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

Example 1 with MathModel

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

the class PDEExportDataPanel method createSimulationSelector.

private ExportSpecs.SimulationSelector createSimulationSelector() {
    ExportSpecs.SimulationSelector simulationSelector = new ExportSpecs.SimulationSelector() {

        private ExportSpecs.SimNameSimDataID[] multiSimNameSimDataIDs;

        // private ExportSpecs.ExportParamScanInfo exportParamScanInfo;
        private int[] selectedParamScanIndexes;

        private Simulation[] simulations;

        public SimNameSimDataID[] getSelectedSimDataInfo() {
            // }
            if (multiSimNameSimDataIDs == null) {
                return new ExportSpecs.SimNameSimDataID[] { currentSimNameSimDataID };
            }
            return multiSimNameSimDataIDs;
        }

        public void selectSimulations() {
            getNumAvailableSimulations();
            String[][] rowData = new String[simulations.length][5];
            for (int i = 0; i < rowData.length; i++) {
                rowData[i][0] = simulations[i].getName();
                rowData[i][1] = simulations[i].getMeshSpecification().getSamplingSize().toString();
                rowData[i][2] = simulations[i].getSolverTaskDescription().getExpectedNumTimePoints() + "";
                rowData[i][3] = simulations[i].getSolverTaskDescription().getTimeBounds().getEndingTime() + "";
                rowData[i][4] = simulations[i].getSolverTaskDescription().getOutputTimeSpec().getShortDescription();
            }
            try {
                int[] choices = DialogUtils.showComponentOKCancelTableList(PDEExportDataPanel.this, "Choose Sims to export together", new String[] { "Simulation", "Mesh x,y,z", "NumTimePoints", "EndTime", "Output Descr." }, rowData, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
                if (choices != null) {
                    multiSimNameSimDataIDs = new ExportSpecs.SimNameSimDataID[choices.length];
                    for (int i = 0; i < choices.length; i++) {
                        multiSimNameSimDataIDs[i] = new ExportSpecs.SimNameSimDataID(simulations[choices[i]].getName(), simulations[choices[i]].getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), SimResultsViewer.getParamScanInfo(simulations[choices[i]], (currentSimNameSimDataID == null ? 0 : currentSimNameSimDataID.getDefaultJobIndex())));
                    }
                }
            } catch (UserCancelException uce) {
            // ignore
            }
        }

        public void selectParamScanInfo() {
            String[][] rowData = new String[currentSimNameSimDataID.getExportParamScanInfo().getParamScanJobIndexes().length][currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames().length];
            for (int i = 0; i < rowData.length; i++) {
                for (int j = 0; j < rowData[i].length; j++) {
                    rowData[i][j] = currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantValues()[i][j];
                }
            }
            try {
                int[] choices = DialogUtils.showComponentOKCancelTableList(PDEExportDataPanel.this, "Choose ParameterScans to export together", currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames(), rowData, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
                if (choices != null && choices.length > 0) {
                    selectedParamScanIndexes = new int[choices.length];
                    // String[][] selectedParamScanValues = new String[choices.length][currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames().length];
                    for (int i = 0; i < choices.length; i++) {
                        selectedParamScanIndexes[i] = choices[i];
                    // for (int j = 0; j < currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames().length; j++) {
                    // selectedParamScanValues[i][j] = currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantValues()[choices[i]][j];
                    // }
                    }
                // exportParamScanInfo =
                // new ExportSpecs.ExportParamScanInfo(selectedParamScanIndexes, selectedParamScanIndexes[0], currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames(), selectedParamScanValues);
                } else {
                    selectedParamScanIndexes = null;
                }
            } catch (UserCancelException uce) {
            // ignore
            }
        }

        public int[] getselectedParamScanIndexes() {
            return selectedParamScanIndexes;
        }

        public int getNumAvailableParamScans() {
            if (currentSimNameSimDataID == null || currentSimNameSimDataID.getExportParamScanInfo() == null) {
                return 0;
            }
            return currentSimNameSimDataID.getExportParamScanInfo().getParamScanJobIndexes().length;
        }

