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Can't use ShapeRednerer when using 3D

Let me explain what I am trying here:
my application will use 3d rendering for most part, but for development and debugging I'm trying to use ShapeRenderer for things like drawing paths, debugging collisions etc.
But I can't get anything to display on screen and I'm lost. I'm suspecting a camera issue, but please advise and suggest a solution. Here's what I'm doing:
public void create () {
assets = new AssetManager();
assets.load("button.g3db", Model.class);
camera = new PerspectiveCamera(75, Gdx.graphics.getWidth(),Gdx.graphics.getHeight());
camera.position.set(0f, 0f, 5f);
camera.lookAt(0f,0f,0f);
camera.near = 1f;
camera.far = 100.0f;
shapeRenderer = new ShapeRenderer();
shapeRenderer.setProjectionMatrix(camera.combined);
modelBatch = new ModelBatch();
//some Bezier curve to draw for debuging
Bezier<Vector3> points = ButtonUtils.getButtonEscapePath();
int k = 100;
pointsArray = new Vector3[k];
for(int i = 0; i < k; ++i)
{
pointsArray[i] = new Vector3();
points.valueAt(pointsArray[i], ((float)i)/((float)k-1));
}
environment = new Environment();
DirectionalLight light = new DirectionalLight();
light.set(0.8f, 0.8f, 0.8f, new Vector3(-1f, -0.8f, -0.2f));
environment.set(new ColorAttribute(ColorAttribute.AmbientLight, 0.4f, 0.4f, 0.4f, 1f));
environment.add(light);
}
public void render () {
Gdx.gl.glViewport(0, 0, Gdx.graphics.getWidth(), Gdx.graphics.getHeight());
Gdx.gl.glClearColor(0, 0, 0, 1);
Gdx.gl.glClear(GL20.GL_COLOR_BUFFER_BIT | GL20.GL_DEPTH_BUFFER_BIT);
camera.update();
modelBatch.begin(camera);
modelBatch.render(button, environment);
modelBatch.end();
//drawing debug circles around 3D object
shapeRenderer.begin(ShapeRenderer.ShapeType.Line);
shapeRenderer.setColor(Color.WHITE);
shapeRenderer.circle(button.getPosition().x, button.getPosition().y, 50f, 50);
shapeRenderer.end();
//drawing Bezier curve
int k = 100;
shapeRenderer.begin(ShapeRenderer.ShapeType.Line);
for(int i = 0; i < k-1; ++i)
{
shapeRenderer.line(pointsArray[i], pointsArray[i+1]);
}
shapeRenderer.end();
}
edit: tiny correction, I can get something on the screen, what I mean is 3d models display just fine, it's ShapeRenderer stuff that won't display.

Taking a screenshot with JOGL

I am looking for a way to screenshot my GLCanvas programmatically without awt Robot.
Here is my current setup:
Constructor:
glcaps = new GLCapabilities(GLProfile.get(GLProfile.GL2));
glcaps.setDoubleBuffered(true);
glcaps.setHardwareAccelerated(true);
glcanvas = new GLCanvas(glcaps);
glcanvas.setSize(720, 720);
glcanvas.addGLEventListener(this);
glcanvas is declared as an instance variable: GLCanvas glcanvas
OpenGL init:
#Override
public void init(GLAutoDrawable glad) {
GL2 gl = glad.getGL().getGL2();
glu = new GLU();
gl.glEnable(GL2.GL_DEPTH_TEST);
gl.glDepthFunc(GL2.GL_LEQUAL);
gl.glShadeModel(GL2.GL_SMOOTH);
gl.glHint(GL2.GL_PERSPECTIVE_CORRECTION_HINT, GL2.GL_NICEST);
gl.glClearColor(0f, 0f, 0f, 1f);
// Some camera related code not shown
}
OpenGL display:
public void display(GLAutoDrawable glad) {
GL2 gl = glad.getGL().getGL2();
gl.glClear(GL2.GL_COLOR_BUFFER_BIT | GL2.GL_DEPTH_BUFFER_BIT);
...
