diffractem
Pre-processing and data management for serial electron diffraction data.
Science Score: 23.0%
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✓DOI references
Found 2 DOI reference(s) in README -
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2 of 9 committers (22.2%) from academic institutions -
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Low similarity (13.3%) to scientific vocabulary
Keywords
Repository
Pre-processing and data management for serial electron diffraction data.
Basic Info
Statistics
- Stars: 16
- Watchers: 4
- Forks: 8
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
diffractem
Pre-processing software for serial electron diffraction (SerialED) data. See https://doi.org/10.1101/682575 for example results.
Diffractem is intended for usage within Jupyter notebooks - get a set of examples here: https://github.com/robertbuecker/serialed-examples.
Installation
diffractem is tailored to pre-processing SerialED data primarily for crystallographic analysis using CrystFEL, version 0.10.0 or higher: https://www.desy.de/~twhite/crystfel/index.html.
To make most of diffractem's functionality, if you do not have it already, please download and install CrystFEL following the installation instructions given on its homepage.
During the build process of CrystFEL using meson, the pinkIndexer component will automatically be downloaded and installed.
Create conda enivronment
We strongly suggest to use the Anaconda3 Python distribution/package manager, and create a dedicated environment within it for diffractem.
If you do not have Anaconda installed, it is sufficient to obtain the minimal Miniconda of the conda package manager at https://docs.conda.io/en/latest/miniconda.
Once installed, please create a new anaconda environment for diffractem, and activate it:
conda create -n diffractem -c conda-forge python=3.10 numpy scipy pandas dask distributed jupyterlab ipywidgets ipympl tifffile h5py
conda activate diffractem
Install diffractem
Finally install diffractem itself, either from PyPi:
pip install diffractem
or, if you want to play/develop a bit more and stay up-to-date, you can clone this git repository and install diffractem in developer mode:
git clone https://github.com/robertbuecker/diffractem
cd diffractem
pip install -e .
Now you should be ready to go! To get started, why don't you download the example notebooks:
git clone https://github.com/robertbuecker/serialed-examples
And get example raw data at MPDL Edmond: https://edmond.mpdl.mpg.de/imeji/collection/32lI6YJ7DZaF5L_K.
And when you're ready to go: just make your own branches of the notebooks for your own projects, and have fun!
diffractem, (C) 2019-2022 Robert Bücker, robert.buecker@rigaku.com
peakfinder8, (C) 2014-2019 Deutsches Elektronen-Synchrotron DESY
Owner
- Name: Robert Bücker
- Login: robertbuecker
- Kind: user
- Location: Frankfurt
- Company: Rigaku Europe SE
- Website: https://orcid.org/0000-0001-7654-4707
- Twitter: antonietrebor
- Repositories: 11
- Profile: https://github.com/robertbuecker
GitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Robert Bücker | r****r@m****e | 200 |
| Robert Buecker | b****r@c****e | 143 |
| Robert Buecker | r****r@c****e | 46 |
| Robert Bücker | r****r | 3 |
| Robert McLeod | r****d@h****m | 2 |
| robertbuecker | r****e@m****e | 1 |
| Robert Buecker | b****r@m****e | 1 |
| Robert Buecker | b****r@m****e | 1 |
| Robert Bücker | r****r@r****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 19 days
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 2.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- robbmcleod (1)
Top Labels
Issue Labels
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Packages
- Total packages: 1
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Total downloads:
- pypi 67 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 17
- Total maintainers: 1
pypi.org: diffractem
Some tools for working with serial electron microscopy data.
- Homepage: https://github.com/robertbuecker/diffractem
- Documentation: https://diffractem.readthedocs.io/
- License: GNU Lesser General Public License v2 or later (LGPLv2+)
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Latest release: 0.4.1
published about 4 years ago
Rankings
Maintainers (1)
Dependencies
- PyQt5 *
- astropy *
- dask *
- distributed *
- h5py *
- hdf5plugin *
- ipykernel *
- jupyter-sphinx *
- m2r2 *
- matplotlib *
- nbsphinx *
- nbsphinx-link *
- numba *
- opencv-python-headless *
- pandas *
- pyqtgraph *
- pyyaml *
- scikit-image *
- scikit-learn *
- scipy *
- sphinx-autodoc-typehints *
- tables *
- tifffile *
- Cython *
- PyQt5 *
- PyYAML *
- astropy *
- dask *
- distributed *
- h5py *
- hdf5plugin *
- ipython *
- ipywidgets *
- matplotlib *
- numba *
- numpy *
- pandas *
- pyqtgraph *
- recommonmark *
- scikit_image *
- scikit_learn *
- scipy *
- setuptools *
- skimage *
- tifffile *
- tqdm *
- dask *
- h5py *
- hdf5plugin *
- numpy *
- pandas *