JavaFX 2 vs Java3D

Java3D

• The Java 3D API is a high-level library for creating 3D-graphics including animation and transformation of 3D-objects.
• The Java 3D API operates with objects that are placed in the scene graph that is the tree of 3D-objects and is intended to render.
• Java3D application can run as a desktop application or as an applet or as a desktop application and an applet.
• The Java 3D API is presented by the basic package javax.media.j3d and support packages com.sun.j3d.utils, java.awt, javax.vecmath.
• In fact, the Java 3D API is a wrapper of the graphic systems OpenGL and DirectX.

Java3D installation

• Download the distributive at http://www.oracle.com/technetwork/java/javase/tech/index-jsp-138252.html.
• Run the installation program. The result will appear in the JDK directory as the folder Java3D.
• The installed files on the Java3D folder work as the runtime over JDK for programs that use the Java 3D API.
• To develop programs using the Java 3D API download the NetBeans plugin at http://plugins.netbeans.org/plugin/32144/java-3d and install it using the option Tools | Plugins | Downloaded | Add Plugins.
• You can then include the import of the Java 3D API libraries in a Java application project.

Java3D programming model

• To create a Java3D application first creates the VirtualUniverse object.
• Each Java3D application has only one object VirtualUniverse, which represents a virtual space that is associated with a scene graph.
• Further create the BranchGroup object that represents the root node of the branch of the scene graph.
• Create the Transform3D object representing the three-dimensional transformations and, based on it, create the TransformGroup object that represents the node of the scene graph.
• Create a 3D-object, which is added to the node TransformGroup.
• The TransformGroup node is added to the node BranchGroup and the BranchGroup node is added to the virtual space VirtualUniverse.
• In the BranchGroup node, besides 3D-objects, you can add light sources illuminating 3D-objects.
• For 3D-objects it is possible to define the appearance by adding colors, materials, textures and effects.
• With the Canvas3D object it is possible to create 3D-graphics in the program way.
• Animations of the 3D-object are controlled by changing the object Transform3D in time.
• The following code is a simple Java3D-program that displays the rotated cube:

package javaapplication3d;
import com.sun.j3d.utils.geometry.ColorCube;
import com.sun.j3d.utils.universe.SimpleUniverse;
import javax.media.j3d.BranchGroup;
import javax.media.j3d.Transform3D;
import javax.media.j3d.TransformGroup;
public class JavaApplication3D {
public JavaApplication3D()
{
SimpleUniverse universe = new SimpleUniverse();
BranchGroup group = new BranchGroup();
ColorCube cube=new ColorCube(0.3);
Transform3D rotate = new Transform3D();
rotate.rotX(10);
TransformGroup rotateGroup = new TransformGroup();
rotateGroup.setTransform(rotate);
rotateGroup.addChild(cube);
group.addChild(rotateGroup);
universe.getViewingPlatform().setNominalViewingTransform();
universe.addBranchGraph(group);
}
public static void main(String[] args) {
     JavaApplication3D javaApplication3D = new JavaApplication3D();
}
}

JavaFX 2

• The JavaFX technology provides a powerful graphical user interface for large-scale data-oriented applications, media-rich applications that deliver diverse media content to users, Mashup applications that integrate a variety of web resources for users, high-quality graphical components and animation to web sites, various types of custom programs that saturated graphics, animation and interactive elements.
• The same Java code created on the basis of the JavaFX platform can be launched as the desktop application or it can be deployed as the Java Web Start application or it can be displayed in the web browser as the JavaFX applet embedded in an HTML page.
• The JavaFX 2 Platform provides modern GUI-components, the rich set of graphics and media libraries, and the high-performance execution environment for applications.
• For an alternative declarative description of the GUI the JavaFX platform offers the FXML language.
• Also, the JavaFX 2 platform provides the new graphical and media engines, which improve the display of graphics and playback of multimedia content, embedding HTML-content in the application, the new plugin for web browsers, and the wide range of the GUI components with the support of CSS3.
• Currently JavaFX 2 provides:
• JavaFX SDK that provides the JavaFX Packager tool for compiling, packaging, and deploying JavaFX applications, Ant library for building JavaFX applications, the JavaFX doclet for Javadoc, JavaFX API, and documentation.
• JavaFX Runtime for desktop applications and JavaFX applets.
• Support of the JavaFX 2 platform for NetBeans IDE 7.
•  Examples of JavaFX applications.
• The JavaFX 2 platform is integrated into the platform JDK 7 and does not require separate installation.
• The site of the JavaFX 2 platform is located at http://javafx.com/.

