Examples with AnnotatedFunction cbit.vcell.solver.AnnotatedFunction used on opensource projects

Example 51 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class MergedData method readFunctions.

/**
 * Insert the method's description here.
 * Creation date: (1/15/2004 11:48:25 AM)
 */
private void readFunctions(OutputContext outputContext) throws FileNotFoundException, IOException {
    Vector<AnnotatedFunction> annotatedFuncsVector = FunctionFileGenerator.readFunctionsFile(getFunctionsFile(), dataInfo.getID());
    // add user-defined functions from output context, if any
    if (outputContext != null) {
        for (int i = 0; i < outputContext.getOutputFunctions().length; i++) {
            annotatedFuncsVector.add(outputContext.getOutputFunctions()[i]);
        }
    }
    // 
    // Convert this annotatedfunctionsVector into the field annotatedFunctionsList.
    // 
    annotatedFunctionList.clear();
    for (int i = 0; i < annotatedFuncsVector.size(); i++) {
        AnnotatedFunction annotatedFunction = annotatedFuncsVector.elementAt(i);
        try {
            functionBindAndSubstitute(annotatedFunction);
            addFunctionToList(annotatedFunction);
        } catch (ExpressionException e) {
            throw new RuntimeException("Could not add function " + annotatedFunction.getName() + " to annotatedFunctionList");
        }
    }
}

Example 52 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class MergedData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    getFunctionDataIdentifiers(outputContext);
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}

Example 53 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class SundialsSolver method createFunctionList.

public Vector<AnnotatedFunction> createFunctionList() {
    // 
    // add appropriate Function columns to result set
    // 
    Vector<AnnotatedFunction> funcList = super.createFunctionList();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    if (getSensitivityParameter() != null) {
        try {
            AnnotatedFunction saf = new AnnotatedFunction(getSensitivityParameter().getName(), new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getDomain(), "", VariableType.NONSPATIAL, FunctionCategory.PREDEFINED);
            if (!funcList.contains(saf)) {
                funcList.add(saf);
            }
            Variable[] variables = simSymbolTable.getVariables();
            StateVariable[] stateVars = createStateVariables();
            for (int i = 0; i < variables.length; i++) {
                if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
                    Function depSensFunction = (Function) variables[i];
                    Expression depSensFnExpr = new Expression(depSensFunction.getExpression());
                    depSensFnExpr = simSymbolTable.substituteFunctions(depSensFnExpr);
                    depSensFnExpr = getFunctionSensitivity(depSensFnExpr, getSensitivityParameter(), stateVars);
                    // depSensFnExpr = depSensFnExpr.flatten(); 	// already bound and flattened in getFunctionSensitivity, no need here.....
                    String depSensFnName = new String("sens_" + depSensFunction.getName() + "_wrt_" + getSensitivityParameter().getName());
                    if (depSensFunction != null) {
                        AnnotatedFunction af = new AnnotatedFunction(depSensFnName, depSensFnExpr.flatten(), variables[i].getDomain(), "", VariableType.NONSPATIAL, FunctionCategory.PREDEFINED);
                        funcList.add(af);
                    }
                }
            }
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        }
    }
    return funcList;
}

Example 54 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class ODESimData method readNCDataFile.

