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

Example 26 with FieldFunctionArguments

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

the class DataProcessingInstructions method getSampleImageFieldData.

public FieldDataIdentifierSpec getSampleImageFieldData(User user) {
    if (scriptInput != null) {
        int index = scriptInput.indexOf("SampleImage");
        StringTokenizer st = new StringTokenizer(scriptInput.substring(index));
        // SampleImage
        st.nextToken();
        // numRegions
        st.nextToken();
        if (getScriptName().equals(VFRAP)) {
            // zSlice
            st.nextToken();
        }
        // key
        String key = st.nextToken();
        index = scriptInput.indexOf(FieldFunctionDefinition.FUNCTION_name);
        if (index >= 0) {
            st = new StringTokenizer(scriptInput.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 27 with FieldFunctionArguments

use of cbit.vcell.field.FieldFunctionArguments 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 28 with FieldFunctionArguments

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

the class RunRefSimulationFastOp method getROIDataGenerator.

private ROIDataGenerator getROIDataGenerator(LocalContext localWorkspace, ROI[] rois) throws ImageException, IOException {
    // create ROI image
    short[] roiFieldData = null;
    if (rois.length > 0) {
        Origin origin = new Origin(0, 0, 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 = 0; 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
        VCImage vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ());
        RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
        CartesianMesh simpleCartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
        ExternalDataIdentifier newROIExtDataID = createNewExternalDataInfo(localWorkspace, ROI_SUMDATA_NAME).getExternalDataIdentifier();
        try {
            FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = simpleCartesianMesh;
            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(ROI_SUMDATA_NAME, ROI_SUMDATA_VARNAME, new Expression(0), VariableType.VOLUME), /*FieldFunctionArguments, sample image*/
        false);
    }
    return null;
}

Example 29 with FieldFunctionArguments

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

the class Generate2DSimBioModelOp method generateBioModel.