The JavaFX 2 browser plugin is not browser add-ons and its work is provided by the JavaScript-code that embeds the JavaFX-code as a JavaFX-applet on the web page, connecting the JavaFX Runtime installed on the local computer.

JavaFX installation

• To install the JavaFX 2 platform just download and install the JDK 7 (http://www.oracle.com/technetwork/java/javase/downloads/index.html).
• To develop applications based on the JavaFX 2 platform just download and install the NetBeans IDE 7 (http://netbeans.org/downloads/).
• With the selection of the option New Project | JavaFX project in the menu File of the NetBeans IDE the project templates JavaFX Application, JavaFX Preloaderand JavaFX FXML Application will be shown.

JavaFX programming model

• The same Java code of the JavaFX application can be launched as the desktop application or it can be deployed as the Java Web Start application or it can be displayed in the web browser as the JavaFX applet embedded in an HTML page.
• The entry point to the JavaFX-application is a Java-class that extends the abstract class javafx.application.Application and contains the method main ():

public class JavaFXApp extends Application {

public static void main(String[] args) {
launch(args);
}
public void init(){
. . .
}

@Override
public void start(Stage primaryStage) {

.. .
primaryStage.setScene(scene);
primaryStage.setVisible(true);
}
public void stop(){
. . .
}
}

In the main() method of the main JavaFX application class the launch() method of the Application class is called that is responsible for loading the JavaFX application. In addition, the main JavaFX application class must override the abstract start() method of the Application class, which provides the creation and display of the JavaFX application scene.

The methods init() and stop() of the Application class can be used to initialize the data and to release the resources of the JavaFX application.

Since the init() method is called before creating the main JavaFX Application Thread, then the initialization of the JavaFX application in the init() method with the scene graph nodes should be implemented using the static method javafx.application.Platform.runLater().

To perform the JavaScript code on the Web page containing the JavaFX application, the main JavaFX application class can use the getHostServices() method of the Application class and the object netscape.javascript.JSObject.

Processing of input parameters in the main JavaFX application class can be made by calling the getParameters() method of the Application class.

To improve the display and handling of the JavaFX application startup and launching it is possible in several ways. The first way is to use the onGetSplash handler of the JavaScript library Deployment Toolkit API to create a splash screen for the JavaFX applet embedded in the Web page. The other way is to apply CSS-styles to the default Preloader. And finally, it is possible to create the custom preloader class that extends the abstract class javafx.application.Preloader and to refer to it in the JNLP deployment descriptor of the JavaFX application. In this regard, for communication of the main JavaFX application class with the preloader it is possible to use the notifyPreloader() method of the Application class.

The start() method of the Application class has the javafx.stage.Stage object as a parameter that represents the main window graphic container of the JavaFX application. This Stage object is created by the runtime when running the JavaFX application and passed to the start() method of the main JavaFX application class what allows to use the methods of the Stage class for the setting and showing of the JavaFX application scene. Instead the Stage object as the argument of the method start(), the developer can create a custom instance of the Stage class to show the JavaFX application scene.

Before the setting and display the scene in the main window graphic container Stage of the JavaFX application is necessary to create a scene graph consisting of a root node and its children, and on its basis to create a scene object javafx.scene.Scene.

As a rule, the javafx.scene.Group object is used as the root node, which is created using the constructor. The Group object is used as an argument of the constructor when creating a javafx.scene.Scene object.

Child nodes of the scene graph that represent the graphics, GUI controls, media content are added to the root node using the getChildren().add() method or the getChildren().addAll() method. Child nodes can have visual effects, blend modes, CSS styles, opacity, transformation, event handlers, and can participate in keyframe animation, in animation with built-in timeline, etc.

Below is the code of the JavaFX 2 application that displayed the rotated cube:

import javafx.application.Application;

import javafx.scene.Group;

import javafx.scene.Scene;

import javafx.scene.paint.Color;

import javafx.scene.text.Font;

import javafx.stage.Stage;

public class JavaFXApp extends Application {

   

    @Override

    public void start(Stage primaryStage) {

       Cube c = new Cube(50,Color.BLUE,2);

       c.setLayoutX(50);

       c.setLayoutY(50);

Group root = new Group();

root.getChildren().addAll(cmHome,cmServices, cmBlog, cmContacts, content1,content2);       

        Scene scene = new Scene(root, 800, 600);

        scene.setFill(Color.BLACK);      

        primaryStage.setScene(scene);

        primaryStage.show();

    }

    public static void main(String[] args) {

        launch(args);

