pyuvdata 3.2.0__tar.gz → 3.2.1__tar.gz

{pyuvdata-3.2.0 → pyuvdata-3.2.1}/.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
           args: ['--fix=no']
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.6
+    rev: v0.11.8
     hooks:
       - id: ruff
       - id: ruff-format

{pyuvdata-3.2.0 → pyuvdata-3.2.1}/CHANGELOG.md

@@ -1,9 +1,18 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
-## [Unreleased]
+## [3.2.1] - 2025-05-01
 
-## [3.2.0] - 2025-04-25
+### Fixed
+- A bug where the `Telescope.get_x_orientation` would not return `"east"` or `"north"`
+if the feed angles if outside of the range of 0 to 90 degrees (e.g. 180 and 270 degrees
+for x- and y-polarization should return "north".).
+- A bug in reading in uvfits files with baseline coordinates that have the '--' suffix,
+which is allowed in uvfits files.
+- A bug in reading in uvfits files where the antenna frame is given by an arbitrary
+number of repeated '?', which is allowed in uvfits.
+
+## [3.2.0] - 2025-04-28
 
 ### Added
 - A new page to the docs labeled "Conventions" has been added.
@@ -74,7 +83,7 @@ now set to `(0, 0)`, was originally `(1e-5, 1e-8)` (relative and absolute tolera
 respectively).
 - Flex-jones `UVCal` objects now recorded to MeasurementSet format as "T Jones" subtype.
 - Only import lunarsky if needed.
-- `UVData.select`, `UVBeam.select`, `UVFlag.select`, `UVFlag.select` have been
+- `UVData.select`, `UVBeam.select`, `UVCal.select`, `UVFlag.select` have been
 significantly refactored and made to behave more uniformly.
 - Allowing `UVParameter.__eq__` to use `UVParameter.compare_value` if the item being
 compared and `UVParameter.value` share the same class.
@@ -87,7 +96,7 @@ written with the wrong conjugation when setting `flip_conj=True`.
 - Bug in `UVData.write_ms` where the baseline conjugation scheme did not conform to
 what CASA nominally expects.
 - Bug in `utils.tools.slicify` and `utils.tools._convert_to_slices` where
-reverse-ordered slices (i.e., where the step was negative) where not correctly handled.
+reverse-ordered slices (i.e., where the step was negative) were not correctly handled.
 - Bug in MWA beams that caused beams pointed away from zenith to be wrong because
 the delays were not assigned to the right dipoles.
 - Bug in `UVData.sum_vis` where it errored if there were different filenames on

{pyuvdata-3.2.0 → pyuvdata-3.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyuvdata
-Version: 3.2.0
+Version: 3.2.1
 Summary: A pythonic interface for radio astronomy interferometry data
 Author-email: Bryna Hazelton <brynah@phys.washington.edu>, Adam Beardsley <adam.beardsley@winona.edu>, Daniel Jacobs <daniel.c.jacobs@gmail.com>, Garrett Keating <garrett.keating@cfa.harvard.edu>, Nicholas Kern <nkern@mit.edu>, Matthew Kolopanis <matthew.kolopanis@gmail.com>, Adam Lanman <alanman@mit.edu>, Paul La Plante <paul.laplante@unlv.edu>, Steven Murray <murray.steveng@gmail.com>, Jonathan Pober <jonathan_pober@brown.edu>, Pyxie Star <pyxiestar@gmail.com>
 Maintainer-email: Bryna Hazelton <brynah@phys.washington.edu>, Matthew Kolopanis <matthew.kolopanis@gmail.com>, Garrett Keating <garrett.keating@cfa.harvard.edu>, Steven Murray <murray.steveng@gmail.com>

