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

Example 1 with FunctionColumnDescription

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

the class ParameterEstimationTaskSimulatorIDA method getOdeSolverResultSet.

private ODESolverResultSet getOdeSolverResultSet(ParameterEstimationTask parameterEstimationTask, OptimizationSpec optSpec, OptimizationResultSet optResultSet) throws Exception {
    if (optResultSet == null) {
        return null;
    }
    String[] parameterNames = optResultSet.getOptSolverResultSet().getParameterNames();
    double[] bestEstimates = optResultSet.getOptSolverResultSet().getBestEstimates();
    // if we don't have parameter names or best estimates, return null. if we have them, we can run a simulation and generate a solution
    if (parameterNames == null || parameterNames.length == 0 || bestEstimates == null || bestEstimates.length == 0) {
        return null;
    }
    // check if we have solution or not, if not, generate a solution since we have the best estimates
    if (optResultSet.getSolutionNames() == null) {
        RowColumnResultSet rcResultSet = getRowColumnRestultSetByBestEstimations(parameterEstimationTask, parameterNames, bestEstimates);
        optResultSet.setSolutionFromRowColumnResultSet(rcResultSet);
    }
    String[] solutionNames = optResultSet.getSolutionNames();
    if (solutionNames != null && solutionNames.length > 0) {
        ODESolverResultSet odeSolverResultSet = new ODESolverResultSet();
        // add data column descriptions
        for (int i = 0; i < solutionNames.length; i++) {
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(solutionNames[i]));
        }
        // 
        // add row data
        // 
        int numRows = optResultSet.getSolutionValues(0).length;
        for (int i = 0; i < numRows; i++) {
            odeSolverResultSet.addRow(optResultSet.getSolutionRow(i));
        }
        // 
        // make temporary simulation (with overrides for parameter values)
        // 
        MathDescription mathDesc = parameterEstimationTask.getSimulationContext().getMathDescription();
        Simulation simulation = new Simulation(mathDesc);
        SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(simulation, 0);
        // 
        for (int i = 0; i < optSpec.getParameters().length; i++) {
            cbit.vcell.opt.Parameter parameter = optSpec.getParameters()[i];
            simulation.getMathOverrides().putConstant(new Constant(parameter.getName(), new Expression(parameter.getInitialGuess())));
        }
        // 
        for (int i = 0; i < parameterNames.length; i++) {
            simulation.getMathOverrides().putConstant(new Constant(parameterNames[i], new Expression(optResultSet.getOptSolverResultSet().getBestEstimates()[i])));
        }
        // 
        // add functions (evaluating them at optimal parameter)
        // 
        Vector<AnnotatedFunction> annotatedFunctions = simSymbolTable.createAnnotatedFunctionsList(mathDesc);
        for (AnnotatedFunction f : annotatedFunctions) {
            Expression funcExp = f.getExpression();
            for (int j = 0; j < parameterNames.length; j++) {
                funcExp.substituteInPlace(new Expression(parameterNames[j]), new Expression(optResultSet.getOptSolverResultSet().getBestEstimates()[j]));
            }
            odeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(funcExp, f.getName(), null, f.getName(), false));
        }
        return odeSolverResultSet;
    } else {
        return null;
    }
}

Example 2 with FunctionColumnDescription

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

the class ODESolverPlotSpecificationPanel method initConnections.

/**
 * Initializes connections
 * @exception java.lang.Exception The exception description.
 */
@SuppressWarnings({ "serial", "unchecked" })
private void initConnections() throws java.lang.Exception {
    // user code begin {1}
    // user code end
    getFilterPanel().addPropertyChangeListener(ivjEventHandler);
    getYAxisChoice().addListSelectionListener(ivjEventHandler);
    this.addPropertyChangeListener(ivjEventHandler);
    getXAxisComboBox_frm().addItemListener(ivjEventHandler);
    getLogSensCheckbox().addActionListener(ivjEventHandler);
    getSensitivityParameterSlider().addChangeListener(ivjEventHandler);
    connPtoP1SetTarget();
    connPtoP3SetTarget();
    getYAxisChoice().setCellRenderer(new DefaultListCellRenderer() {

