diff --git a/03_nc_to_npy_for_openvdb.py b/03_nc_to_npy_for_openvdb.py index c858fe7..8d3e730 100644 --- a/03_nc_to_npy_for_openvdb.py +++ b/03_nc_to_npy_for_openvdb.py @@ -66,6 +66,8 @@ class volume_maker: with cp.cuda.Device(gpu_id): im = cp.array(im) + print(im.shape) + print(clean, remove_small) if clean: im = cucim.skimage.morphology.binary_opening(im, footprint=cucim.skimage.morphology.ball(fp_radius)) if remove_small: im = cucim.skimage.morphology.remove_small_objects(im, min_size=minsize) im = cp.asnumpy(im) @@ -73,7 +75,7 @@ class volume_maker: mempool.free_all_blocks() else: - print(clean, remove_small) + print(str(clean), str(remove_small)) if clean: im = ndimage.binary_opening(im, structure=ball(fp_radius)) if remove_small: im = morphology.remove_small_objects(im, min_size=minsize) diff --git a/04_npy_to_openvdb_in_blender.py b/04_npy_to_openvdb_in_blender.py index c6a42cd..c835829 100644 --- a/04_npy_to_openvdb_in_blender.py +++ b/04_npy_to_openvdb_in_blender.py @@ -14,8 +14,9 @@ import numpy as np import pyopenvdb as openvdb -toppath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/4/all_phases_npy' -topoutpath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/4/combined_vdb' +toppath = '/mnt/SSD/fische_r/blender_visualization/4/nc_to_npy_per_ts/phase_0' +# topoutpath = '/mnt/SSD/fische_r/blender_visualization/4/nc_to_npy_per_ts/phase_vdb/' +topoutpath = toppath+'_vdb' if not os.path.exists(topoutpath): os.mkdir(topoutpath) @@ -48,11 +49,12 @@ def check_npy_folder(toppath): def convert_npy_to_vdb(file,toppath, topoutpath, x1,x2,y1,y2,z1,z2): im = np.load(os.path.join(toppath,file)) imc = im[x1:x2,y1:y2,z1:z2] - # im = im*1.0 - im1 = imc == 0 - im2 = imc == 2 - imc = im1*1.0 + im2*2.0 + # im1 = imc == 0 + # im2 = imc == 2 + + # imc = im1*1.0 + im2*2.0 + imc = im*1.0 grid = openvdb.FloatGrid() grid.copyFromArray(imc.astype(float))