public BioModel generateBioModel(Extent extent, ROI cellROI_2D, double[] timeStamps, Integer indexFirstPostbleach, double primaryDiffusionRate, double primaryFraction, double bleachMonitorRate, Double secondaryDiffusionRate, double secondaryFraction, Double bindingSiteConcentration, double bindingOnRate, double bindingOffRate, String extracellularName, String cytosolName, User owner, KeyValue simKey) throws PropertyVetoException, ExpressionException, ModelException, GeometryException, ImageException, MappingException, MathException, MatrixException {
    if (owner == null) {
        throw new IllegalArgumentException("Owner is not defined");
    }
    double df = primaryDiffusionRate;
    double ff = primaryFraction;
    double bwmRate = bleachMonitorRate;
    double dc = 0.0;
    double fc = 0.0;
    if (secondaryDiffusionRate != null) {
        dc = secondaryDiffusionRate;
        fc = secondaryFraction;
    }
    double bs = 0.0;
    double onRate = 0.0;
    double offRate = 0.0;
    if (bindingSiteConcentration != null) {
        bs = bindingSiteConcentration;
        onRate = bindingOnRate;
        offRate = bindingOffRate;
    }
    // immobile fraction
    double fimm = 1 - ff - fc;
    if (fimm < epsilon && fimm > (0 - epsilon)) {
        fimm = 0;
    }
    if (fimm < (1 + epsilon) && fimm > (1 - epsilon)) {
        fimm = 1;
    }
    int startingIndexForRecovery = indexFirstPostbleach;
    TimeBounds timeBounds = new TimeBounds(0.0, timeStamps[timeStamps.length - 1] - timeStamps[startingIndexForRecovery]);
    double timeStepVal = timeStamps[startingIndexForRecovery + 1] - timeStamps[startingIndexForRecovery];
    ROI cellROI = cellROI_2D;
    int numX = cellROI.getISize().getX();
    int numY = cellROI.getISize().getY();
    int numZ = cellROI.getISize().getZ();
    short[] shortPixels = cellROI.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new IllegalArgumentException("Cell ROI has no ExtraCellular.");
    }
    String EXTRACELLULAR_NAME = extracellularName;
    String CYTOSOL_NAME = cytosolName;
    int subVolume0PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(0).setName((subVolume0PixVal == EXTRACELLULAR_PIXVAL ? EXTRACELLULAR_NAME : CYTOSOL_NAME));
    int subVolume1PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(1).setName((subVolume1PixVal == CYTOSOL_PIXVAL ? CYTOSOL_NAME : EXTRACELLULAR_NAME));
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    model.addFeature(EXTRACELLULAR_NAME);
    Feature extracellular = (Feature) model.getStructure(EXTRACELLULAR_NAME);
    model.addFeature(CYTOSOL_NAME);
    Feature cytosol = (Feature) model.getStructure(CYTOSOL_NAME);
    // Membrane mem = model.addMembrane(EXTRACELLULAR_CYTOSOL_MEM_NAME);
    // model.getStructureTopology().setInsideFeature(mem, cytosol);
    // model.getStructureTopology().setOutsideFeature(mem, extracellular);
    String roiDataName = ROI_EXTDATA_NAME;
    final int SPECIES_COUNT = 4;
    final int FREE_SPECIES_INDEX = 0;
    final int BS_SPECIES_INDEX = 1;
    final int COMPLEX_SPECIES_INDEX = 2;
    final int IMMOBILE_SPECIES_INDEX = 3;
    Expression[] diffusionConstants = null;
    Species[] species = null;
    SpeciesContext[] speciesContexts = null;
    Expression[] initialConditions = null;
    diffusionConstants = new Expression[SPECIES_COUNT];
    species = new Species[SPECIES_COUNT];
    speciesContexts = new SpeciesContext[SPECIES_COUNT];
    initialConditions = new Expression[SPECIES_COUNT];
    // total initial condition
    FieldFunctionArguments postBleach_first = new FieldFunctionArguments(roiDataName, "postbleach_first", new Expression(0), VariableType.VOLUME);
    FieldFunctionArguments prebleach_avg = new FieldFunctionArguments(roiDataName, "prebleach_avg", new Expression(0), VariableType.VOLUME);
    Expression expPostBleach_first = new Expression(postBleach_first.infix());
    Expression expPreBleach_avg = new Expression(prebleach_avg.infix());
    Expression totalIniCondition = Expression.div(expPostBleach_first, expPreBleach_avg);
    // Free Species
    diffusionConstants[FREE_SPECIES_INDEX] = new Expression(df);
    species[FREE_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_MOBILE, "Mobile bleachable species");
    speciesContexts[FREE_SPECIES_INDEX] = new SpeciesContext(null, species[FREE_SPECIES_INDEX].getCommonName(), species[FREE_SPECIES_INDEX], cytosol);
    initialConditions[FREE_SPECIES_INDEX] = Expression.mult(new Expression(ff), totalIniCondition);
    // Immobile Species (No diffusion)
    // Set very small diffusion rate on immobile to force evaluation as state variable (instead of FieldData function)
    // If left as a function errors occur because functions involving FieldData require a database connection
    final String IMMOBILE_DIFFUSION_KLUDGE = "1e-14";
    diffusionConstants[IMMOBILE_SPECIES_INDEX] = new Expression(IMMOBILE_DIFFUSION_KLUDGE);
    species[IMMOBILE_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_IMMOBILE, "Immobile bleachable species");
    speciesContexts[IMMOBILE_SPECIES_INDEX] = new SpeciesContext(null, species[IMMOBILE_SPECIES_INDEX].getCommonName(), species[IMMOBILE_SPECIES_INDEX], cytosol);
    initialConditions[IMMOBILE_SPECIES_INDEX] = Expression.mult(new Expression(fimm), totalIniCondition);
    // BS Species
    diffusionConstants[BS_SPECIES_INDEX] = new Expression(IMMOBILE_DIFFUSION_KLUDGE);
    species[BS_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_BINDING_SITE, "Binding Site species");
    speciesContexts[BS_SPECIES_INDEX] = new SpeciesContext(null, species[BS_SPECIES_INDEX].getCommonName(), species[BS_SPECIES_INDEX], cytosol);
    initialConditions[BS_SPECIES_INDEX] = Expression.mult(new Expression(bs), totalIniCondition);
    // Complex species
    diffusionConstants[COMPLEX_SPECIES_INDEX] = new Expression(dc);
    species[COMPLEX_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_SLOW_MOBILE, "Slower mobile bleachable species");
    speciesContexts[COMPLEX_SPECIES_INDEX] = new SpeciesContext(null, species[COMPLEX_SPECIES_INDEX].getCommonName(), species[COMPLEX_SPECIES_INDEX], cytosol);
    initialConditions[COMPLEX_SPECIES_INDEX] = Expression.mult(new Expression(fc), totalIniCondition);
    // add reactions to species if there is bleachWhileMonitoring rate.
    for (int i = 0; i < initialConditions.length; i++) {
        model.addSpecies(species[i]);
        model.addSpeciesContext(speciesContexts[i]);
        // reaction with BMW rate, which should not be applied to binding site
        if (!(species[i].getCommonName().equals(SPECIES_NAME_PREFIX_BINDING_SITE))) {
            SimpleReaction simpleReaction = new SimpleReaction(model, cytosol, speciesContexts[i].getName() + "_bleach", true);
            model.addReactionStep(simpleReaction);
            simpleReaction.addReactant(speciesContexts[i], 1);
            MassActionKinetics massActionKinetics = new MassActionKinetics(simpleReaction);
            simpleReaction.setKinetics(massActionKinetics);
            KineticsParameter kforward = massActionKinetics.getForwardRateParameter();
            simpleReaction.getKinetics().setParameterValue(kforward, new Expression(new Double(bwmRate)));
        }
    }
    // add the binding reaction: F + BS <-> C
    SimpleReaction simpleReaction2 = new SimpleReaction(model, cytosol, "reac_binding", true);
    model.addReactionStep(simpleReaction2);
    simpleReaction2.addReactant(speciesContexts[FREE_SPECIES_INDEX], 1);
    simpleReaction2.addReactant(speciesContexts[BS_SPECIES_INDEX], 1);
    simpleReaction2.addProduct(speciesContexts[COMPLEX_SPECIES_INDEX], 1);
    MassActionKinetics massActionKinetics = new MassActionKinetics(simpleReaction2);
    simpleReaction2.setKinetics(massActionKinetics);
    KineticsParameter kforward = massActionKinetics.getForwardRateParameter();
    KineticsParameter kreverse = massActionKinetics.getReverseRateParameter();
    simpleReaction2.getKinetics().setParameterValue(kforward, new Expression(new Double(onRate)));
    simpleReaction2.getKinetics().setParameterValue(kreverse, new Expression(new Double(offRate)));
    // create simulation context
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i]);
        scs.getInitialConditionParameter().setExpression(initialConditions[i]);
        scs.getDiffusionParameter().setExpression(diffusionConstants[i]);
    }
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    // Add total fluorescence as function of mobile(optional: and slower mobile) and immobile fractions
    mathDesc.addVariable(new Function(SPECIES_NAME_PREFIX_COMBINED, new Expression(species[FREE_SPECIES_INDEX].getCommonName() + "+" + species[COMPLEX_SPECIES_INDEX].getCommonName() + "+" + species[IMMOBILE_SPECIES_INDEX].getCommonName()), null));
    simContext.setMathDescription(mathDesc);
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, mathDesc);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getMeshSpecification().setSamplingSize(cellROI.getISize());
    // newSimulation.getSolverTaskDescription().setTimeStep(timeStep); // Sundials doesn't need time step
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    // use exp time step as output time spec
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    return bioModel;
}

