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ACES-CMZ / reduction_ACES

Reduction scripts and tools for ACES
https://worldwidetelescope.org/webclient/?wtml=https://data.rc.ufl.edu/pub/adamginsburg/ACES/mosaics/mosaics.wtml
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Execution Block ID uid://A001/X15a0/Xa6 Sgr_A_st_b_03_TM1 #150

Open keflavich opened 2 years ago

keflavich commented 2 years ago

Sgr_A_st_b_03_TM1 uid://A001/X15a0/Xa6

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d-l-walker commented 2 years ago

There are a few outliers in the plots in stage 17 (timegaincal), but these are very minor and mostly cosmetic. I don't think this warrants recalibration.

There are various issues with the imaging that need resolving. This is Sgr B2 M / South / Extended, so I guess no surprise here. I will work on the reimaging soon. Eventually we will want to image this together with the adjacent regions, especially because there are very bright sources at the edges of the mosaics.

Continuum residual

uid___A001_X15a0_Xa6 s36_0 Sgr_A_star_sci spw25_27_29_31_33_35 cont I iter1 residual tt0 sky

SPWs 25 & 27. Self-absorption? Likely from Sgr B2 M.

uid___A001_X15a0_Xa6 s38_0 Sgr_A_star_sci spw25 cube I iter1 image spectrum uid___A001_X15a0_Xa6 s38_0 Sgr_A_star_sci spw27 cube I iter1 residual sky uid___A001_X15a0_Xa6 s38_0 Sgr_A_star_sci spw27 cube I iter1 image spectrum

Slope in SPW 29. Re-do uvcontsub with fitorder=0. Also significant emission in residual.

uid___A001_X15a0_Xa6 s38_0 Sgr_A_star_sci spw29 cube I iter1 image spectrum uid___A001_X15a0_Xa6 s38_0 Sgr_A_star_sci spw29 cube I iter1 residual sky

keflavich commented 2 years ago

The spw33 clean failed because the chanwidth was specified incorrectly; I think we need chanwidths to be exact

