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import numpy as np
import pyvista as pv
import argparse
import os
import glob
import trimesh
def parse_command_line():
print('---'*10)
print('Parsing Command Line Arguments')
parser = argparse.ArgumentParser(description='Defacing protocol')
parser.add_argument('-bp', metavar='base path', type=str,
help="Absolute path of the base directory")
parser.add_argument('-gp', metavar='ground truth path', type=str,
help="Relative path of the ground truth model")
parser.add_argument('-pp', metavar='prediction path', type=str,
help="Relative path of the prediction model")
argv = parser.parse_args()
return argv
def distanceVertex2Mesh(mesh, vertex):
faces_as_array = mesh.faces.reshape((mesh.n_faces, 4))[:, 1:]
mesh_box = trimesh.Trimesh(vertices=mesh.points,
faces=faces_as_array)
cp, cd, ci = trimesh.proximity.closest_point(mesh_box, vertex)
return cd
def main():
args = parse_command_line()
base = args.bp
gt_path = args.gp
pred_path = args.pp
output_dir = os.path.join(base, 'output')
try:
os.mkdir(output_dir)
except:
print(f'{output_dir} already exists')
for i in glob.glob(os.path.join(base, gt_path) + '/*.vtk'):
filename = os.path.basename(i).split('.')[0]
#side = os.path.basename(i).split('.')[0].split('_')[0]
#scan_name = os.path.basename(i).split('.')[0].split('_')[0]
#scan_id = os.path.basename(i).split('.')[0].split('_')[1]
output_sub_dir = os.path.join(
base, 'output', filename)
try:
os.mkdir(output_sub_dir)
except:
print(f'{output_sub_dir} already exists')
gt_mesh = pv.read(i)
pred_mesh = pv.read(os.path.join(
base, pred_path, filename + '.vtk'))
pred_vertices = np.array(pred_mesh.points)
cd = distanceVertex2Mesh(gt_mesh, pred_vertices)
pred_mesh['dist'] = cd
pred_mesh.save(os.path.join(output_sub_dir, filename + '.vtk'))
if __name__ == '__main__':
main()
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