pyRS

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Data reduction workflow

The workflow is as follows. The word "script" is used to denote a distict step in processing the data rather than actual script.

1. Start with a nexus file. As in, /HFIR/HB2B/IPTS-22731/nexus/HB2B_439.nxs.h5
2. This is read in by something that will split into sub-scans and create a project file [script 1 - currently convert_nexus_to_hidra.py]
3. This is read in by something that will create powder patterns and add them to the project file [script 2 - currently reduce_HB2B.py]
4. This is read in by the gui to do the peak fitting and add the results to the project file [script 3 - currently somewhere in the gui]

5. This is read in by the gui and used to create the summary .csv file [script 4 - currently being written]

   Some other things to note

   • scripts 1-2 will be refactored/combined to create a new reduce_HB2B.py that can be run by autoreduction
   • scripts 2-4 (more like functionality 2-4) will all live in the gui in some way
   • going back any number of steps will delete the following steps from the project file. This is to prevent users from having a project file with powder patterns that are not associated with the peak fitting from the project file.

Developer Quick Start

If you've never used PyRS before, you can get started quickly by doing the following.

1. Install basic dependencies: Conda, Python, and PyQt. Conda installation requires linux.
2. Create a new Conda environment with additional dependencies:

Installation using an anaconda environment

Anaconda environments are only supported on OSx (x86) and Linux using python 3.10

1. Configure anaconda environment:

.. code-block::

conda install -c conda-forge mamba

.. code-block::

mamba env create --name pyrs --file environment.yml

2. Activate the conda environment

.. code-block::

conda activate pyrs

3. From the PyRS directory, run the setup script in developer mode

.. code-block::

python setup.py build

4. From the PyRS directory, start the user interface

.. code-block::

PYTHONPATH=$PWD:$PYTHONPATH python scripts/pyrsplot

Running and developing PyRS

To start main window from analysis machine

.. code-block::

PYTHONPATH=$PWD:$PYTHONPATH python scripts/pyrsplot

To develop

To run all of the tests

.. code-block::

python -m pytest

Running specific tests can be done through standard ways https://docs.pytest.org/en/stable/usage.html`_. For example

.. code-block::

python -m pytest tests/unit

will only run the unit tests

Related packages

• Mantid <https://github.com/mantidproject/mantid>_ - The Mantid project provides a framework that supports high-performance computing and visualisation of scientific data.
• Steca2 <https://gitlab-public.fz-juelich.de/mlz/steca/-/tree/main>_ - The stress and texture calculator used by the Heinz Maier-Leibnitz Zentrum Garching facility.

Contributing to pyRS

If you want to suggest changes of a feature or the inclusion of new features, you can either 1) fork the repository to work on it and create an issue to discuss it before proceeding with a pull request, or 2) create an issue with your suggestion for others to discuss and potentially work on it.

Reporting bugs or asking for help

Please report any bugs or ask for help by creating a new issue.

Funding

This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.