Updated for synchronized methods in growing lists, regeneration of (860cbc5f) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/tileprocessor/lwoc/LwocLeaf.java

+26 −3

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@ package com.elphel.imagej.tileprocessor.lwoc;
		import java.util.ArrayList;

		public class LwocLeaf {
		private static final long serialVersionUID = 1L;
		ArrayList <LwocMesh> meshes;
		ArrayList <LwocMesh> mesh_centers;
		ArrayList <LwocScene> scenes;
		@@ -36,21 +37,43 @@ public class LwocLeaf {
		scenes = new ArrayList <LwocScene>(); // cameras located in this node
		}

		public void addScene(LwocScene scene,
		public void initMeshes() {
		meshes = new ArrayList <LwocMesh>(); // all meshes BB intersecting this node
		}
		public synchronized void addScene( // IS synchronized needed?
		LwocScene scene,
		boolean check_existed) {
		if (!check_existed \|\| !scenes.contains(scene)) {
		scenes.add(scene);
		}
		}

		public void addMeshCenter(LwocMesh mesh,
		public synchronized void addMeshCenter( // IS synchronized needed?
		LwocMesh mesh,
		boolean check_existed) {
		if (!check_existed \|\| !mesh_centers.contains(mesh)) {
		mesh_centers.add(mesh);
		}
		}

		public void addMesh(LwocMesh mesh,
		public synchronized void removeScene(
		LwocScene scene) {
		while (scenes.remove(scene)); // will remove all
		}

		public synchronized void removeMeshCenter(
		LwocMesh mesh) {
		while (mesh_centers.remove(mesh)); // will remove all
		}

		public synchronized void removeMesh(
		LwocMesh mesh) {
		while (meshes.remove(mesh)); // will remove all
		}


		public synchronized void addMesh( // synchronized IS needed
		LwocMesh mesh,
		boolean check_existed) {
		if (!check_existed \|\| !meshes.contains(mesh)) {
		meshes.add(mesh);

src/main/java/com/elphel/imagej/tileprocessor/lwoc/LwocMesh.java

+1 −0

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@ import java.util.ArrayList;
		import java.util.concurrent.atomic.AtomicInteger;

		public class LwocMesh {
		private static final long serialVersionUID = 1L;
		static AtomicInteger MESH_ID = new AtomicInteger();
		static ArrayList<LwocMesh> LWOC_MESHES;
		int id; // assign unique ID

src/main/java/com/elphel/imagej/tileprocessor/lwoc/LwocOctree.java

+109 −139

Original line number	Diff line number	Diff line
		@@ -29,6 +29,7 @@ import java.util.List;
		import java.util.concurrent.atomic.AtomicInteger;
		import com.elphel.imagej.common.MultiThreading;
		public class LwocOctree {
		private static final long serialVersionUID = 1L;
		public static final int NUM_CHILDREN = 8;
		public static double MIN_HSIZE = 0.3; // meter - do not subdivide more
		// can not be used as intersecting meshes' bb will not decrease number after splitting
		@@ -37,14 +38,10 @@ public class LwocOctree {
		public static LwocOctree lwoc_root = null;
		static ArrayList<LwocOctree> LWOK_OCTREE = new ArrayList<LwocOctree>();
		static AtomicInteger OCTREE_ID = new AtomicInteger();
		// synchronized lists to handle thread-unsafe operations: growing world and splitting leaves
		/// static List<LwocScene> pendingScenes; // synchronized - add not-yet-added scenes pending growing world
		/// static List<LwocMesh> pendingMeshes; // synchronized - add not-yet-added meshes pending growing world
		/// static List<LwocOctree> pendingLeafNodes;// synchronized - leaf nodes needed to be split

		static AtomicInteger numPendingScenes;
		static AtomicInteger numPendingMeshes;
		static AtomicInteger numPendingLeafNodes;
		static List<LwocScene> pendingScenes; // synchronized - add not-yet-added scenes pending growing world
		static List<LwocMesh> pendingMeshes; // synchronized - add not-yet-added meshes pending growing world
		static List<LwocOctree> pendingLeafNodes;// synchronized - leaf nodes needed to be split


		int id; // assign unique ID
		@@ -53,6 +50,26 @@ public class LwocOctree {
		LwocLeaf leaf; //
		double [] center; // x-center, y-center, z-center
		double hsize;

		public static void addPendingScene(LwocScene scene) {
		synchronized(pendingScenes) {
		pendingScenes.add(scene);
		}
		}

		public static void addPendingMesh(LwocMesh mesh) {
		synchronized(pendingMeshes) {
		pendingMeshes.add(mesh);
		}
		}

		public static void addPendingLeafNode(LwocOctree node) {
		synchronized(pendingLeafNodes) {
		pendingLeafNodes.add(node);
		}
		}


