Add documentation to the visualization project.

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/Visualization.java

@@ -22,6 +22,7 @@
  * The fact that you are presently reading this means that you have had
  * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization;
 
 import fr.amap.lidar.amapvox.visualization.views.VisualizationScene;
@@ -30,12 +31,9 @@ import fr.amap.commons.util.debug.Debugger;
 import fr.amap.commons.util.swing.jprogress.JProgressFrame;
 import java.io.InputStream;
 import fr.amap.lidar.amapvox.visualization.views.MainView;
-import java.io.FileInputStream;
-import java.io.FileReader;
 
 /**
- * Visualization class of the Voxelization project.
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Main class of the Voxelization project.
  */
 public class Visualization {
 

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/controllers/OptionsController.java

@@ -22,6 +22,7 @@
  * The fact that you are presently reading this means that you have had
  * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization.controllers;
 
 import java.awt.Color;
@@ -32,21 +33,35 @@ import fr.amap.lidar.amapvox.visualization.opengl.util.Skyboxes;
 import fr.amap.lidar.amapvox.visualization.util.ProjectProperties;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Controller of the options view.
  */
 public class OptionsController {
 
+    /**
+     * The current visualization scene.
+     */
     private VisualizationScene scene;
 
+    /**
+     * Create an options controller with empty scene.
+     */
     public OptionsController() {
         this.scene = null;
     }
 
+    /**
+     * Set the current visualization scene.
+     * @param scene 
+     */
     public final void setScene(final VisualizationScene scene) {
         this.scene = scene;
     }
 
+    /**
+     * Chnage the background of the scene.
+     * @param background
+     * @throws IOException 
+     */
     public final void changeBackground(final String background)
             throws IOException {
         if (scene != null) {
@@ -55,6 +70,10 @@ public class OptionsController {
         }
     }
 
+    /**
+     * Change the color bar of the voxel space.
+     * @param name 
+     */
     public final void changeColorBar(final String name) {
         final Color[] colorBar = ColorBars.getColorBar(name);
         scene.getVoxelSpaceComponent().setColorBar(colorBar);
@@ -62,17 +81,29 @@ public class OptionsController {
         ProjectProperties.setProperty("colorBar", name);
     }
 
+    /**
+     * Change the draw fast property of the voxel space.
+     * @param enabled 
+     */
     public final void changeDrawFast(final boolean enabled) {
         scene.getVoxelSpaceComponent().setDrawFastEnabled(enabled);
         ProjectProperties.setProperty("drawFastEnabled", Boolean.toString(enabled));
     }
     
+    /**
+     * Change the voxel size
+     * @param size 
+     */
     public final void changeVoxelSize(final int size) {
         final float normalizedSize = (float) size / 100;
         scene.getVoxelSpaceComponent().setDrawingMode(normalizedSize);
         ProjectProperties.setProperty("voxelSize", Integer.toString(size));
     }
     
+    /**
+     * Enable or disable the reflections of the voxel space.
+     * @param enabled 
+     */
     public final void changeEnableReflection(final boolean enabled) {
         if (scene != null) {
             scene.getVoxelSpaceComponent().setReflectionEnabled(enabled);
@@ -80,6 +111,10 @@ public class OptionsController {
         }
     }
     
+    /**
+     * Hide or show the grid entity.
+     * @param hide 
+     */
     public final void setHideGrid(final boolean hide) {
         if (scene != null) {
             scene.setHideGrid(hide);
@@ -88,6 +123,10 @@ public class OptionsController {
         }
     }
     
+    /**
+     * Hide or show the boundingbox entity.
+     * @param hide 
+     */
     public final void setHideBoundingbox(final boolean hide) {
         if (scene != null) {
             scene.setHideBoundingBox(hide);
@@ -96,6 +135,10 @@ public class OptionsController {
         }
     }
     
+    /**
+     * Set the voxels shape.
+     * @param index 
+     */
     public final void setShape(final int index) {
         if (scene != null) {
             scene.getVoxelSpaceComponent().setDrawPixel(index == 0);

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/controllers/PropertiesController.java

