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

Example 66 with Geometry

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

the class ClientDocumentManager method getGeometry.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 4:02:44 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public Geometry getGeometry(GeometryInfo geometryInfo) throws DataAccessException {
    Geometry geometry = null;
    try {
        XMLSource geomSource = new XMLSource(getGeometryXML(geometryInfo.getVersion().getVersionKey()));
        geometry = XmlHelper.XMLToGeometry(geomSource);
    } catch (XmlParseException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    }
    try {
        if (geometry.getDimension() > 0 && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
            geometry.getGeometrySurfaceDescription().updateAll();
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
    // throw new DataAccessException("Geometric surface generation error:\n"+e.getMessage());
    }
    return geometry;
}

Example 67 with Geometry

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

the class ClientDocumentManager method getGeometryFromDatabaseXML.

/**
 * Insert the method's description here.
 * Creation date: (9/22/2004 5:22:40 PM)
 * @return cbit.vcell.mathmodel.MathModel
 * @param mathModelXML java.lang.String
 */
private Geometry getGeometryFromDatabaseXML(String geometryXML) throws DataAccessException {
    try {
        Geometry geometry = XmlHelper.XMLToGeometry(new XMLSource(geometryXML));
        geometry.refreshDependencies();
        try {
            if (geometry.getDimension() > 0) {
                geometry.getGeometrySurfaceDescription().updateAll();
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new DataAccessException("Geometric surface generation error:\n" + e.getMessage());
        }
        return geometry;
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new DataAccessException(e.getClass().getName() + ": " + e.getMessage());
    }
}

Example 68 with Geometry

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

the class SimulationContext method setGeometry.

/**
 * This method was created in VisualAge.
 */
public void setGeometry(Geometry geometry) throws MappingException {
    Geometry oldGeometry = this.getGeometry();
    if (geometry != oldGeometry) {
        getGeometryContext().setGeometry(geometry);
        try {
            refreshCharacteristicSize();
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException(e.getMessage());
        }
        refreshSpatialObjects();
        oldGeometry.getGeometrySpec().removePropertyChangeListener(this);
        getGeometry().getGeometrySpec().addPropertyChangeListener(this);
        if (geometry != null && geometry.getDimension() > 0) {
            try {
                if (fieldBioEvents != null) {
                    setBioEvents(null);
                }
                if (fieldRateRules != null) {
                    setRateRules(null);
                }
                if (fieldAnalysisTasks != null) {
                    setAnalysisTasks(null);
                }
                if (oldGeometry != null && oldGeometry.getDimension() == 0) {
                    // && geometry != null && geometry.getDimension() > 0
                    initializeForSpatial();
                }
            } catch (PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new MappingException(e.getMessage());
            }
        }
    // now firing from geoContext
    // firePropertyChange("geometry",oldGeometry,geometry);
    }
}

Example 69 with Geometry

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

the class SimulationContext method copySimulationContext.

