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

Example 1 with SurfaceGeometricRegion

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

the class ClientRequestManager method createMathModel.

/**
 * Insert the method's description here. Creation date: (5/24/2004 12:22:11 PM)
 *
 * @param windowID java.lang.String
 */
private MathModel createMathModel(String name, Geometry geometry) {
    MathModel mathModel = new MathModel(null);
    MathDescription mathDesc = mathModel.getMathDescription();
    try {
        mathDesc.setGeometry(geometry);
        if (geometry.getDimension() == 0) {
            mathDesc.addSubDomain(new CompartmentSubDomain("Compartment", CompartmentSubDomain.NON_SPATIAL_PRIORITY));
        } else {
            try {
                if (geometry.getDimension() > 0 && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                    geometry.getGeometrySurfaceDescription().updateAll();
                }
            } catch (ImageException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Geometric surface generation error: \n" + e.getMessage());
            } catch (GeometryException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Geometric surface generation error: \n" + e.getMessage());
            }
            SubVolume[] subVolumes = geometry.getGeometrySpec().getSubVolumes();
            for (int i = 0; i < subVolumes.length; i++) {
                mathDesc.addSubDomain(new CompartmentSubDomain(subVolumes[i].getName(), subVolumes[i].getHandle()));
            }
            // 
            // add only those MembraneSubDomains corresponding to surfaces that acutally
            // exist in geometry.
            // 
            GeometricRegion[] regions = geometry.getGeometrySurfaceDescription().getGeometricRegions();
            for (int i = 0; i < regions.length; i++) {
                if (regions[i] instanceof SurfaceGeometricRegion) {
                    SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) regions[i];
                    SubVolume subVolume1 = ((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[0]).getSubVolume();
                    SubVolume subVolume2 = ((VolumeGeometricRegion) surfaceRegion.getAdjacentGeometricRegions()[1]).getSubVolume();
                    CompartmentSubDomain compartment1 = mathDesc.getCompartmentSubDomain(subVolume1.getName());
                    CompartmentSubDomain compartment2 = mathDesc.getCompartmentSubDomain(subVolume2.getName());
                    MembraneSubDomain membraneSubDomain = mathDesc.getMembraneSubDomain(compartment1, compartment2);
                    if (membraneSubDomain == null) {
                        SurfaceClass surfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(subVolume1, subVolume2);
                        membraneSubDomain = new MembraneSubDomain(compartment1, compartment2, surfaceClass.getName());
                        mathDesc.addSubDomain(membraneSubDomain);
                    }
                }
            }
        }
        mathDesc.isValid();
        mathModel.setName(name);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
    return mathModel;
}

Example 2 with SurfaceGeometricRegion

use of cbit.vcell.geometry.surface.SurfaceGeometricRegion 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();
        if (lg.isTraceEnabled())
            lg.trace(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;
        if (lg.isTraceEnabled())
            lg.trace(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;
        if (lg.isTraceEnabled())
            lg.trace(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) {
        throw new DataAccessException(e.toString(), e);
    } finally {
        // Release resources include resultset
        stmt.close();
    }
}

Example 3 with SurfaceGeometricRegion

use of cbit.vcell.geometry.surface.SurfaceGeometricRegion 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) {
        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 4 with SurfaceGeometricRegion

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

the class SmoldynFileWriter method writeSurfaces.

