Examples with ODESolverResultSet cbit.vcell.solver.ode.ODESolverResultSet used on opensource projects

Example 11 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet 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 12 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet 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 13 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class SbmlVcmlConverter method solveSimulation.

/**
 * solves the simulation that is passed in throught the simulation job.
 */
private static void solveSimulation(SimulationJob simJob, String filePathName, SimSpec argSimSpec) /* Hashtable argSpUnitsHash, double argTimeFactor, Model.ReservedSymbol kMoleSymbol*/
{
    ODESolverResultSet odeSolverResultSet = null;
    try {
        /*		// Generate .idaInput string		
		File idaInputFile = new File(filePathName.replace(".vcml", ".idaInput"));
		PrintWriter idaPW = new java.io.PrintWriter(idaInputFile);
		IDAFileWriter idaFileWriter = new IDAFileWriter(idaPW, simJob);
		idaFileWriter.write();
		idaPW.close();

		// use the SundialsStandaloneSolver
		File idaOutputFile = new File(filePathName.replace(".vcml", ".ida"));
		Executable executable = new Executable(new String[]{"SundialsSolverStandalone", idaInputFile.getAbsolutePath(), idaOutputFile.getAbsolutePath()});
		executable.start();
*/
        // Generate .cvodeInput string
        File cvodeInputFile = new File(filePathName.replace(".vcml", ".cvodeInput"));
        PrintWriter cvodePW = new java.io.PrintWriter(cvodeInputFile);
        SimulationTask simTask = new SimulationTask(simJob, 0);
        CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simTask);
        cvodeFileWriter.write();
        cvodePW.close();
        // use the cvodeStandalone solver
        // use the SundialsStandaloneSolver
        File cvodeOutputFile = new File(filePathName.replace(".vcml", ".ida"));
        /*
		Executable executable = new Executable(new String[]{"d:/workspace/VCell_5.3_VCell/SundialsSolverStandalone_x64", cvodeInputFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath()});
		executable.start();
		*/
        // use the cvodeStandalone solver
        // use the SundialsStandaloneSolver
        File[] exes = SolverUtilities.getExes(SolverDescription.CombinedSundials);
        assert exes.length == 1 : "one and only one smoldyn solver expected";
        File sundialsExe = exes[0];
        Executable executable = new Executable(new String[] { sundialsExe.getAbsolutePath(), cvodeInputFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath() });
        executable.start();
        // get the result
        odeSolverResultSet = VCellSBMLSolver.getODESolverResultSet(simJob, cvodeOutputFile.getPath());
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Error running NativeIDA solver : " + e.getMessage());
    }
    // now write out the results into CSV file
    try {
        if (odeSolverResultSet != null) {
            File csvFile = new File(filePathName.replace(".vcml", ".csv"));
            PrintStream outputStream = new PrintStream(new BufferedOutputStream(new FileOutputStream(csvFile)));
            outputStream.print("time");
            for (int i = 0; i < argSimSpec.getVarsList().length; i++) {
                outputStream.print("," + argSimSpec.getVarsList()[i]);
            }
            outputStream.println();
            // extract data for time and species
            double[][] data = new double[argSimSpec.getVarsList().length + 1][];
            int column = odeSolverResultSet.findColumn("t");
            data[0] = odeSolverResultSet.extractColumn(column);
            int origDataLength = data[0].length;
            for (int i = 0; i < argSimSpec.getVarsList().length; i++) {
                column = odeSolverResultSet.findColumn(argSimSpec.getVarsList()[i]);
                if (column == -1) {
                    Variable var = simJob.getSimulationSymbolTable().getVariable(argSimSpec.getVarsList()[i]);
                    data[i + 1] = new double[data[0].length];
                    if (var instanceof cbit.vcell.math.Constant) {
                        double value = ((cbit.vcell.math.Constant) var).getExpression().evaluateConstant();
                        for (int j = 0; j < data[i + 1].length; j++) {
                            data[i + 1][j] = value;
                        }
                    } else {
                        throw new RuntimeException("Did not find " + argSimSpec.getVarsList()[i] + " in simulation");
                    }
                } else {
                    data[i + 1] = odeSolverResultSet.extractColumn(column);
                }
            }
            double endTime = (simJob.getSimulation().getSolverTaskDescription().getTimeBounds().getEndingTime());
            // for each time, print row
            int index = 0;
            double[] sampleTimes = new double[numTimeSteps + 1];
            for (int i = 0; i <= numTimeSteps; i++) {
                sampleTimes[i] = endTime * i / numTimeSteps;
            }
            for (int i = 0; i < sampleTimes.length; i++) {
                // find largest index whose time is not past sample time
                while (true) {
                    // if already at last time point, then if it equals the sampleTime, we're done if it doesn't then we don't have this time point.
                    if (index == odeSolverResultSet.getRowCount() - 1) {
                        if (data[0][index] == sampleTimes[i]) {
                            break;
                        } else {
                            throw new RuntimeException("sampleTime does not match at last time point");
                        }
                    }
                    // haven't gotten to last time point yet, stop when next time step is past sampleTime.
                    if (data[0][index + 1] > sampleTimes[i]) {
                        break;
                    }
                    // sampleTime must be later in our data list.
                    index++;
                }
                // if (data[0][index] == sampleTimes[i]) {
                if (Math.abs(data[0][index] - sampleTimes[i]) < 1e-12) {
                    // if timeFactor is not 1.0, time is not in seconds (mins or hrs); if timeFactor is 60, divide sampleTime/60; if it is 3600, divide sampleTime/3600.
                    // if (argTimeFactor != 1.0) {
                    // outputStream.print(data[0][index]/argTimeFactor);
                    // } else {
                    outputStream.print(data[0][index]);
                    // }
                    for (int j = 0; j < argSimSpec.getVarsList().length; j++) {
                        // SBMLImporter.SBVCConcentrationUnits spConcUnits = (SBMLImporter.SBVCConcentrationUnits)argSpUnitsHash.get(argSimSpec.getVarsList()[j]);
                        // if (spConcUnits != null) {
                        // VCUnitDefinition sbunits = spConcUnits.getSBConcentrationUnits();
                        // VCUnitDefinition vcunits = spConcUnits.getVCConcentrationUnits();
                        // SBMLUnitParameter unitFactor = SBMLUtils.getConcUnitFactor("spConcParam", vcunits, sbunits, kMoleSymbol);
                        // outputStream.print("," + data[j + 1][index] * unitFactor.getExpression().evaluateConstant()); 		//earlier, hack unitfactor = 0.000001
                        // earlier, hack unitfactor = 0.000001
                        outputStream.print("," + data[j + 1][index]);
                    }
                    // }
                    outputStream.println();
                } else {
                    // if data[0][index] < sampleTime, must interpolate
                    double fraction = (sampleTimes[i] - data[0][index]) / (data[0][index + 1] - data[0][index]);
                    // if argTimeFactor is not 1.0, time is not in seconds (mins or hrs); if argTimeFactor is 60, divide sampleTime/60; if it is 3600, divide sampleTime/3600.
                    // if (argTimeFactor != 1.0) {
                    // outputStream.print(sampleTimes[i]/argTimeFactor);
                    // } else {
                    outputStream.print(sampleTimes[i]);
                    // }
                    for (int j = 0; j < argSimSpec.getVarsList().length; j++) {
                        double interpolatedValue = 0.0;
                        double[] speciesVals = null;
                        double[] times = null;
                        // Currently using 2nd order interpolation
                        if (index == 0) {
                            // can only do 1st order interpolation
                            times = new double[] { data[0][index], data[0][index + 1] };
                            speciesVals = new double[] { data[j + 1][index], data[j + 1][index + 1] };
                            interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                        } else {
                            if (index >= 1 && index <= origDataLength - 3) {
                                double val_1 = Math.abs(sampleTimes[i] - data[0][index - 1]);
                                double val_2 = Math.abs(sampleTimes[i] - data[0][index + 2]);
                                if (val_1 < val_2) {
                                    times = new double[] { data[0][index - 1], data[0][index], data[0][index + 1] };
                                    speciesVals = new double[] { data[j + 1][index - 1], data[j + 1][index], data[j + 1][index + 1] };
                                } else {
                                    times = new double[] { data[0][index], data[0][index + 1], data[0][index + 2] };
                                    speciesVals = new double[] { data[j + 1][index], data[j + 1][index + 1], data[j + 1][index + 2] };
                                }
                                interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                            } else {
                                times = new double[] { data[0][index - 1], data[0][index], data[0][index + 1] };
                                speciesVals = new double[] { data[j + 1][index - 1], data[j + 1][index], data[j + 1][index + 1] };
                                interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                            }
                        }
                        // end if-else - calc of interpolated value
                        // interpolatedValue = interpolatedValue * unitFactor.getExpression().evaluateConstant();
                        outputStream.print("," + interpolatedValue);
                    }
                    // end for - sp values for each time point (row)
                    outputStream.println();
                }
            }
            outputStream.close();
        } else {
            throw new RuntimeException("Result set was null, could not write to CSV file");
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Errors saving results to CSV file" + e.getMessage());
    }
}

