|Icon| `diffpy.pdfmorph <https://diffpy.github.io/diffpy.pdfmorph>`_
====================================================================
.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
:target: https://diffpy.github.io/diffpy.pdfmorph
:height: 100px
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Tools for manipulating and comparing PDF profiles
PDFmorph is a Python software package designed to increase the insight
researchers can obtain from measured atomic pair distribution functions
(PDFs) in a model-independent way. The program was designed to help a
researcher answer the question: "Has my material undergone a phase
transition between these two measurements?"
One approach is to compare the two PDFs in a plot and view the difference
curve underneath. However, significant signal can be seen in the
difference curve from benign effects such as thermal expansion (peak
shifts) and increased thermal motion (peak broadening) or a change in
scale due to differences in incident flux, for example. PDFmorph will
do its best to correct for these benign effects before computing and
plotting the difference curve. One measured PDF (typically that collected
at higher temperature) is identified as the target PDF and the second
PDF is then morphed by "stretching" (changing the r-axis to simulate a
uniform lattice expansion), "smearing" (broadening peaks through a
uniform convolution to simulate increased thermal motion), and "scaling"
(self-explanatory). PDFmorph will vary the amplitude of the morphing
transformations to obtain the best fit between the morphed and the target
PDFs, then plot them on top of each other with the difference plotted
below.
There are also a few other morphing transformations in the program.
Finally, we note that PDFmorph should work on other spectra that are not
PDFs, though it has not been extensively tested beyond the PDF.
For more information about the diffpy.pdfmorph library, please consult our `online documentation <https://diffpy.github.io/diffpy.pdfmorph>`_.
Citation
--------
If you use diffpy.pdfmorph in a scientific publication, we would like you to cite this package as
diffpy.pdfmorph Package, https://github.com/diffpy/diffpy.pdfmorph
REQUIREMENTS
------------------------------------------------------------------------
PDFmorph is currently run from the command line, which requires opening
and typing into a terminal window or Windows command prompt. It is
recommended that you consult online resources and become somewhat
familiar before using PDFmorph.
PDFmorph can be run with Python 3.10 or higher. It makes use of several third party
libraries that you'll need to run the app and its components.
* `NumPy` - library for scientific computing with Python
* `matplotlib` - Python 2D plotting library
* `SciPy` - library for highly technical Python computing
* `diffpy.utils` - `shared helper utilities <https://github.com/diffpy/diffpy.utils/>`_ for wx GUI
These dependencies will be installed automatically if you use the conda
installation procedure described below.
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.pdfmorph_env`` ::
conda create -n diffpy.pdfmorph_env python=3
conda activate diffpy.pdfmorph_env
Then, to fully install ``diffpy.pdfmorph`` in our active environment, run ::
conda install diffpy.pdfmorph
Another option is to use ``pip`` to download and install the latest release from
`Python Package Index <https://pypi.python.org>`_.
To install using ``pip`` into your ``diffpy.pdfmorph_env`` environment, we will also have to install dependencies ::
pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdfmorph/main/requirements/run.txt
and then install the package ::
pip install diffpy.pdfmorph
If you prefer to install from sources, after installing the dependencies, obtain the source archive from
`GitHub <https://github.com/diffpy/diffpy.pdfmorph/>`_. Once installed, ``cd`` into your ``diffpy.pdfmorph`` directory
and run the following ::
pip install .
USING PDFmorph
------------------------------------------------------------------------
For detailed instructions and full tutorial, consult the user manual
on our `website <www.diffpy.org/diffpy.pdfmorph/>`.
Once the required software, including PDFmorph is all installed, open
up a terminal and check installation has worked properly by running ::
source activate pdfmorph_env #if the environment isn't already active
pdfmorph -h #get some helpful information
pdfmorph --version
If installed correctly, this last command should return the version
of PDFmorph that you have installed on your system. To begin using
PDFmorph, run a command like ::
pdfmorph <target PDF file> <morphed PDF file>
where both PDFs file are text files which contain PDF data, such as ``.gr``
or ``.cgr`` files that are produced by ``PDFgetX2``, ``PDFgetX3``,
or ``PDFgui``. Though some file extensions other than ``.gr`` or ``.cgr``,
but with the same content structure, have been shown to work with
PDFmorph, it is recommended to stick with ``.gr`` files.
Enjoy!
Support and Contribute
----------------------
`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.pdfmorph. Please join the diffpy.pdfmorph users community by joining the Google group. The diffpy.pdfmorph project welcomes your expertise and enthusiasm!