private void writeSurfaces() throws SolverException, ImageException, PropertyVetoException, GeometryException, ExpressionException {
    GeometrySurfaceDescription geometrySurfaceDescription = resampledGeometry.getGeometrySurfaceDescription();
    SurfaceClass[] surfaceClasses = geometrySurfaceDescription.getSurfaceClasses();
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    SubVolume[] surfaceGeometrySubVolumes = geometrySpec.getSubVolumes();
    GeometricRegion[] AllGeometricRegions = resampledGeometry.getGeometrySurfaceDescription().getGeometricRegions();
    ArrayList<SurfaceGeometricRegion> surfaceRegionList = new ArrayList<SurfaceGeometricRegion>();
    ArrayList<VolumeGeometricRegion> volumeRegionList = new ArrayList<VolumeGeometricRegion>();
    for (GeometricRegion geometricRegion : AllGeometricRegions) {
        if (geometricRegion instanceof SurfaceGeometricRegion) {
            surfaceRegionList.add((SurfaceGeometricRegion) geometricRegion);
        } else if (geometricRegion instanceof VolumeGeometricRegion) {
            volumeRegionList.add((VolumeGeometricRegion) geometricRegion);
        } else {
            throw new SolverException("unsupported geometric region type " + geometricRegion.getClass());
        }
    }
    printWriter.println("# geometry");
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.dim + " " + dimension);
    if (bHasNoSurface) {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_compartment + " " + surfaceGeometrySubVolumes.length);
    } else {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_compartment + " " + (surfaceGeometrySubVolumes.length + 1));
        // plus the surface which are bounding walls
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_surface + " " + (surfaceClasses.length + dimension));
    }
    printWriter.println();
    // write boundaries and wall surfaces
    writeWallSurfaces();
    // for 3D ... smoldyn normal convension is triangle right-hand-rule normal points to the outside compartment subdomain.
    if (!bHasNoSurface) {
        membraneSubdomainTriangleMap = new HashMap<MembraneSubDomain, ArrayList<TrianglePanel>>();
        // write surfaces
        printWriter.println("# surfaces");
        int triangleGlobalCount = 0;
        int membraneIndex = -1;
        SurfaceCollection surfaceCollection = geometrySurfaceDescription.getSurfaceCollection();
        // pre-allocate collections used repeatedly in following loops; clear before reusing
        HashMap<Node, Set<String>> nodeTriMap = new HashMap<>();
        ArrayList<TrianglePanel> triList = new ArrayList<TrianglePanel>();
        // use a sorted set to ensure neighbors written out is same order for reproducibility
        SortedSet<String> neighborsForCurrentNode = new TreeSet<String>();
        for (int sci = 0; sci < surfaceClasses.length; sci++) {
            nodeTriMap.clear();
            triList.clear();
            int triLocalCount = 0;
            SurfaceClass surfaceClass = surfaceClasses[sci];
            GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(surfaceClass);
            for (GeometricRegion gr : geometricRegions) {
                SurfaceGeometricRegion sgr = (SurfaceGeometricRegion) gr;
                VolumeGeometricRegion volRegion0 = (VolumeGeometricRegion) sgr.getAdjacentGeometricRegions()[0];
                VolumeGeometricRegion volRegion1 = (VolumeGeometricRegion) sgr.getAdjacentGeometricRegions()[1];
                SubVolume subVolume0 = volRegion0.getSubVolume();
                SubVolume subVolume1 = volRegion1.getSubVolume();
                CompartmentSubDomain compart0 = mathDesc.getCompartmentSubDomain(subVolume0.getName());
                CompartmentSubDomain compart1 = mathDesc.getCompartmentSubDomain(subVolume1.getName());
                MembraneSubDomain membraneSubDomain = mathDesc.getMembraneSubDomain(compart0, compart1);
                if (membraneSubDomain == null) {
                    throw new SolverException(VCellErrorMessages.getSmoldynUnexpectedSurface(compart0, compart1));
                }
                int exteriorRegionID = volRegion0.getRegionID();
                int interiorRegionID = volRegion1.getRegionID();
                if (membraneSubDomain.getInsideCompartment() == compart0) {
                    exteriorRegionID = volRegion1.getRegionID();
                    interiorRegionID = volRegion0.getRegionID();
                }
                for (int j = 0; j < surfaceCollection.getSurfaceCount(); j++) {
                    Surface surface = surfaceCollection.getSurfaces(j);
                    if ((surface.getInteriorRegionIndex() == exteriorRegionID && surface.getExteriorRegionIndex() == interiorRegionID) || (surface.getInteriorRegionIndex() == interiorRegionID && surface.getExteriorRegionIndex() == exteriorRegionID)) {