    }

}

package javafxapp;

import javafx.animation.Animation;

import javafx.animation.KeyFrame;

import javafx.animation.KeyValue;

import javafx.animation.Timeline;

import javafx.event.EventHandler;

import javafx.scene.Group;

import javafx.scene.control.Hyperlink;

import javafx.scene.control.HyperlinkBuilder;

import javafx.scene.input.MouseEvent;

import javafx.scene.layout.StackPane;

import javafx.scene.paint.Color;

import javafx.scene.shape.Rectangle;

import javafx.scene.shape.RectangleBuilder;

import javafx.scene.text.Font;

import javafx.scene.transform.Rotate;

import javafx.util.Duration;

public class Cube extends Group {

        final Rotate rx = new Rotate(0,Rotate.X_AXIS);

        final Rotate ry = new Rotate(0,Rotate.Y_AXIS);

        final Rotate rz = new Rotate(0,Rotate.Z_AXIS);      

       

public MenuContainer(double size, Color colorContainer, double shade) {

            rx.setAngle(15);

            ry.setAngle(15);

            rz.setAngle(0);

            this.getTransforms().addAll(rz, ry, rx);

          final Group group=this;

            //

final Rectangle   backFace =   RectangleBuilder.create() // back face

.width(size*2).height(size)

.fill(colorContainer.deriveColor(0.0, 1.0, (1 - 0.3*shade), 1.0))

.translateX(-0.5*size)

.translateY(-0.5*size)

.translateZ(0.5*size)                   

.build()

;

           

              //

final Rectangle   bottomFace =  RectangleBuilder.create() // bottom face

.width(size*2).height(size)

.fill(colorContainer.deriveColor(0.0, 1.0, (1 - 0.3*shade), 1.0))

.translateX(-0.5*size)

.translateY(0)

.rotationAxis(Rotate.X_AXIS)

.rotate(90)                  

.build();

 //

 //

final Rectangle   rightFace =   RectangleBuilder.create() // right face

.width(size).height(size)

.fill(colorContainer.deriveColor(0.0, 1.0, (1 - 0.3*shade), 1.0))

.translateX(1*size)

.translateY(-0.5*size)

.rotationAxis(Rotate.Y_AXIS)

.rotate(90)                  

.build();

 //

 //

final Rectangle   leftFace =   RectangleBuilder.create() // left face

.width(size).height(size)

.fill(colorContainer.deriveColor(0.0, 1.0, (1 - 0.3*shade), 1.0))

.translateX(-1*size)

.translateY(-0.5*size)

.rotationAxis(Rotate.Y_AXIS)

.rotate(90)                  

.build();

 //

 //

final Rectangle   topFace =  RectangleBuilder.create() // top face

.width(size*2).height(size)

.fill(colorContainer.deriveColor(0.0, 1.0, (1 - 0.2*shade), 1.0))

.translateX(-0.5*size)

.translateY(-1*size)

.rotationAxis(Rotate.X_AXIS)

.rotate(90)                   

.build();

 //

 //

          

final Rectangle   face = RectangleBuilder.create() // face

.width(size*2).height(size)

.fill(colorContainer)                 

.build();

face.setTranslateX(-0.5*size);

face.setTranslateY(-0.5*size);

face.setTranslateZ(-0.5*size);

            

final   Timeline animation = new Timeline();

animation.getKeyFrames().addAll(

new KeyFrame(Duration.ZERO, new KeyValue(rx.angleProperty(), 15d)),                      

new KeyFrame(new Duration(1000), new KeyValue(rx.angleProperty(), 375d))                      

);

animation.setCycleCount(Animation.INDEFINITE);

group.setOnMouseDragged(new EventHandler<MouseEvent>() {

@Override

public void handle(MouseEvent event) {         

animation.play();   

double x= event.getSceneX();

double y = event.getSceneY();        

group.setLayoutX(x);

group.setLayoutY(y);

group.setOnMouseReleased(new EventHandler<MouseEvent>() {

@Override

public void handle(MouseEvent event) {

animation.stop();

rx.angleProperty().set(15);

}

});

} });

//

getChildren() .addAll(backFace,bottomFace,rightFace,leftFace,topFace,face);

