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

Example 6 with Simulation

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

the class SmoldynFileWriter method writeDataProcessor.

private void writeDataProcessor() throws DataAccessException, IOException, MathException, DivideByZeroException, ExpressionException {
    Simulation simulation = simTask.getSimulation();
    DataProcessingInstructions dpi = simulation.getDataProcessingInstructions();
    if (dpi == null) {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " begin " + DataProcessingInstructions.ROI_TIME_SERIES);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " end");
    } else {
        FieldDataIdentifierSpec fdis = dpi.getSampleImageFieldData(simulation.getVersion().getOwner());
        if (fdis == null) {
            throw new DataAccessException("Can't find sample image in data processing instructions");
        }
        File userDirectory = outputFile.getParentFile();
        String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
        DataSetControllerImpl dsci = new DataSetControllerImpl(null, userDirectory.getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
        CartesianMesh origMesh = dsci.getMesh(fdis.getExternalDataIdentifier());
        SimDataBlock simDataBlock = dsci.getSimDataBlock(null, fdis.getExternalDataIdentifier(), fdis.getFieldFuncArgs().getVariableName(), fdis.getFieldFuncArgs().getTime().evaluateConstant());
        VariableType varType = fdis.getFieldFuncArgs().getVariableType();
        VariableType dataVarType = simDataBlock.getVariableType();
        if (!varType.equals(VariableType.UNKNOWN) && !varType.equals(dataVarType)) {
            throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
        }
        double[] origData = simDataBlock.getData();
        String filename = SimulationJob.createSimulationJobID(Simulation.createSimulationID(simulation.getKey()), simTask.getSimulationJob().getJobIndex()) + SimulationData.getDefaultFieldDataFileNameForSimulation(fdis.getFieldFuncArgs());
        File fdatFile = new File(userDirectory, filename);
        DataSet.writeNew(fdatFile, new String[] { fdis.getFieldFuncArgs().getVariableName() }, new VariableType[] { simDataBlock.getVariableType() }, new ISize(origMesh.getSizeX(), origMesh.getSizeY(), origMesh.getSizeZ()), new double[][] { origData });
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " begin " + dpi.getScriptName());
        StringTokenizer st = new StringTokenizer(dpi.getScriptInput(), "\n\r");
        while (st.hasMoreTokens()) {
            String str = st.nextToken();
            if (str.trim().length() > 0) {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " " + str);
            }
        }
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " SampleImageFile " + fdis.getFieldFuncArgs().getVariableName() + " " + fdis.getFieldFuncArgs().getTime().infix() + " " + fdatFile);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " end");
    }
}

Example 7 with Simulation

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

the class StandaloneSEDMLTest method doit.

