diff --git a/particlespy/particle_analysis.py b/particlespy/particle_analysis.py index 2010289..16a10b8 100644 --- a/particlespy/particle_analysis.py +++ b/particlespy/particle_analysis.py @@ -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 @@ -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 @@ -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'] @@ -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'] diff --git a/particlespy/segptcls.py b/particlespy/segptcls.py index b4c9d44..d0d941c 100644 --- a/particlespy/segptcls.py +++ b/particlespy/segptcls.py @@ -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"])