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Execution Block ID uid://A001/X15a0/X184 Sgr_A_st_am_03_TM1 #259

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keflavich opened this issue Sep 20, 2022 · 26 comments
Open
6 of 15 tasks

Execution Block ID uid://A001/X15a0/X184 Sgr_A_st_am_03_TM1 #259

keflavich opened this issue Sep 20, 2022 · 26 comments
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@keflavich
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keflavich commented Sep 20, 2022

Sgr_A_st_am_03_TM1
uid://A001/X15a0/X184

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Reprocessed Product Links:

@keflavich keflavich added EB Execution Block TM1 labels Sep 20, 2022
@d-l-walker
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I'm doing the QA2 for this SB, and it has a similar issue to #126 in that it is an irregular and elongated mosaic. It's not quite as severe as the other instance, but the PSF is still just outside the mosaic and causing the synthesised beams to misbehave. I'm going to do the manual imaging at the QA2 stage for this, which will take a while, but I just wanted to flag this.

@keflavich
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keflavich commented Jul 24, 2023

The auto-script-writing failed because there are no clean parameters:

INFO: Processing Sgr_A_st_am_03_TM1 = uid://A001/X15a0/X184 from /orange/adamginsburg/ACES//data/2021.1.00172.L/weblogs/pipeline-20221012T211956 [aces.pipeline_scripts.recover_tclean_commands]
Traceback (most recent call last):
  File "/orange/adamginsburg/miniconda3/envs/python39/bin//aces_recover_tclean_commands", line 8, in <module>
    sys.exit(main())
  File "/orange/adamginsburg/ACES/reduction_ACES/aces/pipeline_scripts/recover_tclean_commands.py", line 128, in main
    raise ValueError("No parameters found")
ValueError: No parameters found

This is mostly a note for me; I need to put in an exception for this case, which I did in c780237

@d-l-walker d-l-walker self-assigned this Nov 15, 2023
@d-l-walker
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@keflavich any idea what the status of this is? I've assigned myself since I did the manual QA2. I know that we need to re-do the imaging with full spectral resolution, and that it's a bit awkward due to the over-sized image to account for the PSF offset.

I don't see any final products in /member.uid___A001_X15a0_X184/calibrated/working/, so I assume this still needs some attention. Would it be easier for me to take on the re-imaging locally given that this region deviates from the usual procedure? Or would you prefer to add a special exception into the reduction PL?

@d-l-walker
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Update: @keflavich is going to look into this in the next ~ week. If it's easier to do so, I will run the un-size-mitigated cleaning locally.

@keflavich
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@d-l-walker can you add the parameters as you did for al in #290?

@keflavich
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I've added the continuum parameters in 12b4e64

@keflavich
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Scripts weren't being written because I had to manually link the files from calibrated/ to calibrated/working/ (this note is for future reference, in case we have to come back and reproduce this part of the workflow sometime)

@d-l-walker
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@keflavich I added the cube parameters to your PR in 50738ae

I also tweaked the continuum parameters that you had added:

  • Updated the imagename to include the MOUS ID
  • Changed SPW IDs in continuum selection from [0,1,2,3,4,5] -> [25,27,29,31,33,35]

@keflavich
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Got a failure:

2023-11-29 14:19:04     INFO    ::casa
2023-11-29 14:19:05     INFO    ::casa
2023-11-29 14:19:05     INFO    ::casa
2023-11-29 14:19:05     INFO    ::casa
2023-11-29 14:19:07     INFO    ::casa  Python version 3.8.10
2023-11-29 14:19:07     INFO    ::casa  CASA Version CASALITH 6.5.5.21
2023-11-29 14:19:09     INFO    ::casa  Using configuration file /scratch/local/16719365/config.py
2023-11-29 14:19:09     INFO    ::casa
2023-11-29 14:19:09     INFO    ::casa  Checking Measures tables in data repository sub-directory /blue/adamginsburg/adamginsburg/casa/casa-6.5.5-21-py3.8/lib/py/lib/python3.8/site-packages/casadata/__data__/geodetic
2023-11-29 14:19:09     INFO    ::casa    IERSeop2000 (version date, last date in table (UTC)): 2023/03/10/15:00, 2023/02/08/00:00:00
2023-11-29 14:19:09     INFO    ::casa    IERSeop97 (version date, last date in table (UTC)): 2023/03/10/15:00, 2023/02/08/00:00:00
2023-11-29 14:19:09     INFO    ::casa    IERSpredict (version date, last date in table (UTC)): 2023/04/09/15:00, 2023/07/08/00:00:00
2023-11-29 14:19:09     INFO    ::casa    TAI_UTC (version date, last date in table (UTC)): 2023/04/04/15:00, 2017/01/01/00:00:00
2023-11-29 14:19:09     INFO    tclean_script::tclean_script::casa      Temporary directory used is /scratch/local/16719365
2023-11-29 14:19:09     INFO    tclean_script::tclean_script::casa      Started CASA in /scratch/local/16719365
2023-11-29 14:19:09     INFO    tclean_script::tclean_script::casa      Splitting /orange/adamginsburg/ACES/rawdata/2021.1.00172.L/science_goal.uid___A001_X1590_X30a8/group.uid___A001_X1590_X30a9/member.uid___A001_X15a0_X184/calibrated/uid___A002_Xfe90b7_X773a.ms.split.cal with defaults
2023-11-29 14:19:11     INFO    MSTransformManager::parseMsSpecParams   Input file name is /orange/adamginsburg/ACES/rawdata/2021.1.00172.L/science_goal.uid___A001_X1590_X30a8/group.uid___A001_X1590_X30a9/member.uid___A001_X15a0_X184/calibrated/uid___A002_Xfe90b7_X773a.ms.split.cal
2023-11-29 14:19:11     INFO    MSTransformManager::parseMsSpecParams   Data column is CORRECTED
2023-11-29 14:19:11     INFO    MSTransformManager::parseMsSpecParams   Output file name is /blue/adamginsburg/adamginsburg/ACES/workdir/am_spw29_cube_TM1_A001_X15a0_X184/uid___A002_Xfe90b7_X773a_spw29.ms.split.cal
2023-11-29 14:19:11     INFO    MSTransformManager::parseDataSelParams  field selection is Sgr_A_star
2023-11-29 14:19:11     INFO    MSTransformManager::parseDataSelParams  spw selection is 29
2023-11-29 14:19:11     WARN    MSTransformManager::checkDataColumnsToFill      CORRECTED_DATA column requested but not available in input MS
2023-11-29 14:19:11     INFO    MSTransformManager::initDataSelectionParams     Selected Fields Ids are [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150]
2023-11-29 14:19:11     INFO    MSTransformManager::initDataSelectionParams     Selected SPWs Ids are Axis Lengths: [1, 4]  (NB: Matrix in Row/Column order)
2023-11-29 14:19:11     INFO    MSTransformManager::initDataSelectionParams+    [29, 0, 1919, 1]
2023-11-29 14:19:11     INFO    MSTransformManager::open        Select data
2023-11-29 14:19:11     INFO    MSTransformManager::createOutputMSStructure     Create output MS structure
2023-11-29 14:19:11     SEVERE  split::::casa   Exception Reported: Error in split: Desired column (CORRECTED_DATA) not found in the input MS (/orange/adamginsburg/ACES/rawdata/2021.1.00172.L/science_goal.uid___A001_X1590_X30a8/group.uid___A001_X1590_X30a9/member.uid___A001_X15a0_X184/calibrated/uid___A002_Xfe90b7_X773a.ms.split.cal).
2023-11-29 14:19:11     INFO    split::::casa   Traceback (most recent call last):
2023-11-29 14:19:11     INFO    split::::casa+    File "/blue/adamginsburg/adamginsburg/casa/casa-6.5.5-21-py3.8/lib/py/lib/python3.8/site-packages/casashell/private/split.py", line 862, in __call__
2023-11-29 14:19:11     INFO    split::::casa+      _return_result_ = _split_t( _pc.document['vis'],_pc.document['outputvis'],_pc.document['keepmms'],_pc.document['field'],_pc.document['spw'],_pc.document['scan'],_pc.document['antenna'],_pc.document['correlation'],_pc.document['timerange'],_pc.document['intent'],_pc.document['array'],_pc.document['uvrange'],_pc.document['observation'],_pc.document['feed'],_pc.document['datacolumn'],_pc.document['keepflags'],_pc.document['width'],_pc.document['timebin'],_pc.document['combine'] )
2023-11-29 14:19:11     INFO    split::::casa+    File "/blue/adamginsburg/adamginsburg/casa/casa-6.5.5-21-py3.8/lib/py/lib/python3.8/site-packages/casatasks/private/task_split.py", line 163, in split
2023-11-29 14:19:11     INFO    split::::casa+      mtlocal.open()
2023-11-29 14:19:11     INFO    split::::casa+    File "/blue/adamginsburg/adamginsburg/casa/casa-6.5.5-21-py3.8/lib/py/lib/python3.8/site-packages/casatools/mstransformer.py", line 36, in open
2023-11-29 14:19:11     INFO    split::::casa+      return self._swigobj.open()
2023-11-29 14:19:11     INFO    split::::casa+    File "/blue/adamginsburg/adamginsburg/casa/casa-6.5.5-21-py3.8/lib/py/lib/python3.8/site-packages/casatools/__casac__/mstransformer.py", line 176, in open
2023-11-29 14:19:11     INFO    split::::casa+      return _mstransformer.mstransformer_open(self)
2023-11-29 14:19:11     INFO    split::::casa+  RuntimeError: Desired column (CORRECTED_DATA) not found in the input MS (/orange/adamginsburg/ACES/rawdata/2021.1.00172.L/science_goal.uid___A001_X1590_X30a8/group.uid___A001_X1590_X30a9/member.uid___A001_X15a0_X184/calibrated/uid___A002_Xfe90b7_X773a.ms.split.cal).

