Best way to deal with Collision in JavaFX

Question

This question I'ts no exactly a fix for the current game I'm working on, but I am showing it as an example to explain my problem. I just want to know the best way to handle collision in JavaFX.

My problem is that I cant seem to make collision work with javaFX using the .intercept() function. the way I'm doing it is making a Pane that has the image and different overlapping rectangles that make the collision box. then i add this pane to another pane(the game world). then when I try to get the collision boxes that i want to compare and use .intercept() function it doesn't work, they seem to always collide no matter what, I am using .setLayoutX and Y to move my pane(the ship pane) if that matters and yes I am using .getBoundsOnParent()

The only way i have found that kind of works is comparing the panes themselves but that doesn't work since it just tries to compare the fills.

This is my ship:

This is my Collision Box:

Here is colliding by using the whole pane(see it doesn't work)

Answer 1

(i just want to feel like i am helping a game developer)

From my little knowledge in game development i think they are actually intercepting but not appearing as such, you see you have a rectangle ship-in respect to its bounds

  ________________
 |               |
 |               |
 |    ship one   | // your rectangle shaped ship in layout
 |               |
 |_______________|           //about to collide with another rectangle shaped
         ________________
        |               |
        |               |
        |  ship two     | // your rectangle shaped ship in layout
        |               |
        |_______________|
 //collision
          //same as these two potions
            !
  __________v______
 |          !     |
 | ship one !     |  
 |          !     |
 |        __v_____|______
 |_______|_______| <- --|<----- //this portion(s) does not exist in your shaped ship
         |              |
         |              |
         | ship two     |
         |______________|

Here you can see both rectangles are touching each other, so you have a collision but your shaped ship dont appear that way because they are not rectangles, your blue vertical portion starts at the middle-same goes for the other, if you look at your image carefully you see that they are touching each other but maybe with a 2dip space. so if i am to give one of my ignorant solutions(i am now trying to enter deep into game development hence that vocab) i will say move your objects past their surface area..

EDIT

Also you are using boundsInParent- which is bigger or than local bounds, a boundsInParent leaves extra room for your nodes so they can go through transformation, rotation etc, without having to overlap other nodes, that explains the etxra 2dip space or my theory

Hope it wasn't bad enough