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

Example 46 with MathDescription

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

the class MathDebuggerPanel method expandBoth.

private void expandBoth() throws PropertyVetoException, MappingException, MathException, ExpressionException {
    setStatus("Canonical Math for both mathDescriptions: \n");
    MathDescription[] canonicalMathDescs = MathUtilities.getCanonicalMathDescriptions(SimulationSymbolTable.createMathSymbolTableFactory(), getMathModel1().getMathDescription(), getMathModel2().getMathDescription());
    MathModel newMathModel = new MathModel(null);
    newMathModel.setName("Math1");
    newMathModel.setMathDescription(canonicalMathDescs[0]);
    setMathModel1(newMathModel);
    newMathModel = new MathModel(null);
    newMathModel.setName("Math2");
    newMathModel.setMathDescription(canonicalMathDescs[1]);
    setMathModel2(newMathModel);
}

Example 47 with MathDescription

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

the class MathDescEditor method setMathDescription.

/**
 * Set the MathDescription to a new value.
 * @param newValue cbit.vcell.math.MathDescription
 */
public void setMathDescription(MathDescription newValue) {
    if (ivjMathDescription != newValue) {
        try {
            MathDescription oldValue = getMathDescription();
            ivjMathDescription = newValue;
            getVCMLPane().setText(getMathDescription().getVCML_database());
            getVCMLPane().setCaretPosition(0);
            firePropertyChange("mathDescription", oldValue, newValue);
        } catch (java.lang.Throwable ivjExc) {
            handleException(ivjExc);
        }
    }
}

Example 48 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 49 with MathDescription

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

the class MathDescriptionDbDriver method getMathDescriptionSQL.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param mathDescKey cbit.sql.KeyValue
 */
private MathDescription getMathDescriptionSQL(QueryHashtable dbc, Connection con, User user, KeyValue mathDescKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    String sql;
    Field[] f = { userTable.userid, new cbit.sql.StarField(mathDescTable) };
    Table[] t = { mathDescTable, userTable };
    String condition = mathDescTable.id.getQualifiedColName() + " = " + mathDescKey + " AND " + userTable.id.getQualifiedColName() + " = " + mathDescTable.ownerRef.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // System.out.println(sql);
    MathDescription mathDescription = null;
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            // 
            // note: must call mathDescTable.getMathDescription() first (rset.getBytes(language) must be called first)
            // 
            mathDescription = mathDescTable.getMathDescription(rset, con, dbSyntax);
            // 
            // get Geometry reference and assign to mathDescription
            // 
            java.math.BigDecimal bigD = rset.getBigDecimal(MathDescTable.table.geometryRef.toString());
            KeyValue geomRef = null;
            if (!rset.wasNull()) {
                geomRef = new KeyValue(bigD);
            } else {
                throw new DataAccessException("Error:  Geometry Reference Cannot be Null for MathDescription");
            }
            Geometry geom = (Geometry) geomDB.getVersionable(dbc, con, user, VersionableType.Geometry, geomRef, false);
            try {
                mathDescription.setGeometry(geom);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new DataAccessException("DataAccess Exception: " + e.getMessage());
            }
        } else {
            throw new ObjectNotFoundException("MathDescription id=" + mathDescKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return mathDescription;
}

Example 50 with MathDescription

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

the class MathVerifier method testMathGeneration.

