def get_semseg_axon_model():
try:
from elektronn3.models.base import InferenceModel
except Exception as e: # ImportError as e:
log_main.error(
"elektronn3 could not be imported ({}). Please see 'https://github."
"com/ELEKTRONN/elektronn3' for more information.".format(e))
path = global_params.config.mpath_axonsem
m = InferenceModel(path)
m._path = path
return m
def get_tripletnet_model_large_e3():
"""Those networks are typically trained with `naive_view_normalization_new` """
try:
from elektronn3.models.base import InferenceModel
except Exception as e: # ImportError as e:
log_main.error(
"elektronn3 could not be imported ({}). Please see 'https://github."
"com/ELEKTRONN/elektronn3' for more information.".format(e))
m_path = global_params.config.mpath_tnet_large
m = InferenceModel(m_path)
return m
def get_celltype_model_large_e3():
"""Those networks are typically trained with `naive_view_normalization_new`
Unlike the other e3 InferenceModel instances, here the view normalization
is applied in the downstream inference method (`predict_sso_celltype`)
because the celltype model also gets scalar values as input which should
not be normalized."""
try:
from elektronn3.models.base import InferenceModel
except Exception as e: # ImportError as e:
log_main.error(
"elektronn3 could not be imported ({}). Please see 'https://github."
"com/ELEKTRONN/elektronn3' for more information.".format(e))
path = global_params.config.mpath_celltype_large_e3
m = InferenceModel(path)
return m
def get_glia_model_e3():
"""Those networks are typically trained with `naive_view_normalization_new` """
from elektronn3.models.base import InferenceModel
path = global_params.config.mpath_glia_e3
m = InferenceModel(path, normalize_func=naive_view_normalization_new)
return m
'location.')
# set working directory to obtain models
global_params.wd = path_to_workingdir
model_p = args.modelpath
if model_p is None:
m = get_semseg_axon_model()
else:
try:
from elektronn3.models.base import InferenceModel
except ImportError as e:
msg = "elektronn3 could not be imported ({}). Please see 'https://github." \
"com/ELEKTRONN/elektronn3' for more information.".format(e)
raise ImportError(msg)
m = InferenceModel(model_p)
m._path = model_p
# get model for compartment detection
view_props = global_params.view_properties_semsegax
view_props["verbose"] = True
# load SSO instance from k.zip file
sso = init_sso_from_kzip(cell_kzip_fn, sso_id=1)
# run prediction and store result in new kzip
cell_kzip_fn_axon = cell_kzip_fn[:-6] + '_axon.k.zip'
semseg_of_sso_nocache(sso,
dest_path=cell_kzip_fn_axon,
model=m,
**view_props)