        public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
            super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
            ODEDataInterface mdi = getMyDataInterface();
            if (mdi == null) {
                return this;
            }
            String varName = (String) value;
            ColumnDescription cd = null;
            try {
                cd = mdi.getColumnDescription(varName);
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
            }
            if (cd instanceof FunctionColumnDescription && ((FunctionColumnDescription) cd).getIsUserDefined()) {
                if (function_icon == null) {
                    function_icon = new ImageIcon(getClass().getResource("/icons/function_icon.png"));
                }
                setIcon(function_icon);
            }
            if (mdi.getDataSymbolMetadataResolver() != null && mdi.getDataSymbolMetadataResolver().getDataSymbolMetadata(varName) != null) {
                DataSymbolMetadata dsm = mdi.getDataSymbolMetadataResolver().getDataSymbolMetadata(varName);
                String tooltipString = dsm.tooltipString;
                if (tooltipString == null) {
                    tooltipString = varName;
                }
                setToolTipText(tooltipString);
            }
            return this;
        }
    });
}

Example 3 with FunctionColumnDescription

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

the class MathTestingUtilities method getConstructedResultSet.

/**
 * Insert the method's description here.
 * Creation date: (1/17/2003 3:47:43 PM)
 * @return cbit.vcell.solver.ode.ODESolverResultSet
 * @param sim cbit.vcell.solver.Simulation
 */
public static ODESolverResultSet getConstructedResultSet(MathDescription mathDesc, double[] time) throws Exception {
    if (mathDesc.getGeometry().getDimension() != 0) {
        throw new RuntimeException("can only handle non-spatial simulations.");
    }
    Simulation sim = new Simulation(mathDesc);
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(sim, 0);
    ODESolverResultSet resultSet = new ODESolverResultSet();
    resultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
    for (int i = 0; i < time.length; i++) {
        resultSet.addRow(new double[] { time[i] });
    }
    java.util.Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
    String errorString = "Variable(s) : ";
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        java.util.Enumeration<Equation> enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = enumEquations.nextElement();
            Expression constructedSolution = equation.getExactSolution();
            if (constructedSolution != null) {
                constructedSolution = new Expression(constructedSolution);
                constructedSolution.bindExpression(simSymbolTable);
                constructedSolution = simSymbolTable.substituteFunctions(constructedSolution);
                constructedSolution = constructedSolution.flatten();
                resultSet.addFunctionColumn(new FunctionColumnDescription(constructedSolution, equation.getVariable().getName(), null, equation.getVariable().getName(), false));
            } else {
                errorString = errorString + equation.getVariable().getName() + ", ";
            }
        }
    }
    if (!errorString.equals("Variable(s) : ")) {
        throw new RuntimeException(errorString + " don't have a constructed solution");
    }
    return resultSet;
}

Example 4 with FunctionColumnDescription

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

the class MathTestingUtilities method getExactResultSet.

/**
 * Insert the method's description here.
 * Creation date: (1/17/2003 3:47:43 PM)
 * @return cbit.vcell.solver.ode.ODESolverResultSet
 * @param sim cbit.vcell.solver.Simulation
 */
public static ODESolverResultSet getExactResultSet(MathDescription mathDesc, double[] time, Constant sensitivityParam) throws Exception {
    if (mathDesc.getGeometry().getDimension() != 0) {
        throw new RuntimeException("can only handle non-spatial simulations.");
    }
    Simulation sim = new Simulation(mathDesc);
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(sim, 0);
    ODESolverResultSet resultSet = new ODESolverResultSet();
    resultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
    for (int i = 0; i < time.length; i++) {
        resultSet.addRow(new double[] { time[i] });
    }
    java.util.Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        java.util.Enumeration<Equation> enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = enumEquations.nextElement();
            Expression exactSolution = equation.getExactSolution();
            if (exactSolution != null) {
                exactSolution = new Expression(exactSolution);
                exactSolution.bindExpression(simSymbolTable);
                exactSolution = simSymbolTable.substituteFunctions(exactSolution);
                exactSolution.bindExpression(simSymbolTable);
                exactSolution = exactSolution.flatten();
                resultSet.addFunctionColumn(new FunctionColumnDescription(exactSolution, equation.getVariable().getName(), null, equation.getVariable().getName(), false));
                if (sensitivityParam != null) {
                    exactSolution = equation.getExactSolution();
                    Expression exactSensitivity = new Expression(exactSolution);
                    exactSensitivity.bindExpression(simSymbolTable);
                    exactSensitivity = simSymbolTable.substituteFunctions(exactSensitivity);
                    exactSensitivity.bindExpression(simSymbolTable);
                    exactSensitivity = exactSensitivity.differentiate(sensitivityParam.getName());
                    exactSensitivity = exactSensitivity.flatten();
                    VolVariable volVar = (VolVariable) equation.getVariable();
                    String sensName = SensVariable.getSensName(volVar, sensitivityParam);
                    resultSet.addFunctionColumn(new FunctionColumnDescription(exactSensitivity, sensName, null, sensName, false));
                }
            } else {
                throw new RuntimeException("variable " + equation.getVariable().getName() + " doesn't have an exact solution");
            }
        }
    }
    return resultSet;
}

