Examples with MathDescription cbit.vcell.math.MathDescription used on opensource projects

Example 1 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class MatlabOdeFileCoder method write_V6_MFile.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
public void write_V6_MFile(java.io.PrintWriter pw, String functionName) throws MathException, ExpressionException {
    MathDescription mathDesc = simulation.getMathDescription();
    if (!mathDesc.isValid()) {
        throw new MathException("invalid math description\n" + mathDesc.getWarning());
    }
    if (mathDesc.isSpatial()) {
        throw new MathException("spatial math description, cannot create ode file");
    }
    if (mathDesc.hasFastSystems()) {
        throw new MathException("math description contains algebraic constraints, cannot create .m file");
    }
    // 
    // print function declaration
    // 
    pw.println("function [T,Y,yinit,param, allNames, allValues] = " + functionName + "(argTimeSpan,argYinit,argParam)");
    pw.println("% [T,Y,yinit,param] = " + functionName + "(argTimeSpan,argYinit,argParam)");
    pw.println("%");
    pw.println("% input:");
    pw.println("%     argTimeSpan is a vector of start and stop times (e.g. timeSpan = [0 10.0])");
    pw.println("%     argYinit is a vector of initial conditions for the state variables (optional)");
    pw.println("%     argParam is a vector of values for the parameters (optional)");
    pw.println("%");
    pw.println("% output:");
    pw.println("%     T is the vector of times");
    pw.println("%     Y is the vector of state variables");
    pw.println("%     yinit is the initial conditions that were used");
    pw.println("%     param is the parameter vector that was used");
    pw.println("%     allNames is the output solution variable names");
    pw.println("%     allValues is the output solution variable values corresponding to the names");
    pw.println("%");
    pw.println("%     example of running this file: [T,Y,yinit,param,allNames,allValues] = myMatlabFunc; <-(your main function name)");
    pw.println("%");
    VariableHash varHash = new VariableHash();
    for (Variable var : simulationSymbolTable.getVariables()) {
        varHash.addVariable(var);
    }
    Variable[] variables = varHash.getTopologicallyReorderedVariables();
    CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
    // 
    // collect "true" constants (Constants without identifiers)
    // 
    // 
    // collect "variables" (VolVariables only)
    // 
    // 
    // collect "functions" (Functions and Constants with identifiers)
    // 
    Vector<Constant> constantList = new Vector<Constant>();
    Vector<VolVariable> volVarList = new Vector<VolVariable>();
    Vector<Variable> functionList = new Vector<Variable>();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof Constant) {
            Constant constant = (Constant) variables[i];
            String[] symbols = constant.getExpression().getSymbols();
            if (symbols == null || symbols.length == 0) {
                constantList.addElement(constant);
            } else {
                functionList.add(constant);
            }
        } else if (variables[i] instanceof VolVariable) {
            volVarList.addElement((VolVariable) variables[i]);
        } else if (variables[i] instanceof Function) {
            functionList.addElement(variables[i]);
        }
    }
    Constant[] constants = (Constant[]) BeanUtils.getArray(constantList, Constant.class);
    VolVariable[] volVars = (VolVariable[]) BeanUtils.getArray(volVarList, VolVariable.class);
    Variable[] functions = (Variable[]) BeanUtils.getArray(functionList, Variable.class);
    int numVars = volVarList.size() + functionList.size();
    String varNamesForStringArray = "";
    String varNamesForValueArray = "";
    for (Variable var : volVarList) {
        varNamesForStringArray = varNamesForStringArray + "'" + var.getName() + "';";
        varNamesForValueArray = varNamesForValueArray + var.getName() + " ";
    }
    for (Variable func : functionList) {
        varNamesForStringArray = varNamesForStringArray + "'" + func.getName() + "';";
        varNamesForValueArray = varNamesForValueArray + func.getName() + " ";
    }
    pw.println("");
    pw.println("%");
    pw.println("% Default time span");
    pw.println("%");
    double beginTime = 0.0;
    double endTime = simulation.getSolverTaskDescription().getTimeBounds().getEndingTime();
    pw.println("timeSpan = [" + beginTime + " " + endTime + "];");
    pw.println("");
    pw.println("% output variable lengh and names");
    pw.println("numVars = " + numVars + ";");
    pw.println("allNames = {" + varNamesForStringArray + "};");
    pw.println("");
    pw.println("if nargin >= 1");
    pw.println("\tif length(argTimeSpan) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% TimeSpan overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\ttimeSpan = argTimeSpan;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% Default Initial Conditions");
    pw.println("%");
    pw.println("yinit = [");
    for (int j = 0; j < volVars.length; j++) {
        Expression initial = subDomain.getEquation(volVars[j]).getInitialExpression();
        double defaultInitialCondition = 0;
        try {
            initial.bindExpression(mathDesc);
