Examples with FieldDataParameterVariable cbit.vcell.field.FieldDataParameterVariable used on opensource projects

Example 1 with FieldDataParameterVariable

use of cbit.vcell.field.FieldDataParameterVariable 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 2 with FieldDataParameterVariable

use of cbit.vcell.field.FieldDataParameterVariable in project vcell by virtualcell.

the class DataSetControllerImpl method evaluateFunction.

/**
 * Insert the method's description here.
 * Creation date: (10/13/00 9:13:52 AM)
 * @return cbit.vcell.simdata.SimDataBlock
 * @param user cbit.vcell.server.User
 * @param simResults cbit.vcell.simdata.SimResults
 * @param function cbit.vcell.math.Function
 * @param time double
 */
private SimDataBlock evaluateFunction(OutputContext outputContext, final VCDataIdentifier vcdID, VCData simData, AnnotatedFunction function, double time) throws ExpressionException, DataAccessException, IOException, MathException {
    Expression exp = new Expression(function.getExpression());
    exp = SolverUtilities.substituteSizeAndNormalFunctions(exp, function.getFunctionType().getVariableDomain());
    exp.bindExpression(simData);
    exp = fieldFunctionSubstitution(outputContext, vcdID, exp);
    // 
    // get Dependent datasets
    // 
    // variables are indexed by a number, t=0, x=1, y=2, z=3, a(i) = 4+i where a's are other variables
    // these variables
    // 
    CartesianMesh mesh = null;
    if (function.getFunctionType().equals(VariableType.POSTPROCESSING)) {
        mesh = ((SimulationData) simData).getPostProcessingMesh(function.getName(), outputContext);
    }
    if (mesh == null) {
        mesh = getMesh(vcdID);
    }
    String[] dependentIDs = exp.getSymbols();
    Vector<SimDataHolder> dataSetList = new Vector<SimDataHolder>();
    Vector<DataSetIdentifier> dependencyList = new Vector<DataSetIdentifier>();
    int varIndex = TXYZ_OFFSET;
    int dataLength = 0;
    long lastModified = 0;
    VariableType variableType = function.getFunctionType();
    if (variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.POSTPROCESSING)) {
        dataLength = mesh.getNumVolumeElements();
    } else if (variableType.equals(VariableType.MEMBRANE)) {
        dataLength = mesh.getNumMembraneElements();
    } else if (variableType.equals(VariableType.VOLUME_REGION)) {
        dataLength = mesh.getNumVolumeRegions();
    } else if (variableType.equals(VariableType.MEMBRANE_REGION)) {
        dataLength = mesh.getNumMembraneRegions();
    }
    VariableType computedVariableType = null;
    int computedDataLength = 0;
    for (int i = 0; dependentIDs != null && i < dependentIDs.length; i++) {
        SymbolTableEntry ste = exp.getSymbolBinding(dependentIDs[i]);
        if (ste instanceof DataSetIdentifier) {
            DataSetIdentifier dsi = (DataSetIdentifier) ste;
            dependencyList.addElement(dsi);
            dsi.setIndex(varIndex++);
            if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX) || dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                String volVarName = dsi.getName().substring(0, dsi.getName().lastIndexOf("_"));
                SimDataBlock simDataBlock = getSimDataBlock(outputContext, vcdID, volVarName, time);
                lastModified = simDataBlock.getPDEDataInfo().getTimeStamp();
                // 
                if (simDataBlock.getVariableType().equals(VariableType.VOLUME)) {
                    computedVariableType = VariableType.MEMBRANE;
                    computedDataLength = mesh.getMembraneElements().length;
                // 
                // if inside/outside volume element dependent, then can only be a membrane type
                // 
                } else if (simDataBlock.getVariableType().equals(VariableType.VOLUME_REGION) && variableType == null) {
                    computedVariableType = VariableType.MEMBRANE_REGION;
                    computedDataLength = mesh.getNumMembraneRegions();
                }
                dataSetList.addElement(simDataBlock);
            } else {
                SimDataBlock simDataBlock = getSimDataBlock(outputContext, vcdID, dsi.getName(), time);
                if (variableType == null || simDataBlock.getVariableType().isExpansionOf(variableType)) {
                    lastModified = simDataBlock.getPDEDataInfo().getTimeStamp();
                    computedDataLength = simDataBlock.getData().length;
                    computedVariableType = simDataBlock.getVariableType();
                }
                dataSetList.addElement(simDataBlock);
            }
        } else if (ste instanceof ReservedVariable) {
            ReservedVariable rv = (ReservedVariable) ste;
            if (rv.isTIME()) {
                rv.setIndex(0);
            } else if (rv.isX()) {
                rv.setIndex(1);
            } else if (rv.isY()) {
                rv.setIndex(2);
            } else if (rv.isZ()) {
                rv.setIndex(3);
            }
        } else if (ste instanceof FieldDataParameterVariable) {
            // Field Data
            ((FieldDataParameterVariable) ste).setIndex(varIndex++);
            final double[] steResampledFieldData = ((FieldDataParameterVariable) ste).getResampledFieldData();
            final VariableType newVariableType = (steResampledFieldData.length == mesh.getNumVolumeElements() ? VariableType.VOLUME : (steResampledFieldData.length == mesh.getNumMembraneElements() ? VariableType.MEMBRANE : null));
            if (newVariableType == null) {
                throw new DataAccessException("Couldn't determine VariableType for FieldData");
            }
            if (variableType != null && !variableType.equals(newVariableType)) {
                throw new DataAccessException("Incompatible VariableType for FieldData");
            }
            SimDataHolder newSimDataHolder = new SimDataHolder() {

