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

Example 46 with MathModel

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

the class TopLevelWindowManager method prepareDocumentToLoad.

public void prepareDocumentToLoad(VCDocument doc, boolean bInNewWindow) throws Exception {
    if (doc instanceof BioModel) {
        Simulation[] simulations = ((BioModel) doc).getSimulations();
        ArrayList<VCSimulationIdentifier> simIDs = new ArrayList<VCSimulationIdentifier>();
        for (int i = 0; i < simulations.length; i++) {
            SimulationInfo simulationInfo = simulations[i].getSimulationInfo();
            if (simulationInfo != null) {
                simIDs.add(simulationInfo.getAuthoritativeVCSimulationIdentifier());
            }
        }
        RequestManager rm = getRequestManager();
        ConnectionStatus stat = rm.getConnectionStatus();
        if (stat.getStatus() == ConnectionStatus.CONNECTED) {
            rm.getDocumentManager().preloadSimulationStatus(simIDs.toArray(new VCSimulationIdentifier[0]));
        }
    } else if (doc instanceof MathModel) {
        Geometry geometry = ((MathModel) doc).getMathDescription().getGeometry();
        geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
        Simulation[] simulations = ((MathModel) doc).getSimulations();
        // VCSimulationIdentifier simIDs[] = new VCSimulationIdentifier[simulations.length];
        ArrayList<VCSimulationIdentifier> simIDs = new ArrayList<>();
        for (int i = 0; i < simulations.length; i++) {
            if (simulations[i].getSimulationInfo() != null) {
                simIDs.add(simulations[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier());
            }
        }
        getRequestManager().getDocumentManager().preloadSimulationStatus(simIDs.toArray(new VCSimulationIdentifier[0]));
    } else if (doc instanceof Geometry) {
        ((Geometry) doc).precomputeAll(new GeometryThumbnailImageFactoryAWT());
    }
}

Example 47 with MathModel

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

the class SimulationWorkspaceModelInfo method getMembraneName.

/**
 * Insert the method's description here.
 * Creation date: (9/19/2005 1:30:44 PM)
 * @return java.lang.String
 * @param subVolumeIdIn int
 * @param subVolumeIdOut int
 */
public String getMembraneName(int subVolumeIdIn, int subVolumeIdOut, boolean bFromGeometry) {
    String results = null;
    if (simulationOwner instanceof MathModel) {
        MathModel mathModel = (MathModel) simulationOwner;
        final GeometrySpec geometrySpec = mathModel.getMathDescription().getGeometry().getGeometrySpec();
        if (geometrySpec.getSubVolume(subVolumeIdIn) != null && geometrySpec.getSubVolume(subVolumeIdOut) != null) {
            SubVolume svIn = geometrySpec.getSubVolume(subVolumeIdIn);
            SubVolume svOut = geometrySpec.getSubVolume(subVolumeIdOut);
            SurfaceClass membrane = mathModel.getMathDescription().getGeometry().getGeometrySurfaceDescription().getSurfaceClass(svIn, svOut);
            results = membrane.getName();
        }
    } else if (simulationOwner instanceof SimulationContext) {
        SimulationContext simContext = (SimulationContext) simulationOwner;
        SubVolume svIn = simContext.getGeometry().getGeometrySpec().getSubVolume(subVolumeIdIn);
        SubVolume svOut = simContext.getGeometry().getGeometrySpec().getSubVolume(subVolumeIdOut);
        if (bFromGeometry) {
            SurfaceClass membrane = simContext.getMathDescription().getGeometry().getGeometrySurfaceDescription().getSurfaceClass(svIn, svOut);
            results = membrane.getName();
        } else {
            if (svIn != null && svOut != null) {
                GeometryClass[] geometryClasses = simContext.getGeometry().getGeometryClasses();
                for (int i = 0; i < geometryClasses.length; i++) {
                    if (geometryClasses[i] instanceof SurfaceClass) {
                        SurfaceClass surface = (SurfaceClass) geometryClasses[i];
                        if (surface.isAdjacentTo(svIn) && surface.isAdjacentTo(svOut)) {
                            StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings(surface);
                            if (structureMappings != null && structureMappings.length > 0) {
                                results = surface.getName() + "(";
                                for (int j = 0; j < structureMappings.length; j++) {
                                    results += structureMappings[j].getStructure().getName() + " ";
                                }
                                results += ")";
                                return results;
                            }
                        }
                    }
                }
            }
        }
    }
    return results;
}

Example 48 with MathModel

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

the class VCellClientDataServiceImpl method getSimsFromOpenModels.

