Examples with Geometry cbit.vcell.geometry.Geometry used on opensource projects

Example 1 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class SmoldynFileWriter method writeCompartments.

private void writeCompartments() throws ImageException, PropertyVetoException, GeometryException, ExpressionException {
    MeshSpecification meshSpecification = simulation.getMeshSpecification();
    ISize sampleSize = meshSpecification.getSamplingSize();
    int numX = sampleSize.getX();
    int numY = dimension < 2 ? 1 : sampleSize.getY();
    int numZ = dimension < 3 ? 1 : sampleSize.getZ();
    int numXY = numX * numY;
    boolean bCellCentered = simulation.hasCellCenteredMesh();
    double dx = meshSpecification.getDx(bCellCentered);
    double dy = meshSpecification.getDy(bCellCentered);
    double dz = meshSpecification.getDz(bCellCentered);
    Origin origin = resampledGeometry.getGeometrySpec().getOrigin();
    printWriter.println("# compartments");
    resampledGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
    for (SubVolume subVolume : resampledGeometry.getGeometrySpec().getSubVolumes()) {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_compartment + " " + subVolume.getName());
        for (SurfaceClass sc : resampledGeometry.getGeometrySurfaceDescription().getSurfaceClasses()) {
            if (sc.getAdjacentSubvolumes().contains(subVolume)) {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.surface + " " + sc.getName());
            }
        }
        if (boundaryXSubVolumes.contains(subVolume)) {
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_X);
        }
        if (dimension > 1) {
            if (boundaryYSubVolumes.contains(subVolume)) {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Y);
            }
            if (dimension > 2) {
                if (boundaryZSubVolumes.contains(subVolume)) {
                    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Z);
                }
            }
        }
        // if (DEBUG) {
        // tmppw.println("points" + pointsCount + "=[");
        // pointsCount ++;
        // }
        // gather all the points in all the regions
        Geometry interiorPointGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), resampledGeometry, resampledGeometry.getGeometrySurfaceDescription().getVolumeSampleSize());
        SubVolume interiorPointSubVolume = interiorPointGeometry.getGeometrySpec().getSubVolume(subVolume.getName());
        GeometricRegion[] geometricRegions = interiorPointGeometry.getGeometrySurfaceDescription().getGeometricRegions(interiorPointSubVolume);
        RegionInfo[] regionInfos = interiorPointGeometry.getGeometrySurfaceDescription().getRegionImage().getRegionInfos();
        for (GeometricRegion geometricRegion : geometricRegions) {
            VolumeGeometricRegion volumeGeometricRegion = (VolumeGeometricRegion) geometricRegion;
            ArrayList<SelectPoint> selectPointList = new ArrayList<SelectPoint>();
            for (RegionInfo regionInfo : regionInfos) {
                if (regionInfo.getRegionIndex() != volumeGeometricRegion.getRegionID()) {
                    continue;
                }
                int volIndex = 0;
                for (int k = 0; k < numZ; k++) {
                    for (int j = 0; j < numY; j++) {
                        int starti = -1;
                        int endi = 0;
                        for (int i = 0; i < numX; i++, volIndex++) {
                            boolean bInRegion = false;
                            if (regionInfo.isIndexInRegion(volIndex)) {
                                bInRegion = true;
                                if (starti == -1) {
                                    starti = i;
                                    endi = i;
                                } else {
                                    endi++;
                                }
                            }
                            if ((!bInRegion || i == numX - 1) && starti != -1) {
                                int midi = (endi + starti) / 2;
                                int midVolIndex = k * numXY + j * numX + midi;
                                boolean bOnBoundary = false;
                                int[] neighbors = { j == 0 ? -1 : midVolIndex - numX, j == numY - 1 ? -1 : midVolIndex + numX, k == 0 ? -1 : midVolIndex - numXY, k == numZ - 1 ? -1 : midVolIndex + numXY };
                                for (int n = 0; n < 2 * (dimension - 1); n++) {
                                    if (neighbors[n] == -1 || !regionInfo.isIndexInRegion(neighbors[n])) {
                                        bOnBoundary = true;
                                        break;
                                    }
                                }
                                if (!bOnBoundary) {
                                    selectPointList.add(new SelectPoint(starti, endi, j, k));
                                }
                                starti = -1;
                            }
                        }
                    // end i
                    }
                // end j
                }
            // end k
            }
            for (int m = 0; m < selectPointList.size(); m++) {
                SelectPoint thisPoint = selectPointList.get(m);
                boolean bPrint = true;
                for (int n = 0; n < selectPointList.size(); n++) {
                    if (n == m) {
                        continue;
                    }
                    SelectPoint point = selectPointList.get(n);
                    if (thisPoint.k == point.k && Math.abs(thisPoint.j - point.j) == 1 || thisPoint.j == point.j && Math.abs(thisPoint.k - point.k) == 1) {
                        if (point.same(thisPoint) && m < n) {
                            // found same one later, print the later one
                            bPrint = false;
                            break;
                        }
                        if (point.contains(thisPoint) && point.length() < 2 * thisPoint.length()) {
                            // found a longer one, but not too much longer
                            bPrint = false;
                            break;
                        }
                    }
                }
                if (bPrint) {
                    int midi = (thisPoint.starti + thisPoint.endi) / 2;
                    double coordX = origin.getX() + dx * midi;
                    printWriter.print(SmoldynVCellMapper.SmoldynKeyword.point + " " + coordX);
                    if (dimension > 1) {
                        double coordY = origin.getY() + dy * thisPoint.j;
                        printWriter.print(" " + coordY);
                        if (dimension > 2) {
                            double coordZ = origin.getZ() + dz * thisPoint.k;
                            printWriter.print(" " + coordZ);
                        }
                    }
                    printWriter.println();
                }
            }
        }
        // end for (GeometricRegion
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_compartment);
        printWriter.println();
    }
// end for (SubVolume
}

Example 2 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class SmoldynFileWriter method init.