}

}

Comparison JavaFX 2 and Java3D

• Both JavaFX 2 and Java3D include API and runtime.
• Java3D requires a separate installation. JavaFX 2 is included in JDK 7. 
• Both JavaFX 2 and Java3D can create 3D-graphics. 
• Java3D provides ready 3D-objects. JavaFX 2 allows creating 3D-objects from 2D-primitives. 
• JavaFX 2 provides GUI-components, but Java3D is not. 
• Both JavaFX 2 and Java3D provide transformation and animation facilities. 
• The JavaFX 2 code automatically compiled into the desktop application and the applet. For Java3D-applet creation the additional code is required. 
• Both JavaFX 2 and Java3D operate a scene graph. 
• JavaFX 2 provides a declarative description of the scene graph and the visual editor of the scene graph, but Java3D is not. 
• Java3D supports textures, but JavaFX 2 is not. 
• The JavaFX 2 code should be performed in a separate JavaFX Application Thread. The Java3D code runs in the main thread. 
• The entry point of the JavaFX-application is a Java-class that extends the abstract class javafx.application.Application and contains the method main(). The entry point of Java3D-application is the usual Java-class with the method main()

Building a 3D Sample Application

package application;

import javafx.animation.Timeline;
import javafx.application.Application;
import javafx.event.EventHandler;
import javafx.scene.Group;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.input.KeyEvent;
import javafx.scene.input.MouseEvent;
import javafx.scene.paint.Color;
import javafx.scene.paint.PhongMaterial;
import javafx.scene.shape.Box;
import javafx.stage.Stage;
import javafx.scene.PerspectiveCamera;
import javafx.scene.shape.Cylinder;
import javafx.scene.shape.Sphere;
import javafx.scene.transform.Rotate;
import javafx.util.Duration;

public class Main extends Application {
final Group root = new Group();
final Group axisGroup = new Group();

final Xform world = new Xform();
final PerspectiveCamera camera = new PerspectiveCamera(true);
final Xform cameraXform = new Xform();
final Xform cameraXform2 = new Xform();
final Xform cameraXform3 = new Xform();
final double cameraDistance = 450;
final Xform moleculeGroup = new Xform();

private Timeline timeline;
boolean timelinePlaying = false;
double ONE_FRAME = 1.0 / 24.0;
double DELTA_MULTIPLIER = 200.0;
double CONTROL_MULTIPLIER = 0.1;
double SHIFT_MULTIPLIER = 0.1;
double ALT_MULTIPLIER = 0.5;

double mousePosX;
double mousePosY;
double mouseOldX;
double mouseOldY;
double mouseDeltaX;
double mouseDeltaY;

private void buildScene() {
System.out.println("buildScene");
root.getChildren().add(world);
}

private void buildAxes() {
System.out.println("buildAxes()");
final PhongMaterial redMaterial = new PhongMaterial();
redMaterial.setDiffuseColor(Color.DARKRED);
redMaterial.setSpecularColor(Color.RED);

final PhongMaterial greenMaterial = new PhongMaterial();
greenMaterial.setDiffuseColor(Color.DARKGREEN);
greenMaterial.setSpecularColor(Color.GREEN);

final PhongMaterial blueMaterial = new PhongMaterial();
blueMaterial.setDiffuseColor(Color.DARKBLUE);
blueMaterial.setSpecularColor(Color.BLUE);

final Box xAxis = new Box(240.0, 1, 1);
final Box yAxis = new Box(1, 240.0, 1);
final Box zAxis = new Box(1, 1, 240.0);

xAxis.setMaterial(redMaterial);
yAxis.setMaterial(greenMaterial);
zAxis.setMaterial(blueMaterial);

axisGroup.getChildren().addAll(xAxis, yAxis, zAxis);
world.getChildren().addAll(axisGroup);
}

@Override
public void start(Stage primaryStage) {
System.out.println("start");
buildScene();
buildCamera();
buildAxes();
buildMolecule();

Scene scene = new Scene(root, 1024, 768, true);
scene.setFill(Color.GREY);
handleKeyboard(scene, world);
        handleMouse(scene, world);

primaryStage.setTitle("Molecule Sample Application");
primaryStage.setScene(scene);
primaryStage.show();
scene.setCamera(camera);

}

private void buildCamera() {
root.getChildren().add(cameraXform);
cameraXform.getChildren().add(cameraXform2);
cameraXform2.getChildren().add(cameraXform3);
cameraXform3.getChildren().add(camera);
cameraXform3.setRotateZ(180.0);

camera.setNearClip(0.1);
camera.setFarClip(10000.0);
camera.setTranslateZ(-cameraDistance);
cameraXform.ry.setAngle(320.0);
cameraXform.rx.setAngle(40);
}

//
// This buildMolecule file contains the buildMolecule() method that is used
// in
// the MoleculeSampleApp application that you can build using the Getting
// Started with
// JavaFX 3D Graphics tutorial.
//

private void buildMolecule() {

final PhongMaterial redMaterial = new PhongMaterial();
redMaterial.setDiffuseColor(Color.DARKRED);
redMaterial.setSpecularColor(Color.RED);

final PhongMaterial whiteMaterial = new PhongMaterial();
whiteMaterial.setDiffuseColor(Color.WHITE);
whiteMaterial.setSpecularColor(Color.LIGHTBLUE);

final PhongMaterial greyMaterial = new PhongMaterial();
greyMaterial.setDiffuseColor(Color.DARKGREY);
greyMaterial.setSpecularColor(Color.GREY);