		// just for testing
		// List<List<LwocScene>> group = new ArrayList<List<LwocScene>>(4);

		@@ -79,9 +96,9 @@ public class LwocOctree {
		* processes by a single-thread method.
		*/
		public static void resetPending() {
		numPendingScenes.set(0); // = Collections.synchronizedList(new ArrayList<LwocScene>());
		numPendingMeshes.set(0); // = Collections.synchronizedList(new ArrayList<LwocMesh>());
		numPendingLeafNodes.set(0); // = Collections.synchronizedList(new ArrayList<LwocOctree>());
		pendingScenes = new ArrayList<LwocScene>();
		pendingMeshes = new ArrayList<LwocMesh>();
		pendingLeafNodes = new ArrayList<LwocOctree>();
		}
		// use per-thread lists and then combine them avoiding synchronizations?
		//Pass list to any function that may grow it
		@@ -99,7 +116,7 @@ public class LwocOctree {
		* @return if world needs growing.
		*/
		public static boolean pendingGrow() {
		return (numPendingScenes.get() + numPendingMeshes.get()) > 0;
		return (pendingScenes.size() + pendingMeshes.size()) > 0;
		}

		/**
		@@ -107,7 +124,7 @@ public class LwocOctree {
		* @return if any leaf nodes require splitting
		*/
		public static boolean pendingSplit() {
		return numPendingLeafNodes.get() > 0;
		return pendingLeafNodes.size() > 0;
		}

		/**
		@@ -152,23 +169,18 @@ public class LwocOctree {
		* Add scene to the world in a thread-safe mode, or put it to pending list if the world
		* needs growing.
		* @param scene Scene to add.
		* @param pendingScenes per thread list of scenes to be combined after merging threads
		* @param pendingLeafNodes per thread list of nodes to be combined after merging threads
		* @param check_existed - do not add duplicate scenes and nodes
		* @return An octree node where scene is added or null if the world needs growing
		*/
		public static LwocOctree addScene(
		LwocScene scene,
		ArrayList<LwocScene> pendingScenes,
		ArrayList<LwocOctree> pendingLeafNodes,
		boolean check_existed
		) {// returns null and adds to pendingScenes if needs growing
		LwocOctree node = getLeafNode(scene.getCameraXYZ());
		if (node == null) {
		if (pendingScenes != null) {
		if (!check_existed \|\| !pendingScenes.contains(scene)) {
		pendingScenes.add(scene);
		numPendingScenes.getAndIncrement();
		addPendingScene(scene);
		}
		}
		} else {
		@@ -177,8 +189,7 @@ public class LwocOctree {
		if (node.leaf.getScenes().size() > MAX_CAMERAS) {
		if (node.hsize > MIN_HSIZE) {
		if (!check_existed \|\| !pendingLeafNodes.contains(node)) {
		pendingLeafNodes.add(node);
		numPendingLeafNodes.getAndIncrement();
		addPendingLeafNode(node);
		}
		}
		}
		@@ -188,13 +199,9 @@ public class LwocOctree {