                        // Polygon polygon = surface.getPolygons(k);
                        for (Polygon polygon : surface) {
                            if (polygonMembaneElementMap != null) {
                                membraneIndex = polygonMembaneElementMap.get(polygon).getMembraneIndex();
                            }
                            Node[] nodes = polygon.getNodes();
                            if (dimension == 2) {
                                // ignore z
                                Vect3d unitNormal = new Vect3d();
                                polygon.getUnitNormal(unitNormal);
                                unitNormal.set(unitNormal.getX(), unitNormal.getY(), 0);
                                int point0 = 0;
                                Vect3d v0 = new Vect3d(nodes[point0].getX(), nodes[point0].getY(), 0);
                                int point1 = 1;
                                Vect3d v1 = null;
                                for (point1 = 1; point1 < nodes.length; point1++) {
                                    if (v0.getX() != nodes[point1].getX() || v0.getY() != nodes[point1].getY()) {
                                        v1 = new Vect3d(nodes[point1].getX(), nodes[point1].getY(), 0);
                                        break;
                                    }
                                }
                                if (v1 == null) {
                                    throw new RuntimeException("failed to generate surface");
                                }
                                Vect3d v01 = Vect3d.sub(v1, v0);
                                Vect3d unit01n = v01.cross(unitNormal);
                                unit01n.unit();
                                if (Math.abs(unit01n.getZ() - 1.0) < 1e-6) {
                                    // v0 to v1 opposes vcell surface normal. it's already flipped.
                                    Triangle triangle;
                                    if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                        // we have to flipped it back
                                        triangle = new Triangle(nodes[point1], nodes[point0], null);
                                    } else {
                                        triangle = new Triangle(nodes[point0], nodes[point1], null);
                                    }
                                    triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle));
                                } else if (Math.abs(unit01n.getZ() + 1.0) < 1e-6) {
                                    // v0 to v1 is in direction of vcell surface normal.
                                    Triangle triangle;
                                    if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                        triangle = new Triangle(nodes[point0], nodes[point1], null);
                                    } else {
                                        triangle = new Triangle(nodes[point1], nodes[point0], null);
                                    }
                                    triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle));
                                } else {
                                    throw new RuntimeException("failed to generate surface");
                                }
                            } else if (dimension == 3) {
                                Triangle triangle1;
                                Triangle triangle2;
                                if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                    // interior
                                    triangle1 = new Triangle(nodes[0], nodes[1], nodes[2]);
                                    triangle2 = new Triangle(nodes[0], nodes[2], nodes[3]);
                                } else {
                                    triangle1 = new Triangle(nodes[2], nodes[1], nodes[0]);
                                    triangle2 = new Triangle(nodes[3], nodes[2], nodes[0]);
                                }
                                triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle1));
                                triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle2));
                            }
                        }
                    }
                }
            }
            // add triangles to node hash
            for (TrianglePanel triPanel : triList) {
                for (Node node : triPanel.triangle.getNodes()) {
                    if (node == null) {
                        continue;
