rheed-viz

Database, dimensionality reduction, and visualization dashboard for RHEED data

How it works

Environment Setup

To setup the environment, run conda env update --file env.cpu.yml, which will create a conda environment called rheed-viz

Next setup the default local database, responding to the commands as follows (blank means hit enter):

molarcli install local

Where do you want to install Molar 🦷 (./molar_data_dir):
Password for Postgres admin: rheed
Server url (http://localhost):
Allow the backend to send email? [y/n]: n
Backend port (8000):
Number of workers for the backend (2):
Full name: default
Email: default@rheed.com
Password: rheed
Do you want to start it now? [y/n]: y

If you get a permissions error on linux, you can change the user group of docker using the following command: sudo usermod -G docker your_username; su - your_username

Start the RHEED database

python database-setup/dbsetup.py

Launching app

Streamlit frontend uses requirements.txt Run locally with streamlit run app.py

RHEED jpg data

• Pre-processed, dimensionality reduced images are in ./data/ saved as npz files. They can be loaded as shown in Rheed-viz.ipynb
• Process AVI movies by installing ffmpeg and doing ffmpeg -i MovieName.avi -vf fps=<num_fps> c01_%04d.jpg -hide_banner
• Raw jpgs: https://figshare.com/s/73b8ab6cb131acbbe9d4

References

[1] Fabius, Otto, and Joost R. Van Amersfoort. "Variational recurrent auto-encoders." arXiv preprint arXiv:1412.6581 (2014).

[2] Gliebe, Kimberly, and Alp Sehirlioglu. "Distinct thin film growth characteristics determined through comparative dimension reduction techniques." Journal of Applied Physics 130.12 (2021): 125301.

[3] Zheng Ren, & Ilija Zeljkovic. (2021). FeSe/SrTiO3(001) RHEED movie [Data set]. Zenodo. https://doi.org/10.5281/zenodo.4725825