Examples with Extent org.vcell.util.Extent used on opensource projects

Example 6 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class ChomboMeshValidator method main.

public static void main(String[] args) {
    int blockFactor = 4;
    // Extent[] extents2D = new Extent[] { new Extent(1, 1, 1), new Extent(2, 3, 1), new Extent(5.00001, 2.5, 1) };
    // for (Extent extent : extents2D) {
    // ChomboMeshValidator validator = new ChomboMeshValidator(2, extent, blockFactor);
    // ChomboMeshRecommendation chomboMeshRecommendation = validator.computeMeshSpecs();
    // System.out.println("==Test Case 2D==" + validator);
    // for (ChomboMeshSpec ms : chomboMeshRecommendation.validMeshSpecList) {
    // System.out.println(ms);
    // }
    // }
    Extent[] extents3D = new Extent[] { new Extent(158, 34, 4) };
    for (Extent extent : extents3D) {
        ChomboMeshValidator validator = new ChomboMeshValidator(3, extent, blockFactor);
        ChomboMeshRecommendation chomboMeshRecommendation = validator.computeMeshSpecs();
        System.out.println("==Test Case 3D==" + validator);
        System.out.println(chomboMeshRecommendation);
    }
}

Example 7 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class SimulationContext method refreshCharacteristicSize.

/**
 * This method was created in VisualAge.
 * @return java.lang.Double
 */
private void refreshCharacteristicSize() throws PropertyVetoException {
    Geometry geo = getGeometryContext().getGeometry();
    int dimension = geo.getDimension();
    if (dimension == 0) {
        setCharacteristicSize(null);
        return;
    }
    Extent extent = geo.getExtent();
    if (characteristicSize == null) {
        // 
        // if characteristicSize is not specified, estimate a 'good' value
        // 
        VCImage image = geo.getGeometrySpec().getImage();
        if (image != null) {
            double pixelSizeX = extent.getX() / image.getNumX();
            double pixelSizeY = extent.getY() / image.getNumY();
            double pixelSizeZ = extent.getZ() / image.getNumZ();
            switch(dimension) {
                case 1:
                    {
                        setCharacteristicSize(new Double(pixelSizeX));
                        break;
                    }
                case 2:
                    {
                        setCharacteristicSize(new Double(Math.min(pixelSizeX, pixelSizeY)));
                        break;
                    }
                case 3:
                    {
                        setCharacteristicSize(new Double(Math.min(pixelSizeX, Math.min(pixelSizeY, pixelSizeZ))));
                        break;
                    }
                default:
                    {
                        throw new RuntimeException("unexpected geometry dimension = '" + dimension + "'");
                    }
            }
        } else {
            // 
            // image doesn't exist, apply heuristics
            // 
            // 
            // 
            // choose spatial steps to give reasonable size mesh ( < MaxNumberElements)
            // 
            // start with very small elements (~0.01 * smallest dimension)
            // 
            // if number of elements exceed 100,000 then take larger steps
            // 
            long MaxNumberElements = 1000000;
            long MaxPerDimension = 500;
            long totalElements = MaxNumberElements + 1;
            double elementLength = Math.min(extent.getX(), Math.min(extent.getY(), extent.getZ())) / (MaxPerDimension);
            while (true) {
                // 
                // calculate total elements based on characteristic length
                // 
                int numY = -1;
                int numZ = -1;
                int numX = (int) Math.round(extent.getX() / elementLength);
                if (dimension > 1) {
                    numY = (int) Math.round(extent.getY() / elementLength);
                } else {
                    numY = 1;
                }
                if (dimension > 2) {
                    numZ = (int) Math.round(extent.getZ() / elementLength);
                } else {
                    numZ = 1;
                }
                totalElements = numX * numY * numZ;
                if ((numX <= MaxPerDimension) && (numY <= MaxPerDimension) && (numZ <= MaxPerDimension) && (totalElements <= MaxNumberElements)) {
                    break;
                } else {
                    elementLength *= 1.125;
                }
            }
            setCharacteristicSize(new Double(elementLength));
        }
    }
}

Example 8 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class FRAPStudy method createNewRefBioModel.

public static BioModel createNewRefBioModel(FRAPStudy sourceFrapStudy, String baseDiffusionRate, TimeStep tStep, KeyValue simKey, User owner, FieldDataIdentifierSpec psfFDIS, int startingIndexForRecovery) throws Exception {
    if (owner == null) {
        throw new Exception("Owner is not defined");
    }
    ROI cellROI_2D = sourceFrapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    Extent extent = sourceFrapStudy.getFrapData().getImageDataset().getExtent();
    TimeBounds timeBounds = FRAPOptData.getEstimatedRefTimeBound(sourceFrapStudy);
    double timeStepVal = FRAPOptData.REFERENCE_DIFF_DELTAT;
    int numX = cellROI_2D.getRoiImages()[0].getNumX();
    int numY = cellROI_2D.getRoiImages()[0].getNumY();
    int numZ = cellROI_2D.getRoiImages().length;
    short[] shortPixels = cellROI_2D.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 Exception("Cell ROI has no ExtraCellular.");
    }
    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);
    Feature extracellular = model.addFeature(EXTRACELLULAR_NAME);
    Feature cytosol = model.addFeature(CYTOSOL_NAME);
    Membrane plasmaMembrane = model.addMembrane(PLASMAMEMBRANE_NAME);
    String roiDataName = FRAPStudy.ROI_EXTDATA_NAME;
    final int ONE_DIFFUSION_SPECIES_COUNT = 1;
    final int MOBILE_SPECIES_INDEX = 0;
    Expression[] diffusionConstants = new Expression[ONE_DIFFUSION_SPECIES_COUNT];
    Species[] species = new Species[ONE_DIFFUSION_SPECIES_COUNT];
    SpeciesContext[] speciesContexts = new SpeciesContext[ONE_DIFFUSION_SPECIES_COUNT];
    Expression[] initialConditions = new Expression[ONE_DIFFUSION_SPECIES_COUNT];
    // Mobile Species
    diffusionConstants[MOBILE_SPECIES_INDEX] = new Expression(baseDiffusionRate);
    species[MOBILE_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_MOBILE, "Mobile bleachable species");
    speciesContexts[MOBILE_SPECIES_INDEX] = new SpeciesContext(null, species[MOBILE_SPECIES_INDEX].getCommonName(), species[MOBILE_SPECIES_INDEX], cytosol);
    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());
    initialConditions[MOBILE_SPECIES_INDEX] = Expression.div(expPostBleach_first, expPreBleach_avg);
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    MembraneMapping plasmaMembraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(plasmaMembrane);
    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);
    plasmaMembraneMapping.setGeometryClass(pmSurfaceClass);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    plasmaMembraneMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    for (int i = 0; i < initialConditions.length; i++) {
        model.addSpecies(species[i]);
        model.addSpeciesContext(speciesContexts[i]);
    }
    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 PSF function
    mathDesc.addVariable(new Function(Simulation.PSF_FUNCTION_NAME, new Expression(psfFDIS.getFieldFuncArgs().infix()), 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, simContext.getMathDescription());
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
    newSimulation.getSolverTaskDescription().setTimeStep(new TimeStep(timeStepVal, timeStepVal, timeStepVal));
    return bioModel;
}

Example 9 with Extent

use of org.vcell.util.Extent 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 10 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class FRAPData method changeImageExtent.

public void changeImageExtent(double imageSizeX, double imageSizeY) {
    double imageSizeZ = getImageDataset().getExtent().getZ();
    getImageDataset().setExtent(new Extent(imageSizeX, imageSizeY, imageSizeZ));
}