        public int getNumAvailableSimulations() {
            if (simulations == null) {
                VCDocument thisDocument = (getDataViewerManager() instanceof DocumentWindowManager ? ((DocumentWindowManager) getDataViewerManager()).getVCDocument() : null);
                if (thisDocument instanceof BioModel) {
                    String thisSimContextName = dataInfoProvider.getSimulationModelInfo().getContextName();
                    SimulationContext[] simContexts = ((BioModel) thisDocument).getSimulationContexts();
                    SimulationContext thisSimulationContext = null;
                    for (int i = 0; i < simContexts.length; i++) {
                        if (thisSimContextName.equals(thisDocument.getName() + "::" + simContexts[i].getName())) {
                            thisSimulationContext = simContexts[i];
                            break;
                        }
                    }
                    simulations = thisSimulationContext.getSimulations();
                } else if (thisDocument instanceof MathModel) {
                    simulations = ((MathModel) thisDocument).getSimulations();
                } else {
                    simulations = new Simulation[0];
                }
            }
            return simulations.length;
        }
    };
    return simulationSelector;
}

Example 2 with MathModel

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

the class ClientRequestManager method newDocument.

/**
 * Insert the method's description here.
 * Creation date: (5/21/2004 4:20:47 AM)
 * @param documentType int
 */
public AsynchClientTask[] newDocument(TopLevelWindowManager requester, final VCDocument.DocumentCreationInfo documentCreationInfo) {
    // gcwtodo
    AsynchClientTask createNewDocumentTask = new AsynchClientTask("Creating New Document", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocument doc = (VCDocument) hashTable.get("doc");
            DocumentWindowManager windowManager = createDocumentWindowManager(doc);
            DocumentWindow dw = getMdiManager().createNewDocumentWindow(windowManager);
            if (windowManager != null) {
                hashTable.put("windowManager", windowManager);
            }
            setFinalWindow(hashTable, dw);
        }
    };
    if (documentCreationInfo.getDocumentType() == VCDocumentType.MATHMODEL_DOC && documentCreationInfo.getOption() == VCDocument.MATH_OPTION_SPATIAL_NEW) {
        final AsynchClientTask createSpatialMathModelTask = new AsynchClientTask("creating mathmodel", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                Geometry geometry = null;
                geometry = (Geometry) hashTable.get("doc");
                MathModel mathModel = createMathModel("Untitled", geometry);
                mathModel.setName("MathModel" + (getMdiManager().getNumCreatedDocumentWindows() + 1));
                hashTable.put("doc", mathModel);
            }
        };
        requester.createGeometry(null, new AsynchClientTask[] { createSpatialMathModelTask, createNewDocumentTask }, "Choose geometry type to start MathModel creation", "Create MathModel", null);
        return null;
    }
    /* asynchronous and not blocking any window */
    AsynchClientTask[] taskArray = null;
    if (documentCreationInfo.getPreCreatedDocument() == null) {
        AsynchClientTask[] taskArray1 = createNewDocument(requester, documentCreationInfo);
        taskArray = new AsynchClientTask[taskArray1.length + 1];
        System.arraycopy(taskArray1, 0, taskArray, 0, taskArray1.length);
    } else {
        taskArray = new AsynchClientTask[2];
        taskArray[0] = new AsynchClientTask("Setting document...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                hashTable.put("doc", documentCreationInfo.getPreCreatedDocument());
            }
        };
    }
    taskArray[taskArray.length - 1] = createNewDocumentTask;
    return taskArray;
}

Example 3 with MathModel

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

the class ClientRequestManager method changeGeometry0.