// Orient camera and draw a simple cube
...
gl.glFlush();
}
Screenshot method:
BufferedImage b = new BufferedImage(glcanvas.getWidth(), glcanvas.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics g = b.createGraphics();
glcanvas.setupPrint(glcanvas.getWidth(), glcanvas.getWidth(), 50, 50, 50);
glcanvas.print(g);
try {
ImageIO.write(b, "png", new File("test.png"));
} catch (IOException ex) {
// Error handling
}
glcanvas.releasePrint();
g.dispose();
This method works, as in executes without crashing, but the png file I get is just black with no cube. I also tried using glReadPixels but that does not work either as it just gives me a buffer full of 0's (black).
I think that the problem is that I am not reading glcanvas from the draw thread. Is this the error, and if so, how can I solve it?
All answers appreciated!

First, you have to be sure that you read the framebuffer after what you want to catch has been rendered.
Second, you can do something like this:
protected void saveImage(GL3 gl3, int width, int height) {
try {
BufferedImage screenshot = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
Graphics graphics = screenshot.getGraphics();
ByteBuffer buffer = GLBuffers.newDirectByteBuffer(width * height * 4);
// be sure you are reading from the right fbo (here is supposed to be the default one)
// bind the right buffer to read from
gl3.glReadBuffer(GL_BACK);
// if the width is not multiple of 4, set unpackPixel = 1
gl3.glReadPixels(0, 0, width, height, GL_RGBA, GL_UNSIGNED_BYTE, buffer);
for (int h = 0; h < height; h++) {
for (int w = 0; w < width; w++) {
// The color are the three consecutive bytes, it's like referencing
// to the next consecutive array elements, so we got red, green, blue..
// red, green, blue, and so on..+ ", "
graphics.setColor(new Color((buffer.get() & 0xff), (buffer.get() & 0xff),
(buffer.get() & 0xff)));
buffer.get(); // consume alpha
graphics.drawRect(w, height - h, 1, 1); // height - h is for flipping the image
}
}
// This is one util of mine, it make sure you clean the direct buffer
BufferUtils.destroyDirectBuffer(buffer);
File outputfile = new File("D:\\Downloads\\texture.png");
ImageIO.write(screenshot, "png", outputfile);
} catch (IOException ex) {
}
}
I filled some comment inside, if something is still unclear, don't hesitate to ask further

Basic openGL 3.2 Setup with lwjgl - Object not rendered

I am little bit desperate here.
I am trying to update/refactor an existing code written in legacy opengl to make use of the "modern way" of opengl version 3.2+.
It is written in Java with lwjgl. I already stripped away most of the functionality to test the basic setup. For me at the moment it is really just about setting up the vbo with vertices loaded from an obj file and render it. My problem is, that the display window stays empty. If it would display me just something, I would be really happy.
Maybe you guys can help me what I am missing here.
public class Mobile {
private final String texturePath = "../CGSS15Ex3MobileDS/dataEx3/Textures";
private int
width = 1200,
height = 800,
fps = 0,
cameraDist = 2000,
fillMode = GL_LINE,
ticksPerSecond = 60,
frameCounter = 0,
vaoId,
vboId,
vboiID,
pId,
vsId,
fsId;
private long
time,
lastTime,
lastFPS,
lastKeySpace,
frameCounterTime,
avgTime = 0;
private float
dx = 0f, // mouse x distance
dy = 0f, // mouse y distance
diffTime = 0f, // frame length
mouseSensitivity = 0.5f,
movementSpeed = 800.0f; // move 10 units per second.
