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"description": "# bfit\n\n![](\"https://img.shields.io/pypi/v/bfit?label=PyPI%20Version\"/)
\n![](\"https://img.shields.io/pypi/format/bfit?label=PyPI%20Format\"/)
\n![](\"https://img.shields.io/github/languages/code-size/dfujim/bfit\"/)
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\n![](\"https://img.shields.io/pypi/l/bfit\"/)
\n[](https://doi.org/10.21105/joss.03598)\n\n![](\"https://img.shields.io/github/commits-since/dfujim/bfit/latest/master\"/)
\n![](\"https://img.shields.io/github/last-commit/dfujim/bfit\"/)
\n\n[bfit] is a [Python] application aimed to aid in the analysis of \u03b2-detected\nnuclear magnetic/quadrupole resonance (\u03b2-NMR and \u03b2-NQR) data taken at [TRIUMF].\nThese techniques are similar to muon spin rotation ([\u03bcSR]) and \"conventional\"\nnuclear magnetic resonance ([NMR]), but use radioactive nuclei as their [NMR]\nprobe in place of the [muon] or a stable isotope.\nThe instruments and research program are governed through [TRIUMF]'s [CMMS],\nwith more information given at .\nAn overview of instrumentation details and scientific applications of the\n\u03b2-NMR/\u03b2-NQR techniques can be found in several recent journal articles:\n\n- W. A. MacFarlane.\n Implanted-ion \u03b2NMR: a new probe for nanoscience.\n \n Solid State Nucl. Magn. Reson. 68-69, 1-12 (2015).\n- G. D. Morris.\n \u03b2-NMR.\n \n Hyperfine Interact. 225, 173-182 (2014).\n\nThe intended user of [bfit] is anyone performing experiments with or analyzing\ndata taken from [TRIUMF]'s \u03b2-NMR or \u03b2-NQR spectrometers - independent of whether\nthey are a new student, visiting scientist, or someone with decades of experience.\n(e.g., someone from the \"local\" [TRIUMF]/[CMMS]/[UBC] group).\nA key goal of the project is to alleviate much of the technical tedium that is\noften encountered during any analysis.\nMore generally, [bfit] has been written to fulfill the following needs:\n\n* Provide the means for quick on-line analyses during beam time.\n* Provide a useful and flexible API for refined analyses in [Python],\n to be used in conjunction with [bdata] and the [SciPy] ecosystem.\n* Provide an intuitive, user-friendly interface for non-programmers.\n* Be easily maintainable and distributable.\n\n## Citing\n\nIf you use [bfit] in your work, please cite:\n\nD. Fujimoto, \"bfit: A Python Application For Beta-Detected NMR,\" [J. Open Source Softw. 6, 3598 (2021).](https://doi.org/10.21105/joss.03598)\n\n## Useful Links\n\n* [bfit]\n * [Wiki]\n * [API Reference]\n * [API Tutorial]\n * [GUI Tutorial]\n* [mudpy]\n* [bdata]\n\n## Community Guidelines\n\n* Contributing:\n * Please submit your contribution to [bfit] through the list of\n [Pull Requests]!\n* Reporting issues and/or seeking support:\n * Please file a new ticket in [bfit]'s list of [Issues] - I will get an email\n notification of your problem and try to fix it ASAP!\n\n## Installation and Use\n\n### Dependencies\n\nThe following packages/applications are needed _prior_ to [bfit] installation:\n- [Python] 3.6 or higher: a dynamically typed programming language. [[install](https://wiki.python.org/moin/BeginnersGuide/Download)]\n- [Tkinter] : [Python]'s de facto standard GUI package. [[install](https://tkdocs.com/tutorial/install.html)]\n\n### Install Instructions\n\n| | Command |\n|:-- | :--|\nFrom the [PyPI] as user (recommended) | `pip install --user bfit` |\nFrom the [PyPI] as root | `pip install bfit` |\nFrom source | `python3 setup.py install` |\n\nNote that `pip` should point to a (version 3) [Python] executable\n(e.g., `python3`, `python3.8`, etc.).\nIf the above does not work, try using `pip3` or `python3 -m pip` instead.\n\n### Optional Setup\n\nFor convenience,\nyou may want to tell [bfit] where the data is stored on your machine.