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

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Example 6 with ReservedVariable

use of cbit.vcell.math.ReservedVariable 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);
}
Also used : VariableType(cbit.vcell.math.VariableType) DivideByZeroException(cbit.vcell.parser.DivideByZeroException) CartesianMesh(cbit.vcell.solvers.CartesianMesh) SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry) ReservedVariable(cbit.vcell.math.ReservedVariable) Expression(cbit.vcell.parser.Expression) Coordinate(org.vcell.util.Coordinate) Vector(java.util.Vector) DataAccessException(org.vcell.util.DataAccessException) FieldDataParameterVariable(cbit.vcell.field.FieldDataParameterVariable)

Aggregations

ReservedVariable (cbit.vcell.math.ReservedVariable)6 SymbolTableEntry (cbit.vcell.parser.SymbolTableEntry)6 Expression (cbit.vcell.parser.Expression)3 Vector (java.util.Vector)3 KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)2 ModelParameter (cbit.vcell.model.Model.ModelParameter)2 SpeciesContext (cbit.vcell.model.SpeciesContext)2 FieldDataParameterVariable (cbit.vcell.field.FieldDataParameterVariable)1 GeometryClass (cbit.vcell.geometry.GeometryClass)1 SubVolume (cbit.vcell.geometry.SubVolume)1 SurfaceClass (cbit.vcell.geometry.SurfaceClass)1 Equation (cbit.vcell.math.Equation)1 InsideVariable (cbit.vcell.math.InsideVariable)1 MemVariable (cbit.vcell.math.MemVariable)1 MembraneRegionVariable (cbit.vcell.math.MembraneRegionVariable)1 MembraneSubDomain (cbit.vcell.math.MembraneSubDomain)1 OutsideVariable (cbit.vcell.math.OutsideVariable)1 PdeEquation (cbit.vcell.math.PdeEquation)1 SubDomain (cbit.vcell.math.SubDomain)1 Variable (cbit.vcell.math.Variable)1
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