Merge branch 'dev_GUI' into 'dev'

Open source release of CityDoctorGUI and other extensions.

See merge request !6

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/CppFeature.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import de.hft.stuttgart.citydoctor2.datastructure.BoundarySurface;
+import de.hft.stuttgart.citydoctor2.datastructure.Geometry;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing;
+import de.hft.stuttgart.citydoctor2.datastructure.Lod;
+import de.hft.stuttgart.citydoctor2.datastructure.Polygon;
+import de.hft.stuttgart.citydoctor2.datastructure.Vertex;
+
+/**
+ * @author wewetzer
+ * @version 1.0
+ */
+public class CppFeature extends CppReferenceHandlingBase {
+	
+	private native long createCppFeature(String type) throws OutOfMemoryError;
+
+	private native void disposeCppFeature(long ptrToCppFeature) throws NativePointerCastException;
+
+	// setting geometry and attributes
+	private native boolean setGeometry(long ptrToFeature, int geomType, double[] pointArray, int[] pointIdMap,
+			int[] polygonArray, int[] polygonIdMap) throws NativeException;
+
+	private native boolean setLoD(long ptrToFeature, int LoD) throws NativeException;
+	
+
+	// gets the id of a corresponding C++ entity to a given Java entity id
+	private native int getCppPointId(long ptrToFeature, int javaPointId) throws NativeException;
+
+	private native int getCppPolygonId(long ptrToFeature, int javaPolygonId) throws NativeException;
+
+	private native double[] getPoints(long ptrToFeature) throws NativeException;
+
+
+	// debug native methods
+	private native void printMesh(long ptrToFeature) throws NativeException;
+
+	private native void writeMeshToInventor(long ptrToFeature, String fileName) throws NativeException;
+
+
+	private String type;
+
+	public CppFeature(String type) {
+		this.type = type;
+		createCppObject();
+	}
+
+	/**
+	 * Creates an C++ feature object
+	 * 
+	 * @throws IllegalStateException      Thrown if the encapsulated "long-Pointer"
+	 *                                    isn't 0
+	 * @throws NativeOutOfMemoryException If there is no more memory on the native
+	 *                                    side
+	 * 
+	 * @see {@link disposeCppObject}
+	 * @see de.hft.stuttgart.citydoctor2.connect.edge.CppReferenceHandlingBase#createCppObject()
+	 */
+	private void createCppObject() {
+		if (0L != ptrToCppObject) {
+			throw new IllegalStateException("Can't create new C++ object, there is already one!");
+		}
+		// Maybe an exception is thrown
+		ptrToCppObject = createCppFeature(type);
+	}
+
+	@Override
+	public void disposeCppObject() throws NativePointerCastException {
+		if (0L != ptrToCppObject) {
+			disposeCppFeature(ptrToCppObject);
+			ptrToCppObject = 0L;
+		}
+	}
+
+	
+	public void setGeometry(Geometry geometry) throws NativeException {
+		checkNullPointer();
+		CppGeometryData geometryData = createCppFeatureInput(geometry);
+		setGeometry(ptrToCppObject, 0, geometryData.pointArr, geometryData.pointIdMap, geometryData.polygonArr, geometryData.polygonIdMap);
+	}	
+	
+	public void setLoD(Lod lod) throws NativeException {
+		checkNullPointer();
+		int LoD = -1;
+		if(lod == Lod.LOD0) {
+			LoD = 0;
+		}
+		else if(lod == Lod.LOD1) {
+			LoD = 1;
+		}
+		else if(lod == Lod.LOD2) {
+			LoD = 2;
+		}
+		else if(lod == Lod.LOD3) {
+			LoD = 3;
+		}
+		else if(lod == Lod.LOD4) {
+			LoD = 4;
+		}
+		
+		setLoD(ptrToCppObject, LoD);
+	}	
+	
+
+	/**
+	 * Returns the id of the corresponding C++ point to a given Java point id
+	 * 
+	 * @param javaPointId The given Java point id
+	 * @return The corresponding C++ point id
+	 * @throws IllegalArgumentException If the feature pointer is 0
+	 * @throws NativeException          If an error occurred during the execution of
+	 *                                  the native code
+	 */
+	public int getCppPointId(int javaPointId) throws NativeException {
+		checkNullPointer();
+		return this.getCppPointId(ptrToCppObject, javaPointId);
+	}
+
+	/**
+	 * Returns the id of the corresponding C++ polygon to a given java polygon
+	 * id
+	 * 
+	 * @param javaPolygonId The given Java polygon id
+	 * @return The corresponding C++ polygon id
+	 * @throws IllegalArgumentException If the feature pointer is 0
+	 * @throws NativeException          If an error occurred during the execution of
+	 *                                  the native code
+	 */
+	public int getCppPolygonId(int javaPolygonId) throws NativeException {
+		checkNullPointer();
+		return this.getCppPolygonId(ptrToCppObject, javaPolygonId);
+	}
+
+
+	public double[] getPoints() throws NativeException {
+		checkNullPointer();
+		return this.getPoints(ptrToCppObject);
+	}
+
+	/**
+	 * Debug method, that prints the mesh
+	 * 
+	 * @throws IllegalArgumentException If the feature pointer is 0
+	 * @throws NativeException          If an error occurred during the execution of
+	 *                                  the native code
+	 */
+	public void printMesh() throws NativeException {
+		checkNullPointer();
+		this.printMesh(ptrToCppObject);
+	}
+
+	/**
+	 * Writes the current stored level of detail 1 mesh in the file "filename.iv" as
+	 * Open Inventor file.
+	 * 
+	 * @param fileName The name of the output file
+	 * @throws IllegalArgumentException If the feature pointer is 0
+	 * @throws NativeException          If an error occurred during the execution of
+	 *                                  the native code n
+	 */
+	public void writeMeshToInventor(String fileName) throws NativeException {
+		checkNullPointer();
+		this.writeMeshToInventor(ptrToCppObject, fileName);
+	}
+
+	/**
+	 * Writes the current stored level of detail 2 mesh in the file "filename.iv" as
+	 * Open Inventor file.
+	 * 
+	 * @param fileName The name of the output file
+	 * @throws IllegalArgumentException If the feature pointer is 0
+	 * @throws NativeException          If an error occurred during the execution of
+	 *                                  the native code n
+	 */
+
+	private void printGeomDataAsCppCode(CppGeometryData cppGeoData) {
+
+		System.out.println("\n \n \n");
+
+		double[] pnts = cppGeoData.pointArr;
+		System.out.println("const size_t numCoords = " + pnts.length / 3 + ";");
+		System.out.println("Coordinate3d * coords[" + pnts.length / 3 + "];");
+		for (int i = 0; i < pnts.length; i += 3) {
+			System.out.print("coords[ " + i / 3 + " ] = new Coordinate3d( ");
+			System.out.println(pnts[i] + ", " + pnts[i + 1] + ", " + pnts[i + 2] + " );");
+		}
+
+		System.out.println("");
+		int[] polys = cppGeoData.polygonArr;
+		System.out.println("const size_t numPolys = " + cppGeoData.polygonIdMap.length + ";");
+		System.out.println("const size_t sizePolys = " + polys.length + ";");
+		System.out.print("int polyArr[] = {");
+		for (int i = 0; i < polys.length - 1; ++i) {
+			if (-1 == polys[i]) {
+				System.out.println();
+				System.out.print("   " + polys[i] + ", ");
+			} else if (-2 == polys[i]) {
+				System.out.print("   " + polys[i] + ", ");
+			} else {
+				System.out.print("   " + polys[i] + ", ");
+			}
+		}
+		System.out.println("   " + polys[polys.length - 1] + " \n};\n");
+
+		if (cppGeoData.boundarySurfaceTypeArr.length > 0) {
+			System.out.println("BoundarySurfaceType types[numPolys] = {");
+			for (int i = 0; i < cppGeoData.boundarySurfaceTypeArr.length; i++) {
+				switch (cppGeoData.boundarySurfaceTypeArr[i]) {
+				case (1): {
+					System.out.println("   roofsurface,");
+					break;
+				}
+				case (2): {
+					System.out.println("   wallsurface,");
+					break;
+				}
+				case (3): {
+					System.out.println("   groundsurface,");
+					break;
+				}
+				default: {
+					System.out.println("   undefined,");
+				}
+				}
+				;
+			}
+			System.out.println("};");
+			System.out.println("return createHouse( coords, numCoords, polyArr, numPolys, sizePolys, types, true);");
+		}
+	}
+
+	/**
+	 * generates all the necessary geometric input for the CppFeature
+	 * 
+	 * @param geom
+	 */
+	private CppGeometryData createCppFeatureInput(Geometry geometry) {
+
+		// ====================================================================
+		// Vertices
+		List<Vertex> vertices = geometry.getVertices();
+		double[] pointArr = new double[vertices.size() * 3];
+		int[] pointIdMap = new int[vertices.size()];
+
+		Map<Vertex, Integer> vertexToIndexMap = new HashMap<>(vertices.size());
+		for (int i = 0; i < vertices.size(); i++) {
+			Vertex v = vertices.get(i);
+			vertexToIndexMap.put(v, i);
+			pointArr[i * 3 + 0] = v.getX();
+			pointArr[i * 3 + 1] = v.getY();
+			pointArr[i * 3 + 2] = v.getZ();
+			pointIdMap[i] = i;
+		}
+
+		// ====================================================================
+		// Polygons & BoundarySurfaceType
+
+		List<Polygon> polygons = geometry.getPolygons();
+		int numReferencedVertices = 0;
+		int[] polygonIdMap = new int[polygons.size()];
+		for (int i = 0; i < polygons.size(); i++) {
+			Polygon p = polygons.get(i);
+			polygonIdMap[i] = i;
+			numReferencedVertices += p.getExteriorRing().getVertices().size();
+			for (LinearRing lr : p.getInnerRings()) {
+				numReferencedVertices += lr.getVertices().size();
+			}
+		}
+
+		int[] polygonArr = new int[numReferencedVertices];
