diff --git a/03_nc_to_npy_for_openvdb.py b/03_nc_to_npy_for_openvdb.py index 95a1f79..463ebf3 100644 --- a/03_nc_to_npy_for_openvdb.py +++ b/03_nc_to_npy_for_openvdb.py @@ -54,7 +54,7 @@ class volume_maker: self.topoutfolder = args.output_path self.array_name = args.segmented_name self.ph = args.phase - self.mask = args.masks + self.mask = args.mask self.mask_name = args.mask_name @@ -81,6 +81,8 @@ class volume_maker: if self.mask: # TODO: check if mask is int-binary 0-1 and adjust if necessary + a,b,c,d,e,f = self.data.attrs['cropping of seg data'] + im = im[a:b,c:d,e:f] mask = self.data[self.mask_name].sel(timestep = ts).data im = im*mask diff --git a/04_npy_to_openvdb_in_blender_combined.py b/04_npy_to_openvdb_in_blender_combined.py index b0e2b8d..a6794c1 100644 --- a/04_npy_to_openvdb_in_blender_combined.py +++ b/04_npy_to_openvdb_in_blender_combined.py @@ -14,9 +14,9 @@ import numpy as np import pyopenvdb as openvdb -toppath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/5/membrane_npy' -toppath2 = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/5/crack_npy' -topoutpath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/5/combined_vdb' +toppath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/5II/membrane_npy' +toppath2 = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/5II/crack_npy' +topoutpath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/5II/combined_vdb' if not os.path.exists(topoutpath): os.mkdir(topoutpath)