als_microct-recon

Description

Jupyter notebooks to reconstruct and visualize microCT data from ALS beamline 8.3.2

Getting Started

On NERSC, no setup or installation is required. Just log into https://jupyter.nersc.gov/ and use "microCT" nodes, then follow the instructions in "README_to_get_notebooks.txt" (if you don't see microCT-specific nodes, make sure the beamline scientist adds you to the NERSC microCT group).

Installing on local machine

• Install git (eg. https://git-scm.com/downloads) and python/conda (eg. https://docs.conda.io/en/latest/miniconda.html)

• Clone repo

git clone git@github.com:perlmutter/battery_microct.git

• Create environment

cd als_microct-recon
conda env create -f environment.yml

if conda cannot solve environment, check that channel priority is flexible

conda config --get channel_priority
conda config --set channel_priority flexible

• Create kernel

conda activate als832
ipython kernel install --user --name=als832

• You should now be able to run launch Jupyter lab and run ALS_recon.ipynb with the als832 kernel

jupyter lab

Authors

David Perlmutter (dperl@lbl.gov) Lipi Gupta (lipigupta@lbl.gov) Dula Parkinson (dyparkinson@lbl.gov)

License

This project is licensed under the [NAME HERE] License - see the LICENSE.md file for details

Acknowledgments