private void changeGeometry0(final TopLevelWindowManager requester, final SimulationContext simContext) {
    AsynchClientTask selectDocumentTypeTask = createSelectDocTask(requester);
    AsynchClientTask selectLoadGeomTask = createSelectLoadGeomTask(requester);
    AsynchClientTask processGeometryTask = new AsynchClientTask("Processing geometry...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get(GEOMETRY_KEY);
            if (requester instanceof MathModelWindowManager) {
                // User can cancel here
                continueAfterMathModelGeomChangeWarning((MathModelWindowManager) requester, newGeometry);
            }
            if (newGeometry.getDimension() > 0 && newGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                newGeometry.getGeometrySurfaceDescription().updateAll();
            }
        }
    };
    AsynchClientTask setNewGeometryTask = new AsynchClientTask("Setting new Geometry...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get(GEOMETRY_KEY);
            if (newGeometry != null) {
                if (requester instanceof BioModelWindowManager) {
                    simContext.setGeometry(newGeometry);
                } else if (requester instanceof MathModelWindowManager) {
                    MathModel mathModel = (MathModel) ((MathModelWindowManager) requester).getVCDocument();
                    mathModel.getMathDescription().setGeometry(newGeometry);
                }
            }
        }
    };
    Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { selectDocumentTypeTask, selectLoadGeomTask, processGeometryTask, setNewGeometryTask }, false);
}

Example 4 with MathModel

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

the class ClientRequestManager method createMathModel.

/**
 * Insert the method's description here.
 * Creation date: (5/24/2004 12:22:11 PM)
 * @param windowID java.lang.String
 */
private MathModel createMathModel(String name, Geometry geometry) {
    MathModel mathModel = new MathModel(null);
    MathDescription mathDesc = mathModel.getMathDescription();
    try {
        mathDesc.setGeometry(geometry);
        if (geometry.getDimension() == 0) {
            mathDesc.addSubDomain(new CompartmentSubDomain("Compartment", CompartmentSubDomain.NON_SPATIAL_PRIORITY));
        } else {
            try {
                if (geometry.getDimension() > 0 && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                    geometry.getGeometrySurfaceDescription().updateAll();
                }
            } catch (ImageException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Geometric surface generation error: \n" + e.getMessage());
            } catch (GeometryException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Geometric surface generation error: \n" + e.getMessage());
            }
            SubVolume[] subVolumes = geometry.getGeometrySpec().getSubVolumes();
            for (int i = 0; i < subVolumes.length; i++) {
                mathDesc.addSubDomain(new CompartmentSubDomain(subVolumes[i].getName(), subVolumes[i].getHandle()));
            }
            // 
            // add only those MembraneSubDomains corresponding to surfaces that acutally exist in geometry.
            // 
            GeometricRegion[] regions = geometry.getGeometrySurfaceDescription().getGeometricRegions();
            for (int i = 0; i < regions.length; i++) {
                if (regions[i] instanceof SurfaceGeometricRegion) {
                    SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) regions[i];
                    SubVolume subVolume1 = ((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[0]).getSubVolume();
                    SubVolume subVolume2 = ((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[1]).getSubVolume();
                    CompartmentSubDomain compartment1 = mathDesc.getCompartmentSubDomain(subVolume1.getName());
                    CompartmentSubDomain compartment2 = mathDesc.getCompartmentSubDomain(subVolume2.getName());
                    MembraneSubDomain membraneSubDomain = mathDesc.getMembraneSubDomain(compartment1, compartment2);
                    if (membraneSubDomain == null) {
                        SurfaceClass surfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(subVolume1, subVolume2);
                        membraneSubDomain = new MembraneSubDomain(compartment1, compartment2, surfaceClass.getName());
                        mathDesc.addSubDomain(membraneSubDomain);
                    }
                }
            }
        }
        mathDesc.isValid();
        mathModel.setName(name);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
    return mathModel;
}

Example 5 with MathModel

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

the class MathModel_SBMLExporter method getSBMLString.

