Examples with OutputTimeSpec cbit.vcell.solver.OutputTimeSpec used on opensource projects

Example 16 with OutputTimeSpec

use of cbit.vcell.solver.OutputTimeSpec in project vcell by virtualcell.

the class RuleBasedTest method checkNonspatialStochasticSimContext.

private static void checkNonspatialStochasticSimContext(SimulationContext srcSimContext, File baseDirectory, int numTrials) throws Exception {
    if (!srcSimContext.getApplicationType().equals(Application.NETWORK_STOCHASTIC) || srcSimContext.getGeometry().getDimension() != 0) {
        throw new RuntimeException("simContext is of type " + srcSimContext.getApplicationType() + " and geometry dimension of " + srcSimContext.getGeometry().getDimension() + ", expecting nonspatial stochastic");
    }
    BioModel origBioModel = srcSimContext.getBioModel();
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(XmlHelper.bioModelToXML(origBioModel)));
    bioModel.refreshDependencies();
    // create ODE and RuleBased
    SimulationContext newODEApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewODEApp", false, Application.NETWORK_DETERMINISTIC);
    SimulationContext newRuleBasedApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewRuleBasedApp", false, Application.RULE_BASED_STOCHASTIC);
    newODEApp.setBioModel(bioModel);
    newRuleBasedApp.setBioModel(bioModel);
    ArrayList<AnnotatedFunction> outputFunctionsList = srcSimContext.getOutputFunctionContext().getOutputFunctionsList();
    // OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
    newODEApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    newRuleBasedApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    NetworkGenerationRequirements networkGenerationRequirements = NetworkGenerationRequirements.AllowTruncatedStandardTimeout;
    bioModel.addSimulationContext(newODEApp);
    newODEApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    bioModel.addSimulationContext(newRuleBasedApp);
    newRuleBasedApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    srcSimContext.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    // Create non-spatialStoch, ODE and RuleBased sims
    Simulation nonspatialStochAppNewSim = srcSimContext.addNewSimulation(STOCH_SIM_NAME, /*SimulationOwner.DEFAULT_SIM_NAME_PREFIX*/
    new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    Simulation newODEAppNewSim = newODEApp.addNewSimulation(ODE_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    Simulation newRuleBasedAppNewSim = newRuleBasedApp.addNewSimulation(NFS_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    nonspatialStochAppNewSim.setSimulationOwner(srcSimContext);
    newODEAppNewSim.setSimulationOwner(newODEApp);
    newRuleBasedAppNewSim.setSimulationOwner(newRuleBasedApp);
    try {
        bioModel.getModel().getSpeciesContexts();
        ArrayList<String> varNameList = new ArrayList<String>();
        for (SpeciesContextSpec scs : srcSimContext.getReactionContext().getSpeciesContextSpecs()) {
            varNameList.add(scs.getSpeciesContext().getName());
        }
        String[] varNames = varNameList.toArray(new String[0]);
        OutputTimeSpec outputTimeSpec = nonspatialStochAppNewSim.getSolverTaskDescription().getOutputTimeSpec();
        ArrayList<Double> sampleTimeList = new ArrayList<Double>();
        if (outputTimeSpec instanceof UniformOutputTimeSpec) {
            double endingTime = nonspatialStochAppNewSim.getSolverTaskDescription().getTimeBounds().getEndingTime();
            double dT = ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep();
            int currTimeIndex = 0;
            while (currTimeIndex * dT <= (endingTime + 1e-8)) {
                sampleTimeList.add(currTimeIndex * dT);
                currTimeIndex++;
            }
        }
        double[] sampleTimes = new double[sampleTimeList.size()];
        for (int i = 0; i < sampleTimes.length; i++) {
            sampleTimes[i] = sampleTimeList.get(i);
        }
        TimeSeriesMultitrialData sampleDataStoch1 = new TimeSeriesMultitrialData("stochastic1", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataStoch2 = new TimeSeriesMultitrialData("stochastic2", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataDeterministic = new TimeSeriesMultitrialData("determinstic", varNames, sampleTimes, 1);
        runsolver(nonspatialStochAppNewSim, baseDirectory, numTrials, sampleDataStoch1);
        runsolver(newODEAppNewSim, baseDirectory, 1, sampleDataDeterministic);
        runsolver(newRuleBasedAppNewSim, baseDirectory, numTrials, sampleDataStoch2);
        writeVarDiffData(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeKolmogorovSmirnovTest(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeChiSquareTest(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeData(baseDirectory, sampleDataStoch1);
        writeData(baseDirectory, sampleDataStoch2);
        writeData(baseDirectory, sampleDataDeterministic);
    } finally {
        srcSimContext.removeSimulation(nonspatialStochAppNewSim);
        newODEApp.removeSimulation(newODEAppNewSim);
        newRuleBasedApp.removeSimulation(newRuleBasedAppNewSim);
    }
}