            defaultInitialCondition = initial.evaluateConstant();
            pw.println("\t" + defaultInitialCondition + ";\t\t% yinit(" + (j + 1) + ") is the initial condition for '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[j].getName()) + "'");
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            pw.println("\t" + initial.infix_Matlab() + ";\t\t% yinit(" + (j + 1) + ") is the initial condition for '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[j].getName()) + "'");
        // throw new RuntimeException("error evaluating initial condition for variable "+volVars[j].getName());
        }
    }
    pw.println("];");
    pw.println("if nargin >= 2");
    pw.println("\tif length(argYinit) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% initial conditions overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\tyinit = argYinit;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% Default Parameters");
    pw.println("%   constants are only those \"Constants\" from the Math Description that are just floating point numbers (no identifiers)");
    pw.println("%   note: constants of the form \"A_init\" are really initial conditions and are treated in \"yinit\"");
    pw.println("%");
    pw.println("param = [");
    int paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + constants[i].getExpression().infix_Matlab() + ";\t\t% param(" + (paramIndex + 1) + ") is '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + "'");
        paramIndex++;
    }
    pw.println("];");
    pw.println("if nargin >= 3");
    pw.println("\tif length(argParam) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% parameter values overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\tparam = argParam;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% invoke the integrator");
    pw.println("%");
    pw.println("[T,Y] = ode15s(@f,timeSpan,yinit,odeset('OutputFcn',@odeplot),param,yinit);");
    pw.println("");
    pw.println("% get the solution");
    pw.println("all = zeros(size(T), numVars);");
    pw.println("for i = 1:size(T)");
    pw.println("\tall(i,:) = getRow(T(i), Y(i,:), yinit, param);");
    pw.println("end");
    pw.println("");
    pw.println("allValues = all;");
    pw.println("end");
    // get row data for solution
    pw.println("");
    pw.println("% -------------------------------------------------------");
    pw.println("% get row data");
    pw.println("function rowValue = getRow(t,y,y0,p)");
    // 
    // print volVariables (in order and assign to var vector)
    // 
    pw.println("\t% State Variables");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()) + " = y(" + (i + 1) + ");");
    }
    // 
    // print constants
    // 
    pw.println("\t% Constants");
    paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + " = p(" + (paramIndex + 1) + ");");
        paramIndex++;
    }
    // 
    // print variables
    // 
    pw.println("\t% Functions");
    for (int i = 0; i < functions.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(functions[i].getName()) + " = " + functions[i].getExpression().infix_Matlab() + ";");
    }
    pw.println("");
    pw.println("\trowValue = [" + varNamesForValueArray + "];");
    pw.println("end");
    // 
    // print ode-rate
    // 
    pw.println("");
    pw.println("% -------------------------------------------------------");
    pw.println("% ode rate");
    pw.println("function dydt = f(t,y,p,y0)");
    // 
    // print volVariables (in order and assign to var vector)
    // 
    pw.println("\t% State Variables");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()) + " = y(" + (i + 1) + ");");
    }
    // 
    // print constants
    // 
    pw.println("\t% Constants");
    paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + " = p(" + (paramIndex + 1) + ");");
        paramIndex++;
    }
    // 
    // print variables
    // 
    pw.println("\t% Functions");
    for (int i = 0; i < functions.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(functions[i].getName()) + " = " + functions[i].getExpression().infix_Matlab() + ";");
    }
    pw.println("\t% Rates");
    pw.println("\tdydt = [");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t\t" + subDomain.getEquation(volVars[i]).getRateExpression().infix_Matlab() + ";    % rate for " + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()));
    }
    pw.println("\t];");
    pw.println("end");
}

Example 2 with MathDescription

use of cbit.vcell.math.MathDescription 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 3 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class ClientRequestManager method openAfterChecking.

private void openAfterChecking(VCDocumentInfo documentInfo, final TopLevelWindowManager requester, final boolean inNewWindow) {
    final String DOCUMENT_INFO = "documentInfo";
    final String SEDML_TASK = "SedMLTask";
    final String SEDML_MODELS = "SedMLModels";
    final String BNG_UNIT_SYSTEM = "bngUnitSystem";
    final String BMDB_DEFAULT_APPLICATION = "Deterministic";
    /* asynchronous and not blocking any window */
    bOpening = true;
    Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
    // may want to insert corrected VCDocumentInfo later if our import debugger
    // corrects it (BNGL Debugger).
