LEC-5422-Public/Tomcat-Blender
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

post process erosion

Browse Source
This commit is contained in:
fische_r
2024-01-25 10:07:21 +01:00
parent bf03c1f44f
commit 5330989f93
1 changed files with 4 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
03_nc_to_npy_for_openvdb.py
View File

@@ -77,6 +77,7 @@ class volume_maker:
self.mask = args.mask
self.mask_name = args.mask_name
self.mask_dilate = args.mask_dilate
self.erode = args.erode
def clean_binary_image(self, im, clean = True, remove_small=True, minsize = 20, fp_radius = 1, i=0, GPU = True, GPU_avail=GPU_avail):
@@ -88,6 +89,7 @@ class volume_maker:
im = cp.array(im)
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)
if self.erode >0: im = cucim.skimage.morphology.binary_erosion(im, footprint=cucim.skimage.morphology.ball(self.erode))
im = cp.asnumpy(im)
mempool = cp.get_default_memory_pool()
mempool.free_all_blocks()
@@ -95,6 +97,7 @@ class volume_maker:
else:
if clean: im = ndimage.binary_opening(im, structure=ball(fp_radius))
if remove_small: im = morphology.remove_small_objects(im, min_size=minsize)
if self.erode >0: im = ndimage.binary_erosion(im, structure=ball(self.erode))
return im
@@ -181,6 +184,7 @@ if __name__ == '__main__':
parser.add_argument('-mk', '--mask', type = str2bool, default = False, help='wheter to use the mask in the segmented data (if available)')
parser.add_argument('-mn', '--mask_name', type = str, default = '', help='name of the mask in the segmented data (if available)')
parser.add_argument('-md', '--mask_dilate', type = int, default = 8, help='dilation radius of mask')
parser.add_argument('-er', '--erode', type = int, default = 0, help='erosion radius')
args = parser.parse_args()