private void init() throws SolverException {
    simulation = simTask.getSimulation();
    mathDesc = simulation.getMathDescription();
    simulationSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    particleVariableList = new ArrayList<ParticleVariable>();
    Variable[] variables = simulationSymbolTable.getVariables();
    for (Variable variable : variables) {
        if (variable instanceof ParticleVariable) {
            if (variable.getDomain() == null) {
                throw new SolverException("Particle Variables are required to be defined in a subdomain using syntax Subdomain::Variable.");
            }
            particleVariableList.add((ParticleVariable) variable);
        }
    }
    // write geometry
    Geometry geometry = mathDesc.getGeometry();
    dimension = geometry.getDimension();
    try {
        // clone and resample geometry
        resampledGeometry = (Geometry) BeanUtils.cloneSerializable(geometry);
        GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
        ISize newSize = simulation.getMeshSpecification().getSamplingSize();
        geoSurfaceDesc.setVolumeSampleSize(newSize);
        geoSurfaceDesc.updateAll();
        bHasNoSurface = geoSurfaceDesc.getSurfaceClasses() == null || geoSurfaceDesc.getSurfaceClasses().length == 0;
    } catch (Exception e) {
        e.printStackTrace();
        throw new SolverException(e.getMessage());
    }
    if (!bGraphicOpenGL) {
        writeMeshFile();
    }
    colors = ColorUtil.generateAutoColor(particleVariableList.size() + resampledGeometry.getGeometrySurfaceDescription().getSurfaceClasses().length, bg, new Integer(5));
}

Example 3 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class SBMLImporter method getBioModel.

// /**
// * @ TODO: This method doesn't take care of adjusting species in nested
// parameter rules with the species_concetration_factor.
// * @param kinetics
// * @param paramExpr
// * @throws ExpressionException
// */
// private void substituteOtherGlobalParams(Kinetics kinetics, Expression
// paramExpr) throws ExpressionException, PropertyVetoException {
// String[] exprSymbols = paramExpr.getSymbols();
// if (exprSymbols == null || exprSymbols.length == 0) {
// return;
// }
// Model vcModel = vcBioModel.getSimulationContext(0).getModel();
// for (int kk = 0; kk < exprSymbols.length; kk++) {
// ModelParameter mp = vcModel.getModelParameter(exprSymbols[kk]);
// if (mp != null) {
// Expression expr = mp.getExpression();
// if (expr != null) {
// Expression newExpr = new Expression(expr);
// substituteGlobalParamRulesInPlace(newExpr, false);
// // param has constant value, add it as a kinetic parameter if it is not
// already in the kinetics
// kinetics.setParameterValue(exprSymbols[kk], newExpr.infix());
// kinetics.getKineticsParameter(exprSymbols[kk]).setUnitDefinition(getSBMLUnit(sbmlModel.getParameter(exprSymbols[kk]).getUnits(),
// null));
// if (newExpr.getSymbols() != null) {
// substituteOtherGlobalParams(kinetics, newExpr);
// }
// }
// }
// }
// }
/**
 * parse SBML file into biomodel logs errors to log4j if present in source
 * document
 *
 * @return new Biomodel
 * @throws IOException
 * @throws XMLStreamException
 */
public BioModel getBioModel() throws XMLStreamException, IOException {
    SBMLDocument document;
    String output = "didn't check";
    try {
        if (sbmlFileName != null) {
            // Read SBML model into libSBML SBMLDocument and create an SBML model
            SBMLReader reader = new SBMLReader();
            document = reader.readSBML(sbmlFileName);
            // document.checkConsistencyOffline();
            // long numProblems = document.getNumErrors();
            // 
            // System.out.println("\n\nSBML Import Error Report");
            // ByteArrayOutputStream os = new ByteArrayOutputStream();
            // PrintStream ps = new PrintStream(os);
            // document.printErrors(ps);
            // String output = os.toString();
            // if (numProblems > 0 && lg.isEnabledFor(Level.WARN)) {
            // lg.warn("Num problems in original SBML document : " + numProblems);
            // lg.warn(output);
            // }
            sbmlModel = document.getModel();
            if (sbmlModel == null) {
                throw new SBMLImportException("Unable to read SBML file : \n" + output);
            }
        } else {
            if (sbmlModel == null) {
                throw new IllegalStateException("Expected non-null SBML model");
            }
            document = sbmlModel.getSBMLDocument();
        }
        // Convert SBML Model to VCell model
        // An SBML model will correspond to a simcontext - which needs a
        // Model and a Geometry
        // SBML handles only nonspatial geometries at this time, hence
        // creating a non-spatial default geometry
        String modelName = sbmlModel.getId();
        if (modelName == null || modelName.trim().equals("")) {
            modelName = sbmlModel.getName();
        }
        // name, say 'newModel'
        if (modelName == null || modelName.trim().equals("")) {
            modelName = "newModel";
        }
        // get namespace based on SBML model level and version to use in
        // SBMLAnnotationUtil
        this.level = sbmlModel.getLevel();
        // this.version = sbmlModel.getVersion();
        String ns = document.getNamespace();
        try {
            // create SBML unit system for the model and create the bioModel.