@keflavich
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Should we just be using the data column, not corrected_data, since we're operating on the .split.cal files?

@pyhsiehATalma
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There are two re-imaging cubes of spw33, they are,

(1) Sgr_A_star_sci33.cube.I.manual.pbcor.fits-> There is no divergence in the cube, but it only has 1917 channels (
size mitigated issue?)
(2) uid___A001_X15a0_X184.Sgr_A_star_sci33.cube.I.manual.image.pbcor. It has native spectral resolution and full bandwidth, but it has divergence around channel 626.

@d-l-walker
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d-l-walker commented Jan 24, 2024

Thanks @pyhsiehATalma! Yes, the full resolution one should be the new one, but I don't think it had been checked until now, so thanks for checking the cube!

I can submit a PR to increase the cyclefactor, which will hopefully fix the issue.

Edit: Per discussion in telecon, we'll probably proceed with the mild divergence for now, as this cube takes a long time to clean.

@keflavich
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image
channel 626

@pyhsiehATalma
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channel 670
@d-l-walker I am sorry that I didn't notice there is another high level divergence at channel 670 in the new cube.

截圖 2024-01-25 15 46 20

For the purpose of combination, I can reimage the narrowband within the -300 km/s to 300 km/s velocity range locally. For archival purposes, would you like to rerun the pipeline?

@d-l-walker
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Thanks @pyhsiehATalma. This is much more significant that the previous one you posted. @keflavich I think this necessitates re-cleaning now, right?

@keflavich
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Yes, with new parameters.

@keflavich
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Bumped cyclefactor to 2.5 in 0051bbc

@keflavich
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This field has a huge beam:


uid___A001_X15a0_X184.Sgr_A_star_sci25.cube.I.manual.image.pbcor.statcont.contsub.fits Beam: BMAJ=3.1414519769151603 arcsec BMIN=1.9806471924264 arcsec &
uid___A001_X15a0_X184.Sgr_A_star_sci27.cube.I.manual.image.pbcor.statcont.contsub.fits Beam: BMAJ=3.22112800908468 arcsec BMIN=1.96514224566408 arcsec &
uid___A001_X15a0_X184.Sgr_A_star_sci29.cube.I.manual.image.pbcor.statcont.contsub.fits Beam: BMAJ=3.03171861786696 arcsec BMIN=1.90907300590992 arcsec &
uid___A001_X15a0_X184.Sgr_A_star_sci31.cube.I.manual.image.pbcor.statcont.contsub.fits Beam: BMAJ=3.1911897771432 arcsec BMIN=1.94215439145888 arcsec &
uid___A001_X15a0_X184.Sgr_A_star_sci33.cube.I.manual.image.pbcor.statcont.contsub.fits Beam: BMAJ=2.8374902861425197 arcsec BMIN=1.91982815008056 arcsec &
uid___A001_X15a0_X184.Sgr_A_star_sci35.cube.I.manual.image.pbcor.statcont.contsub.fits Beam: BMAJ=2.64573553220712 arcsec BMIN=1.78163167820976 arcsec &

This is problematic, as it is the limiting factor in full-field mosaics.

I think we may need to taper to force a higher resolution here, or just leave this field out of the final images (which is what I'm doing right now).

@keflavich
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The weblog indicates that the beam should be smaller, 2.32x1.47 arcsec:
https://data.rc.ufl.edu/secure/adamginsburg/ACES/weblogs/humanreadable/Sgr_A_st_am_03_TM1/html/t2-4m.html?sidebar=sidebar_stage24&ms=all&subpage=t2-4m_details.html
but we're getting 3.14x1.98, which is a lot bigger.

