Note
Click here to download the full example code
Pickling#
This tutorial shows how to use Python's pickle module to quickly store and load neurons.
All neuron types including whole NeuronLists can be "pickled" 
. If you don't know what that is: pickling is storing the actual Python object as a bytes stream. This is incredibly fast and works very well for short-term storage but has a few downsides:
- Pickle files can only be re-opened in Python
- The pickled object is (sort of) specific to your current Python enviroment. If you e.g. update Python, NAVis or even just
numpyorpandasyou may not be able to open the file again. - Pickle files can contain arbitrary Python code. Never open a pickle file from an untrusted source!
With that out of the way, pickling is incredibly easy:
import navis
import pickle
# Load some example neurons
nl = navis.example_neurons(3, kind='mesh')
# Pickle neurons to file
with open('/Users/philipps/Downloads//meshes.pkl', 'wb') as f:
pickle.dump(nl, f)
To "unpickle", i.e. read the file back into Python:
# Read neurons back from pickle file
with open('/Users/philipps/Downloads//meshes.pkl', 'rb') as f:
nl = pickle.load(f)
This tutorial has hopefully given you some entry points on how to load your data. See also the I/O API reference.
Total running time of the script: ( 0 minutes 0.000 seconds)
Download Python source code: tutorial_io_04_pickle.py