+		int[] boundarySurfaceTypeArr = new int[polygons.size()];
+		int polyCounter = 0;
+		for (int polyIndex = 0; polyIndex < polygons.size(); polyIndex++) {
+			Polygon p = polygons.get(polyIndex);
+			// exterior ring = -1
+			polygonArr[polyCounter++] = -1;
+			for (int i = 0; i < p.getExteriorRing().getVertices().size() - 1; i++) {
+				Vertex v = p.getExteriorRing().getVertices().get(i);
+				int id = vertexToIndexMap.get(v);
+				polygonArr[polyCounter++] = id;
+			}
+			for (LinearRing lr : p.getInnerRings()) {
+				// interior ring = -2
+				polygonArr[polyCounter++] = -2;
+				for (int i = 0; i < lr.getVertices().size() - 1; i++) {
+					Vertex v = lr.getVertices().get(i);
+					int id = vertexToIndexMap.get(v);
+					polygonArr[polyCounter++] = id;
+				}
+			}
+
+			if (geometry.getLod() == Lod.LOD2) {
+				BoundarySurface bs = p.getPartOfSurface();
+				if (bs != null) {
+					boundarySurfaceTypeArr[polyIndex] = bs.getType().ordinal();
+				} else {
+					boundarySurfaceTypeArr[polyIndex] = 999999;
+				}
+			}
+		}
+		return new CppGeometryData(pointArr, pointIdMap, polygonArr, polygonIdMap, boundarySurfaceTypeArr);
+	}
+
+	private class CppGeometryData {
+		private double[] pointArr;
+		private int[] pointIdMap;
+		private int[] polygonArr;
+		private int[] polygonIdMap;
+		private int[] boundarySurfaceTypeArr;
+
+		private CppGeometryData(double[] pointArr, int[] pointIdMap, int[] polygonArr, int[] polygonIdMap,
+				int[] bfTypeArr) {
+			this.pointArr = pointArr;
+			this.pointIdMap = pointIdMap;
+			this.polygonArr = polygonArr;
+			this.polygonIdMap = polygonIdMap;
+			this.boundarySurfaceTypeArr = bfTypeArr;
+		}
+	}
+
+	public String getType() {
+		return type;
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/CppHealResult.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+import de.hft.stuttgart.citydoctor2.datastructure.ConcretePolygon;
+import de.hft.stuttgart.citydoctor2.datastructure.Geometry;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing.LinearRingType;
+import de.hft.stuttgart.citydoctor2.datastructure.Polygon;
+import de.hft.stuttgart.citydoctor2.datastructure.Vertex;
+
+public class CppHealResult extends CppReferenceHandlingBase {
+
+	private native void delete(long ptr);
+
+	private native int[] getChangedOrAddedVertexIds(long ptr);
+
+	private native double[] getChangedOrAddedVertexValues(long ptr);
+
+	private native int[] getChangedOrAddedPolygonIds(long ptr);
+
+	private native int[] getChangedOrAddedPolygon(long ptr, int id);
+	
+	
+
+	public CppHealResult(long ptr) {
+		ptrToCppObject = ptr;
+	}
+
+	@Override
+	public void disposeCppObject() {
+		if (ptrToCppObject != 0) {
+			delete(ptrToCppObject);
+			ptrToCppObject = 0;
+		}
+	}
+
+	public void mergeIntoGeometry(Geometry geom) {
+		Map<Integer, Vertex> vertexMap = updateVertices(geom);
+		
+		int[] changedPolygons = getChangedOrAddedPolygonIds(ptrToCppObject);
+		List<Polygon> deletedPolygons = new ArrayList<>();
+		for (int i = 0; i < changedPolygons.length; i++) {
+			int polyId = changedPolygons[i];
+			int[] vertices = getChangedOrAddedPolygon(ptrToCppObject, polyId);
+			if (vertices == null || vertices.length == 0) {
+				if (polyId >= geom.getPolygons().size()) {
+					throw new IllegalStateException("Cannot delete a polygon which does not exist");
+				}
+				Polygon p = geom.getPolygons().get(polyId);
+				deletedPolygons.add(p);
+			} else {
+				Polygon p;
+				if (polyId < geom.getPolygons().size()) {
+					p = geom.getPolygons().get(polyId);
+					// empty the polygon
+					p.removeRings();
+				} else {
+					p = new ConcretePolygon();
+					geom.addPolygon(p);
+				}
+				createPolygon(geom, vertexMap, vertices, p);
+			}
+		}
+		for (Polygon p : deletedPolygons) {
+			geom.getPolygons().remove(p);
+		}
+	}
+
+	private void createPolygon(Geometry geom, Map<Integer, Vertex> vertexMap, int[] vertices, Polygon p) {
+		LinearRing lr = null;
+		for (int j = 0; j < vertices.length; j++) {
+			if (vertices[j] == -1) {
+				if (p.getExteriorRing() != null) {
+					throw new IllegalStateException("Cannot create a polygon with more than 1 exterior rings");
+				}
+				lr = new LinearRing(LinearRingType.EXTERIOR);
+				p.setExteriorRing(lr);
+			} else if (vertices[j] == -2) {
+				lr = new LinearRing(LinearRingType.INTERIOR);
+				p.addInteriorRing(lr);
+			} else {
+				Objects.requireNonNull(lr, "No ring type specified, before supplying vertices");
+				int index = vertices[j];
+				Vertex v;
+				if (index < geom.getVertices().size()) {
+					v = geom.getVertices().get(index);
+				} else {
+					v = vertexMap.get(index);
+				}
+				Objects.requireNonNull(v, "Polygon references vertex, which does not exist");
+				lr.addVertex(v);
+			}
+		}
+		// close the rings
+		p.getExteriorRing().addVertex(p.getExteriorRing().getVertices().get(0));
+		for (LinearRing inner : p.getInnerRings()) {
+			inner.addVertex(inner.getVertices().get(0));
+		}
+	}
+
+	private Map<Integer, Vertex> updateVertices(Geometry geom) {
+		int[] changedVertices = getChangedOrAddedVertexIds(ptrToCppObject);
+		double[] changedVertexValues = getChangedOrAddedVertexValues(ptrToCppObject);
+		Map<Integer, Vertex> vertexMap = new HashMap<>();
+		for (int i = 0; i < changedVertices.length; i++) {
+			int id = changedVertices[i];
+			double x = changedVertexValues[i * 3 + 0];
+			double y = changedVertexValues[i * 3 + 1];
+			double z = changedVertexValues[i * 3 + 2];
+			if (id >= geom.getVertices().size()) {
+				// new vertex
+				Vertex newV = new Vertex(x, y, z);
+				vertexMap.put(id, newV);
+				System.out.println("New Vertex: " + newV);
+			} else {
+				// change vertex
+				Vertex changedV = geom.getVertices().get(id);
+				System.out.print("Changed Vertex from " + changedV + " to ");
+				changedV.setX(x);
+				changedV.setY(y);
+				changedV.setZ(z);
+				System.out.println(changedV);
+			}
+		}
+		return vertexMap;
+	}
+
+	public void print() {
+		int[] changedVertices = getChangedOrAddedVertexIds(ptrToCppObject);
+		System.out.println("Changed or added vertex ids: " + Arrays.toString(changedVertices));
+		double[] changedVertexValues = getChangedOrAddedVertexValues(ptrToCppObject);
+		if (changedVertices.length * 3 != changedVertexValues.length) {
+			throw new IllegalStateException("Number of indices and number of values do not match");
+		}
+		for (int i = 0; i < changedVertices.length; i++) {
+			System.out.println(String.format("Vertex %d = [%f, %f, %f]", changedVertices[i],
+					changedVertexValues[i * 3 + 0], changedVertexValues[i * 3 + 1], changedVertexValues[i * 3 + 2]));
+		}
+		System.out.println();
+		int[] changedPolygons = getChangedOrAddedPolygonIds(ptrToCppObject);
+		System.out.println("Changed or added polygon ids: " + Arrays.toString(changedPolygons));
+		for (int i = 0; i < changedPolygons.length; i++) {
+			int polyId = changedPolygons[i];
+			System.out.println("Polygon " + polyId + ":");
+			int[] vertices = getChangedOrAddedPolygon(ptrToCppObject, polyId);
+			if (vertices == null || vertices.length == 0) {
+				System.out.println("deleted");
+			} else {
+				for (int j = 0; j < vertices.length; j++) {
+					if (vertices[j] == -1) {
+						System.out.println("Exterior ring:");
+					} else if (vertices[j] == -2) {
+						System.out.println("Interior ring:");
+					} else {
+						System.out.println(vertices[j]);
+					}
+				}
+			}
+		}
+	}
+
+	public boolean isEmpty() {
+		int[] changedVertices = getChangedOrAddedVertexIds(ptrToCppObject);
+		int[] changedPolygons = getChangedOrAddedPolygonIds(ptrToCppObject);
+		if(changedVertices.length == 0 && changedPolygons.length == 0)
+			return true;
+	
+		return false;
+	}
+	
+	
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/CppHealing.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+public abstract class CppHealing extends CppReferenceHandlingBase {
+	// Checks will operate on this VPDFeature
+	CppFeature feature;
+
+	public CppHealing(CppFeature feature) {
+		this.feature = feature;
+	}
+
+	public CppFeature getNestedFeature() {
+		return feature;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see java.lang.Object#equals(java.lang.Object)
+	 */
+
+//*************************************************************************************
+// vorerst auskommentiert, da CppChecks nicht mehr verwendet wird
+
+// @Override
+// public boolean equals(Object obj)
+// {
+//     if (obj instanceof CppChecks)
+//     {
+//         return (super.equals(obj) && (feature == ((CppChecks)obj).feature));
+//     }
+//     else
+//     {
+//         return super.equals(obj);
+//     }
+// }
+//**************************************************************************************
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see java.lang.Object#hashCode()
+	 */
+	@Override
+	public int hashCode() {
+		int hash = super.hashCode();
+		hash = hash * 19 + feature.hashCode() * 3;
+		return hash;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see java.lang.Object#toString()
+	 */
+	@Override
+	public String toString() {
+		StringBuffer sf = new StringBuffer();
+		sf.append(super.toString());
+		sf.append("Feature:\n\t");
+		sf.append(feature);
+		return sf.toString();
+	}
+}
\ No newline at end of file

