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

Example 6 with Geometry

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

the class ClientRequestManager method changeGeometry0.

private void changeGeometry0(final TopLevelWindowManager requester, final SimulationContext simContext) {
    AsynchClientTask selectDocumentTypeTask = createSelectDocTask(requester);
    AsynchClientTask selectLoadGeomTask = createSelectLoadGeomTask(requester);
    AsynchClientTask processGeometryTask = new AsynchClientTask("Processing geometry...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get(GEOMETRY_KEY);
            if (requester instanceof MathModelWindowManager) {
                // User can cancel here
                continueAfterMathModelGeomChangeWarning((MathModelWindowManager) requester, newGeometry);
            }
            if (newGeometry.getDimension() > 0 && newGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                newGeometry.getGeometrySurfaceDescription().updateAll();
            }
        }
    };
    AsynchClientTask setNewGeometryTask = new AsynchClientTask("Setting new Geometry...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get(GEOMETRY_KEY);
            if (newGeometry != null) {
                if (requester instanceof BioModelWindowManager) {
                    simContext.setGeometry(newGeometry);
                } else if (requester instanceof MathModelWindowManager) {
                    MathModel mathModel = (MathModel) ((MathModelWindowManager) requester).getVCDocument();
                    mathModel.getMathDescription().setGeometry(newGeometry);
                }
            }
        }
    };
    Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { selectDocumentTypeTask, selectLoadGeomTask, processGeometryTask, setNewGeometryTask }, false);
}

Example 7 with Geometry

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

the class ClientRequestManager method getSaveImageAndGeometryTask.

private AsynchClientTask getSaveImageAndGeometryTask() {
    final AsynchClientTask saveImageAndGeometryTask = new AsynchClientTask("creating geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            getClientTaskStatusSupport().setMessage("Getting new Geometry name...");
            String newGeometryName = null;
            while (true) {
                newGeometryName = ClientRequestManager.this.getMdiManager().getDatabaseWindowManager().showSaveDialog(((Geometry) hashTable.get("doc")).getDocumentType(), (Component) hashTable.get(ClientRequestManager.GUI_PARENT), (newGeometryName == null ? "NewGeometry" : newGeometryName));
                if (newGeometryName == null || newGeometryName.trim().length() == 0) {
                    newGeometryName = null;
                    DialogUtils.showWarningDialog((Component) hashTable.get(ClientRequestManager.GUI_PARENT), "New Geometry name cannot be empty.");
                    continue;
                }
                // Check name conflict
                GeometryInfo[] geometryInfos = ClientRequestManager.this.getDocumentManager().getGeometryInfos();
                boolean bNameConflict = false;
                for (int i = 0; i < geometryInfos.length; i++) {
                    if (geometryInfos[i].getVersion().getOwner().equals(ClientRequestManager.this.getDocumentManager().getUser())) {
                        if (geometryInfos[i].getVersion().getName().equals(newGeometryName)) {
                            bNameConflict = true;
                            break;
                        }
                    }
                }
                if (bNameConflict) {
                    DialogUtils.showWarningDialog((Component) hashTable.get(ClientRequestManager.GUI_PARENT), "A Geometry with name " + newGeometryName + " already exists.  Choose a different name.");
                    continue;
                } else {
                    break;
                }
            }
            getClientTaskStatusSupport().setMessage("Saving image portion of Geometry...");
            saveImageAutoName(ClientRequestManager.this, ((Geometry) hashTable.get("doc")).getGeometrySpec().getImage());
            getClientTaskStatusSupport().setMessage("Saving final Geometry...");
            ClientRequestManager.this.getDocumentManager().saveAsNew((Geometry) hashTable.get("doc"), newGeometryName);
        }
    };
    return saveImageAndGeometryTask;
}

Example 8 with Geometry

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

the class MathModel_SBMLExporter method addGeometry.