public static void doit(File archiveFile) throws Exception {
    ArchiveComponents ac = null;
    ac = Libsedml.readSEDMLArchive(new FileInputStream(archiveFile));
    SEDMLDocument sedmlDoc = ac.getSedmlDocument();
    SedML sedml = sedmlDoc.getSedMLModel();
    if (sedml == null || sedml.getModels().isEmpty()) {
        throw new RuntimeException("sedml null or empty");
    }
    ModelResolver resolver = new ModelResolver(sedml);
    // resolver.add(new FileModelResolver());
    resolver.add(new ArchiveModelResolver(ac));
    resolver.add(new BioModelsModelsRetriever());
    resolver.add(new URLResourceRetriever());
    // resolver.add(new RelativeFileModelResolver(FileUtils.getFullPath(archiveFile.getAbsolutePath())));
    // 
    // iterate through all the elements and show them at the console
    // 
    List<org.jlibsedml.Model> mmm = sedml.getModels();
    for (Model mm : mmm) {
        System.out.println(mm.toString());
    }
    List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
    for (org.jlibsedml.Simulation ss : sss) {
        System.out.println(ss.toString());
    }
    List<AbstractTask> ttt = sedml.getTasks();
    for (AbstractTask tt : ttt) {
        System.out.println(tt.toString());
    }
    List<DataGenerator> ddd = sedml.getDataGenerators();
    for (DataGenerator dd : ddd) {
        System.out.println(dd.toString());
    }
    List<Output> ooo = sedml.getOutputs();
    for (Output oo : ooo) {
        System.out.println(oo.toString());
    }
    // 
    // extract models referenced in tasks.
    // 
    KisaoOntology kisaoInstance = KisaoOntology.getInstance();
    // HashMap<String,Model> flattenedModels = new HashMap<String, Model>();
    List<AbstractTask> taskList = sedml.getTasks();
    for (AbstractTask task : taskList) {
        String modelReference = task.getModelReference();
        org.jlibsedml.Model sedmlOriginalModel = sedml.getModelWithId(modelReference);
        String sbmlModelString = resolver.getModelString(sedmlOriginalModel);
        // sbmlSource with all the changes applied
        XMLSource sbmlSource = new XMLSource(sbmlModelString);
        org.jlibsedml.Simulation sedmlSimulation = sedml.getSimulation(task.getSimulationReference());
        Algorithm algorithm = sedmlSimulation.getAlgorithm();
        KisaoTerm sedmlKisao = kisaoInstance.getTermById(algorithm.getKisaoID());
        // 
        // try to find a VCell solverDescription to match the Kisao term
        // 
        // UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
        // Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
        // identify the vCell solvers that would match best the sedml solver kisao id
        List<SolverDescription> solverDescriptions = new ArrayList<>();
        for (SolverDescription sd : SolverDescription.values()) {
            KisaoTerm solverKisaoTerm = kisaoInstance.getTermById(sd.getKisao());
            if (solverKisaoTerm == null) {
                break;
            }
            boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
            if (isExactlySame && !solverKisaoTerm.isObsolete()) {
                // we make a list with all the solvers that match the kisao
                solverDescriptions.add(sd);
            }
        }
        if (solverDescriptions.isEmpty()) {
            throw new RuntimeException("cannot find the solverDescription with exact match for Kisao term '" + sedmlKisao + "'");
        }
        // choose first one
        SolverDescription solverDescription = solverDescriptions.get(0);
        // find out everything else we need about the application we're going to use,
        // some of the info will be needed when we parse the sbml file
        boolean bSpatial = false;
        Application appType = Application.NETWORK_DETERMINISTIC;
        Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
        for (SolverDescription.SolverFeature sf : sfList) {
            switch(sf) {
                case Feature_Rulebased:
                    appType = Application.RULE_BASED_STOCHASTIC;
                    break;
                case Feature_Stochastic:
                    appType = Application.NETWORK_STOCHASTIC;
                    break;
                case Feature_Deterministic:
                    appType = Application.NETWORK_DETERMINISTIC;
                    break;
                case Feature_Spatial:
                    bSpatial = true;
                    break;
                default:
                    break;
            }
        }
        BioModel bioModel = (BioModel) XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
        // 
        // we already have an application loaded from the sbml file, with initial conditions and stuff
        // which may be not be suitable because the sedml kisao may need a different app type
        // so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
        // 
        // the new application we're making from the old one
        SimulationContext newSimulationContext = null;
        if (bioModel.getSimulationContexts().length == 1) {
            SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
            String newSCName = bioModel.getFreeSimulationContextName();
            newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, newSCName, bSpatial, appType);
            bioModel.addSimulationContext(newSimulationContext);
            bioModel.removeSimulationContext(oldSimulationContext);
        } else {
            newSimulationContext = bioModel.addNewSimulationContext("App1", appType);
        }
        // 
        // making the new vCell simulation based on the sedml simulation
        // 
        newSimulationContext.refreshDependencies();
        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(progressListener);
        newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
        newSimulation.setName(sedmlSimulation.getName());
        bioModel.addSimulation(newSimulation);
        // and set the vCell simulation parameters accordingly
        if (sedmlSimulation instanceof UniformTimeCourse) {
        } else if (sedmlSimulation instanceof OneStep) {
        } else if (sedmlSimulation instanceof SteadyState) {
        } else {
        }
        System.out.println(XmlHelper.bioModelToXML(bioModel));
    }
}

Example 8 with Simulation

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

the class SimulationServiceImpl method computeModel.

private SimulationInfo computeModel(BioModel bioModel, SimulationSpec simSpec, ClientTaskStatusSupport statusCallback) {
    try {
        SimulationContext simContext = bioModel.getSimulationContext(0);
        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(statusCallback);
        Simulation newsim = simContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX, callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
        SimulationInfo simulationInfo = new SimulationInfo();
        simulationInfo.setId(Math.abs(new Random().nextInt(1000000)));
        // ----------- run simulation(s)
        final File localSimDataDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
        Simulation simulation = new TempSimulation(newsim, false);
        final SimulationServiceContext simServiceContext = new SimulationServiceContext();
        simServiceContext.simInfo = simulationInfo;
        simServiceContext.simState = SimulationState.running;
        simServiceContext.simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
        simServiceContext.vcDataIdentifier = simServiceContext.simTask.getSimulationJob().getVCDataIdentifier();
        simServiceContext.solver = createQuickRunSolver(localSimDataDir, simServiceContext.simTask);
        simServiceContext.localSimDataDir = localSimDataDir;
        if (simServiceContext.solver == null) {
            throw new RuntimeException("null solver");
        }
        sims.put(simulationInfo.id, simServiceContext);
        simServiceContext.solver.addSolverListener(new SolverListener() {

            public void solverStopped(SolverEvent event) {
                simServiceContext.simState = SimulationState.failed;
                System.err.println("Simulation stopped");
            }

            public void solverStarting(SolverEvent event) {
                simServiceContext.simState = SimulationState.running;
                updateStatus(event);
            }

            public void solverProgress(SolverEvent event) {
                simServiceContext.simState = SimulationState.running;
                updateStatus(event);
            }

            public void solverPrinted(SolverEvent event) {
                simServiceContext.simState = SimulationState.running;
            }