Example 14 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class BNGDataPlotListModel method setOdeSolverResultSet.

/**
 * Sets the dataSource property (cbit.vcell.modelopt.gui.DataSource) value.
 * @param dataSource The new value for the property.
 * @see #getDataSource
 */
public void setOdeSolverResultSet(ODESolverResultSet odeSolverResultSet) {
    ODESolverResultSet oldValue = fieldOdeSolverResultSet;
    fieldOdeSolverResultSet = odeSolverResultSet;
    firePropertyChange("odeSolverResultSet", oldValue, odeSolverResultSet);
}

Example 15 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class BNGOutputPanel method setTextArea.

/**
 * Comment
 */
private void setTextArea(javax.swing.event.ListSelectionEvent listSelectionEvent) {
    int listSelectionIndex = (int) getOutputFormatsList().getSelectedIndex();
    if (listSelectionIndex == -1) {
        return;
    }
    if (((String) getOutputFormatsList().getSelectedValue()).endsWith("dat")) {
        ((java.awt.CardLayout) getOutputsTextPanel().getLayout()).show(getOutputsTextPanel(), getbngDataPlotPanel().getName());
        String fileContentStr = getbngOutput1().getBNGFileContent(listSelectionIndex);
        // Read the data from the cdat/gdat file contents to create a data source for the bngDataPlotPane
        ODESolverResultSet odeSolverResultSet = getOdeSolverResultSet(fileContentStr);
        getbngDataPlotPanel().setOdeSolverResultSet(odeSolverResultSet);
        getbngDataPlotPanel().selectAll();
    } else {
        ((java.awt.CardLayout) getOutputsTextPanel().getLayout()).show(getOutputsTextPanel(), getOutputTextScrollPane().getName());
        String fileContentStr = getbngOutput1().getBNGFileContent(listSelectionIndex);
        getOutputTextArea().setText(fileContentStr);
    }
}