@Override
public List<SimulationDataSetRef> getSimsFromOpenModels() {
    ArrayList<SimulationDataSetRef> simulationDataSetRefs = new ArrayList<SimulationDataSetRef>();
    for (TopLevelWindowManager windowManager : vcellClient.getMdiManager().getWindowManagers()) {
        Simulation[] simulations = null;
        VCDocument modelDocument = null;
        if (windowManager instanceof BioModelWindowManager) {
            BioModelWindowManager selectedBioWindowManager = (BioModelWindowManager) windowManager;
            BioModel bioModel = selectedBioWindowManager.getBioModel();
            simulations = bioModel.getSimulations();
            modelDocument = bioModel;
        // simOwnerCount = bioModel.getNumSimulationContexts();
        } else if (windowManager instanceof MathModelWindowManager) {
            MathModelWindowManager selectedMathWindowManager = (MathModelWindowManager) windowManager;
            MathModel mathModel = selectedMathWindowManager.getMathModel();
            simulations = mathModel.getSimulations();
            modelDocument = mathModel;
        // simOwnerCount = 1;
        }
        if (simulations != null) {
            for (Simulation simulation : simulations) {
                if (!isVtkSupported(simulation)) {
                    continue;
                }
                Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
                Extent extent = simulation.getMathDescription().getGeometry().getExtent();
                SimulationInfo simInfo = simulation.getSimulationInfo();
                SimulationStatus simStatus = vcellClient.getRequestManager().getServerSimulationStatus(simInfo);
                for (int jobIndex = 0; jobIndex < simulation.getScanCount(); jobIndex++) {
                    if (simStatus != null && simStatus.getHasData()) {
                        SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simulation, modelDocument, jobIndex, false);
                        simulationDataSetRefs.add(simulationDataSetReference);
                    }
                }
            }
        }
    }
    File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    String[] simtaskFilenames = localSimDir.list((dir, name) -> (name.endsWith(".simtask.xml")));
    for (String simtaskFilename : simtaskFilenames) {
        try {
            SimulationTask simTask = XmlHelper.XMLToSimTask(org.apache.commons.io.FileUtils.readFileToString(new File(localSimDir, simtaskFilename)));
            VCDocument modelDocument = null;
            SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simTask.getSimulation(), modelDocument, simTask.getSimulationJob().getJobIndex(), true);
            simulationDataSetRefs.add(simulationDataSetReference);
        } catch (ExpressionException | XmlParseException | IOException e) {
            e.printStackTrace();
        }
    }
    return simulationDataSetRefs;
}

Example 49 with MathModel

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

the class ClientRequestManager method continueAfterMathModelGeomChangeWarning.

public static void continueAfterMathModelGeomChangeWarning(MathModelWindowManager mathModelWindowManager, Geometry newGeometry) throws UserCancelException {
    MathModel mathModel = mathModelWindowManager.getMathModel();
    if (mathModel != null && mathModel.getMathDescription() != null) {
        Geometry oldGeometry = mathModel.getMathDescription().getGeometry();
        if (oldGeometry != null && oldGeometry.getDimension() == 0) {
            return;
        }
        boolean bMeshResolutionChange = true;
        if (oldGeometry == null) {
            bMeshResolutionChange = false;
        }
        if (newGeometry != null && oldGeometry != null && oldGeometry.getDimension() == newGeometry.getDimension()) {
            bMeshResolutionChange = false;
        }
        boolean bHasSims = (mathModel.getSimulations() != null) && (mathModel.getSimulations().length > 0);
        StringBuffer meshResolutionChangeSB = new StringBuffer();
        if (bHasSims && bMeshResolutionChange) {
            ISize newGeomISize = MeshSpecification.calulateResetSamplingSize(newGeometry);
            for (int i = 0; i < mathModel.getSimulations().length; i++) {
                if (mathModel.getSimulations()[i].getMeshSpecification() != null) {
                    String simName = mathModel.getSimulations()[i].getName();
                    ISize simMeshSize = mathModel.getSimulations()[i].getMeshSpecification().getSamplingSize();
                    meshResolutionChangeSB.append((i != 0 ? "\n" : "") + "'" + simName + "' Mesh" + simMeshSize + " will be reset to " + newGeomISize + "");
                }
            }
        }
        String result = DialogUtils.showWarningDialog(JOptionPane.getFrameForComponent(mathModelWindowManager.getComponent()), "After changing MathModel geometry please note:\n" + "  1.  Check Geometry subvolume names match MathModel compartment names." + (bHasSims && bMeshResolutionChange ? "\n" + "  2.  All existing simulations mesh sizes will be reset" + " because the new Geometry spatial dimension(" + newGeometry.getDimension() + "D)" + " does not equal the current Geometry spatial dimension(" + oldGeometry.getDimension() + "D)" + "\n" + meshResolutionChangeSB.toString() : ""), new String[] { "Continue", "Cancel" }, "Continue");
        if (result != null && result.equals("Continue")) {
            return;
        }
    } else {
        return;
    }
    throw UserCancelException.CANCEL_GENERIC;
}

Example 50 with MathModel

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

the class CopasiServicePython method makeOptProblem.

public static OptProblem makeOptProblem(ParameterEstimationTask parameterEstimationTask) throws IOException, ExpressionException, SBMLException, XMLStreamException {
    OptimizationSpec optimizationSpec = parameterEstimationTask.getModelOptimizationMapping().getOptimizationSpec();
    SimulationContext simulationContext = parameterEstimationTask.getSimulationContext();
    MathMappingCallback callback = new MathMappingCallback() {