                public double[] getData() {
                    return steResampledFieldData;
                }

                public VariableType getVariableType() {
                    return newVariableType;
                }
            };
            dataSetList.addElement(newSimDataHolder);
            dependencyList.add(new DataSetIdentifier(ste.getName(), newVariableType, ((FieldDataParameterVariable) ste).getDomain()));
            if (variableType == null) {
                computedVariableType = newVariableType;
                computedDataLength = newSimDataHolder.getData().length;
            }
        }
    }
    if (computedDataLength <= 0) {
        if (lg.isWarnEnabled())
            lg.warn("dependencies for function '" + function + "' not found, assuming datalength of volume");
        computedDataLength = mesh.getDataLength(VariableType.VOLUME);
        computedVariableType = VariableType.VOLUME;
    // try {
    // computedDataLength = mesh.getDataLength(VariableType.VOLUME);
    // computedVariableType = VariableType.VOLUME;
    // }catch (MathException e){
    // lg.error(e.getMessage(), e);
    // throw new RuntimeException("MathException, cannot determine domain for function '"+function+"'");
    // }catch (FileNotFoundException e){
    // lg.error(e.getMessage(), e);
    // throw new RuntimeException("Mesh not found, cannot determine domain for function '"+function+"'");
    // }
    }
    if (!variableType.equals(computedVariableType)) {
        System.err.println("function [" + function.getName() + "] variable type [" + variableType.getTypeName() + "] is not equal to computed variable type [" + computedVariableType.getTypeName() + "].");
    }
    if (dataLength == 0) {
        dataLength = computedDataLength;
        variableType = computedVariableType;
    }
    // 
    // Gradient Info for special processing
    // 
    boolean isGrad = hasGradient(exp);
    if (isGrad && !variableType.equals(VariableType.VOLUME)) {
        throw new DataAccessException("Gradient function is not implemented for datatype " + variableType.getTypeName());
    }
    double[] args = new double[varIndex + (isGrad ? 12 * varIndex : 0)];
    double[] data = new double[dataLength];
    // time
    args[0] = time;
    // x
    args[1] = 0.0;
    // y
    args[2] = 0.0;
    // z
    args[3] = 0.0;
    String dividedByZeroMsg = "";
    for (int i = 0; i < dataLength; i++) {
        // 
        if (variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.POSTPROCESSING)) {
            Coordinate coord = mesh.getCoordinateFromVolumeIndex(i);
            args[1] = coord.getX();
            args[2] = coord.getY();
            args[3] = coord.getZ();
            for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
                SimDataHolder simDataHolder = dataSetList.elementAt(j);
                if (simDataHolder.getVariableType().equals(VariableType.VOLUME) || simDataHolder.getVariableType().equals(VariableType.POSTPROCESSING)) {
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[i];
                } else if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION)) {
                    int volumeIndex = mesh.getVolumeRegionIndex(i);
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[volumeIndex];
                } else if (simDataHolder.getVariableType().equals(VariableType.POINT_VARIABLE)) {
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[0];
                }
            }
            if (isGrad) {
                getSpatialNeighborData(mesh, i, varIndex, time, dataSetList, args);
            }
        } else if (variableType.equals(VariableType.VOLUME_REGION)) {
            for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
                SimDataHolder simDataHolder = dataSetList.elementAt(j);
                if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION)) {
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[i];
                } else if (simDataHolder.getVariableType().equals(VariableType.POINT_VARIABLE)) {
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[0];
                }
            }
        } else if (variableType.equals(VariableType.MEMBRANE)) {
            Coordinate coord = mesh.getCoordinateFromMembraneIndex(i);
            args[1] = coord.getX();
            args[2] = coord.getY();
            args[3] = coord.getZ();
            for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
                DataSetIdentifier dsi = (DataSetIdentifier) dependencyList.elementAt(j);
                SimDataHolder simDataHolder = dataSetList.elementAt(j);
                if (simDataHolder.getVariableType().equals(VariableType.VOLUME)) {
                    if (mesh.isChomboMesh()) {
                        String varName = dsi.getName();
                        if (dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                            varName = varName.substring(0, varName.lastIndexOf(InsideVariable.INSIDE_VARIABLE_SUFFIX));