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/CppHealingResultChangeType.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+public enum CppHealingResultChangeType {
+	
+	ADD, DELETE, CHANGE, REPLACE
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/CppHealingResultType.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+public enum CppHealingResultType {
+	
+	VERTEX, POLYGON, EDGE
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/CppPolygonHealing.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+// im alten CD:
+//
+public class CppPolygonHealing extends CppHealing {
+
+	// ----- native methods
+	// create and release stored C++ polygon check object
+	private native long createCppPolygonHealing(long ptrToCppFeature) throws OutOfMemoryError;
+
+	private native void disposeCppPolygonHealing(long ptrToCppFeature) throws NativePointerCastException;
+
+	// healing
+	private native long healPlanarity(long ptrToCppFeature, int[] polyIds)
+			throws NativeException, IllegalArgumentException;
+    
+    private native long healSolidNotClosed(long ptrToCppFeature)
+			throws NativeException, IllegalArgumentException;
+    
+
+	public CppPolygonHealing(CppFeature feature) {
+		super(feature);
+	}
+
+	/**
+	 * Creates an C++ object to use the native solid check methods.
+	 * 
+	 * @throws IllegalStateException Thrown if the encapsulated "long-Pointer" isn't
+	 *                               0
+	 * @throws OutOfMemoryError      If there is no more memory on the native side
+	 * 
+	 * @see {@link disposeCppObject}
+	 * @see de.hft.stuttgart.citydoctor.connect.edGe.CppReferenceHandlingBase#createCppObject()
+	 */
+	public void createCppObject() throws IllegalStateException, OutOfMemoryError {
+		if (0L != ptrToCppObject) {
+			throw new IllegalStateException("Can't create new C++ object, there is allready one!");
+		}
+		// Maybe an exception is thrown and there should be no crap in ptrToCppObject
+		long tmpPointer = createCppPolygonHealing(feature.ptrToCppObject);
+		ptrToCppObject = tmpPointer;
+
+	}
+
+	@Override
+	public void disposeCppObject() throws NativePointerCastException {
+		if (0L != ptrToCppObject) {
+			disposeCppPolygonHealing(this.ptrToCppObject);
+			ptrToCppObject = 0L;
+		}
+	}
+
+	public CppHealResult healPlanarity(int[] polyIds) throws NativeException, IllegalArgumentException {
+		checkNullPointer();
+		return new CppHealResult( healPlanarity( this.feature.ptrToCppObject, polyIds ));
+	}
+
+   
+    public CppHealResult healSolidNotClosed() throws NativeException, IllegalArgumentException{
+        checkNullPointer();
+        return new CppHealResult( healSolidNotClosed( this.feature.ptrToCppObject ));
+    }
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/CppReferenceHandlingBase.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+/**
+ * This class is part of the JNI interface which controls the access to the
+ * check- and heal kernel in native C++ code.<br>
+ * It's represent a base class for classes which encapsulates a C++ object.
+ * Therefor two abstract methods {@link createCppObject} and
+ * {@link disposeCppObject} are defined, to create and dispose a C++ object. All
+ * non-abstract subclasses are requested to implement at least the two native
+ * methods<br>
+ * <br>
+ * <code> 
+ * native long create[MeaningfulName](long ptrToCppFeature);<br>
+ * native void dispose[MeaningfulName](long ptrToCppPolygonCheck);
+ * </code><br>
+ * <br>
+ * 
+ * @author wewetzer
+ * @version 1.0
+ * 
+ */
+public abstract class CppReferenceHandlingBase {
+	
+	// This long holds the address of an C++ object
+	long ptrToCppObject = 0L;
+
+	/**
+	 * This method frees the occupied memory of the created C++ object. The method
+	 * should be called after the instance of an child class is nor longer needed,
+	 * to avoid memory leaks.
+	 * 
+	 * @see {@link createCppObject}
+	 */
+	public abstract void disposeCppObject();
+
+	/**
+	 * Checks if the pointer to the corresponding C++ object is 0. In this case an
+	 * exception is thrown. This method should be called at first in every method,
+	 * that uses native methods!
+	 * 
+	 * @throws IllegalArgumentException if the pointer to the corresponding C++
+	 *                                  object i 0
+	 */
+	public void checkNullPointer() {
+		if (0L == ptrToCppObject) {
+			throw new IllegalArgumentException("C++ object pointer is null");
+		}
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj) {
+			return true;
+		}
+		if (obj == null) {
+			return false;
+		}
+		if (getClass() != obj.getClass()) {
+			return false;
+		}
+		CppReferenceHandlingBase other = (CppReferenceHandlingBase) obj;
+		return ptrToCppObject == other.ptrToCppObject;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see java.lang.Object#finalize()
+	 */
+	@Override
+	protected void finalize() throws Throwable {
+		if (0L != ptrToCppObject) {
+			disposeCppObject();
+		}
+	}
+
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + (int) (ptrToCppObject ^ (ptrToCppObject >>> 32));
+		return result;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see java.lang.Object#toString()
+	 */
+	@Override
+	public String toString() {
+		return ("ptrToCppObject\n\t" + ptrToCppObject + "\n");
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/CppTestHeal.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+public class CppTestHeal {
+	
+	private CppTestHeal() {
+		// only static usage
+	}
+	
+	private static native long healGeometry(long ptrToCppFeature);
+	
+	public static CppHealResult healGeometry(CppFeature feature) {
+		return new CppHealResult(healGeometry(feature.ptrToCppObject));
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/NativeException.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+/**
+ * This class represents the parent class of all exceptions thrown by the native
+ * c++ library for the check- and healkernel for the project CityDoctor. An
+ * additionally sting field has been added to identify the thrown Exception, if
+ * not a specialized exception has been caught. This keeps the code clearly
+ * arranged, because most of the exception that will be thrown represents an
+ * severe error in C++, so there it doesn't makes sense to carry on with the
+ * java program
+ * 
+ * @author wewetzer
+ * @version 1.0
+ */
+public abstract class NativeException extends RuntimeException {
+	private static final long serialVersionUID = 443321035265866910L;
+	String exceptionType = "not specified";
+
+	/**
+	 * Standard constructor.
+	 */
+	public NativeException() {
+		super("Message not specified");
+	}
+
+	/**
+	 * Constructs a NativeException with the given message an the given type
+	 * 
+	 * @param message The message of the exception
+	 */
+	public NativeException(String message) {
+		super(message);
+	}
+
+	/**
+	 * Returns the type of the exception
+	 * 
+	 * @return The type of the exception
+	 */
+	public String getType() {
+		return exceptionType;
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/connect/edge/NativePointerCastException.java