 /*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
+ * This software is governed by the CeCILL-B license under French law and
+ * abiding by the rules of distribution of free software. You can use, modify
+ * and/ or redistribute the software under the terms of the CeCILL-B license as
+ * circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and rights to copy, modify
+ * and redistribute granted by the license, users are provided only with a
+ * limited warranty and the software's author, the holder of the economic
+ * rights, and the successive licensors have only limited liability.
+ * 
+ * In this respect, the user's attention is drawn to the risks associated with
+ * loading, using, modifying and/or developing or reproducing the software by
+ * the user in light of its specific status of free software, that may mean that
+ * it is complicated to manipulate, and that also therefore means that it is
+ * reserved for developers and experienced professionals having in-depth
+ * computer knowledge. Users are therefore encouraged to load and test the
+ * software's suitability as regards their requirements in conditions enabling
+ * the security of their systems and/or data to be ensured and, more generally,
+ * to use and operate it in the same conditions as regards security.
+ * 
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization.controllers;
 
 import fr.amap.lidar.amapvox.visualization.opengl.entities.util.VoxelFilter;
 import fr.amap.lidar.amapvox.visualization.views.VisualizationScene;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Controller of the properties view.
  */
 public class PropertiesController {
     
+    /**
+     * The current scene.
+     */
     private VisualizationScene scene;
 
+    /**
+     * Create a property controller with an empty scene.
+     */
     public PropertiesController() {
         this.scene = null;
     }
     
+    /**
+     * Change the current scene.
+     * @param scene 
+     */
     public final void setScene(final VisualizationScene scene) {
         this.scene = scene;
     }
 
+    /**
+     * Get the current scene.
+     * @return 
+     */
     public final VisualizationScene getScene() {
         return scene;
     }
     
+    /**
+     * Change the displayed property of the voxel space.
+     * @param property 
+     */
     public final void changeCurrentProperty(final String property) {
         if (scene != null) {
             scene.getVoxelSpaceComponent().setProperty(property);
@@ -35,6 +72,12 @@ public class PropertiesController {
         }
     }
     
+    /**
+     * Change the min and max of the current property values.
+     * (not used by the UI)
+     * @param min
+     * @param max 
+     */
     public final void changeMinAndMax(final float min, final float max) {
         if (scene != null) {
             scene.getVoxelSpaceComponent().setColorMinAndMax(min, max);
@@ -42,6 +85,10 @@ public class PropertiesController {
         }
     }
     
+    /**
+     * Add or replace a particular filter of a voxel property.
+     * @param filter 
+     */
     public final void changeFilter(final VoxelFilter filter) {
         if (scene != null && filter != null) {
             scene.getVoxelSpaceComponent().setFilter(filter);
@@ -49,6 +96,10 @@ public class PropertiesController {
         }
     }
     
+    /**
+     * Remove a filter of a voxel property.
+     * @param filter 
+     */
     public final void removeFilter(final int filter) {
         if (scene != null) {
             scene.getVoxelSpaceComponent().removeFilter(filter);
@@ -56,6 +107,9 @@ public class PropertiesController {
         }
     }
     
+    /**
+     * Remove all voxel filters.
+     */
     public final void clearFilters() {
         if (scene != null) {
             scene.getVoxelSpaceComponent().resetFilters();

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/controllers/ToolbarController.java

 /*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
+ * This software is governed by the CeCILL-B license under French law and
+ * abiding by the rules of distribution of free software. You can use, modify
+ * and/ or redistribute the software under the terms of the CeCILL-B license as
+ * circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and rights to copy, modify
+ * and redistribute granted by the license, users are provided only with a
+ * limited warranty and the software's author, the holder of the economic
+ * rights, and the successive licensors have only limited liability.
+ * 
+ * In this respect, the user's attention is drawn to the risks associated with
+ * loading, using, modifying and/or developing or reproducing the software by
+ * the user in light of its specific status of free software, that may mean that
+ * it is complicated to manipulate, and that also therefore means that it is
+ * reserved for developers and experienced professionals having in-depth
+ * computer knowledge. Users are therefore encouraged to load and test the
+ * software's suitability as regards their requirements in conditions enabling
+ * the security of their systems and/or data to be ensured and, more generally,
+ * to use and operate it in the same conditions as regards security.
+ * 
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization.controllers;
 
 import fr.amap.commons.util.swing.jprogress.JProgressFrame;
@@ -14,25 +34,44 @@ import java.io.InputStream;
 import fr.amap.lidar.amapvox.visualization.views.VisualizationScene;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Controller of the toolbar view.
  */
 public class ToolbarController {
     
+    /**
+     * The current visualization scene.
+     */
     private VisualizationScene scene;
 
+    /**
+     * Create a new toolbar controller with an empty visualization scene.
+     */
     public ToolbarController() {
         this.scene = null;
     }
 
+    /**
+     * Set the current visualization scene.
+     * @param scene 
+     */
     public final void setScene(final VisualizationScene scene) {
         this.scene = scene;
     }
 
+    /**
+     * Get the current visualization scene.
+     * @return 
+     */
     public final VisualizationScene getScene() {
         return scene;
     }
     
