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

Example 1 with ODESolverResultSet

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

the class ParameterEstimationRunTaskPanel method plot.

private void plot() {
    try {
        java.util.Vector<DataSource> dataSourceList = new java.util.Vector<DataSource>();
        java.util.Vector<String> nameVector = new java.util.Vector<String>();
        ModelOptimizationSpec modelOptimizationSpec = parameterEstimationTask.getModelOptimizationSpec();
        final ReferenceDataMappingSpec[] mappingSpecs = modelOptimizationSpec.getReferenceDataMappingSpecs();
        int timeIndex = modelOptimizationSpec.getReferenceDataTimeColumnIndex();
        ReferenceData referenceData = modelOptimizationSpec.getReferenceData();
        if (referenceData != null) {
            dataSourceList.add(new DataSource.DataSourceReferenceData("EXPT", timeIndex, referenceData));
            String[] refColumnNames = referenceData.getColumnNames();
            for (int i = 0; i < refColumnNames.length; i++) {
                if (i == timeIndex) {
                    continue;
                }
                nameVector.add(refColumnNames[i]);
                break;
            }
        }
        ParameterEstimationTaskSimulatorIDA parestSimulator = new ParameterEstimationTaskSimulatorIDA();
        ODESolverResultSet odeSolverResultSet = parestSimulator.getOdeSolverResultSet(parameterEstimationTask);
        if (odeSolverResultSet != null) {
            dataSourceList.add(new DataSource.DataSourceRowColumnResultSet("EST", odeSolverResultSet));
            if (mappingSpecs != null) {
                for (int i = 0; i < mappingSpecs.length; i++) {
                    if (i == timeIndex) {
                        continue;
                    }
                    Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(mappingSpecs[i].getModelObject());
                    nameVector.add(var.getName());
                    break;
                }
            }
        }
        DataSource[] dataSources = (DataSource[]) BeanUtils.getArray(dataSourceList, DataSource.class);
        MultisourcePlotPane multisourcePlotPane = new MultisourcePlotPane();
        multisourcePlotPane.setGroupingListSorter(new Comparator<SortDataReferenceHelper>() {

            @Override
            public int compare(SortDataReferenceHelper o1, SortDataReferenceHelper o2) {
                DataSource ds01 = o1.dataReference.getDataSource();
                DataSource ds02 = o2.dataReference.getDataSource();
                // System.out.println(ds01.getClass().getSimpleName()+" "+o1.dataReference.getIdentifier()+" "+ds02.getClass().getSimpleName()+" "+o2.dataReference.getIdentifier());
                if (ds01 instanceof DataSource.DataSourceReferenceData) {
                    if (ds02 instanceof DataSource.DataSourceReferenceData) {
                        // both reference data, sort names
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            // Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return o1.dataReference.getIdentifier().compareToIgnoreCase(o2.dataReference.getIdentifier());
                        } else if (mspec01 != null && mspec02 != null) {
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else {
                            return 1;
                        }
                    } else {
                        // compare ref to ode
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(var.getName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return -1;
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else if (mspec02 != null && mspec01 == null) {
                            return 1;
                        } else {
                            // BeanUtils.forceStringSize(mspec02.getReferenceDataColumnName(), 25, " ", true));
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        }
                    }
                } else {
                    if (ds02 instanceof DataSource.DataSourceRowColumnResultSet) {
                        // both OdeSolverResultSet data, sort names
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(var.getName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(var.getName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return o1.dataReference.getIdentifier().compareToIgnoreCase(o2.dataReference.getIdentifier());
                        } else if (mspec01 != null && mspec02 != null) {
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else {
                            return 1;
                        }
                    } else {
                        // compare ode to ref
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o2.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o1.dataReference.getIdentifier().equals(var.getName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return 1;
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else if (mspec02 != null && mspec01 == null) {
                            return 1;
                        } else {
                            // BeanUtils.forceStringSize(mspec02.getReferenceDataColumnName(), 25, " ", true));
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        }
                    }
                }
            }
        });
        multisourcePlotPane.setDataSources(dataSources);
        String[] nameArray = new String[nameVector.size()];
        nameArray = (String[]) BeanUtils.getArray(nameVector, String.class);
        multisourcePlotPane.select(nameArray);
        DialogUtils.showComponentCloseDialog(JOptionPane.getFrameForComponent(this), multisourcePlotPane, "Data Plot");
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 2 with ODESolverResultSet

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

the class VCellSedMLSolver method doWork.

