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

Example 11 with OutputTimeSpec

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

the class StandaloneRuleBasedTest method checkNonspatialStochasticSimContext.

private static void checkNonspatialStochasticSimContext(SimulationContext srcSimContext, File baseDirectory, int numTrials, long bngTimeoutDuration) 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 networkGenRequirements = NetworkGenerationRequirements.getComputeFull(bngTimeoutDuration);
    bioModel.addSimulationContext(newODEApp);
    newODEApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    bioModel.addSimulationContext(newRuleBasedApp);
    newRuleBasedApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    srcSimContext.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    // Create non-spatialStoch, ODE and RuleBased sims
    Simulation nonspatialStochAppNewSim = srcSimContext.addNewSimulation(STOCH_SIM_NAME, /*SimulationOwner.DEFAULT_SIM_NAME_PREFIX*/
    new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    Simulation newODEAppNewSim = newODEApp.addNewSimulation(ODE_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    Simulation newRuleBasedAppNewSim = newRuleBasedApp.addNewSimulation(NFS_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    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);
        StochtestFileUtils.writeVarDiffData(new File(baseDirectory, VARDIFF_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeKolmogorovSmirnovTest(new File(baseDirectory, KS_TEST_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeChiSquareTest(new File(baseDirectory, ChiSquared_TEST_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeData(sampleDataStoch1, new File(baseDirectory, "data." + sampleDataStoch1.datasetName + ".json"));
        StochtestFileUtils.writeData(sampleDataStoch2, new File(baseDirectory, "data." + sampleDataStoch2.datasetName + ".json"));
        StochtestFileUtils.writeData(sampleDataDeterministic, new File(baseDirectory, "data." + sampleDataDeterministic.datasetName + ".json"));
    } finally {
        srcSimContext.removeSimulation(nonspatialStochAppNewSim);
        newODEApp.removeSimulation(newODEAppNewSim);
        newRuleBasedApp.removeSimulation(newRuleBasedAppNewSim);
    }
}

Example 12 with OutputTimeSpec

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

the class OutputOptionsPanel method actionOutputOptionButtonState.

private void actionOutputOptionButtonState(java.awt.event.ActionEvent actionEvent) {
    try {
        if (solverTaskDescription == null) {
            return;
        }
        OutputTimeSpec outputTimeSpec = solverTaskDescription.getOutputTimeSpec();
        if (actionEvent.getSource() == getDefaultOutputRadioButton() && !outputTimeSpec.isDefault()) {
            solverTaskDescription.setOutputTimeSpec(new DefaultOutputTimeSpec());
        } else if (actionEvent.getSource() == getUniformOutputRadioButton() && !outputTimeSpec.isUniform()) {
            double outputTime = 0.0;
            if (solverTaskDescription.getSolverDescription().isSemiImplicitPdeSolver()) {
                String floatStr = "" + (float) (((DefaultOutputTimeSpec) outputTimeSpec).getKeepEvery() * solverTaskDescription.getTimeStep().getDefaultTimeStep());
                outputTime = Double.parseDouble(floatStr);
            } else {
                TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
                Range outputTimeRange = NumberUtils.getDecimalRange(timeBounds.getStartingTime(), timeBounds.getEndingTime() / 100, true, true);
                outputTime = outputTimeRange.getMax();
            }
            solverTaskDescription.setOutputTimeSpec(new UniformOutputTimeSpec(outputTime));
        } else if (actionEvent.getSource() == getExplicitOutputRadioButton() && !outputTimeSpec.isExplicit()) {
            TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
            solverTaskDescription.setOutputTimeSpec(new ExplicitOutputTimeSpec(new double[] { timeBounds.getStartingTime(), timeBounds.getEndingTime() }));
        }
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 13 with OutputTimeSpec

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

the class OutputOptionsPanel method setNewOutputOption.

