JOSS - XRTpy (#205)

* Creating a folder for JOSS realted topics. * Adding title and tags * Adding authors and affiliations * Adding a bib for references * Adding Summary and testing references in text. * Adding the statement of need * Adding xrtpy_effective_area_plot.pdf * Adding xrtpy_temperature_from_filter_ratio_plot.pdf * Adding xrtpy_temperature_response_plot.pdf * Adding Statement of Need * Testing methods for adding pdf images and referencing correctly * Adding and reference two other images and thier info * Adding Acknowledgements * Adding more to Statement of need * Small edits * Adding references to the coronal abundances * Put sentences on single lines * Adding Landi:2002 * Adding Feldman:1992 * Adding references * Adding references * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Updating abundance info * Adding articles referecnes * Adding references * Adding Development section * Fixing linkings * suggestion made by namurphy * suggestion made by namurphy * suggestion made by namurphy * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Minor edits * Minor edits * rearrange in alphabetical order * small change to affiliation name The official name of the CfA has an & between Harvard and Smithsonian, not a - * Small rewording Rewording of the sentence that begins "In fostering collaboration..." * Adding Will T. Barnes * Minor edit * Adding reference links * Minor edit * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> * Update joss/paper.md Co-authored-by: Nick Murphy <[email protected]> --------- Co-authored-by: Nick Murphy <[email protected]> Co-authored-by: Jonathan Slavin <[email protected]>
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diff --git a/joss/paper.bib b/joss/paper.bib
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+@article{Asplund:2009,
+  title = {The Chemical Composition of the Sun},
+  author = {Asplund, Martin and Grevesse, Nicolas and Sauval, A. Jacques and Scott, Pat},
+  journal = {Annual Review of Astronomy and Astrophysics},
+  volume = {47},
+  pages = {481-522},
+  year = {2009},
+  doi = {10.1146/annurev.astro.46.060407.145222},
+  url = {https://doi.org/10.1146/annurev.astro.46.060407.145222},
+  note = {Volume publication date: 22 September 2009}
+}
+
+@ARTICLE{Fludra-and-Schmelz:1999,
+  author = {{Fludra}, A. and {Schmelz}, J.~T.},
+  title = "{The absolute coronal abundances of sulfur, calcium, and iron from
+Yohkoh-BCS flare spectra}",
+  journal = "{Astronomy \& Astrophysics}",
+  keywords = {SUN: ABUNDANCES, SUN: CORONA, SUN: FLARES, SUN: X-RAYS, GAMMA RAYS},
+  year = 1999,
+  month = aug,
+  volume = {348},
+  pages = {286-294},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/1999A&A...348..286F},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@article{Feldman:1992,
+  title = {The Potential for Plasma Diagnostics from Stellar Extreme-Ultraviolet Observations},
+  author = {Feldman, U. and Mandelbaum, P. and Seely, J.F. and Doschek, G.A. and Gursky, H.},
+  journal = {Astrophysical Journal Supplement Series},
+  volume = {81},
+  pages = {387},
+  year = {1992},
+  doi = {10.1086/191698}
+}
+
+@ARTICLE{Golub:2007,
+  author = {{Golub}, L. and {Deluca}, E. and {Austin}, G. and {Bookbinder}, J.
+and {Caldwell}, D. and {Cheimets}, P. and {Cirtain}, J. and {Cosmo}, M. and
+{Reid}, P. and {Sette}, A. and {Weber}, M. and {Sakao}, T. and {Kano}, R. and
+{Shibasaki}, K. and {Hara}, H. and {Tsuneta}, S. and {Kumagai}, K. and
+{Tamura}, T. and {Shimojo}, M. and {McCracken}, J. and {Carpenter}, J. and
+{Haight}, H. and {Siler}, R. and {Wright}, E. and {Tucker}, J. and {Rutledge},
+H. and {Barbera}, M. and {Peres}, G. and {Varisco}, S.},
+  title = "{The X-Ray Telescope (XRT) for the Hinode Mission}",
+  journal = "{Solar Physics}",
+  year = 2007,
+  volume = {243},
+  number = {1},
+  pages = {63-86},
+  doi = {10.1007/s11207-007-0182-1}
+}
+
+@ARTICLE{Grevesse:2007,
+  author = {{Grevesse}, N. and {Asplund}, M. and {Sauval}, A.~J.},
+  title = "{The Solar Chemical Composition}",
+  journal = {\ssr},
+  keywords = {Sun: abundances, photosphere, corona},
+  year = 2007,
+  month = jun,
+  volume = {130},
+  number = {1-4},
+  pages = {105-114},
+  doi = {10.1007/s11214-007-9173-7},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2007SSRv..130..105G},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Guidoni:2015,
+  author = {{Guidoni}, S. E. and McKenzie, D. E. and Longcope, D. W. and
+Plowman, J. E. and Yoshimura, K.},
+  title = "{Temperature and Electron Density Diagnostics of a
+Candle-flame-shaped Flare}",
+  journal = {\ssr},
+  keywords = {magnetic reconnection; shock waves; Sun: flares; Sun: UV radiation; Sun: X-rays; gamma rays},
+  year = 2015,
+  month = Feb,
+  volume = {800},
+  number = {54},
+  pages = {},
+  doi = {10.1007/s11214-007-9173-7},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJ...800...54G/},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Kosugi:2007,
+  author = {{Kosugi}, T. and {Matsuzaki}, K. and {Sakao}, T. and {Shimizu}, T.