            ModelUnitSystem modelUnitSystem;
            try {
                modelUnitSystem = createSBMLUnitSystemForVCModel();
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SBMLImportException("Inconsistent unit system. Cannot import SBML model into VCell", Category.INCONSISTENT_UNIT, e);
            }
            Geometry geometry = new Geometry(BioModelChildSummary.COMPARTMENTAL_GEO_STR, 0);
            vcBioModel = new BioModel(null, modelUnitSystem);
            SimulationContext simulationContext = new SimulationContext(vcBioModel.getModel(), geometry, null, null, Application.NETWORK_DETERMINISTIC);
            vcBioModel.addSimulationContext(simulationContext);
            simulationContext.setName(vcBioModel.getSimulationContext(0).getModel().getName());
        // vcBioModel.getSimulationContext(0).setName(vcBioModel.getSimulationContext(0).getModel().getName()+"_"+vcBioModel.getSimulationContext(0).getGeometry().getName());
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new SBMLImportException("Could not create simulation context corresponding to the input SBML model", e);
        }
        // SBML annotation
        sbmlAnnotationUtil = new SBMLAnnotationUtil(vcBioModel.getVCMetaData(), vcBioModel, ns);
        translateSBMLModel();
        try {
            // **** TEMPORARY BLOCK - to name the biomodel with proper name,
            // rather than model id
            String biomodelName = sbmlModel.getName();
            // if name is not set, use id
            if ((biomodelName == null) || biomodelName.trim().equals("")) {
                biomodelName = sbmlModel.getId();
            }
            // if id is not set, use a default, say, 'newModel'
            if ((biomodelName == null) || biomodelName.trim().equals("")) {
                biomodelName = "newBioModel";
            }
            vcBioModel.setName(biomodelName);
        // **** end - TEMPORARY BLOCK
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new SBMLImportException("Could not create Biomodel", e);
        }
        sbmlAnnotationUtil.readAnnotation(vcBioModel, sbmlModel);
        sbmlAnnotationUtil.readNotes(vcBioModel, sbmlModel);
        vcBioModel.refreshDependencies();
        Issue[] warningIssues = localIssueList.toArray(new Issue[localIssueList.size()]);
        if (warningIssues != null && warningIssues.length > 0) {
            StringBuffer messageBuffer = new StringBuffer("Issues encountered during SBML Import:\n");
            int issueCount = 0;
            for (int i = 0; i < warningIssues.length; i++) {
                if (warningIssues[i].getSeverity() == Issue.SEVERITY_WARNING || warningIssues[i].getSeverity() == Issue.SEVERITY_INFO) {
                    messageBuffer.append(warningIssues[i].getCategory() + " " + warningIssues[i].getSeverityName() + " : " + warningIssues[i].getMessage() + "\n");
                    issueCount++;
                }
            }
            if (issueCount > 0) {
                try {
                    logger.sendMessage(VCLogger.Priority.MediumPriority, VCLogger.ErrorType.OverallWarning, messageBuffer.toString());
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                }
            // PopupGenerator.showWarningDialog(requester,messageBuffer.toString(),new
            // String[] { "OK" }, "OK");
            }
        }
    } catch (Exception e) {
        throw new SBMLImportException("Unable to read SBML file : \n" + output, e);
    }
    return vcBioModel;
}

Example 4 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class SBMLImporter method addGeometry.

protected void addGeometry() {
    // get a Geometry object via SpatialModelPlugin object.
    org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = getSbmlGeometry();
    if (sbmlGeometry == null) {
        return;
    }
    int dimension = 0;
    Origin vcOrigin = null;
    Extent vcExtent = null;
    {
        // local code block
        // get a CoordComponent object via the Geometry object.
        ListOf<CoordinateComponent> listOfCoordComps = sbmlGeometry.getListOfCoordinateComponents();
        if (listOfCoordComps == null) {
            throw new RuntimeException("Cannot have 0 coordinate compartments in geometry");
        }
        // coord component
        double ox = 0.0;
        double oy = 0.0;
        double oz = 0.0;
        double ex = 1.0;
        double ey = 1.0;
        double ez = 1.0;
        for (CoordinateComponent coordComponent : listOfCoordComps) {
            double minValue = coordComponent.getBoundaryMinimum().getValue();
            double maxValue = coordComponent.getBoundaryMaximum().getValue();
            switch(coordComponent.getType()) {
                case cartesianX:
                    {
                        ox = minValue;
                        ex = maxValue - minValue;
                        break;
                    }
                case cartesianY:
                    {
                        oy = minValue;
                        ey = maxValue - minValue;
                        break;
                    }
                case cartesianZ:
                    {
                        oz = minValue;
                        ez = maxValue - minValue;
                        break;
                    }
            }
            dimension++;
        }
        vcOrigin = new Origin(ox, oy, oz);
        vcExtent = new Extent(ex, ey, ez);
    }
    // from geometry definition, find out which type of geometry : image or
    // analytic or CSG
    AnalyticGeometry analyticGeometryDefinition = null;
    CSGeometry csGeometry = null;
    SampledFieldGeometry segmentedSampledFieldGeometry = null;
    SampledFieldGeometry distanceMapSampledFieldGeometry = null;
    ParametricGeometry parametricGeometry = null;
    for (int i = 0; i < sbmlGeometry.getListOfGeometryDefinitions().size(); i++) {
        GeometryDefinition gd_temp = sbmlGeometry.getListOfGeometryDefinitions().get(i);
        if (!gd_temp.isSetIsActive()) {
            continue;
        }
        if (gd_temp instanceof AnalyticGeometry) {
            analyticGeometryDefinition = (AnalyticGeometry) gd_temp;
        } else if (gd_temp instanceof SampledFieldGeometry) {
            SampledFieldGeometry sfg = (SampledFieldGeometry) gd_temp;
            String sfn = sfg.getSampledField();
            ListOf<SampledField> sampledFields = sbmlGeometry.getListOfSampledFields();
            if (sampledFields.size() > 1) {
                throw new RuntimeException("only one sampled field supported");