2022-08-21 23:29:45     INFO    tclean::::casa  ##########################################
2022-08-21 23:29:45     INFO    tclean::::casa  ##### Begin Task: tclean             #####
2022-08-21 23:29:45     INFO    tclean::::casa  tclean( vis=['/blue/adamginsburg/adamginsburg/ACES/workdir/b_spw33_cube/uid___A002_Xf99bb0_X2491_spw33.ms', '/blue/adamginsburg/adamginsburg/ACES/workdir/b_spw33_cube/uid___A002_Xf99bb0_X3f39_spw33.ms', '/blue/adamginsburg/adamginsburg/ACES/workdir/b_spw33_cube/uid___A002_Xf99bb0_X4ae1_spw33.ms'], selectdata=True, field='Sgr_A_star', spw='', timerange='', uvrange='', antenna=['0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45&', '0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46&', '0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46&'], scan=['6,9,12,15,18', '6,9,12,15,18', '6,9,12,15,18'], observation='', intent='OBSERVE_TARGET#ON_SOURCE', datacolumn='corrected', imagename='/blue/adamginsburg/adamginsburg/ACES/workdir/b_spw33_cube/uid___A001_X15a0_Xa6.s38_0.Sgr_A_star_sci.spw33.cube.I.iter1', imsize=[2160, 2048], cell=['0.21arcsec'], phasecenter='ICRS 17:47:12.6400 -028.25.37.295', stokes='I', projection='SIN', startmodel='', specmode='cube', reffreq='', nchan=3836, start='97.6660537907GHz', width='488244Hz', outframe='LSRK', veltype='radio', restfreq=[], interpolation='linear', perchanweightdensity=True, gridder='mosaic', facets=1, psfphasecenter='', wprojplanes=1, vptable='', mosweight=True, aterm=True, psterm=False, wbawp=True, conjbeams=False, cfcache='', usepointing=False, computepastep=360.0, rotatepastep=360.0, pointingoffsetsigdev=[], pblimit=0.2, normtype='flatnoise', deconvolver='hogbom', scales=[], nterms=2, smallscalebias=0.0, restoration=True, restoringbeam='common', pbcor=True, outlierfile='', weighting='briggsbwtaper', robust=0.5, noise='1.0Jy', npixels=0, uvtaper=[''], niter=50000000, gain=0.1, threshold='0.01Jy', nsigma=0.0, cycleniter=-1, cyclefactor=2.0, minpsffraction=0.05, maxpsffraction=0.8, interactive=0, usemask='auto-multithresh', mask='', pbmask=0.0, sidelobethreshold=3.0, noisethreshold=5.0, lownoisethreshold=1.5, negativethreshold=7.0, smoothfactor=1.0, minbeamfrac=0.3, cutthreshold=0.01, growiterations=50, dogrowprune=True, minpercentchange=1.0, verbose=False, fastnoise=False, restart=True, savemodel='none', calcres=True, calcpsf=True, psfcutoff=0.35, parallel=False )
2022-08-21 23:29:45     INFO    tclean::::casa  Verifying Input Parameters
2022-08-21 23:29:45     INFO    SynthesisImagerVi2::selectData  MS : /blue/adamginsburg/adamginsburg/ACES/workdir/b_spw33_cube/uid___A002_Xf99bb0_X2491_spw33.ms | Selecting on fields : Sgr_A_star | Selecting on antenna names : 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45& | Selecting on scan : 6,9,12,15,18 | Selecting on Scan Intent/State : OBSERVE_TARGET#ON_SOURCE | [Opened in readonly mode]
2022-08-21 23:29:46     INFO    SynthesisImagerVi2::selectData    NRows selected : 456435
2022-08-21 23:29:46     INFO    SynthesisImagerVi2::selectData  MS : /blue/adamginsburg/adamginsburg/ACES/workdir/b_spw33_cube/uid___A002_Xf99bb0_X3f39_spw33.ms | Selecting on fields : Sgr_A_star | Selecting on antenna names : 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46& | Selecting on scan : 6,9,12,15,18 | Selecting on Scan Intent/State : OBSERVE_TARGET#ON_SOURCE | [Opened in readonly mode]
2022-08-21 23:29:46     INFO    SynthesisImagerVi2::selectData    NRows selected : 476721
2022-08-21 23:29:47     INFO    SynthesisImagerVi2::selectData  MS : /blue/adamginsburg/adamginsburg/ACES/workdir/b_spw33_cube/uid___A002_Xf99bb0_X4ae1_spw33.ms | Selecting on fields : Sgr_A_star | Selecting on antenna names : 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46& | Selecting on scan : 6,9,12,15,18 | Selecting on Scan Intent/State : OBSERVE_TARGET#ON_SOURCE | [Opened in readonly mode]
2022-08-21 23:29:47     INFO    SynthesisImagerVi2::selectData    NRows selected : 476721
2022-08-21 23:29:48     INFO    SynthesisImagerVi2::defineImage         Define image coordinates for [/blue/adamginsburg/adamginsburg/ACES/workdir/b_spw33_cube/uid___A001_X15a0_Xa6.s38_0.Sgr_A_star_sci.spw33.cube.I.iter1] :
2022-08-21 23:29:49     WARN    MSTransformRegridder::calcChanFreqs      phaseCenter='Direction: [-0.0490499, -0.878055, -0.476039]'  *** Requested new channel width (488244 Hz) is smaller than smallest original channel width
2022-08-21 23:29:49     WARN    MSTransformRegridder::calcChanFreqs+         which is 488246 Hz
2022-08-21 23:29:49     SEVERE  MSTransformRegridder::calcChanFreqs     calcChanFreqs failed, check input start and width parameters
2022-08-21 23:29:49     SEVERE  SynthesisImagerVi2::defineImage (file src/code/synthesis/ImagerObjects/SynthesisImagerVi2.cc, line 594) Error in building Coordinate System and Image Shape : 2022-08-21 23:29:49       SEVERE  MSTransformRegridder::calcChanFreqs     calcChanFreqs failed, check input start and width parameters
2022-08-21 23:29:49     SEVERE  tclean::::casa  Task tclean raised an exception of class RuntimeError with the following message: 2022-08-21 23:29:49   SEVERE  SynthesisImagerVi2::defineImage (file src/code/synthesis/ImagerObjects/SynthesisImagerVi2.cc, line 594) Error in building Coordinate System and Image Shape : 2022-08-21 23:29:49       SEVERE  MSTransformRegridder::calcChanFreqs     calcChanFreqs failed, check input start and width parameters
2022-08-21 23:29:49     INFO    tclean::::casa  Task tclean complete. Start time: 2022-08-21 19:29:45.261100 End time: 2022-08-21 19:29:48.859718
2022-08-21 23:29:49     INFO    tclean::::casa  ##### End Task: tclean               #####
2022-08-21 23:29:49     INFO    tclean::::casa  ##########################################
keflavich commented 2 years ago

The reimaging remains broken. Probably the data are not calibrated?

image

keflavich commented 2 years ago

@djeff1887 Could you also have a closer look at this one? You should already have a pretty good sense of where the hot cores are.

keflavich commented 2 years ago

@djeff1887 could you report what you did on your Charlottesville visit here? Especially what imaging parameters you (successfully) used for spw33?