// Molecule Hierarchy
// [*] moleculeXform
// [*] oxygenXform
// [*] oxygenSphere
// [*] hydrogen1SideXform
// [*] hydrogen1Xform
// [*] hydrogen1Sphere
// [*] bond1Cylinder
// [*] hydrogen2SideXform
// [*] hydrogen2Xform
// [*] hydrogen2Sphere
// [*] bond2Cylinder

Xform moleculeXform = new Xform();
Xform oxygenXform = new Xform();
Xform hydrogen1SideXform = new Xform();
Xform hydrogen1Xform = new Xform();
Xform hydrogen2SideXform = new Xform();
Xform hydrogen2Xform = new Xform();

Sphere oxygenSphere = new Sphere(40.0);
oxygenSphere.setMaterial(redMaterial);

Sphere hydrogen1Sphere = new Sphere(30.0);
hydrogen1Sphere.setMaterial(whiteMaterial);
hydrogen1Sphere.setTranslateX(0.0);

Sphere hydrogen2Sphere = new Sphere(30.0);
hydrogen2Sphere.setMaterial(whiteMaterial);
hydrogen2Sphere.setTranslateZ(0.0);

Cylinder bond1Cylinder = new Cylinder(5, 100);
bond1Cylinder.setMaterial(greyMaterial);
bond1Cylinder.setTranslateX(50.0);
bond1Cylinder.setRotationAxis(Rotate.Z_AXIS);
bond1Cylinder.setRotate(90.0);

Cylinder bond2Cylinder = new Cylinder(5, 100);
bond2Cylinder.setMaterial(greyMaterial);
bond2Cylinder.setTranslateX(50.0);
bond2Cylinder.setRotationAxis(Rotate.Z_AXIS);
bond2Cylinder.setRotate(90.0);

moleculeXform.getChildren().add(oxygenXform);
moleculeXform.getChildren().add(hydrogen1SideXform);
moleculeXform.getChildren().add(hydrogen2SideXform);
oxygenXform.getChildren().add(oxygenSphere);
hydrogen1SideXform.getChildren().add(hydrogen1Xform);
hydrogen2SideXform.getChildren().add(hydrogen2Xform);
hydrogen1Xform.getChildren().add(hydrogen1Sphere);
hydrogen2Xform.getChildren().add(hydrogen2Sphere);
hydrogen1SideXform.getChildren().add(bond1Cylinder);
hydrogen2SideXform.getChildren().add(bond2Cylinder);

hydrogen1Xform.setTx(100.0);
hydrogen2Xform.setTx(100.0);
hydrogen2SideXform.setRotateY(104.5);

moleculeGroup.getChildren().add(moleculeXform);

world.getChildren().addAll(moleculeGroup);
}

/**
* The main() method is ignored in correctly deployed JavaFX application.
* main() serves only as fallback in case the application can not be
* launched through deployment artifacts, e.g., in IDEs with limited FX
* support. NetBeans ignores main().
*
* @param args
*            the command line arguments
*/
public static void main(String[] args) {
System.setProperty("prism.dirtyopts", "false");
launch(args);
}

private void handleMouse(Scene scene, final Node root) {
scene.setOnMousePressed(new EventHandler<MouseEvent>() {
public void handle(MouseEvent me) {
mousePosX = me.getSceneX();
mousePosY = me.getSceneY();
mouseOldX = me.getSceneX();
mouseOldY = me.getSceneY();
}
});
scene.setOnMouseDragged(new EventHandler<MouseEvent>() {
public void handle(MouseEvent me) {
mouseOldX = mousePosX;
mouseOldY = mousePosY;
mousePosX = me.getSceneX();
mousePosY = me.getSceneY();
mouseDeltaX = (mousePosX - mouseOldX);
mouseDeltaY = (mousePosY - mouseOldY);

double modifier = 1.0;
double modifierFactor = 0.1;

