def create_atlas(level):
if level == 'high':
MESH_PATH = os.path.join(DATA_PATH, 'atlas_data', atlas_name, 'mesh',
'0.9')
else:
MESH_PATH = os.path.join(DATA_PATH, 'atlas_data', atlas_name, 'mesh',
'0.1')
sqlController = SqlController('MD589')
structures = sqlController.get_structures_list()
acts = []
for structure in tqdm(structures):
filepath = os.path.join(MESH_PATH, f'{structure}.stl')
if os.path.exists(filepath):
act = load(filepath)
color = sqlController.get_structure_color_rgb(structure)
act.color(color)
acts.append(act)
show(acts)
HOME = os.path.expanduser("~")
PATH = os.path.join(HOME, 'programming/pipeline_utility')
sys.path.append(PATH)
atlas_name = 'atlasV9'
surface_level = 0.8
from utilities.file_location import DATA_PATH
ATLAS_PATH = os.path.join(DATA_PATH, 'atlas_data', atlas_name)
OUTPUT = os.path.join(ATLAS_PATH, 'mesh')
os.makedirs(OUTPUT, exist_ok=True)
from utilities.atlas.imported_atlas_utilities import volume_to_polydata, save_mesh_stl
from utilities.sqlcontroller import SqlController
sqlController = SqlController('MD589')
structures = sqlController.get_structures_list()
structures.remove('R')
for structure in tqdm(structures):
volume_filepath = os.path.join(ATLAS_PATH, 'structure', f'{structure}.npy')
volume = np.load(volume_filepath)
origin_filepath = os.path.join(ATLAS_PATH, 'origin', f'{structure}.txt')
origin = np.loadtxt(origin_filepath)
volume_origin = (volume >= surface_level, origin)
#volume_origin = (volume, origin)
aligned_structure = volume_to_polydata(volume=volume_origin,
num_simplify_iter=3,
smooth=True,
return_vertex_face_list=False)
mesh_filepath = os.path.join(OUTPUT, '{}.stl'.format(structure))