djeff1887 commented 2 years ago

@keflavich I used the tclean command from spw31 (with the tweaks you made on Aug 22) to image a concatenated ms with multiscale clean using scales that were multiples of 5. I also had cyclefactor=2, although that was also directly from the pipeline. My tclean command is below.


tclean(vis='../calibrated_final.ms', field='Sgr_A_star', spw=['33'], 
       antenna=['0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45&'], scan=['6,9,12,15,18'], intent='OBSERVE_TARGET#ON_SOURCE', datacolumn='corrected', imagename='uid___A001_X15a0_Xa6.s38_0.Sgr_A_star_sci.spw33.cube.I.iter1_multiscale1-5-25-100', imsize=[2160, 2048], cell=['0.21arcsec'], phasecenter='ICRS 17:47:12.6400 -028.25.37.295', stokes='I', specmode='cube', nchan=956, start='97.6660537907GHz', width='0.488245MHz', outframe='LSRK', perchanweightdensity=True, gridder='mosaic', mosweight=True, usepointing=False, pblimit=0.2, deconvolver='multiscale', scales=[1,5,25,100], restoration=True, restoringbeam='common', pbcor=True, weighting='briggsbwtaper', robust=0.5, npixels=0, niter=20000000, threshold='0.123Jy', nsigma=0.0, cyclefactor=2.0, interactive=0, usemask='auto-multithresh', sidelobethreshold=3.0, noisethreshold=5.0, lownoisethreshold=1.5, negativethreshold=7.0, minbeamfrac=0.3, growiterations=50, dogrowprune=True, minpercentchange=1.0, fastnoise=False, restart=False, savemodel='none', calcres=True, calcpsf=True, parallel=True)```
keflavich commented 2 years ago

Did it result in a good image? Share a screenshot if so.

djeff1887 commented 2 years ago

It did: here's the image, mask, model, and residual from a random channel (269, for reference). We were planning to experiment with some deeper cleaning using the same parameters since there's still a lot of structure in the residual, but there wasn't enough time.

I will note that it's possible that there's some "glare" coming from N being off-screen in these images... it's hard to tell, but the areas to the north of N look suspicious when scrolling through the cube.

image

keflavich commented 2 years ago

@djeff1887 could you make sure the successful imaging parameters are in the override_tclean_commands.json file and that they have been run correctly?

keflavich commented 1 year ago

@djeff1887 check if these are OK

d-l-walker commented 1 year ago

@djeff1887 just echoing @keflavich's previous comment -- what's the status of this one? Is SPW 33 finished?

Also, I just checked and I don't think the channel parameters were ever updated, so we still have the size-mitigated cubes for everything (except SPW 33). I'll verify this, and then update the tclean commands as necessary.

d-l-walker commented 1 year ago

@keflavich I've updated the channel parameters in #389. I'm trying to figure out why it's failing the code style checks, but once I've done that could you merge and re-run the cleaning for all except SPW 33?

SPW 33 is not size mitigated, and it appears to have a higher cyclefactor, so presumably it's consistent with what @djeff1887 did when he worked on this, but it would be good to confirm that.

d-l-walker commented 10 months ago

@keflavich I think the re-clean needs to be executed again after the update to undo size mitigation in #389. The cubes on globus (~/member.uid___A001_X15a0_Xa6/calibrated/working/) still appear to be size mitigated.

keflavich commented 10 months ago

I re-triggered imaging.

pyhsiehATalma commented 10 months ago

截圖 2024-01-24 18 53 30

Same issue (absorption) of spw 33 (CS2-1), using a mask for absorption is probably necessary to remove the sidelobe (donut feature) from the absorption.

usemask = auto-multithresh negativethreshold (double=0.0) = negativethreshold * rms in residual image + location(median)

pyhsiehATalma commented 10 months ago

For the purpose of mosaic and combination, I subtract continuum emission using imcontsub over a narrow cube (CS2-1 line, -300 km/s - 300 km/s). The results are shown below. It seems to work ok (not perfect) to remove the continuum emission. I still don't understand why those artificial structures (like sidelobes from continuum) could be removed by subtracting continuum in image base.

截圖 2024-01-29 11 42 23

djeff1887 commented 9 months ago

We've stumbled onto these odd tear-like features in spw35. They resemble debris on a camera lens: they don't change when you scroll through the cube. Not immediately sure what they are, but Adam noted that they are likely caused by curvature in Sgr B2M's spectra. They also seem to be roughly concentric, centered on M. image image

d-l-walker commented 9 months ago

QA for latest continuum selection/imaging:

region_b_continuum

keflavich commented 6 months ago

Continuum was missing in latest reimaging from spw33_35 and full aggregate. Fixed in f207e656424347a7c55132c03b3a74a6bbb62e4c. Rerunning