Examples with VariableSymbolTable cbit.vcell.parser.VariableSymbolTable used on opensource projects

Example 1 with VariableSymbolTable

use of cbit.vcell.parser.VariableSymbolTable in project vcell by virtualcell.

the class RowColumnResultSet method createResultSetSymbolTable.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2003 4:32:00 PM)
 * @return cbit.vcell.parser.SymbolTable
 */
private VariableSymbolTable createResultSetSymbolTable(boolean bIncludeFunctions) {
    // 
    // create symbol table for binding expression against data columns and functions (of data columns)
    // 
    VariableSymbolTable resultSetSymbolTable = new VariableSymbolTable();
    for (int i = 0; i < getColumnDescriptionsCount(); i++) {
        ColumnDescription colDesc = getColumnDescriptions(i);
        if (colDesc instanceof ODESolverResultSetColumnDescription) {
            Domain domain = null;
            VolVariable vVar = new VolVariable(colDesc.getName(), domain);
            vVar.setIndex(i);
            resultSetSymbolTable.addVar(vVar);
        } else if (bIncludeFunctions && colDesc instanceof FunctionColumnDescription) {
            FunctionColumnDescription funcColDesc = (FunctionColumnDescription) colDesc;
            Domain domain = null;
            Function func = new Function(funcColDesc.getName(), new Expression(funcColDesc.getExpression()), domain);
            func.setIndex(i);
            resultSetSymbolTable.addVar(func);
        }
    }
    return resultSetSymbolTable;
}

Example 2 with VariableSymbolTable

use of cbit.vcell.parser.VariableSymbolTable in project vcell by virtualcell.

the class DataSetControllerImpl method fieldFunctionSubstitution.

private Expression fieldFunctionSubstitution(OutputContext outputContext, final VCDataIdentifier vcdID, Expression functionExpression) throws ExpressionException, DataAccessException, IOException, MathException {
    SimResampleInfoProvider simResampleInfoProvider = null;
    Expression origExpression = new Expression(functionExpression);
    if (vcdID instanceof VCSimulationDataIdentifier) {
        simResampleInfoProvider = ((VCSimulationDataIdentifier) vcdID);
    } else if (vcdID instanceof VCSimulationDataIdentifierOldStyle) {
        simResampleInfoProvider = ((VCSimulationDataIdentifierOldStyle) vcdID);
    } else if (vcdID instanceof ExternalDataIdentifier) {
        simResampleInfoProvider = ((ExternalDataIdentifier) vcdID);
    } else {
        return origExpression;
    }
    FieldFunctionArguments[] fieldfuncArgumentsArr = FieldUtilities.getFieldFunctionArguments(origExpression);
    if (fieldfuncArgumentsArr == null || fieldfuncArgumentsArr.length == 0) {
        return origExpression;
    }
    String[] origSymbols = origExpression.getSymbols();
    Vector<SymbolTableEntry> originalSymbolTablEntrryV = new Vector<SymbolTableEntry>();
    for (int i = 0; origSymbols != null && i < origSymbols.length; i++) {
        if (!originalSymbolTablEntrryV.contains(origExpression.getSymbolBinding(origSymbols[i]))) {
            originalSymbolTablEntrryV.add(origExpression.getSymbolBinding(origSymbols[i]));
        }
    }
    Expression exp = new Expression(origExpression);
    // 
    // Handle Field Data Function field(...)
    // 
    double[][] resampledFieldDatas = null;
    HashMap<String, Integer> substSymbolIndexH = new HashMap<String, Integer>();
    // if(fieldfuncArgumentsArr != null && fieldfuncArgumentsArr.length > 0){
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecArr = getFieldDataIdentifierSpecs(fieldfuncArgumentsArr, simResampleInfoProvider.getOwner());
    // Substitute Field Data Functions for simple symbols for lookup-------
    for (int i = 0; i < fieldfuncArgumentsArr.length; i += 1) {
        for (int j = 0; j < fieldDataIdentifierSpecArr.length; j++) {
            if (fieldfuncArgumentsArr[i].equals(fieldDataIdentifierSpecArr[j].getFieldFuncArgs())) {
                String substFieldName = fieldfuncArgumentsArr[i].getFieldName() + "_" + fieldfuncArgumentsArr[i].getVariableName() + "_" + fieldfuncArgumentsArr[i].getTime().evaluateConstant();
                substFieldName = TokenMangler.fixTokenStrict(substFieldName);
                if (exp.hasSymbol(substFieldName)) {
                    throw new DataAccessException("Substitute Field data name is not unique");
                }
                String fieldFuncString = SimulationData.createCanonicalFieldFunctionSyntax(fieldDataIdentifierSpecArr[j].getExternalDataIdentifier().getName(), fieldfuncArgumentsArr[i].getVariableName(), fieldfuncArgumentsArr[i].getTime().evaluateConstant(), fieldfuncArgumentsArr[i].getVariableType().getTypeName());
                exp.substituteInPlace(new Expression(fieldFuncString), new Expression(substFieldName));
                substSymbolIndexH.put(substFieldName, i);
                break;
            }
        }
    }
    // ----------------------------------------------------------------------
    boolean[] bResample = new boolean[fieldDataIdentifierSpecArr.length];
    Arrays.fill(bResample, true);
    writeFieldFunctionData(outputContext, fieldDataIdentifierSpecArr, bResample, getMesh(simResampleInfoProvider), simResampleInfoProvider, getMesh(simResampleInfoProvider).getNumMembraneElements(), FVSolverStandalone.HESM_KEEP_AND_CONTINUE);
    resampledFieldDatas = new double[fieldfuncArgumentsArr.length][];
    for (int i = 0; i < fieldfuncArgumentsArr.length; i += 1) {
        // File resampledFile =
        // new File(getUserDir(vcsdID.getOwner()),
        // vcsdID.getID()+
        // FieldDataIdentifierSpec.getDefaultFieldDataFileNameForSimulation(fieldfuncArgumentsArr[i])
        // );
        // File resampledFile = new File(getPrimaryUserDir(simResampleInfoProvider.getOwner(), true),
        // SimulationData.createCanonicalResampleFileName(
        // simResampleInfoProvider, fieldfuncArgumentsArr[i]));
        File resampledFile = ((SimulationData) getVCData(simResampleInfoProvider)).getFieldDataFile(simResampleInfoProvider, fieldfuncArgumentsArr[i]);
        resampledFieldDatas[i] = DataSet.fetchSimData(fieldfuncArgumentsArr[i].getVariableName(), resampledFile);
    }
    // }
    // Rebind all the symbols
    String[] dependentIDs = exp.getSymbols();
    VariableSymbolTable varSymbolTable = new VariableSymbolTable();
    for (int i = 0; dependentIDs != null && i < dependentIDs.length; i++) {
        SymbolTableEntry newSymbolTableEntry = null;
        for (int j = 0; j < originalSymbolTablEntrryV.size(); j++) {
            if (originalSymbolTablEntrryV.elementAt(j).getName().equals(dependentIDs[i])) {
                newSymbolTableEntry = originalSymbolTablEntrryV.elementAt(j);
                break;
            }
        }
        if (newSymbolTableEntry == null) {
            if (substSymbolIndexH.containsKey(dependentIDs[i])) {
                int resampledDataIndex = substSymbolIndexH.get(dependentIDs[i]).intValue();
                FieldDataParameterVariable fieldDataParameterVariable = new FieldDataParameterVariable(dependentIDs[i], resampledFieldDatas[resampledDataIndex]);
                newSymbolTableEntry = fieldDataParameterVariable;
            }
        }
        if (newSymbolTableEntry == null) {
            throw new DataAccessException("Field Data Couldn't find substituted expression while evaluating function");
        }
        varSymbolTable.addVar(newSymbolTableEntry);
    }
    exp.bindExpression(varSymbolTable);
    return exp;
}

