overlapping_tesselations.py

import numpy as np
import pyvista as pv
import nibabel as nib
from arr_stacking import *
from skimage import measure

def tesselation_function(input_file_path, output_file_path, offset, iters):
    # Load the MRI data which is a NIftI file (.nii)
    mri_file_path = input_file_path
    
    #Loading the brain data 
    brain = nib.load(mri_file_path)
    
    #Converting to a NumPy array
    binary_brain_mask_inp = brain.get_fdata()
    
    binary_brain_mask = np.sum(binary_brain_mask_inp, axis=3)
    
    # print(binary_brain_mask.shape)
    
    # Creating the surface mesh using the marching cubes algorithm
    vertices, faces, _, _ = measure.marching_cubes(binary_brain_mask, 0.5)
    
    faces_1 = stack_arrs(faces)
    
    # Using the output from the marching cubes algorithm, a PyVista mesh is created
    mesh = pv.PolyData(vertices, faces_1)
    
    # Mesh Decimation
    mesh = mesh.smooth(iters)
    
    # Overlapping regions are created using mesh translation
    
    overlap_mesh = mesh.copy()
    overlap_mesh.translate([offset, 0, 0])
    
    # Mesh combination
    final_mesh = mesh + overlap_mesh
    
    # Final mesh decimation
    final_mesh = final_mesh.smooth(iters)
    
    # Saving the required file in the ".stl" format
    output_mesh_file = output_file_path
    final_mesh.save(output_mesh_file)

    print("Tesselation Saved!")