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

Example 61 with Extent

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

the class VCellBasicCellRenderer method getTreeCellRendererComponent.

/**
 * Insert the method's description here.
 * Creation date: (7/27/2000 6:41:57 PM)
 * @return java.awt.Component
 */
public java.awt.Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    // 
    if (!leaf && expanded) {
        setIcon(fieldFolderOpenIcon);
    } else if (!leaf && !expanded) {
        setIcon(fieldFolderClosedIcon);
    }
    try {
        if (value instanceof BioModelNode) {
            BioModelNode node = (BioModelNode) value;
            boolean bLoaded = false;
            // 
            // Check if node is a SolverResultSetInfo
            // 
            Object userObject = node.getUserObject();
            if (userObject instanceof SimulationInfo) {
                // 
                // Check if node is a SimulationInfo
                // 
                setComponentProperties(component, (SimulationInfo) userObject);
                int maxErrorLevel = getMaxErrorLevel(node);
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    setIcon(fieldSimulationWarningIcon);
                    component.setToolTipText("Simulation contains possibly invalid results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    setIcon(fieldSimulationErrorIcon);
                    component.setToolTipText("Simulation contains invalid results");
                }
            } else if (userObject instanceof String && node.getChildCount() == 0) {
                component.setToolTipText(null);
                component.setText((String) userObject);
            } else if (userObject instanceof BioModelInfo) {
                // 
                // Check if node is a BioModelInfo
                // 
                setComponentProperties(component, (BioModelInfo) userObject);
                bLoaded = isLoaded((BioModelInfo) userObject);
                int maxErrorLevel = getMaxErrorLevel(node);
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    setIcon(fieldBioModelWarningIcon);
                    component.setToolTipText("BioModel version: Has possibly invalid simulation results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    setIcon(fieldBioModelErrorIcon);
                    component.setToolTipText("BioModel version: Has invalid simulation results");
                }
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof BioModelInfo) {
                // 
                // Check if node is a BioModelName (String), with children (at least one version of biomodel), and if the child is a
                // BioModelInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("BioModel");
                component.setText(label);
                // 
                // check if child is loaded
                // 
                int maxErrorLevel = BioModelNode.ERROR_NONE;
                for (int i = 0; i < node.getChildCount(); i++) {
                    maxErrorLevel = Math.max(maxErrorLevel, getMaxErrorLevel((BioModelNode) node.getChildAt(i)));
                }
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    if (!leaf && expanded) {
                        setIcon(fieldFolderOpenWarningIcon);
                    } else if (!leaf && !expanded) {
                        setIcon(fieldFolderClosedWarningIcon);
                    }
                    component.setToolTipText("BioModel: one or more versions may have invalid simulation results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    if (!leaf && expanded) {
                        setIcon(fieldFolderOpenErrorIcon);
                    } else if (!leaf && !expanded) {
                        setIcon(fieldFolderClosedErrorIcon);
                    }
                    component.setToolTipText("BioModel: one or more versions have invalid simulation results");
                }
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    BioModelInfo bioModelInfo = (BioModelInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(bioModelInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof BioModelInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (BioModel name)
                // and if the child's child is a BioModelInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof MathModelInfo) {
                // 
                // Check if node is a MathModelInfo node
                // 
                setComponentProperties(component, (MathModelInfo) userObject);
                bLoaded = isLoaded((MathModelInfo) userObject);
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof MathModelInfo) {
                // 
                // Check if node is a MathModel name (String), with children (at least one version of mathmodel), and
                // if the child is a MathModelInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("Mathematical Model");
                component.setText(label);
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    MathModelInfo mathModelInfo = (MathModelInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(mathModelInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof MathModelInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (Mathmodel name)
                // and if the child's child is a MathModelInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof cbit.vcell.geometry.GeometryInfo) {
                // 
                // Check if node is a GeometryInfo
                // 
                setComponentProperties(component, (GeometryInfo) userObject);
                bLoaded = isLoaded((GeometryInfo) userObject);
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof GeometryInfo) {
                // 
                // Check if node is a Geometry name (String), with children (at least one version of Geometry), and
                // if the child is a GeometryInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("Geometry");
                component.setText(label);
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    GeometryInfo geometryInfo = (GeometryInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(geometryInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof GeometryInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (Geometry name)
                // and if the child's child is a GeometryInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof String && node.getChildCount() > 0) {
                component.setToolTipText(null);
                component.setText((String) userObject);
            // }else if (node.getUserObject() instanceof MathInfo) {
            // setComponentProperties(component,(MathInfo)node.getUserObject());
            } else if (userObject instanceof VCImageInfo) {
                setComponentProperties(component, (VCImageInfo) userObject);
            } else if (userObject instanceof Extent) {
                setComponentProperties(component, (Extent) userObject);
            } else if (userObject instanceof Annotation) {
                setComponentProperties(component, (Annotation) userObject);
            } else if (userObject instanceof MathModel) {
                setComponentProperties(component, (MathModel) userObject);
            } else if (userObject instanceof BioModel) {
                setComponentProperties(component, (BioModel) userObject);
            } else if (userObject instanceof SimulationContext) {
                setComponentProperties(component, (SimulationContext) userObject);
                bLoaded = isLoaded((SimulationContext) userObject);
            } else if (userObject instanceof Simulation) {
                setComponentProperties(component, (Simulation) userObject);
            } else if (userObject instanceof MathDescription) {
                setComponentProperties(component, (MathDescription) userObject);
            } else if (userObject instanceof Geometry) {
                setComponentProperties(component, (Geometry) userObject);
            } else if (userObject instanceof User) {
                setComponentProperties(component, (User) userObject);
            } else {
                setComponentProperties(component, userObject);
            }
            if (selectedFont == null && component.getFont() != null) {
                selectedFont = component.getFont().deriveFont(Font.BOLD);
            }
            if (unselectedFont == null && component.getFont() != null) {
                unselectedFont = component.getFont().deriveFont(Font.PLAIN);
            }
            if (bLoaded) {
                component.setFont(selectedFont);
            } else {
                component.setFont(unselectedFont);
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    return component;
}

Example 62 with Extent

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

the class GeometrySpec method setExtent.