If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.pdfmorph/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfmorph/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
Feel free to fork the project and contribute. To install diffpy.pdfmorph
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 contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdfmorph/blob/main/CODE_OF_CONDUCT.rst>`_.
Contact
-------
For more information on diffpy.pdfmorph please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.
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"description": "|Icon| `diffpy.pdfmorph <https://diffpy.github.io/diffpy.pdfmorph>`_\n====================================================================\n\n.. |Icon| image:: https://avatars.githubusercontent.com/diffpy\n :target: https://diffpy.github.io/diffpy.pdfmorph\n :height: 100px\n\n|PyPi| |Forge| |PythonVersion| |PR|\n\n|CI| |Codecov| |Black| |Tracking|\n\n.. |Black| image:: https://img.shields.io/badge/code_style-black-black\n :target: https://github.com/psf/black\n\n.. |CI| image:: https://github.com/diffpy/diffpy.pdfmorph/actions/workflows/main.yml/badge.svg\n :target: https://github.com/diffpy/diffpy.pdfmorph/actions/workflows/main.yml\n\n.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.pdfmorph/branch/main/graph/badge.svg\n :target: https://codecov.io/gh/diffpy/diffpy.pdfmorph\n\n.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.pdfmorph\n :target: https://anaconda.org/conda-forge/diffpy.pdfmorph\n\n.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff\n\n.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.pdfmorph\n :target: https://pypi.org/project/diffpy.pdfmorph/\n\n.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.pdfmorph\n :target: https://pypi.org/project/diffpy.pdfmorph/\n\n.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue\n :target: https://github.com/diffpy/diffpy.pdfmorph/issues\n\nTools for manipulating and comparing PDF profiles\n\nPDFmorph is a Python software package designed to increase the insight\nresearchers can obtain from measured atomic pair distribution functions\n(PDFs) in a model-independent way. The program was designed to help a\nresearcher answer the question: \"Has my material undergone a phase\ntransition between these two measurements?\"\n\nOne approach is to compare the two PDFs in a plot and view the difference\ncurve underneath. However, significant signal can be seen in the\ndifference curve from benign effects such as thermal expansion (peak\nshifts) and increased thermal motion (peak broadening) or a change in\nscale due to differences in incident flux, for example. PDFmorph will\ndo its best to correct for these benign effects before computing and\nplotting the difference curve. One measured PDF (typically that collected\nat higher temperature) is identified as the target PDF and the second\nPDF is then morphed by \"stretching\" (changing the r-axis to simulate a\nuniform lattice expansion), \"smearing\" (broadening peaks through a\nuniform convolution to simulate increased thermal motion), and \"scaling\"\n(self-explanatory). 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It makes use of several third party\nlibraries that you'll need to run the app and its components.\n\n* `NumPy` - library for scientific computing with Python\n* `matplotlib` - Python 2D plotting library\n* `SciPy` - library for highly technical Python computing\n* `diffpy.utils` - `shared helper utilities <https://github.com/diffpy/diffpy.utils/>`_ for wx GUI\n\nThese dependencies will be installed automatically if you use the conda\ninstallation procedure described below.\n\nInstallation\n------------\n\nThe preferred method is to use `Miniconda Python\n<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_\nand install from the \"conda-forge\" channel of Conda packages.\n\nTo add \"conda-forge\" to the conda channels, run the following in a terminal. ::\n\n conda config --add channels conda-forge\n\nWe want to install our packages in a suitable conda environment.\nThe following creates and activates a new environment named ``diffpy.pdfmorph_env`` ::\n\n conda create -n diffpy.pdfmorph_env python=3\n conda activate diffpy.pdfmorph_env\n\nThen, to fully install ``diffpy.pdfmorph`` in our active environment, run ::\n\n conda install diffpy.pdfmorph\n\nAnother option is to use ``pip`` to download and install the latest release from\n`Python Package Index <https://pypi.python.org>`_.\nTo install using ``pip`` into your ``diffpy.pdfmorph_env`` environment, we will also have to install dependencies ::\n\n pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdfmorph/main/requirements/run.txt\n\nand then install the package ::\n\n pip install diffpy.pdfmorph\n\nIf you prefer to install from sources, after installing the dependencies, obtain the source archive from\n`GitHub <https://github.com/diffpy/diffpy.pdfmorph/>`_. 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