Examples with MathModel cbit.vcell.mathmodel.MathModel used on opensource projects

Example 51 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class OptXmlWriter method getCoapsiOptProblemDescriptionXML.

public static Element getCoapsiOptProblemDescriptionXML(ParameterEstimationTask parameterEstimationTask, MathMappingCallback mathMappingCallback) throws IOException, XmlParseException, ExpressionException, SBMLException, XMLStreamException {
    OptimizationSpec optimizationSpec = parameterEstimationTask.getModelOptimizationMapping().getOptimizationSpec();
    Element optProblemDescriptionElement = new Element(OptXmlTags.OptProblemDescription_Tag);
    File modelSbmlFile = File.createTempFile("mathModel", ".xml", ResourceUtil.getVcellHome());
    SimulationContext simulationContext = parameterEstimationTask.getSimulationContext();
    simulationContext.refreshMathDescription(mathMappingCallback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
    MathModel vcellMathModel = new MathModel(null);
    vcellMathModel.setMathDescription(simulationContext.getMathDescription());
    // get math model string
    String sbmlString = MathModel_SBMLExporter.getSBMLString(vcellMathModel, 2, 4);
    // String modelSbml = XmlHelper.exportSBML(simulationContext.getBioModel(), 3, 1, 0, false, simulationContext, null);
    XmlUtil.writeXMLStringToFile(sbmlString, modelSbmlFile.getAbsolutePath(), true);
    Element element = new Element(OptXmlTags.MathModelSbmlFile_Tag);
    element.addContent(modelSbmlFile.getAbsolutePath());
    optProblemDescriptionElement.addContent(element);
    if (optimizationSpec.isComputeProfileDistributions()) {
        optProblemDescriptionElement.setAttribute(OptXmlTags.ComputeProfileDistributions_Attr, optimizationSpec.isComputeProfileDistributions() + "");
    }
    optProblemDescriptionElement.addContent(getVCellOptionsXML(parameterEstimationTask.getOptimizationSolverSpec()));
    optProblemDescriptionElement.addContent(getParameterDescriptionXML(optimizationSpec));
    Element dataElement = getCopasiDataXML(parameterEstimationTask);
    optProblemDescriptionElement.addContent(dataElement);
    element = getCopasiOptimizationMethodXML(parameterEstimationTask.getOptimizationSolverSpec().getCopasiOptimizationMethod());
    optProblemDescriptionElement.addContent(element);
    return optProblemDescriptionElement;
}

Example 52 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class HybridSolverTester method runHybridTest.

public void runHybridTest(String site) {
    try {
        double[] timePoints = null;
        File mathModelFile = new File(mathModelVCMLFileName);
        XMLSource vcmlSource = new XMLSource(mathModelFile);
        MathModel mathModel = XmlHelper.XMLToMathModel(vcmlSource);
        File simDataDir = mathModelFile.getParentFile();
        Simulation sim = mathModel.getSimulations()[0];
        // run multiple trials and each run will have a simID = origSimID + i
        for (int i = 0; i < numRuns; i++) {
            System.out.println("--------------Trial No: " + (startTrialNo + i) + "----------------");
            // replace random seed
            sim.getSolverTaskDescription().getSmoldynSimulationOptions().setRandomSeed(new Integer(startTrialNo + i));
            // create sim job
            int jobIndex = startTrialNo + i;
            SimulationTask simTask = new SimulationTask(new SimulationJob(sim, jobIndex, null), 0);
            /*
				 * When you want to run the multiple trials on local uncomment the line below.
				 */
            // ResourceUtil.prepareSolverExecutable(sim.getSolverTaskDescription().getSolverDescription());
            /*
				 * When you want to run the multiple trials on server (without VCell user interface), use the next line of code 
				 * Corresponding changes should be made in the shell script runhybridtest for the location of executable on server
				 */
            FVSolverStandalone fvSolver = new FVSolverStandalone(simTask, simDataDir, false);
            fvSolver.startSolver();
            SolverStatus status = fvSolver.getSolverStatus();
            while (status.getStatus() != SolverStatus.SOLVER_FINISHED && status.getStatus() != SolverStatus.SOLVER_ABORTED) {
                System.out.println("progress: " + (int) (fvSolver.getProgress() * 100) + "%");
                // ask status every 2 seconds
                Thread.sleep(2000);
                status = fvSolver.getSolverStatus();
            }
            if (status.getStatus() == SolverStatus.SOLVER_FINISHED) {
                // get data
                VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(sim.getVersion().getVersionKey(), sim.getVersion().getOwner());
                VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
                File hdf5File = new File(simDataDir, vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
                DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(vcSimDataID, false, null), hdf5File);
                if (i == 0) {
                    // do only one time
                    timePoints = dataProcessingOutputInfo.getVariableTimePoints();
                    for (int j = 0; j < varNames.length; j++) {
                        // row: numTimePoints, col:first col time + numRuns
                        double[][] data = new double[numRuns + 1][timePoints.length];
                        data[0] = timePoints;
                        results.add(data);
                    }
                }
                // write into results after each run
                for (int j = 0; j < varNames.length; j++) {
                    results.get(j)[i + 1] = dataProcessingOutputInfo.getVariableStatValues().get(varNames[j]);
                }
                // delete the file generated for this run
                deleteSimFiles(simDataDir, vcSimDataID);
            } else {
                throw new Exception("Sover did not finish normally." + status);
            }
        }
        // write to output file, tab delimited
        if (results != null && results.size() > 0) {
            for (int j = 0; j < varNames.length; j++) {
                File file = new File(simDataDir, "SimID_" + sim.getVersion().getVersionKey().toString() + "_" + varNames[j] + "_" + startTrialNo + ".txt");
                PrintWriter pw = new PrintWriter(file);
                double[][] data = results.get(j);
                if (data != null) {
                    for (int k = 0; k < data.length; k++) {
                        if (!bPrintTime && k == 0) {
                            continue;
                        }
                        String rowStr = (k == 0) ? "Time\t" : ("trialNo_" + (startTrialNo + k - 1) + "\t");
                        double[] rowData = data[k];
                        for (int q = 0; q < rowData.length; q++) {
                            rowStr += rowData[q] + "\t";
                        }
                        pw.println(rowStr);
                    }
                }
                pw.close();
            }
        }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 53 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class XmlHelper method XMLToMathModel.

