Metadata-Version: 2.4
Name: diffpy.labpdfproc
Version: 0.3.1rc4
Summary: Tools for processing x-ray powder diffraction data from laboratory sources.
Author-email: Yucong Chen <yc4372@columbia.edu>, Till Schertenleib <ts@chem.ku.dk>, Caden Myers <cjm2304@columbia.edu>, Simon Billinge <sbillinge@ucsb.edu>
Maintainer-email: Simon Billinge <sbillinge@ucsb.edu>
Project-URL: Homepage, https://github.com/diffpy/diffpy.labpdfproc/
Project-URL: Issues, https://github.com/diffpy/diffpy.labpdfproc/issues/
Keywords: powder XRD,absorption correction,PDF,diffpy
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: <3.15,>=3.10
Description-Content-Type: text/x-rst
License-File: LICENSE.rst
License-File: AUTHORS.rst
Requires-Dist: numpy
Requires-Dist: diffpy.utils
Requires-Dist: pandas
Requires-Dist: scipy
Requires-Dist: gooey
Dynamic: license-file

|Icon| |title|_
===============

.. |title| replace:: diffpy.labpdfproc
.. _title: https://diffpy.github.io/diffpy.labpdfproc

.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
        :target: https://diffpy.github.io/diffpy.labpdfproc
        :height: 100px

|PyPI| |Forge| |PythonVersion| |PR|

|CI| |Codecov| |Black| |Tracking|

.. |Black| image:: https://img.shields.io/badge/code_style-black-black
        :target: https://github.com/psf/black

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        :target: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov-on-merge-to-main.yml

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        :target: https://codecov.io/gh/diffpy/diffpy.labpdfproc

.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.labpdfproc
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        :target: https://pypi.org/project/diffpy.labpdfproc/

.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.labpdfproc
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Tools for processing x-ray powder diffraction data from laboratory sources.

PDFgetX3 has revolutionized how PDF methods can be applied to solve nanostructure problems.
However, the program was designed for use with Rapid Acquisition PDF (RAPDF) data from synchrotron sources.
A key approximation inherent in the use of PDFgetX3 for RAPDF data is that absorption effects are negligible.
This is typically not the case for laboratory x-ray diffractometers, where absorption effects can be significant.

This app is designed to preprocess data from laboratory x-ray diffractometers before using PDFgetX3 to obtain PDFs.
The app currently carries out an absorption correction assuming a parallel beam capillary geometry
which is the most common geometry for lab PDF measurements.

The theory is described in the following paper:

        Chen, Y., Schertenleib, T., Yang, A., Schouwink, P., Queen, W. L., and Billinge, S. J. L.,
        *Absorption Correction for Reliable Pair Distribution Functions from Low Energy X-ray Sources*.
        Crystal Growth & Design, 2026, 26 (3), 1036–1047.
        https://doi.org/10.1021/acs.cgd.5c00551


The related experimental data acquisition protocols are described in the following paper:

        Schertenleib, T., Schmuckler, D., Chen, Y., Jin, G. B., Queen, W. L., and Billinge, S. J. L. (2025).
        *Testing Protocols for Obtaining Reliable Pair Distribution Functions from Laboratory X-Ray Sources Using PDFgetX3*.
        Chem. Methods, 2500001.
        https://doi.org/10.1002/cmtd.202500001


For more information about the diffpy.labpdfproc library, please consult our `online documentation <https://diffpy.github.io/diffpy.labpdfproc>`_.

Citation
--------

If you use diffpy.labpdfproc in a scientific publication, we would like you to cite this package as

        Chen, Y., Schertenleib, T., Yang, A., Schouwink, P., Queen, W. L., and Billinge, S. J. L.,
        *Absorption Correction for Reliable Pair Distribution Functions from Low Energy X-ray Sources*.
        Crystal Growth & Design, 2026, 26 (3), 1036–1047.
        https://doi.org/10.1021/acs.cgd.5c00551

Installation
------------

The preferred method is to use `Miniconda Python
<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
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.labpdfproc_env`` ::

        conda create -n diffpy.labpdfproc_env diffpy.labpdfproc
        conda activate diffpy.labpdfproc_env

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 <https://pypi.python.org>`_.
To install using ``pip`` into your ``diffpy.labpdfproc_env`` environment, type ::

        pip install diffpy.labpdfproc

If you prefer to install from sources, after installing the dependencies, obtain the source archive from
`GitHub <https://github.com/diffpy/diffpy.labpdfproc/>`_. Once installed, ``cd`` into your ``diffpy.labpdfproc`` directory
and run the following ::

        pip install .

This package also provides command-line utilities. To check the software has been installed correctly, type ::

        labpdfproc --version

You can also type the following command to verify the installation. ::

        python -c "import diffpy.labpdfproc; print(diffpy.labpdfproc.__version__)"


To view the basic usage and available commands, type ::

        labpdfproc -h

Getting Started
---------------

You may consult our `online documentation <https://diffpy.github.io/diffpy.labpdfproc>`_ for tutorials and API references.

Support and Contribute
----------------------

If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.labpdfproc/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.labpdfproc/pulls>`_.

Feel free to fork the project and contribute. To install diffpy.labpdfproc
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.

1. Install pre-commit in your working environment by running ``conda install pre-commit``.

2. 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 <https://github.com/diffpy/diffpy.labpdfproc/blob/main/CODE-OF-CONDUCT.rst>`_.

Contact
-------

For more information on diffpy.labpdfproc please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu)``.

Acknowledgements
----------------

``diffpy.labpdfproc`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