/**
 * Insert the method's description here.
 * Creation date: (4/11/2006 11:38:26 AM)
 * @return org.sbml.libsbml.Model
 * @param mathModel cbit.vcell.mathmodel.MathModel
 * @throws XMLStreamException
 * @throws SBMLException
 */
public static String getSBMLString(cbit.vcell.mathmodel.MathModel mathModel, long level, long version) throws cbit.vcell.parser.ExpressionException, java.io.IOException, SBMLException, XMLStreamException {
    if (mathModel.getMathDescription().isSpatial()) {
        throw new RuntimeException("spatial models export to SBML not supported");
    }
    if (mathModel.getMathDescription().hasFastSystems()) {
        throw new RuntimeException("math models with fast systems cannot be exported to SBML");
    }
    if (mathModel.getMathDescription().isNonSpatialStoch()) {
        throw new RuntimeException("stochastic math models cannot be exported to SBML");
    }
    if (!mathModel.getMathDescription().isValid()) {
        throw new RuntimeException("math model has an invalid Math Description, cannot export to SBML");
    }
    String dummyID = "ID_0";
    String compartmentId = "compartment";
    SBMLDocument sbmlDocument = new SBMLDocument((int) level, (int) version);
    Model sbmlModel = sbmlDocument.createModel();
    sbmlModel.setId("MathModel_" + TokenMangler.mangleToSName(mathModel.getName()));
    if (mathModel.getMathDescription().isSpatial()) {
        addGeometry(sbmlModel, mathModel);
    }
    Compartment compartment = sbmlModel.createCompartment();
    compartment.setId(compartmentId);
    // ------ For spatial SBML when implemented -----
    // if (vcMathModel.getMathDescription().isSpatial()){
    // // for spatial model, compartment(s) created in addGeometry(), based on number of subVolumes/surfaceClasses.
    // addGeometry();
    // } else {
    // // for non-spatial mathmodel, only 1 compartment; create it here.
    // String compartmentId = "compartment";
    // org.sbml.libsbml.Compartment compartment = sbmlModel.createCompartment();
    // compartment.setId(compartmentId);
    // }
    MathDescription mathDesc = mathModel.getMathDescription();
    Enumeration<Variable> enumVars = mathDesc.getVariables();
    while (enumVars.hasMoreElements()) {
        Variable vcVar = (Variable) enumVars.nextElement();
        // 
        if (vcVar instanceof cbit.vcell.math.VolVariable) {
        // 
        // skip for now, define later when defining ODEEquations.
        // 
        // org.sbml.libsbml.Species species = model.createSpecies();
        // species.setId(vcVar.getName());
        // species.setCompartment(compartmentId);
        } else if (vcVar instanceof cbit.vcell.math.Constant && ((cbit.vcell.math.Constant) vcVar).getExpression().isNumeric()) {
            Parameter param = sbmlModel.createParameter();
            param.setId(TokenMangler.mangleToSName(vcVar.getName()));
            param.setConstant(true);
            param.setValue(vcVar.getExpression().evaluateConstant());
        } else if (vcVar instanceof cbit.vcell.math.Constant || vcVar instanceof cbit.vcell.math.Function) {
            Parameter param = sbmlModel.createParameter();
            param.setId(TokenMangler.mangleToSName(vcVar.getName()));
            param.setConstant(false);
            // 
            // Function or Constant with expressions - create assignment rule and add to model.
            // 
            ASTNode mathNode = getFormulaFromExpression(vcVar.getExpression(), MathType.REAL);
            AssignmentRule assignmentRule = sbmlModel.createAssignmentRule();
            dummyID = TokenMangler.getNextEnumeratedToken(dummyID);
            assignmentRule.setId(dummyID);
            assignmentRule.setVariable(TokenMangler.mangleToSName(vcVar.getName()));
            assignmentRule.setMath(mathNode);
        // Create a parameter for this function/non-numeric constant, set its value to be 'not-constant',
        // add to model.
        }
    }
    cbit.vcell.math.CompartmentSubDomain subDomain = (cbit.vcell.math.CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
    // System.out.println(model.toSBML());
    Enumeration<Equation> enumEqu = subDomain.getEquations();
    while (enumEqu.hasMoreElements()) {
        cbit.vcell.math.Equation equ = (cbit.vcell.math.Equation) enumEqu.nextElement();