                    }
                    Set<String> triNameSet = nodeTriMap.get(node);
                    if (triNameSet == null) {
                        triNameSet = new HashSet<String>();
                        nodeTriMap.put(node, triNameSet);
                    }
                    triNameSet.add(triPanel.name);
                }
            }
            SubVolume[] adjacentSubvolums = surfaceClass.getAdjacentSubvolumes().toArray(new SubVolume[0]);
            CompartmentSubDomain csd0 = simulation.getMathDescription().getCompartmentSubDomain(adjacentSubvolums[0].getName());
            CompartmentSubDomain csd1 = simulation.getMathDescription().getCompartmentSubDomain(adjacentSubvolums[1].getName());
            MembraneSubDomain membraneSubDomain = simulation.getMathDescription().getMembraneSubDomain(csd0, csd1);
            membraneSubdomainTriangleMap.put(membraneSubDomain, triList);
            final boolean initialMoleculesOnMembrane = (closestTriangles != null);
            if (initialMoleculesOnMembrane) {
                findClosestTriangles(membraneSubDomain, triList);
            }
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + surfaceClass.getName());
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.all + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
            // printWriter.println(SmoldynKeyword.action + " " + SmoldynKeyword.all + "(" + SmoldynKeyword.up + ") " + SmoldynKeyword.both + " " + SmoldynKeyword.reflect);
            // get color after species
            Color c = colors[sci + particleVariableList.size()];
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + c.getRed() / 255.0 + " " + c.getGreen() / 255.0 + " " + c.getBlue() / 255.0 + " 0.1");
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.tri + " " + triList.size());
            for (TrianglePanel trianglePanel : triList) {
                Triangle triangle = trianglePanel.triangle;
                printWriter.print(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.tri);
                switch(dimension) {
                    case 1:
                        printWriter.print(" " + triangle.getNodes(0).getX());
                        break;
                    case 2:
                        printWriter.print(" " + triangle.getNodes(0).getX() + " " + triangle.getNodes(0).getY());
                        printWriter.print(" " + triangle.getNodes(1).getX() + " " + triangle.getNodes(1).getY());
                        break;
                    case 3:
                        for (Node node : triangle.getNodes()) {
                            printWriter.print(" " + node.getX() + " " + node.getY() + " " + node.getZ());
                        }
                        break;
                }
                printWriter.println(" " + trianglePanel.name);
            }
            for (TrianglePanel triPanel : triList) {
                neighborsForCurrentNode.clear();
                for (Node node : triPanel.triangle.getNodes()) {
                    if (node == null) {
                        continue;
                    }
                    neighborsForCurrentNode.addAll(nodeTriMap.get(node));
                }
                neighborsForCurrentNode.remove(triPanel.name);
                // printWriter.print(SmoldynKeyword.neighbors + " " +triPanel.name);
                // to allow smoldyn read line length as 256, chop the neighbors to multiple lines
                int maxNeighborCount = 4;
                // 
                int count = 0;
                for (String neigh : neighborsForCurrentNode) {
                    if (count % maxNeighborCount == 0) {
                        printWriter.println();
                        printWriter.print(SmoldynVCellMapper.SmoldynKeyword.neighbors + " " + triPanel.name);
                    }
                    printWriter.print(" " + neigh);
                    count++;
                }
            }
            printWriter.println();
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
            printWriter.println();
        }
    // write compartment
    // printWriter.println("# bounding wall compartment");
    // printWriter.println(SmoldynKeyword.start_compartment + " " + VCellSmoldynKeyword.bounding_wall_compartment);
    // printWriter.println(SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_X);
    // if (dimension > 1) {
    // printWriter.println(SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Y);
    // if (dimension > 2) {
    // printWriter.println(SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Z);
    // }
    // }
    // printWriter.println(SmoldynKeyword.end_compartment);
    // printWriter.println();
    }
}

