Paper

paper/paper.bib

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+@online{unzueta_gamma,
+    author = {Ayllon Unzueta, Mauricio},
+    title = {{\tt NASA-gamma}},
+    year = {2021},
+    url = {https://github.com/mauricioAyllon/NASA-gamma/},
+    urldate = {2021-10-12}
+}
+
+@online{sandia_interspec,
+    author = {{Sandia National Laboratories}},
+    title = {{\tt InterSpec v1.0.8}},
+    year = {2021},
+    url = {https://github.com/sandialabs/InterSpec/},
+    urldate = {2021-10-12}
+}
+
+@online{morrell_curie,
+    author = {Morrell, Jonathan},
+    title = {{\tt curie}},
+    year = {2021},
+    url = {https://github.com/jtmorrell/curie},
+    urldate = {2021-10-12}
+}
+
+@techreport{xcom,
+    author = {Berger,M.J. and Hubbell,J.H. and Seltzer,S.M. and Chang,J. and Coursey,J.S. and Sukumar,R. and Zucker,D.S. and Olsen,K.},
+    title = {XCOM: Photon Cross Sections Database},
+    institution = {NIST Standard Reference Database 8},
+    year = {2010},
+    doi = {10.18434/T48G6X},
+}
+
+@online{nndc,
+    author = {{National Nuclear Data Center}},
+    title = {{NuDat} 2},
+    year = 2021,
+    url = {https://www.nndc.bnl.gov/nudat2/help/index.jsp},
+    urldate = {2021-03-04}
+}
+
+@article{vavrek2020reconstructing,
+  title={Reconstructing the Position and Intensity of Multiple Gamma-Ray Point Sources with a Sparse Parametric Algorithm},
+  author={Vavrek, Jayson R and Hellfeld, Daniel and Bandstra, Mark S and Negut, Victor and Meehan, Kathryn and Vanderlip, William Joe and Cates, Joshua W and Pavlovsky, Ryan and Quiter, Brian J and Cooper, Reynold J and others},
+  journal={IEEE Transactions on Nuclear Science},
+  volume={67},
+  number={11},
+  pages={2421--2430},
+  year={2020},
+  publisher={IEEE}
+}
+
+@article{bandstra2020modeling,
+  title={Modeling Aerial Gamma-Ray Backgrounds using Non-negative Matrix Factorization},
+  author={Bandstra, MS and Joshi, THY and Bilton, KJ and Zoglauer, A and Quiter, BJ},
+  journal={IEEE Transactions on Nuclear Science},
+  volume={67},
+  number={5},
+  pages={777--790},
+  year={2020},
+  publisher={IEEE}
+}
+
+@article{salathe2021determining,
+  title={Determining urban material activities with a vehicle-based multi-sensor system},
+  author={Salathe, M and Quiter, BJ and Bandstra, MS and Curtis, JC and Meyer, R and Chow, CH},
+  journal={Physical Review Research},
+  volume={3},
+  number={2},
+  pages={023070},
+  year={2021},
+  publisher={APS}
+}
+
+@inproceedings{lamb2021cylindrical,
+  title={{CAMIS: A Cylindrical Active Mask Imaging System}},
+  author={Lamb, C and Hanks, J and Hellfeld, D and Ellin, J and Marshall, M and Cooper, R and Quiter, B and Vetter, K},
+  year={2021},
+  booktitle={{2021 IEEE Nuclear Science Symposium and Medical Imaging Conference}},
+}
+
+@online{radwatch,
+  title={{Berkeley RadWatch}},
+  url={https://radwatch.berkeley.edu/},
+  urldate = {2022-05-31}
+}

paper/paper.md

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+---
+title: "Becquerel: a Python package for analyzing nuclear spectroscopic measurements"
+tags:
+  - Python
+  - nuclear engineering
+  - spectroscopy
+  - calibration
+  - peak fitting
+  - nuclear data
+authors:
+  - name: Jayson R. Vavrek^[corresponding author]
+    affiliation: 1
+  - name: Mark S. Bandstra
+    affiliation: 1
+  - name: Brian Plimley
+    affiliation: 1
+  - name: Joseph C. Curtis
+    affiliation: 1
+  - name: Marco Salathe
+    affiliation: 1
+  - name: Chun Ho Chow
+    affiliation: 1
+  - name: Micah Folsom
+    affiliation: 1
+  - name: Tenzing H.Y. Joshi
+    affiliation: 1
+  - name: Daniel Hellfeld
+    affiliation: 1
+  - name: J. Ali Hanks
+    affiliation: 2
+affiliations:
+  - name: Applied Nuclear Physics group, Lawrence Berkeley National Laboratory
+    index: 1
+  - name: Department of Nuclear Engineering, University of California, Berkeley
+    index: 2
+date: 04 Mar 2021
+bibliography: paper.bib
+---
+
+# Summary
+
+Nuclear spectroscopic analysis follows a typical workflow: collect binmode or listmode spectra of radiation detections, apply a calibration from detector observables to energy deposition, fit spectral peaks to determine the number of counts detected above background, and then relate changes in net counts to measurement parameters. While there are several open-source general scientific computing packages such as `ROOT` and `numpy` suitable for handling spectroscopic data, no dedicated solution exists for both managing and analyzing spectroscopic measurements, forcing students and researchers to develop their own codes independently (e.g., [@unzueta_gamma], [@sandia_interspec], [@morrell_curie]).
+
+`becquerel` is a Python package for analyzing nuclear spectroscopic measurements that seeks to prevent this wide duplication of efforts. It provides open-source standard analysis tools, including peak finding and fitting, automated energy calibrations, spectrum rebinning, and file I/O across several widely-used formats in nuclear spectroscopy. Built atop the Python scientific stack of `numpy`, `scipy`, `pandas`, and `numba`, `becquerel` is fast, flexible, and easy to use given even an introductory knowledge of Python. In addition, `becquerel` provides a comprehensive test suite, coverage metrics, and several example notebooks for quickly getting started with various analyses. Finally, it also provides a convenient Python interface to the NIST XCOM [@xcom] and NNDC [@nndc] nuclear databases, eliminating the need for ad-hoc downloads or manual data entry.
+
+`becquerel` was developed to be useable by a wide range of nuclear scientists and engineers, from undergraduates in laboratory courses to academic and national laboratory researchers. It has already been used to facilitate analyses in several works, including [@vavrek2020reconstructing], [@bandstra2020modeling], [@salathe2021determining], [@lamb2021cylindrical], and the Berkeley RadWatch project [@radwatch], and will facilitate the rapid development of future spectroscopic analyses and workflows.
+
+# Acknowledgements
+
+We acknowledge funding support from the U.S. Department of Energy and Department of Defense, and licensing support from Berkeley Lab's Intellectual Property Office.
+
+# References