if (me.isControlDown()) {
modifier = 0.1;
}
if (me.isShiftDown()) {
modifier = 10.0;
}
if (me.isPrimaryButtonDown()) {
cameraXform.ry.setAngle(cameraXform.ry.getAngle()
- mouseDeltaX * modifierFactor * modifier * 2.0); // +
cameraXform.rx.setAngle(cameraXform.rx.getAngle()
+ mouseDeltaY * modifierFactor * modifier * 2.0); // -
} else if (me.isSecondaryButtonDown()) {
double z = camera.getTranslateZ();
double newZ = z + mouseDeltaX * modifierFactor * modifier;
camera.setTranslateZ(newZ);
} else if (me.isMiddleButtonDown()) {
cameraXform2.t.setX(cameraXform2.t.getX() + mouseDeltaX
* modifierFactor * modifier * 0.3); // -
cameraXform2.t.setY(cameraXform2.t.getY() + mouseDeltaY
* modifierFactor * modifier * 0.3); // -
}
}
});
}

private void handleKeyboard(Scene scene, final Node root) {
final boolean moveCamera = true;
scene.setOnKeyPressed(new EventHandler<KeyEvent>() {
public void handle(KeyEvent event) {
Duration currentTime;
switch (event.getCode()) {
case Z:
if (event.isShiftDown()) {
cameraXform.ry.setAngle(0.0);
cameraXform.rx.setAngle(0.0);
camera.setTranslateZ(-300.0);
}
cameraXform2.t.setX(0.0);
cameraXform2.t.setY(0.0);
break;
case X:
if (event.isControlDown()) {
if (axisGroup.isVisible()) {
System.out.println("setVisible(false)");
axisGroup.setVisible(false);
} else {
System.out.println("setVisible(true)");
axisGroup.setVisible(true);
}
}
break;
case S:
if (event.isControlDown()) {
if (moleculeGroup.isVisible()) {
moleculeGroup.setVisible(false);
} else {
moleculeGroup.setVisible(true);
}
}
break;
case SPACE:
if (timelinePlaying) {
timeline.pause();
timelinePlaying = false;
} else {
timeline.play();
timelinePlaying = true;
}
break;
case UP:
if (event.isControlDown() && event.isShiftDown()) {
cameraXform2.t.setY(cameraXform2.t.getY() - 10.0
* CONTROL_MULTIPLIER);
} else if (event.isAltDown() && event.isShiftDown()) {
cameraXform.rx.setAngle(cameraXform.rx.getAngle()
- 10.0 * ALT_MULTIPLIER);
} else if (event.isControlDown()) {
cameraXform2.t.setY(cameraXform2.t.getY() - 1.0
* CONTROL_MULTIPLIER);
} else if (event.isAltDown()) {
cameraXform.rx.setAngle(cameraXform.rx.getAngle() - 2.0
* ALT_MULTIPLIER);
} else if (event.isShiftDown()) {
double z = camera.getTranslateZ();
double newZ = z + 5.0 * SHIFT_MULTIPLIER;
camera.setTranslateZ(newZ);
}
break;
case DOWN:
if (event.isControlDown() && event.isShiftDown()) {
cameraXform2.t.setY(cameraXform2.t.getY() + 10.0
* CONTROL_MULTIPLIER);
} else if (event.isAltDown() && event.isShiftDown()) {
cameraXform.rx.setAngle(cameraXform.rx.getAngle()
+ 10.0 * ALT_MULTIPLIER);
} else if (event.isControlDown()) {
cameraXform2.t.setY(cameraXform2.t.getY() + 1.0
* CONTROL_MULTIPLIER);
} else if (event.isAltDown()) {
cameraXform.rx.setAngle(cameraXform.rx.getAngle() + 2.0
* ALT_MULTIPLIER);
} else if (event.isShiftDown()) {
double z = camera.getTranslateZ();
double newZ = z - 5.0 * SHIFT_MULTIPLIER;
camera.setTranslateZ(newZ);
}
break;
case RIGHT:
if (event.isControlDown() && event.isShiftDown()) {
cameraXform2.t.setX(cameraXform2.t.getX() + 10.0
* CONTROL_MULTIPLIER);
} else if (event.isAltDown() && event.isShiftDown()) {
cameraXform.ry.setAngle(cameraXform.ry.getAngle()
- 10.0 * ALT_MULTIPLIER);
} else if (event.isControlDown()) {
cameraXform2.t.setX(cameraXform2.t.getX() + 1.0
* CONTROL_MULTIPLIER);
} else if (event.isAltDown()) {
cameraXform.ry.setAngle(cameraXform.ry.getAngle() - 2.0
* ALT_MULTIPLIER);
}
break;
case LEFT:
if (event.isControlDown() && event.isShiftDown()) {
cameraXform2.t.setX(cameraXform2.t.getX() - 10.0
* CONTROL_MULTIPLIER);
} else if (event.isAltDown() && event.isShiftDown()) {
cameraXform.ry.setAngle(cameraXform.ry.getAngle()
+ 10.0 * ALT_MULTIPLIER); // -
} else if (event.isControlDown()) {
cameraXform2.t.setX(cameraXform2.t.getX() - 1.0
* CONTROL_MULTIPLIER);
} else if (event.isAltDown()) {
cameraXform.ry.setAngle(cameraXform.ry.getAngle() + 2.0
* ALT_MULTIPLIER); // -
}
break;
}
}
});
}