That link also says this field shouldn't have passed QA because the beam is too large. @d-l-walker ideas?

@d-l-walker
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@keflavich yeah that's strange. I've just checked the products that I manually imaged, and I see:
SPW 35: Restoring beam = 2.2872" X 1.31029", -88.8137 deg
SPW 25: Restoring beam = 2.86723" X 1.51524", -86.4075 deg
Continuum: Restoring beam = 2.51007" X 1.54627", -88.3095 deg

Not great, but better than what you're seeing here for the cubes. Also using robust=0.5. I think this technically just squeezes into the acceptable range based on SPW 35 as our representative window.

As far as I can tell, you're still manually forcing the PSF to be inside the mosaic with the re-cleans, right?

The beams that you're reporting are broadly consistent with, though slightly larger than, what we were seeing during the QA2 stage prior to fixing the issue with the PSF 🤔

My suspicion is that this must be related to the weird mosaic shape and PSF issue still. I've just checked, and while there is a difference between the phasecenter that I used vs. what you're using (see below. mine = red square, yours = yellow), they're both firmly inside the mosaic, so I'm not sure why that would cause any issues.

TL;DR: I don't know. Seems suspiciously similar to the issues we saw prior to fixing the PSF, but that should be addressed based on what I can see ... I'll keep digging.

Screenshot 2024-02-12 at 11 34 01

@pyhsiehATalma
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pyhsiehATalma commented Feb 14, 2024

Hi @keflavich @d-l-walker , I am also curious about this larger beam issue, so I did some tests (robust=0). I have found that the reason for the large beam is the gridder="mosaic" and mosweight=True option, as the beam size is approximately 2.1"x1.6" when I use the gridder="standard" option on the same mosaic image.

Here is the explanation of the gridder='mosaic' option and its warning. The gridder='mosaic' option will trigger mosweight=True by default.

https://casadocs.readthedocs.io/en/stable/notebooks/synthesis_imaging.html

When doing Brigg’s style weighting (including uniform) in tclean, the mosweight subparameter of the mosaic gridder determines whether to weight each field in a mosaic independently (mosweight = True), or to calculate the weight density from the average uv distribution of all the fields combined (mosweight = False). The underlying issue with more uniform robust weighting is how the weight density maps onto the uv-grid, which can give high weight to areas of the uv-plane that are not actually more sensitive. The setting mosweight = True has long been known as potentially useful in cases where a mosaic has non-uniform sensitivity, but it was found that it is also very important for more uniform values of robust Briggs weighting in the presence of relatively poor uv-coverage. For example, snap-shot ALMA mosaics with mosweight = False typically show an increase in noise in the corners or in the areas furthest away from the phase-center. Therefore, as of CASA 5.4, the mosweight sub-parameter in tclean has the default value mosweight = True.

WARNING: the default setting of mosweight=True under the mosaic gridder in tclean has the following disadvantages: (1) it may potentially cause memory issues for large VLA mosaics; (2) the major and minor axis of the synthesized beam may be ~10% larger than with mosweight=False. Please change to mosweight=False to get around these issues.

So, perhaps using mosweight=True, larger beam can occur because areas (or shorter baselines) with higher sensitivity (and therefore more weight) contribute more to the final PSF.

I found the beam size is 2"x1.6" using gridder='mosaic' and mosweight=False, but I haven't had a time to check the image quality.

@ashleythomasbarnes
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7B4E42DF-4EAA-4DC6-9B0F-12603D573FFB

@SpacialTree
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Continuum QA

This field has none of the new continuum images made, there is only the old spw25_27_29_31_33_35 continuum image. There are also no mfs images.

spw25_27_29_31_33_35
uid___A001_X15a0_X184 Sgr_A_star_sci spw25_27_29_31_33_35 cont I manual image tt0-image-2024-03-04-13-47-38

@SpacialTree
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Continuum QA

This field is still missing any other continuum images except the aggregate.

uid___A001_X15a0_X184 Sgr_A_star_sci v1aggregated_spw25_27_29_31_33_35 cont I manual image tt0-image-2024-04-03-11-48-45

@SpacialTree
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Continuum QA

Still missing new continuum images.

@keflavich
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We never resolved the beam size issues. @pyhsiehATalma did you ever check the image quality? Is it safe to switch to mosweight=False?

@github-project-automation github-project-automation bot moved this to Execution Blocks under QA in Data Reduction Aug 30, 2024
@keflavich keflavich added the Done! label Oct 2, 2024
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