def ct_of_ssv(self, ssv_id):
"""
Returns the CT for a given SSV ID.
:param sv_id:
:return:
"""
# TODO: changed to new cell type predictions, work this in everywhere
ssv = self.ssd.get_super_segmentation_object(int(ssv_id))
ssv.nb_cpus = self.nb_cpus
ssv.load_attr_dict()
label = ""
if "celltype_cnn_e3_probas" in ssv.attr_dict: # new prediction
l = ssv.attr_dict["celltype_cnn_e3"]
# ct_label_dc = {0: "EA", 1: "MSN", 2: "GP", 3: "INT"}
# label = ct_label_dc[l]
label = int2str_converter(l, gt_type='ctgt_v2')
certainty = ssv.certainty_celltype()
elif "celltype_cnn" in ssv.attr_dict:
ct_label_dc = {0: "EA", 1: "MSN", 2: "GP", 3: "INT"}
l = ssv.attr_dict["celltype_cnn"]
label = ct_label_dc[l]
certainty = 'nan'
else:
log_gate.warning("Celltype prediction not present in attribute "
"dict of SSV {} at {}.".format(ssv_id, ssv.attr_dict_path))
return {'ct': label, 'certainty': certainty}
def ssv_skeleton(self, ssv_id):
"""
Get mesh vertices for ssv_id.
:param ssv_id: int
:return: dict
"""
self.logger.info('Loading ssv skeleton {}'.format(ssv_id))
ssv = self.ssd.get_super_segmentation_object(int(ssv_id))
ssv.nb_cpus = self.nb_cpus
ssv.load_skeleton()
skeleton = ssv.skeleton
if skeleton is None:
return {}
skel_attr = ["nodes", "edges", "diameters"]
pred_key_ax = "{}_avg{}".format(global_params.view_properties_semsegax['semseg_key'],
global_params.DIST_AXONESS_AVERAGING)
keys = [
# "axoness_avg{}".format(avg_dst),
# "axoness_avg{}_comp_maj".format(avg_dst),
global_params.view_properties_semsegax['semseg_key'],
pred_key_ax,
'myelin_avg10000', # TODO: use global_params.py value !
'myelin', # TODO: use global_params.py value !
"axoness_k{}".format(global_params.map_properties_semsegax['k']),
"axoness_k{}_comp_maj".format(global_params.map_properties_semsegax['k'])]
for k in keys:
if k in skeleton:
skel_attr.append(k)
if type(skeleton[k]) is list:
skeleton[k] = np.array(skeleton[k])
else:
log_gate.warning("Couldn't find requested key in "
"skeleton '{}'. Existing keys: {}".format(k, skeleton.keys()))
return {k: skeleton[k].flatten().tolist() for k in
skel_attr}