+    /**
+     * Open a new voxel space file.
+     * @param file
+     * @param progressFrame
+     * @throws FileNotFoundException 
+     */
     public final void openVoxelSpaceFile(final File file, 
             final JProgressFrame progressFrame) 
             throws FileNotFoundException {
@@ -43,6 +82,10 @@ public class ToolbarController {
         }
     }
     
+    /**
+     * Change the current camera angle.
+     * @param viewType 
+     */
     public final void setCameraView(final ViewType viewType) {
         if (scene != null) {
             scene.getCameraController().setView(viewType);

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/controllers/ViewController.java

@@ -31,22 +31,39 @@ import fr.amap.lidar.amapvox.visualization.views.VisualizationScene;
 import java.awt.Color;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Controller of the view view.
  */
 public class ViewController {
     
+    /**
+     * The OpenGL canvas used to draw 3D elements.
+     */
     private GLNewtCanvas canvas;
+    
+    /**
+     * The current visualization scene.
+     */
     private VisualizationScene scene;
 
+    /**
+     * Create a view controller with an empty canvas and an empty scene.
+     */
     public ViewController() {
         this.canvas = null;
     }
 
+    /**
+     * Set the OpenGL canvas of the view component.
+     * @param canvas 
+     */
     public void setCanvas(final GLNewtCanvas canvas) {
         this.canvas = canvas;
     }
     
+    /**
+     * Set the current visualization scene.
+     * @param scene 
+     */
     public final void setScene(final Scene scene) {
         if (canvas != null) {
             canvas.getGLEventListener().setScene(scene);
@@ -54,6 +71,10 @@ public class ViewController {
         }
     }
     
+    /**
+     * Get the current used color bar.
+     * @return 
+     */
     public final Color[] getCurrentColorBar() {
         if (scene != null) {
             return scene.getVoxelSpaceComponent().getColorBar();

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/base/Component.java

@@ -25,25 +25,43 @@
 package fr.amap.lidar.amapvox.visualization.opengl.entities.base;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Class to add to an entity to give it a behaviour.
  */
 public abstract class Component extends Behaviour {
     
+    /**
+     * The entity of this component.
+     */
     protected Entity parent;
 
+    /**
+     * Create an abstract component.
+     */
     public Component() {
         super();
     }
     
+    /**
+     * Set the entity of this component.
+     * @param parent 
+     */
     public final void setParent(final Entity parent) {
         this.parent = parent;
     }
 
+    /**
+     * Get the entity of this component.
+     * @return 
+     */
     public final Entity getParent() {
         return parent;
     }
     
+    /**
+     * Implement it to receive messages from the scene.
+     * @param name
+     * @param object 
+     */
     protected abstract void receiveMessage(final String name, final Object object);
     
 }

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/base/Entity.java

@@ -81,27 +81,52 @@ public final class Entity extends Behaviour {
         transform.setParent(parent.getTransform());
     }
 
+    /**
+     * Set the layout of this entity.
+     * @param layout 
+     */
     public final void setLayout(final String layout) {
         this.layout = layout;
     }
 
+    /**
+     * Get the layout of this entity.
+     * @return 
+     */
     public final String getLayout() {
         return layout;
     }
     
+    /**
+     * Set the scene where this entity is contained.
+     * @param scene 
+     */
     public final void setScene(final Scene scene) {
         this.scene = scene;
     }
 
+    /**
+     * Get the scene where this entity is contained.
+     * @return 
+     */
     public final Scene getScene() {
         return scene;
     }
     
+    /**
+     * Add a component to this entity.
+     * @param component 
+     */
     public final void addComponent(final Component component) {
         component.setParent(this);
         components.add(component);
     }
     
+    /**
+     * Check if this entity has the specified component.
+     * @param type
+     * @return 
+     */
     public final boolean hasComponent(final Class<? extends Component> type) {
         for (Component component : components) {
             if (type.isInstance(component)) {
@@ -112,6 +137,12 @@ public final class Entity extends Behaviour {
         return false;
     }
     
+    /**
+     * Get the specified component type from this entity.
+     * @param <T>
+     * @param type
+     * @return 
+     */
     public final <T extends Component> T getComponent(final Class<T> type) {
         for (Component component : components) {
             if (type.isInstance(component)) {
@@ -122,10 +153,18 @@ public final class Entity extends Behaviour {
         return null;
     }
     
+    /**
+     * Check if this entity has been modify during the frame.
+     * @return 
+     */
     public final boolean isModified() {
         return modified || transform.isModified();
     }
     
+    /**
+     * Set if this entity has been modifyed during this frame.
+     * @param modified 
+     */
     public final void setModified(final boolean modified) {
         this.modified = modified;
     }
@@ -138,6 +177,11 @@ public final class Entity extends Behaviour {
         return transform;
     }
     