+package de.hft.stuttgart.citydoctor2.connect.edge;
+
+/**
+ * @author wewetzer
+ * @version 1.0
+ */
+public class NativePointerCastException extends NativeException
+{
+    // version control for serialization
+    private static final long serialVersionUID = 1L;
+
+    public NativePointerCastException()
+    {
+        exceptionType = "Native pointer cast exception";
+    }
+
+
+    public NativePointerCastException(String message)
+    {
+        super(message);
+        exceptionType = "Native pointer cast exception";        
+    }
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healer/GeometryFilter.java

+package de.hft.stuttgart.citydoctor2.healer;
+
+import java.util.Objects;
+import java.util.Set;
+
+import de.hft.stuttgart.citydoctor2.check.Check;
+import de.hft.stuttgart.citydoctor2.check.CheckId;
+import de.hft.stuttgart.citydoctor2.check.RequirementType;
+import de.hft.stuttgart.citydoctor2.check.Requirement;
+import de.hft.stuttgart.citydoctor2.datastructure.Geometry;
+
+public class GeometryFilter extends Check {
+	
+	private GeometryListener l;
+	
+	@Override
+	public void check(Geometry geom) {
+		l.visit(geom);
+	}
+
+	public GeometryFilter(GeometryListener l) {
+		Objects.requireNonNull(l);
+		this.l = l;
+	}
+
+	@Override
+	public RequirementType getType() {
+		return null;
+	}
+
+	@Override
+	public Check createNewInstance() {
+		return null;
+	}
+
+	@Override
+	public CheckId getCheckId() {
+		return null;
+	}
+
+	@Override
+	public Set<Requirement> appliesToRequirements() {
+		return null;
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healer/GeometryListener.java

+package de.hft.stuttgart.citydoctor2.healer;
+
+import de.hft.stuttgart.citydoctor2.datastructure.Geometry;
+
+public interface GeometryListener {
+
+	public void visit(Geometry geom);
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healer/Healer.java