private Fork fork;
private CameraController camera;
FloatBuffer kugelBuff, indexBuff;
int kugelVertCount;
static LinkedList<Integer> textureIDs = new LinkedList<>();
public Mobile() {
run();
}
private void run() {
init();
while (!exit()) {
update();
draw();
updateFPS();
}
fini();
}
private void init() {
// OpenGL Setup
// create display
try {
PixelFormat pixelFormat = new PixelFormat();
ContextAttribs contextAtrributes = new ContextAttribs(3, 2)
.withProfileCore(true)
.withForwardCompatible(true);
Display.setDisplayMode(new DisplayMode(width, height));
Display.setTitle("Mobile by Aaron Scheu");
Display.create(pixelFormat, contextAtrributes);
GL11.glClearColor(0.3f, 0.3f, 0.3f, 0f);
GL11.glViewport(0, 0, width, height);
} catch (LWJGLException e) {
e.printStackTrace();
System.exit(-1);
}
// setup scene //
setupSphere();
setupShaders();
setupTex();
// set Timer
frameCounterTime = lastFPS = getTime();
System.out.println("Start timer ...");
}
private void setupTex() {
for (String file : getTextureFiles(texturePath)) {
try {
TextureReader.Texture texture = TextureReader.readTexture(file);
textureIDs.add(glGenTextures());
GL13.glActiveTexture(GL13.GL_TEXTURE0);
GL11.glBindTexture(GL11.GL_TEXTURE_2D, textureIDs.getLast());
// Upload tex and generate mipmap for scaling
glTexImage2D(
GL_TEXTURE_2D, 0, GL_RGB, texture.getWidth(), texture.getHeight(), 0,
GL_RGB, GL_UNSIGNED_BYTE, texture.getPixels()
);
GL30.glGenerateMipmap(GL11.GL_TEXTURE_2D);
// Setup the ST coordinate system
GL11.glTexParameteri(GL11.GL_TEXTURE_2D, GL11.GL_TEXTURE_WRAP_S, GL11.GL_REPEAT);
GL11.glTexParameteri(GL11.GL_TEXTURE_2D, GL11.GL_TEXTURE_WRAP_T, GL11.GL_REPEAT);
// Setup what to do when the texture has to be scaled
GL11.glTexParameteri(GL11.GL_TEXTURE_2D, GL11.GL_TEXTURE_MAG_FILTER,
GL11.GL_NEAREST);
GL11.glTexParameteri(GL11.GL_TEXTURE_2D, GL11.GL_TEXTURE_MIN_FILTER,
GL11.GL_LINEAR_MIPMAP_LINEAR);
} catch(IOException e) {
System.out.println(e);
}
}
}
private void setupShaders() {
// Load the vertex shader
// vsId = GLDrawHelper.compileShader("../CGSS15Ex3MobileDS/dataEx3/Shader/phong_vertex.glsl", GL20.GL_VERTEX_SHADER);
vsId = GLDrawHelper.compileShader("shader/vert_shader.glsl", GL20.GL_VERTEX_SHADER);
// Load the fragment shader
// fsId = GLDrawHelper.compileShader("../CGSS15Ex3MobileDS/dataEx3/Shader/phong_fragment.glsl", GL20.GL_FRAGMENT_SHADER);
fsId = GLDrawHelper.compileShader("shader/frac_shader.glsl", GL20.GL_FRAGMENT_SHADER);
// Create a new shader program that links both shaders
pId = GL20.glCreateProgram();
GL20.glAttachShader(pId, vsId);
GL20.glAttachShader(pId, fsId);
// Bind shader data to vbo attribute list
// GL20.glBindAttribLocation(pId, 0, "vert_in");
// GL20.glBindAttribLocation(pId, 1, "col_in");
// GL20.glBindAttribLocation(pId, 2, "tex0_in");
// GL20.glBindAttribLocation(pId, 3, "norm_in");