/**
 * This method was created by a SmartGuide.
 * @param x double
 * @param y double
 */
public void setExtent(Extent aExtent) throws PropertyVetoException {
    if (!this.extent.compareEqual(aExtent)) {
        Extent oldExtent = this.extent;
        fireVetoableChange("extent", oldExtent, extent);
        // 
        if (vcImage != null) {
            vcImage.setExtent(aExtent);
        }
        this.extent = aExtent;
        firePropertyChange("extent", oldExtent, getExtent());
    }
    return;
}

Example 63 with Extent

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

the class FRAPStudy method getCartesianMesh.

public CartesianMesh getCartesianMesh() throws Exception {
    CartesianMesh cartesianMesh = null;
    ImageDataset imgDataSet = getFrapData().getImageDataset();
    Extent extent = imgDataSet.getExtent();
    ISize isize = imgDataSet.getISize();
    Origin origin = new Origin(0, 0, 0);
    if (getBioModel() == null) {
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
    } else {
        RegionImage regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        if (regionImage == null) {
            getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().updateAll();
            regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        }
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    }
    return cartesianMesh;
}

Example 64 with Extent

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

the class FRAPStudy method createNewSimBioModel.

public static BioModel createNewSimBioModel(FRAPStudy sourceFrapStudy, Parameter[] params, TimeStep tStep, KeyValue simKey, User owner, 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());
    double df = params[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess();
    double ff = params[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess();
    double bwmRate = params[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess();
    double dc = 0;
    double fc = 0;
    double bs = 0;
    double onRate = 0;
    double offRate = 0;
    if (params.length == FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF) {
        dc = params[FRAPModel.INDEX_SECONDARY_DIFF_RATE].getInitialGuess();
        fc = params[FRAPModel.INDEX_SECONDARY_FRACTION].getInitialGuess();
    } else if (params.length == FRAPModel.NUM_MODEL_PARAMETERS_BINDING) {
        dc = params[FRAPModel.INDEX_SECONDARY_DIFF_RATE].getInitialGuess();
        fc = params[FRAPModel.INDEX_SECONDARY_FRACTION].getInitialGuess();
        bs = params[FRAPModel.INDEX_BINDING_SITE_CONCENTRATION].getInitialGuess();
        onRate = params[FRAPModel.INDEX_ON_RATE].getInitialGuess();
        offRate = params[FRAPModel.INDEX_OFF_RATE].getInitialGuess();
    }
    // immobile fraction
    double fimm = 1 - ff - fc;
    if (fimm < FRAPOptimizationUtils.epsilon && fimm > (0 - FRAPOptimizationUtils.epsilon)) {
        fimm = 0;
    }
    if (fimm < (1 + FRAPOptimizationUtils.epsilon) && fimm > (1 - FRAPOptimizationUtils.epsilon)) {
        fimm = 1;
    }
    Extent extent = sourceFrapStudy.getFrapData().getImageDataset().getExtent();
    double[] timeStamps = sourceFrapStudy.getFrapData().getImageDataset().getImageTimeStamps();
    TimeBounds timeBounds = new TimeBounds(0.0, timeStamps[timeStamps.length - 1] - timeStamps[startingIndexForRecovery]);
    double timeStepVal = timeStamps[startingIndexForRecovery + 1] - timeStamps[startingIndexForRecovery];
    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);
    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 = FRAPStudy.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(FRAPStudy.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(FRAPStudy.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(FRAPStudy.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(FRAPStudy.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(FRAPStudy.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);
    // Membrane plasmaMembrane = model.getStructureTopology().getMembrane(cytosol, 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));
    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(FRAPStudy.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_2D.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 65 with Extent

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

the class FRAPStudy method getPSFFieldData.

public static FieldDataIdentifierSpec getPSFFieldData(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] psfFieldData = null;
    psfFieldData = new short[9];
    psfFieldData[4] = (short) 1;
    // create field data
    int NumTimePoints = 1;
    // 8 rois integrated into 1 image
    int NumChannels = 1;
    short[][][] pixData = new short[NumTimePoints][NumChannels][1];
    pixData[0][0] = psfFieldData;
    // get extental data id
    ExternalDataIdentifier newPsfExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.PSF_DATA_NAME).getExternalDataIdentifier();
    CartesianMesh cartesianMesh;
    try {
        Origin origin = new Origin(0, 0, 0);
        Extent ext = new Extent(1, 1, 1);
        ISize isize = new ISize(3, 3, 1);
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, ext, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], ext, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
        FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
        fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
        fdos.cartesianMesh = cartesianMesh;
        fdos.shortSpecData = pixData;
        fdos.specEDI = newPsfExtDataID;
        fdos.varNames = new String[] { "psfVar" };
        fdos.owner = LocalWorkspace.getDefaultOwner();
        fdos.times = new double[] { 0.0 };
        fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
        fdos.origin = origin;
        fdos.extent = ext;
        fdos.isize = isize;
        localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        FieldFunctionArguments psfFieldFunc = new FieldFunctionArguments(PSF_DATA_NAME, "psfVar", new Expression(0.0), VariableType.VOLUME);
        FieldDataIdentifierSpec fdis = new FieldDataIdentifierSpec(psfFieldFunc, newPsfExtDataID);
        return fdis;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return null;
    }
}