+and {Sone}, Y. and {Tachikawa}, S. and {Hashimoto}, T. and {Minesugi}, K. and
+{Ohnishi}, A. and {Yamada}, T. and {Tsuneta}, S. and {Hara}, H. and
+{Ichimoto}, K. and {Suematsu}, Y. and {Shimojo}, M. and {Watanabe}, T. and
+{Shimada}, S. and {Davis}, J.~M. and {Hill}, L.~D. and {Owens}, J.~K. and
+{Title}, A.~M. and {Culhane}, J.~L. and {Harra}, L.~K. and {Doschek}, G.~A.
+and {Golub}, L.},
+  title = "{The Hinode (Solar-B) Mission: An Overview}",
+  journal = "{Solar Physics}",
+  year = 2007,
+  volume = {243},
+  number = {1},
+  pages = {3-17},
+  doi = {10.1007/s11207-007-9014-6}
+}
+
+@article{Landi:2002,
+  title = {CHIANTI—An Atomic Database for Emission Lines. V. Comparison with an Isothermal Spectrum Observed with SUMER},
+  author = {Landi, E. and Feldman, U. and Dere, K.P.},
+  journal = {Astrophysical Journal Letters},
+  volume = {139},
+  pages = {L281},
+  doi = {10.1086/337949},
+  year = {2002}
+}
+
+@ARTICLE{Narukage:2011,
+  author = { {Narukage}, N. and {Sakao}, T. and {Kano}, R. and {Hara}, H. and
+{Shimojo}, M. and {Bando}, T. and {Urayama}, F. and {DeLuca}, E. and {Golub},
+L. and {Weber}, M. and {Grigis}, P. and {Cirtain}, J. and {Tsuneta}, S.},
+  title = "{Coronal-Temperature-Diagnostic Capability of the Hinode/X-Ray
+Telescope Based on Self-Consistent Calibration}",
+  journal = "{Solar Physics}",
+  year = 2011,
+  volume = {269},
+  number = {1},
+  pages = {169-236},
+  doi = {10.1007/s11207-010-9685-2}
+}
+
+@ARTICLE{Narukage:2014,
+  author = { {Narukage}, N. and {Sakao}, T. and {Kano}, R. and {Shimojo}, M.
+and {Winebarger}, A. and {Weber}, M. and {Reeves}, K. },
+  title = "{ Coronal-Temperature-Diagnostic Capability of the Hinode/X-Ray
+Telescope Based on Self-consistent Calibration. II. Calibration with On-Orbit
+Data }",
+  journal = "{Solar Physics}",
+  year = 2014,
+  number = {3},
+  volume = {289},
+  pages = {1029-1042},
+  doi = {10.1007/s11207-013-0368-7}
+}
+
+@article{Schmelz:2012,
+  title = {Composition of the Solar Corona, Solar Wind, and Solar Energetic Particles},
+  author = {Schmelz, J. T. and Reames, D. V. and von Steiger, R. and Basu, S.},
+  journal = {The Astrophysical Journal},
+  volume = {755},
+  number = {1},
+  pages = {33},
+  year = {2012},
+  doi = {10.1088/0004-637X/755/1/33},
+  publisher = {The American Astronomical Society}
+}
+
+@article{Scott:2015,
+  title = {The Elemental Composition of the Sun II. The Iron Group Elements Sc to Ni},
+  author = {Scott, Pat and Asplund, Martin and Grevesse, Nicolas and Bergemann, Maria and Sauval, A. Jacques},
+  journal = {Astronomy & Astrophysics (A&A)},
+  volume = {573},
+  pages = {A26},
+  year = {2015},
+  doi = {10.1051/0004-6361/201424110},
+  number = {1},
+  section = {The Sun},
+  publisher = {EDP Sciences},
+  url = {https://www.aanda.org/articles/aa/abs/2015/01/aa24110-14/aa24110-14.html},
+  note = {Published online: 11 December 2014}
+}
diff --git a/joss/paper.md b/joss/paper.md
@@ -0,0 +1,117 @@
+---
+title: 'XRTpy : A Hinode-X-Ray Telescope Python Package'
+
+tags:
+  - Python
+  - Astronomy
+  - X-Ray Telescope
+  - Solar Physics
+  - Helio
+
+authors:
+  - name: Joy Velasquez
+    orcid: 0009-0005-4804-0946
+    equal-contrib: true
+    affiliation: "1"
+  - name: Nicholas A. Murphy
+    orcid: 0000-0001-6628-8033
+    affiliation: "1"
+    corresponding: true
+  - name: Katharine K. Reeves
+    orcid: 0000-0002-6903-6832
+    affiliation: "1"
+    equal-contrib: true
+  - name: Jonathan Slavin
+    orcid: 0000-0002-7597-6935
+    affiliation: "1"
+    corresponding: true
+  - name: Mark Weber
+    orcid: 0000-0001-7098-7064
+    affiliation: "1"
+    corresponding: true
+  - name: Will T. Barnes
+    orcid: 0000-0001-9642-6089
+    affiliation: "2,3"
+
+affiliations:
+ - name: Center for Astrophysics | Harvard-Smithsonian 60 Garden Street, Cambridge, MA, USA
+   index : 1
+ - name: American University, 4400 Massachusetts Avenue NW, Washington, DC 20016, USA
+   index : 2