    hashTable.put(DOCUMENT_INFO, documentInfo);
    hashTable.put("isBMDB", false);
    hashTable.put("isSEDML", false);
    // start a thread that gets it and updates the GUI by creating a new document
    // desktop
    String taskName = null;
    if (documentInfo instanceof ExternalDocInfo) {
        taskName = "Importing document";
        ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
        File file = externalDocInfo.getFile();
        if (file != null && !file.getName().isEmpty() && file.getName().endsWith("bngl")) {
            BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitOrigin.DEFAULT);
            String fileText;
            String originalFileText;
            try {
                fileText = BeanUtils.readBytesFromFile(file, null);
                originalFileText = new String(fileText);
            } catch (IOException e1) {
                e1.printStackTrace();
                DialogUtils.showErrorDialog(requester.getComponent(), "<html>Error reading file " + file.getPath() + "</html>");
                return;
            }
            Reader reader = externalDocInfo.getReader();
            boolean bException = true;
            while (bException) {
                try {
                    BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
                    boolean bStochastic = true;
                    boolean bRuleBased = true;
                    SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("temp NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
                    List<SimulationContext> appList = new ArrayList<SimulationContext>();
                    appList.add(ruleBasedSimContext);
                    RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                    RbmUtils.reactionRuleLabelIndex = 0;
                    RbmUtils.reactionRuleNames.clear();
                    ASTModel astModel = RbmUtils.importBnglFile(reader);
                    // for now, hasUnitSystem() always returns false
                    if (astModel.hasUnitSystem()) {
                        bngUnitSystem = astModel.getUnitSystem();
                    }
                    if (astModel.hasCompartments()) {
                        Structure struct = bioModel.getModel().getStructure(0);
                        if (struct != null) {
                            bioModel.getModel().removeStructure(struct);
                        }
                    }
                    BnglObjectConstructionVisitor constructionVisitor = null;
                    if (!astModel.hasMolecularDefinitions()) {
                        System.out.println("Molecular Definition Block missing.");
                        constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
                    } else {
                        constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, true);
                    }
                    astModel.jjtAccept(constructionVisitor, rbmModelContainer);
                    bException = false;
                } catch (final Exception e) {
                    e.printStackTrace(System.out);
                    BNGLDebuggerPanel panel = new BNGLDebuggerPanel(fileText, e);
                    int oKCancel = DialogUtils.showComponentOKCancelDialog(requester.getComponent(), panel, "Bngl Debugger: " + file.getName());
                    if (oKCancel == JOptionPane.CANCEL_OPTION || oKCancel == JOptionPane.DEFAULT_OPTION) {
                        throw new UserCancelException("Canceling Import");
                    }
                    // inserting <potentially> corrected DocumentInfo
                    fileText = panel.getText();
                    externalDocInfo = new ExternalDocInfo(panel.getText());
                    reader = externalDocInfo.getReader();
                    hashTable.put(DOCUMENT_INFO, externalDocInfo);
                }
            }
            if (!originalFileText.equals(fileText)) {
                // file has been modified
                String message = "Importing <b>" + file.getName() + "</b> into vCell. <br>Overwrite the file on the disk?<br>";
                message = "<html>" + message + "</html>";
                Object[] options = { "Overwrite and Import", "Import Only", "Cancel" };
                int returnCode = JOptionPane.showOptionDialog(requester.getComponent(), message, "Bngl Debugger", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, options, options[2]);
                if (returnCode == JOptionPane.YES_OPTION) {
                    try {
                        FileWriter fw = new FileWriter(file);
                        fw.write(fileText);
                        fw.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                } else if (returnCode == JOptionPane.CANCEL_OPTION || returnCode == JOptionPane.CLOSED_OPTION) {
                    return;
                }
            }
            if (!(bngUnitSystem.getOrigin() == BngUnitOrigin.PARSER)) {
                BNGLUnitsPanel panel = new BNGLUnitsPanel(bngUnitSystem);
                int oKCancel = DialogUtils.showComponentOKCancelDialog(requester.getComponent(), panel, " Bngl Units Selector", null, false);
                if (oKCancel == JOptionPane.CANCEL_OPTION || oKCancel == JOptionPane.DEFAULT_OPTION) {
                    // TODO: or do nothing and continue with default values?