// Test Shader
GL20.glBindAttribLocation(pId, 0, "in_Position");
GL20.glBindAttribLocation(pId, 1, "in_Color");
GL20.glBindAttribLocation(pId, 2, "in_TextureCoord");
GL20.glLinkProgram(pId);
GL20.glValidateProgram(pId);
}
private void setupSphere() {
Model sphere = null;
try {
sphere = OBJLoader.loadModel(new File("sphere.obj"));
} catch (IOException e) {
e.printStackTrace();
Display.destroy();
System.exit(1);
}
kugelBuff = GLDrawHelper.directFloatBuffer(sphere.getVVVNNNTT());
indexBuff = GLDrawHelper.directFloatBuffer(sphere.getVertIndices());
kugelVertCount = sphere.getVertCount();
// Create a new Vertex Array Object in memory and select it (bind)
vaoId = GL30.glGenVertexArrays();
GL30.glBindVertexArray(vaoId);
// Create a new Vertex Buffer Object in memory and select it (bind)
vboId = GL15.glGenBuffers();
GL15.glBindBuffer(GL15.GL_ARRAY_BUFFER, vboId);
GL15.glBufferData(GL15.GL_ARRAY_BUFFER, kugelBuff, GL15.GL_STATIC_DRAW);
// Attribute Pointer - list id, size, type, normalize, sprite, offset
GL20.glVertexAttribPointer(0, 3, GL11.GL_FLOAT, false, 8*4, 0); // Vertex
// GL20.glVertexAttribPointer(1, 3, GL11.GL_FLOAT, false, 3, 0); // Color
GL20.glVertexAttribPointer(2, 2, GL11.GL_FLOAT, false, 8*4, 6*4); // UV Tex
// GL20.glVertexAttribPointer(3, 3, GL11.GL_FLOAT, false, 8*4, 3*4); // Normals
GL15.glBindBuffer(GL15.GL_ARRAY_BUFFER, 0);
// Deselect (bind to 0) the VAO
GL30.glBindVertexArray(0);
// Create a new VBO for the indices and select it (bind) - INDICES
vboiID = GL15.glGenBuffers();
GL15.glBindBuffer(GL15.GL_ELEMENT_ARRAY_BUFFER, vboiID);
GL15.glBufferData(GL15.GL_ELEMENT_ARRAY_BUFFER, indexBuff, GL15.GL_STATIC_DRAW);
GL15.glBindBuffer(GL15.GL_ELEMENT_ARRAY_BUFFER, 0);
}
private void update() {
// limit framerate
// Display.sync(ticksPerSecond);
// get time
time = getTime();
diffTime = (time - lastTime)/1000.0f;
lastTime = time;
// Distance mouse has been moved
dx = Mouse.getDX();
dy = Mouse.getDY();
// toggle wireframe
if(Keyboard.isKeyDown(Keyboard.KEY_SPACE)) {
if (time - lastKeySpace > 100) {
fillMode = fillMode == GL_FILL ? GL_LINE : GL_FILL;
glPolygonMode(GL_FRONT_AND_BACK, fillMode);
}
lastKeySpace = time;
}
// mouse control
camera.yaw(dx * mouseSensitivity);
camera.pitch(dy * mouseSensitivity);
// WASD control
if (Keyboard.isKeyDown(Keyboard.KEY_W)) {
camera.walkForward(movementSpeed * diffTime);
}
if (Keyboard.isKeyDown(Keyboard.KEY_S)) {
camera.walkBackwards(movementSpeed * diffTime);
}
if (Keyboard.isKeyDown(Keyboard.KEY_A)) {
camera.strafeLeft(movementSpeed * diffTime);
}
if (Keyboard.isKeyDown(Keyboard.KEY_D)) {
camera.strafeRight(movementSpeed * diffTime);
}
}
private boolean exit() {
return Display.isCloseRequested() || Keyboard.isKeyDown(Keyboard.KEY_ESCAPE);
}
// runner is finished, clean up
private void fini() {
// glDisable(GL_DEPTH_BITS);