/**
 * Comment
 */
private void setNewOutputOption() {
    try {
        OutputTimeSpec ots = null;
        if (getDefaultOutputRadioButton().isSelected()) {
            int keepEvery = Integer.parseInt(getKeepEveryTextField().getText());
            if (solverTaskDescription.getSolverDescription().isSemiImplicitPdeSolver()) {
                ots = new DefaultOutputTimeSpec(keepEvery);
            } else {
                int keepAtMost = Integer.parseInt(getKeepAtMostTextField().getText());
                ots = new DefaultOutputTimeSpec(keepEvery, keepAtMost);
            }
        } else if (getUniformOutputRadioButton().isSelected()) {
            double outputTime = Double.parseDouble(getOutputTimeStepTextField().getText());
            ots = new UniformOutputTimeSpec(outputTime);
        } else if (getExplicitOutputRadioButton().isSelected()) {
            ots = ExplicitOutputTimeSpec.fromString(getOutputTimesTextField().getText());
        }
        try {
            solverTaskDescription.setOutputTimeSpec(ots);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException(e.getMessage());
        }
    } catch (Exception e) {
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 14 with OutputTimeSpec

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

the class XmlReader method getSolverTaskDescription.

/**
 * This method returns a SolverTaskDescription Object from a XML Element.
 * Creation date: (5/22/2001 10:51:23 AM)
 * @return cbit.vcell.solver.SolverTaskDescription
 * @param param org.jdom.Element
 * @param simulation cbit.vcell.solver.Simulation
 */
private SolverTaskDescription getSolverTaskDescription(Element param, Simulation simulation) throws XmlParseException {
    // *** create new SolverTaskDescription ***
    SolverTaskDescription solverTaskDesc = new SolverTaskDescription(simulation);
    // Added July 22nd, 2007, used as condition for stochSimOptions or stochHybridOprtions
    SolverDescription sd = null;
    // Retrieve attributes
    String taskType = param.getAttributeValue(XMLTags.TaskTypeTag);
    int keepEvery = -1;
    int keepAtMost = -1;
    if (param.getAttributeValue(XMLTags.KeepEveryTag) != null) {
        keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryTag));
        keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostTag));
    }
    boolean useSymJacob = new Boolean(param.getAttributeValue(XMLTags.UseSymbolicJacobianAttrTag)).booleanValue();
    String solverName = param.getAttributeValue(XMLTags.SolverNameTag);
    // get sentivity parameter
    Element sensparamElement = param.getChild(XMLTags.ConstantTag, vcNamespace);
    Constant sensitivityparam = null;
    if (sensparamElement != null) {
        sensitivityparam = getConstant(sensparamElement);
    }
    // set Attributes
    try {
        // set solver
        sd = SolverDescription.fromDatabaseName(solverName);
        if (sd == null) {
            System.err.println("====================================== couldn't find solver description name ==========================================");
        }
        solverTaskDesc.setSolverDescription(sd);
        if (taskType.equalsIgnoreCase(XMLTags.UnsteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_UNSTEADY);
        } else if (taskType.equalsIgnoreCase(XMLTags.SteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_STEADY);
        } else {
            throw new XmlParseException("Unexpected task type: " + taskType);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the taskType: " + taskType, e);
    }
    int numProcessors = parseIntWithDefault(param, XMLTags.NUM_PROCESSORS, 1);
    try {
        solverTaskDesc.setNumProcessors(numProcessors);
        solverTaskDesc.setUseSymbolicJacobian(useSymJacob);
        // get TimeBound
        solverTaskDesc.setTimeBounds(getTimeBounds(param.getChild(XMLTags.TimeBoundTag, vcNamespace)));
        // get TimeStep
        solverTaskDesc.setTimeStep(getTimeStep(param.getChild(XMLTags.TimeStepTag, vcNamespace)));
        // get ErrorTolerance