Example 17 with OutputTimeSpec

use of cbit.vcell.solver.OutputTimeSpec in project vcell by virtualcell.

the class SimulationListPanel method initConnections.

/**
 * Initializes connections
 * @exception java.lang.Exception The exception description.
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void initConnections() throws java.lang.Exception {
    // user code begin {1}
    // user code end
    getNewButton().addActionListener(ivjEventHandler);
    getEditButton().addActionListener(ivjEventHandler);
    getDeleteButton().addActionListener(ivjEventHandler);
    getRunButton().addActionListener(ivjEventHandler);
    // getPythonResultsButton().addActionListener(ivjEventHandler);
    getNativeResultsButton().addActionListener(ivjEventHandler);
    getMoreActionsButton().addActionListener(ivjEventHandler);
    getScrollPaneTable().addPropertyChangeListener(ivjEventHandler);
    getOutputFunctionsPanel().addPropertyChangeListener(ivjEventHandler);
    getScrollPaneTable().getSelectionModel().addListSelectionListener(ivjEventHandler);
    DefaultScrollTableCellRenderer renderer = new DefaultScrollTableCellRenderer() {

        @Override
        public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
            super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
            if (value instanceof OutputTimeSpec) {
                SimulationWorkspace sw = getSimulationWorkspace();
                SimulationOwner so = sw.getSimulationOwner();
                UnitInfo unitInfo = so.getUnitInfo();
                Objects.requireNonNull(unitInfo);
                OutputTimeSpec ots = (OutputTimeSpec) value;
                String text = ots.describe(unitInfo);
                setText(text);
            } else if (value instanceof Double) {
                setText(value + "");
            }
            boolean bFinitVolumeRerun = false;
            if (value instanceof SolverDescription) {
                SolverDescription solverDescription = (SolverDescription) value;
                try {
                    if (FINITEVOLUME_CUTTOFF != null && solverDescription.equals(SolverDescription.FiniteVolume)) /*Compiled Solver*/
                    {
                        SimulationStatus simStatus = getSimulationWorkspace().getSimulationStatus(getSimulationListTableModel1().getValueAt(row));
                        if (simStatus.getHasData()) {
                            int statusIndex = 0;
                            while (simStatus.getJobStatus(statusIndex) != null) {
                                if (simStatus.getJobStatus(statusIndex).getEndDate().compareTo(FINITEVOLUME_CUTTOFF) > 0) {
                                    bFinitVolumeRerun = true;
                                    break;
                                }
                                statusIndex++;
                            }
                        }
                    }
                } catch (Exception e) {
                    // ignore, let table cell render anyway
                    e.printStackTrace();
                }
                setText(solverDescription.getShortDisplayLabel());
                setToolTipText(solverDescription.getDisplayLabel());
            } else {
                setToolTipText(getText());
            }
            if (bFinitVolumeRerun) {
                setText(getText() + (bFinitVolumeRerun ? "(*)" : ""));
                setToolTipText(getToolTipText() + (bFinitVolumeRerun ? " (data regenerated using FiniteVolumeStandalone)" : ""));
            }
            return this;
        }
    };
    getScrollPaneTable().setDefaultRenderer(OutputTimeSpec.class, renderer);
    getScrollPaneTable().setDefaultRenderer(Double.class, renderer);
    getScrollPaneTable().setDefaultRenderer(String.class, renderer);
    getScrollPaneTable().setDefaultRenderer(SolverDescription.class, renderer);
    getScrollPaneTable().setDefaultEditor(OutputTimeSpec.class, new DefaultCellEditor(new JTextField()));
    getScrollPaneTable().setDefaultRenderer(SimulationStatus.class, new DefaultScrollTableCellRenderer() {