Example 3 with VariableSymbolTable

use of cbit.vcell.parser.VariableSymbolTable in project vcell by virtualcell.

the class OdeFileWriter method createSymbolTable.

/**
 * OdeFileCoder constructor comment.
 * @throws Exception
 */
private void createSymbolTable() throws Exception {
    // 
    // Create symbol table for binding sensitivity variable expressions. (Cannot bind to simulation,
    // since it does not have the sensitivity variables corresponding to the volume variables).
    // 
    varsSymbolTable = new VariableSymbolTable();
    // SymbolTableEntry.index doesn't matter ... just code generating binding by var names not index.
    varsSymbolTable.addVar(ReservedVariable.TIME);
    int count = 0;
    Variable[] variables = simTask.getSimulationJob().getSimulationSymbolTable().getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof VolVariable) {
            VolVariable vVar = (VolVariable) variables[i];
            vVar.setIndex(count);
            varsSymbolTable.addVar(vVar);
            count++;
        } else if (variables[i] instanceof Function) {
            Function func = (Function) variables[i];
            func.setIndex(count);
            varsSymbolTable.addVar(func);
            count++;
        } else if (variables[i] instanceof Constant) {
            Constant constant = (Constant) variables[i];
            constant.setIndex(count);
            varsSymbolTable.addVar(constant);
            count++;
        } else if (variables[i] instanceof ParameterVariable) {
            ParameterVariable param = (ParameterVariable) variables[i];
            param.setIndex(count);
            varsSymbolTable.addVar(param);
            count++;
        }
    }
    // Get the vector of sensVariables, needed for creating SensStateVariables
    Vector<SensStateVariable> sensVars = new Vector<SensStateVariable>();
    for (int i = 0; i < getStateVariableCount(); i++) {
        if (simTask.getSimulation().getSolverTaskDescription().getSensitivityParameter() != null) {
            if (getStateVariable(i) instanceof SensStateVariable) {
                sensVars.addElement((SensStateVariable) getStateVariable(i));
            }
        }
    }
    for (int j = count; j < (count + sensVars.size()); j++) {
        SensVariable sVar = (SensVariable) (sensVars.elementAt(j - count).getVariable());
        sVar.setIndex(j);
        varsSymbolTable.addVar(sVar);
    }
}