The following installation steps assumes that Anaconda is installed. AxoID was only tested on Ubuntu.
First, download the repository:
git clone https://github.com/NeLy-EPFL/AxoID
cd AxoID
Then, create an environment with Python 3.6:
conda create -n axoid python=3.6
where axoid will be the name of the conda environment (you can choose any name).
Then, you have to enter this environment (you will have to enter it each time you want to use AxoID) with
source activate axoid
or the name you have given it (in order to quit the environment, you can use conda deactivate). The command line should have (axoid) at the beginning when you are in the environment.
If you intend to use the Jupyter Notebooks, you need to install jupyter:
conda install jupyter
Finally, you can install the axoid package and its dependencies with (be sure to be in the AxoID/ folder)
pip install -e .
Optic flow warping: If you intend to let AxoID call the optic flow warping, you will need the motion_compensation repository. Follow the instructions there to install it.
Once it is installed and working, you will need to edit the paths in motion_compensation_path.py to the motion_compensation script, and MATLAB release.
Without this, AxoID will not be able to warp the data, and it is the user's responsability to do so beforehand.
Inside the new conda environment just created, the axoid package should have been installed and therefore can be imported in Python (using import axoid).
Additionally, two new commands were added to run easily AxoID and its GUI:
axoid /path/to/experiment [--option VALUE]
to run the main pipeline on the experiment, and
axoid-gui /path/to/experiment [--option VALUE]
to run the user correction GUI on the experiment, after it was processed by AxoID.
For more information, see Running AxoID