        solverTaskDesc.setErrorTolerance(getErrorTolerance(param.getChild(XMLTags.ErrorToleranceTag, vcNamespace)));
        // get StochSimOptions
        if (simulation != null && simulation.getMathDescription() != null) {
            if (simulation.getMathDescription().isNonSpatialStoch() && param.getChild(XMLTags.StochSimOptionsTag, vcNamespace) != null) {
                // Amended July 22nd, 2007 to read either stochSimOptions or stochHybridOptions
                solverTaskDesc.setStochOpt(getStochSimOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                if (sd != null && !sd.equals(SolverDescription.StochGibson)) {
                    solverTaskDesc.setStochHybridOpt(getStochHybridOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                }
            }
        }
        // get OutputOptions
        if (keepEvery != -1) {
            solverTaskDesc.setOutputTimeSpec(new DefaultOutputTimeSpec(keepEvery, keepAtMost));
        }
        OutputTimeSpec ots = getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace));
        if (ots != null) {
            solverTaskDesc.setOutputTimeSpec(getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace)));
        }
        // set SensitivityParameter
        solverTaskDesc.setSensitivityParameter(sensitivityparam);
        // set StopAtSpatiallyUniform
        Element stopSpatiallyElement = param.getChild(XMLTags.StopAtSpatiallyUniform, vcNamespace);
        if (stopSpatiallyElement != null) {
            Element errTolElement = stopSpatiallyElement.getChild(XMLTags.ErrorToleranceTag, vcNamespace);
            if (errTolElement != null) {
                solverTaskDesc.setStopAtSpatiallyUniformErrorTolerance(getErrorTolerance(errTolElement));
            }
        }
        String runParameterScanSeriallyAttributeValue = param.getAttributeValue(XMLTags.RunParameterScanSerially);
        if (runParameterScanSeriallyAttributeValue != null) {
            solverTaskDesc.setSerialParameterScan(new Boolean(runParameterScanSeriallyAttributeValue).booleanValue());
        }
        Element nfsimSimulationOptionsElement = param.getChild(XMLTags.NFSimSimulationOptions, vcNamespace);
        if (nfsimSimulationOptionsElement != null) {
            NFsimSimulationOptions nfsimSimulationOptions = getNFSimSimulationOptions(nfsimSimulationOptionsElement);
            solverTaskDesc.setNFSimSimulationOptions(nfsimSimulationOptions);
        }
        Element smoldySimulationOptionsElement = param.getChild(XMLTags.SmoldynSimulationOptions, vcNamespace);
        if (smoldySimulationOptionsElement != null) {
            SmoldynSimulationOptions smoldynSimulationOptions = getSmoldySimulationOptions(smoldySimulationOptionsElement);
            solverTaskDesc.setSmoldynSimulationOptions(smoldynSimulationOptions);
        }
        Element sundialsPdeSolverOptionsElement = param.getChild(XMLTags.SundialsSolverOptions, vcNamespace);
        if (sundialsPdeSolverOptionsElement != null) {
            SundialsPdeSolverOptions sundialsPdeSolverOptions = getSundialsPdeSolverOptions(sundialsPdeSolverOptionsElement);
            solverTaskDesc.setSundialsPdeSolverOptions(sundialsPdeSolverOptions);
        }
        Element chomboElement = param.getChild(XMLTags.ChomboSolverSpec, vcNamespace);
        if (chomboElement != null) {
            ChomboSolverSpec chombo = getChomboSolverSpec(solverTaskDesc, chomboElement, simulation.getMathDescription().getGeometry().getDimension());
            solverTaskDesc.setChomboSolverSpec(chombo);
        }
        Element mbElement = param.getChild(XMLTags.MovingBoundarySolverOptionsTag, vcNamespace);
        if (mbElement != null) {
            MovingBoundarySolverOptions mb = getMovingBoundarySolverOptions(solverTaskDesc, mbElement);
            solverTaskDesc.setMovingBoundarySolverOptions(mb);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    }
    return solverTaskDesc;
}

Example 15 with OutputTimeSpec

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

the class StochtestRunService method runOne.