        @Override
        public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
            Object obj = getSimulationStatusDisplay(row);
            if (obj instanceof JProgressBar) {
                return (JProgressBar) obj;
            }
            super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
            if (value instanceof SimulationStatus) {
                setText(obj.toString());
                String details = ((SimulationStatus) value).getDetails();
                setToolTipText(details);
            }
            return this;
        }
    });
}

Example 18 with OutputTimeSpec

use of cbit.vcell.solver.OutputTimeSpec in project vcell by virtualcell.

the class SimulationListTableModel method setValueAt.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2004 2:01:23 PM)
 * @param aValue java.lang.Object
 * @param rowIndex int
 * @param columnIndex int
 */
public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Simulation simulation = getValueAt(rowIndex);
    try {
        switch(columnIndex) {
            case COLUMN_NAME:
                if (aValue instanceof String) {
                    String newName = (String) aValue;
                    if (!simulation.getName().equals(newName)) {
                        simulation.setName(newName);
                    }
                }
                break;
            case COLUMN_ENDTIME:
                if (aValue instanceof Double) {
                    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
                    double newEndTime = (Double) aValue;
                    if (newEndTime != solverTaskDescription.getTimeBounds().getEndingTime()) {
                        ClientTaskManager.changeEndTime(ownerTable, solverTaskDescription, newEndTime);
                        simulation.setIsDirty(true);
                    }
                }
                break;
            case COLUMN_OUTPUT:
                if (aValue instanceof String) {
                    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
                    OutputTimeSpec ots = solverTaskDescription.getOutputTimeSpec();
                    OutputTimeSpec newOts = null;
                    if (ots instanceof DefaultOutputTimeSpec) {
                        int newValue = Integer.parseInt((String) aValue);
                        newOts = new DefaultOutputTimeSpec(newValue, ((DefaultOutputTimeSpec) ots).getKeepAtMost());
                    } else if (ots instanceof UniformOutputTimeSpec) {
                        try {
                            boolean bValid = true;
                            double outputTime = Double.parseDouble((String) aValue);
                            if (solverTaskDescription.getOutputTimeSpec().isUniform()) {
                                if (solverTaskDescription.getSolverDescription().hasVariableTimestep()) {
                                    newOts = new UniformOutputTimeSpec(outputTime);
                                } else {
                                    double timeStep = solverTaskDescription.getTimeStep().getDefaultTimeStep();
                                    double suggestedInterval = outputTime;
                                    if (outputTime < timeStep) {
                                        suggestedInterval = timeStep;
                                        bValid = false;
                                    } else {
                                        if (!BeanUtils.isIntegerMultiple(outputTime, timeStep)) {
                                            double n = outputTime / timeStep;
                                            int intn = (int) Math.round(n);
                                            suggestedInterval = (intn * timeStep);
                                            if (suggestedInterval != outputTime) {
                                                bValid = false;
                                            }
                                        }
                                    }
                                    if (bValid) {
                                        newOts = new UniformOutputTimeSpec(outputTime);
                                    } else {
                                        String ret = PopupGenerator.showWarningDialog(ownerTable, "Output Interval", "Output Interval must " + "be integer multiple of time step.\n\nChange Output Interval to " + suggestedInterval + "?", new String[] { UserMessage.OPTION_YES, UserMessage.OPTION_NO }, UserMessage.OPTION_YES);
                                        if (ret.equals(UserMessage.OPTION_YES)) {
                                            newOts = new UniformOutputTimeSpec(suggestedInterval);
                                        }
                                    }
                                }
                            }
                        } catch (NumberFormatException ex) {
                            DialogUtils.showErrorDialog(ownerTable, "Wrong number format " + ex.getMessage().toLowerCase());
                        }
                    } else if (ots instanceof ExplicitOutputTimeSpec) {
                        newOts = ExplicitOutputTimeSpec.fromString((String) aValue);
                    }
                    if (newOts != null && !newOts.compareEqual(ots)) {
                        solverTaskDescription.setOutputTimeSpec(newOts);
                        simulation.setIsDirty(true);
                    }
                }
                break;
        }
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(ownerTable, ex.getMessage());
    }
}

