diff --git a/atlas_gen/atlas_scripts/kim_unified_atlas_v2.py b/atlas_gen/atlas_scripts/kim_unified_atlas_v2.py index f47500b..ab79ca6 100644 --- a/atlas_gen/atlas_scripts/kim_unified_atlas_v2.py +++ b/atlas_gen/atlas_scripts/kim_unified_atlas_v2.py @@ -11,24 +11,24 @@ # import sys # sys.path.append("./") -from atlas_gen.mesh_utils import create_region_mesh +from atlas_gen.mesh_utils import create_region_mesh, Region from atlas_gen.wrapup import wrapup_atlas_from_data -from brainatlas_api.structure_tree_util import get_structures_tree, Region +from brainatlas_api.structure_tree_util import get_structures_tree if __name__ == "__main__": - PARALLEL = True # disable parallel mesh extraction for easier debugging + PARALLEL = False # disable parallel mesh extraction for easier debugging # ---------------------------------------------------------------------------- # # PREP METADATA # # ---------------------------------------------------------------------------- # - RES_UM = 50 + RES_UM = 25 VERSION = 1 ATLAS_NAME = f"kim_unified" SPECIES = "Mus musculus" ATLAS_LINK = "https://kimlab.io/brain-map/atlas/" CITATION = "Chon et al. 2019, https://doi.org/10.1038/s41467-019-13057-w" - ORIENTATION = "asr" + ORIENTATION = "als" ROOT_ID = 997 # ---------------------------------------------------------------------------- # diff --git a/atlas_gen/mesh_utils.py b/atlas_gen/mesh_utils.py index 8f7e4e1..e7639c9 100644 --- a/atlas_gen/mesh_utils.py +++ b/atlas_gen/mesh_utils.py @@ -166,7 +166,6 @@ def create_region_mesh(args): if not np.max(mask): print(f"Empty mask for {node.tag}") else: - print("Creating mesh for ", node.tag) if node.identifier == ROOT_ID: extract_mesh_from_mask( mask, obj_filepath=savepath, smooth=True