private static void addGeometry(Model sbmlModel, MathModel vcMathModel) {
    SpatialModelPlugin mplugin = (SpatialModelPlugin) sbmlModel.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
    // Creates a geometry object via SpatialModelPlugin object.
    org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = mplugin.getGeometry();
    sbmlGeometry.setCoordinateSystem(GeometryKind.cartesian);
    Geometry vcGeometry = vcMathModel.getGeometry();
    // 
    // list of CoordinateComponents : 1 if geometry is 1-d, 2 if geometry is 2-d, 3 if geometry is 3-d
    // 
    int dimension = vcGeometry.getDimension();
    Extent vcExtent = vcGeometry.getExtent();
    Origin vcOrigin = vcGeometry.getOrigin();
    // add x coordinate component
    CoordinateComponent coordCompX = sbmlGeometry.createCoordinateComponent();
    coordCompX.setSpatialId("CoordCompX");
    coordCompX.setType(CoordinateKind.cartesianX);
    Boundary minX = coordCompX.getBoundaryMaximum();
    minX.setSpatialId("Xmin");
    minX.setValue(vcOrigin.getX());
    Boundary maxX = coordCompX.getBoundaryMaximum();
    maxX.setSpatialId("Xmax");
    maxX.setValue(vcOrigin.getX() + (vcExtent.getX()));
    Parameter parameterX = sbmlModel.createParameter();
    // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.X
    parameterX.setId(ReservedVariable.X.getName());
    SpatialSymbolReference coordXSpatialRef = new SpatialSymbolReference();
    coordXSpatialRef.setSpatialRef(coordCompX.getSpatialId());
    SpatialParameterPlugin parameterXSpatialPlugin = (SpatialParameterPlugin) parameterX.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
    parameterXSpatialPlugin.setParamType(coordXSpatialRef);
    // add y coordinate component
    if (dimension == 2 || dimension == 3) {
        CoordinateComponent coordCompY = sbmlGeometry.createCoordinateComponent();
        coordCompY.setSpatialId("CoordCompY");
        coordCompY.setType(CoordinateKind.cartesianY);
        Boundary minY = coordCompY.getBoundaryMinimum();
        minY.setId("Ymin");
        minY.setValue(vcOrigin.getY());
        Boundary maxY = coordCompY.getBoundaryMaximum();
        maxY.setId("Ymax");
        maxY.setValue(vcOrigin.getY() + (vcExtent.getY()));
        Parameter parameterY = sbmlModel.createParameter();
        // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.Y
        parameterY.setId(ReservedVariable.Y.getName());
        SpatialSymbolReference coordYSpatialRef = new SpatialSymbolReference();
        coordYSpatialRef.setSpatialRef(coordCompY.getSpatialId());
        SpatialParameterPlugin parameterYSpatialPlugin = (SpatialParameterPlugin) parameterY.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        parameterYSpatialPlugin.setParamType(coordYSpatialRef);
    }
    // add z coordinate component
    if (dimension == 3) {
        CoordinateComponent coordCompZ = sbmlGeometry.createCoordinateComponent();
        coordCompZ.setSpatialId("CoordCompZ");
        coordCompZ.setType(CoordinateKind.cartesianZ);
        Boundary minZ = coordCompZ.getBoundaryMinimum();
        minZ.setId("Zmin");
        minZ.setValue(vcOrigin.getZ());
        Boundary maxZ = coordCompZ.getBoundaryMaximum();
        maxZ.setId("Zmax");
        maxZ.setValue(vcOrigin.getZ() + (vcExtent.getZ()));
        Parameter parameterZ = sbmlModel.createParameter();
        // note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.Y
        parameterZ.setId(ReservedVariable.Z.getName());
        SpatialSymbolReference coordZSpatialRef = new SpatialSymbolReference();
        coordZSpatialRef.setSpatialRef(coordCompZ.getSpatialId());
        SpatialParameterPlugin parameterZSpatialPlugin = (SpatialParameterPlugin) parameterZ.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        parameterZSpatialPlugin.setParamType(coordZSpatialRef);
    }
    // 
    // list of domain types : subvolumes and surface classes from VC
    // Also create compartments - one compartment for each geometryClass. set id and spatialDimension based on type of geometryClass.
    // 
    boolean bAnalyticGeom = false;
    boolean bImageGeom = false;
    GeometryClass[] vcGeomClasses = vcGeometry.getGeometryClasses();
    int numVCGeomClasses = vcGeomClasses.length;
    for (int i = 0; i < numVCGeomClasses; i++) {
        DomainType domainType = sbmlGeometry.createDomainType();
        domainType.setId(vcGeomClasses[i].getName());
        if (vcGeomClasses[i] instanceof SubVolume) {
            if (((SubVolume) vcGeomClasses[i]) instanceof AnalyticSubVolume) {
                bAnalyticGeom = true;
            } else if (((SubVolume) vcGeomClasses[i]) instanceof ImageSubVolume) {
                bImageGeom = true;
            }
