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Update segptcls.py to make clear_borders optional #88

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Update segptcls.py to make clear_borders optional #88

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ec12ba1
Update segptcls.py to make clear_borders optional
TomSlater May 20, 2026
a7242ce
Update particle_analysis.py to add clear_borders to parameters object
TomSlater May 20, 2026
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5 changes: 4 additions & 1 deletion particlespy/particle_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -302,7 +302,7 @@ class parameters(object):

def generate(self,threshold='otsu',watershed=False,watershed_size=0,
watershed_erosion=0,invert=False,min_size=0,store_im=False,
pad=5,rb_kernel=0,gaussian=0,local_size=1):
pad=5,rb_kernel=0,gaussian=0,local_size=1,clear_borders=True):
self.segment = {}
self.segment['threshold'] = threshold
self.segment['watershed'] = watershed
Expand All @@ -313,6 +313,7 @@ def generate(self,threshold='otsu',watershed=False,watershed_size=0,
self.segment['rb_kernel'] = rb_kernel
self.segment['gaussian'] = gaussian
self.segment['local_size'] = local_size
self.segment['clear_borders'] = clear_borders

self.store = {}
self.store['store_im'] = store_im
Expand Down Expand Up @@ -346,6 +347,7 @@ def save(self,filename=os.path.dirname(inspect.getfile(process))+'/parameters/pa
segment.attrs["rb_kernel"] = self.segment['rb_kernel']
segment.attrs["gaussian"] = self.segment['gaussian']
segment.attrs["local_size"] = self.segment['local_size']
segment.attrs["clear_borders"] = self.segment['clear_borders']
store.attrs['store_im'] = self.store['store_im']
store.attrs['pad'] = self.store['pad']
store.attrs['store_maps'] = self.store['store_maps']
Expand Down Expand Up @@ -376,6 +378,7 @@ def load(self,filename=os.path.dirname(inspect.getfile(process))+'/parameters/pa
self.segment['rb_kernel'] = segment.attrs["rb_kernel"]
self.segment['gaussian'] = segment.attrs["gaussian"]
self.segment['local_size'] = segment.attrs["local_size"]
self.segment['clear_borders'] = segment.attrs["clear_borders"]
self.store['store_im'] = store.attrs['store_im']
self.store['pad'] = store.attrs['pad']
self.store['store_maps'] = store.attrs['store_maps']
Expand Down
3 changes: 2 additions & 1 deletion particlespy/segptcls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,8 @@ def process(im, param):
if param.segment["watershed"]!=False:
labels = p_watershed(labels,param.segment["watershed_size"],param.segment["watershed_erosion"])

labels = clear_border(labels)
if params.segment["clear_border"]!=False:
labels = clear_border(labels)

if param.segment["min_size"]!=0:
labels = remove_small_objects(labels,param.segment["min_size"])
Expand Down
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