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

Example 96 with Expression

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

the class FRAPStudy method getROIDataGenerator.

public ROIDataGenerator getROIDataGenerator(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] roiFieldData = null;
    ROI[] rois = getFrapData().getRois();
    if (rois.length > 0) {
        Extent extent = rois[0].getRoiImages()[0].getExtent();
        ISize isize = rois[0].getISize();
        int numROIX = rois[0].getISize().getX();
        int numROIY = rois[0].getISize().getY();
        roiFieldData = new short[numROIX * numROIY];
        short regionCounter = 1;
        for (int roiIdx = FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.ordinal(); roiIdx < rois.length; roiIdx++) {
            short[] roiImg = rois[roiIdx].getPixelsXYZ();
            for (int pixelIdx = 0; pixelIdx < (numROIX * numROIY); pixelIdx++) {
                if (roiImg[pixelIdx] > 0) {
                    roiFieldData[pixelIdx] = regionCounter;
                }
            }
            regionCounter++;
        }
        // create field data
        int NumTimePoints = 1;
        // 8 rois integrated into 1 image
        int NumChannels = 1;
        short[][][] pixData = new short[NumTimePoints][NumChannels][];
        pixData[0][0] = roiFieldData;
        // get extental data id
        ExternalDataIdentifier newROIExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_SUMDATA_NAME).getExternalDataIdentifier();
        CartesianMesh cartesianMesh;
        try {
            cartesianMesh = getCartesianMesh();
            Origin origin = new Origin(0, 0, 0);
            FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = cartesianMesh;
            fdos.shortSpecData = pixData;
            fdos.specEDI = newROIExtDataID;
            fdos.varNames = new String[] { "roiSumDataVar" };
            fdos.owner = LocalWorkspace.getDefaultOwner();
            fdos.times = new double[] { 0.0 };
            fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
            fdos.origin = origin;
            fdos.extent = extent;
            fdos.isize = isize;
            localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return new ROIDataGenerator(ROI_EXTDATA_NAME, /*name*/
        new int[] { 0 }, /* volumePoints*/
        new int[0], /* membranePoints*/
        regionCounter, /*numRegions*/
        0, /*zSlice*/
        newROIExtDataID.getKey(), /* fieldDataKey, sample image*/
        new FieldFunctionArguments(FRAPStudy.ROI_SUMDATA_NAME, "roiSumDataVar", new Expression(0), VariableType.VOLUME), /*FieldFunctionArguments, sample image*/
        false);
    }
    return null;
}

Example 97 with Expression

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

the class ROIDataGenerator method getSampleImageFieldData.

public FieldDataIdentifierSpec getSampleImageFieldData(User user) {
    // key
    String key = fieldDataKey.toString();
    String fieldInput = fieldFuncArguments.infix();
    StringTokenizer st = null;
    int index = fieldInput.indexOf(FieldFunctionDefinition.FUNCTION_name);
    if (index >= 0) {
        st = new StringTokenizer(fieldInput.substring(index), "\n");
        if (st.hasMoreTokens()) {
            String fieldFunction = st.nextToken();
            try {
                Expression exp = new Expression(fieldFunction);
                FieldFunctionArguments[] ffa = FieldUtilities.getFieldFunctionArguments(exp);
                return new FieldDataIdentifierSpec(ffa[0], new ExternalDataIdentifier(KeyValue.fromString(key), user, ffa[0].getFieldName()));
            } catch (ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException(e.getMessage());
            } catch (Exception e) {
                e.printStackTrace();
                throw new RuntimeException("Failed to load data processing script.");
            }
        }
    }
    return null;
}

Example 98 with Expression

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

the class ReactionDominantTest method solve.

private OptimizationResultSet solve() throws ExpressionException, IOException {
    Expression Fbleached_bleachFastExp = new Expression(Fbleached_bleachFast);
    Expression OmegaExp = new Expression(strOmega);
    Expression Omega_cExp = new Expression(strOmega_c);
    Expression WExp = new Expression(strW);
    Fbleached_bleachFastExp.substituteInPlace(OmegaExp, new Expression(Omega));
    Fbleached_bleachFastExp.substituteInPlace(Omega_cExp, new Expression(Omega_c));
    Fbleached_bleachFastExp.substituteInPlace(WExp, new Expression(W));
    Parameter[] parameters = new Parameter[] { para_alpha, para_Kon_star, para_Koff };
    // Expression Fbleached_bleachFast = Fbleached_bleachFastExp.flatten();
    // choose optimization solver, currently we have Powell and CFSQP
    PowellOptimizationSolver optService = new PowellOptimizationSolver();
    OptimizationSpec optSpec = new OptimizationSpec();
    // create simple reference data
    double[][] realData = new double[2][t.length];
    for (int i = 0; i < t.length; i++) {
        realData[0][i] = t[i];
        realData[1][i] = data_bleached[i];
    }
    String[] colNames = new String[] { "t", "intensity" };
    double[] weights = new double[] { 1.0, 1.0 };
    SimpleReferenceData refData = new SimpleReferenceData(colNames, weights, realData);
    // send to optimization service
    ExplicitFitObjectiveFunction.ExpressionDataPair oneExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(Fbleached_bleachFastExp.flatten(), 1);
    ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs = new ExplicitFitObjectiveFunction.ExpressionDataPair[] { oneExpDataPair };
    optSpec.setObjectiveFunction(new ExplicitFitObjectiveFunction(expDataPairs, refData));
    optSpec.setComputeProfileDistributions(true);
    // get the initial guess to send it to the f() function. ....
    for (int i = 0; i < parameters.length; i++) {
        optSpec.addParameter(parameters[i]);
    }
    // Parameters in OptimizationSolverSpec are solver type and objective function change tolerance.
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(OptimizationSolverSpec.SOLVERTYPE_POWELL, 0.000001);
    OptSolverCallbacks optSolverCallbacks = new DefaultOptSolverCallbacks();
    OptimizationResultSet optResultSet = null;
    optResultSet = optService.solve(optSpec, optSolverSpec, optSolverCallbacks);
    String[] paramNames = optResultSet.getOptSolverResultSet().getParameterNames();
    ArrayList<ProfileDistribution> profileDistributionList = optResultSet.getOptSolverResultSet().getProfileDistributionList();
    for (int i = 0; i < profileDistributionList.size(); i++) {
        outputProfileLikelihood(profileDistributionList.get(i), i, paramNames[i], new File(fileDir));
    }
    return optResultSet;
}