            domainType.setSpatialDimensions(3);
        } else if (vcGeomClasses[i] instanceof SurfaceClass) {
            domainType.setSpatialDimensions(2);
        }
    }
    // 
    // list of domains, adjacent domains : from VC geometricRegions
    // 
    GeometrySurfaceDescription vcGSD = vcGeometry.getGeometrySurfaceDescription();
    if (vcGSD.getRegionImage() == null) {
        try {
            vcGSD.updateAll();
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to generate region images for geometry");
        }
    }
    GeometricRegion[] vcGeometricRegions = vcGSD.getGeometricRegions();
    ISize sampleSize = vcGSD.getVolumeSampleSize();
    int numX = sampleSize.getX();
    int numY = sampleSize.getY();
    int numZ = sampleSize.getZ();
    double ox = vcOrigin.getX();
    double oy = vcOrigin.getY();
    double oz = vcOrigin.getZ();
    RegionInfo[] regionInfos = vcGSD.getRegionImage().getRegionInfos();
    Compartment compartment = null;
    for (int i = 0; i < vcGeometricRegions.length; i++) {
        // domains
        Domain domain = sbmlGeometry.createDomain();
        domain.setId(vcGeometricRegions[i].getName());
        compartment = sbmlModel.createCompartment();
        compartment.setId("compartment" + i);
        if (vcGeometricRegions[i] instanceof VolumeGeometricRegion) {
            domain.setDomainType(((VolumeGeometricRegion) vcGeometricRegions[i]).getSubVolume().getName());
            // domain.setImplicit(false);
            compartment.setSpatialDimensions(3);
            InteriorPoint interiorPt = domain.createInteriorPoint();
            int regionID = ((VolumeGeometricRegion) vcGeometricRegions[i]).getRegionID();
            boolean bFound = false;
            int regInfoIndx = 0;
            for (int j = 0; j < regionInfos.length; j++) {
                regInfoIndx = j;
                if (regionInfos[j].getRegionIndex() == regionID) {
                    int volIndx = 0;
                    for (int z = 0; z < numZ && !bFound; z++) {
                        for (int y = 0; y < numY && !bFound; y++) {
                            for (int x = 0; x < numX && !bFound; x++) {
                                if (regionInfos[j].isIndexInRegion(volIndx)) {
                                    bFound = true;
                                    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;
                                    interiorPt.setCoord1(coordX);
                                    interiorPt.setCoord2(coordY);
                                    interiorPt.setCoord3(coordZ);
                                }
                                volIndx++;
                            }
                        // end - for x
                        }
                    // end - for y
                    }
                // end - for z
                }
            // end if
            }
            // end for regionInfos
            if (!bFound) {
                throw new RuntimeException("Unable to find interior point for region '" + regionInfos[regInfoIndx].toString());
            }
        } else if (vcGeometricRegions[i] instanceof SurfaceGeometricRegion) {
            SurfaceGeometricRegion vcSurfaceGeomReg = (SurfaceGeometricRegion) vcGeometricRegions[i];
            GeometricRegion geomRegion0 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[0];
            GeometricRegion geomRegion1 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[1];
            SurfaceClass surfaceClass = vcGSD.getSurfaceClass(((VolumeGeometricRegion) geomRegion0).getSubVolume(), ((VolumeGeometricRegion) geomRegion1).getSubVolume());
            domain.setDomainType(surfaceClass.getName());
            // domain.setImplicit(true);
            compartment.setSpatialDimensions(2);
            // adjacent domains : 2 adjacent domain objects for each surfaceClass in VC.
            // adjacent domain 1
            AdjacentDomains adjDomain = sbmlGeometry.createAdjacentDomain();
            adjDomain.setId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + geomRegion0.getName()));
            adjDomain.setDomain1(vcSurfaceGeomReg.getName());
            adjDomain.setDomain2(geomRegion0.getName());
            // adjacent domain 2
            adjDomain = sbmlGeometry.createAdjacentDomain();
            adjDomain.setId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + geomRegion1.getName()));
            adjDomain.setDomain1(vcSurfaceGeomReg.getName());
            adjDomain.setDomain2(geomRegion1.getName());
        }
        // 
        // Mathmodel does not have structureMapping, hence creating compartmentMapping while creating domains.
        // @TODO : how to assign unitSize for compartmentMapping?