            }
            InterpolationKind ik = sampledFields.get(0).getInterpolationType();
            switch(ik) {
                case linear:
                    distanceMapSampledFieldGeometry = sfg;
                    break;
                case nearestneighbor:
                    segmentedSampledFieldGeometry = sfg;
                    break;
                default:
                    lg.warn("Unsupported " + sampledFields.get(0).getName() + " interpolation type " + ik);
            }
        } else if (gd_temp instanceof CSGeometry) {
            csGeometry = (CSGeometry) gd_temp;
        } else if (gd_temp instanceof ParametricGeometry) {
            parametricGeometry = (ParametricGeometry) gd_temp;
        } else {
            throw new RuntimeException("unsupported geometry definition type " + gd_temp.getClass().getSimpleName());
        }
    }
    if (analyticGeometryDefinition == null && segmentedSampledFieldGeometry == null && distanceMapSampledFieldGeometry == null && csGeometry == null) {
        throw new SBMLImportException("VCell supports only Analytic, Image based (segmentd or distance map) or Constructed Solid Geometry at this time.");
    }
    GeometryDefinition selectedGeometryDefinition = null;
    if (csGeometry != null) {
        selectedGeometryDefinition = csGeometry;
    } else if (analyticGeometryDefinition != null) {
        selectedGeometryDefinition = analyticGeometryDefinition;
    } else if (segmentedSampledFieldGeometry != null) {
        selectedGeometryDefinition = segmentedSampledFieldGeometry;
    } else if (distanceMapSampledFieldGeometry != null) {
        selectedGeometryDefinition = distanceMapSampledFieldGeometry;
    } else if (parametricGeometry != null) {
        selectedGeometryDefinition = parametricGeometry;
    } else {
        throw new SBMLImportException("no geometry definition found");
    }
    Geometry vcGeometry = null;
    if (selectedGeometryDefinition == analyticGeometryDefinition || selectedGeometryDefinition == csGeometry) {
        vcGeometry = new Geometry("spatialGeom", dimension);
    } else if (selectedGeometryDefinition == distanceMapSampledFieldGeometry || selectedGeometryDefinition == segmentedSampledFieldGeometry) {
        SampledFieldGeometry sfg = (SampledFieldGeometry) selectedGeometryDefinition;
        // get image from sampledFieldGeometry
        // get a sampledVol object via the listOfSampledVol (from
        // SampledGeometry) object.
        // gcw gcw gcw
        String sfn = sfg.getSampledField();
        SampledField sf = null;
        for (SampledField sampledField : sbmlGeometry.getListOfSampledFields()) {
            if (sampledField.getSpatialId().equals(sfn)) {
                sf = sampledField;
            }
        }
        int numX = sf.getNumSamples1();
        int numY = sf.getNumSamples2();
        int numZ = sf.getNumSamples3();
        int[] samples = new int[sf.getSamplesLength()];
        StringTokenizer tokens = new StringTokenizer(sf.getSamples(), " ");
        int count = 0;
        while (tokens.hasMoreTokens()) {
            int sample = Integer.parseInt(tokens.nextToken());
            samples[count++] = sample;
        }
        byte[] imageInBytes = new byte[samples.length];
        if (selectedGeometryDefinition == distanceMapSampledFieldGeometry) {
            // 
            for (int i = 0; i < imageInBytes.length; i++) {
                // if (interpolation(samples[i])<0){
                if (samples[i] < 0) {
                    imageInBytes[i] = -1;
                } else {
                    imageInBytes[i] = 1;
                }
            }
        } else {
            for (int i = 0; i < imageInBytes.length; i++) {
                imageInBytes[i] = (byte) samples[i];
            }
        }
        try {
            // System.out.println("ident " + sf.getId() + " " + sf.getName());
            VCImage vcImage = null;
            CompressionKind ck = sf.getCompression();
            DataKind dk = sf.getDataType();
            if (ck == CompressionKind.deflated) {
                vcImage = new VCImageCompressed(null, imageInBytes, vcExtent, numX, numY, numZ);
            } else {
                switch(dk) {
                    case UINT8:
                    case UINT16:
                    case UINT32:
                        vcImage = new VCImageUncompressed(null, imageInBytes, vcExtent, numX, numY, numZ);
                    default:
                }
            }
            if (vcImage == null) {
                throw new SbmlException("Unsupported type combination " + ck + ", " + dk + " for sampled field " + sf.getName());
            }
            vcImage.setName(sf.getId());
            ListOf<SampledVolume> sampledVolumes = sfg.getListOfSampledVolumes();
            final int numSampledVols = sampledVolumes.size();
            if (numSampledVols == 0) {
                throw new RuntimeException("Cannot have 0 sampled volumes in sampledField (image_based) geometry");
            }
            // check to see if values are uniquely integer , add set up scaling if necessary
            double scaleFactor = checkPixelScaling(sampledVolumes, 1);
            if (scaleFactor != 1) {
                double checkScaleFactor = checkPixelScaling(sampledVolumes, scaleFactor);
                VCAssert.assertTrue(checkScaleFactor != scaleFactor, "Scale factor check failed");
            }
            VCPixelClass[] vcpixelClasses = new VCPixelClass[numSampledVols];
            // get pixel classes for geometry
            for (int i = 0; i < numSampledVols; i++) {
                SampledVolume sVol = sampledVolumes.get(i);
                // from subVolume, get pixelClass?
                final int scaled = (int) (scaleFactor * sVol.getSampledValue());
                vcpixelClasses[i] = new VCPixelClass(null, sVol.getDomainType(), scaled);
            }
            vcImage.setPixelClasses(vcpixelClasses);
            // now create image geometry
            vcGeometry = new Geometry("spatialGeom", vcImage);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to create image from SampledFieldGeometry : " + e.getMessage());
        }
    }
    GeometrySpec vcGeometrySpec = vcGeometry.getGeometrySpec();
    vcGeometrySpec.setOrigin(vcOrigin);
    try {
        vcGeometrySpec.setExtent(vcExtent);
    } catch (PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Unable to set extent on VC geometry : " + e.getMessage(), e);
    }
    // get listOfDomainTypes via the Geometry object.