+package de.hft.stuttgart.citydoctor2.healer;
+
+import java.io.BufferedOutputStream;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.citygml4j.core.ade.ADEException;
+import org.citygml4j.core.model.CityGMLVersion;
+import org.citygml4j.core.model.core.AbstractCityObject;
+import org.citygml4j.core.model.core.AbstractCityObjectProperty;
+import org.citygml4j.core.model.core.CityModel;
+import org.citygml4j.core.util.geometry.GeometryFactory;
+import org.citygml4j.xml.CityGMLContext;
+import org.citygml4j.xml.writer.CityGMLOutputFactory;
+import org.citygml4j.xml.writer.CityGMLWriteException;
+import org.citygml4j.xml.writer.CityGMLWriter;
+
+import de.hft.stuttgart.citydoctor2.CityDoctorValidation;
+import de.hft.stuttgart.citydoctor2.check.AbstractCheck;
+import de.hft.stuttgart.citydoctor2.check.CheckError;
+import de.hft.stuttgart.citydoctor2.check.Checker;
+import de.hft.stuttgart.citydoctor2.check.HealingMethod;
+import de.hft.stuttgart.citydoctor2.check.ModificationListener;
+import de.hft.stuttgart.citydoctor2.check.ValidationConfiguration;
+import de.hft.stuttgart.citydoctor2.check.error.AttributeMissingError;
+import de.hft.stuttgart.citydoctor2.check.error.AttributeValueWrongError;
+import de.hft.stuttgart.citydoctor2.checkresult.utility.CheckReportWriteException;
+import de.hft.stuttgart.citydoctor2.checks.SvrlContentHandler;
+import de.hft.stuttgart.citydoctor2.datastructure.CityDoctorModel;
+import de.hft.stuttgart.citydoctor2.datastructure.CityObject;
+import de.hft.stuttgart.citydoctor2.datastructure.Geometry;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing;
+import de.hft.stuttgart.citydoctor2.datastructure.Polygon;
+import de.hft.stuttgart.citydoctor2.datastructure.Vertex;
+import de.hft.stuttgart.citydoctor2.exceptions.CityDoctorWriteException;
+import de.hft.stuttgart.citydoctor2.parameter.ArgumentParser;
+import de.hft.stuttgart.citydoctor2.parser.CityGmlConsumer;
+import de.hft.stuttgart.citydoctor2.parser.CityGmlParseException;
+import de.hft.stuttgart.citydoctor2.parser.CityGmlParser;
+import de.hft.stuttgart.citydoctor2.parser.InvalidGmlFileException;
+import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
+import de.hft.stuttgart.citydoctor2.reporting.XmlStreamReporter;
+import de.hft.stuttgart.citydoctor2.reporting.pdf.PdfStreamReporter;
+import de.hft.stuttgart.citydoctor2.utils.Localization;
+import de.hft.stuttgart.quality.QualityADEModule;
+
+public class Healer {
+
+	private static final Logger logger = LogManager.getLogger(Healer.class);
+
+	private int numIterations = 200;
+	private int schematronIterations = 2;
+
+	private Checker checker;
+	private ModificationListener l;
+	private HealingPlan plan;
+
+	static {
+//		CppInitializer.initCpp();
+	}
+
+	public static void main(String[] args) throws CityGmlParseException, IOException,
+			InvalidGmlFileException, CityDoctorWriteException {
+		ArgumentParser argParser = new ArgumentParser(args);
+		String inputFile = CityDoctorValidation.getInputFile(argParser, false);
+		String outputFile = getOutputFile(argParser);
+		String xmlOutput = CityDoctorValidation.getXmlOutput(argParser);
+		String pdfOutput = CityDoctorValidation.getPdfOutput(argParser);
+		ValidationConfiguration config = CityDoctorValidation.getValidationConfig(argParser, true);
+		startHealingProcess(inputFile, outputFile, xmlOutput, pdfOutput, config);
+	}
+
+	private static void startHealingProcess(String inputFile, String outputFile, String xmlOutput, String pdfOutput,
+			ValidationConfiguration config) throws CityGmlParseException, IOException,
+			InvalidGmlFileException, CityDoctorWriteException {
+		ParserConfiguration parserConfig = config.getParserConfiguration();
+
+		if (config.isUseStreaming()) {
+			Healer.streamHeal(new File(inputFile), outputFile, xmlOutput, pdfOutput, config);
+		} else {
+			CityDoctorModel model = CityGmlParser.parseCityGmlFile(inputFile, parserConfig);
+			Checker c = new Checker(config, model);
+			Healer healer = new Healer(c, (ModificationListener) null);
+			healer.healModel(model);
+			model.saveAs(outputFile, true);
+		}
+	}
+
+	public static void streamHeal(File inputFile, String outputFileName, String xmlOutput, String pdfOutput,
+			ValidationConfiguration config) throws CityGmlParseException, IOException {
+		if (!inputFile.exists() || !inputFile.isFile()) {
+			logger.error("Inputfile does not exist or is not a file: {}", inputFile.getAbsolutePath());
+		}
+		Checker c = new Checker(config, null);
+		Healer healer = new Healer(c, (ModificationListener) null);
+		try (BufferedOutputStream xmlBos = Checker.getXmlOutputMaybe(xmlOutput);
+				BufferedOutputStream pdfBos = Checker.getPdfOutputMaybe(pdfOutput)) {
+			String fileName = inputFile.getName();
+			XmlStreamReporter xmlReporter;
+			if (xmlBos != null) {
+				xmlReporter = new XmlStreamReporter(xmlBos, fileName, config);
+			} else {
+				xmlReporter = null;
+			}
+			PdfStreamReporter pdfReporter;
+			if (pdfBos != null) {
+				pdfReporter = new PdfStreamReporter(pdfBos, fileName, config);
+			} else {
+				pdfReporter = null;
+			}
+
+			CityGmlConsumer coConsumer = new CityGmlConsumer() {
+
+				@Override
+				public void accept(CityObject co) {
+					healer.healCityObject(co);
+				}
+
+			};
+			CityGmlParser.streamCityGml(inputFile, config.getParserConfiguration(), coConsumer, outputFileName);
+			Checker.writeReport(xmlReporter);
+			Checker.writeReport(pdfReporter);
+		} catch (CheckReportWriteException e) {
+			logger.error(Localization.getText("Checker.failReports"), e);
+		}
+	}
+
+	private static String getOutputFile(ArgumentParser argParser) {
+		String outputFile;
+		if (!argParser.containsOption("out")) {
+			logger.error("No output file specified. (-out [FILE])");
+			System.exit(10);
+		}
+		List<String> outFiles = argParser.getValues("out");
+		if (outFiles.size() != 1) {
+			logger.error("Specify exactly one file as output.");
+			System.exit(11);
+		}
+		outputFile = outFiles.get(0);
+		return outputFile;
+	}
+
+	public static void heal(File in, File configFile, File out)
+			throws FileNotFoundException, CityGmlParseException, InvalidGmlFileException, CityDoctorWriteException {
+		ValidationConfiguration config;
+		if (configFile == null) {
+			config = ValidationConfiguration.loadStandardValidationConfig();
+		} else {
+			config = ValidationConfiguration.loadValidationConfig(configFile.getAbsolutePath());
+		}
+		CityDoctorModel model = CityGmlParser.parseCityGmlFile(in.getAbsolutePath(), config.getParserConfiguration());
+		Checker c = new Checker(config, model);
+		Healer healer = new Healer(c, (ModificationListener) null);
+		healer.healModel(model);
+		model.saveAs(out.getAbsolutePath(), true);
+	}
+
+	public Healer(Checker c) {
+		this(c, (ModificationListener) null);
+	}
+
+	public Healer(Checker c, ModificationListener l) {