}

Private tag numbers available for use in DICOM

Private tags are typically just documented by a device manufacturer in the DICOM Conformance Statement for the product adding the private tags. The method for adding private tags was designed to prevent conflicts between manufacturers. When adding tags, you should develop in such away to prevent conflicts. Ie, to give an example, a typical DICOM tag is composed of a 2 byte group and a 2 byte element:

(gggg,eeee)

The group needs to be an odd number greater than 0008. Your private attributes are typically in a private block that have an associated private creator data element. The private creator is encoded as such:

(gggg,00bb)

where bb in the tag is an open private block in the DICOM object and has a value in the rage of 10-FF. This private block is where conflicts between vendors are dealt with. You must assign your private tags in the object to one of these blocks.

Finally, the private elements themselves are within the block:

(gggg,bbxx)

Where the block is encoded in the tag, and then the elements themselves are defined by xx. Your conformance statement should list your private identification code, the DICOM VR of the tag, the element number (xx) of the tag, along with a description of the tag so that other vendors can use the tag, if necessary.

If you want a more detailed explanation, it can be found in Part 5 of the DICOM Standard, starting at page 45.

Create image thumbnail in java using ImageJ API

For more information on how to implement Photos sharing website using Java, Spring, Tomcat, Imagej download Fotovault (opensource Photo sharing project) Fotovault - Photo Sharing Project

Below is the code example to create thumbnails in Java.

Download ImageJ jar from

http://rsbweb.nih.gov/ij/download.html

and include it in your classpath.

The below code example proportionately/evenly crops the image to make the image a perfect square and creates a thumbnail of 100 X 100 pixels.
cropAndResize method takes the fileAbsolutePath and Save as image suffix (thumbnail name suffix).

	private String cropAndResize(String fileAbsolutePath, String fileSaveAsNameSuffix) {
	try {
	Opener opener = new Opener();
	ImagePlus imp = opener.openImage(fileAbsolutePath);
	ImageProcessor ip = imp.getProcessor();
	StackProcessor sp = new StackProcessor(imp.getStack(), ip);
	int width = imp.getWidth();
	int height = imp.getHeight();
	int cropWidth = 0;
	int cropHeight = 0;
	if(width > height) {
	cropWidth = height;
	cropHeight = height;
	} else {
	cropWidth = width;
	cropHeight = width;
	}
	int x = -1;
	int y = -1;
	if(width == height) {
	x = 0;
	y = 0;
	} else if(width > height) {
	x = (width - height) / 2;
	y=0;
	} else if (width < height) {
	x = 0;
	y = (height - width) / 2;
	}
	logger.debug(imp.getWidth());
	logger.debug(imp.getHeight());
	logger.debug("cropWidth " + cropWidth);
	logger.debug("cropHeight" + cropHeight);
	ImageStack croppedStack = sp.crop(x, y, cropWidth, cropHeight);
	imp.setStack(null, croppedStack);
	logger.debug(imp.getWidth());
	logger.debug(imp.getHeight());
	sp = new StackProcessor(imp.getStack(), imp.getProcessor());
	ImageStack resizedStack = sp.resize(100, 100, true);
	imp.setStack(null, resizedStack);
	StringBuffer filePath = new StringBuffer(fileAbsolutePath);
	filePath.replace(filePath.lastIndexOf("."),
	filePath.lastIndexOf("."), fileSaveAsNameSuffix);
	String saveAsFilePath = filePath.toString();
	IJ.save(imp, saveAsFilePath);
	return saveAsFilePath;
	} catch (Exception e) {
	logger.error("Error while resizing Image.");
	e.printStackTrace();
	return null;
	}
	}

view raw CreateImageThumbnail hosted with ❤ by GitHub

Dynamic Cylinder

When a BY_REFERENCE GeometryArray object is created, the user creates geometry arrays and populates those arrays with geometry data. There are no geometry arrays internal to the Geometry object no copy of the geometry data made. Instead the BY_REFERENCE GeometryArray object simply stores a reference to the user array(s) of geometry data.

There are two good reasons for using BY_REFERENCE GeometryArray:

1. if the geometry data is dynamic
2. if the geometry data requires too much memory

This program shows how to implement the dynamic geometry data by a BY_REFERENCE GeometryArray.