Example 19 with OutputTimeSpec

use of cbit.vcell.solver.OutputTimeSpec in project vcell by virtualcell.

the class OdeFileWriter method write.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
public void write(String[] parameterNames) throws Exception {
    createStateVariables();
    createSymbolTable();
    Simulation simulation = simTask.getSimulation();
    if (simulation.getSolverTaskDescription().getUseSymbolicJacobian()) {
        throw new RuntimeException("symbolic jacobian option not yet supported in interpreted Stiff solver");
    }
    writeJMSParamters();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
    ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
    printWriter.println("SOLVER " + getSolverName());
    printWriter.println("STARTING_TIME " + timeBounds.getStartingTime());
    printWriter.println("ENDING_TIME " + timeBounds.getEndingTime());
    printWriter.println("RELATIVE_TOLERANCE " + errorTolerance.getRelativeErrorTolerance());
    printWriter.println("ABSOLUTE_TOLERANCE " + errorTolerance.getAbsoluteErrorTolerance());
    printWriter.println("MAX_TIME_STEP " + simulation.getSolverTaskDescription().getTimeStep().getMaximumTimeStep());
    OutputTimeSpec ots = simulation.getSolverTaskDescription().getOutputTimeSpec();
    if (ots.isDefault()) {
        printWriter.println("KEEP_EVERY " + ((DefaultOutputTimeSpec) ots).getKeepEvery());
    } else if (ots.isUniform()) {
        printWriter.println("OUTPUT_TIME_STEP " + ((UniformOutputTimeSpec) ots).getOutputTimeStep());
    } else if (ots.isExplicit()) {
        printWriter.println("OUTPUT_TIMES " + ((ExplicitOutputTimeSpec) ots).getNumTimePoints());
        printWriter.println(((ExplicitOutputTimeSpec) ots).toSpaceSeperatedMultiLinesOfString());
    }
    if (parameterNames != null && parameterNames.length != 0) {
        printWriter.println("NUM_PARAMETERS " + parameterNames.length);
        for (int i = 0; i < parameterNames.length; i++) {
            printWriter.println(parameterNames[i]);
        }
    }
    HashMap<Discontinuity, String> discontinuityNameMap = new HashMap<Discontinuity, String>();
    String eventString = null;
    if (simulation.getMathDescription().hasEvents()) {
        eventString = writeEvents(discontinuityNameMap);
    }
    String equationString = writeEquations(discontinuityNameMap);
    if (discontinuityNameMap.size() > 0) {
        printWriter.println("DISCONTINUITIES " + discontinuityNameMap.size());
        for (Discontinuity od : discontinuityNameMap.keySet()) {
            printWriter.println(discontinuityNameMap.get(od) + " " + od.getDiscontinuityExp().flatten().infix() + "; " + od.getRootFindingExp().flatten().infix() + ";");
        }
    }
    if (eventString != null) {
        printWriter.print(eventString);
    }
    printWriter.println("NUM_EQUATIONS " + getStateVariableCount());
    printWriter.println(equationString);
}

Example 20 with OutputTimeSpec

use of cbit.vcell.solver.OutputTimeSpec in project vcell by virtualcell.

the class NFSimSolver method getMathExecutableCommand.