    ListOf<DomainType> listOfDomainTypes = sbmlGeometry.getListOfDomainTypes();
    if (listOfDomainTypes == null || listOfDomainTypes.size() < 1) {
        throw new SBMLImportException("Cannot have 0 domainTypes in geometry");
    }
    // get a listOfDomains via the Geometry object.
    ListOf<Domain> listOfDomains = sbmlGeometry.getListOfDomains();
    if (listOfDomains == null || listOfDomains.size() < 1) {
        throw new SBMLImportException("Cannot have 0 domains in geometry");
    }
    // ListOfGeometryDefinitions listOfGeomDefns =
    // sbmlGeometry.getListOfGeometryDefinitions();
    // if ((listOfGeomDefns == null) ||
    // (sbmlGeometry.getNumGeometryDefinitions() > 1)) {
    // throw new
    // RuntimeException("Can have only 1 geometry definition in geometry");
    // }
    // use the boolean bAnalytic to create the right kind of subvolume.
    // First match the somVol=domainTypes for spDim=3. Deal witl spDim=2
    // afterwards.
    GeometrySurfaceDescription vcGsd = vcGeometry.getGeometrySurfaceDescription();
    Vector<DomainType> surfaceClassDomainTypesVector = new Vector<DomainType>();
    try {
        for (DomainType dt : listOfDomainTypes) {
            if (dt.getSpatialDimensions() == 3) {
                // subvolume
                if (selectedGeometryDefinition == analyticGeometryDefinition) {
                    // will set expression later - when reading in Analytic
                    // Volumes in GeometryDefinition
                    vcGeometrySpec.addSubVolume(new AnalyticSubVolume(dt.getId(), new Expression(1.0)));
                } else {
                // add SubVolumes later for CSG and Image-based
                }
            } else if (dt.getSpatialDimensions() == 2) {
                surfaceClassDomainTypesVector.add(dt);
            }
        }
        // analytic vol is needed to get the expression for subVols
        if (selectedGeometryDefinition == analyticGeometryDefinition) {
            // get an analyticVol object via the listOfAnalyticVol (from
            // AnalyticGeometry) object.
            ListOf<AnalyticVolume> aVolumes = analyticGeometryDefinition.getListOfAnalyticVolumes();
            if (aVolumes.size() < 1) {
                throw new SBMLImportException("Cannot have 0 Analytic volumes in analytic geometry");
            }
            for (AnalyticVolume analyticVol : aVolumes) {
                // get subVol from VC geometry using analyticVol spatialId;
                // set its expr using analyticVol's math.
                SubVolume vcSubvolume = vcGeometrySpec.getSubVolume(analyticVol.getDomainType());
                CastInfo<AnalyticSubVolume> ci = BeanUtils.attemptCast(AnalyticSubVolume.class, vcSubvolume);
                if (!ci.isGood()) {
                    throw new RuntimeException("analytic volume '" + analyticVol.getId() + "' does not map to any VC subvolume.");
                }
                AnalyticSubVolume asv = ci.get();
                try {
                    Expression subVolExpr = getExpressionFromFormula(analyticVol.getMath());
                    asv.setExpression(subVolExpr);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new SBMLImportException("Unable to set expression on subVolume '" + asv.getName() + "'. " + e.getMessage(), e);
                }
            }
        }
        SampledFieldGeometry sfg = BeanUtils.downcast(SampledFieldGeometry.class, selectedGeometryDefinition);
        if (sfg != null) {
            ListOf<SampledVolume> sampledVolumes = sfg.getListOfSampledVolumes();
            int numSampledVols = sampledVolumes.size();
            if (numSampledVols == 0) {
                throw new SBMLImportException("Cannot have 0 sampled volumes in sampledField (image_based) geometry");
            }
            VCPixelClass[] vcpixelClasses = new VCPixelClass[numSampledVols];
            ImageSubVolume[] vcImageSubVols = new ImageSubVolume[numSampledVols];
            // get pixel classes for geometry
            int idx = 0;
            for (SampledVolume sVol : sampledVolumes) {
                // from subVolume, get pixelClass?
                final String name = sVol.getDomainType();
                final int pixelValue = SBMLUtils.ignoreZeroFraction(sVol.getSampledValue());
                VCPixelClass pc = new VCPixelClass(null, name, pixelValue);
                vcpixelClasses[idx] = pc;
                // Create the new Image SubVolume - use index of this for
                // loop as 'handle' for ImageSubVol?
                ImageSubVolume isv = new ImageSubVolume(null, pc, idx);
                isv.setName(name);
                vcImageSubVols[idx++] = isv;
            }
            vcGeometry.getGeometrySpec().setSubVolumes(vcImageSubVols);
        }
        if (selectedGeometryDefinition == csGeometry) {
            ListOf<org.sbml.jsbml.ext.spatial.CSGObject> listOfcsgObjs = csGeometry.getListOfCSGObjects();
            ArrayList<org.sbml.jsbml.ext.spatial.CSGObject> sbmlCSGs = new ArrayList<org.sbml.jsbml.ext.spatial.CSGObject>(listOfcsgObjs);
            // we want the CSGObj with highest ordinal to be the first
            // element in the CSG subvols array.
