LEC-5422-Public/Tomcat-Blender
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This commit is contained in:
fische_r
2024-01-24 10:47:06 +01:00
parent 47481a47b3
commit 95b0c242f1
1 changed files with 5 additions and 7 deletions
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12
03_nc_to_npy_for_openvdb.py
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@@ -74,7 +74,6 @@ class volume_maker:
with cp.cuda.Device(gpu_id):
im = cp.array(im)
print(im.shape)
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)
@@ -87,12 +86,13 @@ class volume_maker:
return im
def xarray_to_npy(self, im, ts, i=0, GPU = True, GPU_avail=GPU_avail, overwrite=False):
def xarray_to_npy(self, imdata, ts, i=0, GPU = True, GPU_avail=GPU_avail, overwrite=False):
outpath = os.path.join(self.topoutfolder, self.array_name+'_phase_'+str(self.ph)+'_ts_'+f'{ts:04d}'+'.npy')
if not os.path.exists(outpath) and not overwrite:
# im = im.data
im = imdata.sel(timestep=ts).data
if self.mask:
# TODO: check if mask is int-binary 0-1 and adjust if necessary
@@ -122,10 +122,8 @@ class volume_maker:
im = im+1
if not self.ph<0:
print(type(im), type(self.ph))
im = im == self.ph
print(im.shape)
im = self.clean_binary_image(im, i=i, clean = self.clean , remove_small=self.remove_small, minsize = self.minsize, fp_radius = self.footprint); print(im.shape)
im = self.clean_binary_image(im, i=i, clean = self.clean , remove_small=self.remove_small, minsize = self.minsize, fp_radius = self.footprint)
@@ -149,8 +147,8 @@ class volume_maker:
timesteps = imdata.timestep.data
length = len(timesteps)
Parallel(n_jobs=n_jobs, temp_folder=temp_folder)(delayed(self.xarray_to_npy)(imdata.sel(timestep=timesteps[i]).data, timesteps[i], i) for i in range(length))
Parallel(n_jobs=n_jobs, temp_folder=temp_folder)(delayed(self.xarray_to_npy)(imdata, timesteps[i], i) for i in range(length))
# .sel(timestep=timesteps[i]).data
else:
print('processing time step ',str(self.ts))
self.xarray_to_npy(imdata.sel(timestep=self.ts).data, self.ts)