removed octree attribute in AdjacencyMap

pom.xml

@@ -182,7 +182,7 @@
                 <executions>
                     <execution>
                         <goals>
-                            <goal>check</goal>
+                            <goal>format</goal>
                         </goals>
                     </execution>
                 </executions>

src/main/java/es/usc/citius/lab/joctomap/octree/JOctree.java

@@ -43,8 +43,6 @@
  * @author adrian.gonzalez
  */
 public class JOctree extends NativeObject{
-
-        private String path;
 
 	/**
 	 * Initializes the JOctree with a pointer to the native OcTree object of
@@ -424,14 +422,5 @@ public JOctreeNode search(float x, float y, float z){
 	 * @return octree with the given resolution
 	 */
 	public static native JOctree create(float res);
-
-        /**
-         * Retrieves the path from which the octree was loaded.
-         * 
-         * @return 
-         */
-        public String getPath() {
-            return path;
-        }
 
 }

src/main/java/es/usc/citius/lab/joctomap/util/AdjacencyMap.java

@@ -26,15 +26,12 @@
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
 import java.io.Serializable;
 
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 /**
  * This class implements a builder for calculating the adjacency map of an Octomap.
@@ -49,7 +46,6 @@
 public class AdjacencyMap implements Serializable{
 
     private Map<JOctreeKey, List<JOctreeKey>> adjacencies;
-    private JOctree octree;
     //contains the information of size and center of each leaf in the octree
     private Map<JOctreeKey, Pair<Float, Point3D>> nodesInfo;
     private double EPSILON = 1e-3;
@@ -63,7 +59,6 @@ public class AdjacencyMap implements Serializable{
      */
     private AdjacencyMap(JOctree octree){
         this.adjacencies = new HashMap<JOctreeKey, List<JOctreeKey>>();
-        this.octree = octree;
         this.nodesInfo = new HashMap<JOctreeKey, Pair<Float, Point3D>>();
         //create cache
         Cache cacheOfKeys = new Cache();
@@ -116,10 +111,8 @@ private AdjacencyMap(){
     public static AdjacencyMap create(JOctree octree){
         //initialize structures
         AdjacencyMap map = new AdjacencyMap();
-        //assign octree
-        map.octree = octree;
         //fill with JNI method
-        map.initializeJNI();
+        map.initializeJNI(octree);
         //retrieve result
         return map;
     }
@@ -139,7 +132,7 @@ public static AdjacencyMap createJava(JOctree octree){
      * This fills the structures of the adjacency map using full-native
      * implementation method for efficiency.
      */
-    private native void initializeJNI();
+    private native void initializeJNI(JOctree octree);
 
     /**
      * Retrieves the adjacencies for a current key.
@@ -159,10 +152,6 @@ public Map<JOctreeKey, Pair<Float, Point3D>> getNodesInfo() {
         return nodesInfo;
     }
 
-    public JOctree getOctree() {
-        return octree;
-    }
-
     /**
      * Retrieves the information of a node stored after exploring the adjacencies.
      *
@@ -194,8 +183,6 @@ public boolean write(String filename){
         //open output stream
         try{
             DataOutputStream outputStream = new DataOutputStream(new FileOutputStream(outputFile));
-            //write name of octree
-            outputStream.writeUTF(this.octree.getPath());
             //write adjacencies & nodesInfo
             outputStream.writeInt(adjacencies.size());
             for(Map.Entry<JOctreeKey, List<JOctreeKey>> current : adjacencies.entrySet()){
@@ -239,10 +226,6 @@ public static AdjacencyMap read(String filename){
         //open input stream (will be closed after this statement)
         try{
             DataInputStream inputStream = new DataInputStream(new FileInputStream(inputFile));
-            //read name of the octree
-            String octreePath = inputStream.readUTF();
-            //load octree
-            map.octree = JOctree.read(octreePath);
             //read map instance
             int sizeMap = inputStream.readInt();
             map.adjacencies = new HashMap<JOctreeKey, List<JOctreeKey>>(sizeMap);

src/main/resources/joctomap-natives/include/adjacencymap.h

@@ -25,10 +25,10 @@ extern "C" {
 /*
  * Class:     es_usc_citius_lab_joctomap_util_AdjacencyMap
  * Method:    initializeJNI
- * Signature: ()V
+ * Signature: (Les/usc/citius/lab/joctomap/octree/JOctree;)V
  */
 JNIEXPORT void JNICALL Java_es_usc_citius_lab_joctomap_util_AdjacencyMap_initializeJNI
-  (JNIEnv *, jobject);
+  (JNIEnv *, jobject, jobject);
 