@Override
protected String[] getMathExecutableCommand() {
    String executableName = null;
    try {
        executableName = SolverUtilities.getExes(SolverDescription.NFSim)[0].getAbsolutePath();
    } catch (IOException e) {
        throw new RuntimeException("failed to get executable for solver " + SolverDescription.NFSim.getDisplayLabel() + ": " + e.getMessage(), e);
    }
    String inputFilename = getInputFilename();
    String outputFilename = getOutputFilename();
    String speciesOutputFilename = getSpeciesOutputFilename();
    NFsimSimulationOptions nfsso = simTask.getSimulation().getSolverTaskDescription().getNFSimSimulationOptions();
    ArrayList<String> adv = new ArrayList<String>();
    boolean observableComputationOff = nfsso.getObservableComputationOff();
    if (observableComputationOff == true) {
        // false is by default, no need to specify
        adv.add("-notf");
    }
    Integer moleculeDistance = nfsso.getMoleculeDistance();
    if (moleculeDistance != null) {
        adv.add("-utl");
        adv.add(moleculeDistance + "");
    }
    boolean aggregateBookkeeping = nfsso.getAggregateBookkeeping();
    if (aggregateBookkeeping == true || simTask.getSimulation().getMathDescription().hasSpeciesObservable()) {
        // false is by default, no need to specify
        adv.add("-cb");
    }
    Integer maxMoleculesPerType = nfsso.getMaxMoleculesPerType();
    if (maxMoleculesPerType != null) {
        adv.add("-gml");
        adv.add(maxMoleculesPerType + "");
    }
    Integer equilibrateTime = nfsso.getEquilibrateTime();
    if (equilibrateTime != null) {
        adv.add("-eq");
        adv.add(equilibrateTime + "");
    }
    boolean preventIntraBonds = nfsso.getPreventIntraBonds();
    if (preventIntraBonds == true) {
        // false is by default, no need to specify
        adv.add("-bscb");
    }
    TimeBounds tb = getSimulationJob().getSimulation().getSolverTaskDescription().getTimeBounds();
    double dtime = tb.getEndingTime() - tb.getStartingTime();
    String timeSpecOption1 = "-oSteps";
    String timeSpecOption2 = "10";
    OutputTimeSpec outputTimeSpec = getSimulationJob().getSimulation().getSolverTaskDescription().getOutputTimeSpec();
    if (outputTimeSpec instanceof DefaultOutputTimeSpec) {
        DefaultOutputTimeSpec dots = (DefaultOutputTimeSpec) outputTimeSpec;
        int steps = dots.getKeepAtMost();
        timeSpecOption1 = "-oSteps";
        timeSpecOption2 = Integer.toString(steps);
    } else if (outputTimeSpec instanceof UniformOutputTimeSpec) {
        UniformOutputTimeSpec dots = (UniformOutputTimeSpec) outputTimeSpec;
        double steps = dtime / dots.getOutputTimeStep();
        timeSpecOption1 = "-oSteps";
        int stepsi = (int) Math.round(steps);
        timeSpecOption2 = Integer.toString(stepsi);
    } else {
        throw new RuntimeException("Unsupported output time spec class");
    }
    String[] baseCommands = { "-xml", inputFilename, "-o", outputFilename, "-sim", Double.toString(dtime), "-ss", speciesOutputFilename };
    ArrayList<String> cmds = new ArrayList<String>();
    cmds.add(executableName);
    Integer seed = nfsso.getRandomSeed();
    if (seed != null) {
        cmds.add("-seed");
        cmds.add(seed.toString());
    } else {
        long randomSeed = System.currentTimeMillis();
        randomSeed = randomSeed + simTask.getSimulationJob().getJobIndex();
        // multiply with a large prime number to spread numbers that are too close and in sequence
        randomSeed = randomSeed * 89611;
        Integer rs = (int) randomSeed;
        String str = rs.toString();
        if (str.startsWith("-")) {
            // NFSim wants a positive integer, for anything else is initializing with 0
            str = str.substring(1);
        }
        cmds.add("-seed");
        cmds.add(str);
    // PrintWriter writer;
    // try {
    // writer = new PrintWriter("c:\\TEMP\\aaa\\" + randomSeed + ".txt", "UTF-8");
    // writer.println(str);
    // writer.close();
    // } catch (FileNotFoundException | UnsupportedEncodingException e) {
    // // Auto-generated catch block
    // e.printStackTrace();
    // }
    }
    cmds.add("-vcell");
    cmds.addAll(new ArrayList<String>(Arrays.asList(baseCommands)));
    cmds.add(timeSpecOption1);
    cmds.add(timeSpecOption2);
    cmds.addAll(adv);
    if (bMessaging) {
        cmds.add("-v");
    }
    return cmds.toArray(new String[cmds.size()]);
}