                    return;
                } else {
                    bngUnitSystem = panel.getUnits();
                }
            }
            hashTable.put(BNG_UNIT_SYSTEM, bngUnitSystem);
        } else if (file != null && !file.getName().isEmpty() && file.getName().toLowerCase().endsWith(".sedml")) {
            try {
                XMLSource xmlSource = externalDocInfo.createXMLSource();
                File sedmlFile = xmlSource.getXmlFile();
                SedML sedml = Libsedml.readDocument(sedmlFile).getSedMLModel();
                if (sedml == null || sedml.getModels().isEmpty()) {
                    return;
                }
                // AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(),
                // file.getName());
                List<SedML> sedmls = new ArrayList<>();
                sedmls.add(sedml);
                hashTable.put(SEDML_MODELS, sedmls);
            // hashTable.put(SEDML_TASK, chosenTask);
            } catch (Exception e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read document: " + e.getMessage(), e);
            }
        } else if (file != null && !file.getName().isEmpty() && (file.getName().toLowerCase().endsWith(".sedx") || file.getName().toLowerCase().endsWith(".omex"))) {
            try {
                ArchiveComponents ac = null;
                ac = Libsedml.readSEDMLArchive(new FileInputStream(file));
                List<SEDMLDocument> docs = ac.getSedmlDocuments();
                List<SedML> sedmls = new ArrayList<>();
                for (SEDMLDocument doc : docs) {
                    SedML sedml = doc.getSedMLModel();
                    if (sedml == null) {
                        throw new RuntimeException("Failed importing " + file.getName());
                    }
                    if (sedml.getModels().isEmpty()) {
                        throw new RuntimeException("Unable to find any model in " + file.getName());
                    }
                    sedmls.add(sedml);
                }
                // AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(),
                // file.getName());
                hashTable.put(SEDML_MODELS, sedmls);
            // hashTable.put(SEDML_TASK, chosenTask);
            } catch (Exception e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read archive: " + e.getMessage(), e);
            }
        }
    } else {
        taskName = "Loading document '" + documentInfo.getVersion().getName() + "' from database";
    }
    AsynchClientTask task0 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (!inNewWindow) {
                // request was to replace the document in an existing window
                getMdiManager().blockWindow(requester.getManagerID());
            }
        }
    };
    AsynchClientTask task1 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocument doc = null;
            List<VCDocument> docs = new ArrayList<>();
            boolean isBMDB = false;
            boolean isSEDML = false;
            VCDocumentInfo documentInfo = (VCDocumentInfo) hashTable.get(DOCUMENT_INFO);
            if (documentInfo instanceof BioModelInfo) {
                BioModelInfo bmi = (BioModelInfo) documentInfo;
                doc = getDocumentManager().getBioModel(bmi);
            } else if (documentInfo instanceof MathModelInfo) {
                MathModelInfo mmi = (MathModelInfo) documentInfo;
                doc = getDocumentManager().getMathModel(mmi);
            } else if (documentInfo instanceof GeometryInfo) {
                GeometryInfo gmi = (GeometryInfo) documentInfo;
                doc = getDocumentManager().getGeometry(gmi);
            } else if (documentInfo instanceof ExternalDocInfo) {
                ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
                File file = externalDocInfo.getFile();
                if (file != null && !file.getName().isEmpty() && (file.getName().toLowerCase().endsWith(".sedx") || file.getName().toLowerCase().endsWith(".omex"))) {
                    TranslationLogger transLogger = new TranslationLogger(requester);
                    // iterate through one or more SEDML objects
                    List<SedML> sedmls = (List<SedML>) hashTable.get(SEDML_MODELS);
                    for (SedML sedml : sedmls) {
                        // default to import all tasks
                        List<VCDocument> vcdocs = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, sedml, null, null, false);
                        for (VCDocument vcdoc : vcdocs) {
                            docs.add(vcdoc);
                        }
                    }
                    // treat the same since OMEX is just and archive with SED-ML file(s)
                    isSEDML = true;
                } else if (!externalDocInfo.isXML()) {
                    if (hashTable.containsKey(BNG_UNIT_SYSTEM)) {
                        // not XML, look for BNGL etc.
                        // we use the BngUnitSystem already created during the 1st pass
                        BngUnitSystem bngUnitSystem = (BngUnitSystem) hashTable.get(BNG_UNIT_SYSTEM);
                        BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
                        SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
                        SimulationContext odeSimContext = bioModel.addNewSimulationContext("BioNetGen app", SimulationContext.Application.NETWORK_DETERMINISTIC);
                        List<SimulationContext> appList = new ArrayList<SimulationContext>();
                        appList.add(ruleBasedSimContext);
                        appList.add(odeSimContext);
                        // set convention for initial conditions in generated application for seed
                        // species (concentration or count)
                        ruleBasedSimContext.setUsingConcentration(bngUnitSystem.isConcentration());
                        odeSimContext.setUsingConcentration(bngUnitSystem.isConcentration());
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        RbmUtils.reactionRuleLabelIndex = 0;
                        RbmUtils.reactionRuleNames.clear();
                        Reader reader = externalDocInfo.getReader();
                        ASTModel astModel = RbmUtils.importBnglFile(reader);
                        if (bioModel.getModel() != null && bioModel.getModel().getVcMetaData() != null) {
                            VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
                            vcMetaData.setFreeTextAnnotation(bioModel, astModel.getProlog());
                        }
                        if (astModel.hasCompartments()) {
                            Structure struct = bioModel.getModel().getStructure(0);
                            if (struct != null) {
                                bioModel.getModel().removeStructure(struct);
                            }
                        }
                        BnglObjectConstructionVisitor constructionVisitor = null;
                        if (!astModel.hasMolecularDefinitions()) {
                            System.out.println("Molecular Definition Block missing. Extracting it from Species, Reactions, Obserbables.");
                            constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
                        } else {
                            constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, true);
                        }
                        // we'll convert the kinetic parameters to BngUnitSystem inside the
                        // visit(ASTKineticsParameter...)