+		plan = HealingMethods.createHealingPlanFromAllMethods();
+		checker = c;
+		if (l == null) {
+			// create useless modification listener to avoid having to check on == null
+			l = new ModificationListener() {
+
+				@Override
+				public void polygonRemoved(Polygon p) {
+					// not observing anything
+				}
+
+				@Override
+				public void polygonAdded(Polygon p) {
+					// not observing anything
+				}
+			};
+		}
+		this.l = l;
+	}
+
+	public Healer(Checker c, ModificationListener l, HealingPlan plan) {
+		this(c, l);
+		this.plan = Objects.requireNonNull(plan);
+	}
+
+	public Healer(Checker c, HealingPlan plan) {
+		this(c);
+		this.plan = Objects.requireNonNull(plan);
+	}
+
+	public void setNumberOfIterations(int iterations) {
+		if (iterations < 1) {
+			throw new IllegalArgumentException("Iterations may not be lower than 1");
+		}
+		numIterations = iterations;
+	}
+
+	public void healModel(CityDoctorModel model) {
+		model.createFeatureStream().forEach(this::healCityObject);
+	}
+
+	public void healCityObject(CityObject co) {
+		logger.info("Repairing feature {}", co.getGmlId());
+		String schematronPath = checker.getConfig().getSchematronFilePath();
+		if (schematronPath != null && !schematronPath.isEmpty()) {
+			healSemanticErrors(co);
+		}
+		// healing geometries
+		GeometryFilter filter = new GeometryFilter(g -> heal(g, co));
+		co.accept(filter);
+	}
+
+	private void healSemanticErrors(CityObject co) {
+		// if a schematron file has been declared this needs to execute
+		for (int i = 0; i < schematronIterations; i++) {
+			co.clearAllContainedCheckResults();
+			executeSchematron(co);
+			List<CheckError> errors = new ArrayList<>();
+			co.collectContainedErrors(errors);
+			boolean healedSomething = false;
+			for (CheckError err : errors) {
+				if (err instanceof AttributeMissingError || err instanceof AttributeValueWrongError) {
+					for (HealingMethod m : plan.getHealingMethods()) {
+						if (err.accept(m, l)) {
+							healedSomething = true;
+							break;
+						}
+					}
+				}
+			}
+			if (!healedSomething) {
+				// nothing was changed, don't check for anything more
+				break;
+			}
+		}
+
+		// recheck for geometry errors as they were removed when executing the
+		// schematron stuff
+		co.prepareForChecking();
+		checker.executeChecksForCheckable(co);
+		if (checker.getConfig().getParserConfiguration().useLowMemoryConsumption()) {
+			co.clearMetaInformation();
+		}
+	}
+
+	private void executeSchematron(CityObject co) {
+		ValidationConfiguration config = checker.getConfig();
+		try {
+			GeometryFactory factory = GeometryFactory.newInstance();
+			// write geometries in citygml4j datastructure
+			co.reCreateGeometries(factory, checker.getConfig().getParserConfiguration());
+			byte[] gml = writeCityGml(co.getGmlObject());
+			// remove them again to save memory
+			co.unsetGmlGeometries();
+			SvrlContentHandler handler = Checker.executeSchematronValidationIfAvailable(config,
+					new ByteArrayInputStream(gml));
+			if (handler != null) {
+				handler.getFeatureErrors().computeIfPresent(co.getGmlId().getGmlString(), (key, list) -> {
+					Checker.handleSchematronErrorsForCityObject(list, co);
+					return list;
+				});
+			}
+		} catch (CityGMLWriteException e) {
+			throw new IllegalStateException(e);
+		}
+	}
+
+	/**
+	 * Writes one feature to a byte array.
+	 * 
+	 * @param aco the feature to write
+	 * @return the byte array containing the feature
+	 * @throws ADEException
+	 * @throws CityGMLBuilderException
+	 * @throws CityGMLWriteException
+	 */
+	private byte[] writeCityGml(AbstractCityObject aco) throws CityGMLWriteException {
+		CityModel model = new CityModel();
+		model.getCityObjectMembers().add(new AbstractCityObjectProperty(aco));
+		CityGMLContext context = CityGmlParser.getContext();
+		CityGMLOutputFactory outputFactory = context.createCityGMLOutputFactory(CityGMLVersion.v2_0);
+		ByteArrayOutputStream out = new ByteArrayOutputStream();
+		try (CityGMLWriter writer = outputFactory.createCityGMLWriter(out)) {
+			writer.withIndent("  ");
+			writer.withDefaultPrefixes();
+			writer.withPrefix("qual", QualityADEModule.NAMESPACE_URI);
+			writer.withSchemaLocation(QualityADEModule.NAMESPACE_URI,
+					QualityADEModule.NAMESPACE_URI + "/qualityAde.xsd");
+			writer.withDefaultSchemaLocations();
+			writer.write(model);
+			writer.flush();
+			return out.toByteArray();
+		}
+	}
+
+	public void heal(Geometry geom, CityObject co) {
+		heal(geom, co, numIterations);
+	}
+
+	public void heal(Geometry geom, CityObject co, int numIterations) {
+		if (checker.getConfig().getParserConfiguration().useLowMemoryConsumption()) {
+			co.prepareForChecking();
+		}
+		if (!co.isValidated()) {
+			// check it if it has not been checked yet
+			checker.executeChecksForCheckable(co);
+		}
+
+		try {
+			for (int i = 0; i < numIterations; i++) {
+				List<CheckError> errors = collectErrorsFromGeometry(geom);
+				if (errors.isEmpty()) {
+					break;
+				} else {
+					logger.debug("Found errors: ");
+					for (CheckError err : errors) {
+						logger.debug(err.getErrorId());
+					}
+				}
+				boolean cannotBeHealed = executeHealingLoop(errors);
+
+				logger.debug("End heal iteration: {}", (i + 1));
+				if (cannotBeHealed) {
+					logger.debug("Geometry: {} cannot be healed", geom.getGmlId());
+					// break iteration loop, nothing more to be done
+					break;
+				}
+				co.prepareForChecking();
+				filterOutDuplicateVertices(co);
+				// recheck for errors
+				checker.executeChecksForCheckable(co);
+			}
+		} catch (Exception e) {
+			logger.debug("Failed to heal geometry", e);
+		} finally {
+			if (checker.getConfig().getParserConfiguration().useLowMemoryConsumption()) {
+				co.clearMetaInformation();
+			}
+		}
+	}
+
+	private void filterOutDuplicateVertices(CityObject co) {
+		Map<Vertex, Vertex> map = new HashMap<>();
+		co.accept(new AbstractCheck() {
+			@Override
+			public void check(LinearRing ring) {
+				for (int i = 0; i < ring.getVertices().size(); i++) {
+					Vertex v = ring.getVertices().get(i);
+					Vertex duplicate = map.get(v);
+					if (duplicate == null) {
+						map.put(v, v);
+					} else if (duplicate != v) {
+						ring.getVertices().set(i, duplicate);
+					}
+				}
+			}
+		});
+	}
+
+	private boolean executeHealingLoop(List<CheckError> errors) {
+		for (HealingMethod method : plan.getHealingMethods()) {
+			for (CheckError err : errors) {
+				if (err.accept(method, l)) {
+					// geometry got changed, update, recheck, restart
+					return false;
+				}
+			}
+		}
+		return true;
+	}
+
+	private List<CheckError> collectErrorsFromGeometry(Geometry geom) {
+		List<CheckError> errors = new ArrayList<>();
+		geom.collectContainedErrors(errors);
+		return errors;
+	}
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healer/HealingMethodPrototype.java

