Adding new classes

src/main/java/com/elphel/imagej/common/MultiThreading.java

+package com.elphel.imagej.common;
+
+public class MultiThreading {
+	public static int THREADS_MAX = 100;
+	/* Create a Thread[] array as large as the number of processors available.
+	 * From Stephan Preibisch's Multithreading.java class. See:
+	 * http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
+	 */
+	public static Thread[] newThreadArray() {
+		return newThreadArray (THREADS_MAX);
+	}
+	public static Thread[] newThreadArray(int maxCPUs) {
+		int n_cpus = Runtime.getRuntime().availableProcessors();
+		if (n_cpus>maxCPUs)n_cpus=maxCPUs;
+		return new Thread[n_cpus];
+	}
+/* Start all given threads and wait on each of them until all are done.
+	 * From Stephan Preibisch's Multithreading.java class. See:
+	 * http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
+	 */
+	public static void startAndJoin(Thread[] threads) // USED in lwir
+	{
+		for (int ithread = 0; ithread < threads.length; ++ithread)
+		{
+			threads[ithread].setPriority(Thread.NORM_PRIORITY);
+			threads[ithread].start();
+		}
+		try
+		{
+			for (int ithread = 0; ithread < threads.length; ++ithread)
+				threads[ithread].join();
+		} catch (InterruptedException ie)
+		{
+			throw new RuntimeException(ie);
+		}
+	}
+}

src/main/java/com/elphel/imagej/tileprocessor/MultiLayerDSL.java

+/**
+ ** MultiLayerDSL - Handle multilayer/multivalue disparity/strength/lma values 
+ **
+ ** Copyright (C) 2022 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  TexturedModel.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+
+package com.elphel.imagej.tileprocessor;
+
+public class MultiLayerDSL {
+
+}

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

+/**
+ **
+ ** LwocLeaf.java - Octree leaf of the world built from LWIR16 images
+ **
+ ** Copyright (C) 2022 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  LwocLeaf.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+
+package com.elphel.imagej.tileprocessor.lwoc;
+
+import java.util.ArrayList;
+
+public class LwocLeaf {
+	ArrayList <LwocMesh>  meshes;
+	ArrayList <LwocMesh>  mesh_centers;
+	ArrayList <LwocScene> scenes;
+	public LwocLeaf() {
+		meshes =       new ArrayList <LwocMesh>();  // all meshes BB intersecting this node
+		mesh_centers = new ArrayList <LwocMesh>();  // mesh centers in this node
+		scenes =       new ArrayList <LwocScene>(); // cameras located in this node
+	}
+	
+	public void addScene(LwocScene scene) {
+		scenes.add(scene);
+	}
+	
+	public void addMeshCenter(LwocMesh mesh) {
+		mesh_centers.add(mesh);
+	}
+
+	public void addMesh(LwocMesh mesh,
+			boolean check_existed) {
+		if (!check_existed || meshes.contains(mesh)) {
+			meshes.add(mesh);
+		}
+	}
+	
+	public ArrayList <LwocMesh> getMeshes(){
+		return meshes;
+	}
+	
+	public ArrayList <LwocMesh> getMeshCenters(){
+		return mesh_centers;
+	}
+	
+	public ArrayList <LwocScene> getScenes(){
+		return scenes;
+	}
+}

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

+/**
+ **
+ ** LwocMesh.java - Single mesh of the world built from LWIR16 images
+ **
+ ** Copyright (C) 2022 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  LwocMesh.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+
+package com.elphel.imagej.tileprocessor.lwoc;
+
+import java.util.ArrayList;
+import java.util.concurrent.atomic.AtomicInteger;
+
+public class LwocMesh {
+	static AtomicInteger       MESH_ID = new AtomicInteger();
+	static ArrayList<LwocMesh> LWOC_MESHES;
+	int                        id;         // assign unique ID
+	String                     stimestamp; // mesh is always referenced to a single scene
+	double []                  world_xyz;  // world coordinates of the center
+	double []                  hdims_xyz;  // world bounding box half-dimensions along x,y,z
+	
+	public static void resetMeshes() {
+		MESH_ID.set(0);
+		LWOC_MESHES = new ArrayList<LwocMesh>();
+	}
+	// maybe use mesh properties instead of id?
+	public boolean equals (LwocMesh other_mesh) {
+		return id == other_mesh.id;
+	}
+	public LwocMesh(
+			String    stimestamp
+			) {
+		this.stimestamp = stimestamp;
+		id = MESH_ID.getAndIncrement();
+		LWOC_MESHES.add(this);
+	}
+	
+	public double [] getCenter() {
+		return world_xyz;
+	}
+	
+	public double [] getDims() {
+		return hdims_xyz;
+	}
+}