            Collections.sort(sbmlCSGs, new Comparator<org.sbml.jsbml.ext.spatial.CSGObject>() {

                @Override
                public int compare(org.sbml.jsbml.ext.spatial.CSGObject lhs, org.sbml.jsbml.ext.spatial.CSGObject rhs) {
                    // minus one to reverse sort
                    return -1 * Integer.compare(lhs.getOrdinal(), rhs.getOrdinal());
                }
            });
            int n = sbmlCSGs.size();
            CSGObject[] vcCSGSubVolumes = new CSGObject[n];
            for (int i = 0; i < n; i++) {
                org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = sbmlCSGs.get(i);
                CSGObject vcellCSGObject = new CSGObject(null, sbmlCSGObject.getDomainType(), i);
                vcellCSGObject.setRoot(getVCellCSGNode(sbmlCSGObject.getCSGNode()));
            }
            vcGeometry.getGeometrySpec().setSubVolumes(vcCSGSubVolumes);
        }
        // Call geom.geomSurfDesc.updateAll() to automatically generate
        // surface classes.
        // vcGsd.updateAll();
        vcGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Unable to create VC subVolumes from SBML domainTypes : " + e.getMessage(), e);
    }
    // should now map each SBML domain to right VC geometric region.
    GeometricRegion[] vcGeomRegions = vcGsd.getGeometricRegions();
    ISize sampleSize = vcGsd.getVolumeSampleSize();
    RegionInfo[] regionInfos = vcGsd.getRegionImage().getRegionInfos();
    int numX = sampleSize.getX();
    int numY = sampleSize.getY();
    int numZ = sampleSize.getZ();
    double ox = vcOrigin.getX();
    double oy = vcOrigin.getY();
    double oz = vcOrigin.getZ();
    for (Domain domain : listOfDomains) {
        String domainType = domain.getDomainType();
        InteriorPoint interiorPt = domain.getListOfInteriorPoints().get(0);
        if (interiorPt == null) {
            DomainType currDomainType = null;
            for (DomainType dt : sbmlGeometry.getListOfDomainTypes()) {
                if (dt.getSpatialId().equals(domainType)) {
                    currDomainType = dt;
                }
            }
            if (currDomainType.getSpatialDimensions() == 2) {
                continue;
            }
        }
        Coordinate sbmlInteriorPtCoord = new Coordinate(interiorPt.getCoord1(), interiorPt.getCoord2(), interiorPt.getCoord3());
        for (int j = 0; j < vcGeomRegions.length; j++) {
            if (vcGeomRegions[j] instanceof VolumeGeometricRegion) {
                int regionID = ((VolumeGeometricRegion) vcGeomRegions[j]).getRegionID();
                for (int k = 0; k < regionInfos.length; k++) {
                    // (using gemoRegion regionID).
                    if (regionInfos[k].getRegionIndex() == regionID) {
                        int volIndx = 0;
                        Coordinate nearestPtCoord = null;
                        double minDistance = Double.MAX_VALUE;
                        // represented by SBML 'domain[i]'.
                        for (int z = 0; z < numZ; z++) {
                            for (int y = 0; y < numY; y++) {
                                for (int x = 0; x < numX; x++) {
                                    if (regionInfos[k].isIndexInRegion(volIndx)) {
                                        double unit_z = (numZ > 1) ? ((double) z) / (numZ - 1) : 0.5;
                                        double coordZ = oz + vcExtent.getZ() * unit_z;
                                        double unit_y = (numY > 1) ? ((double) y) / (numY - 1) : 0.5;
                                        double coordY = oy + vcExtent.getY() * unit_y;
                                        double unit_x = (numX > 1) ? ((double) x) / (numX - 1) : 0.5;
                                        double coordX = ox + vcExtent.getX() * unit_x;
                                        // for now, find the shortest dist
                                        // coord. Can refine algo later.
                                        Coordinate vcCoord = new Coordinate(coordX, coordY, coordZ);
                                        double distance = sbmlInteriorPtCoord.distanceTo(vcCoord);
                                        if (distance < minDistance) {
                                            minDistance = distance;
                                            nearestPtCoord = vcCoord;
                                        }
                                    }
                                    volIndx++;
                                }
                            // end - for x
                            }
                        // end - for y
                        }
                        // with domain name
                        if (nearestPtCoord != null) {
                            GeometryClass geomClassSBML = vcGeometry.getGeometryClass(domainType);
                            // we know vcGeometryReg[j] is a VolGeomRegion
                            GeometryClass geomClassVC = ((VolumeGeometricRegion) vcGeomRegions[j]).getSubVolume();
                            if (geomClassSBML.compareEqual(geomClassVC)) {
                                vcGeomRegions[j].setName(domain.getId());
                            }
                        }
                    }
                // end if (regInfoIndx = regId)
                }
            // end - for regInfo
            }
        }
    // end for - vcGeomRegions
    }
    // deal with surfaceClass:spDim2-domainTypes
    for (int i = 0; i < surfaceClassDomainTypesVector.size(); i++) {
        DomainType surfaceClassDomainType = surfaceClassDomainTypesVector.elementAt(i);
        // 'surfaceClassDomainType'
        for (Domain d : listOfDomains) {
            if (d.getDomainType().equals(surfaceClassDomainType.getId())) {
                // get the adjacent domains of this 'surface' domain
                // (surface domain + its 2 adj vol domains)
                Set<Domain> adjacentDomainsSet = getAssociatedAdjacentDomains(sbmlGeometry, d);
                // get the domain types of the adjacent domains in SBML and
                // store the corresponding subVol counterparts from VC for
                // adj vol domains
                Vector<SubVolume> adjacentSubVolumesVector = new Vector<SubVolume>();
                Vector<VolumeGeometricRegion> adjVolGeomRegionsVector = new Vector<VolumeGeometricRegion>();
                Iterator<Domain> iterator = adjacentDomainsSet.iterator();
                while (iterator.hasNext()) {
                    Domain dom = iterator.next();
                    DomainType dt = getBySpatialID(sbmlGeometry.getListOfDomainTypes(), dom.getDomainType());
                    if (dt.getSpatialDimensions() == 3) {
                        // for domain type with sp. dim = 3, get
                        // correspoinding subVol from VC geometry.