// Delete all textures
textureIDs.stream().forEach(GL11::glDeleteTextures);
// Delete the shaders
GL20.glUseProgram(0);
GL20.glDetachShader(pId, vsId);
GL20.glDetachShader(pId, fsId);
GL20.glDeleteShader(vsId);
GL20.glDeleteShader(fsId);
GL20.glDeleteProgram(pId);
// Select the VAO
GL30.glBindVertexArray(vaoId);
// Disable the VBO index from the VAO attributes list
GL20.glDisableVertexAttribArray(0);
GL20.glDisableVertexAttribArray(1);
// Delete the vertex VBO
GL15.glBindBuffer(GL15.GL_ARRAY_BUFFER, 0);
GL15.glDeleteBuffers(vboId);
// Delete the index VBO
// GL15.glBindBuffer(GL15.GL_ELEMENT_ARRAY_BUFFER, 0);
// GL15.glDeleteBuffers(vboiId);
// Delete the VAO
GL30.glBindVertexArray(0);
GL30.glDeleteVertexArrays(vaoId);
Display.destroy();
}
private void updateFPS() {
long time = getTime();
String title;
if (time - lastFPS > 1000) {
// Display.setTitle("FPS: " + fps);
title = "FPS: " + fps + " || avg time per frame: " + (avgTime != 0 ? avgTime/1000f : "-/-") + " ms";
Display.setTitle(title);
fps = 0;
lastFPS += 1000;
}
fps++;
// Frame Count over 1000
if (frameCounter == 1000) {
avgTime = time - frameCounterTime;
// System.out.println("Time for 1000 frames: " + avgTime + " ms.");
frameCounter = 0;
frameCounterTime = time;
}
frameCounter++;
}
private long getTime() {
return (Sys.getTime() * 1000 / Sys.getTimerResolution());
}
private void draw() {
GL11.glClear(GL11.GL_COLOR_BUFFER_BIT);
GL20.glUseProgram(pId);
// Bind the texture
GL13.glActiveTexture(GL13.GL_TEXTURE0);
GL11.glBindTexture(GL11.GL_TEXTURE_2D, textureIDs.get(0));
// Bind to the VAO that has all the information about the vertices
GL30.glBindVertexArray(vaoId);
GL20.glEnableVertexAttribArray(0);
// GL20.glEnableVertexAttribArray(1);
GL20.glEnableVertexAttribArray(2);
GL20.glEnableVertexAttribArray(3);
// Bind to the index VBO that has all the information about the order of the vertices
GL15.glBindBuffer(GL15.GL_ELEMENT_ARRAY_BUFFER, vboiID);
// Draw the vertices
GL11.glDrawElements(GL11.GL_TRIANGLES, kugelVertCount, GL11.GL_UNSIGNED_BYTE, 0);
// Put everything back to default (deselect)
GL15.glBindBuffer(GL15.GL_ELEMENT_ARRAY_BUFFER, 0);
GL20.glDisableVertexAttribArray(0);
// GL20.glDisableVertexAttribArray(1);
GL20.glDisableVertexAttribArray(2);
GL20.glDisableVertexAttribArray(3);
GL30.glBindVertexArray(0);
GL20.glUseProgram(0);
Display.update();
}
private static String[] getTextureFiles(String directory) {
File pathfile = new File(directory);
File[] files = pathfile.listFiles( (File dir, String name) ->
name.endsWith(".jpg") || name.endsWith(".png")
);
return Arrays.stream(files).map(File::toString).toArray(String[]::new);
}
public static void main(String[] args) {
new Mobile();
}
}
Sorry for the code mess. Maybe this is better readable.
https://codeshare.io/1SEQK

Don't be desperate, amaridev.
