Examples with VolumeGeometricRegion cbit.vcell.geometry.surface.VolumeGeometricRegion used on opensource projects

Example 11 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion in project vcell by virtualcell.

the class GeometricRegionTable method getVolumeRegion.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 */
public VolumeGeometricRegion getVolumeRegion(java.sql.ResultSet rset, cbit.vcell.geometry.Geometry geometry) throws java.sql.SQLException, DataAccessException {
    String _name = rset.getString(this.name.toString());
    double _size = rset.getBigDecimal(this.size.toString()).doubleValue();
    String _sizeUnitSymbol = rset.getString(this.sizeUnit.toString());
    cbit.vcell.units.VCUnitDefinition _sizeUnit = geometry.getUnitSystem().getInstance(_sizeUnitSymbol);
    int _regionID = rset.getInt(this.regionID.toString());
    KeyValue _subvolumeKey = new KeyValue(rset.getBigDecimal(this.subVolumeRef.toString()));
    // 
    // find subvolume with correct key
    // 
    cbit.vcell.geometry.SubVolume _subVolume = null;
    cbit.vcell.geometry.SubVolume[] subvolumes = geometry.getGeometrySpec().getSubVolumes();
    for (int i = 0; i < subvolumes.length; i++) {
        if (subvolumes[i].getKey().compareEqual(_subvolumeKey)) {
            _subVolume = subvolumes[i];
            break;
        }
    }
    VolumeGeometricRegion volumeRegion = new VolumeGeometricRegion(_name, _size, _sizeUnit, _subVolume, _regionID);
    return volumeRegion;
}

Example 12 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion in project vcell by virtualcell.

the class GeomDbDriver method getSurfaceDescription.

/**
 * Insert the method's description here.
 * Creation date: (7/29/00 2:10:42 PM)
 * @param con java.sql.Connection
 * @param geom cbit.vcell.geometry.Geometry
 */
private void getSurfaceDescription(Connection con, Geometry geom) throws SQLException, DataAccessException {
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    try {
        String sql = null;
        // 
        // read sampleSize and filterFrequency from GeometrySurfaceTable.
        // 
        sql = " SELECT " + geoSurfaceTable.getTableName() + ".* " + " FROM " + geoSurfaceTable.getTableName() + " WHERE " + geoSurfaceTable.geometryRef.getQualifiedColName() + " = " + geom.getVersion().getVersionKey();
        System.out.println(sql);
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            geoSurfaceTable.populateGeometrySurfaceDescription(rset, geom.getGeometrySurfaceDescription());
            rset.close();
        } else {
            if (lg.isWarnEnabled()) {
                lg.warn("surface description not found for geometry " + geom.getVersion().toString());
            }
            rset.close();
            return;
        }
        // 
        // read volume regions from GeometricRegionTable
        // 
        sql = " SELECT " + geoRegionTable.name.getQualifiedColName() + ", " + geoRegionTable.size.getQualifiedColName() + ", " + geoRegionTable.sizeUnit.getQualifiedColName() + ", " + geoRegionTable.subVolumeRef.getQualifiedColName() + ", " + geoRegionTable.regionID.getQualifiedColName() + " FROM " + geoRegionTable.getTableName() + " WHERE " + geoRegionTable.geometryRef.getQualifiedColName() + " = " + geom.getVersion().getVersionKey() + " AND " + geoRegionTable.type + " = " + GeometricRegionTable.TYPE_VOLUME;
        System.out.println(sql);
        rset = stmt.executeQuery(sql);
        Vector<GeometricRegion> regionList = new Vector<GeometricRegion>();
        while (rset.next()) {
            VolumeGeometricRegion volumeRegion = geoRegionTable.getVolumeRegion(rset, geom);
            regionList.add(volumeRegion);
        }
        VolumeGeometricRegion[] volumeRegions = (VolumeGeometricRegion[]) BeanUtils.getArray(regionList, VolumeGeometricRegion.class);
        // 
        // read surface regions from GeometricRegionTable
        // 
        sql = " SELECT " + "surfTable." + geoRegionTable.name.getUnqualifiedColName() + ", " + "surfTable." + geoRegionTable.size.getUnqualifiedColName() + ", " + "surfTable." + geoRegionTable.sizeUnit.getUnqualifiedColName() + ", " + "vol1Table.name as " + GeometricRegionTable.VOLUME1_NAME_COLUMN + ", " + "vol2Table.name as " + GeometricRegionTable.VOLUME2_NAME_COLUMN + " " + " FROM " + geoRegionTable.getTableName() + " surfTable, " + geoRegionTable.getTableName() + " vol1Table, " + geoRegionTable.getTableName() + " vol2Table " + " WHERE surfTable." + geoRegionTable.geometryRef.getUnqualifiedColName() + " = " + geom.getVersion().getVersionKey() + " AND vol1Table.id = surfTable." + geoRegionTable.volRegion1.getUnqualifiedColName() + " AND vol2Table.id = surfTable." + geoRegionTable.volRegion2.getUnqualifiedColName() + " AND surfTable." + geoRegionTable.type.getUnqualifiedColName() + " = " + GeometricRegionTable.TYPE_SURFACE;
        System.out.println(sql);
        rset = stmt.executeQuery(sql);
        while (rset.next()) {
            SurfaceGeometricRegion surfaceRegion = geoRegionTable.getSurfaceRegion(rset, volumeRegions, geom.getUnitSystem());
            regionList.add(surfaceRegion);
        }
        // 
        // set regions onto the geometrySurfaceDescription
        // 
        GeometricRegion[] regions = (GeometricRegion[]) BeanUtils.getArray(regionList, GeometricRegion.class);
        geom.getGeometrySurfaceDescription().setGeometricRegions(regions);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.toString());
    } finally {
        // Release resources include resultset
        stmt.close();
    }
}

Example 13 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion in project vcell by virtualcell.

the class GeomDbDriver method insertGeometrySurfaceDescriptionSQL.

