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

Example 6 with ODESolverResultSetColumnDescription

use of cbit.vcell.math.ODESolverResultSetColumnDescription 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 7 with ODESolverResultSetColumnDescription

use of cbit.vcell.math.ODESolverResultSetColumnDescription 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 8 with ODESolverResultSetColumnDescription

use of cbit.vcell.math.ODESolverResultSetColumnDescription 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);
}

Example 9 with ODESolverResultSetColumnDescription

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

the class ODESimData method readIn.

/**
 * JMW : This really should be synchronized...
 */
public void readIn(DataInputStream input) throws IOException {
    formatID = input.readUTF();
    if (formatID.equals(SIMPLE_ODE_DATA_FORMAT_ID)) {
        this.mathName = input.readUTF();
        // read data from old format file
        double saveInterval = input.readDouble();
        int savedNumber = input.readInt();
        int variableNumber = input.readInt();
        String[] variableNames = new String[variableNumber];
        double[][] dataValues = new double[savedNumber][variableNumber];
        for (int i = 0; i < variableNumber; i++) {
            int flag = input.readInt();
            variableNames[i] = input.readUTF();
            for (int j = 0; j < savedNumber; j++) {
                dataValues[j][i] = input.readDouble();
            }
        }
        // now put data in new data structure
        int rowCount = savedNumber;
        int columnCount = variableNumber + 1;
        addDataColumn(new ODESolverResultSetColumnDescription("t", "t"));
        for (int c = 1; c < columnCount; c++) {
            addDataColumn(new ODESolverResultSetColumnDescription(variableNames[c - 1], variableNames[c - 1]));
        }
        double[] values = new double[columnCount];
        for (int c = 0; c < columnCount; c++) values[c] = 0.0;
        for (int r = 0; r < rowCount; r++) {
            values[0] = r * saveInterval / 1000.0;
            addRow(values);
        }
        for (int c = 1; c < columnCount; c++) {
            for (int r = 0; r < rowCount; r++) {
                setValue(r, c, dataValues[r][c - 1]);
            }
        }
    } else if (formatID.equals(GENERIC_ODE_DATA_FORMAT_ID)) {
        this.mathName = input.readUTF();
        int rowCount = input.readInt();
        int columnCount = input.readInt();
        for (int c = 0; c < columnCount; c++) {
            String columnName = input.readUTF();
            String columnDisplayName = input.readUTF();
            addDataColumn(new ODESolverResultSetColumnDescription(columnName, columnDisplayName));
        }
        double[] values = new double[columnCount];
        for (int r = 0; r < rowCount; r++) {
            for (int c = 0; c < columnCount; c++) {
                values[c] = input.readDouble();
            }
            addRow(values);
        }
    } else if (formatID.equals(COMPACT_ODE_DATA_FORMAT_ID)) {
        this.mathName = input.readUTF();
        int rowCount = input.readInt();
        int columnCount = input.readInt();
        for (int c = 0; c < columnCount; c++) {
            String columnName = input.readUTF();
            String columnDisplayName = input.readUTF();
            String columnParameterName = input.readUTF();
            if (columnParameterName.equals("null")) {
                columnParameterName = null;
            }
            addDataColumn(new ODESolverResultSetColumnDescription(columnName, columnParameterName, columnDisplayName));
        }
        double[] values = new double[columnCount];
        for (int r = 0; r < rowCount; r++) {
            for (int c = 0; c < columnCount; c++) {
                values[c] = input.readDouble();
            }
            addRow(values);
        }
        try {
            int functionCount = input.readInt();
            for (int c = 0; c < functionCount; c++) {
                String columnName = input.readUTF();
                String columnDisplayName = input.readUTF();
                String columnParameterName = input.readUTF();
                if (columnParameterName.equals("null")) {
                    columnParameterName = null;
                }
                String expressionString = input.readUTF();
                try {
                    Expression expression = new Expression(expressionString);
                    addFunctionColumn(new FunctionColumnDescription(expression, columnName, columnParameterName, columnDisplayName, false));
                } catch (ExpressionBindingException e) {
                    e.printStackTrace(System.out);
                    System.out.println("ODESimData.readIn(): unable to bind expression '" + expressionString + "'");
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    System.out.println("ODESimData.readIn(): unable to parse expression '" + expressionString + "'");
                }
            }
        } catch (EOFException e) {
        }
    } else {
        throw new IOException("DataInputStream is wrong format '" + formatID + "'");
    }
}

Example 10 with ODESolverResultSetColumnDescription

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

the class ODESimData method readIDADataFile.

public static ODESimData readIDADataFile(VCDataIdentifier vcdId, File dataFile, int keepMost, File functionsFile) throws DataAccessException {
    // read ida file
    System.out.println("reading ida file : " + dataFile);
    ODESimData odeSimData = new ODESimData();
    odeSimData.formatID = IDA_DATA_FORMAT_ID;
    odeSimData.mathName = vcdId.getID();
    BufferedReader bufferedReader = null;
    try {
        bufferedReader = new BufferedReader(new InputStreamReader(new FileInputStream(dataFile)));
        // Read header
        String line = bufferedReader.readLine();
        if (line == null) {
            // throw exception
            return null;
        }
        StringTokenizer st = new StringTokenizer(line, ":");
        while (st.hasMoreTokens()) {
            odeSimData.addDataColumn(new ODESolverResultSetColumnDescription(st.nextToken()));
        }
        // Read data
        while ((line = bufferedReader.readLine()) != null) {
            st = new StringTokenizer(line);
            double[] values = new double[odeSimData.getDataColumnCount()];
            int count = 0;
            while (st.hasMoreTokens()) {
                values[count++] = Double.valueOf(st.nextToken()).doubleValue();
            }
            if (count == odeSimData.getDataColumnCount()) {
                odeSimData.addRow(values);
            } else {
                break;
            }
        }
    // 
    } catch (Exception e) {
        e.printStackTrace(System.out);
        return null;
    } finally {
        try {
            if (bufferedReader != null) {
                bufferedReader.close();
            }
        } catch (Exception ex) {
            ex.printStackTrace(System.out);
        }
    }
    if (!odeSimData.getColumnDescriptions(0).getName().equals(SimDataConstants.HISTOGRAM_INDEX_NAME)) {
        Vector<AnnotatedFunction> funcList;
        try {
            funcList = FunctionFileGenerator.readFunctionsFile(functionsFile, vcdId.getID());
            for (AnnotatedFunction func : funcList) {
                try {
                    Expression expression = new Expression(func.getExpression());
                    odeSimData.addFunctionColumn(new FunctionColumnDescription(expression, func.getName(), null, func.getName(), false));
                } catch (ExpressionException e) {
                    throw new RuntimeException("Could not add function " + func.getName() + " to annotatedFunctionList");
                }
            }
        } catch (FileNotFoundException e1) {
            e1.printStackTrace(System.out);
            throw new DataAccessException(e1.getMessage());
        } catch (IOException e1) {
            e1.printStackTrace(System.out);
            throw new DataAccessException(e1.getMessage());
        }
    }
    if (keepMost > 0) {
        odeSimData.trimRows(keepMost);
    }
    return odeSimData;
}