                        astModel.jjtAccept(constructionVisitor, rbmModelContainer);
                        // set the volume in the newly created application to
                        // BngUnitSystem.bnglModelVolume
                        // TODO: set the right values if we import compartments from the bngl file!
                        // if(!bngUnitSystem.isConcentration()) {
                        Expression sizeExpression = new Expression(bngUnitSystem.getVolume());
                        ruleBasedSimContext.getGeometryContext().getStructureMapping(0).getSizeParameter().setExpression(sizeExpression);
                        odeSimContext.getGeometryContext().getStructureMapping(0).getSizeParameter().setExpression(sizeExpression);
                        // }
                        // we remove the NFSim application if any seed species is clamped because NFSim
                        // doesn't know what to do with it
                        boolean bClamped = false;
                        for (SpeciesContextSpec scs : ruleBasedSimContext.getReactionContext().getSpeciesContextSpecs()) {
                            if (scs.isConstant()) {
                                bClamped = true;
                                break;
                            }
                        }
                        if (bClamped) {
                            bioModel.removeSimulationContext(ruleBasedSimContext);
                        }
                        // // TODO: DON'T delete this code
                        // // the code below is needed if we also want to create simulations, example for 1 rule based simulation
                        // // it is rule-based so it wont have to flatten, should be fast.
                        // MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
                        // NetworkGenerationRequirements networkGenerationRequirements = null; // network generation should not be executed.
                        // ruleBasedSimContext.refreshMathDescription(callback,networkGenerationRequirements);
                        // Simulation sim = ruleBasedSimContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX,callback,networkGenerationRequirements);
                        doc = bioModel;
                    }
                } else {
                    // is XML
                    try (TranslationLogger transLogger = new TranslationLogger(requester)) {
                        XMLSource xmlSource = externalDocInfo.createXMLSource();
                        org.jdom.Element rootElement = xmlSource.getXmlDoc().getRootElement();
                        String xmlType = rootElement.getName();
                        String modelXmlType = null;
                        if (xmlType.equals(XMLTags.VcmlRootNodeTag)) {
                            // For now, assuming that <vcml> element has only one child (biomodel, mathmodel
                            // or geometry).
                            // Will deal with multiple children of <vcml> Element when we get to model
                            // composition.
                            @SuppressWarnings("unchecked") List<Element> childElementList = rootElement.getChildren();
                            // assuming first child is the biomodel,
                            Element modelElement = childElementList.get(0);
                            // mathmodel or geometry.
                            modelXmlType = modelElement.getName();
                        }
                        if (xmlType.equals(XMLTags.BioModelTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.BioModelTag))) {
                            doc = XmlHelper.XMLToBioModel(xmlSource);
                        } else if (xmlType.equals(XMLTags.MathModelTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.MathModelTag))) {
                            doc = XmlHelper.XMLToMathModel(xmlSource);
                        } else if (xmlType.equals(XMLTags.GeometryTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.GeometryTag))) {
                            doc = XmlHelper.XMLToGeometry(xmlSource);
                        } else if (xmlType.equals(XMLTags.SbmlRootNodeTag)) {
                            Namespace namespace = rootElement.getNamespace(XMLTags.SBML_SPATIAL_NS_PREFIX);
                            isBMDB = externalDocInfo.isBioModelsNet();
                            boolean bIsSpatial = (namespace == null) ? false : true;
                            doc = XmlHelper.importSBML(transLogger, xmlSource, bIsSpatial);
                        } else if (xmlType.equals(XMLTags.CellmlRootNodeTag)) {
                            if (requester instanceof BioModelWindowManager) {
                                doc = XmlHelper.importBioCellML(transLogger, xmlSource);
                            } else {
                                doc = XmlHelper.importMathCellML(transLogger, xmlSource);
                            }
                        } else if (xmlType.equals(MicroscopyXMLTags.FRAPStudyTag)) {
                            doc = VFrapXmlHelper.VFRAPToBioModel(hashTable, xmlSource, getDocumentManager(), requester);
                        } else if (xmlType.equals(XMLTags.SedMLTypeTag)) {
                            // we know it is a single SedML since it is an actual XML source
                            List<SedML> sedmls = (List<SedML>) hashTable.get(SEDML_MODELS);
                            SedML sedml = sedmls.get(0);
                            // default to import all tasks
                            docs = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, sedml, null, externalDocInfo.getFile().getAbsolutePath(), false);
                            isSEDML = true;
                        } else {
                            // unknown XML format
                            throw new RuntimeException("unsupported XML format, first element tag is <" + rootElement.getName() + ">");
                        }