public static ODESimData readNCDataFile(VCDataIdentifier vcdId, File dataFile, File functionsFile) throws DataAccessException {
    // read ida file
    System.out.println("reading NetCDF file : " + dataFile);
    ODESimData odeSimData = new ODESimData();
    odeSimData.formatID = NETCDF_DATA_FORMAT_ID;
    odeSimData.mathName = vcdId.getID();
    // read .stoch file, this funciton here equals to getODESolverRestultSet()+getStateVariableResultSet()  in ODE.
    try {
        NetCDFEvaluator ncEva = new NetCDFEvaluator();
        NetCDFReader ncReader = null;
        try {
            ncEva.setNetCDFTarget(dataFile.getAbsolutePath());
            ncReader = ncEva.getNetCDFReader();
        } catch (Exception e) {
            e.printStackTrace(System.err);
            throw new RuntimeException("Cannot open simulation result file: " + dataFile.getAbsolutePath() + "!");
        }
        // Read result according to trial number
        if (ncReader.getNumTrials() == 1) {
            // Read header
            String[] varNames = ncReader.getSpeciesNames_val();
            // first column will be time t.
            odeSimData.addDataColumn(new ODESolverResultSetColumnDescription("t"));
            // following columns are stoch variables
            for (int i = 0; i < varNames.length; i++) {
                odeSimData.addDataColumn(new ODESolverResultSetColumnDescription(varNames[i]));
            }
            // Read data
            // data only, no time points
            ArrayDouble data = (ArrayDouble) ncEva.getTimeSeriesData(1);
            double[] timePoints = ncReader.getTimePoints();
            System.out.println("time points length is " + timePoints.length);
            // shape[0]:num of timepoints, shape[1]: num of species
            int[] shape = data.getShape();
            if (// one species
            shape.length == 1) {
                ArrayDouble.D1 temData = (ArrayDouble.D1) data;
                System.out.println("one species in time series data and size is " + temData.getSize());
                for (// rows
                int k = 0; // rows
                k < timePoints.length; // rows
                k++) {
                    double[] values = new double[odeSimData.getDataColumnCount()];
                    values[0] = timePoints[k];
                    for (int i = 1; i < odeSimData.getDataColumnCount(); i++) {
                        values[i] = temData.get(k);
                    }
                    odeSimData.addRow(values);
                }
            }
            if (// more than one species
            shape.length == 2) {
                ArrayDouble.D2 temData = (ArrayDouble.D2) data;
                System.out.println("multiple species in time series, the length of time series is :" + data.getShape()[0] + ", and the total number of speceis is: " + data.getShape()[1]);
                for (// rows
                int k = 0; // rows
                k < timePoints.length; // rows
                k++) {
                    double[] values = new double[odeSimData.getDataColumnCount()];
                    values[0] = timePoints[k];
                    for (int i = 1; i < odeSimData.getDataColumnCount(); i++) {
                        values[i] = temData.get(k, i - 1);
                    }
                    odeSimData.addRow(values);
                }
            }
        } else if (ncReader.getNumTrials() > 1) {
            // Read header
            String[] varNames = ncReader.getSpeciesNames_val();
            // first column will be time t.
            odeSimData.addDataColumn(new ODESolverResultSetColumnDescription("TrialNo"));
            // following columns are stoch variables
            for (int i = 0; i < varNames.length; i++) {
                odeSimData.addDataColumn(new ODESolverResultSetColumnDescription(varNames[i]));
            }
            // Read data
            // data only, no trial numbers
            ArrayDouble data = (ArrayDouble) ncEva.getDataOverTrials(ncReader.getTimePoints().length - 1);
            int[] trialNum = ncEva.getNetCDFReader().getTrialNumbers();
            // System.out.println("total trials are "+trialNum.length);
            // shape[0]:number of trials, shape[1]: num of species
            int[] shape = data.getShape();
            if (// one species
            shape.length == 1) {
                ArrayDouble.D1 temData = (ArrayDouble.D1) data;
                // System.out.println("one species over trials, size is: "+temData.getSize());
                for (// rows
                int k = 0; // rows
                k < trialNum.length; // rows
                k++) {
                    double[] values = new double[odeSimData.getDataColumnCount()];
                    values[0] = trialNum[k];
                    for (int i = 1; i < odeSimData.getDataColumnCount(); i++) {
                        values[i] = temData.get(k);
                    }
                    odeSimData.addRow(values);
                }
            }
            if (// more than one species
            shape.length == 2) {
                ArrayDouble.D2 temData = (ArrayDouble.D2) data;
                // System.out.println("multiple species in multiple trials, the length of trials is :"+data.getShape()[0]+", and the total number of speceis is: "+data.getShape()[1]);
                for (// rows
                int k = 0; // rows
                k < trialNum.length; // rows
                k++) {
                    double[] values = new double[odeSimData.getDataColumnCount()];
                    values[0] = trialNum[k];
                    for (int i = 1; i < odeSimData.getDataColumnCount(); i++) {
                        values[i] = temData.get(k, i - 1);
                    }
                    odeSimData.addRow(values);
                }
            }
        } else {
            throw new RuntimeException("Number of trials should be a countable positive value, from 1 to N.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.err);
        throw new RuntimeException("Problem encountered in parsing hybrid simulation results.\n" + e.getMessage());
    }
    if (!odeSimData.getColumnDescriptions(0).getName().equals(SimDataConstants.HISTOGRAM_INDEX_NAME)) {
        Vector<AnnotatedFunction> funcList;
        try {
            funcList = FunctionFileGenerator.readFunctionsFile(functionsFile, vcdId.getID());
            for (AnnotatedFunction func : funcList) {
                try {
                    Expression expression = new Expression(func.getExpression());
                    odeSimData.addFunctionColumn(new FunctionColumnDescription(expression, func.getName(), null, func.getName(), false));
                } catch (ExpressionException e) {
                    throw new RuntimeException("Could not add function " + func.getName() + " to annotatedFunctionList");
                }
            }
        } catch (FileNotFoundException e1) {
            e1.printStackTrace(System.out);
            throw new DataAccessException(e1.getMessage());
        } catch (IOException e1) {
            e1.printStackTrace(System.out);
            throw new DataAccessException(e1.getMessage());
        }
    }
    return odeSimData;
}