        if (equ instanceof cbit.vcell.math.OdeEquation) {
            // For ODE equations, add the ode variable as a parameter, add rate as a rate rule and init condition as an initial assignment rule.
            Parameter param = sbmlModel.createParameter();
            param.setId(TokenMangler.mangleToSName(equ.getVariable().getName()));
            param.setConstant(false);
            // try to obtain the constant to which the init expression evaluates.
            RateRule rateRule = sbmlModel.createRateRule();
            rateRule.setVariable(TokenMangler.mangleToSName(equ.getVariable().getName()));
            rateRule.setMath(getFormulaFromExpression(equ.getRateExpression(), MathType.REAL));
            InitialAssignment initialAssignment = sbmlModel.createInitialAssignment();
            dummyID = TokenMangler.getNextEnumeratedToken(dummyID);
            initialAssignment.setId(dummyID);
            initialAssignment.setMath(getFormulaFromExpression(equ.getInitialExpression(), MathType.REAL));
            initialAssignment.setVariable(TokenMangler.mangleToSName(equ.getVariable().getName()));
        } else {
            throw new RuntimeException("equation type " + equ.getClass().getName() + " not supported");
        }
    }
    Iterator<Event> vcellEvents = mathDesc.getEvents();
    while (vcellEvents.hasNext()) {
        Event vcellEvent = vcellEvents.next();
        addSbmlEvent(sbmlModel, vcellEvent);
    }
    System.out.println(new SBMLWriter().writeSBMLToString(sbmlDocument));
    // validate the sbml document
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.GENERAL_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.IDENTIFIER_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.MATHML_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.MODELING_PRACTICE, false);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.OVERDETERMINED_MODEL, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.SBO_CONSISTENCY, false);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.UNITS_CONSISTENCY, false);
    sbmlDocument.checkConsistency();
    // sbmlDocument.checkConsistencyOffline();
    long internalErrCount = sbmlDocument.getNumErrors();
    if (internalErrCount > 0) {
        StringBuffer sbmlErrbuf = new StringBuffer();
        for (int i = 0; i < internalErrCount; i++) {
            SBMLError sbmlErr = sbmlDocument.getError(i);
            if (sbmlErr.isError() || sbmlErr.isFatal()) {
                sbmlErrbuf.append(sbmlErr.getCategory() + " :: " + sbmlErr.getSeverity() + " :: " + sbmlErr.getMessage() + "\n");
            }
        }
        if (sbmlErrbuf.length() > 0) {
            throw new RuntimeException("SBML Internal consistency checks failed: \n" + sbmlErrbuf.toString());
        }
    }
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.GENERAL_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.IDENTIFIER_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.UNITS_CONSISTENCY, false);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.MATHML_CONSISTENCY, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.SBO_CONSISTENCY, false);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.OVERDETERMINED_MODEL, true);
    sbmlDocument.setConsistencyChecks(CHECK_CATEGORY.MODELING_PRACTICE, false);
    sbmlDocument.checkConsistency();
    // sbmlDocument.checkConsistencyOffline();
    long errCount = sbmlDocument.getNumErrors();
    if (errCount > 0) {
        StringBuffer sbmlErrbuf = new StringBuffer();
        for (int i = 0; i < errCount; i++) {
            SBMLError sbmlErr = sbmlDocument.getError(i);
            if (sbmlErr.isError() || sbmlErr.isFatal()) {
                sbmlErrbuf.append(sbmlErr.getCategory() + " :: " + sbmlErr.getSeverity() + " :: " + sbmlErr.getMessage() + "\n");
            }
        }
        if (sbmlErrbuf.length() > 0) {
            throw new RuntimeException("SBML validation failed: \n" + sbmlErrbuf.toString());
        }
    }
    // end of validation
    // start writing
    SBMLWriter sbmlWriter = new SBMLWriter();
    String sbmlStr = sbmlWriter.writeSBMLToString(sbmlDocument);
    // Error check - use libSBML's document.printError to print to outputstream
    System.out.println("\n\nSBML Export Error Report");
    sbmlDocument.printErrors(System.out);
    return sbmlStr;
}