 

public class DynamicCylinder extends JFrame {   private float height = 0.5f;   private float radius = 0.02f;   private int verticesNum = 40;   private float[] vertices = new float[verticesNum * 3];   private Shape3D cylinder=new Shape3D(createGeometry());      private JTextField heightTxt=new JTextField("0.5",5);   private JTextField radiusTxt=new JTextField("0.02",5);      public DynamicCylinder() {     ...          // Prepare the control panel for changing the height and radius of      // the cylinder     JPanel panel=new JPanel();     panel.add(new JLabel("Height:"));     panel.add(heightTxt);     panel.add(new JLabel("Radius:"));     panel.add(radiusTxt);     JButton okBtn=new JButton("Ok");     okBtn.addActionListener(new ActionListener(){       public void actionPerformed(ActionEvent e) {         setHeight(Float.parseFloat(heightTxt.getText()));         setRadius(Float.parseFloat(radiusTxt.getText()));       }            });     panel.add(okBtn);     getContentPane().add(panel,BorderLayout.SOUTH);   }   public BranchGroup createSceneGraph() {     BranchGroup objRoot = new BranchGroup();     // Set the proper capabilities     cylinder.setCapability(Shape3D.ALLOW_GEOMETRY_READ);          objRoot.addChild(cylinder);     return objRoot;   }   private Geometry createGeometry() {     updateVertices();     // Create the geometry by reference     TriangleStripArray quadArray = new TriangleStripArray(verticesNum,         GeometryArray.COORDINATES | GeometryArray.BY_REFERENCE,         new int[] { verticesNum });     quadArray.setCoordRefFloat(vertices);     // Set the capabilities     quadArray.setCapability(GeometryArray.ALLOW_REF_DATA_READ);     quadArray.setCapability(GeometryArray.ALLOW_REF_DATA_WRITE);     return quadArray;   }      private void updateVertices() {       float perR = (float) (2 * Math.PI / (verticesNum / 2 - 1));             for (int i = 0; i < verticesNum; i += 2) {         vertices[ (i + 1) * 3] = vertices[i *             3] = (float) (radius * Math.cos(i / 2 * perR));         vertices[ (i + 1) * 3 + 2] = vertices[i * 3 +             2] = (float) (radius * Math.sin(i / 2 * perR));         vertices[i * 3 + 1] = height;         vertices[ (i + 1) * 3 + 1] = 0;       }     }      public void setHeight(float height) {       float oldHeight = this.height;       this.height = height;       // Update the geometry       this.updateGeometry();     }      public void setRadius(float radius) {       float oldRadius = this.radius;       this.radius = radius;       // Update the geometry       this.updateGeometry();     }      private void updateGeometry() {       GeometryArray geometryArray = (GeometryArray)cylinder.getGeometry();       geometryArray.updateData(new GeometryUpdater(){         public void updateData(Geometry geometry){           updateVertices();         }       });     }   public static void main(String[] args) {     ...   } }

ImageJ New Plugins

In a joint project, we work towards using ImageJ in the context of neuroanatomy. The people involved are:

• Baker, Dean
• Jenett, Arnim
• Grübel, Kornelia
• Heisenberg, Martin
• Larkworthy, Tom
• Longair, Mark
• Schindelin, Johannes
• Schmid, Benjamin

AmiraMesh Reader / Writer

In the Würzburg group, we work a lot with Amira, and we work a lot with ImageJ.

To make the work easier, we wrote plugins to read and write 3d stacks in the Amira Mesh format in ImageJ.

Amira Surface Viewer

Amira can write 3d surface files. These can be loaded and visualized in ImageJ with the ShowAmiraSurface plugin.

ROI Brush

Tom Larkworthy wrote the ROI Brush, a tool which does not paint, but instead (un)selects circular regions.

Delaunay / Voronoi diagram

Gabriel Landini had this on his wishlist...

Two Point Correlation

This plugin plots a correlation / distance graph. It was requested by Paul Stutzman, but I have not heard back from him.

Scrollable StackWindow

With this plugin, you can select the current slice with your mouse wheel.

Align Image

Use this plugin to align an image to a template image, by selecting a line in both images.

Moving Least Squares

Warp an image using a technique presented by Schaefer et al. in Image Deformation Using Moving Least Squares.

IsoSurface Extractor

This plugin makes an isosurface from an image stack. It displays the result in a 3d window (you can zoom, pan and rotate the surface), and optionally saves the result as a VRML.

3D Viewer

This plugin offers 3D visualisation of image s