Example 30 with FieldFunctionArguments

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

the class MathDescriptionDbDriver method insertMathDescExternalDataLink.

private void insertMathDescExternalDataLink(Connection con, User user, MathDescription mathDesc, KeyValue newMathDescKey) throws DataAccessException {
    try {
        ExternalDataIdentifier[] extDataIDArr = fieldDataDBOperation(con, keyFactory, user, FieldDataDBOperationSpec.createGetExtDataIDsSpec(user)).extDataIDArr;
        boolean[] bExtDataInserted = new boolean[extDataIDArr.length];
        FieldFunctionArguments[] fieldFuncArgsArr = FieldUtilities.getFieldFunctionArguments(mathDesc);
        for (int i = 0; i < fieldFuncArgsArr.length; i += 1) {
            for (int k = 0; k < extDataIDArr.length; k += 1) {
                if (!bExtDataInserted[k] && extDataIDArr[k].getName().equals(fieldFuncArgsArr[i].getFieldName())) {
                    bExtDataInserted[k] = true;
                    KeyValue newKey = keyFactory.getNewKey(con);
                    updateCleanSQL(con, "INSERT INTO " + MathDescExternalDataLinkTable.table.getTableName() + " VALUES " + MathDescExternalDataLinkTable.table.getSQLValueList(newKey, newMathDescKey, extDataIDArr[k].getKey()));
                    break;
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("Error inserting MathDescription-ExtrnalData link\n" + e.getMessage());
    }
}