Example 99 with Expression

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

the class AbstractMathMapping method getFluxCorrectionParameter.

/**
 * This method was created in VisualAge.
 * @return Expression
 */
public KFluxParameter getFluxCorrectionParameter(StructureMapping sourceStructureMapping, StructureMapping targetStructureMapping) throws MappingException, ExpressionException {
    for (int i = 0; i < fieldMathMappingParameters.length; i++) {
        if (fieldMathMappingParameters[i] instanceof KFluxParameter) {
            KFluxParameter kfluxParameter = (KFluxParameter) fieldMathMappingParameters[i];
            if (kfluxParameter.getSourceStructureMapping() == sourceStructureMapping && kfluxParameter.getTargetStructureMapping() == targetStructureMapping) {
                return kfluxParameter;
            }
        }
    }
    // 
    // not found, add new parameter
    // 
    String sourceName = sourceStructureMapping.getStructure().getNameScope().getName();
    String targetName = targetStructureMapping.getStructure().getNameScope().getName();
    Parameter sourceSizeParameter = null;
    Parameter targetSizeParameter = null;
    if (sourceStructureMapping.getGeometryClass() instanceof CompartmentSubVolume) {
        sourceSizeParameter = sourceStructureMapping.getSizeParameter();
    } else {
        sourceSizeParameter = sourceStructureMapping.getUnitSizeParameter();
    }
    if (targetStructureMapping.getGeometryClass() instanceof CompartmentSubVolume) {
        targetSizeParameter = targetStructureMapping.getSizeParameter();
        if (targetSizeParameter == null || targetSizeParameter.getExpression() == null) {
            throw new MappingException("structure mapping sizes not set for application " + simContext.getName());
        }
    } else {
        targetSizeParameter = targetStructureMapping.getUnitSizeParameter();
    }
    Expression fluxCorrectionExp = Expression.div(new Expression(sourceSizeParameter, simContext.getNameScope()), new Expression(targetSizeParameter, simContext.getNameScope()));
    VCUnitDefinition sourceSizeUnit = sourceSizeParameter.getUnitDefinition();
    VCUnitDefinition targetSizeUnit = targetSizeParameter.getUnitDefinition();
    VCUnitDefinition unit = sourceSizeUnit.divideBy(targetSizeUnit);
    fluxCorrectionExp.bindExpression(this);
    String parameterName = PARAMETER_K_FLUX_PREFIX + sourceName + "_" + targetName;
    KFluxParameter kFluxParameter = new KFluxParameter(parameterName, fluxCorrectionExp, unit, sourceStructureMapping, targetStructureMapping);
    MathMappingParameter[] newMathMappingParameters = (MathMappingParameter[]) BeanUtils.addElement(this.fieldMathMappingParameters, kFluxParameter);
    try {
        setMathMapppingParameters(newMathMappingParameters);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
    return kFluxParameter;
}

Example 100 with Expression

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

the class AbstractMathMapping method substituteGlobalParameters.

private Expression substituteGlobalParameters(Expression exp) throws ExpressionException {
    Expression exp2 = new Expression(exp);
    // 
    // do until no more globals to substitute
    // 
    int count = 0;
    ModelParameter[] modelParams = simContext.getModel().getModelParameters();
    while (true) {
        if (count++ > 30) {
            throw new ExpressionBindingException("infinite loop in eliminating function nesting");
        }
        // 
        // get all symbols (identifiers), make list of globals used
        // 
        String[] symbols = exp2.getSymbols();
        Vector<ModelParameter> globalsVector = new Vector<ModelParameter>();
        if (symbols != null) {
            for (int i = 0; i < symbols.length; i++) {
                for (int j = 0; j < modelParams.length; j++) {
                    if (symbols[i].equals(modelParams[j].getName())) {
                        globalsVector.addElement(modelParams[j]);
                    }
                }
            }
        }
        // 
        if (globalsVector.size() == 0) {
            break;
        }
        // 
        for (int i = 0; i < globalsVector.size(); i++) {
            ModelParameter mp = globalsVector.elementAt(i);
            Expression mpExp = new Expression(mp.getName());
            exp2.substituteInPlace(mpExp, mp.getExpression());
        }
    }
    // exp2.bindExpression(simContext.getModel());
    return exp2;
}