            public void solverFinished(SolverEvent event) {
                try {
                    getDataSetController(simServiceContext).getDataSetTimes(simServiceContext.vcDataIdentifier);
                    simServiceContext.simState = SimulationState.done;
                } catch (DataAccessException e) {
                    simServiceContext.simState = SimulationState.failed;
                    e.printStackTrace();
                }
                updateStatus(event);
            }

            public void solverAborted(SolverEvent event) {
                simServiceContext.simState = SimulationState.failed;
                System.err.println(event.getSimulationMessage().getDisplayMessage());
            }

            private void updateStatus(SolverEvent event) {
                if (statusCallback == null)
                    return;
                statusCallback.setMessage(event.getSimulationMessage().getDisplayMessage());
                statusCallback.setProgress((int) (event.getProgress() * 100));
            }
        });
        simServiceContext.solver.startSolver();
        return simServiceContext.simInfo;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        // remember the exceptiopn ... fail the status ... save the error message
        return new SimulationInfo().setId(1);
    }
}

Example 9 with Simulation

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

the class XmlReader method getSimulation.

/**
 * This method returns a Simulation object from a XML element.
 * Creation date: (4/26/2001 12:14:30 PM)
 * @return cbit.vcell.solver.Simulation
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
Simulation getSimulation(Element param, MathDescription mathDesc) throws XmlParseException {
    // retrive metadata (if any)
    SimulationVersion simulationVersion = getSimulationVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // create new simulation
    Simulation simulation = null;
    if (simulationVersion != null) {
        simulation = new Simulation(simulationVersion, mathDesc);
    } else {
        simulation = new Simulation(mathDesc);
    }
    // set attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    try {
        simulation.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // simulation.setDescription(unMangle(annotation));
        // }
        // Add Annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            simulation.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        throw new XmlParseException(e);
    }
    // Retrieve MathOverrides
    simulation.setMathOverrides(getMathOverrides(param.getChild(XMLTags.MathOverridesTag, vcNamespace), simulation));
    // Retrieve SolverTaskDescription
    try {
        simulation.setSolverTaskDescription(getSolverTaskDescription(param.getChild(XMLTags.SolverTaskDescriptionTag, vcNamespace), simulation));
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the SolverTaskDescroiption object to the Simulation object " + name, e);
    }
    Element dataProcessingInstructionsElement = param.getChild(XMLTags.DataProcessingInstructionsTag, vcNamespace);
    if (dataProcessingInstructionsElement != null) {
        String scriptName = dataProcessingInstructionsElement.getAttributeValue(XMLTags.DataProcessingScriptNameAttrTag);
        String scriptInput = dataProcessingInstructionsElement.getText();
        simulation.setDataProcessingInstructions(new DataProcessingInstructions(scriptName, scriptInput));
    }
    // Retrieve MeshEspecification (if any)
    Element tempElement = param.getChild(XMLTags.MeshSpecTag, vcNamespace);
    if (tempElement != null) {
        try {
            simulation.setMeshSpecification(getMeshSpecification(tempElement, mathDesc.getGeometry()));
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace();
            throw new XmlParseException("A ProperyVetoException was fired when setting the MeshSpecification to a new Simulation!", e);
        }
    }
    return simulation;
}

Example 10 with Simulation

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

the class ParameterEstimationTaskSimulatorIDA method getRowColumnRestultSetByBestEstimations.

public RowColumnResultSet getRowColumnRestultSetByBestEstimations(ParameterEstimationTask parameterEstimationTask, String[] paramNames, double[] paramValues) throws Exception {
    // create a temp simulation based on math description
    KeyValue key = new KeyValue("" + Math.abs(new Random().nextLong()));
    SimulationVersion dummyVersion = new SimulationVersion(key, "name", new User("temp", new KeyValue("1")), null, null, null, null, null, null, null);
    Simulation simulation = new Simulation(dummyVersion, parameterEstimationTask.getSimulationContext().getMathDescription());
    ReferenceData refData = parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    double[] times = refData.getDataByColumn(0);
    double endTime = times[times.length - 1];
    ExplicitOutputTimeSpec exTimeSpec = new ExplicitOutputTimeSpec(times);
    // set simulation ending time and output interval
    simulation.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
    simulation.getSolverTaskDescription().setOutputTimeSpec(exTimeSpec);
    // set parameters as math overrides
    MathOverrides mathOverrides = simulation.getMathOverrides();
    for (int i = 0; i < paramNames.length; i++) {
        mathOverrides.putConstant(new Constant(paramNames[i], new Expression(paramValues[i])));
    }
    SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
    IDASolverStandalone idaSolver = new IDASolverStandalone(simTask, ResourceUtil.getLocalSimDir("temp"), false);
    // startSolver();
    idaSolver.runSolver();
    Thread.sleep(1000);
    long startTimeMS = System.currentTimeMillis();
    while (idaSolver.getSolverStatus().isRunning() && System.currentTimeMillis() < (startTimeMS + 10000L)) {
        Thread.sleep(500);
    }
    ODESolverResultSet resultset = idaSolver.getODESolverResultSet();
    return resultset;
}