+    /**
+     * Send a message to each components.
+     * @param name
+     * @param object 
+     */
     public final void sendMessage(final String name, final Object object) {
         components.forEach((component) -> {
             component.receiveMessage(name, object);

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/base/Scene.java

@@ -45,8 +45,8 @@ import fr.amap.lidar.amapvox.visualization.opengl.resources.programs.SkyboxProgr
 import fr.amap.lidar.amapvox.visualization.opengl.resources.textures.TextureCubemap;
 
 /**
- * A parent object that can be used to regroup many entities and make them work.
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * A parent object that can be used to regroup 
+ * many entities and make them work.
  */
 public class Scene extends Behaviour {
 
@@ -90,6 +90,9 @@ public class Scene extends Behaviour {
      */
     protected boolean somethingsModified;
 
+    /**
+     * If the scene has been drawed twice.
+     */
     private boolean drawDouble;
 
     /**
@@ -144,14 +147,25 @@ public class Scene extends Behaviour {
         }
     }
 
+    /**
+     * Check if somethings has been modified in the scene during the frame.
+     * @return 
+     */
     public final boolean isSomethingsHasBeenTransformed() {
         return somethingsModified && !drawDouble;
     }
 
+    /**
+     * Set that somethings has been modified during the frame.
+     */
     public final void setSomethingsModified() {
         somethingsModified = true;
     }
 
+    /**
+     * Change the background image of the scene.
+     * @param cubemap 
+     */
     public final void setBackground(final TextureCubemap cubemap) {
         this.skyboxCubemap = cubemap;
 

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/base/Transform.java

@@ -32,7 +32,6 @@ import org.joml.Vector4f;
 /**
  * A transformation class that have a tridimentionnal position vector, 
  * a rotation quaternion and tridimensionnal scale vector and a parent transform.
- * @author Tristan Muller (tristan.muller@cirad.fr)
  */
 public final class Transform {
     
@@ -119,6 +118,10 @@ public final class Transform {
         return scale;
     }
     
+    /**
+     * Get the position of this transform compared to its parent hierarchy.
+     * @return 
+     */
     public final Vector3f getWorldPosition() {
         final Vector4f worldPos = new Vector4f(position, 1);
         
@@ -129,10 +132,18 @@ public final class Transform {
         return new Vector3f(worldPos.x, worldPos.y, worldPos.z);
     }
     
+    /**
+     * Get the rotation of this transform.
+     * @return 
+     */
     public final Quaternionf getWorldRotation() {
         return rotation;
     }
     
+    /**
+     * Get the scale of this transform compared to its parent hierarchy.
+     * @return 
+     */
     public final Vector3f getWorldScale() {
         final Vector3f worldScale = new Vector3f(scale);
         
@@ -162,6 +173,11 @@ public final class Transform {
         return modified;
     }
     
+    /**
+     * Get the translation matrix.
+     * @deprecated Moved in the GLSL shaders.
+     * @return 
+     */
     public final Matrix4f getTranslationMatrix() {
         /* Generate an identity matrix */
         final Matrix4f transformation = new Matrix4f().identity();
@@ -179,6 +195,11 @@ public final class Transform {
         return transformation;
     }
     
+    /**
+     * Get the rotation matrix.
+     * @deprecated Moved in the GLSL shaders.
+     * @return 
+     */
     public final Matrix4f getRotationMatrix() {
         /* Generate an identity matrix */
         final Matrix4f transformation = new Matrix4f().identity();
@@ -199,6 +220,7 @@ public final class Transform {
     /**
      * Get the transformation matrix from the parent transformation matrix 
      * and the current position, rotation and scale (also called a "model" matrix).
+     * @deprecated Moved in the GLSL shaders.
      * @return 
      */
     public final Matrix4f getTransformation() {

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/extended/Camera.java

@@ -83,14 +83,29 @@ public final class Camera extends Component {
      */
     private Matrix4f projection;
 
+    /**
+     * The framebuffer assiciated with this camera.
+     */
     private FrameBuffer frameBuffer;
 
+    /**
+     * The post process list of this camera.
+     */
     private final List<PostProcess> postProcesses;
     
+    /**
+     * The rendered layouts.
+     */
     private final List<String> renderedLayouts;
     
+    /**
+     * If the zoom functionnality is enabled.
+     */
     private boolean zoomEnabled;
     
+    /**
+     * The zooming callback function.
+     */
     private Consumer<Float> onZoomCallback;
 
     /**
@@ -109,6 +124,11 @@ public final class Camera extends Component {
         this.renderedLayouts = new ArrayList();
     }
 