                        GeometryClass gc = vcGeometry.getGeometryClass(dt.getId());
                        adjacentSubVolumesVector.add((SubVolume) gc);
                        // store volGeomRegions corresponding to this (vol)
                        // geomClass in adjVolGeomRegionsVector : this
                        // should return ONLY 1 region for subVol.
                        GeometricRegion[] geomRegion = vcGsd.getGeometricRegions(gc);
                        adjVolGeomRegionsVector.add((VolumeGeometricRegion) geomRegion[0]);
                    }
                }
                // there should be only 2 subVols in this vector
                if (adjacentSubVolumesVector.size() != 2) {
                    throw new RuntimeException("Cannot have more or less than 2 subvolumes that are adjacent to surface (membrane) '" + d.getId() + "'");
                }
                // get the surface class with these 2 adj subVols. Set its
                // name to that of 'surfaceClassDomainType'
                SurfaceClass surfacClass = vcGsd.getSurfaceClass(adjacentSubVolumesVector.get(0), adjacentSubVolumesVector.get(1));
                surfacClass.setName(surfaceClassDomainType.getSpatialId());
                // get surfaceGeometricRegion that has adjVolGeomRegions as
                // its adjacent vol geom regions and set its name from
                // domain 'd'
                SurfaceGeometricRegion surfaceGeomRegion = getAssociatedSurfaceGeometricRegion(vcGsd, adjVolGeomRegionsVector);
                if (surfaceGeomRegion != null) {
                    surfaceGeomRegion.setName(d.getId());
                }
            }
        // end if - domain.domainType == surfaceClassDomainType
        }
    // end for - numDomains
    }
    // structureMappings in VC from compartmentMappings in SBML
    try {
        // set geometry first and then set structureMappings?
        vcBioModel.getSimulationContext(0).setGeometry(vcGeometry);
        // update simContextName ...
        vcBioModel.getSimulationContext(0).setName(vcBioModel.getSimulationContext(0).getName() + "_" + vcGeometry.getName());
        Model vcModel = vcBioModel.getSimulationContext(0).getModel();
        ModelUnitSystem vcModelUnitSystem = vcModel.getUnitSystem();
        Vector<StructureMapping> structMappingsVector = new Vector<StructureMapping>();
        SpatialCompartmentPlugin cplugin = null;
        for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
            Compartment c = sbmlModel.getCompartment(i);
            String cname = c.getName();
            cplugin = (SpatialCompartmentPlugin) c.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            CompartmentMapping compMapping = cplugin.getCompartmentMapping();
            if (compMapping != null) {
                // final String id = compMapping.getId();
                // final String name = compMapping.getName();
                CastInfo<Structure> ci = SBMLHelper.getTypedStructure(Structure.class, vcModel, cname);
                if (ci.isGood()) {
                    Structure struct = ci.get();
                    String domainType = compMapping.getDomainType();
                    GeometryClass geometryClass = vcGeometry.getGeometryClass(domainType);
                    double unitSize = compMapping.getUnitSize();
                    Feature feat = BeanUtils.downcast(Feature.class, struct);
                    if (feat != null) {
                        FeatureMapping featureMapping = new FeatureMapping(feat, vcBioModel.getSimulationContext(0), vcModelUnitSystem);
                        featureMapping.setGeometryClass(geometryClass);
                        if (geometryClass instanceof SubVolume) {
                            featureMapping.getVolumePerUnitVolumeParameter().setExpression(new Expression(unitSize));
                        } else if (geometryClass instanceof SurfaceClass) {
                            featureMapping.getVolumePerUnitAreaParameter().setExpression(new Expression(unitSize));
                        }
                        structMappingsVector.add(featureMapping);
                    } else if (struct instanceof Membrane) {
                        MembraneMapping membraneMapping = new MembraneMapping((Membrane) struct, vcBioModel.getSimulationContext(0), vcModelUnitSystem);
                        membraneMapping.setGeometryClass(geometryClass);
                        if (geometryClass instanceof SubVolume) {
                            membraneMapping.getAreaPerUnitVolumeParameter().setExpression(new Expression(unitSize));
                        } else if (geometryClass instanceof SurfaceClass) {
                            membraneMapping.getAreaPerUnitAreaParameter().setExpression(new Expression(unitSize));
                        }
                        structMappingsVector.add(membraneMapping);
                    }
                }
            }
        }
        StructureMapping[] structMappings = structMappingsVector.toArray(new StructureMapping[0]);
        vcBioModel.getSimulationContext(0).getGeometryContext().setStructureMappings(structMappings);
        // if type from SBML parameter Boundary Condn is not the same as the
        // boundary type of the
        // structureMapping of structure of paramSpContext, set the boundary
        // condn type of the structureMapping
        // to the value of 'type' from SBML parameter Boundary Condn.