        // 
        SpatialCompartmentPlugin cplugin = (SpatialCompartmentPlugin) compartment.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
        CompartmentMapping compMapping = cplugin.getCompartmentMapping();
        String compMappingId = TokenMangler.mangleToSName(domain.getDomainType() + "_" + compartment.getId());
        compMapping.setId(compMappingId);
        compMapping.setDomainType(TokenMangler.mangleToSName(domain.getDomainType()));
    // try {
    // compMapping.setUnitSize(1.0);
    // } catch (ExpressionException e) {
    // e.printStackTrace(System.out);
    // throw new RuntimeException("Unable to create compartment mapping for structureMapping '" + compMapping.getId() +"' : " + e.getMessage());
    // }
    }
    AnalyticGeometry sbmlAnalyticGeom = null;
    SampledFieldGeometry sbmlSFGeom = null;
    // both image and analytic subvolumes?? == not handled in SBML at this time.
    if (bAnalyticGeom && !bImageGeom) {
        sbmlAnalyticGeom = sbmlGeometry.createAnalyticGeometry();
        sbmlAnalyticGeom.setId(TokenMangler.mangleToSName(vcGeometry.getName()));
    } else if (bImageGeom && !bAnalyticGeom) {
        // assuming image based geometry if not analytic geometry
        sbmlSFGeom = sbmlGeometry.createSampledFieldGeometry();
        sbmlSFGeom.setId(TokenMangler.mangleToSName(vcGeometry.getName()));
    } else if (bAnalyticGeom && bImageGeom) {
        throw new RuntimeException("Export to SBML of a combination of Image-based and Analytic geometries is not supported yet.");
    } else if (!bAnalyticGeom && !bImageGeom) {
        throw new RuntimeException("Unknown geometry type.");
    }
    // 
    for (int i = 0; i < vcGeomClasses.length; i++) {
        if (vcGeomClasses[i] instanceof AnalyticSubVolume) {
            // add analytiVols to sbmlAnalyticGeometry
            if (sbmlAnalyticGeom != null) {
                AnalyticVolume analyticVol = sbmlAnalyticGeom.createAnalyticVolume();
                analyticVol.setId(vcGeomClasses[i].getName());
                analyticVol.setDomainType(vcGeomClasses[i].getName());
                analyticVol.setFunctionType(FunctionKind.layered);
                analyticVol.setOrdinal(i);
                Expression expr = ((AnalyticSubVolume) vcGeomClasses[i]).getExpression();
                try {
                    String mathMLStr = ExpressionMathMLPrinter.getMathML(expr, true);
                    ASTNode mathMLNode = ASTNode.readMathMLFromString(mathMLStr);
                    analyticVol.setMath(mathMLNode);
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Error converting VC subvolume expression to mathML" + e.getMessage());
                }
            } else {
                throw new RuntimeException("SBML AnalyticGeometry is null.");
            }
        } else if (vcGeomClasses[i] instanceof ImageSubVolume) {
            // add sampledVols to sbmlSFGeometry
            if (sbmlSFGeom != null) {
                SampledVolume sampledVol = sbmlSFGeom.createSampledVolume();
                sampledVol.setId(vcGeomClasses[i].getName());
                sampledVol.setDomainType(vcGeomClasses[i].getName());
                sampledVol.setSampledValue(((ImageSubVolume) vcGeomClasses[i]).getPixelValue());
            } else {
                throw new RuntimeException("SBML SampledFieldGeometry is null.");
            }
        }
    }
    if (sbmlSFGeom != null) {
        // add sampledField to sampledFieldGeometry
        SampledField sampledField = sbmlGeometry.createSampledField();
        VCImage vcImage = vcGeometry.getGeometrySpec().getImage();
        sampledField.setId(vcImage.getName());
        sampledField.setNumSamples1(vcImage.getNumX());
        if (vcImage.getNumY() > 1) {
            sampledField.setNumSamples2(vcImage.getNumY());
        }
        if (vcImage.getNumZ() > 1) {
            sampledField.setNumSamples3(vcImage.getNumZ());
        }
        sampledField.setInterpolationType(InterpolationKind.nearestneighbor);
        sampledField.setDataType(DataKind.UINT8);
        // add image from vcGeometrySpec to sampledField.
        try {
            StringBuffer sb = new StringBuffer();
            byte[] imagePixelsBytes = vcImage.getPixelsCompressed();
            for (int i = 0; i < imagePixelsBytes.length; i++) {
                int uint8_sample = ((int) imagePixelsBytes[i]) & 0xff;
                sb.append(uint8_sample + " ");
            }
            sampledField.setSamplesLength(vcImage.getNumXYZ());
            sampledField.setSamples(sb.toString().trim());
        } catch (ImageException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to export image from VCell to SBML : " + e.getMessage());
        }
    }
}