        @Override
        public void setProgressFraction(float fractionDone) {
            Thread.dumpStack();
            System.out.println("---> stdout mathMapping: progress = " + (fractionDone * 100.0) + "% done");
        }

        @Override
        public void setMessage(String message) {
            Thread.dumpStack();
            System.out.println("---> stdout mathMapping: message = " + message);
        }

        @Override
        public boolean isInterrupted() {
            return false;
        }
    };
    simulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
    MathModel vcellMathModel = new MathModel(null);
    vcellMathModel.setMathDescription(simulationContext.getMathDescription());
    // get math model string
    String sbmlString = MathModel_SBMLExporter.getSBMLString(vcellMathModel, 2, 4);
    OptProblem optProblem = new OptProblem();
    optProblem.setMathModelSbmlContents(sbmlString);
    optProblem.setNumberOfOptimizationRuns(parameterEstimationTask.getOptimizationSolverSpec().getNumOfRuns());
    for (Parameter p : optimizationSpec.getParameters()) {
        ParameterDescription pdesc = new ParameterDescription(p.getName(), p.getScale(), p.getLowerBound(), p.getUpperBound(), p.getInitialGuess());
        optProblem.addToParameterDescriptionList(pdesc);
    }
    SimpleReferenceData refData = (SimpleReferenceData) parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    // check if t is at the first column
    int timeIndex = refData.findColumn(ReservedVariable.TIME.getName());
    if (timeIndex != 0) {
        throw new RuntimeException("t must be the first column");
    }
    DataSet dataset = new DataSet();
    for (int rowIndex = 0; rowIndex < refData.getNumDataRows(); rowIndex++) {
        DataRow dataRow = new DataRow();
        double[] array = refData.getDataByRow(rowIndex);
        for (double d : array) {
            dataRow.addToData(d);
        }
        dataset.addToRows(dataRow);
    }
    optProblem.setExperimentalDataSet(dataset);
    optProblem.addToReferenceVariableList(new ReferenceVariable(ReservedVariable.TIME.getName(), ReferenceVariableType.independent));
    // add all other dependent variables, recall that the dependent variables start from 2nd column onward in reference data
    for (int i = 1; i < refData.getNumDataColumns(); i++) {
        ReferenceDataMappingSpec rdms = parameterEstimationTask.getModelOptimizationSpec().getReferenceDataMappingSpec(refData.getColumnNames()[i]);
        optProblem.addToReferenceVariableList(new ReferenceVariable(rdms.getModelObject().getName(), ReferenceVariableType.dependent));
    }
    cbit.vcell.opt.CopasiOptimizationMethod vcellCopasiOptimizationMethod = parameterEstimationTask.getOptimizationSolverSpec().getCopasiOptimizationMethod();
    OptimizationMethodType optMethodType = OptimizationMethodType.valueOf(vcellCopasiOptimizationMethod.getType().name());
    CopasiOptimizationMethod thriftOptMethod = new CopasiOptimizationMethod();
    thriftOptMethod.setOptimizationMethodType(optMethodType);
    for (cbit.vcell.opt.CopasiOptimizationParameter optParam : vcellCopasiOptimizationMethod.getParameters()) {
        org.vcell.optimization.thrift.CopasiOptimizationParameter p = new org.vcell.optimization.thrift.CopasiOptimizationParameter();
        p.setValue(optParam.getValue());
        org.vcell.optimization.thrift.OptimizationParameterType optParmType = null;
        org.vcell.optimization.thrift.OptimizationParameterDataType optDataType = null;
        switch(optParam.getType()) {
            case Cooling_Factor:
                optParmType = OptimizationParameterType.Cooling_Factor;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case IterationLimit:
                optParmType = OptimizationParameterType.IterationLimit;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Number_of_Generations:
                optParmType = OptimizationParameterType.Number_of_Generations;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Number_of_Iterations:
                optParmType = OptimizationParameterType.Number_of_Iterations;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Pf:
                optParmType = OptimizationParameterType.Pf;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Population_Size:
                optParmType = OptimizationParameterType.Population_Size;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Random_Number_Generator:
                optParmType = OptimizationParameterType.Random_Number_Generator;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Rho:
                optParmType = OptimizationParameterType.Rho;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Scale:
                optParmType = OptimizationParameterType.Scale;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Seed:
                optParmType = OptimizationParameterType.Seed;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Start_Temperature:
                optParmType = OptimizationParameterType.Start_Temperature;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Std_Deviation:
                optParmType = OptimizationParameterType.Std_Deviation;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Swarm_Size:
                optParmType = OptimizationParameterType.Swarm_Size;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Tolerance:
                optParmType = OptimizationParameterType.Tolerance;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            default:
                throw new RuntimeException("unsupported parameter type :" + optParam.getType().name() + " in COPASI optimization solver");
        }
        p.setParamType(optParmType);
        p.setDataType(optDataType);
        thriftOptMethod.addToOptimizationParameterList(p);
    }
    optProblem.setOptimizationMethod(thriftOptMethod);
    return optProblem;
}