MS writer improvements

[kartographer]

Description

Adds some functionality to the write_ms method, which enforces that CASA-preferred polarization ordering is used on write, and allows the user to specify whether to flip the baseline conjugation scheme used.

Motivation and Context

This addresses some issues that LWA users were running into when passing data through puvdata. Two issues in particular were identified in #1355. First, some CASA tasks clearly want the polarization order to be set up in a particular way, so the writer now always writes out in "CASA order". Second, there's an open question as to if some methods and functions (both internal and external to the CASA package) require different baseline conventions, which would be understandable given the conflicting documentation. Though I believe the pyuvdata standard is correct for most applications, I've added a switch that users can use to flip the convention.

In the course of addressing the above, I did make a few small tweaks to the writer and added/modified a couple of functions in utils to help with polarization ordering and to make indexing faster under most circumstances via use of slices.

Closes #1355.

Types of changes

• Bug fix (non-breaking change which fixes an issue)

Checklist:

• I have read the contribution guide.
• My code follows the code style of this project.

Bug fix checklist:

• My fix includes a new test that breaks as a result of the bug (if possible).
• All new and existing tests pass.
• I have updated the CHANGELOG.

[codecov]

Codecov Report

Merging #1363 (eb3c56c) into main (bd03009) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1363   +/-   ##
=======================================
  Coverage   99.92%   99.92%           
=======================================
  Files          36       36           
  Lines       20202    20228   +26     
=======================================
+ Hits        20186    20212   +26     
  Misses         16       16           

Files	Coverage Δ
pyuvdata/utils.py	100.00% <100.00%> (ø)
pyuvdata/uvdata/ms.py	99.89% <100.00%> (+<0.01%)	⬆️
pyuvdata/uvdata/uvdata.py	100.00% <100.00%> (ø)

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[bhazelton]

Thanks @kartographer ! Just a few comments.

[bhazelton]

@rlbyrne we'd be happy to hear any feedback from you on this if you have time to look at it or test it.

[bhazelton]

Looks great, thanks!

[rlbyrne]

@kartographer Apologies that I'm only getting around to testing this now.

I am getting an error with the new ms writer. When I read an .uvfits file and then immediately write to an .ms file, I get this message:

  File "<stdin>", line 1, in <module>
  File "/opt/devel/rbyrne/envs/pyuvdata/lib/python3.8/site-packages/pyuvdata/uvdata/uvdata.py", line 12731, in write_ms
    ms_obj.write_ms(
  File "/opt/devel/rbyrne/envs/pyuvdata/lib/python3.8/site-packages/pyuvdata/uvdata/ms.py", line 1219, in write_ms
    ms.putcol(col, temp_vals)
  File "/opt/devel/rbyrne/envs/pyuvdata/lib/python3.8/site-packages/casacore/tables/table.py", line 1155, in putcol
    self._putcol(columnname, startrow, nrow, rowincr, value)
RuntimeError: ArrayColumn::putColumn - column DATA has 62128, array has 4 rows: Table array conformance error

If I run uv.reorder_pols(order="CASA", run_check=False) before writing I do not get the error. Any thoughts? I can put this in an issue as well.