Example 9 with Geometry

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

the class XmlReader method getGeometry.

/**
 * This method returns a Geometry object from a XML representation.
 * Creation date: (4/26/2001 12:12:18 PM)
 * @return cbit.vcell.geometry.Geometry
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
public Geometry getGeometry(Element param) throws XmlParseException {
    // Get the Extent object
    Extent newextent = getExtent(param.getChild(XMLTags.ExtentTag, vcNamespace));
    // Get VCimage information
    VCImage newimage = null;
    if (param.getChild(XMLTags.ImageTag, vcNamespace) != null) {
        try {
            newimage = getVCImage(param.getChild(XMLTags.ImageTag, vcNamespace), newextent);
        } catch (Throwable e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    int newdimension = Integer.parseInt(param.getAttributeValue(XMLTags.DimensionAttrTag));
    // Get Version
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Try to construct the geometry upon four different cases
    Geometry newgeometry = null;
    if (version != null && newimage != null) {
        newgeometry = new Geometry(version, newimage);
    } else if (version != null) {
        newgeometry = new Geometry(version, newdimension);
    } else if (newimage != null) {
        newgeometry = new Geometry(name, newimage);
    } else {
        newgeometry = new Geometry(name, newdimension);
    }
    // set attributes
    try {
        if (!newgeometry.getName().equalsIgnoreCase(name)) {
            newgeometry.setName(name);
        }
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // newgeometry.setDescription( unMangle(annotation) );
        // }
        // Add annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null && annotation.length() > 0) {
            newgeometry.setDescription(unMangle(annotation));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred when setting the name " + name + " to a Geometry object!", e);
    }
    // Add the Extent
    try {
        newgeometry.getGeometrySpec().setExtent(newextent);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred while trying to set the Extent for the Geometry " + name, e);
    }
    // Add the Origin
    newgeometry.getGeometrySpec().setOrigin(getOrigin(param.getChild(XMLTags.OriginTag, vcNamespace)));
    // Add the SubVolumes
    List<Element> children = param.getChildren(XMLTags.SubVolumeTag, vcNamespace);
    SubVolume[] newsubvolumes = new SubVolume[children.size()];
    int subvolumeCounter = 0;
    for (Element child : children) {
        newsubvolumes[subvolumeCounter] = getSubVolume(child);
        subvolumeCounter++;
    }
    try {
        newgeometry.getGeometrySpec().setSubVolumes(newsubvolumes);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e);
    }
    if (newgeometry.getDimension() > 0) {
        // Add SurfaceClasses
        List<Element> surfaceClassChildren = param.getChildren(XMLTags.SurfaceClassTag, vcNamespace);
        SurfaceClass[] newSurfaceClassArr = new SurfaceClass[surfaceClassChildren.size()];
        int surfClassCounter = 0;
        for (Element surfClassChild : surfaceClassChildren) {
            newSurfaceClassArr[surfClassCounter] = getSurfaceClass(surfClassChild, newgeometry);
            surfClassCounter++;
        }
        try {
            newgeometry.getGeometrySurfaceDescription().setSurfaceClasses(newSurfaceClassArr);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace();
            throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e);
        }
    }
    // read Filaments (if any)
    Iterator<Element> iterator = param.getChildren(XMLTags.FilamentTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = iterator.next();
        String filname = unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag));
        Iterator<Element> curveiterator = tempElement.getChildren().iterator();
        while (curveiterator.hasNext()) {
            ControlPointCurve curve = getControlPointCurve(curveiterator.next());
            newgeometry.getGeometrySpec().getFilamentGroup().addCurve(filname, curve);
        }
    }
    // read Surface description (if any)
    Element sd = param.getChild(XMLTags.SurfaceDescriptionTag, vcNamespace);
    if (sd != null) {
        GeometrySurfaceDescription dummy = getGeometrySurfaceDescription(sd, newgeometry);
    }
    try {
        newgeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), false, false);
    } catch (GeometryException e) {
        e.printStackTrace(System.out);
    } catch (ImageException e) {
        e.printStackTrace(System.out);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
    }
    return newgeometry;
}

Example 10 with Geometry

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

the class XmlReader method getMathModel.