Example 5 with SurfaceGeometricRegion

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

the class SmoldynSurfaceTessellator method writeSurfaces.

protected void writeSurfaces() throws SolverException, ImageException, PropertyVetoException, GeometryException, ExpressionException {
    GeometrySurfaceDescription geometrySurfaceDescription = resampledGeometry.getGeometrySurfaceDescription();
    SurfaceClass[] surfaceClasses = geometrySurfaceDescription.getSurfaceClasses();
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    SubVolume[] surfaceGeometrySubVolumes = geometrySpec.getSubVolumes();
    GeometricRegion[] AllGeometricRegions = resampledGeometry.getGeometrySurfaceDescription().getGeometricRegions();
    ArrayList<SurfaceGeometricRegion> surfaceRegionList = new ArrayList<SurfaceGeometricRegion>();
    ArrayList<VolumeGeometricRegion> volumeRegionList = new ArrayList<VolumeGeometricRegion>();
    for (GeometricRegion geometricRegion : AllGeometricRegions) {
        if (geometricRegion instanceof SurfaceGeometricRegion) {
            surfaceRegionList.add((SurfaceGeometricRegion) geometricRegion);
        } else if (geometricRegion instanceof VolumeGeometricRegion) {
            volumeRegionList.add((VolumeGeometricRegion) geometricRegion);
        } else {
            throw new SolverException("unsupported geometric region type " + geometricRegion.getClass());
        }
    }
    printWriter.println("# geometry");
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.dim + " " + dimension);
    if (bHasNoSurface) {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_compartment + " " + surfaceGeometrySubVolumes.length);
    } else {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_compartment + " " + (surfaceGeometrySubVolumes.length + 1));
        // plus the surface which are bounding walls
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_surface + " " + (surfaceClasses.length + dimension));
    }
    printWriter.println();
    // write boundaries and wall surfaces
    writeWallSurfaces();
    // for 3D ... smoldyn normal convension is triangle right-hand-rule normal points to the outside compartment subdomain.
    if (!bHasNoSurface) {
        membraneSubdomainTriangleMap = new HashMap<MembraneSubDomain, ArrayList<TrianglePanel>>();
        // write surfaces
        printWriter.println("# surfaces");
        int triangleGlobalCount = 0;
        int membraneIndex = -1;
        SurfaceCollection surfaceCollection = geometrySurfaceDescription.getSurfaceCollection();
        // pre-allocate collections used repeatedly in following loops; clear before reusing
        HashMap<Node, Set<String>> nodeTriMap = new HashMap<>();
        ArrayList<TrianglePanel> triList = new ArrayList<TrianglePanel>();
        // use a sorted set to ensure neighbors written out is same order for reproducibility
        SortedSet<String> neighborsForCurrentNode = new TreeSet<String>();
        for (int sci = 0; sci < surfaceClasses.length; sci++) {
            nodeTriMap.clear();
            triList.clear();
            int triLocalCount = 0;
            SurfaceClass surfaceClass = surfaceClasses[sci];
            GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(surfaceClass);
            for (GeometricRegion gr : geometricRegions) {
                SurfaceGeometricRegion sgr = (SurfaceGeometricRegion) gr;
                VolumeGeometricRegion volRegion0 = (VolumeGeometricRegion) sgr.getAdjacentGeometricRegions()[0];
                VolumeGeometricRegion volRegion1 = (VolumeGeometricRegion) sgr.getAdjacentGeometricRegions()[1];
                SubVolume subVolume0 = volRegion0.getSubVolume();
                SubVolume subVolume1 = volRegion1.getSubVolume();
                CompartmentSubDomain compart0 = mathDesc.getCompartmentSubDomain(subVolume0.getName());
                CompartmentSubDomain compart1 = mathDesc.getCompartmentSubDomain(subVolume1.getName());
                MembraneSubDomain membraneSubDomain = mathDesc.getMembraneSubDomain(compart0, compart1);
                if (membraneSubDomain == null) {
                    throw new SolverException(VCellErrorMessages.getSmoldynUnexpectedSurface(compart0, compart1));
                }
                int exteriorRegionID = volRegion0.getRegionID();
                int interiorRegionID = volRegion1.getRegionID();
                if (membraneSubDomain.getInsideCompartment() == compart0) {
                    exteriorRegionID = volRegion1.getRegionID();
                    interiorRegionID = volRegion0.getRegionID();
                }
                for (int j = 0; j < surfaceCollection.getSurfaceCount(); j++) {
                    Surface surface = surfaceCollection.getSurfaces(j);
                    if ((surface.getInteriorRegionIndex() == exteriorRegionID && surface.getExteriorRegionIndex() == interiorRegionID) || (surface.getInteriorRegionIndex() == interiorRegionID && surface.getExteriorRegionIndex() == exteriorRegionID)) {
                        // Polygon polygon = surface.getPolygons(k);
                        for (Polygon polygon : surface) {
                            if (polygonMembaneElementMap != null) {
                                membraneIndex = polygonMembaneElementMap.get(polygon).getMembraneIndex();
                            }
                            Node[] nodes = polygon.getNodes();
                            if (dimension == 2) {
                                // ignore z
                                Vect3d unitNormal = new Vect3d();
                                polygon.getUnitNormal(unitNormal);
                                unitNormal.set(unitNormal.getX(), unitNormal.getY(), 0);
                                int point0 = 0;
                                Vect3d v0 = new Vect3d(nodes[point0].getX(), nodes[point0].getY(), 0);
                                int point1 = 1;
                                Vect3d v1 = null;
                                for (point1 = 1; point1 < nodes.length; point1++) {
                                    if (v0.getX() != nodes[point1].getX() || v0.getY() != nodes[point1].getY()) {
                                        v1 = new Vect3d(nodes[point1].getX(), nodes[point1].getY(), 0);
                                        break;
                                    }
                                }
                                if (v1 == null) {
                                    throw new RuntimeException("failed to generate surface");
                                }
                                Vect3d v01 = Vect3d.sub(v1, v0);
                                Vect3d unit01n = v01.cross(unitNormal);
                                unit01n.unit();
                                if (Math.abs(unit01n.getZ() - 1.0) < 1e-6) {
