The execution order of the code

[liyunkai-carpediem]

• resector version: 0.2.10
• Python version:3.7
• Operating System:linux

Description

I want to delve into the code and not run it as pre-packaged methods. I have found the generated geodesic polyhedron and I would like to ask which part of the code is responsible for adding simplex noise to it , as well as the code for random affine transformations.

[fepegar]

Hi @liyunkai-carpediem. You can just search for the code:

https://github.com/fepegar/resector/blob/ed63b3de5562fb011fb88916c4da8d170415cd6f/resector/mesh.py#L64-L87

https://github.com/fepegar/resector/blob/ed63b3de5562fb011fb88916c4da8d170415cd6f/resector/mesh.py#L109-L124

[liyunkai-carpediem]

Dear sir, Thanks a lot for giving me an answer, I am very excited!!! And I have found the relative codes in the following path: "scripts/test/perlin_sphere.py" I think they are the same(?)

1. So what is the difference between the folder "scripts" and "resector"?
2. I have found there is a code called "perlin_image.py", I ran it, getting a result of"simplex.nii", maybe it is a noise for adding it into the sphere? But I noticed that we use “noise” library to do so. So what is the function of "perlin_image.py"?

3. when I run the following code, I have noticed that there are 5 shapes generated. Which one will be the final shape I will be used later?

   for _ in range(5):
   offset = np.random.randint(1000)
   output_path = f'/tmp/geodesic_polyhedron_noise_{offset}.vtp'
   
   volume = np.random.randint(100, 10000)
   center = np.random.randint(-50, 50, size=(3))
   k = 4/3 * np.pi
   radius = (volume / k) ** (1/3)
   ratio = np.random.uniform(0.8, 1)
   a = radius
   b = radius * ratio
   c = radius / ratio
   radii = a, b, c
   angles = np.random.uniform(0, 180, size=3)
   
   output_poly_data = get_resection_poly_data(
       input_poly_data,
       offset,
       center,
       radii,
       angles,
   )

Thanks a lot.

[liyunkai-carpediem]

When I run the mesh_to_vol, I met some problems. My code is here:

from resector.io import read_poly_data, write
from resector.mesh import mesh_to_volume

mesh_path = '/storage/liyunkai/resector-master/geodesic_polyhedron_noise_102.vtp'
reference_path = '/storage/liyunkai/MICCAI_FeTS2022_TrainingData/FeTS2022_00000/FeTS2022_00000_seg.nii.gz'

poly_data = read_poly_data(mesh_path)

image = mesh_to_volume(poly_data, reference_path)
write(image, '/storage/liyunkai/resector-master/result/stenciled.nii.gz')

And the error is:

/storage/liyunkai/resector-master/resector/mesh.py:281: UserWarning: Empty stencil mask for reference /tmp/tmpub2oik3h.nii
  warnings.warn(f'Empty stencil mask for reference {reference_path}')

the file is empty, but how?