I have (a bunch of 3D) stacks of tomographic data, in those I have deduced a certain (3D) coordinate around which I need to cut out a spherical region.

My code produces me the following image which gives an overview of what I do. I calculate the orange and green points, based on the dashed white and dashed green region. Around the midpoint of these, I'd like to cut out a spherical region, the representation of it is now marked with a circle in the image (also drawn by my code).

Constructing a sphere with skimage.morphology.ball and multiplying this with the original image is easy to do, but how can I set the center of the sphere at the desired 3D location in the image? The ~30 3D stacks of images are all of different size with different regions, but I have all the necessary coordinates ready for further use.

CodePudding user response：

0. you have some radius r and an index (i,j,k) into the data.

1. kernel = skimage.morphology.ball(r) returns a mask/kernel which is a = 2*r 1 along each side. It's cube-shaped.

2. Take a cube-shaped slice, the size of your kernel, out of the tree trunk tomograph. Starting indices depend on where you need the center to be and what radius the kernel has.

   piece = data[i-r:i-r a, j-r:j-r a, k-r:k-r a]

3. Apply the binary "ball" mask/kernel to the slice.

   piece *= kernel