public void runOne() throws IllegalArgumentException, SQLException, DataAccessException, XmlParseException, PropertyVetoException, ExpressionException, MappingException, GeometryException, ImageException, IOException {
    StochtestRun stochtestRun = StochtestDbUtils.acceptNextWaitingStochtestRun(conFactory);
    String biomodelXML = null;
    if (stochtestRun != null) {
        String networkGenProbs = null;
        try {
            User user = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new KeyValue(PropertyLoader.ADMINISTRATOR_ID));
            ServerDocumentManager serverDocumentManager = new ServerDocumentManager(this.dbServerImpl);
            biomodelXML = serverDocumentManager.getBioModelXML(new QueryHashtable(), user, stochtestRun.stochtest.biomodelRef, true);
            BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(biomodelXML));
            bioModel.refreshDependencies();
            SimulationContext srcSimContext = null;
            for (SimulationContext sc : bioModel.getSimulationContexts()) {
                if (sc.getKey().equals(stochtestRun.stochtest.simContextRef)) {
                    srcSimContext = sc;
                }
            }
            if (srcSimContext == null) {
                throw new RuntimeException("cannot find simcontext with key=" + stochtestRun.stochtest.simContextRef);
            }
            // 
            for (SpeciesContextSpec scs : srcSimContext.getReactionContext().getSpeciesContextSpecs()) {
                scs.setConstant(false);
            }
            SimulationContext simContext = srcSimContext;
            StochtestMathType parentMathType = stochtestRun.parentMathType;
            StochtestMathType mathType = stochtestRun.mathType;
            if (parentMathType != mathType) {
                if (parentMathType == StochtestMathType.nonspatialstochastic && mathType == StochtestMathType.rules) {
                    simContext = SimulationContext.copySimulationContext(srcSimContext, "generatedRules", false, Application.RULE_BASED_STOCHASTIC);
                } else if (parentMathType == StochtestMathType.rules && mathType == StochtestMathType.nonspatialstochastic) {
                    simContext = SimulationContext.copySimulationContext(srcSimContext, "generatedSSA", false, Application.NETWORK_STOCHASTIC);
                } else {
                    throw new RuntimeException("unexpected copy of simcontext from " + parentMathType + " to " + mathType);
                }
                bioModel.addSimulationContext(simContext);
            }
            MathMappingCallback mathMappingCallback = new MathMappingCallback() {

                @Override
                public void setProgressFraction(float fractionDone) {
                }

                @Override
                public void setMessage(String message) {
                }

                @Override
                public boolean isInterrupted() {
                    return false;
                }
            };
            MathMapping mathMapping = simContext.createNewMathMapping(mathMappingCallback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
            MathDescription mathDesc = mathMapping.getMathDescription(mathMappingCallback);
            simContext.setMathDescription(mathDesc);
            if (simContext.isInsufficientIterations()) {
                networkGenProbs = "insufficientIterations";
            } else if (simContext.isInsufficientMaxMolecules()) {
                networkGenProbs = "insufficientMaxMolecules";
            }
            File baseDirectory = StochtestFileUtils.createDirFile(baseDir, stochtestRun);
            try {
                OutputTimeSpec outputTimeSpec = new UniformOutputTimeSpec(0.5);
                double endTime = 10.0;
                computeTrials(simContext, stochtestRun, baseDirectory, outputTimeSpec, endTime, numTrials);
                StochtestDbUtils.finalizeAcceptedStochtestRun(conFactory, stochtestRun, StochtestRun.StochtestRunStatus.complete, null, networkGenProbs);
            } finally {
                StochtestFileUtils.clearDir(baseDirectory);
            }
        } catch (Exception e) {
            StochtestDbUtils.finalizeAcceptedStochtestRun(conFactory, stochtestRun, StochtestRun.StochtestRunStatus.failed, e.getMessage(), networkGenProbs);
            // 
            if (biomodelXML != null) {
                XmlUtil.writeXMLStringToFile(biomodelXML, new File(baseDir, "stochtestrun_" + stochtestRun.stochtest.key + ".vcml").getPath(), false);
            }
            // 
            // write exception trace to .txt file
            // 
            StringWriter stringWriter = new StringWriter();
            PrintWriter printWriter = new PrintWriter(stringWriter);
            e.printStackTrace(printWriter);
            printWriter.flush();
            System.out.println(stringWriter.getBuffer().toString());
            XmlUtil.writeXMLStringToFile(stringWriter.getBuffer().toString(), new File(baseDir, "stochtestrun_" + stochtestRun.stochtest.key + "_error.txt").getPath(), false);
        }
    } else {
        System.out.println("no jobs waiting");
        try {
            Thread.sleep(5000);
        } catch (InterruptedException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
}