+package de.hft.stuttgart.citydoctor2.healer;
+
+import de.hft.stuttgart.citydoctor2.check.HealingMethod;
+
+public class HealingMethodPrototype {
+	
+	public HealingMethod method;
+	
+	public static HealingMethodPrototype of(HealingMethod method) {
+		return new HealingMethodPrototype(method);
+	}
+	
+	public HealingMethodPrototype(HealingMethod method) {
+		this.method = method;
+	}
+
+	public HealingMethod createMethod() {
+		return method.createNew();
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healer/HealingMethods.java

+package de.hft.stuttgart.citydoctor2.healer;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import de.hft.stuttgart.citydoctor2.healing.GeometrySimplifier;
+import de.hft.stuttgart.citydoctor2.healing.HealAllPolygonsWrongOrientationError;
+import de.hft.stuttgart.citydoctor2.healing.HealConsecutivePointsSameError;
+import de.hft.stuttgart.citydoctor2.healing.HealHoleOutsideError;
+import de.hft.stuttgart.citydoctor2.healing.HealMainBuilding;
+import de.hft.stuttgart.citydoctor2.healing.HealMissingSolid;
+import de.hft.stuttgart.citydoctor2.healing.HealNonManifoldEdgeError;
+import de.hft.stuttgart.citydoctor2.healing.HealPlanarPolygonError;
+import de.hft.stuttgart.citydoctor2.healing.HealPolygonWithoutSurface;
+import de.hft.stuttgart.citydoctor2.healing.HealPolygonWrongOrientationError;
+import de.hft.stuttgart.citydoctor2.healing.HealRingNotClosedError;
+import de.hft.stuttgart.citydoctor2.healing.HealRingSelfIntError;
+import de.hft.stuttgart.citydoctor2.healing.HealSameOrientationError;
+import de.hft.stuttgart.citydoctor2.healing.HealSolidNotClosedError;
+import de.hft.stuttgart.citydoctor2.healing.HealTooFewPoints;
+import de.hft.stuttgart.citydoctor2.healing.HealWrongDormers;
+
+public class HealingMethods {
+	
+	private static List<HealingMethodPrototype> healingMethods;
+	
+	private HealingMethods() {
+		// only static access
+	}
+	
+	static {
+		healingMethods = new ArrayList<>();
+		healingMethods.add(HealingMethodPrototype.of(new HealMissingSolid()));
+		healingMethods.add(HealingMethodPrototype.of(new HealMainBuilding()));
+		healingMethods.add(HealingMethodPrototype.of(new HealConsecutivePointsSameError()));
+		healingMethods.add(HealingMethodPrototype.of(new HealTooFewPoints()));
+		healingMethods.add(HealingMethodPrototype.of(new HealRingNotClosedError()));
+		healingMethods.add(HealingMethodPrototype.of(new HealRingSelfIntError()));
+		healingMethods.add(HealingMethodPrototype.of(new HealPlanarPolygonError()));
+//		healingMethods.add(HealingMethodPrototype.of(new HealPlanarPolygonCpp()));
+		healingMethods.add(HealingMethodPrototype.of(new HealSameOrientationError()));
+		healingMethods.add(HealingMethodPrototype.of(new HealHoleOutsideError()));
+		healingMethods.add(HealingMethodPrototype.of(new HealNonManifoldEdgeError()));
+		healingMethods.add(HealingMethodPrototype.of(new HealSolidNotClosedError()));
+//		healingMethods.add(HealingMethodPrototype.of(new HealSolidNotClosedCpp()));
+		healingMethods.add(HealingMethodPrototype.of(new HealPolygonWrongOrientationError()));
+		healingMethods.add(HealingMethodPrototype.of(new GeometrySimplifier()));
+		healingMethods.add(HealingMethodPrototype.of(new HealWrongDormers()));
+		healingMethods.add(HealingMethodPrototype.of(new HealAllPolygonsWrongOrientationError()));
+		healingMethods.add(HealingMethodPrototype.of(new HealPolygonWithoutSurface()));
+		healingMethods = Collections.unmodifiableList(healingMethods);
+	}
+	
+	public static HealingPlan createHealingPlanFromAllMethods() {
+		HealingPlan plan = new HealingPlan();
+		for (HealingMethodPrototype proto : healingMethods) {
+			plan.addHealingMethod(proto.createMethod());
+		}
+		return plan;
+	}
+	
+	public static List<HealingMethodPrototype> getAvailableHealingMethods() {
+		return healingMethods;
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healer/HealingPlan.java

+package de.hft.stuttgart.citydoctor2.healer;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import de.hft.stuttgart.citydoctor2.check.HealingMethod;
+
+public class HealingPlan {
+	
+	private List<HealingMethod> methods;
+	
+	public HealingPlan() {
+		methods = new ArrayList<>();
+	}
+	
+	public void addHealingMethod(HealingMethod method) {
+		methods.add(method);
+	}
+	
+	public List<HealingMethod> getHealingMethods() {
+		return methods;
+	}
+
+	@Override
+	public String toString() {
+		return "HealingPlan [methods=" + methods + "]";
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healing/GeometrySimplifier.java

+package de.hft.stuttgart.citydoctor2.healing;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import de.hft.stuttgart.citydoctor2.check.HealingID;
+import de.hft.stuttgart.citydoctor2.check.HealingMethod;
+import de.hft.stuttgart.citydoctor2.check.ModificationListener;
+import de.hft.stuttgart.citydoctor2.check.error.MultipleConnectedComponentsError;
+import de.hft.stuttgart.citydoctor2.datastructure.ConcretePolygon;
+import de.hft.stuttgart.citydoctor2.datastructure.Edge;
+import de.hft.stuttgart.citydoctor2.datastructure.Geometry;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing.LinearRingType;
+import de.hft.stuttgart.citydoctor2.datastructure.Polygon;
+import de.hft.stuttgart.citydoctor2.datastructure.Vertex;
+import de.hft.stuttgart.citydoctor2.healing.math.EdgeGraph;
+import de.hft.stuttgart.citydoctor2.math.Plane;
+
+public class GeometrySimplifier implements HealingMethod {
+
+	private static final Logger logger = LogManager.getLogger(GeometrySimplifier.class);
+
+	private static final double EPSILON = 0.1;
+	
+	@Override
+	public HealingID getID() {
+		return HealingID.S_GEOMETRIC_SIMPLIFIER;
+	}
+
+	@Override
+	public boolean visit(MultipleConnectedComponentsError err, ModificationListener l) {
+		logger.debug("Executing Repair for MultipleConnectedComponentsError");
+		// first merge similar polygons
+		for (List<Polygon> component : err.getComponents()) {
+			for (int i = 0; i < component.size() - 1; i++) {
+				Polygon p0 = component.get(i);
+				Plane plane = new Plane(p0.calculateNormalNormalized(), p0.getExteriorRing().getVertices().get(0));
+				for (int j = i + 1; j < component.size(); j++) {
+					Polygon p1 = component.get(j);
+					if (isPolygonInPlane(plane, p1) && isPolygonConnectedViaEdge(p0, p1, err.getGeometry())) {
+						ConcretePolygon p = mergePolygons(p0, p1);
+						p1.remove();
+						err.getGeometry().replacePolygon(p0, p);
+						return true;
+					}
+				}
+			}
+		}
+		return false;
+	}
+	
+	private boolean isPolygonConnectedViaEdge(Polygon p1, Polygon p2, Geometry g) {
+		List<Edge> edges = g.getEdgesAdjacentTo(p1);
+		for (Edge e : edges) {
+			if (e.getAdjacentPolygons().contains(p2)) {
+				return true;
+			}
+		}
+		return false;
+	}
+	
+	private ConcretePolygon mergePolygons(Polygon p1, Polygon p2) {
+		Geometry geom = p1.getParent();
+		List<Edge> edgesP1 = geom.getEdgesAdjacentTo(p1);
+		List<Edge> edgesP2 = geom.getEdgesAdjacentTo(p2);
+		Set<Edge> setOfEdgesFromP1 = new HashSet<>(edgesP1);
+		Set<Edge> duplicateEdges = new HashSet<>();
+		for (Edge e : edgesP2) {
+			if (setOfEdgesFromP1.contains(e)) {
+				duplicateEdges.add(e);
+			}
+		}
+		if (duplicateEdges.isEmpty()) {
+			throw new IllegalStateException(
+					"Trying to merge two polygon which are not connected " + p1.getGmlId() + ", " + p2.getGmlId());
+		}
+		List<Edge> newEdges = new ArrayList<>();
+		filterDuplicateEdges(edgesP1, duplicateEdges, newEdges);
+		filterDuplicateEdges(edgesP2, duplicateEdges, newEdges);
+		if (newEdges.isEmpty()) {
+			return copyPolygon(p1);
+		}
+		List<List<Edge>> rings = findCyclesInEdges(newEdges);
+		// find the exterior ring in the new rings
+		ConcretePolygon p = new ConcretePolygon();
+		List<LinearRing> newRings = new ArrayList<>();
+		for (List<Edge> edges : rings) {
+			LinearRing ring = createRingFromEdges(edges);
+			newRings.add(ring);
+		}
+		if (rings.size() == 1) {
+			// only one ring -> the ring is an exterior
+			LinearRing ext = newRings.get(0);
+			ext.setType(LinearRingType.EXTERIOR);
+
+			p.setParent(geom);
+			p.setExteriorRing(ext);
+			return p;
+		} else {
+			for (LinearRing lr : newRings) {
+				if (isRingExterior(newRings, lr)) {
+					return createPolygon(newRings, lr, p);
+				}
+			}
+			throw new IllegalStateException(
+					"Merging polygons produced intersecting edges," + " no exterior ring could be found");
+		}
+
+	}
+
+	private ConcretePolygon copyPolygon(Polygon p1) {
+		ConcretePolygon newPoly = new ConcretePolygon();
+		ConcretePolygon original = p1.getOriginal();
+		LinearRing ext = new LinearRing(LinearRingType.EXTERIOR);
+		newPoly.setExteriorRing(ext);
+		for (Vertex v : original.getExteriorRing().getVertices()) {
+			ext.addVertex(v);
+		}
+		for (LinearRing lr : original.getInnerRings()) {
+			LinearRing inner = new LinearRing(LinearRingType.INTERIOR);
+			newPoly.addInteriorRing(inner);
+			for (Vertex v : lr.getVertices()) {
+				inner.addVertex(v);
+			}
+		}
+		return newPoly;
+	}
+
+	private ConcretePolygon createPolygon(List<LinearRing> newRings, LinearRing lr, ConcretePolygon p) {
+		lr.setType(LinearRingType.EXTERIOR);
+		p.setExteriorRing(lr);
+		for (LinearRing innerRing : newRings) {
+			if (lr == innerRing) {
+				continue;
+			}
+			p.addInteriorRing(innerRing);
+		}
+		return p;
+	}
+
+	private boolean isRingExterior(List<LinearRing> newRings, LinearRing lr) {
+		for (LinearRing other : newRings) {
+			if (lr == other) {
+				continue;
+			}
+			for (Vertex v : lr.getVertices()) {
+				if (other.isPointInside(v)) {
+					return false;
+				}
+			}
+		}
+		return true;
+	}
+
+	private LinearRing createRingFromEdges(List<Edge> edges) {
+		Edge startEdge = edges.get(0);
+		Vertex start = startEdge.getFrom();
+		Vertex currentVertex = startEdge.getTo();
+		edges.remove(0);
+		LinearRing lr = new LinearRing(LinearRingType.INTERIOR);
+		lr.addVertex(start);
+		lr.addVertex(currentVertex);
+		while (!edges.isEmpty()) {
+			boolean removedEdge = false;
+			for (Edge e : edges) {
+				Vertex oppositeV = e.getOppositeVertex(currentVertex);
+				if (oppositeV != null) {
+					lr.addVertex(oppositeV);
+					currentVertex = oppositeV;
+					edges.remove(e);
+					removedEdge = true;
+					break;
+				}
+			}
+			if (!removedEdge) {
+				// avoid endless loop in case of errors
+				logger.error("Could not create ring from edges, edges are not a loop");
+				break;
+			}
+		}
+		return lr;
+	}
+
+	private void filterDuplicateEdges(List<Edge> edges, Set<Edge> duplicateEdges, List<Edge> newEdges) {
+		for (Edge e : edges) {
+			if (!duplicateEdges.contains(e)) {
+				newEdges.add(e);
+			}
+		}
+	}
+
+	private List<List<Edge>> findCyclesInEdges(List<Edge> edges) {
+		EdgeGraph graph = new EdgeGraph();
+		for (Edge e : edges) {
+			graph.addEdge(e, edges);
+		}
+		return graph.getCycles();
+	}
+
+	private boolean isPolygonInPlane(Plane plane, Polygon potentialPoly) {
+		for (Vertex v : potentialPoly.getExteriorRing().getVertices()) {
+			if (plane.getDistance(v) > EPSILON) {
+				return false;
+			}
+		}
+		return true;
+	}
+
+	@Override
+	public GeometrySimplifier createNew() {
+		return new GeometrySimplifier();
+	}
+
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healing/HealAllPolygonsWrongOrientationError.java