pyuvdata-3.2.1/paper.bib

@@ -0,0 +1,164 @@
+@TECHREPORT{aipy,
+  author = {Aaron Parsons},
+  title = {Astronomical Interferometry in PYthon},
+  year = {2007},
+  file = {http://astro.berkeley.edu/~aparsons/aipy.pdf},
+  url = {https://casper.berkeley.edu/astrobaki/index.php/AIPY}}
+@TECHREPORT{uvfits,
+  author = {Eric W. Greisen},
+  title = {AIPS FITS File Format},
+  number = {AIPS Memo 117},
+  institution = {National Radio Astronomy Observatory},
+  abstract = {AIPS has been writing images and uv data in FITS-format files
+              for a very long time. While these files have been used widely in
+              the community, there is a perception that a detailed document is
+              still required. This memo is an attempt to meet that perception.
+              AIPS FITS files for uv are conventions layered upon the standard
+              FITS format to assist in the interchange of data recorded by
+              interferometric telescopes, particularly by radio telescopes such
+              as the EVLA and VLBA.},
+  keywords = {radio astronomy, uvfits},
+  month = {February},
+  year = {2016},
+  pages = {107},
+  file = {ftp://ftp.aoc.nrao.edu/pub/software/aips/TEXT/PUBL/AIPSMEM117.PS},
+  url = {http://www.aips.nrao.edu/aipsmemo.html},
+}
+
+@INPROCEEDINGS{miriad,
+  author = {{Sault}, R.~J. and {Teuben}, P.~J. and {Wright}, M.~C.~H.},
+  title = "{A Retrospective View of MIRIAD}",
+  booktitle = {Astronomical Data Analysis Software and Systems IV},
+  abstract = {Miriad is a radio interferometry data-reduction package, designed
+              for taking raw data through to the image analysis stage. The
+              Miriad project, begun in 1988, is now middle-aged. With the wisdom
+              of hindsight, we review design decisions and some of Miriad's
+              characteristics.},
+  year = 1995,
+  series = {Astronomical Society of the Pacific Conference Series},
+  volume = 77,
+  eprint = {astro-ph/0612759},
+  editor = {{Shaw}, R.~A. and {Payne}, H.~E. and {Hayes}, J.~J.~E.},
+  pages = {433},
+  adsurl = {http://adsabs.harvard.edu/abs/1995ASPC...77..433S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+  url = {http://www.atnf.csiro.au/computing/software/miriad/}
+}
+
+@ARTICLE{fhd,
+  author = {{Sullivan}, I.~S. and {Morales}, M.~F. and {Hazelton}, B.~J. and
+	          {Arcus}, W. and {Barnes}, D. and {Bernardi}, G. and {Briggs}, F.~H. and
+	          {Bowman}, J.~D. and {Bunton}, J.~D. and {Cappallo}, R.~J. and
+	          {Corey}, B.~E. and {Deshpande}, A. and {deSouza}, L. and {Emrich}, D. and
+	          {Gaensler}, B.~M. and {Goeke}, R. and {Greenhill}, L.~J. and
+	          {Herne}, D. and {Hewitt}, J.~N. and {Johnston-Hollitt}, M. and
+	          {Kaplan}, D.~L. and {Kasper}, J.~C. and {Kincaid}, B.~B. and
+	          {Koenig}, R. and {Kratzenberg}, E. and {Lonsdale}, C.~J. and
+	          {Lynch}, M.~J. and {McWhirter}, S.~R. and {Mitchell}, D.~A. and
+	          {Morgan}, E. and {Oberoi}, D. and {Ord}, S.~M. and {Pathikulangara}, J. and
+	          {Prabu}, T. and {Remillard}, R.~A. and {Rogers}, A.~E.~E. and
+	          {Roshi}, A. and {Salah}, J.~E. and {Sault}, R.~J. and {Udaya Shankar}, N. and
+	          {Srivani}, K.~S. and {Stevens}, J. and {Subrahmanyan}, R. and
+	          {Tingay}, S.~J. and {Wayth}, R.~B. and {Waterson}, M. and {Webster}, R.~L. and
+	          {Whitney}, A.~R. and {Williams}, A. and {Williams}, C.~L. and
+	          {Wyithe}, J.~S.~B.},
+  title = "{Fast Holographic Deconvolution: A New Technique for Precision Radio Interferometry}",
+  journal = {\apj},
+  archivePrefix = "arXiv",
+  eprint = {1209.1653},
+  primaryClass = "astro-ph.IM",
+  keywords = {dark ages, reionization, first stars, techniques: image processing, techniques: interferometric},
+  year = 2012,
+  month = nov,
+  volume = 759,
+  eid = {17},
+  pages = {17},
+  doi = {10.1088/0004-637X/759/1/17},
+  adsurl = {http://adsabs.harvard.edu/abs/2012ApJ...759...17S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+  url = {https://github.com/EoRImaging/FHD}
+}
+