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

+/**
+ **
+ ** LwocScene.java - Scene of the world built from LWIR16 images
+ **
+ ** Copyright (C) 2022 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  LwocScene.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+
+package com.elphel.imagej.tileprocessor.lwoc;
+
+import java.util.ArrayList;
+import java.util.concurrent.atomic.AtomicInteger;
+import com.elphel.imagej.tileprocessor.GeometryCorrection;
+
+public class LwocScene {
+	static AtomicInteger SCENE_ID = new AtomicInteger();
+	static ArrayList<LwocScene> LWOC_SCENES;
+	
+	int       id;         // assign unique ID
+	String    stimestamp;
+	GeometryCorrection geometryCorrection;
+	double [] camera_xyz;
+	double [] camera_atr;
+	double [] camera_xyz_dt;
+	double [] camera_atr_dt;
+	double [][][] tile_layers_dsm; // per tile, per layer, {disparity, strength, mode}. For mode -
+	// interpret as Double doubleToLongBits(), [22] - used LMA, 0..15 - which sensors were used
+
+	public static void resetScenes() {
+		SCENE_ID.set(0);
+		LWOC_SCENES = new ArrayList<LwocScene>();
+	}
+	
+	public LwocScene (
+		String             stimestamp,
+		GeometryCorrection geometryCorrection,
+		double []          camera_xyz,
+		double []          camera_atr,
+		double []          camera_xyz_dt,
+		double []          camera_atr_dt,
+		double [][][]      tile_layers_dsm) {
+		
+		this.stimestamp =         stimestamp;
+		this.geometryCorrection = geometryCorrection;
+		this.camera_xyz =         camera_xyz;
+		this.camera_atr =         camera_atr;
+		this.camera_xyz_dt =      camera_xyz_dt;
+		this.camera_atr_dt =      camera_atr_dt;
+		this.tile_layers_dsm =    tile_layers_dsm;
+		id = SCENE_ID.getAndIncrement();
+		LWOC_SCENES.add(this);
+	};
+	// add functionality to save/restore
+	public double [] getCameraXYZ() {
+		return camera_xyz;
+	}
+	public double [] getCameraATR() {
+		return camera_atr;
+	}
+	public double [] getCameraXYZdt() {
+		return camera_xyz_dt;
+	}
+	public double [] getCameraATRdt() {
+		return camera_atr_dt;
+	}
+	public double [][][] getTileLayersDSM() {
+		return tile_layers_dsm;
+	}
+
+	
+	
+	public String getTimestamp() {
+    	return stimestamp;
+    }
+	
+	public static String getTimestamp(double dts) {
+    	return String.format("%.6f", dts).replace('.', '-');
+    }
+
+	public double getDoubleTimestamp() {
+    	return Double.parseDouble(stimestamp.replace('_', '.'));
+    }
+	
+	public static double getDoubleTimestamp(String sts) {
+    	return Double.parseDouble(sts.replace('_', '.'));
+    }
+	
+	public int getIntTimestamp() {
+    	return (int) Math.round(1E6*getDoubleTimestamp());
+    }
+	public void setTimeStamp(String ts) {
+    	stimestamp =  ts;
+    }
+	public void setTimeStamp(double dts) {
+    	stimestamp = getTimestamp(dts);
+    }
+	public void setTimeStamp(int its) {
+    	stimestamp =  String.format("%d_%06d", its / 1000000, its % 1000000);
+    }
+}