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by default do not overwerite (hard coded)

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fische_r
2024-01-23 16:45:38 +01:00
parent 85b0e370e6
commit da385232a6
1 changed files with 31 additions and 28 deletions
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59
03_nc_to_npy_for_openvdb.py
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@@ -78,42 +78,45 @@ class volume_maker:
return im
def xarray_to_npy(self, im, ts, i=0, GPU = True, GPU_avail=GPU_avail):
def xarray_to_npy(self, im, ts, i=0, GPU = True, GPU_avail=GPU_avail, overwrite=False):
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
if GPU and GPU_avail:
gpu_id = i%5 #num_GPU #use gpus 1 through 4, leaving the big A40 (0) alone or i%5 to use all 5
outpath = os.path.join(self.topoutfolder, self.array_name+'_phase_'+str(self.ph)+'_ts_'+f'{ts:04d}'+'.npy')
with cp.cuda.Device(gpu_id):
mask = cp.array(mask)
mask = cucim.skimage.morphology.binary_dilation(mask, footprint=cucim.skimage.morphology.ball(self.mask_dilate))
mask = cp.asnumpy(mask)
mempool = cp.get_default_memory_pool()
mempool.free_all_blocks()
if os.path.exists(outpath) and not overwrite:
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
else:
mask = ndimage.binary_dilation(mask, structure=ball(self.mask_dilate))
if GPU and GPU_avail:
gpu_id = i%5 #num_GPU #use gpus 1 through 4, leaving the big A40 (0) alone or i%5 to use all 5
# manual shift because membrane =0
im = im -1
with cp.cuda.Device(gpu_id):
mask = cp.array(mask)
mask = cucim.skimage.morphology.binary_dilation(mask, footprint=cucim.skimage.morphology.ball(self.mask_dilate))
mask = cp.asnumpy(mask)
mempool = cp.get_default_memory_pool()
mempool.free_all_blocks()
else:
mask = ndimage.binary_dilation(mask, structure=ball(self.mask_dilate))
# manual shift because membrane =0
im = im -1
im = im*mask
# reshift
im = im+1
im = im*mask
# reshift
im = im+1
if not self.ph<0:
im = im == self.ph
im = self.clean_binary_image(im, i=i, clean = self.clean , remove_small=self.remove_small, minsize = self.minsize, fp_radius = self.footprint)
if not self.ph<0:
im = im == self.ph
im = self.clean_binary_image(im, i=i, clean = self.clean , remove_small=self.remove_small, minsize = self.minsize, fp_radius = self.footprint)
outpath = os.path.join(self.topoutfolder, self.array_name+'_phase_'+str(self.ph)+'_ts_'+f'{ts:04d}'+'.npy')
np.save(outpath, im)
def nc_to_set_of_npy(self):