+ - name : NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, MD 20771, USA
+   index : 3
+
+date: 15 December 2023
+bibliography: paper.bib
+---
+
+# Summary
+
+The XRTpy Python package is a specialized tool developed for the analysis of observations made by the X-Ray Telescope (XRT) [@Golub:2007] aboard the Hinode spacecraft [@Kosugi:2007].
+Hinode, a joint mission involving space agencies from Japan, the United States, Europe, and the United Kingdom, was launched with the primary aim of providing multi-wavelength data from the photosphere to the upper corona, enabling continuous observations of the Sun.
+Within this mission, the XRT instrument stands out as a remarkable piece of technology, capable of capturing high-resolution images of the solar corona's hottest material, spanning temperatures from 10<sup>6</sup> to 10<sup>7</sup> K.
+
+# Statement of need
+
+XRTpy is a Python package developed for the analysis of observations from the X-Ray Telescope (XRT) aboard the Hinode spacecraft.
+It offers a comprehensive range of functionalities, including object-oriented representation of instrument configuration, effective area calculations, temperature response computation, light leak subtraction, image sharpening, estimation of electron temperature, and emission measure derivation.
+These capabilities empower researchers to explore and analyze XRT data comprehensively, contributing to a deeper understanding of solar phenomena.
+
+The official analysis routines for Hinode are scripted in the Interactive Data Language (IDL).
+The SolarSoft XRT Analysis Guide serves as the official software and instrument guide for XRT data analysis.
+XRTpy has been carefully written to ensure the consistency and replication of results obtained from the official IDL routines as described in the SolarSoft XRT Analysis Guide.
+Although currently XRTpy does not have all the capabilities of the SolarSoft routines for XRT, the package is in continual development and more functionality will be added in the future.
+This alignment with established practices and standards aims to facilitate a seamless transition for researchers while harnessing the benefits of Python in solar data analysis.
+
+A shift towards Python is underway within both NASA and the wider scientific community.
+With XRTpy, Python users can efficiently analyze and process Hinode/XRT data, bridging the gap between traditional IDL routines and the increasing adoption of Python within the scientific community.
+This transition not only enhances accessibility but also supports the broader trend in the scientific community toward Python-based data analysis tools, thereby fostering a collaborative and efficient environment for solar researchers.
+
+
+# Package Structure
+
+XRTpy is equipped with a range of capabilities tailored for the comprehensive analysis of XRT observations.
+The package is structured into distinct modules, each serving a specific purpose:
+
+ - `xrtpy.response.channel`: This module defines the `Channel` class which offers access to the properties of XRT filters, including information on the CCD, Entrance Filter, Focus-Filter(s), Geometry, and Mirror(s).
+
+ - `xrtpy.response.effective_area`: XRTpy's capability to calculate effective areas for various XRT filter channels, combined with CCD contamination layer thickness information, is crucial for understanding instrumental spectral responses, as depicted in \autoref{fig:Figure 1}.
+
+ - `xrtpy.response.temperature_response`: XRTpy provides the capability of computing the temperature response of all the XRT filter channels. It does this by relying on a spectral emission model, drawing from [@Narukage:2011] and [@Narukage:2014]. Users can choose from a range of CHIANTI abundance sets, including the default model with coronal abundances, hybrid, and photospheric options. \autoref{fig:Figure 2} shows XRTpy's temperature response calculations for all XRT filters across the different CHIANTI  abundance sets.