public static SimulationContext copySimulationContext(SimulationContext srcSimContext, String newSimulationContextName, boolean bSpatial, Application simContextType) throws java.beans.PropertyVetoException, ExpressionException, MappingException, GeometryException, ImageException {
    Geometry newClonedGeometry = new Geometry(srcSimContext.getGeometry());
    newClonedGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
    // if stoch copy to ode, we need to check is stoch is using particles. If yes, should convert particles to concentraton.
    // the other 3 cases are fine. ode->ode, ode->stoch, stoch-> stoch
    SimulationContext destSimContext = new SimulationContext(srcSimContext, newClonedGeometry, simContextType);
    if (srcSimContext.getApplicationType() == Application.NETWORK_STOCHASTIC && !srcSimContext.isUsingConcentration() && simContextType == Application.NETWORK_DETERMINISTIC) {
        try {
            destSimContext.convertSpeciesIniCondition(true);
        } catch (MappingException e) {
            e.printStackTrace();
            throw new java.beans.PropertyVetoException(e.getMessage(), null);
        }
    }
    if (srcSimContext.getGeometry().getDimension() > 0 && !bSpatial) {
        // copy the size over
        destSimContext.setGeometry(new Geometry("nonspatial", 0));
        StructureMapping[] srcStructureMappings = srcSimContext.getGeometryContext().getStructureMappings();
        StructureMapping[] destStructureMappings = destSimContext.getGeometryContext().getStructureMappings();
        for (StructureMapping destStructureMapping : destStructureMappings) {
            for (StructureMapping srcStructureMapping : srcStructureMappings) {
                if (destStructureMapping.getStructure() == srcStructureMapping.getStructure()) {
                    if (srcStructureMapping.getUnitSizeParameter() != null) {
                        Expression sizeRatio = srcStructureMapping.getUnitSizeParameter().getExpression();
                        GeometryClass srcGeometryClass = srcStructureMapping.getGeometryClass();
                        GeometricRegion[] srcGeometricRegions = srcSimContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(srcGeometryClass);
                        if (srcGeometricRegions != null) {
                            double size = 0;
                            for (GeometricRegion srcGeometricRegion : srcGeometricRegions) {
                                size += srcGeometricRegion.getSize();
                            }
                            destStructureMapping.getSizeParameter().setExpression(Expression.mult(sizeRatio, new Expression(size)));
                        }
                    }
                    break;
                }
            }
        }
        // If changing spatial to non-spatial
        // set diffusion to 0, velocity and boundary to null
        // srcSimContext.getReactionContext().getspe
        Parameter[] allParameters = destSimContext.getAllParameters();
        if (allParameters != null && allParameters.length > 0) {
            for (int i = 0; i < allParameters.length; i++) {
                if (allParameters[i] instanceof SpeciesContextSpecParameter) {
                    SpeciesContextSpecParameter speciesContextSpecParameter = (SpeciesContextSpecParameter) allParameters[i];
                    int role = speciesContextSpecParameter.getRole();
                    if (role == SpeciesContextSpec.ROLE_DiffusionRate) {
                        speciesContextSpecParameter.setExpression(new Expression(0));
                    } else if (role == SpeciesContextSpec.ROLE_BoundaryValueXm || role == SpeciesContextSpec.ROLE_BoundaryValueXp || role == SpeciesContextSpec.ROLE_BoundaryValueYm || role == SpeciesContextSpec.ROLE_BoundaryValueYp || role == SpeciesContextSpec.ROLE_BoundaryValueZm || role == SpeciesContextSpec.ROLE_BoundaryValueZp) {
                        speciesContextSpecParameter.setExpression(null);
                    } else if (role == SpeciesContextSpec.ROLE_VelocityX || role == SpeciesContextSpec.ROLE_VelocityY || role == SpeciesContextSpec.ROLE_VelocityZ) {
                        speciesContextSpecParameter.setExpression(null);
                    }
                }
            }
        }
    }
    destSimContext.fixFlags();
    destSimContext.setName(newSimulationContextName);
    return destSimContext;
}

Example 70 with Geometry

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

the class SimulationContext method refreshSpatialObjects.