                        } else if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                            varName = varName.substring(0, varName.lastIndexOf(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX));
                        }
                        args[TXYZ_OFFSET + j] = getChomboExtrapolatedValues(vcdID, varName, time).getData()[i];
                    } else {
                        if (dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                            args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, true, false);
                        } else if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                            args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, false, false);
                        } else {
                            args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, dsi.getDomain(), i, simDataHolder, false);
                        }
                    }
                } else if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION)) {
                    if (dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                        args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, true, true);
                    } else if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                        args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, false, true);
                    } else {
                        args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, dsi.getDomain(), i, simDataHolder, true);
                    }
                } else if (simDataHolder.getVariableType().equals(VariableType.MEMBRANE)) {
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[i];
                } else if (simDataHolder.getVariableType().equals(VariableType.MEMBRANE_REGION)) {
                    int memRegionIndex = mesh.getMembraneRegionIndex(i);
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[memRegionIndex];
                } else if (simDataHolder.getVariableType().equals(VariableType.POINT_VARIABLE)) {
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[0];
                }
            }
        } else if (variableType.equals(VariableType.MEMBRANE_REGION)) {
            for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
                DataSetIdentifier dsi = (DataSetIdentifier) dependencyList.elementAt(j);
                SimDataHolder simDataHolder = dataSetList.elementAt(j);
                if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION) && dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                    // 
                    for (int k = 0; k < mesh.getMembraneElements().length; k++) {
                        if (mesh.getMembraneRegionIndex(k) == i) {
                            args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, true, true);
                            break;
                        }
                    }
                } else if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION) && dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                    // 
                    for (int k = 0; k < mesh.getMembraneElements().length; k++) {
                        if (mesh.getMembraneRegionIndex(k) == i) {
                            args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, false, true);
                            break;
                        }
                    }
                } else if (simDataHolder.getVariableType().equals(VariableType.MEMBRANE)) {
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[i];
                } else if (simDataHolder.getVariableType().equals(VariableType.MEMBRANE_REGION)) {
                    int memRegionIndex = i;
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[memRegionIndex];
                } else if (simDataHolder.getVariableType().equals(VariableType.POINT_VARIABLE)) {
                    args[TXYZ_OFFSET + j] = simDataHolder.getData()[0];
                }
            }
        }
        try {
            data[i] = exp.evaluateVector(args);
        // if(time ==0){
        // System.out.print("non-multi evalFunction ");
        // for (int m = 0; m < args.length; m++) {
        // System.out.print(args[m]);
        // }
        // System.out.println(" "+(args[args.length-2]/args[args.length-1]));
        // }
        } catch (DivideByZeroException e) {
            dividedByZeroMsg = e.getMessage();
            data[i] = Double.POSITIVE_INFINITY;
        }
    }
    if (dividedByZeroMsg.length() != 0) {
        System.out.println("DataSetControllerImpl.evaluateFunction(): DivideByZero " + dividedByZeroMsg);
    }
    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdID.getOwner(), vcdID.getID(), function.getName(), time, lastModified);
    return new SimDataBlock(pdeDataInfo, data, variableType);
}