                                    // v0 to v1 opposes vcell surface normal. it's already flipped.
                                    Triangle triangle;
                                    if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                        // we have to flipped it back
                                        triangle = new Triangle(nodes[point1], nodes[point0], null);
                                    } else {
                                        triangle = new Triangle(nodes[point0], nodes[point1], null);
                                    }
                                    triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle));
                                } else if (Math.abs(unit01n.getZ() + 1.0) < 1e-6) {
                                    // v0 to v1 is in direction of vcell surface normal.
                                    Triangle triangle;
                                    if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                        triangle = new Triangle(nodes[point0], nodes[point1], null);
                                    } else {
                                        triangle = new Triangle(nodes[point1], nodes[point0], null);
                                    }
                                    triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle));
                                } else {
                                    throw new RuntimeException("failed to generate surface");
                                }
                            } else if (dimension == 3) {
                                Triangle triangle1;
                                Triangle triangle2;
                                if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                    // interior
                                    triangle1 = new Triangle(nodes[0], nodes[1], nodes[2]);
                                    triangle2 = new Triangle(nodes[0], nodes[2], nodes[3]);
                                } else {
                                    triangle1 = new Triangle(nodes[2], nodes[1], nodes[0]);
                                    triangle2 = new Triangle(nodes[3], nodes[2], nodes[0]);
                                }
                                triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle1));
                                triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle2));
                            }
                        }
                    }
                }
            }
            // add triangles to node hash
            for (TrianglePanel triPanel : triList) {
                for (Node node : triPanel.triangle.getNodes()) {
                    if (node == null) {
                        continue;
                    }
                    Set<String> triNameSet = nodeTriMap.get(node);
                    if (triNameSet == null) {
                        triNameSet = new HashSet<String>();
                        nodeTriMap.put(node, triNameSet);
                    }
                    triNameSet.add(triPanel.name);
                }
            }
            SubVolume[] adjacentSubvolums = surfaceClass.getAdjacentSubvolumes().toArray(new SubVolume[0]);
            CompartmentSubDomain csd0 = simulation.getMathDescription().getCompartmentSubDomain(adjacentSubvolums[0].getName());
            CompartmentSubDomain csd1 = simulation.getMathDescription().getCompartmentSubDomain(adjacentSubvolums[1].getName());
            MembraneSubDomain membraneSubDomain = simulation.getMathDescription().getMembraneSubDomain(csd0, csd1);
            membraneSubdomainTriangleMap.put(membraneSubDomain, triList);
            final boolean initialMoleculesOnMembrane = (closestTriangles != null);
            if (initialMoleculesOnMembrane) {
                findClosestTriangles(membraneSubDomain, triList);
            }
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + surfaceClass.getName());
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.all + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
            // printWriter.println(SmoldynKeyword.action + " " + SmoldynKeyword.all + "(" + SmoldynKeyword.up + ") " + SmoldynKeyword.both + " " + SmoldynKeyword.reflect);
            Color c = colorForSurface(sci);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + c.getRed() / 255.0 + " " + c.getGreen() / 255.0 + " " + c.getBlue() / 255.0 + " 0.1");
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.tri + " " + triList.size());
            for (TrianglePanel trianglePanel : triList) {
                Triangle triangle = trianglePanel.triangle;
                printWriter.print(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.tri);
                switch(dimension) {
                    case 1:
                        printWriter.print(" " + triangle.getNodes(0).getX());
                        break;
                    case 2:
                        printWriter.print(" " + triangle.getNodes(0).getX() + " " + triangle.getNodes(0).getY());
                        printWriter.print(" " + triangle.getNodes(1).getX() + " " + triangle.getNodes(1).getY());
                        break;
                    case 3:
                        for (Node node : triangle.getNodes()) {
                            printWriter.print(" " + node.getX() + " " + node.getY() + " " + node.getZ());
                        }
                        break;
                }
                printWriter.println(" " + trianglePanel.name);
            }
            for (TrianglePanel triPanel : triList) {
                neighborsForCurrentNode.clear();
                for (Node node : triPanel.triangle.getNodes()) {
                    if (node == null) {
                        continue;
                    }
                    neighborsForCurrentNode.addAll(nodeTriMap.get(node));
                }
                neighborsForCurrentNode.remove(triPanel.name);
                // printWriter.print(SmoldynKeyword.neighbors + " " +triPanel.name);
                // to allow smoldyn read line length as 256, chop the neighbors to multiple lines
                int maxNeighborCount = 4;
                // 
                int count = 0;
                for (String neigh : neighborsForCurrentNode) {
                    if (count % maxNeighborCount == 0) {
                        printWriter.println();
                        printWriter.print(SmoldynVCellMapper.SmoldynKeyword.neighbors + " " + triPanel.name);
                    }
                    printWriter.print(" " + neigh);
                    count++;
                }
            }
            printWriter.println();
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
            printWriter.println();
        }
    }
}