		/**
		* Tend to pending scenes list. Not thread-safe, should be run in a single-thread mode.
		* @param pendingScenes combined list of scenes to be added growing world (merged from per-thread ones)
		* @param pendingLeafNodes a list of nodes that will need splitting (here in single-thread mode - single one)
		* @param check_existed - do not add duplicate scenes and nodes
		*/
		public static void tendPendingScenes(
		ArrayList<LwocScene> pendingScenes,
		ArrayList<LwocOctree> pendingLeafNodes,
		boolean check_existed
		) {
		if (pendingScenes.isEmpty()) {
		@@ -204,8 +211,6 @@ public class LwocOctree {
		growXYZ(scene.getCameraXYZ());
		LwocOctree node= addScene( // should not be null
		scene,
		pendingScenes,
		pendingLeafNodes,
		check_existed);
		assert node != null : "addScene() should not fail after growing world";
		}
		@@ -216,13 +221,9 @@ public class LwocOctree {
		* Tend to pending meshes list. Not thread-safe, should be run in a single-thread mode.
		* Only adds mesh centers and grows the world if needed.
		* @param check_existed do not add duplicate meshes
		* @param pendingMeshes combined list of meshes to be added (merged from per-thread ones). Will only be read.
		* @param pendingLeafNodes a list of nodes that will need splitting (here in single-thread mode - single one). May grow.
		*/
		public static void tendPendingMeshCentersOnly(
		boolean check_existed,
		ArrayList<LwocMesh> pendingMeshes, // will read
		ArrayList<LwocOctree> pendingLeafNodes // may add to
		boolean check_existed
		) {
		if (pendingMeshes.isEmpty()) {
		return; // nothing to do
		@@ -240,9 +241,7 @@ public class LwocOctree {
		}
		boolean ok= addMeshCenter( // should not be null
		mesh,
		check_existed,
		null, // pendingMeshes,
		pendingLeafNodes);
		check_existed);
		assert ok : "addMeshCenter() should not fail after growing world";
		}
		}
		@@ -253,13 +252,9 @@ public class LwocOctree {
		* Only adds mesh themselves that do not trigger node splits.
		* Should be run after tendPendingMeshCentersOnly().
		* @param check_existed do not add duplicate meshes
		* @param pendingMeshes combined list of meshes to be added (merged from per-thread ones).
		* Will only be read.
		*/
		public static void tendPendingMeshes(
		boolean check_existed,
		ArrayList<LwocMesh> pendingMeshes // will read
		) {
		boolean check_existed ) {
		if (pendingMeshes.isEmpty()) {
		return; // nothing to do
		} else {
		@@ -276,8 +271,6 @@ public class LwocOctree {
		/**
		* Recursively (if needed) splits octree nodes to reduce number of scenes/cameras
		* and mesh centers below specified thresholds (limited by the minimal node size)
		* @param pendingLeafNodesIn array list of nodes to be split. Will be filtered to
		* remove any duplicates and non-leaf nodes
		* @param min_hsize Minimal half-size of the node (in meters). Smaller nodes will not be split
		* @param max_mesh_centers Maximal number of mesh centers in a node. Larger number
		* triggers node split.
		@@ -286,17 +279,15 @@ public class LwocOctree {
		* @param check_existed
		*/
		public static void tendPendingLeafNodes(
		ArrayList<LwocOctree> pendingLeafNodesIn,
		final double min_hsize,
		final int max_mesh_centers,
		final int max_cameras, // scenes
		final boolean check_existed) {
		// remove any possible duplicates
		final ArrayList<LwocOctree> pendingLeafNodes = new ArrayList<LwocOctree>();
		for (LwocOctree node:pendingLeafNodesIn) {
		if (!pendingLeafNodes.contains(node) && node.isLeaf()) {// filter already split nodes
		pendingLeafNodes.add(node);
		numPendingLeafNodes.getAndIncrement();
		final ArrayList<LwocOctree> pendingLeafNodesFiltered = new ArrayList<LwocOctree>();
		for (LwocOctree node:pendingLeafNodes) {
		if (!pendingLeafNodesFiltered.contains(node) && node.isLeaf()) {// filter already split nodes
		pendingLeafNodesFiltered.add(node);
		}
		}
		// run splitting multithreaded
		@@ -306,8 +297,8 @@ public class LwocOctree {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int indx_node = ai.getAndIncrement(); indx_node < pendingLeafNodes.size(); indx_node = ai.getAndIncrement()) {
		LwocOctree node = pendingLeafNodes.get(indx_node);
		for (int indx_node = ai.getAndIncrement(); indx_node < pendingLeafNodesFiltered.size(); indx_node = ai.getAndIncrement()) {
		LwocOctree node = pendingLeafNodesFiltered.get(indx_node);
		// Split recursively until satisfied conditions
		node.splitNode(
		min_hsize, // double min_hsize,
		@@ -319,7 +310,6 @@ public class LwocOctree {
		};
		}
		MultiThreading.startAndJoin(threads);
		ai.set(0);
		}

