Python package for running NMF analysis on PDF and XRD data.
This package takes a directory containing diffraction files in .gr (or .xy/.xye) format and performs an NMF decomposition of the components with the goal of determining the number of structural phases present, and when these phases are present if the data provided comes from a time series. Any non .gr ( or .xy/.xye) files or .dat files in the directory will be ignored and skipped in the calculation.
This package is the backend logic for pdfitc.org/NMF. Please consider utilizing pdfitc.org/NMF prior to this tool, if possible. If your NMF analysis requires some feature from this CLI that isn't present on the website, please let us know and we will consider adding the feature to the pdfitc.org interface.
For more information about the diffpy.nmf_mapping library, please consult our online documentation.
If you use this program for a scientific research that leads to publication, we ask that you acknowledge use of the program by citing the following paper in your publication:
Z. A. Thatcher, C.-H. Liu, L. Yang, B. C. McBride, G. Thinh Tran, A. Wustrow, M. A. Karlsen, J. R. Neilson, D. B. Ravnsbæk, and S. J. L. Billinge, nmfMapping: a cloud-based web application for non-negative matrix factorization of powder diffraction and pair distribution function datasets, Acta Crystallogr. A 78, 242-248 (2022).
and please consider citing
C.-H. Liu, C. J. Wright, R. Gu, S. Bandi, A. Wustrow, P. K. Todd, D. O'Nolan, M. L. Beauvais, J. R. Neilson, P. J. Chupas, K. W. Chapman, and S. J. L. Billinge, Validation of non-negative matrix factorization for rapid assessment of large sets of atomic pair distribution function data, J. Appl. Cryst. 54, 768-775 (2022).
The preferred method is to use Miniconda Python and install from the "conda-forge" channel of Conda packages.
To add "conda-forge" to the conda channels, run the following in a terminal.
conda config --add channels conda-forge
We want to install our packages in a suitable conda environment.
The following creates and activates a new environment named diffpy.nmf_mapping_env
conda create -n diffpy.nmf_mapping_env diffpy.nmf_mapping conda activate diffpy.nmf_mapping_env
To confirm that the installation was successful, type
python -c "import diffpy.nmf_mapping; print(diffpy.nmf_mapping.__version__)"
The output should print the latest version displayed on the badges above.
If the above does not work, you can use pip to download and install the latest release from
Python Package Index.
To install using pip into your diffpy.nmf_mapping_env environment, type
pip install diffpy.nmf_mapping
If you prefer to install from sources, after installing the dependencies, obtain the source archive from
GitHub. Once installed, cd into your diffpy.nmf_mapping directory
and run the following
pip install .
You may consult our online documentation for tutorials and API references.
Diffpy user group is the discussion forum for general questions and discussions about the use of diffpy.nmf_mapping. Please join the diffpy.nmf_mapping users community by joining the Google group. The diffpy.nmf_mapping project welcomes your expertise and enthusiasm!
If you see a bug or want to request a feature, please report it as an issue and/or submit a fix as a PR. You can also post it to the Diffpy user group.
Feel free to fork the project and contribute. To install diffpy.nmf_mapping in a development mode, with its sources being directly used by Python rather than copied to a package directory, use the following in the root directory
pip install -e .
To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit hooks.
- Install pre-commit in your working environment by running
conda install pre-commit. - Initialize pre-commit (one time only)
pre-commit install.
Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before trying to commit again.
Improvements and fixes are always appreciated.
Before contributing, please read our Code of Conduct.
For more information on diffpy.nmf_mapping please visit the project web-page or email Prof. Simon Billinge at [email protected].