                        if (externalDocInfo.getDefaultName() != null) {
                            doc.setName(externalDocInfo.getDefaultName());
                        }
                    }
                }
                if (doc == null && docs == null) {
                    File f = externalDocInfo.getFile();
                    if (f != null) {
                        throw new RuntimeException("Unable to determine type of file " + f.getCanonicalPath());
                    }
                    throw new ProgrammingException();
                }
            }
            // create biopax objects using annotation
            if (doc instanceof BioModel) {
                BioModel bioModel = (BioModel) doc;
                try {
                    bioModel.getVCMetaData().createBioPaxObjects(bioModel);
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
            requester.prepareDocumentToLoad(doc, inNewWindow);
            hashTable.put("isBMDB", isBMDB);
            hashTable.put("isSEDML", isSEDML);
            if (!isSEDML) {
                hashTable.put("doc", doc);
            } else {
                hashTable.put("docs", docs);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Showing document", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            try {
                Throwable exc = (Throwable) hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR);
                if (exc == null) {
                    boolean isSEDML = (boolean) hashTable.get("isSEDML");
                    if (isSEDML) {
                        List<VCDocument> docs = (List<VCDocument>) hashTable.get("docs");
                        List<DocumentWindowManager> windowManagers = new ArrayList<DocumentWindowManager>();
                        for (VCDocument doc : docs) {
                            DocumentWindowManager windowManager = createDocumentWindowManager(doc);
                            getMdiManager().createNewDocumentWindow(windowManager);
                            windowManagers.add(windowManager);
                        }
                        hashTable.put("managers", windowManagers);
                        hashTable.put("docs", docs);
                    } else {
                        VCDocument doc = (VCDocument) hashTable.get("doc");
                        DocumentWindowManager windowManager = null;
                        if (inNewWindow) {
                            windowManager = createDocumentWindowManager(doc);
                            // request was to create a new top-level window with this doc
                            getMdiManager().createNewDocumentWindow(windowManager);
                        } else {
                            // request was to replace the document in an existing window
                            windowManager = (DocumentWindowManager) requester;
                            getMdiManager().setCanonicalTitle(requester.getManagerID());
                            windowManager.resetDocument(doc);
                        }
                        hashTable.put(WIN_MGR_KEY, windowManager);
                        hashTable.put("doc", doc);
                    }
                }
            } catch (Exception ex) {
                ex.printStackTrace();
            // TODO: check why getMdiManager().createNewDocumentWindow(windowManager) fails sometimes
            } finally {
                if (!inNewWindow) {
                    getMdiManager().unBlockWindow(requester.getManagerID());
                }
                bOpening = false;
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("Special Layout", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (documentInfo instanceof ExternalDocInfo) {
                ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
                boolean isSEDML = (boolean) hashTable.get("isSEDML");
                if (externalDocInfo.isBioModelsNet() || externalDocInfo.isFromXmlFile() || !isSEDML) {
                    DocumentWindowManager windowManager = (DocumentWindowManager) hashTable.get(WIN_MGR_KEY);
                    if (windowManager instanceof BioModelWindowManager) {
                        ((BioModelWindowManager) windowManager).specialLayout();
                    }
                }
                if (isSEDML) {
                    List<DocumentWindowManager> windowManagers = (List<DocumentWindowManager>) hashTable.get("managers");
                    if (windowManagers != null) {
                        for (DocumentWindowManager manager : windowManagers) {
                            ((BioModelWindowManager) manager).specialLayout();
                        }
                    }
                }
            }
        }
    };
    AsynchClientTask task4 = new AsynchClientTaskFunction(ClientRequestManager::setWindowFocus, "Set window focus", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false);
    AsynchClientTask task6 = new AsynchClientTask("Renaming, please wait...", // TASKTYPE_NONSWING_BLOCKING
    AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, // TASKTYPE_NONSWING_BLOCKING
    false, // TASKTYPE_NONSWING_BLOCKING
    false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocument doc = (VCDocument) hashTable.get("doc");
            if (!(doc instanceof BioModel)) {
                return;
            }
            boolean isBMDB = (boolean) hashTable.get("isBMDB");
            if (documentInfo instanceof ExternalDocInfo) {
                if (isBMDB) {
                    idToNameConversion(doc);
                }
            }
            if (isBMDB) {
                BioModel bioModel = (BioModel) doc;
                SimulationContext simulationContext = bioModel.getSimulationContext(0);
                simulationContext.setName(BMDB_DEFAULT_APPLICATION);
                MathMappingCallback callback = new MathMappingCallback() {

                    @Override
                    public void setProgressFraction(float fractionDone) {