+package de.hft.stuttgart.citydoctor2.healing;
+
+import java.util.Collections;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import de.hft.stuttgart.citydoctor2.check.HealingID;
+import de.hft.stuttgart.citydoctor2.check.HealingMethod;
+import de.hft.stuttgart.citydoctor2.check.ModificationListener;
+import de.hft.stuttgart.citydoctor2.check.error.AllPolygonsWrongOrientationError;
+import de.hft.stuttgart.citydoctor2.datastructure.Geometry;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing;
+import de.hft.stuttgart.citydoctor2.datastructure.Polygon;
+
+public class HealAllPolygonsWrongOrientationError implements HealingMethod {
+	
+	private static final Logger logger = LogManager.getLogger(HealAllPolygonsWrongOrientationError.class);
+	
+	@Override
+	public boolean visit(AllPolygonsWrongOrientationError err, ModificationListener l) {
+		logger.debug("Executing Repair for AllPolygonsWrongOrientationError");
+		Geometry geom = err.getGeometry();
+		for (Polygon p : geom.getPolygons()) {
+			Collections.reverse(p.getExteriorRing().getVertices());
+			for (LinearRing lr : p.getInnerRings()) {
+				Collections.reverse(lr.getVertices());
+			}
+		}
+		return true;
+	}
+
+	@Override
+	public HealAllPolygonsWrongOrientationError createNew() {
+		return new HealAllPolygonsWrongOrientationError();
+	}
+
+	@Override
+	public HealingID getID() {
+		return HealingID.S_ALL_POLYGONS_WRONG_ORIENTATION;
+	}
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healing/HealConsecutivePointsSameError.java

+package de.hft.stuttgart.citydoctor2.healing;
+
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import de.hft.stuttgart.citydoctor2.check.HealingID;
+import de.hft.stuttgart.citydoctor2.check.HealingMethod;
+import de.hft.stuttgart.citydoctor2.check.ModificationListener;
+import de.hft.stuttgart.citydoctor2.check.error.ConsecutivePointSameError;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing;
+import de.hft.stuttgart.citydoctor2.datastructure.Vertex;
+import de.hft.stuttgart.citydoctor2.math.Vector3d;
+
+public class HealConsecutivePointsSameError implements HealingMethod {
+
+	private static final Logger logger = LogManager.getLogger(HealConsecutivePointsSameError.class);
+
+	@Override
+	public boolean visit(ConsecutivePointSameError err, ModificationListener l) {
+		logger.debug("Executing Repair for ConsecutivePointSameError");
+		LinearRing lr = err.getRing();
+		Vertex consV1 = err.getVertex1();
+		Vertex consV2 = err.getVertex2();
+		for (int i = 0; i < lr.getVertices().size() - 1; i++) {
+			Vertex v1 = lr.getVertices().get(i + 0);
+			Vertex v2 = lr.getVertices().get(i + 1);
+			if (v1 == consV1 && v2 == consV2) {
+				Vector3d middle = v1.plus(v2).mult(0.5);
+				v2.setX(middle.getX());
+				v2.setY(middle.getY());
+				v2.setZ(middle.getZ());
+				lr.getVertices().remove(i);
+				return true;
+			}
+		}
+		return false;
+	}
+
+	@Override
+	public HealConsecutivePointsSameError createNew() {
+		return new HealConsecutivePointsSameError();
+	}
+
+	@Override
+	public HealingID getID() {
+		return HealingID.R_CONSECUTIVE_POINTS_SAME;
+	}
+}

CityDoctorParent/Extensions/CityDoctorHealer/src/main/java/de/hft/stuttgart/citydoctor2/healing/HealHoleOutsideError.java

+package de.hft.stuttgart.citydoctor2.healing;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import de.hft.stuttgart.citydoctor2.check.HealingID;
+import de.hft.stuttgart.citydoctor2.check.HealingMethod;
+import de.hft.stuttgart.citydoctor2.check.ModificationListener;
+import de.hft.stuttgart.citydoctor2.check.error.PolygonHoleOutsideError;
+import de.hft.stuttgart.citydoctor2.datastructure.LinearRing;
+
+public class HealHoleOutsideError implements HealingMethod {
+	
+	private static final Logger logger = LogManager.getLogger(HealHoleOutsideError.class);
+	
+	@Override
+	public boolean visit(PolygonHoleOutsideError err, ModificationListener l) {
+		logger.debug("Executing Repair for PolygonHoleOutsideError");
+		for (LinearRing lr : err.getHolesOutside()) {
+			err.getPolygon().removeInnerRing(lr);
+		}
+		return true;
+	}
+
+	@Override
+	public HealHoleOutsideError createNew() {
+		return new HealHoleOutsideError();
+	}
+
+	@Override
+	public HealingID getID() {
+		return HealingID.P_HOLE_OUTSIDE;
+	}
+
+}