+
+ - `xrtpy.response.temperature_from_filter_ratio`: This module contains the `temperature_from_filter_ratio` function, which derives temperature and emission measure maps for a pair of images using the filter ratio method. \autoref{fig:Figure 3} illustrates an example usage of this function.
+
+ - `xrtpy.image_correction.deconvolve`: Deconvolution is a powerful technique for improving image sharpness. The `deconvolve` function applies deconvolution to XRT images, effectively reducing blurring effects caused by the telescope's point spread function.
+
+ - `xrtpy.image_correction.remove_lightleak.py`: The `remove_lightleak` function in this module eliminates light leak (visible stray light) from XRT synoptic composite images. This results in cleaner and more precise images suitable for in-depth analysis.
+
+XRTpy supports multiple elemental abundance sets, including CHIANTI coronal abundances ([@Feldman:1992] and [@Feldman:2014]) , hybrid abundances (based on [Fludra-and-Schmelz:1999] and [@Schmelz:2012]), and photospheric abundances (based on [@Grevesse:2007], [@Scott:2015], and [@Asplund:2009]).
+
+Researchers have the flexibility to select the abundance model that best aligns with their research requirements.
+
+XRTpy's capabilities are designed to empower researchers and scientists to fully exploit the potential of XRT data, offering the scientific community a unique opportunity to study the Sun's dynamic and complex behavior in a user-friendly and efficient manner.
+
+![Figure 1: The Effective area for all XRT filters plotted using XRTpy. .\label{fig:Figure 1}](xrtpy_effective_area_plot.pdf)
+
+![Figure 2: The temperature response is plotted for all XRT filters using XRTpy.  The plot also shows the effects of using different abundance models from CHIANTI for each filter. .\label{fig:Figure 2}](xrtpy_temperature_response_plot.pdf)
+
+![In Figure 3, the application of the `temperature_from_filter_ratio` function is illustrated, demonstrating its role in calculating electron temperature and volume emission measure through filter ratios. The dataset, collected on January 28, 2011, between 01:31:55 and 01:32:05 UTC, comprises two images captured with specific filters. These images offer unique insights into solar conditions during the observed moments, as shown by [@Guidoni:2015]. .\label{fig:Figure 3}](xrtpy_temperature_from_filter_ratio_plot.pdf)
+
+# Development of XRTpy Version 0.4.0
+
+XRTpy version `0.4.0` was released on December 5, 2023. This version, available through the [Python Package Index](https://pypi.org/project/aiapy/) (PyPI), can be installed using `pip` and is compatible with Python 3.9 and later.
+
+In fostering collaboration within the solar physics community, interoperability with other packages is a work in progress that we've started on with the developers of aiapy for SDO/AIA observations, EISpack for Hinode-EIS data analysis, and irispy-lmsal for IRIS observations. This integration provides users with a smooth and comprehensive analysis experience. Further building on the SunPy framework (SunPy Project et al., 2020), XRTpy effectively utilizes the `Map` object for handling Hinode/XRT image data.
+
+The development of XRTpy is an open and collaborative effort, hosted on [Github](https://github.com/HinodeXRT/xrtpy) to ensure transparency and encourage community involvement. The project's documentation is comprehensive and continuously updated, available online via [Read the Docs](https://xrtpy.readthedocs.io/en/stable/). To maintain high-quality standards, XRTpy employs a robust testing framework built on [`pytest`](https://pytest.org) and [`GitHub Actions`](https://github.com/features/actions). This framework covers a range of aspects including different Python versions, online functionality, documentation integrity, software functionality, and code style checks, ensuring a reliable and effective tool for users.
+
+
+# Acknowledgements
+
+The development of XRTpy is supported by NASA contract NNM07AB07C to the Smithsonian Astrophysical Observatory.
+Hinode is a Japanese mission developed and launched by ISAS/JAXA, with NAOJ as domestic partner and NASA and STFC (UK) as international partners.
+It is operated by these agencies in co-operation with ESA and the NSC (Norway).
+The XRTpy team would like to extend gratitude to the Python in Heliophysics Community at large for their contribution to XRTpy.
+N.A.M. acknowledges support from NSF CSSI award 1931388.
+
+# References
diff --git a/joss/xrtpy_effective_area_plot.pdf b/joss/xrtpy_effective_area_plot.pdf
diff --git a/joss/xrtpy_temperature_from_filter_ratio_plot.pdf b/joss/xrtpy_temperature_from_filter_ratio_plot.pdf
diff --git a/joss/xrtpy_temperature_response_plot.pdf b/joss/xrtpy_temperature_response_plot.pdf