+    /**
+     * Add a new post process to this camera.
+     * @param index
+     * @param postProcess 
+     */
     public final void addPostProcess(final int index, final PostProcess postProcess) {
         if (index < postProcesses.size()) {
             this.postProcesses.add(index, postProcess);
@@ -117,6 +137,10 @@ public final class Camera extends Component {
         }
     }
     
+    /**
+     * Add a rendered layout to this camera.
+     * @param layout 
+     */
     public final void addLayout(final String layout) {
         renderedLayouts.add(layout);
     }
@@ -129,6 +153,10 @@ public final class Camera extends Component {
         this.fov = fov;
     }
 
+    /**
+     * Set the zooming callback method.
+     * @param onZoomCallback 
+     */
     public void setOnZoomCallback(Consumer<Float> onZoomCallback) {
         this.onZoomCallback = onZoomCallback;
     }
@@ -175,6 +203,10 @@ public final class Camera extends Component {
         return projection;
     }
 
+    /**
+     * get the current rendered layouts.
+     * @return 
+     */
     public final List<String> getRenderedLayouts() {
         return renderedLayouts;
     }
@@ -186,6 +218,7 @@ public final class Camera extends Component {
 
     @Override
     public void onInputting(final InputEvent event, final InputStatus status) {
+        /* Perform zoom if that is enabled */
         if (status == InputStatus.MOUSE_WHEEL_MOVED && zoomEnabled) {
             final MouseEvent mouseEvent = (MouseEvent) event;
             fov -= mouseEvent.getRotation()[1];

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/extended/CameraController.java

@@ -22,6 +22,7 @@
  * The fact that you are presently reading this means that you have had
  * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization.opengl.entities.extended;
 
 import com.jogamp.newt.event.InputEvent;
@@ -33,18 +34,38 @@ import fr.amap.lidar.amapvox.visualization.opengl.entities.util.ViewType;
 import fr.amap.lidar.amapvox.visualization.opengl.util.InputStatus;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Component to move the camera with the mouse.
  */
 public class CameraController extends Component {
     
+    /**
+     * The mouse rotation quaternion.
+     */
     private final Quaternionf mouseRotation;
+    
+    /**
+     * The last mouse x position.
+     */
     private int lastMouseX;
+    
+    /**
+     * The last mouse y position.
+     */
     private int lastMouseY;
     
+    /**
+     * The width of the screen.
+     */
     private int screenWidth;
+    
+    /**
+     * The height of the screen.
+     */
     private int screenheight;
 
+    /**
+     * Create a camera controller component.
+     */
     public CameraController() {
         this.mouseRotation = new Quaternionf();
     }
@@ -127,11 +148,12 @@ public class CameraController extends Component {
 
     @Override
     public final void onDestroy(final GL3bc gl) {
+        /* Nothing needed to do */
     }
     
     @Override
     protected final void receiveMessage(final String name, final Object object) {
-        
+        /* Nothing needed to do */
     }
     
 }

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/extended/MeshRenderer.java

@@ -22,6 +22,7 @@
  * The fact that you are presently reading this means that you have had
  * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization.opengl.entities.extended;
 
 import com.jogamp.newt.event.InputEvent;
@@ -30,7 +31,6 @@ import fr.amap.lidar.amapvox.visualization.opengl.util.InputStatus;
 
 /**
  * A particular component to draw a mesh in a scene.
- * @author Tristan Muller (tristan.muller@cirad.fr)
  */
 public final class MeshRenderer extends Renderer {
 
@@ -57,6 +57,7 @@ public final class MeshRenderer extends Renderer {
             throw(new NullPointerException("The current material is null."));
         }
         
+        /* Send transform values to the material */
         getMaterial().setPosition(parent.getTransform().getWorldPosition());
         getMaterial().setRotation(parent.getTransform().getWorldRotation());
         getMaterial().setScale(parent.getTransform().getWorldScale());

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/extended/Renderer.java

 /*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
+ * This software is governed by the CeCILL-B license under French law and
+ * abiding by the rules of distribution of free software. You can use, modify
+ * and/ or redistribute the software under the terms of the CeCILL-B license as
+ * circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and rights to copy, modify
+ * and redistribute granted by the license, users are provided only with a
+ * limited warranty and the software's author, the holder of the economic
+ * rights, and the successive licensors have only limited liability.
+ * 
+ * In this respect, the user's attention is drawn to the risks associated with
+ * loading, using, modifying and/or developing or reproducing the software by
+ * the user in light of its specific status of free software, that may mean that
+ * it is complicated to manipulate, and that also therefore means that it is
+ * reserved for developers and experienced professionals having in-depth
+ * computer knowledge. Users are therefore encouraged to load and test the
+ * software's suitability as regards their requirements in conditions enabling
+ * the security of their systems and/or data to be ensured and, more generally,
+ * to use and operate it in the same conditions as regards security.
+ * 
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization.opengl.entities.extended;
 
 import org.joml.Matrix4f;
@@ -15,8 +35,7 @@ import fr.amap.lidar.amapvox.visualization.opengl.resources.programs.Program;
 import fr.amap.lidar.amapvox.visualization.opengl.resources.textures.TextureCubemap;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * A particular component to draw something in a scene.
  */
 public abstract class Renderer extends Component {
     
