Hep-dog/mantid_total_scattering

Implementing total neutron scattering data reduction using the Mantid Framework

Health	Main Release (w/ Mantid Framework)	Dev Release (w/o Mantid Framework)

Total Scattering Data Reduction using Mantid Framework

This project is trying to implement total scattering data reduction for neutron time-of-flight diffractometers using the algorithms currently available in the Mantid framework

This entails taking raw neutron counts from detectors in the diffraction experiment and turning them into the reciprocal-space structure factor patterns, F(Q) or S(Q), and applying a Fourier Transform to real-space to give the pair distribution fuction, PDF.

This is the future backend for the ADDIE project and hopes to support multiple diffractometers performing total scattering measurements.

Structure factor S(Q) -> Pair Distribution Function G(r)

Installation

Pre-requiste: Installing conda

The following commands can get you setup (on Linux machine) to get conda installed (as miniconda):

CONDA_PYTHON=3
MINICONDA_URL="https://repo.continuum.io/miniconda";
MINICONDA_FILE="Miniconda${CONDA_PYTHON}-latest-Linux-x86_64.sh";
wget "${MINICONDA_URL}/${MINICONDA_FILE}";
bash ${MINICONDA_FILE} -b -p $HOME/miniconda;
export PATH="$HOME/miniconda/bin:$PATH";

NOTE: You can change the python version number via the CONDA_PYTHON variable

You will have to excute the last command on every new bash session (export PATH...). Adding this last line to your ~/.bashrc will automatically add it on every bash session startup.

Mantid Framework Included

Anaconda (Recommended)

Setup (w/ pure conda)

Add channels with dependencies, create a conda environment with python_version set to either 2.7.14 or 3.6, and activate the environment

conda config --add channels conda-forge --add channels mantid --add channels mantid/label/nightly
conda create -n mantidts_env python=${python_version}
source activate mantidts_env

Setup (w/ conda + mamba)

NOTE: Mamba is still in "beta".

python_version=3.6
conda config --add channels conda-forge --add channels mantid --add channels mantid/label/nightly
conda install mamba -c conda-forge
mamba update mamba -c conda-forge
mamba create -n mantidts_env python=${python_version}
source activate mantidts_env

Simply replace conda -> mamba in "Install" instruction commands

Install (or Update)

conda install -c neutrons mantid-total-scattering

Go here for how to delete an environment or use:

conda remove --name mantidts_env --all

Notes

If you have an error (see below for example) related to the libGL library, you may not have it installed for the Mantid Framework to work. See instructions here for installing the necessary libraries for different OS

Example error: ImportError: First import of "._api" failed with "libGL.so.1: cannot open shared object file...

If you have an error that another version of Mantid is installed on the machine and being imported via PYTHONPATH, you can use the following as a workaround for CLI tool:

PYTHONPATH="" mantidtotalscattering

Usage (CLI reduction tool)

To launch the total scattering script, complete the input JSON file (found in examples directory), and run:

mantidtotalscattering examples/sns/nomad_simple.json

If you need to specify the path to Mantid build, use:

MANTIDPATH=/path/to/mantid/build/bin PATH=$MANTIDPATH:$PATH PYTHONPATH=$MANTIDPATH:$PATH mantidtotalscattering <json input>

Mantid Framework Not Included (for development)

This is mainly for development if you want to use a local development build of Mantid Framework instead of one included.

PyPI (Recommended)

Install

pip install mantid-total-scattering

Anaconda

Setup

Add channels with dependencies, create a conda environment with python_version set to either 2.7 or 3.6, and activate the environment

conda config --add channels conda-forge
conda create -n mantidts_env python=${python_version}
conda activate mantidts_env

Install

conda install -c neutrons mantid-total-scattering-python-wrapper

Development

Clone the repository to a local directory

git clone https://github.com/neutrons/mantid_total_scattering.git
cd mantid_total_scattering

Tests

To build and run the tests via pytest, use:

/path/to/mantid/build/bin/mantidpython setup.py test

To build and run tests via Docker, use:

docker build -t unit-test-env -f .ci/Dockerfile.nightly_ubuntu16.04_python3 . && docker run -t unit-test-env /bin/bash -c "mantidpython -m pytest"

Tagging a New Version

Mantid Total Scattering uses versioneer. These are the instructions to create a new version, working on a local clone

git branch --track main origin/main  #  create a local main branch set to follow remote main
git checkout main
git fetch -p -t  # fetch all changes from the remote repo
git rebase -v origin/main  # sync with remote main branch
git merge --ff-only origin/next  # merge in all of the changes in branch next
git tag v.0.2.13  # create the tag in the format that versioneer has been configured
git push --tags origin main  # push the tag to remote to kick off the deploy step