+@TECHREPORT{ms,
+  author = {{Kemball}, A.~J. and {Wieringa}, M.~H.},
+  title = "{MeasurementSet definition version 2.0}",
+  year = 2000,
+  month = jan,
+  file = {https://casa.nrao.edu/Memos/229.ps.gz},
+  url = {https://casper.berkeley.edu/astrobaki/index.php/AIPY}}
+}
+
+@TECHREPORT{mir,
+  author = {{Qi}, C.},
+  title = "{The MIR Cookbook}",
+  year = 2022,
+  month = mar,
+  file = {https://lweb.cfa.harvard.edu/~cqi/mircook.pdf},
+  url = {https://lweb.cfa.harvard.edu/~cqi/mircook.html}}
+}
+
+@TECHREPORT{calfits,
+  author = {{Ali}, Z. and  {Hazelton}, B. and {Beardsley}, A. and {La Plante}, P. and {Kunicki}, T. and {the pyuvdata team}},
+  title = "{Memo: UVCal FITS Format}",
+  year = 2017,
+  month = jul,
+  file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/calfits_memo.pdf},
+}
+
+@TECHREPORT{beamfits,
+  author = {{Hazelton}, B. and {the pyuvdata team}},
+  title = "{Memo: UVBeam FITS Format}",
+  year = 2018,
+  month = jan,
+  file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/beamfits_memo.pdf},
+}
+
+@TECHREPORT{uvh5,
+  author = {{La Plante}, P. and {the pyuvdata team}},
+  title = "{Memo: UVH5 file format}",
+  year = 2024,
+  month = apr,
+  file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/uvh5_memo.pdf},
+}
+
+@TECHREPORT{calh5,
+  author = {{Hazelton}, B. and {the pyuvdata team}},
+  title = "{Memo: CalH5 file format}",
+  year = 2024,
+  month = aug,
+  file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/calh5_memo.pdf},
+}
+
+@ARTICLE{casa,
+       author = {{CASA Team} and {Bean}, Ben and {Bhatnagar}, Sanjay and {Castro}, Sandra and {Donovan Meyer}, Jennifer and {Emonts}, Bjorn and {Garcia}, Enrique and {Garwood}, Robert and {Golap}, Kumar and {Gonzalez Villalba}, Justo and {Harris}, Pamela and {Hayashi}, Yohei and {Hoskins}, Josh and {Hsieh}, Mingyu and {Jagannathan}, Preshanth and {Kawasaki}, Wataru and {Keimpema}, Aard and {Kettenis}, Mark and {Lopez}, Jorge and {Marvil}, Joshua and {Masters}, Joseph and {McNichols}, Andrew and {Mehringer}, David and {Miel}, Renaud and {Moellenbrock}, George and {Montesino}, Federico and {Nakazato}, Takeshi and {Ott}, Juergen and {Petry}, Dirk and {Pokorny}, Martin and {Raba}, Ryan and {Rau}, Urvashi and {Schiebel}, Darrell and {Schweighart}, Neal and {Sekhar}, Srikrishna and {Shimada}, Kazuhiko and {Small}, Des and {Steeb}, Jan-Willem and {Sugimoto}, Kanako and {Suoranta}, Ville and {Tsutsumi}, Takahiro and {van Bemmel}, Ilse M. and {Verkouter}, Marjolein and {Wells}, Akeem and {Xiong}, Wei and {Szomoru}, Arpad and {Griffith}, Morgan and {Glendenning}, Brian and {Kern}, Jeff},
+        title = "{CASA, the Common Astronomy Software Applications for Radio Astronomy}",
+      journal = {\pasp},
+     keywords = {Single-dish antennas, Aperture synthesis, Radio astronomy, Radio interferometry, Long baseline interferometry, Astronomy software, Open source software, Software documentation, Astronomy data reduction, Astronomy data analysis, 1460, 53, 1338, 1346, 932, 1855, 1866, 1869, 1861, 1858, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Solar and Stellar Astrophysics},
+         year = 2022,
+        month = nov,
+       volume = {134},
+       number = {1041},
+          eid = {114501},
+        pages = {114501},
+          doi = {10.1088/1538-3873/ac9642},
+archivePrefix = {arXiv},
+       eprint = {2210.02276},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022PASP..134k4501C},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{pyuvdata_v1,
+       author = {{Hazelton}, Bryna J. and {Jacobs}, Daniel C. and {Pober}, Jonathan C. and {Beardsley}, Adam P.},
+        title = "{pyuvdata: an interface for astronomical interferometeric datasets in python}",
+      journal = {The Journal of Open Source Software},
+         year = 2017,
+        month = feb,
+       volume = {2},
+       number = {10},
+          eid = {140},
+        pages = {140},
+          doi = {10.21105/joss.00140},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2017JOSS....2..140H},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}