		// Split recursively until satisfied conditions
		@@ -517,15 +507,11 @@ public class LwocOctree {
		* add to pending list if does not fit in a root node
		* @param mesh new mesh to add
		* @param check_existed Add only if the same mesh did not exist
		* @param pendingMeshes per thread list of meshes to be combined after merging threads
		* @param pendingLeafNodes per thread list of nodes to be combined after merging threads
		* @return number of nodes it was added to (intersecting)
		*/
		public static boolean addMeshCenter( // returns 0 and adds to pendingMeshes if needs growing
		LwocMesh mesh,
		boolean check_existed,
		ArrayList<LwocMesh> pendingMeshes,
		ArrayList<LwocOctree> pendingLeafNodes
		boolean check_existed
		) {
		// should in check before adding?
		// mesh.equals(mesh);
		@@ -538,8 +524,7 @@ public class LwocOctree {
		if (!lwoc_root.contains(corner_xyz)){
		if (pendingMeshes != null) {
		if (!check_existed \|\| !pendingMeshes.contains(mesh)) {
		pendingMeshes.add(mesh);
		numPendingMeshes.getAndIncrement();
		addPendingMesh(mesh);
		}
		}
		return false;
		@@ -548,8 +533,7 @@ public class LwocOctree {
		if (!lwoc_root.contains(corner_xyz)){
		if (pendingMeshes != null) {
		if (!check_existed \|\| !pendingMeshes.contains(mesh)) {
		pendingMeshes.add(mesh);
		numPendingMeshes.getAndIncrement();
		addPendingMesh(mesh);
		}
		}
		return false;
		@@ -563,8 +547,7 @@ public class LwocOctree {
		if (node.leaf.getMeshCenters().size() > MAX_MESH_CENTERS) {
		if (node.hsize > MIN_HSIZE) {
		if (!check_existed \|\| !pendingLeafNodes.contains(node)) {
		pendingLeafNodes.add(node);
		numPendingLeafNodes.getAndIncrement();
		addPendingLeafNode(node);
		}
		}
		}
		@@ -573,6 +556,13 @@ public class LwocOctree {
		}

		// recursive
		/**
		* Recursively add mesh to all leaf nodes that intersect with its bounding box.
		* Usually starts with lwoc_root.
		* @param mesh Mesh instance to be added
		* @param check_existed verify node lists does not already have this mesh if true
		* @return number of nodes to which this mesh was added
		*/
		public int addMesh(
		LwocMesh mesh,
		boolean check_existed) {
		@@ -593,102 +583,82 @@ public class LwocOctree {
		}

		/**
		* Remove mesh to from each node intersecting with the mesh bounding box.
		* Remove mesh center from the world.
		* Should fit in a root node (as it was earlier added)
		* @param mesh new mesh to add
		* @param check_existed Add only if the same mesh did not exist
		* @return The number of nodes it was removed from
		*/
		public static int removeMesh(
		LwocMesh mesh,
		boolean remove_all) { // check and remove duplicates
		// should in check before adding?
		return 0;
		public static void removeMeshCenter(
		LwocMesh mesh) { // check and remove duplicates
		LwocOctree node = getLeafNode(mesh.getCenter());
		node.leaf.removeMeshCenter(mesh);
		}

		/**
		* Prepare list of lists to add scenes in multithreaded environment, one inner
		* list for each thread.
		* @param threads Array of threads, only length is used
		* @return list of lists to provide to threads
		* Remove mesh from each node intersecting with the mesh bounding box.
		* Should fit in a root node (as it was earlier added)
		* @param mesh mesh to remove
		*/
		public static List<List<LwocScene>> getMultiPendingScenes(Thread [] threads){
		List<List<LwocScene>> multiPendingScenes = new ArrayList<List<LwocScene>>(threads.length);
		for (int i = 0; i < threads.length; i++) {
		multiPendingScenes.add(i, new ArrayList<LwocScene>());
		public int removeMesh(
		LwocMesh mesh) { // check and remove duplicates
		if (!intersects(
		mesh.getCenter(),
		mesh.getDims())) {
		return 0;
		}
		return multiPendingScenes;
		if (isLeaf()) {
		leaf.removeMesh(mesh);
		return 1;
		}

		/**
		* Combine a List of list of scenes (created in multithreaded method getMultiPendingScenes())
		* into a single list.
		* @param multiPendingScenes list of list of scenes
		* @return flattened single list of scenes
		*/
		public static List<LwocScene> mergeMultiPendingScenes(List<List<LwocScene>> multiPendingScenes){
		List<LwocScene> pendingScenes = new ArrayList<LwocScene>();
		for (List<LwocScene> scenes:multiPendingScenes) {
		pendingScenes.addAll(scenes);
		int removed = 0;
		for (LwocOctree node: children) {
		removed += node.removeMesh(mesh);
		}
		return pendingScenes;
		return removed;
		}

