(j - count).getVariable());
        sVar.setIndex(j);
        varsSymbolTable.addVar(sVar);
    }
}

Example 3 with ParameterVariable

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

the class ModelOptimizationMapping method computeOptimizationSpec.

/**
 * Insert the method's description here.
 * Creation date: (8/22/2005 9:26:52 AM)
 * @return cbit.vcell.opt.OptimizationSpec
 * @param modelOptimizationSpec cbit.vcell.modelopt.ModelOptimizationSpec
 */
MathSymbolMapping computeOptimizationSpec() throws MathException, MappingException {
    if (getModelOptimizationSpec().getReferenceData() == null) {
        System.out.println("no referenced data defined");
        return null;
    }
    OptimizationSpec optSpec = new OptimizationSpec();
    optSpec.setComputeProfileDistributions(modelOptimizationSpec.isComputeProfileDistributions());
    parameterMappings = null;
    // 
    // get original MathDescription (later to be substituted for local/global parameters).
    // 
    SimulationContext simContext = modelOptimizationSpec.getSimulationContext();
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription origMathDesc = null;
    mathSymbolMapping = null;
    try {
        origMathDesc = mathMapping.getMathDescription();
        mathSymbolMapping = mathMapping.getMathSymbolMapping();
    } catch (MatrixException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    } catch (ModelException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new MathException(e.getMessage());
    }
    // 
    // create objective function (mathDesc and data)
    // 
    ReferenceData referenceData = getRemappedReferenceData(mathMapping);
    if (referenceData == null) {
        throw new RuntimeException("no referenced data defined");
    }
    // 
    // get parameter mappings
    // 
    ParameterMappingSpec[] parameterMappingSpecs = modelOptimizationSpec.getParameterMappingSpecs();
    Vector<ParameterMapping> parameterMappingList = new Vector<ParameterMapping>();
    Variable[] allVars = (Variable[]) BeanUtils.getArray(origMathDesc.getVariables(), Variable.class);
    for (int i = 0; i < parameterMappingSpecs.length; i++) {
        cbit.vcell.model.Parameter modelParameter = parameterMappingSpecs[i].getModelParameter();
        String mathSymbol = null;
        Variable mathVariable = null;
        if (mathSymbolMapping != null) {
            Variable variable = mathSymbolMapping.getVariable(modelParameter);
            if (variable != null) {
                mathSymbol = variable.getName();
            }
            if (mathSymbol != null) {
                mathVariable = origMathDesc.getVariable(mathSymbol);
            }
        }
        if (mathVariable != null) {
            if (parameterMappingSpecs[i].isSelected()) {
                if (parameterMappingSpecs[i].getHigh() < parameterMappingSpecs[i].getLow()) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is greater than its upper bound.");
                }
                if (parameterMappingSpecs[i].getCurrent() < parameterMappingSpecs[i].getLow()) {
                    throw new MathException("The initial guess of '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is smaller than its lower bound.");
                }
                if (parameterMappingSpecs[i].getCurrent() > parameterMappingSpecs[i].getHigh()) {
                    throw new MathException("The initial guess of '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is greater than its upper bound.");
                }
                if (parameterMappingSpecs[i].getLow() < 0) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is negative. All lower bounds must not be negative.");
                }
                if (Double.isInfinite(parameterMappingSpecs[i].getLow())) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is infinity. Lower bounds must not be infinity.");
                }
                if (parameterMappingSpecs[i].getHigh() <= 0) {
                    throw new MathException("The upper bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is negative. All upper bounds must be positive.");
                }
                if (Double.isInfinite(parameterMappingSpecs[i].getHigh())) {
                    throw new MathException("The upper bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is infinity. Upper bounds must not be infinity.");
                }
            }
            double low = parameterMappingSpecs[i].isSelected() && parameterMappingSpecs[i].getLow() == 0 ? 1e-8 : parameterMappingSpecs[i].getLow();
            double high = parameterMappingSpecs[i].getHigh();
            double scale = Math.abs(parameterMappingSpecs[i].getCurrent()) < 1.0E-10 ? 1.0 : Math.abs(parameterMappingSpecs[i].getCurrent());
            double current = parameterMappingSpecs[i].getCurrent();
            low = Math.min(low, current);
            high = Math.max(high, current);
            Parameter optParameter = new Parameter(mathSymbol, low, high, scale, current);
            ParameterMapping parameterMapping = new ParameterMapping(modelParameter, optParameter, mathVariable);
            // 
            if (mathVariable instanceof Constant) {
                Constant origConstant = (Constant) mathVariable;
                for (int j = 0; j < allVars.length; j++) {
                    if (allVars[j].equals(origConstant)) {
                        if (parameterMappingSpecs[i].isSelected()) {
                            allVars[j] = new ParameterVariable(origConstant.getName());
                        } else {
                            allVars[j] = new Constant(origConstant.getName(), new Expression(optParameter.getInitialGuess()));
                        }
                        break;
                    }
                }
            }
            // 
            if (parameterMappingSpecs[i].isSelected()) {
                parameterMappingList.add(parameterMapping);
            }
        }
    }
    parameterMappings = (ParameterMapping[]) BeanUtils.getArray(parameterMappingList, ParameterMapping.class);
    try {
        origMathDesc.setAllVariables(allVars);
    } catch (ExpressionBindingException e) {
        e.printStackTrace(System.out);
        throw new MathException(e.getMessage());
    }
    // 
    for (int i = 0; i < parameterMappings.length; i++) {
        optSpec.addParameter(parameterMappings[i].getOptParameter());
    }
    Vector<Issue> issueList = new Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    optSpec.gatherIssues(issueContext, issueList);
    for (int i = 0; i < issueList.size(); i++) {
        Issue issue = issueList.elementAt(i);
        if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
            throw new RuntimeException(issue.getMessage());
        }
    }
    // 
    // 
    // 
    optimizationSpec = optSpec;
    return mathSymbolMapping;
}