Example 5 with FunctionColumnDescription

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

the class DefaultODESolver method createODESolverResultSet.

/**
 */
private ODESolverResultSet createODESolverResultSet() throws ExpressionException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    // 
    // create symbol table for binding expression
    // 
    String[] symbols = new String[fieldIdentifiers.size()];
    for (int i = 0; i < symbols.length; i++) {
        symbols[i] = ((Variable) fieldIdentifiers.elementAt(i)).getName();
    }
    // Initialize the ResultSet...
    ODESolverResultSet odeSolverResultSet = new ODESolverResultSet();
    odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedVariable.TIME.getName()));
    for (int i = 0; i < getStateVariableCount(); i++) {
        StateVariable stateVariable = getStateVariable(i);
        if (stateVariable instanceof SensStateVariable) {
            SensStateVariable sensStateVariable = (SensStateVariable) stateVariable;
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(sensStateVariable.getVariable().getName(), sensStateVariable.getParameter().getName(), sensStateVariable.getVariable().getName()));
        } else {
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(stateVariable.getVariable().getName()));
        }
    }
    Variable[] variables = simSymbolTable.getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
            Function function = (Function) variables[i];
            Expression exp1 = new Expression(function.getExpression());
            try {
                exp1 = simSymbolTable.substituteFunctions(exp1);
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + function.getName() + " " + e.getMessage());
            }
            odeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(exp1.flatten(), function.getName(), null, function.getName(), false));
        }
    }
    // 
    if (getSensitivityParameter() != null) {
        if (odeSolverResultSet.findColumn(getSensitivityParameter().getName()) == -1) {
            FunctionColumnDescription fcd = new FunctionColumnDescription(new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getName(), null, getSensitivityParameter().getName(), false);
            odeSolverResultSet.addFunctionColumn(fcd);
        }
        StateVariable[] stateVars = (StateVariable[]) org.vcell.util.BeanUtils.getArray(fieldStateVariables, StateVariable.class);
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
                Function depSensFunction = (Function) variables[i];
                Expression depSensFnExpr = new Expression(depSensFunction.getExpression());
                try {
                    depSensFnExpr = simSymbolTable.substituteFunctions(depSensFnExpr);
                } catch (MathException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Substitute function failed on function " + depSensFunction.getName() + " " + e.getMessage());
                }
                depSensFnExpr = getFunctionSensitivity(depSensFnExpr, getSensitivityParameter(), stateVars);
                // depSensFnExpr = depSensFnExpr.flatten(); 	// already bound and flattened in getFunctionSensitivity, no need here ...
                String depSensFnName = new String("sens_" + depSensFunction.getName() + "_wrt_" + getSensitivityParameter().getName());
                if (depSensFunction != null) {
                    FunctionColumnDescription cd = new FunctionColumnDescription(depSensFnExpr.flatten(), depSensFnName, getSensitivityParameter().getName(), depSensFnName, false);
                    odeSolverResultSet.addFunctionColumn(cd);
                }
            }
        }
    }
    return (odeSolverResultSet);
}