pyuvdata-3.2.1/paper.md

@@ -0,0 +1,128 @@
+---
+title: 'pyuvdata v3: an interface for astronomical interferometeric datasets in python'
+tags:
+ - radio astronomy
+ - uvfits
+ - miriad
+authors:
+ - name: Garrett K. Keating
+   orcid: 0000-0002-3490-146X
+   affiliation: 1
+ - name: Bryna J. Hazelton
+   orcid: 0000-0001-7532-645X
+   affiliation: 2, 3
+ - name: Matthew Kolopanis
+   orcid: 0000-0002-2950-2974
+   affiliation: 4
+ - name: Steven Murray
+   orcid: 0000-0003-3059-3823
+   affiliation: 4
+ - name: Adam P. Beardsley
+   orcid: 0000-0001-9428-8233
+   affiliation: 5
+ - name: Daniel C. Jacobs
+   orcid: 0000-0002-0917-2269
+   affiliation: 3
+ - name: Nicholas Kern
+   affiliation: 6
+   orcid: 0000-0002-8211-1892
+ - name: Adam Lanman
+   affiliation: 7
+   orcid: 0000-0003-2116-3573
+ - name: Paul La Plante
+   affiliation: 8
+   orcid: 0000-0002-4693-0102
+ - name: Jonathan C. Pober
+   orcid: 0000-0002-3492-0433
+   affiliation: 9
+ - name: Pyxie Star
+   affiliation: 3
+affiliations:
+ - name: Center for Astrophysics | Harvard & Smithsonian
+   index: 1
+ - name: University of Washington, eScience Institute
+   index: 2
+ - name: University of Washington, Physics Department
+   index: 3
+ - name: Scuola Normale Superiore, Italy
+   index: 4
+ - name: Winona State University, Physics Department
+   index: 5
+ - name: Massachusetts Institute of Technology, Physics Department
+   index: 6
+ - name: Kavli Institute of Astrophysics and Space Research
+   index: 7
+ - name: University of Nevada, Las Vegas, Department of Computer Science
+   index: 8
+ - name: Brown University, Physics Department
+   index: 9
+date: 2 July 2024
+bibliography: paper.bib
+---
+
+# Summary
+pyuvdata is an open-source software package that seeks to provide a well-documented,
+feature-rich interface for many of the different data formats that exist within radio
+interferometry, including support for reading and writing the following formats:
+UVH5 [@uvh5], UVFITS [@uvfits], MIRIAD [@miriad], and measurement set [@ms] visibility
+files. It offers read-only support for FHD [@fhd] and MIR [@mir] visibility save files.
+Additionally, pyuvdata supports reading/writing measurement set, CalFITS [@calfits], and
+CalH5 [@calh5] calibration solutions; and reading of FHD calibration solutions. pyuvdata
+also provides interfaces for and handling of models of antenna primary beams, including
+BeamFITS [@beamfits] (read and write), CST (read-only), MWA beam formats (read-only).
+It also provides interfaces for handling of data flags.
+
+# Statement of Need
+There are several standard formats for astronomical interferometric data, but
+translating between them in a robust and well-understood way has historically been
+challenging.  This is partially due to conflicting assumptions and standards, giving
+rise to significant (though sometimes subtle) differences between formats.
+Interfacing with different data formats -- like one does when they convert from one
+format to another -- thus requires careful accounting for the complex mathematical
+relationships between both data and metadata to ensure proper data fidelity. This is
+required both for leveraging existing community-favored tools that are typically built
+to interface with a specific data format, as well as analyses requiring bespoke tools
+for specialized types of analyses and simulations leveraging data in a variety of
+formats.
+
+pyuvdata has been designed to facilitate interoperability between different instruments
+and codes by providing high quality, well documented conversion routines as well as an
+interface to interact with interferometric data and simulations directly in Python.
+Originally motivated to support new low frequency instruments (e.g. MWA:
+http://www.mwatelescope.org/, PAPER: http://eor.berkeley.edu/, HERA:
+http://reionization.org/), the capabilities of pyuvdata have been steadily expanded
+to support handling of data from several telescopes, ranging from meter to submillimeter
+wavelengths (including SMA: https://cfa.harvard.edu/sma, ALMA, SMA, VLA, ATCA, CARMA,
+LWA, among others).
+
+# Major updates in this version
+In the time since it was initially published [@pyuvdata_v1], pyuvdata has undergone a
+significant expansion in capabilities. In addition to general performance improvements
+and restructuring, the newest version of pyuvdata includes several new major features,
+including:
+
+- The addition of the `UVCal` class, which provides a container for handling calibration
+solutions (bandpass, delays, and gains) for interferometric data. Supported data formats
+include MS, FHD, CalFITS, and CalH5.
+- The addition of the `UVBeam` class, which provides a container for handling models
+of the primary beam for antennas within an interferometric array. Supported data formats
+include BeamFITS, MWA, and CST.
+- The addition of the `UVFlag` class, which provides a container for handling flags/masking
+of bad data for visibility data.
+- Drastically improved handling of astrometry.
+- Increased speed and accuracy of algorithms used to ``phase-up'' data (i.e., change
+the sky position where the interferometer is centered up on).
+- Support for several new visibility data formats, including MIR, MS, and MWA/MWAX.
+- Support for data sets containing multiple spectral windows.
+- Support for data sets containing observations of multiple sources/phase centers.
+- Many new convenience methods for working with interferometric data, including
+splitting and combining data sets, averaging in time and frequency, and applying
+calibration solutions and flags.
+
+# Acknowledgements
+This work was supported by the National Science Foundation (AST-1835421); and by the
+Submillimeter Array, a joint project between the Smithsonian Astrophysical Observatory
+and the Academia Sinica Institute of Astronomy and Astrophysics, and funded by the
+Smithsonian Institution and the Academia Sinica.
+
+# References