                    }

                    @Override
                    public void setMessage(String message) {
                    }

                    @Override
                    public boolean isInterrupted() {
                        return false;
                    }
                };
                MathMapping mathMapping = simulationContext.createNewMathMapping(callback, NetworkGenerationRequirements.ComputeFullNoTimeout);
                MathDescription mathDesc = null;
                try {
                    mathDesc = mathMapping.getMathDescription(callback);
                    simulationContext.setMathDescription(mathDesc);
                    Simulation sim = new Simulation(mathDesc);
                    sim.setName(simulationContext.getBioModel().getFreeSimulationName());
                    simulationContext.addSimulation(sim);
                    bioModel.refreshDependencies();
                } catch (MappingException | MathException | MatrixException | ExpressionException | ModelException e1) {
                    e1.printStackTrace();
                }
                hashTable.put("doc", doc);
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { task0, task1, task6, task2, task3, task4 }, false);
}

Example 4 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class OutputFunctionsListTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    OutputFunctionContext fc = getOutputFunctionContext();
    SimulationOwner so = null;
    if (fc != null) {
        so = fc.getSimulationOwner();
    }
    if (evt.getSource() == fc && evt.getPropertyName().equals(OutputFunctionContext.PROPERTY_OUTPUT_FUNCTIONS)) {
        setData(outputFunctionContext.getOutputFunctionsList());
    }
    if (evt.getSource() instanceof SimulationContext && evt.getSource() == so && evt.getPropertyName().equals(Model.PROPERTY_NAME_MODEL_ENTITY_NAME)) {
        SimulationContext simulationContext = (SimulationContext) so;
        if (fc.getOutputFunctionsList() == null || fc.getOutputFunctionsList().isEmpty()) {
            return;
        }
        Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
        // 
        // WARNING: this should NOT be used under any circumstance for batch renaming
        // MathDescription, MathMapping, expressions are NOT thread safe
        // 
        AsynchClientTask task0 = new AsynchClientTask("Renaming Functions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                MathMappingCallback callback = new MathMappingCallback() {

                    @Override
                    public void setProgressFraction(float fractionDone) {
                    }

                    @Override
                    public void setMessage(String message) {
                    }

                    @Override
                    public boolean isInterrupted() {
                        return false;
                    }
                };
                MathMapping mathMapping = simulationContext.createNewMathMapping(callback, NetworkGenerationRequirements.ComputeFullNoTimeout);
                MathDescription mathDesc = null;
                try {
                    mathDesc = mathMapping.getMathDescription(callback);
                } catch (MappingException | MathException | MatrixException | ExpressionException | ModelException e1) {
                    e1.printStackTrace();
                }
                String oldName = (String) evt.getOldValue();
                String newName = (String) evt.getNewValue();
                ArrayList<AnnotatedFunction> afList = fc.getOutputFunctionsList();
                List<Expression> changedExpressions = new ArrayList<>();
                for (AnnotatedFunction af : afList) {
                    if (af == null) {
                        continue;
                    }
                    Expression exp = af.getExpression();
                    if (exp == null || exp.getSymbols() == null || exp.getSymbols().length == 0) {
                        continue;
                    }
                    String errMsg = "Failed to rename symbol '" + oldName + "' with '" + newName + "' in the Expression of Function '" + af.getName() + "'.";
                    for (String symbol : exp.getSymbols()) {
                        if (symbol.contentEquals(oldName)) {
                            try {
                                exp.substituteInPlace(new Expression(oldName), new Expression(newName));
                                changedExpressions.add(exp);
                            } catch (ExpressionException e) {
                                e.printStackTrace();
                                throw new RuntimeException(errMsg);
                            }
                        }
                    }
                }
                if (changedExpressions.size() > 0) {
                    try {
                        simulationContext.setMathDescription(mathDesc);
                        for (Expression exp : changedExpressions) {
                            exp.bindExpression(outputFunctionContext);
                        }
                    } catch (ExpressionException | PropertyVetoException e) {
                        e.printStackTrace();
                    }
                }
            }
        };
        ClientTaskDispatcher.dispatch(ownerTable, hashTable, new AsynchClientTask[] { task0 }, false);
    }
    if (evt.getPropertyName().equals(GeometryOwner.PROPERTY_NAME_GEOMETRY)) {
        Geometry oldGeometry = (Geometry) evt.getOldValue();
        Geometry newGeometry = (Geometry) evt.getNewValue();
        // changing from ode to pde
        if (oldGeometry.getDimension() == 0 && newGeometry.getDimension() > 0) {
            fireTableStructureChanged();
            setData(getOutputFunctionContext().getOutputFunctionsList());
        }
    }
}

Example 5 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class OutputFunctionsPanel method getPossibleGeometryClassesAndVariableTypes.