@@ -30,6 +49,9 @@ public abstract class Renderer extends Component {
      */
     private Mesh mesh;
 
+    /**
+     * Create a renderer component.
+     */
     public Renderer() {
         this.material = null;
         this.mesh = null;

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/extended/VoxelSpace.java

@@ -49,8 +49,7 @@ import fr.amap.lidar.amapvox.visualization.opengl.resources.textures.TextureCube
 import fr.amap.lidar.amapvox.visualization.opengl.util.InputStatus;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Component used to display a voxel space.
  */
 public class VoxelSpace extends Component {
 
@@ -68,7 +67,10 @@ public class VoxelSpace extends Component {
      * The size of each voxel drawables.
      */
     private float voxelSize;
-    
+
+    /**
+     * If each voxel is displayed has a pixel.
+     */
     private boolean drawPixel;
 
     /**
@@ -86,20 +88,56 @@ public class VoxelSpace extends Component {
      */
     private float colorMax;
 
+    /**
+     * The default program.
+     */
     private final StandardProgram program;
+
+    /**
+     * The fast rendering program.
+     */
     private final StandardProgram fastProgram;
 
+    /**
+     * The materials list.
+     */
     private List<Material> materials;
+
+    /**
+     * The fast rendering materials list.
+     */
     private List<Material> fastMaterials;
 
+    /**
+     * The albedo texture used to display each voxel models.
+     */
     private Texture2D albedo;
-    
+
+    /**
+     * The current rendered property.
+     */
     private String currentProperty;
+
+    /**
+     * If the fast drawing mode is enabled or not.
+     */
     private boolean drawFastEnabled;
-    
+
+    /**
+     * The main camera fov used to resize the pixels.
+     */
     private float cameraFOV = 60;
+
+    /**
+     * The screen aspect used to resize the voxels displayed has pixels.
+     */
     private float screenAspect = 1f;
-    
+
+    /**
+     * Create a voxel space component with the Equatorial colorbar.
+     * @param voxelMesh
+     * @throws IOException
+     */
     public VoxelSpace(final Mesh voxelMesh) throws IOException {
         this.filters = new ConcurrentHashMap();
         this.colorBar = ColorGradient.GRADIENT_GREEN_YELLOW_ORANGE_RED;
@@ -125,6 +163,10 @@ public class VoxelSpace extends Component {
         fastProgram.setMesh(fastMesh);
     }
 
+    /**
+     * Change the voxel space file rendered by this component.
+     * @param file
+     */
     public final void setFile(final VoxelSpaceFile file) {
         this.file = file;
 
@@ -163,6 +205,10 @@ public class VoxelSpace extends Component {
         }
     }
 
+    /**
+     * Remove a filter from the current list.
+     * @param index
+     */
     public final void removeFilter(final int index) {
         filters.remove(index);
         setProperty(currentProperty);
@@ -229,29 +275,34 @@ public class VoxelSpace extends Component {
                     final float n = (v - min) / (max - min);
 
                     /* Hide the filtered voxels */
-                    if (null != next.getFilteringType())
+                    if (null != next.getFilteringType()) {
                         switch (next.getFilteringType()) {
-                        case EQUAL:
-                            if (next.isHiden(n)) {
-                                equalHiden = true;
-                            }   break;
-                        case NOTEQUAL:
-                            notEqualFilter = true;
-                            
-                            if (next.isHiden(n)) {
-                                notEqualHiden = true;
-                            }   break;
-                        case LESSER:
-                            if (next.isHiden(n)) {
-                                lesserHiden = true;
-                            }   break;
-                        case GREATER:
-                            if (next.isHiden(n)) {
-                                greaterHiden = true;
-                            }   break;
+                            case EQUAL:
+                                if (next.isHiden(n)) {
+                                    equalHiden = true;
+                                }
+                                break;
+                            case NOTEQUAL:
+                                notEqualFilter = true;
+
+                                if (next.isHiden(n)) {
+                                    notEqualHiden = true;
+                                }
+                                break;
+                            case LESSER:
+                                if (next.isHiden(n)) {
+                                    lesserHiden = true;
+                                }
+                                break;
+                            case GREATER:
+                                if (next.isHiden(n)) {
+                                    greaterHiden = true;
+                                }
+                                break;
+                        }
                     }
                 }
-                
+
                 if (notEqualFilter) {
                     hiden = notEqualHiden;
                 } else if (equalHiden || (!lesserHiden && greaterHiden) || (lesserHiden && !greaterHiden)) {
@@ -297,56 +348,97 @@ public class VoxelSpace extends Component {
         }
     }
 