static MathModel XMLToMathModel(XMLSource xmlSource, boolean printkeys) throws XmlParseException {
    MathModel mathModel = null;
    if (xmlSource == null) {
        throw new XmlParseException("Invalid xml for Geometry.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    // NOTES:
    // * The root element can be <Biomodel> (old-style vcml) OR <vcml> (new-style vcml)
    // * With the old-style vcml, the namespace was " "
    // * With the new-style vcml, there is an intermediate stage where the namespace for <vcml> root
    // was set to "http://sourceforge.net/projects/VCell/version0.4" for some models and
    // "http://sourceforge.net/projects/vcell/vcml" for some models; and the namespace for child element
    // <biomdel>, etc. was " "
    // * The final new-style vcml has (should have) the namespace "http://sourceforge.net/projects/vcell/vcml"
    // for <vcml> and all children elements.
    // The code below attempts to take care of this situation.
    Element root = xmlDoc.getRootElement();
    Namespace ns = null;
    if (root.getName().equals(XMLTags.VcmlRootNodeTag)) {
        // NEW WAY - with xml string containing xml declaration, vcml element, namespace, etc ...
        ns = root.getNamespace();
        Element mathRoot = root.getChild(XMLTags.MathModelTag, ns);
        if (mathRoot == null) {
            mathRoot = root.getChild(XMLTags.MathModelTag);
            // mathRoot was null, so obtained the <Mathmodel> element with namespace " ";
            // Re-set the namespace so that the correct XMLReader constructor is invoked.
            ns = null;
        }
        root = mathRoot;
    }
    // else - root is assumed to be old-style vcml with <Mathmodel> as root.
    // common for both new-style (with xml declaration, vcml element, etc) and old-style (mathmodel is root)
    // If namespace is null, xml is the old-style xml with mathmodel as root, so invoke XMLReader without namespace argument.
    XmlReader reader = null;
    if (ns == null) {
        reader = new XmlReader(printkeys);
    } else {
        reader = new XmlReader(printkeys, ns);
    }
    mathModel = reader.getMathModel(root);
    mathModel.refreshDependencies();
    return mathModel;
}

Example 54 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class StandaloneRuleBasedTest method main.

public static void main(String[] args) {
    try {
        PropertyLoader.loadProperties();
    } catch (Exception e) {
        e.printStackTrace();
    }
    final int numTrials = 40;
    // 30 seconds
    final long bngTimeoutDurationMS = 30000;
    VCDatabaseVisitor vcDatabaseVisitor = new VCDatabaseVisitor() {

        @Override
        public void visitMathModel(MathModel mathModel, PrintStream logFilePrintStream) {
            throw new IllegalArgumentException("Not Implemented");
        }

        @Override
        public void visitGeometry(Geometry geometry, PrintStream logFilePrintStream) {
            throw new IllegalArgumentException("Not Implemented");
        }

        @Override
        public void visitBioModel(BioModel bioModel, PrintStream logFilePrintStream) {
            SimulationContext[] simulationContexts = bioModel.getSimulationContexts();
            for (SimulationContext simContext : simulationContexts) {
                if ((simContext.getApplicationType() == Application.NETWORK_STOCHASTIC) && simContext.getGeometry().getDimension() == 0) {
                    File baseDirectory = createDirFile(simContext);
                    try {
                        checkNonspatialStochasticSimContext(simContext, baseDirectory, numTrials, bngTimeoutDurationMS);
                    } catch (Exception e) {
                        e.printStackTrace();
                        if (!e.getMessage().contains("Only Mass Action Kinetics supported ")) {
                            StochtestFileUtils.writeMessageTofile(baseDirectory, e.getMessage());
                        }
                    }
                }
            }
        }

        @Override
        public boolean filterMathModel(MathModelInfo mathModelInfo) {
            return false;
        }

        @Override
        public boolean filterGeometry(GeometryInfo geometryInfo) {
            return false;
        }

        @Override
        public boolean filterBioModel(BioModelInfo bioModelInfo) {
            return // bioModelInfo.getVersion().getName().equals("model");
            bioModelInfo.getVersion().getName().equals("simpleModel_Network_orig");
        }
    };
    String currentUserID = "schaff";
    String[] allUsers = new String[] { /*-all*/
    currentUserID, "-" };
    VCDatabaseScanner.scanBioModels(allUsers, vcDatabaseVisitor, false);
}

Example 55 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class MathGenerationDebugger method compareMath_latest.

private void compareMath_latest() {
    try {
        MathModel mathModel1 = new MathModel(null);
        MathModel mathModel2 = new MathModel(null);
        mathModel1.setMathDescription(mathGenerationResults.mathDesc_original);
        mathModel2.setMathDescription(mathGenerationResults.mathDesc_latest);
        getMathDebuggerPanel().setMathModel1(mathModel1);
        getMathDebuggerPanel().setMathModel2(mathModel2);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}