public void refreshSpatialObjects() {
    Geometry geometry = getGeometry();
    if (geometry != null && geometry.getGeometrySurfaceDescription() != null && geometry.getGeometrySurfaceDescription().getGeometricRegions() != null) {
        ArrayList<SpatialObject> unmappedSpatialObjects = new ArrayList<SpatialObject>(Arrays.asList(spatialObjects));
        ArrayList<GeometricRegion> mappedRegions = new ArrayList<GeometricRegion>();
        // 
        for (SpatialObject spatialObject : spatialObjects) {
            if (spatialObject instanceof VolumeRegionObject) {
                VolumeRegionObject volRegionObj = (VolumeRegionObject) spatialObject;
                SubVolume existingSubvolume = volRegionObj.getSubVolume();
                Integer existingRegionID = volRegionObj.getRegionID();
                SubVolume newSubvolume = geometry.getGeometrySpec().getSubVolume(existingSubvolume.getName());
                if (newSubvolume != null && geometry.getGeometrySurfaceDescription().getGeometricRegions() != null) {
                    for (GeometricRegion newRegion : geometry.getGeometrySurfaceDescription().getGeometricRegions(newSubvolume)) {
                        VolumeGeometricRegion newVolRegion = (VolumeGeometricRegion) newRegion;
                        if (newVolRegion.getRegionID() == existingRegionID) {
                            ((VolumeRegionObject) spatialObject).setSubVolume(newSubvolume);
                            mappedRegions.add(newVolRegion);
                            unmappedSpatialObjects.remove(spatialObject);
                        }
                    }
                }
            }
            if (spatialObject instanceof SurfaceRegionObject) {
                SurfaceRegionObject surfaceRegionObj = (SurfaceRegionObject) spatialObject;
                SubVolume existingInsideSubvolume = surfaceRegionObj.getInsideSubVolume();
                SubVolume existingOutsideSubvolume = surfaceRegionObj.getOutsideSubVolume();
                Integer existingInsideRegionID = surfaceRegionObj.getInsideRegionID();
                Integer existingOutsideRegionID = surfaceRegionObj.getOutsideRegionID();
                SubVolume newInsideSubvolume = geometry.getGeometrySpec().getSubVolume(existingInsideSubvolume.getName());
                SubVolume newOutsideSubvolume = geometry.getGeometrySpec().getSubVolume(existingOutsideSubvolume.getName());
                if (newInsideSubvolume != null && newOutsideSubvolume != null) {
                    SurfaceClass surfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(newInsideSubvolume, newOutsideSubvolume);
                    for (GeometricRegion newRegion : geometry.getGeometrySurfaceDescription().getGeometricRegions(surfaceClass)) {
                        SurfaceGeometricRegion newSurfaceRegion = (SurfaceGeometricRegion) newRegion;
                        GeometricRegion[] adjacentRegions = newSurfaceRegion.getAdjacentGeometricRegions();
                        if (adjacentRegions.length == 2 && adjacentRegions[0] instanceof VolumeGeometricRegion && adjacentRegions[1] instanceof VolumeGeometricRegion) {
                            VolumeGeometricRegion adjVolRegion0 = (VolumeGeometricRegion) adjacentRegions[0];
                            VolumeGeometricRegion adjVolRegion1 = (VolumeGeometricRegion) adjacentRegions[1];
                            if (adjVolRegion0.getSubVolume() == newInsideSubvolume && adjVolRegion0.getRegionID() == existingInsideRegionID && adjVolRegion1.getSubVolume() == newOutsideSubvolume && adjVolRegion1.getRegionID() == existingOutsideRegionID) {
                                surfaceRegionObj.setInsideSubVolume(newInsideSubvolume);
                                surfaceRegionObj.setOutsideSubVolume(newOutsideSubvolume);
                                mappedRegions.add(newSurfaceRegion);
                                unmappedSpatialObjects.remove(spatialObject);
                            }
                            if (adjVolRegion0.getSubVolume() == newOutsideSubvolume && adjVolRegion0.getRegionID() == existingOutsideRegionID && adjVolRegion1.getSubVolume() == newInsideSubvolume && adjVolRegion1.getRegionID() == existingInsideRegionID) {
                                surfaceRegionObj.setInsideSubVolume(newInsideSubvolume);
                                surfaceRegionObj.setOutsideSubVolume(newOutsideSubvolume);
                                mappedRegions.add(newSurfaceRegion);
                                unmappedSpatialObjects.remove(spatialObject);
                            }
                        }
                    }
                }
            }
        }
        // 
        // for geometric regions not represented as spatial objects, add them
        // 
        ArrayList<GeometricRegion> unmappedRegions = new ArrayList<GeometricRegion>(Arrays.asList(geometry.getGeometrySurfaceDescription().getGeometricRegions()));
        unmappedRegions.removeAll(mappedRegions);
        for (GeometricRegion unmappedRegion : unmappedRegions) {
            if (unmappedRegion instanceof VolumeGeometricRegion) {
                VolumeGeometricRegion unmappedVolRegion = (VolumeGeometricRegion) unmappedRegion;
                try {
                    VolumeRegionObject vro = new VolumeRegionObject(unmappedVolRegion.getSubVolume(), unmappedVolRegion.getRegionID(), this);
                    addSpatialObject(vro);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                }
            } else if (unmappedRegion instanceof SurfaceGeometricRegion) {
                SurfaceGeometricRegion unmappedSurfRegion = (SurfaceGeometricRegion) unmappedRegion;
                GeometricRegion[] adjacentRegions = unmappedSurfRegion.getAdjacentGeometricRegions();
                if (adjacentRegions.length == 2 && adjacentRegions[0] instanceof VolumeGeometricRegion && adjacentRegions[1] instanceof VolumeGeometricRegion) {
                    VolumeGeometricRegion volRegion0 = (VolumeGeometricRegion) adjacentRegions[0];
                    VolumeGeometricRegion volRegion1 = (VolumeGeometricRegion) adjacentRegions[1];
                    SubVolume insideSubVolume = volRegion0.getSubVolume();
                    SubVolume outsideSubVolume = volRegion1.getSubVolume();
                    int insideRegionID = volRegion0.getRegionID();
                    int outsideRegionID = volRegion1.getRegionID();
                    SurfaceClass surfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(insideSubVolume, outsideSubVolume);
                    try {
                        addSpatialObject(new SurfaceRegionObject(insideSubVolume, insideRegionID, outsideSubVolume, outsideRegionID, this));
                    } catch (PropertyVetoException e) {
                        e.printStackTrace();
                    }
                }
            }
        }
        // 
        try {
            for (SpatialObject unmappedSpatialObject : unmappedSpatialObjects) {
                if (unmappedSpatialObject instanceof VolumeRegionObject) {
                    System.err.println("volume region spatial object '" + unmappedSpatialObject.getName() + "' not found in geometry, delete.");
                    removeSpatialObject(unmappedSpatialObject);
                }
                if (unmappedSpatialObject instanceof SurfaceRegionObject) {
                    System.err.println("surface region spatial object '" + unmappedSpatialObject.getName() + "' not found in geometry, delete.");
                    removeSpatialObject(unmappedSpatialObject);
                }
                if (unmappedSpatialObject instanceof PointObject) {
                    System.err.println("point spatial object '" + unmappedSpatialObject.getName() + "' not found in geometry, this is expected.");
                // removeSpatialObject(unmappedSpatialObject);
                }
            }
        } catch (PropertyVetoException e) {
            e.printStackTrace();
        }
    }
}