When you can't get nothing rendered you have in general two option:
start from something basic and working (like this hello triangle from mine, it's jogl but you can port it to lwjgl very easily) and build on top of that
debug your application step by step
In case you decide for the second one, you may want to disable first and lighting, any matrix multiplication and any texturing:
check your rendering targets setup by testing if you see the clear color you set
check if glViewport and the fragment shader work by running an hardcoded vertex shader with:
gl_Position = vec4(4.0 * float(gl_VertexID % 2) - 1.0, 4.0 * float(gl_VertexID / 2) - 1.0, 0.0, 1.0);
like here, no matrices and a simple
glDrawArrays(GL_TRIANGLES, 3, 0);
you may want also to hardcode the color output
check if you are reading valid vertex attributes, by outputting each of them in turn to the color fragment shader
out Block
{
vec4 color
} outBlock;
...
outBlock.color = position;
in Block
{
vec4 color;
} inBlock;
outputColor = inBlock.color;
enable matrix multiplication and pass a simple hardcoded triangle to check if any matrix (first proj, then view and finally also model) works as expected
start fetching from your real sphere geometry
start fetching color
enable again texturing and start fetching texture coordinates again
output light and materials values to output color and then enable them back as well

Multiple cameras and ScissorStack?

I'm currently trying to make a game, and I'm still novice with using cameras, and I'm thinking that two OrthographicCameras may be necessary, but I'm not sure if that's the most efficient way, or even how to do so.
Basically, I want this to be the layout for it:
The Main Area is where the main stuff is, which is a Server Interface. The Game Level is where the actual game part is in. I am currently using a ScissorStack to cut the region, but with this demo, results make me question how to do this:
public class TestScissorStackAndCamera extends ApplicationAdapter {
private SpriteBatch batch;
private OrthographicCamera camera;
private Sprite sprite;
private int width, height;
#Override
public void create() {
Gdx.gl.glClearColor(0, 0, 0, 0);
width = Gdx.graphics.getWidth();
height = Gdx.graphics.getHeight();
batch = new SpriteBatch();
camera = new OrthographicCamera(width, height);
camera.position.set(width / 2, height / 2, 0);
camera.update();
createSprite();
}
private void createSprite() {
Pixmap map = new Pixmap(width, height, Format.RGBA8888);
map.setColor(Color.RED);
map.fillRectangle(0, 0, width, height);
map.setColor(Color.BLUE);
map.drawLine(width / 2, 0, width / 2, height);
map.drawLine(0, height / 2, width, height / 2);
Texture texture = new Texture(map);
sprite = new Sprite(texture);
}
#Override
public void render() {
Gdx.gl.glClear(GL20.GL_COLOR_BUFFER_BIT);
batch.setProjectionMatrix(camera.combined); // The Question!
batch.begin();
{
Rectangle scissors = new Rectangle();
Rectangle area = new Rectangle(10, 10, width - 20, height - 20);
ScissorStack.calculateScissors(camera, batch.getTransformMatrix(), area, scissors);
ScissorStack.pushScissors(scissors);
batch.draw(sprite, 0, 0);
batch.flush();
ScissorStack.popScissors();
}
batch.end();
}
public static void main(String[] args) {
LwjglApplicationConfiguration config = new LwjglApplicationConfiguration();
config.title = "ScissorStack & Camera Test";
config.resizable = false;
new LwjglApplication(new TestScissorStackAndCamera(), config);
}
}
Questioning batch.setProjectionMatrix(camera.combined)
I marked a line in the code with a comment, The Question!, which is what is affecting the results. If I don't have it, using the camera.translate(...) method, the image is drawn at (0, 0) but what it does is it moves what part is viewed. If I do have that line, when I use the camera.translate(...) method, the image is drawn respectively to the position of the camera.
In respect to the game that I'm currently developing, it behaves awkwardly without the projectionMatrix not being set, but when I do set it, it messes up the positioning of the rest of the game. I even added some testing features, and it's not rendering inside of the correct ScissorStack
How could I go about setting up two cameras, or what could I do to set up what I'm trying to correctly and efficiently?