        ListOf<Parameter> listOfGlobalParams = sbmlModel.getListOfParameters();
        for (Parameter sbmlGlobalParam : sbmlModel.getListOfParameters()) {
            SpatialParameterPlugin spplugin = (SpatialParameterPlugin) sbmlGlobalParam.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            ParameterType paramType = spplugin.getParamType();
            if (!(paramType instanceof BoundaryCondition)) {
                continue;
            }
            BoundaryCondition bCondn = (BoundaryCondition) paramType;
            if (bCondn.isSetVariable()) {
                // get the var of boundaryCondn; find appropriate spContext
                // in vcell;
                SpeciesContext paramSpContext = vcBioModel.getSimulationContext(0).getModel().getSpeciesContext(bCondn.getVariable());
                if (paramSpContext != null) {
                    Structure s = paramSpContext.getStructure();
                    StructureMapping sm = vcBioModel.getSimulationContext(0).getGeometryContext().getStructureMapping(s);
                    if (sm != null) {
                        BoundaryConditionType bct = null;
                        switch(bCondn.getType()) {
                            case Dirichlet:
                                {
                                    bct = BoundaryConditionType.DIRICHLET;
                                    break;
                                }
                            case Neumann:
                                {
                                    bct = BoundaryConditionType.NEUMANN;
                                    break;
                                }
                            case Robin_inwardNormalGradientCoefficient:
                            case Robin_sum:
                            case Robin_valueCoefficient:
                            default:
                                throw new RuntimeException("boundary condition type " + bCondn.getType().name() + " not supported");
                        }
                        for (CoordinateComponent coordComp : getSbmlGeometry().getListOfCoordinateComponents()) {
                            if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMinimum().getSpatialId())) {
                                switch(coordComp.getType()) {
                                    case cartesianX:
                                        {
                                            sm.setBoundaryConditionTypeXm(bct);
                                        }
                                    case cartesianY:
                                        {
                                            sm.setBoundaryConditionTypeYm(bct);
                                        }
                                    case cartesianZ:
                                        {
                                            sm.setBoundaryConditionTypeZm(bct);
                                        }
                                }
                            }
                            if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMaximum().getSpatialId())) {
                                switch(coordComp.getType()) {
                                    case cartesianX:
                                        {
                                            sm.setBoundaryConditionTypeXm(bct);
                                        }
                                    case cartesianY:
                                        {
                                            sm.setBoundaryConditionTypeYm(bct);
                                        }
                                    case cartesianZ:
                                        {
                                            sm.setBoundaryConditionTypeZm(bct);
                                        }
                                }
                            }
                        }
                    } else // sm != null
                    {
                        logger.sendMessage(VCLogger.Priority.MediumPriority, VCLogger.ErrorType.OverallWarning, "No structure " + s.getName() + " requested by species context " + paramSpContext.getName());
                    }
                }
            // end if (paramSpContext != null)
            }
        // end if (bCondn.isSetVar())
        }
        // end for (sbmlModel.numParams)
        vcBioModel.getSimulationContext(0).getGeometryContext().refreshStructureMappings();
        vcBioModel.getSimulationContext(0).refreshSpatialObjects();
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Unable to create VC structureMappings from SBML compartment mappings : " + e.getMessage(), e);
    }
}

Example 5 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class ClientRequestManager method newDocument.

/**
 * Insert the method's description here.
 * Creation date: (5/21/2004 4:20:47 AM)
 * @param documentType int
 */
public AsynchClientTask[] newDocument(TopLevelWindowManager requester, final VCDocument.DocumentCreationInfo documentCreationInfo) {
    // gcwtodo
    AsynchClientTask createNewDocumentTask = new AsynchClientTask("Creating New Document", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocument doc = (VCDocument) hashTable.get("doc");
            DocumentWindowManager windowManager = createDocumentWindowManager(doc);
            DocumentWindow dw = getMdiManager().createNewDocumentWindow(windowManager);
            if (windowManager != null) {
                hashTable.put("windowManager", windowManager);
            }
            setFinalWindow(hashTable, dw);
        }
    };
    if (documentCreationInfo.getDocumentType() == VCDocumentType.MATHMODEL_DOC && documentCreationInfo.getOption() == VCDocument.MATH_OPTION_SPATIAL_NEW) {
        final AsynchClientTask createSpatialMathModelTask = new AsynchClientTask("creating mathmodel", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                Geometry geometry = null;
                geometry = (Geometry) hashTable.get("doc");
                MathModel mathModel = createMathModel("Untitled", geometry);
                mathModel.setName("MathModel" + (getMdiManager().getNumCreatedDocumentWindows() + 1));
                hashTable.put("doc", mathModel);
            }
        };
        requester.createGeometry(null, new AsynchClientTask[] { createSpatialMathModelTask, createNewDocumentTask }, "Choose geometry type to start MathModel creation", "Create MathModel", null);
        return null;
    }
    /* asynchronous and not blocking any window */
    AsynchClientTask[] taskArray = null;
    if (documentCreationInfo.getPreCreatedDocument() == null) {
        AsynchClientTask[] taskArray1 = createNewDocument(requester, documentCreationInfo);
        taskArray = new AsynchClientTask[taskArray1.length + 1];
        System.arraycopy(taskArray1, 0, taskArray, 0, taskArray1.length);
    } else {
        taskArray = new AsynchClientTask[2];
        taskArray[0] = new AsynchClientTask("Setting document...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                hashTable.put("doc", documentCreationInfo.getPreCreatedDocument());
            }
        };
    }
    taskArray[taskArray.length - 1] = createNewDocumentTask;
    return taskArray;
}