/*
public RateRuleVariable[] getRateRuleVariables(Element rateRuleVarsElement, Model model) throws XmlParseException  {
	Iterator<Element> rateRuleVarsIterator = rateRuleVarsElement.getChildren(XMLTags.RateRuleVariableTag, vcNamespace).iterator();
	Vector<RateRuleVariable> rateRuleVarsVector = new Vector<RateRuleVariable>();
	while (rateRuleVarsIterator.hasNext()) {
		Element rrvElement = (Element) rateRuleVarsIterator.next();

		RateRuleVariable newRateRuleVar = null;
		try {
			String rrvName = unMangle(rrvElement.getAttributeValue(XMLTags.NameAttrTag));
		    String rrvStructureName = unMangle(rrvElement.getAttributeValue(XMLTags.StructureAttrTag));
		    // structure can be null
		    Structure rrvStructure = null;
		    if (rrvStructureName != null) {
		    	rrvStructure = (Structure) model.getStructure(rrvStructureName);
		    }
//		    if (structureref == null) {
//		    	throw new XmlParseException("The structure " + rrvStructureName + "could not be resolved!");
//		    }
		    String rrvRoleStr = rrvElement.getAttributeValue(XMLTags.ParamRoleAttrTag);
		    int rrvRole = RateRuleVariable.getParamRoleFromDesc(rrvRoleStr);
		    Element rrvParamElement = rrvElement.getChild(XMLTags.ParameterTag, vcNamespace);
		    ModelParameter rrvParameter = getModelParameter(rrvParamElement, model);
		    newRateRuleVar = new RateRuleVariable(rrvName, rrvStructure, rrvParameter, rrvRole);
			newRateRuleVar.bind();
		} catch (ExpressionBindingException e) {
			e.printStackTrace(System.out);
			throw new XmlParseException(e.getMessage());
		}
		if (newRateRuleVar != null) {
			rateRuleVarsVector.add(newRateRuleVar);
		}
	}
	
	return ((RateRuleVariable[])BeanUtils.getArray(rateRuleVarsVector, RateRuleVariable.class));
}
*/
/**
 * This method returns a MathModel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @return cbit.vcell.mathmodel.MathModel
 * @param param org.jdom.Element
 */
public MathModel getMathModel(Element param) throws XmlParseException {
    // Create it
    // set Metadata (version), if any
    Version versionObject = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    MathModel mathmodel = new MathModel(versionObject);
    // Set attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    try {
        mathmodel.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // mathmodel.setDescription(unMangle(annotation));
        // }
        // Add annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            mathmodel.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("An error occurred while trying to set the name " + param.getAttributeValue(XMLTags.NameAttrTag) + "to a MathModel!", e);
    }
    // set Geometry (if any)
    Element tempElem = param.getChild(XMLTags.GeometryTag, vcNamespace);
    Geometry tempGeometry = getGeometry(tempElem);
    // set MathDescription
    tempElem = param.getChild(XMLTags.MathDescriptionTag, vcNamespace);
    MathDescription mathDesc = getMathDescription(tempElem, tempGeometry);
    if (tempElem != null) {
        mathmodel.setMathDescription(mathDesc);
    } else {
        throw new XmlParseException("MathDescription missing in this MathModel!");
    }
    // set output functions (outputfunctionContext)
    Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace);
    if (outputFunctionsElement != null) {
        ArrayList<AnnotatedFunction> outputFunctions = getOutputFunctions(outputFunctionsElement);
        try {
            // construct OutputFnContext from mathmodel and add output functions that were read in from XML.
            OutputFunctionContext outputFnContext = mathmodel.getOutputFunctionContext();
            for (AnnotatedFunction outputFunction : outputFunctions) {
                outputFnContext.addOutputFunction(outputFunction);
            }
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    // Set simulations contexts (if any)
    List<Element> childList = param.getChildren(XMLTags.SimulationTag, vcNamespace);
    Simulation[] simList = new Simulation[childList.size()];
    int simCounter = 0;
    for (Element simElement : childList) {
        simList[simCounter] = getSimulation(simElement, mathDesc);
        simCounter++;
    }
    try {
        mathmodel.setSimulations(simList);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred when adding the Simulations to the MathModel " + name, e);
    }
    return mathmodel;
}