+    /**
+     * The min and max of the color bar.
+     * @param min
+     * @param max
+     */
     public final void setColorMinAndMax(final float min, final float max) {
         this.colorMin = min;
         this.colorMax = max;
         setProperty(currentProperty);
     }
 
+    /**
+     * Change if the fast drawing mode is enabled or not.
+     * @param drawFastEnabled
+     */
     public final void setDrawFastEnabled(final boolean drawFastEnabled) {
         this.drawFastEnabled = drawFastEnabled;
     }
 
+    /**
+     * Set if the pixels are displayed as pixels.
+     * @param drawPixel
+     */
     public final void setDrawPixel(final boolean drawPixel) {
         this.drawPixel = drawPixel;
     }
 
+    /**
+     * Chnage the current color bar.
+     * @param colorBar
+     */
     public final void setColorBar(final Color[] colorBar) {
         this.colorBar = colorBar;
         setProperty(currentProperty);
     }
 
+    /**
+     * Get the current color bar.
+     * @return
+     */
     public final Color[] getColorBar() {
         return colorBar;
     }
-    
+
+    /**
+     * Get the ground height position of the current voxel space file.
+     * @return
+     */
     public final float getGroundHeightPosition() {
         return -file.getDepth() - 0.01f;
     }
 
+    /**
+     * Set if the reflection are displayed.
+     * @param reflectionEnabled
+     */
     public final void setReflectionEnabled(final boolean reflectionEnabled) {
         program.setReflectionEnabled(reflectionEnabled);
         fastProgram.setReflectionEnabled(reflectionEnabled);
         parent.getScene().setSomethingsModified();
     }
 
+    /**
+     * Set the main camera field of view.
+     * @param cameraFOV
+     */
     public void setCameraFOV(float cameraFOV) {
         this.cameraFOV = cameraFOV;
     }
 
+    /**
+     * Set the voxel size.
+     * @param mode
+     */
     public final void setDrawingMode(final float mode) {
         voxelSize = mode;
-        
+
         for (Material material : materials) {
             material.setScale(new Vector3f(voxelSize));
         }
         for (Material material : fastMaterials) {
             material.setScale(new Vector3f(voxelSize));
         }
-        
+
         parent.getScene().setSomethingsModified();
     }
 
+    /**
+     * Set the current albedo texture used to display each voxels.
+     * @param albedo
+     */
     public final void setAlbedo(final Texture2D albedo) {
         this.albedo = albedo;
 
@@ -355,6 +447,12 @@ public class VoxelSpace extends Component {
         }
     }
 
+    /**
+     * Get the camera Z position to display the entire current voxel space file
+     * datas.
+     * @param fov
+     * @return
+     */
     public final float getCameraRetreat(final float fov) {
         return (float) ((file.getWidth() + file.getHeight() + file.getDepth())
                 / Math.sin(Math.toRadians(fov) * 2));
@@ -377,18 +475,24 @@ public class VoxelSpace extends Component {
 
     @Override
     public final void onDisplay(final GL3bc gl) {
-        if ((parent.getScene().isSomethingsHasBeenTransformed() 
+        if ((parent.getScene().isSomethingsHasBeenTransformed()
                 && drawFastEnabled) || drawPixel) {
+            /* Get each pixel size aspects */
             float voxelSizeAspect = ((file.getWidth() + file.getHeight() + file.getDepth()) / 3);
             voxelSizeAspect = voxelSizeAspect / (voxelSizeAspect + 1);
             float cameraFovAspect = (1 - cameraFOV / (cameraFOV + 1));
             float drawFastAspect = drawPixel ? 1f : 0.9f;
-            gl.glPointSize(voxelSize * (1 - voxelSizeAspect) 
+
+            /* Change the size of the pixels */
+            gl.glPointSize(voxelSize * (1 - voxelSizeAspect)
                     * cameraFovAspect * drawFastAspect * screenAspect * 20);
+
+            /* Draw the fast rendering mode program */
             fastProgram.updateProperties();
             fastProgram.bind(gl);
             fastProgram.draw(gl);
         } else {
+            /* Draw the default program */
             program.updateProperties();
             program.bind(gl);
             program.draw(gl);
@@ -397,7 +501,7 @@ public class VoxelSpace extends Component {
 