public MathGenerationResults testMathGeneration(KeyValue simContextKey) throws SQLException, ObjectNotFoundException, DataAccessException, XmlParseException, MappingException, MathException, MatrixException, ExpressionException, ModelException, PropertyVetoException {
    User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new org.vcell.util.document.KeyValue(PropertyLoader.ADMINISTRATOR_ID));
    if (lg.isTraceEnabled())
        lg.trace("Testing SimContext with key '" + simContextKey + "'");
    // get biomodel refs
    java.sql.Connection con = null;
    java.sql.Statement stmt = null;
    con = conFactory.getConnection(new Object());
    cbit.vcell.modeldb.BioModelSimContextLinkTable bmscTable = cbit.vcell.modeldb.BioModelSimContextLinkTable.table;
    cbit.vcell.modeldb.BioModelTable bmTable = cbit.vcell.modeldb.BioModelTable.table;
    cbit.vcell.modeldb.UserTable userTable = cbit.vcell.modeldb.UserTable.table;
    String sql = "SELECT " + bmscTable.bioModelRef.getQualifiedColName() + "," + bmTable.ownerRef.getQualifiedColName() + "," + userTable.userid.getQualifiedColName() + " FROM " + bmscTable.getTableName() + "," + bmTable.getTableName() + "," + userTable.getTableName() + " WHERE " + bmscTable.simContextRef.getQualifiedColName() + " = " + simContextKey + " AND " + bmTable.id.getQualifiedColName() + " = " + bmscTable.bioModelRef.getQualifiedColName() + " AND " + bmTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    ArrayList<KeyValue> bioModelKeys = new ArrayList<KeyValue>();
    stmt = con.createStatement();
    User owner = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            KeyValue key = new KeyValue(rset.getBigDecimal(bmscTable.bioModelRef.getUnqualifiedColName()));
            bioModelKeys.add(key);
            KeyValue ownerRef = new KeyValue(rset.getBigDecimal(bmTable.ownerRef.getUnqualifiedColName()));
            String userid = rset.getString(userTable.userid.getUnqualifiedColName());
            owner = new User(userid, ownerRef);
        }
    } finally {
        if (stmt != null) {
            stmt.close();
        }
        con.close();
    }
    // use the first biomodel...
    if (bioModelKeys.size() == 0) {
        throw new RuntimeException("zombie simContext ... no biomodels");
    }
    BioModelInfo bioModelInfo = dbServerImpl.getBioModelInfo(owner, bioModelKeys.get(0));
    // 
    // read in the BioModel from the database
    // 
    BigString bioModelXML = dbServerImpl.getBioModelXML(owner, bioModelInfo.getVersion().getVersionKey());
    BioModel bioModelFromDB = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    BioModel bioModelNewMath = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    bioModelFromDB.refreshDependencies();
    bioModelNewMath.refreshDependencies();
    // 
    // get all Simulations for this model
    // 
    Simulation[] modelSimsFromDB = bioModelFromDB.getSimulations();
    // 
    // ---> only for the SimContext we started with...
    // recompute mathDescription, and verify it is equivalent
    // then check each associated simulation to ensure math overrides are applied in an equivalent manner also.
    // 
    SimulationContext[] simContextsFromDB = bioModelFromDB.getSimulationContexts();
    SimulationContext[] simContextsNewMath = bioModelNewMath.getSimulationContexts();
    SimulationContext simContextFromDB = null;
    SimulationContext simContextNewMath = null;
    for (int k = 0; k < simContextsFromDB.length; k++) {
        // find it...
        if (simContextsFromDB[k].getKey().equals(simContextKey)) {
            simContextFromDB = simContextsFromDB[k];
            simContextNewMath = simContextsNewMath[k];
            break;
        }
    }
    if (simContextFromDB == null) {
        throw new RuntimeException("BioModel referred to by this SimContext does not contain this SimContext");
    } else {
        MathDescription origMathDesc = simContextFromDB.getMathDescription();
        // 
        try {
            if (simContextNewMath.getGeometry().getDimension() > 0 && simContextNewMath.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                simContextNewMath.getGeometry().getGeometrySurfaceDescription().updateAll();
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
        // 
        // updated mathDescription loaded into copy of bioModel, then test for equivalence.
        // 
        cbit.vcell.mapping.MathMapping mathMapping = simContextNewMath.createNewMathMapping();
        MathDescription mathDesc_latest = mathMapping.getMathDescription();
        MathMapping_4_8 mathMapping_4_8 = new MathMapping_4_8(simContextNewMath);
        MathDescription mathDesc_4_8 = mathMapping_4_8.getMathDescription();
        String issueString = null;
        org.vcell.util.Issue[] issues = mathMapping.getIssues();
        if (issues != null && issues.length > 0) {
            StringBuffer buffer = new StringBuffer("Issues(" + issues.length + "):\n");
            for (int l = 0; l < issues.length; l++) {
                buffer.append(" <<" + issues[l].toString() + ">>\n");
            }
            issueString = buffer.toString();
        }
        simContextNewMath.setMathDescription(mathDesc_latest);
        MathCompareResults mathCompareResults_latest = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_latest);
        MathCompareResults mathCompareResults_4_8 = null;
        try {
            mathCompareResults_4_8 = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_4_8);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            mathCompareResults_4_8 = new MathCompareResults(Decision.MathDifferent_FAILURE_UNKNOWN, e.getMessage());
        }
        return new MathGenerationResults(bioModelFromDB, simContextFromDB, origMathDesc, mathDesc_latest, mathCompareResults_latest, mathDesc_4_8, mathCompareResults_4_8);
    }
}