		/**
		* Prepare list of lists to add meshes in multithreaded environment, one inner
		* list for each thread.
		* @param threads Array of threads, only length is used
		* @return list of lists to provide to threads
		* Recursively create a list of all leave nodes in the world.
		* @return A list of all leaf nodes
		*/
		public static List<List<LwocMesh>> getMultiPendingMeshes(Thread [] threads){
		List<List<LwocMesh>> multiPendingMeshes = new ArrayList<List<LwocMesh>>(threads.length);
		for (int i = 0; i < threads.length; i++) {
		multiPendingMeshes.add(i, new ArrayList<LwocMesh>());
		public List<LwocOctree> getAllLeafNodes(){
		List<LwocOctree> leaves = new ArrayList<LwocOctree>();
		if (isLeaf()) {
		leaves.add(this);
		} else {
		for (LwocOctree child:children) {
		leaves.addAll(child.getAllLeafNodes());
		}
		return multiPendingMeshes;
		}
		return leaves;
		}

		/**
		* Combine a List of list of meshes (created in multithreaded method getMultiPendingMeshes())
		* into a single list.
		* @param multiPendingMeshes list of list of meshes
		* @return flattened single list of meshes
		* Rebuild meshes lists from mesh_centers for all leaf nodes after restoring the world.
		* Used after restoring world from serialized form
		*/
		public static List<LwocMesh> mergeMultiPendingMeshes(List<List<LwocMesh>> multiPendingMeshes){
		List<LwocMesh> pendingMeshes = new ArrayList<LwocMesh>();
		for (List<LwocMesh> meshes:multiPendingMeshes) {
		pendingMeshes.addAll(meshes);
		}
		return pendingMeshes;
		public static void rebuildMeshLists(
		final boolean check_existed) {
		final List<LwocOctree> leaves = lwoc_root.getAllLeafNodes();
		final List<LwocMesh> meshes = new ArrayList<LwocMesh>();
		for (LwocOctree node : leaves) {
		node.leaf.initMeshes();
		meshes.addAll(node.leaf.getMeshCenters());
		}

		/**
		* Prepare list of lists to add scenes in multithreaded environment, one inner
		* list for each thread.
		* @param threads Array of threads, only length is used
		* @return list of lists to provide to threads
		*/
		public static List<List<LwocOctree>> getMultiPendingLeafNodes(Thread [] threads){
		List<List<LwocOctree>> multiPendingLeafNodes = new ArrayList<List<LwocOctree>>(threads.length);
		for (int i = 0; i < threads.length; i++) {
		multiPendingLeafNodes.add(i, new ArrayList<LwocOctree>());
		final Thread[] threads = MultiThreading.newThreadArray();
		final AtomicInteger ai = new AtomicInteger(0);

		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		for (int indx_mesh = ai.getAndIncrement(); indx_mesh < meshes.size(); indx_mesh = ai.getAndIncrement()) {
		LwocMesh mesh = meshes.get(indx_mesh);
		lwoc_root.addMesh(mesh, check_existed);
		}
		return multiPendingLeafNodes;
		}

		/**
		* Combine a List of list of scenes (created in multithreaded method getMultiPendingScenes())
		* into a single list.
		* @param multiPendingLeafNodes list of list of scenes
		* @return flattened single list of scenes
		*/
		public static List<LwocOctree> mergeMultiPendingLeafNodes(List<List<LwocOctree>> multiPendingLeafNodes){
		List<LwocOctree> pendingLeafNodes = new ArrayList<LwocOctree>();
		for (List<LwocOctree> nodes:multiPendingLeafNodes) {
		pendingLeafNodes.addAll(nodes);
		};
		}
		return pendingLeafNodes;
		MultiThreading.startAndJoin(threads);
		}


		}

src/main/java/com/elphel/imagej/tileprocessor/lwoc/LwocScene.java

+1 −0

Original line number	Diff line number	Diff line
		@@ -29,6 +29,7 @@ import java.util.concurrent.atomic.AtomicInteger;
		import com.elphel.imagej.tileprocessor.GeometryCorrection;

		public class LwocScene {
		private static final long serialVersionUID = 1L;
		static AtomicInteger SCENE_ID = new AtomicInteger();
		static ArrayList<LwocScene> LWOC_SCENES;

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