\nThis is done by defining two environment variables:\n`BNMR_ARCHIVE` and `BNQR_ARCHIVE`.\nThis can be done, for example, in your `.bashrc` script.\nBoth variables expect the data to be stored in directories with a particular\nheirarchy:\n\n```\n/path/\n|---bnmr/\n|---bnqr/\n|-------2017/\n|-------2018/\n|-----------045123.msr\n```\n\nHere, the folders `/path/bnmr/` and `/path/bnqr/` both contain runs\n(i.e., `.msr` files) organized into subdirectories by year of aquasition.\nIn this case, you would set (in your `.bashrc`):\n\n```bash\nexport BNMR_ARCHIVE=/path/bnmr/\nexport BNQR_ARCHIVE=/path/bnqr/\n```\n\nIf [bfit] cannot find the data, it will attempt to download the relavent [MUD]\n(i.e., `.msr`) files from .\nThis is the default behaviour for [bfit] installed from [PyPI].\n\n### First Startup \n\nTo launch the GUI from a terminal simply call `bfit`, if this fails, one can also use the alternative syntax `python3 -m bfit`, where `python3` may be replaced with any (version 3) [Python] executable.\n\n### Testing\n\nTesting your installation of [bfit] is accomplished by running `pytest` within the installation folder. Note that some tests, particularly those involving drawing, fail when run as group in this environment, but they should pass on a subsequent attempts: `pytest --lf`. Further testing information can be found [here](https://github.com/dfujim/bfit/wiki/Installation-and-first-startup).\n\n[Python]: https://www.python.org/\n[SciPy]: https://www.scipy.org/\n[Cython]: https://cython.org/\n[NumPy]: https://numpy.org/\n[pandas]: https://pandas.pydata.org/\n[Matplotlib]: https://matplotlib.org/\n[Tkinter]: https://wiki.python.org/moin/TkInter\n[PyYAML]: https://pyyaml.org/\n[pytest]: https://docs.pytest.org/en/6.2.x/\n[tqdm]: https://github.com/tqdm/tqdm\n[requests]: https://requests.readthedocs.io/en/master/\n[Jupyter]: https://jupyter.org/\n[argparse]: https://docs.python.org/3/library/argparse.html\n\n[YAML]: https://yaml.org/\n[C]: https://en.wikipedia.org/wiki/C_(programming_language)\n[HTTP]: https://en.wikipedia.org/wiki/Hypertext_Transfer_Protocol\n\n[TRIUMF]: https://www.triumf.ca/\n[CMMS]: https://cmms.triumf.ca\n[MUD]: https://cmms.triumf.ca/mud/\n[archive]: https://cmms.triumf.ca/mud/runSel.html\n[`data/BNMR/2020/040123.msr`]: https://cmms.triumf.ca/mud/mud_hdrs.php?ray=Run%2040123%20from%20BNMR%20in%202020&cmd=heads&fn=data/BNMR/2020/040123.msr\n\n[PHYSICA]: https://computing.triumf.ca/legacy/physica/\n[UBC]: https://www.ubc.ca/\n[\u03bcSR]: https://en.wikipedia.org/wiki/Muon_spin_spectroscopy\n[NMR]: https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance\n[muon]: https://en.wikipedia.org/wiki/Muon\n\n[bnmr_1f]: https://gitlab.com/rmlm/bnmr_1f\n[bnmr_2e]: https://gitlab.com/rmlm/bnmr_2e\n[bnmrfit]: https://gitlab.com/rmlm/bnmrfit\n[bnmroffice]: https://github.com/hsaadaoui/bnmroffice\n[musrfit]: https://bitbucket.org/muonspin/musrfit\n[musrfit documentation]: https://lmu.web.psi.ch/musrfit/user/html/index.html\n\n[mudpy]: https://github.com/dfujim/mudpy\n[bdata]: https://github.com/dfujim/bdata\n\n[bfit]: https://github.com/dfujim/bfit\n[Pull Requests]: https://github.com/dfujim/bfit/pulls\n[Issues]: https://github.com/dfujim/bfit/issues\n[PyPI]: https://pypi.org/project/bfit/\n[API Reference]: https://github.com/dfujim/bfit/wiki/API-Reference\n[API Tutorial]: https://github.com/dfujim/bfit/wiki/API-Tutorial\n[GUI Tutorial]: https://github.com/dfujim/bfit/wiki/GUI-Tutorial\n[Wiki]: https://github.com/dfujim/bfit/wiki\n\n[ROOT]: https://github.com/root-project/root\n[MINUIT]: https://doi.org/10.1016/0010-4655(75)90039-9\n[MINUIT2]: https://root.cern/doc/master/Minuit2Page.html\n[iminuit]: https://github.com/scikit-hep/iminuit",
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