/**
 * This method was created in VisualAge.
 * @param vcimage cbit.image.VCImage
 * @param userid java.lang.String
 * @exception java.rmi.RemoteException The exception description.
 */
// default access for this method, to allow retrofitting surfaces to geometries.
void insertGeometrySurfaceDescriptionSQL(InsertHashtable hash, Connection con, Geometry geom, KeyValue geomKey) throws SQLException, cbit.image.ImageException, DataAccessException, ObjectNotFoundException {
    String sql;
    GeometrySurfaceDescription geoSurfaceDescription = geom.getGeometrySurfaceDescription();
    // 
    // store GeometrySurfaceDescription (sampleSize and filterFrequency for now)
    // 
    KeyValue newGeomSurfDescKey = keyFactory.getNewKey(con);
    sql = "INSERT INTO " + geoSurfaceTable.getTableName() + " " + geoSurfaceTable.getSQLColumnList() + " VALUES " + geoSurfaceTable.getSQLValueList(newGeomSurfDescKey, geoSurfaceDescription, geomKey);
    // System.out.println(sql);
    updateCleanSQL(con, sql);
    // 
    // store GeometricRegions
    // 
    GeometricRegion[] regions = geoSurfaceDescription.getGeometricRegions();
    // }
    if (regions == null) {
        System.out.println("Geometry " + geom.getName() + "(" + geom.getVersion() + ") doesn't have region information");
        throw new DataAccessException("geometry '" + geom.getName() + " didn't have region information");
    }
    // 
    for (int i = 0; i < regions.length; i++) {
        if (regions[i] instanceof VolumeGeometricRegion) {
            VolumeGeometricRegion volumeRegion = (VolumeGeometricRegion) regions[i];
            if (hash.getDatabaseKey(volumeRegion) == null) {
                KeyValue newVolumeRegionKey = keyFactory.getNewKey(con);
                KeyValue subvolumeKey = hash.getDatabaseKey(volumeRegion.getSubVolume());
                sql = "INSERT INTO " + geoRegionTable.getTableName() + " " + geoRegionTable.getSQLColumnList() + " VALUES " + geoRegionTable.getSQLValueList(newVolumeRegionKey, volumeRegion, subvolumeKey, geomKey);
                // System.out.println(sql);
                updateCleanSQL(con, sql);
                hash.put(volumeRegion, newVolumeRegionKey);
            }
        }
    }
    // 
    for (int i = 0; i < regions.length; i++) {
        if (regions[i] instanceof SurfaceGeometricRegion) {
            SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) regions[i];
            if (hash.getDatabaseKey(surfaceRegion) == null) {
                KeyValue newSurfaceRegionKey = keyFactory.getNewKey(con);
                KeyValue volumeRegion1Key = hash.getDatabaseKey((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[0]);
                KeyValue volumeRegion2Key = hash.getDatabaseKey((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[1]);
                sql = "INSERT INTO " + geoRegionTable.getTableName() + " " + geoRegionTable.getSQLColumnList() + " VALUES " + geoRegionTable.getSQLValueList(newSurfaceRegionKey, surfaceRegion, volumeRegion1Key, volumeRegion2Key, geomKey);
                // System.out.println(sql);
                updateCleanSQL(con, sql);
                hash.put(surfaceRegion, newSurfaceRegionKey);
            }
        }
    }
}

Example 14 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion 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();
        }
    }
}

Example 15 with VolumeGeometricRegion

use of cbit.vcell.geometry.surface.VolumeGeometricRegion in project vcell by virtualcell.

the class SurfaceRegionObject method getSurfaceRegion.

public SurfaceGeometricRegion getSurfaceRegion(Geometry geometry) {
    GeometricRegion[] regions = geometry.getGeometrySurfaceDescription().getGeometricRegions();
    for (GeometricRegion region : regions) {
        if (region instanceof SurfaceGeometricRegion) {
            SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) region;
            GeometricRegion[] adjacentRegions = surfaceRegion.getAdjacentGeometricRegions();
            if (adjacentRegions.length == 2 && adjacentRegions[0] instanceof VolumeGeometricRegion && adjacentRegions[1] instanceof VolumeGeometricRegion) {
                VolumeGeometricRegion adjVolumeRegion0 = (VolumeGeometricRegion) adjacentRegions[0];
                VolumeGeometricRegion adjVolumeRegion1 = (VolumeGeometricRegion) adjacentRegions[1];
                // match adjacent vol0 with inside and vol1 with outside
                if (adjVolumeRegion0.getSubVolume() == insideSubVolume && adjVolumeRegion0.getRegionID() == insideRegionID && adjVolumeRegion1.getSubVolume() == outsideSubVolume && adjVolumeRegion1.getRegionID() == outsideRegionID) {
                    return surfaceRegion;
                }
                // match adjacent vol1 with inside and vol0 with outside
                if (adjVolumeRegion1.getSubVolume() == insideSubVolume && adjVolumeRegion1.getRegionID() == insideRegionID && adjVolumeRegion0.getSubVolume() == outsideSubVolume && adjVolumeRegion0.getRegionID() == outsideRegionID) {
                    return surfaceRegion;
                }
            }
        }
    }
    return null;
}