private ArrayList<Object> getPossibleGeometryClassesAndVariableTypes(Expression expr) throws ExpressionException, InconsistentDomainException {
    SimulationOwner simulationOwner = getSimulationWorkspace().getSimulationOwner();
    MathDescription mathDescription = simulationOwner.getMathDescription();
    boolean bSpatial = simulationOwner.getGeometry().getDimension() > 0;
    if (!bSpatial) {
        return null;
    }
    // making sure that output function is not direct function of constant.
    expr.bindExpression(outputFunctionContext);
    // new expression itself to be function of constant.
    try {
        expr = MathUtilities.substituteFunctions(expr, outputFunctionContext).flatten();
    } catch (ExpressionBindingException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        expr = MathUtilities.substituteFunctions(expr, outputFunctionContext, true).flatten();
    }
    String[] symbols = expr.getSymbols();
    // using bit operation to determine whether geometry classes for symbols in expression are vol, membrane or both. 01 => vol; 10 => membrane; 11 => both
    int gatherFlag = 0;
    Set<GeometryClass> geomClassSet = new HashSet<GeometryClass>();
    ArrayList<Object> objectsList = new ArrayList<Object>();
    boolean bHasVariable = false;
    VariableType[] varTypes = null;
    if (symbols != null && symbols.length > 0) {
        // making sure that new expression is defined in the same domain
        varTypes = new VariableType[symbols.length];
        for (int i = 0; i < symbols.length; i++) {
            if (ReservedMathSymbolEntries.getReservedVariableEntry(symbols[i]) != null) {
                varTypes[i] = VariableType.VOLUME;
            } else {
                Variable var = mathDescription.getVariable(symbols[i]);
                if (var == null) {
                    var = mathDescription.getPostProcessingBlock().getDataGenerator(symbols[i]);
                }
                varTypes[i] = VariableType.getVariableType(var);
                bHasVariable = true;
                if (var.getDomain() != null) {
                    GeometryClass varGeoClass = simulationOwner.getGeometry().getGeometryClass(var.getDomain().getName());
                    geomClassSet.add(varGeoClass);
                    if (varGeoClass instanceof SubVolume) {
                        gatherFlag |= 1;
                    } else if (varGeoClass instanceof SurfaceClass) {
                        gatherFlag |= 2;
                    }
                }
                if (varTypes[i].equals(VariableType.POSTPROCESSING)) {
                    gatherFlag |= 4;
                }
            }
        }
    }
    if (gatherFlag > 4) {
        throw new RuntimeException("cannot mix post processing variables with membrane or volume variables");
    }
    int numGeomClasses = geomClassSet.size();
    if (numGeomClasses == 0) {
        if (bHasVariable) {
            // if there are no variables (like built in function, vcRegionArea), check with flattened expression to find out the variable type of the new expression
            Function flattenedFunction = new Function(getFunctionNameTextField().getText(), expr, null);
            flattenedFunction.bind(outputFunctionContext);
            VariableType newVarType = SimulationSymbolTable.getFunctionVariableType(flattenedFunction, simulationOwner.getMathDescription(), symbols, varTypes, bSpatial);
            objectsList.add(newVarType);
        } else {
            objectsList.add(VariableType.VOLUME);
            objectsList.add(VariableType.MEMBRANE);
        }
    } else if (numGeomClasses == 1) {
        objectsList.add(geomClassSet.iterator().next());
        if (gatherFlag == 1) {
            objectsList.add(VariableType.MEMBRANE);
        }
    } else if (gatherFlag == 1) {
        // all volumes
        if (numGeomClasses == 2) {
            // all subvolumes, if there are only 2, check for adjacency.
            GeometryClass[] geomClassesArray = geomClassSet.toArray(new GeometryClass[0]);
            SurfaceClass sc = simulationOwner.getGeometry().getGeometrySurfaceDescription().getSurfaceClass((SubVolume) geomClassesArray[0], (SubVolume) geomClassesArray[1]);
            if (sc != null) {
                objectsList.add(sc);
            }
        }
        objectsList.add(VariableType.VOLUME);
    } else if (gatherFlag == 2) {
        // all membranes
        objectsList.add(VariableType.MEMBRANE);
    } else if (gatherFlag == 3) {
        // mixed - both vols and membranes
        // add only membranes?
        objectsList.add(VariableType.MEMBRANE);
    }
    return objectsList;
}