     @Override
     public final void onRescale(final GL3bc gl, final int width, final int height) {
-        /* Nothing needed to do */
+        /* Update the screen aspect used to resize each pixels */
         screenAspect = (float) (width + height);
     }
 

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/util/ViewType.java

@@ -25,14 +25,13 @@
 package fr.amap.lidar.amapvox.visualization.opengl.entities.util;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * The type of view angle to set to a camera component.
  */
 public enum ViewType {
     X_NEG,
     X_POS,
     Y_NEG,
     Y_POS,
-    Z_NEG,
-    Z_POS
+    Z_NEG, /* not used by the project */
+    Z_POS /* not used by the project */
 }

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/util/VoxelFilter.java

@@ -111,10 +111,12 @@ public class VoxelFilter {
      * @return False if between or False.
      */
     public final boolean isHiden(final float value) {        
+        /* Hide NaN values */
         if (hideNaN && Float.isNaN(value)) {
             return true;
         }
         
+        /* Hide voxel */
         switch(filteringType) {
             case NOTEQUAL: return value != this.value;
             case LESSER: return value < this.value;

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/util/VoxelFilteringType.java

@@ -25,8 +25,7 @@
 package fr.amap.lidar.amapvox.visualization.opengl.entities.util;
 
 /**
- *
- * @author Tristan Muller (tristan.muller@cirad.fr)
+ * Voxel filtering mode enum.
  */
 public enum VoxelFilteringType {
     LESSER,

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/entities/util/VoxelSpaceFile.java

@@ -22,6 +22,7 @@
  * The fact that you are presently reading this means that you have had
  * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization.opengl.entities.util;
 
 import fr.amap.commons.util.swing.jprogress.JProgressEvent;
@@ -36,8 +37,6 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/resources/Resource.java

+/*
+ * This software is governed by the CeCILL-B license under French law and
+ * abiding by the rules of distribution of free software. You can use, modify
+ * and/ or redistribute the software under the terms of the CeCILL-B license as
+ * circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and rights to copy, modify
+ * and redistribute granted by the license, users are provided only with a
+ * limited warranty and the software's author, the holder of the economic
+ * rights, and the successive licensors have only limited liability.
+ * 
+ * In this respect, the user's attention is drawn to the risks associated with
+ * loading, using, modifying and/or developing or reproducing the software by
+ * the user in light of its specific status of free software, that may mean that
+ * it is complicated to manipulate, and that also therefore means that it is
+ * reserved for developers and experienced professionals having in-depth
+ * computer knowledge. Users are therefore encouraged to load and test the
+ * software's suitability as regards their requirements in conditions enabling
+ * the security of their systems and/or data to be ensured and, more generally,
+ * to use and operate it in the same conditions as regards security.
+ * 
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL-B license and that you accept its terms.
+ */
+
 package fr.amap.lidar.amapvox.visualization.opengl.resources;
 
 import com.jogamp.opengl.GL3bc;

AMAPVox/AMAPVoxVisualization/src/main/java/fr/amap/lidar/amapvox/visualization/opengl/resources/ResourceManager.java

 /*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
+ * This software is governed by the CeCILL-B license under French law and
+ * abiding by the rules of distribution of free software. You can use, modify
+ * and/ or redistribute the software under the terms of the CeCILL-B license as
+ * circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and rights to copy, modify
+ * and redistribute granted by the license, users are provided only with a
+ * limited warranty and the software's author, the holder of the economic
+ * rights, and the successive licensors have only limited liability.
+ * 
+ * In this respect, the user's attention is drawn to the risks associated with
+ * loading, using, modifying and/or developing or reproducing the software by
+ * the user in light of its specific status of free software, that may mean that
+ * it is complicated to manipulate, and that also therefore means that it is
+ * reserved for developers and experienced professionals having in-depth
+ * computer knowledge. Users are therefore encouraged to load and test the
+ * software's suitability as regards their requirements in conditions enabling
+ * the security of their systems and/or data to be ensured and, more generally,
+ * to use and operate it in the same conditions as regards security.
+ * 
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL-B license and that you accept its terms.
  */
+
 package fr.amap.lidar.amapvox.visualization.opengl.resources;
 
 import java.util.HashMap;
 
-
 /**
- *
+ * Class to regroup resource in a single place (not used by the project).
  * @author Tristan Muller (tristan.muller@cirad.fr)
  */
 public class ResourceManager {