With my actual game (not the mock-up) this is what it is doing. It should be rendering inside of the red lines, but it's not:
If you'd like to see my current code for my GameLevel that is handling the ScissorStack and OrthographicCamera:
public GameLevel(int x, int y, int displayWidth, int displayHeight) {
this.x = x; // x = 10
this.y = y; // y = 10
this.displayWidth = displayWidth; // displayWidth = Gdx.graphics.getWidth() - x - 10
this.displayHeight = displayHeight; // displayHeight = Gdx.graphics.getHeight() - y - 120
camera = new OrthographicCamera(Gdx.graphics.getWidth(), Gdx.graphics.getHeight());
camera.position.set(displayWidth / 2, displayHeight / 2, 0);
// FBLAGame.batch.setProjectionMatrix(camera.combined);
camera.update();
init();
}
...
#Override
public void render() {
Rectangle area = new Rectangle(x, y, displayWidth, displayHeight);
Rectangle scissor = new Rectangle();
Matrix4 matrix = FBLAGame.batch.getTransformMatrix();
ScissorStack.calculateScissors(camera, matrix, area, scissor);
ScissorStack.pushScissors(scissor);
renderLevel();
FBLAGame.batch.flush();
ScissorStack.popScissors();
Pixmap map = new Pixmap(Gdx.graphics.getWidth(), Gdx.graphics.getHeight(), Format.RGBA8888);
map.setColor(Color.RED);
map.drawRectangle((int) area.x, (int) area.y, (int) area.width, (int) area.height);
Texture t = new Texture(map);
map.dispose();
FBLAGame.batch.draw(t, 0, 0);
}

How to pick objects using jogl?

I met some problems about jogl picking. I need to pick each single point and process it, but I always get 0 hit (nothing is picked). Can anyone help me with this?
the display function can correctly get the 2x2 window around the cursor.
public void display(GLAutoDrawable drawable) {
GL2 gl = drawable.getGL().getGL2();
switch(cmd){
case UPDATE:
gl.glPushMatrix();
gl.glMultMatrixf(rot_matrix, 0);
buildPoints(gl);
buildAxes(gl);
gl.glPopMatrix();
break;
case SELECT:
int buffsize = 512;
double x = mouseX, y = mouseY;
int[] viewPort = new int[4];
IntBuffer selectBuffer = Buffers.newDirectIntBuffer(buffsize);
int hits = 0;
gl.glGetIntegerv(GL2.GL_VIEWPORT, viewPort, 0);
gl.glSelectBuffer(buffsize, selectBuffer);
gl.glRenderMode(GL2.GL_SELECT);
gl.glMatrixMode(GL2.GL_PROJECTION);
gl.glPushMatrix();
gl.glLoadIdentity();
glu.gluPickMatrix(x, (double) viewPort[3] - y, 2.0d, 2.0d, viewPort, 0);
//draw graph
gl.glPushMatrix();
gl.glMultMatrixf(rot_matrix, 0);
buildPoints(gl);
buildAxes(gl);
gl.glPopMatrix();
gl.glMatrixMode(GL2.GL_PROJECTION);
gl.glPopMatrix();
gl.glMatrixMode(GL2.GL_MODELVIEW);
gl.glFlush();
hits = gl.glRenderMode(GL2.GL_RENDER);
processHits(hits, selectBuffer);
cmd = UPDATE;
break;
}
}
so I guess maybe the drawing graph part for picking is not correct. Here is the code of buildPoints function.
public void buildPoints(GL2 gl) {
gl.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT);
gl.glPointSize((float) radius / 2);
int pointName = 0;
gl.glBegin(GL.GL_POINTS);
for (point p : pointsList) {
if(cmd == SELECT) gl.glLoadName(pointName);
gl.glPushMatrix();
gl.glTranslatef(p.getX(), p.getY(), p.getZ());
gl.glColor3f(0.95f, 0.207f, 0.031f);
gl.glVertex3f((float) (p.getX() * scaleFactor),
(float) (p.getY() * scaleFactor),
(float) (p.getZ() * scaleFactor));
gl.glPopMatrix();
pointName++;
}
gl.glEnd();
}

I advise you to look at this example of picking using JOGL 2. However, OpenGL build-in picking is deprecated and shouldn't be used. We discussed a lot about it on our official forum, especially in this thread.