def _cache_neuron(self, neuron_actors, neuron_name, params):
"""
Save a loaded neuron
:param neuron_actors: list of neuron's actors
:param neuron_name: name of the neuron
"""
if not neuron_name or neuron_name is None: return
# Create/update entry in metadata
self.cache_metadata[neuron_name] = params
save_json(self.morphology_cache_metadata,
self.cache_metadata,
append=True)
self.cache_metadata = load_json(self.morphology_cache_metadata)
for neurite, actor in neuron_actors.items():
if actor is None: continue
fl = os.path.join(self.morphology_cache,
neuron_name + "_" + neurite + ".vtk")
if isinstance(actor, list):
if not actor: continue
else:
raise ValueError(
"Something went wrong while saving the actor")
actor.write(fl)
def __init__(self, base_dir=None, **kwargs):
"""
Parses a YAML file to get data folders paths. Stores paths to a number of folders used throughtout brainrender.
Other classes (e.g. brainrender.Scene) subclass Paths.
:param base_dir: str with path to directory to use to save data. If none the user's base directiry is used.
:param kwargs: use the name of a folder as key and a path as argument to specify the path of individual subfolders
"""
# Get and make base directory
if base_dir is None:
user_dir = os.path.expanduser("~")
if not os.path.isdir(user_dir):
raise FileExistsError(
"Could not find user base folder (to save brainrender data). Platform: {}"
.format(sys.platform))
self.base_dir = os.path.join(user_dir, ".brainrender")
else:
self.base_dir = base_dir
if not os.path.isdir(self.base_dir):
os.mkdir(self.base_dir)
for fld_name in self._folders:
# Check if user provided a path for this folder, otherwise use default
fld_path = kwargs.pop(fld_name, default_paths[fld_name])
# Make complete path and save it as an attribute of this class
path = os.path.join(self.base_dir, fld_path)
# Create folder if it doesn't exist
if not os.path.isdir(path):
print("Creating folder at: {}".format(path))
os.makedirs(path)
self.__setattr__(fld_name, path)
# Make a file for morphology cache metadata
self.morphology_cache_metadata = os.path.join(self.morphology_cache,
'metadata.json')
if not os.path.isfile(self.morphology_cache_metadata):
save_json(self.morphology_cache_metadata, {})