Example 55 with AnnotatedFunction

use of cbit.vcell.solver.AnnotatedFunction in project vcell by virtualcell.

the class ChomboVtkFileWriter method getVtuVarInfos.

public VtuVarInfo[] getVtuVarInfos(ChomboFiles chomboFiles, OutputContext outputContext, VCData vcData) throws DataAccessException, IOException {
    // 
    // read the time=0 chombo dataset into memory to get the var names (probably a more efficient way of doing this).
    // 
    ChomboDataset chomboDataset;
    try {
        int timeIndex = 0;
        chomboDataset = ChomboFileReader.readDataset(chomboFiles, chomboFiles.getTimeIndices().get(timeIndex));
    } catch (Exception e) {
        throw new DataAccessException("failed to read chombo dataset: " + e.getMessage(), e);
    }
    DataIdentifier[] dataIdentifiers = vcData.getVarAndFunctionDataIdentifiers(outputContext);
    for (DataIdentifier di : dataIdentifiers) {
        System.out.println(((di.getDomain() != null) ? di.getDomain().getName() : "none") + "::" + di.getName() + "-" + di.getVariableType());
    }
    // 
    // for each ChomboDomain get list of built-in (mesh) variables, component (regular) volume variables, and Membrane Variables (still tied to the volume).
    // 
    ArrayList<VtuVarInfo> varInfos = new ArrayList<VtuVarInfo>();
    for (ChomboCombinedVolumeMembraneDomain chomboCombinedVolumeMembraneDomain : chomboDataset.getCombinedVolumeMembraneDomains()) {
        ChomboMeshData chomboMeshData = chomboCombinedVolumeMembraneDomain.getChomboMeshData();
        // 
        // process Volume variables for this combined domain (chombo stores membrane data with volume)
        // 
        {
            String volumeDomainName = chomboCombinedVolumeMembraneDomain.getVolumeDomainName();
            VariableDomain volVariableDomain = VariableDomain.VARIABLEDOMAIN_VOLUME;
            for (String builtinVarName : chomboMeshData.getVolumeBuiltinNames()) {
                String varName = builtinVarName;
                String displayName = "(" + volumeDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = true;
                varInfos.add(new VtuVarInfo(varName, displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (String componentVarName : chomboMeshData.getVisibleVolumeDataNames()) {
                String varName = componentVarName;
                String displayName = "(" + volumeDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = false;
                varInfos.add(new VtuVarInfo(varName, displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (DataIdentifier dataID : dataIdentifiers) {
                if (dataID.isVisible() && dataID.getVariableType().getVariableDomain() == VariableDomain.VARIABLEDOMAIN_VOLUME && (dataID.getDomain() == null || dataID.getDomain().getName().equals(volumeDomainName))) {
                    String displayName = "(" + volumeDomainName + ")  " + dataID.getDisplayName();
                    String expressionString = null;
                    AnnotatedFunction f = vcData.getFunction(outputContext, dataID.getName());
                    if (f != null) {
                        expressionString = f.getExpression().infix();
                    }
                    boolean bMeshVar = false;
                    varInfos.add(new VtuVarInfo(dataID.getName(), displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVar));
                }
            }
        }
        // 
        // process membrane variables for this combined domain (chombo stores membrane data with volume)
        // 
        {
            String memDomainName = chomboCombinedVolumeMembraneDomain.getMembraneDomainName();
            VariableDomain memVariableDomain = VariableDomain.VARIABLEDOMAIN_MEMBRANE;
            for (ChomboMembraneVarData membraneVarData : chomboMeshData.getMembraneVarData()) {
                String varName = membraneVarData.getName();
                String displayName = "(" + membraneVarData.getDomainName() + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = false;
                varInfos.add(new VtuVarInfo(varName, displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (String builtinVarName : chomboMeshData.getMembraneBuiltinNames()) {
                String varName = builtinVarName;
                String displayName = "(" + memDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = true;
                varInfos.add(new VtuVarInfo(varName, displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (DataIdentifier dataID : dataIdentifiers) {
                if (dataID.isVisible() && dataID.getVariableType().getVariableDomain() == VariableDomain.VARIABLEDOMAIN_MEMBRANE && (dataID.getDomain() == null || dataID.getDomain().getName().equals(memDomainName))) {
                    String displayName = "(" + memDomainName + ")  " + dataID.getDisplayName();
                    String expressionString = null;
                    AnnotatedFunction f = vcData.getFunction(outputContext, dataID.getName());
                    if (f != null) {
                        expressionString = f.getExpression().infix();
                    }
                    boolean bMeshVar = false;
                    varInfos.add(new VtuVarInfo(dataID.getName(), displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVar));
                }
            }
        }
    }
    return varInfos.toArray(new VtuVarInfo[0]);
}