 #ifdef __cplusplus
 }

src/main/resources/joctomap-natives/src/adjacencymap.cpp

@@ -23,16 +23,14 @@
 using namespace octomap;
 
 JNIEXPORT void JNICALL Java_es_usc_citius_lab_joctomap_util_AdjacencyMap_initializeJNI
-  (JNIEnv *env, jobject jadjacencymap){
+  (JNIEnv *env, jobject jadjacencymap, jobject joctree){
     //error margin
     float EPSILON = 0.001f;
     //retrieve fields from adjacencymap
     jclass cls_jadjacencymap = env->FindClass(CLS_JADJACENCYMAP);
-    jfieldID field_joctomap = env->GetFieldID(cls_jadjacencymap, FIELD_ADJACENCYMAP_OCTREE, CLS_JOCTREE);
     jfieldID field_nodes_info = env->GetFieldID(cls_jadjacencymap, FIELD_ADJACENCYMAP_NODESINFO, CLS_MAP);
     jfieldID field_adjacencies = env->GetFieldID(cls_jadjacencymap, FIELD_ADJACENCYMAP_ADJACENCIES, CLS_MAP);
     //retrieve objects from fields
-    jobject joctree = env->GetObjectField(jadjacencymap, field_joctomap);
     jobject jnodes_info = env->GetObjectField(jadjacencymap, field_nodes_info);
     jobject jadjacencies = env->GetObjectField(jadjacencymap, field_adjacencies);
     //retrieve HashMap, JOctreeKey, Pair, Point3D class

src/main/resources/joctomap-natives/src/joctree.cpp

@@ -598,9 +598,6 @@ JNIEXPORT jboolean JNICALL Java_es_usc_citius_lab_joctomap_octree_JOctree_write
 	const char *nativeFilename = env->GetStringUTFChars(filename, &iscopy);
 	//write octree in filename
 	bool value = octree->write(nativeFilename);
-        //set path to which the octree was read
-        jfieldID pathField = env->GetFieldID(env->GetObjectClass(obj), FIELD_PATH, CLS_STRING);
-        env->SetObjectField(obj, pathField, filename);
 	//release memory of native char*
 	env->ReleaseStringUTFChars(filename, nativeFilename);
 	//return obtained value
@@ -660,9 +657,6 @@ JNIEXPORT jobject JNICALL Java_es_usc_citius_lab_joctomap_octree_JOctree_read
 	stream.close();
         //create joctree object
 	jobject jtree =  env->NewObject(cls, constructor, ot);
-        //set path from which the octree was read
-        jfieldID pathField = env->GetFieldID(cls, FIELD_PATH, CLS_STRING);
-        env->SetObjectField(jtree, pathField, filename);
         return jtree;
 }
 

src/test/java/es/usc/citius/lab/joctomap/JOctreeTest.java

@@ -103,7 +103,6 @@ public void test02_readFileOt() throws IOException {
 		octree = JOctree.read(inputPath);
 		assertTrue("Octree direction of memory not assigned",
 				octree.getPointer() != 0);
-                assertTrue("Octree input path not assigned", octree.getPath().equals(inputPath));
 	}
 
 	/**
@@ -117,8 +116,7 @@ public void test03_writeFileOtTest() throws IOException {
 		octree.write(fileWrite.getAbsolutePath());
 		// compare by content both files
 		assertTrue("Input and output files with the same content",
-				FileUtils.contentEquals(fileRead, fileWrite));
-                assertTrue("File path not set properly after write", octree.getPath().equals(fileWrite.getAbsolutePath()));
+                    FileUtils.contentEquals(fileRead, fileWrite));
 	}
 
 	/**

src/test/java/es/usc/citius/lab/joctomap/util/AdjacencyMapTest.java

@@ -55,8 +55,8 @@ public AdjacencyMapTest() throws URISyntaxException{
     @Test
     public void test01_calculateAdjacencyMap(){
 
-        assertEquals("Nodes info size do not match with number of leaves.", adjacencyMap.getOctree().size(), adjacencyMap.getNodesInfo().size());
-        assertEquals("Adjacencies info size do not match with number of leaves.", adjacencyMap.getOctree().size(), adjacencyMap.getAdjacencies().size());
+        assertEquals("Nodes info size do not match with number of leaves.", octree.size(), adjacencyMap.getNodesInfo().size());
+        assertEquals("Adjacencies info size do not match with number of leaves.", octree.size(), adjacencyMap.getAdjacencies().size());
         //iterate over the entries of the adjacency map
         for(Map.Entry<JOctreeKey, List<JOctreeKey>> entry : adjacencyMap.getAdjacencies().entrySet()){
             //center of first cell