// everything is done here
public void doWork(ExternalDocInfo externalDocInfo, AbstractTask sedmlTask, SedML sedml) throws Exception {
    // create the VCDocument (bioModel + application + simulation), do sanity checks
    cbit.util.xml.VCLogger sedmlImportLogger = new LocalLogger();
    List<AbstractTask> tasks = new ArrayList<AbstractTask>();
    tasks.add(sedmlTask);
    List<VCDocument> docs = XmlHelper.sedmlToBioModel(sedmlImportLogger, externalDocInfo, sedml, tasks, null, false);
    VCDocument doc = docs.get(0);
    sanityCheck(doc);
    // create the work directory for this task, invoke the solver
    String docName = doc.getName();
    String outString = VCellSedMLSolver.OUT_ROOT_STRING + "/" + docName + "/" + sedmlTask.getId();
    File outDir = new File(outString);
    if (!outDir.exists()) {
        outDir.mkdirs();
    }
    BioModel bioModel = (BioModel) doc;
    SimulationContext simContext = bioModel.getSimulationContext(0);
    MathDescription mathDesc = simContext.getMathDescription();
    String vcml = mathDesc.getVCML();
    try (PrintWriter pw = new PrintWriter(outString + "/vcmlTrace.xml")) {
        pw.println(vcml);
    }
    Simulation sim = bioModel.getSimulation(0);
    SolverTaskDescription std = sim.getSolverTaskDescription();
    SolverDescription sd = std.getSolverDescription();
    String kisao = sd.getKisao();
    if (SolverDescription.CVODE.getKisao().contentEquals(kisao)) {
        ODESolverResultSet odeSolverResultSet = solveCvode(outDir, bioModel);
        System.out.println("Finished: " + docName + ": - task '" + sedmlTask.getId() + "'.");
    } else if (SolverDescription.StochGibson.getKisao().contentEquals(kisao)) {
        ODESolverResultSet odeSolverResultSet = solveGibson(outDir, bioModel);
        System.out.println("Finished: " + docName + ": - task '" + sedmlTask.getId() + "'.");
    } else if (SolverDescription.IDA.getKisao().contentEquals(kisao)) {
        ODESolverResultSet odeSolverResultSet = solveIDA(outDir, bioModel);
        System.out.println("Finished: " + docName + ": - task '" + sedmlTask.getId() + "'.");
    } else {
        System.out.println("Unsupported solver: " + kisao);
    }
    System.out.println("-------------------------------------------------------------------------");
}

Example 3 with ODESolverResultSet

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

the class VCellSedMLSolver method solveGibson.

private static ODESolverResultSet solveGibson(File outDir, BioModel bioModel) throws Exception {
    String docName = bioModel.getName();
    Simulation sim = bioModel.getSimulation(0);
    File gibsonInputFile = new File(outDir, docName + SimDataConstants.STOCHINPUT_DATA_EXTENSION);
    PrintWriter gibsonPW = new java.io.PrintWriter(gibsonInputFile);
    SimulationJob simJob = new SimulationJob(sim, 0, null);
    SimulationTask simTask = new SimulationTask(simJob, 0);
    StochFileWriter stFileWriter = new StochFileWriter(gibsonPW, simTask, false);
    stFileWriter.write();
    gibsonPW.close();
    File gibsonOutputFile = new File(outDir, docName + SimDataConstants.IDA_DATA_EXTENSION);
    writeFunctionFile(outDir, docName, SimDataConstants.FUNCTIONFILE_EXTENSION, simTask);
    String executableName = null;
    try {
        executableName = SolverUtilities.getExes(SolverDescription.StochGibson)[0].getAbsolutePath();
    } catch (IOException e) {
        throw new RuntimeException("failed to get executable for solver " + SolverDescription.StochGibson.getDisplayLabel() + ": " + e.getMessage(), e);
    }
    Executable executable = new Executable(new String[] { executableName, "gibson", gibsonInputFile.getAbsolutePath(), gibsonOutputFile.getAbsolutePath() });
    executable.start();
    ODESolverResultSet odeSolverResultSet = VCellSBMLSolver.getODESolverResultSet(simJob, gibsonOutputFile.getPath());
    return odeSolverResultSet;
}

Example 4 with ODESolverResultSet

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

the class VCellSedMLSolver method solveCvode.

private static ODESolverResultSet solveCvode(File outDir, BioModel bioModel) throws Exception {
    String docName = bioModel.getName();
    Simulation sim = bioModel.getSimulation(0);
    File cvodeInputFile = new File(outDir, docName + SimDataConstants.CVODEINPUT_DATA_EXTENSION);
    PrintWriter cvodePW = new java.io.PrintWriter(cvodeInputFile);
    SimulationJob simJob = new SimulationJob(sim, 0, null);
    SimulationTask simTask = new SimulationTask(simJob, 0);
    CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simTask);
    cvodeFileWriter.write();
    cvodePW.close();
    // use the cvodeStandalone solver
    String outDirPath = outDir.getAbsolutePath();
    int indexOfLastSlash = outDirPath.lastIndexOf("/");
    String task_name = outDirPath.substring(indexOfLastSlash + 1);
    String idaFilePath = outDirPath.substring(0, indexOfLastSlash);
    File cvodeOutputFile = new File(idaFilePath, task_name + SimDataConstants.IDA_DATA_EXTENSION);
    String executableName = null;
    try {
        // we need to specify the vCell install dir in the Eclipse Debug configuration, as VM argument
        // so that the code next knows where to look for the solver
        // -Dvcell.installDir=G:\dan\jprojects\git\vcell
        // OR
        // just type the string with the full path explicitly
        // OR
        // provide a .properties file in the working directory
        executableName = SolverUtilities.getExes(SolverDescription.CVODE)[0].getAbsolutePath();
    } catch (IOException e) {
        throw new RuntimeException("failed to get executable for solver " + SolverDescription.CVODE.getDisplayLabel() + ": " + e.getMessage(), e);
    }
    Executable executable = new Executable(new String[] { executableName, cvodeInputFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath() });
    executable.start();
    ODESolverResultSet odeSolverResultSet = VCellSBMLSolver.getODESolverResultSet(simJob, cvodeOutputFile.getPath());
    return odeSolverResultSet;
}

Example 5 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);
}