Jupyter notebooks to reconstruct and visualize microCT data from ALS beamline 8.3.2
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).
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Install git (eg. https://git-scm.com/downloads) and python/conda (eg. https://docs.conda.io/en/latest/miniconda.html)
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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
David Perlmutter (dperl@lbl.gov) Lipi Gupta (lipigupta@lbl.gov) Dula Parkinson (dyparkinson@lbl.gov)
als microct recon (microct) Copyright (c) 2022, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.