""" This script was written for CASA 5.1.1 Datasets calibrated (in order of date observed): SB1: 2016.1.00484.L Observed 14 May 2017, 17 May 2017, and 19 May 2017 (3 execution blocks) LB1: 2016.1.00484.L Observed 23 September 2017 and 07 October 2017 (2 execution blocks) reducer: S. Andrews """ """ Starting matter """ import os execfile('reduction_utils.py') skip_plots = True # if True, can run script non-interactively """ Input for loading data """ prefix = 'Elias20' SB1_path = '/full_path/to_calibrated/msfile.ms' LB1_path = '/full_path/to_calibrated/msfile.ms' # Note that if you are downloading data from the archive, your SPW numbering # may differ from this script, depending on how you split your data out! data_params = {'SB1': {'vis' : SB1_path, 'name' : 'SB1', 'field': 'Elias_20', 'line_spws': np.array([0,4,8]), # CO SPWs 'line_freqs': np.array([2.30538e11, 2.30538e11, 2.30538e11]), }, 'LB1': {'vis' : LB1_path, 'name' : 'LB1', 'field' : 'Elias_20', 'line_spws': np.array([3,7]), # CO SPWs 'line_freqs': np.array([2.30538e11, 2.30538e11]), } } """ Check data (various options here; an example) """ if not skip_plots: for i in data_params.keys(): plotms(vis=data_params[i]['vis'], xaxis='channel', yaxis='amplitude', field=data_params[i]['field'], ydatacolumn='data', avgtime='1e8', avgscan=True, avgbaseline=True, iteraxis='spw') """ Identify 50 km/s-wide region containing CO emission; then flag that and do a spectral average to a pseudo-continuum MS """ for i in data_params.keys(): flagchannels_string = get_flagchannels(data_params[i], prefix, velocity_range=np.array([-15, 25])) avg_cont(data_params[i], prefix, flagchannels=flagchannels_string) """ Define simple masks and clean scales for imaging """ mask_pa = 154 # position angle of mask in degrees mask_maj = 0.8 # semimajor axis of mask in arcsec mask_min = 0.5 # semiminor axis of mask in arcsec mask_ra = '16h26m18.87s' mask_dec = '-24.28.20.18' SB1_mask = 'ellipse[[%s, %s], [%.1farcsec, %.1farcsec], %.1fdeg]' % \ (mask_ra, mask_dec, mask_maj, mask_min, mask_pa) LB1_mask = 'ellipse[[%s, %s], [%.1farcsec, %.1farcsec], %.1fdeg]' % \ (mask_ra, mask_dec, mask_maj, mask_min, mask_pa) SB_scales = [0, 5, 10] LB_scales = [0, 5, 20, 60, 120] if not skip_plots: """ Image each dataset individually """ # images are saved in the format prefix+'_name_initcont_exec#.ms' image_each_obs(data_params['SB1'], prefix, mask=SB1_mask, scales=SB_scales, threshold='0.15mJy', interactive=False) image_each_obs(data_params['LB1'], prefix, mask=LB1_mask, scales=LB_scales, threshold='0.06mJy', interactive=False) """ Fit Gaussians to roughly estimate centers, inclinations, PAs """ fit_gaussian(prefix+'_SB1_initcont_exec0.image', region=SB1_mask) #Peak : ICRS 16h26m18.866798s -24d28m20.18202s fit_gaussian(prefix+'_SB1_initcont_exec1.image', region=SB1_mask) #Peak : ICRS 16h26m18.866301s -24d28m20.15363s fit_gaussian(prefix+'_SB1_initcont_exec2.image', region=SB1_mask) #Peak : ICRS 16h26m18.864208s -24d28m20.17807s fit_gaussian(prefix+'_LB1_initcont_exec0.image', region=LB1_mask) #Peak : ICRS 16h26m18.866392s -24d28m20.18075s fit_gaussian(prefix+'_LB1_initcont_exec1.image', region=LB1_mask) #Peak : ICRS 16h26m18.866327s -24d28m20.18056s #PA of Gaussian component: 153.35 deg #Inclination of Gaussian component: 52.82 deg """ The emission appears to be aligned. """ """ Split out individual MSs for each execution """ split_all_obs(prefix+'_SB1_initcont.ms', prefix+'_SB1_initcont_exec') split_all_obs(prefix+'_LB1_initcont.ms', prefix+'_LB1_initcont_exec') """ Inspect the flux calibration. """ if not skip_plots: """ Assign rough emission geometry parameters and centers. """ PA, incl = 154, 53 phasecenter = au.radec2deg('16:26:18.87000, -24.28.19.69000') peakpos = au.radec2deg('16:26:18.866, -24.28.20.181') offsets = au.angularSeparation(peakpos[0], peakpos[1], phasecenter[0], phasecenter[1], True) offx, offy = 3600.*offsets[3], 3600.*offsets[2] """ Export MS contents into Numpy save files """ for msfile in [prefix+'_SB1_initcont_exec0.ms', prefix+'_SB1_initcont_exec1.ms', prefix+'_SB1_initcont_exec2.ms', prefix+'_LB1_initcont_exec0.ms', prefix+'_LB1_initcont_exec1.ms']: export_MS(msfile) """ Plot deprojected visibility profiles for all data together """ plot_deprojected([prefix+'_SB1_initcont_exec0.vis.npz', prefix+'_SB1_initcont_exec1.vis.npz', prefix+'_SB1_initcont_exec2.vis.npz', prefix+'_LB1_initcont_exec0.vis.npz', prefix+'_LB1_initcont_exec1.vis.npz'], fluxscale=[1.0, 1.0, 1.0, 1.0, 1.0], offx=offx, offy=offy, PA=PA, incl=incl, show_err=False) # small, but non-negligible discrepancies; use SB1xEB1 as reference """ Now inspect offsets by comparing against a reference """ estimate_flux_scale(reference=prefix+'_SB1_initcont_exec1_shift.vis.npz', comparison=prefix+'_SB1_initcont_exec0_shift.vis.npz', offx=offx, offy=offy, incl=incl, PA=PA) #The ratio of comparison : reference is 0.93053 #The scaling factor for gencal is 0.965 for your comparison measurement estimate_flux_scale(reference=prefix+'_SB1_initcont_exec1_shift.vis.npz', comparison=prefix+'_SB1_initcont_exec2_shift.vis.npz', offx=offx, offy=offy, incl=incl, PA=PA) #The ratio of comparison : reference is 1.00508 #The scaling factor for gencal is 1.003 for your comparison measurement estimate_flux_scale(reference=prefix+'_SB1_initcont_exec1_shift.vis.npz', comparison=prefix+'_LB1_initcont_exec0_shift.vis.npz', offx=offx, offy=offy, incl=incl, PA=PA) #The ratio of comparison : reference is 1.22256 #The scaling factor for gencal is 1.106 for your comparison measurement estimate_flux_scale(reference=prefix+'_SB1_initcont_exec1_shift.vis.npz', comparison=prefix+'_LB1_initcont_exec1.vis.npz', offx=offx, offy=offy, incl=incl, PA=PA) #The ratio of comparison : reference is 1.06908 #The scaling factor for gencal is 1.034 for your comparison measurement """ Correct the flux scales where appropriate. """ rescale_flux(prefix+'_SB1_initcont_exec0.ms', [0.961]) # this is slightly different than measured above; but this is derived using # the *average* offset from all the Oph measurements, to be consistent rescale_flux(prefix+'_LB1_initcont_exec0.ms', [1.106]) rescale_flux(prefix+'_LB1_initcont_exec1.ms', [1.034]) """ SELF-CAL for short-baseline data """ """ Merge the SB executions back into a single MS """ SB_cont_p0 = prefix+'_SB_contp0' os.system('rm -rf %s*' % SB_cont_p0) concat(vis=[prefix+'_SB1_initcont_exec0_rescaled.ms', prefix+'_SB1_initcont_exec1.ms', prefix+'_SB1_initcont_exec2.ms'], concatvis=SB_cont_p0+'.ms', dirtol='0.1arcsec', copypointing=False) """ Set up a clean mask """ common_mask = LB1_mask """ Initial clean """ tclean_wrapper(vis=SB_cont_p0+'.ms', imagename=SB_cont_p0, mask=common_mask, scales=SB_scales, threshold='0.15mJy', savemodel='modelcolumn') """ Define a noise annulus, measure the peak SNR in map """ noise_annulus = "annulus[[%s, %s],['%.2farcsec', '4.25arcsec']]" % \ (mask_ra, mask_dec, 1.1*mask_maj) estimate_SNR(SB_cont_p0+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_SB_contp0.image #Beam 0.268 arcsec x 0.225 arcsec (88.43 deg) #Flux inside disk mask: 101.68 mJy #Peak intensity of source: 35.81 mJy/beam #rms: 9.64e-02 mJy/beam #Peak SNR: 371.42 """ Self-calibration parameters """ SB_contspws = '0~11' SB_refant = 'DA46, DA51' SB1_obs0_timerange = '2017/05/13/00~2017/05/15/00' SB1_obs1_timerange = '2017/05/15/00~2017/05/18/00' SB1_obs2_timerange = '2017/05/18/00~2017/05/20/00' """ First round of phase-only self-cal (short baselines only) """ SB_p1 = prefix+'_SB.p1' os.system('rm -rf '+SB_p1) gaincal(vis=SB_cont_p0+'.ms', caltable=SB_p1, gaintype='T', spw=SB_contspws, refant=SB_refant, calmode='p', solint='30s', minsnr=1.5, minblperant=4) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=SB_p1, xaxis='time', yaxis='phase',subplot=441, iteration='antenna', timerange=SB1_obs0_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=SB_p1, xaxis='time', yaxis='phase',subplot=441, iteration='antenna', timerange=SB1_obs1_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=SB_p1, xaxis='time', yaxis='phase',subplot=441, iteration='antenna', timerange=SB1_obs2_timerange, plotrange=[0,0,-180,180]) """ Apply the solutions """ applycal(vis=SB_cont_p0+'.ms', spw=SB_contspws, gaintable=[SB_p1], interp='linearPD', calwt=True) """ Split off a corrected MS """ SB_cont_p1 = prefix+'_SB_contp1' os.system('rm -rf %s*' % SB_cont_p1) split(vis=SB_cont_p0+'.ms', outputvis=SB_cont_p1+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=SB_cont_p1+'.ms', imagename=SB_cont_p1, mask=common_mask, scales=SB_scales, threshold='0.1mJy', savemodel='modelcolumn') estimate_SNR(SB_cont_p1+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_SB_contp1.image #Beam 0.268 arcsec x 0.225 arcsec (88.45 deg) #Flux inside disk mask: 103.28 mJy #Peak intensity of source: 38.78 mJy/beam #rms: 3.47e-02 mJy/beam #Peak SNR: 1117.70 """ Second round of phase-only self-cal (short baselines only) """ SB_p2 = prefix+'_SB.p2' os.system('rm -rf '+SB_p2) gaincal(vis=SB_cont_p1+'.ms', caltable=SB_p2, gaintype='T', spw=SB_contspws, refant=SB_refant, calmode='p', solint='18s', minsnr=1.5, minblperant=4) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=SB_p2, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=SB1_obs0_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=SB_p2, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=SB1_obs1_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=SB_p2, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=SB1_obs2_timerange, plotrange=[0,0,-180,180]) """ Apply the solutions """ applycal(vis=SB_cont_p1+'.ms', spw=SB_contspws, gaintable=[SB_p2], interp='linearPD', calwt=True) """ Split off a corrected MS """ SB_cont_p2 = prefix+'_SB_contp2' os.system('rm -rf %s*' % SB_cont_p2) split(vis=SB_cont_p1+'.ms', outputvis=SB_cont_p2+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=SB_cont_p2+'.ms', imagename=SB_cont_p2, mask=common_mask, scales=SB_scales, threshold='0.07mJy', savemodel='modelcolumn') estimate_SNR(SB_cont_p2+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_SB_contp2.image #Beam 0.268 arcsec x 0.225 arcsec (88.50 deg) #Flux inside disk mask: 103.60 mJy #Peak intensity of source: 39.07 mJy/beam #rms: 3.43e-02 mJy/beam #Peak SNR: 1137.81 """ Amplitude self-cal (short baselines only) """ SB_ap = prefix+'_SB.ap' os.system('rm -rf '+SB_ap) gaincal(vis=SB_cont_p2+'.ms', caltable=SB_ap, gaintype='T', spw=SB_contspws, refant=SB_refant, calmode='ap', solint='inf', minsnr=3.0, minblperant=4, solnorm=False) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=SB_ap, xaxis='time', yaxis='amp', subplot=441, iteration='antenna', timerange=SB1_obs0_timerange, plotrange=[0,0,0,2]) plotcal(caltable=SB_ap, xaxis='time', yaxis='amp', subplot=441, iteration='antenna', timerange=SB1_obs1_timerange, plotrange=[0,0,0,2]) plotcal(caltable=SB_ap, xaxis='time', yaxis='amp', subplot=441, iteration='antenna', timerange=SB1_obs2_timerange, plotrange=[0,0,0,2]) """ Apply the solutions """ applycal(vis=SB_cont_p2+'.ms', spw=SB_contspws, gaintable=[SB_ap], interp='linearPD', calwt=True) """ Split off a corrected MS """ SB_cont_ap = prefix+'_SB_contap' os.system('rm -rf %s*' % SB_cont_ap) split(vis=SB_cont_p2+'.ms', outputvis=SB_cont_ap+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=SB_cont_ap+'.ms', imagename=SB_cont_ap, mask=common_mask, scales=SB_scales, threshold='0.07mJy', savemodel='modelcolumn') estimate_SNR(SB_cont_ap+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_SB_contap.image #Beam 0.268 arcsec x 0.225 arcsec (88.13 deg) #Flux inside disk mask: 103.14 mJy #Peak intensity of source: 38.81 mJy/beam #rms: 2.89e-02 mJy/beam #Peak SNR: 1341.85 """ SELF-CAL for the combined (short-baseline + long-baseline) data """ """ Merge the SB+LB executions into a single MS """ combined_cont_p0 = prefix+'_combined_contp0' os.system('rm -rf %s*' % combined_cont_p0) concat(vis=[SB_cont_ap+'.ms', prefix+'_LB1_initcont_exec0_rescaled.ms', prefix+'_LB1_initcont_exec1_rescaled.ms'], concatvis=combined_cont_p0+'.ms', dirtol='0.1arcsec', copypointing=False) """ Initial clean """ tclean_wrapper(vis=combined_cont_p0+'.ms', imagename=combined_cont_p0, mask=common_mask, scales=LB_scales, threshold='0.05mJy', savemodel='modelcolumn') estimate_SNR(combined_cont_p0+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_combined_contp0.image #Beam 0.040 arcsec x 0.029 arcsec (81.85 deg) #Flux inside disk mask: 105.18 mJy #Peak intensity of source: 3.10 mJy/beam #rms: 1.22e-02 mJy/beam #Peak SNR: 254.20 """ Self-calibration parameters """ combined_contspws = '0~19' combined_refant = 'DA61@A015,DV09@A007,DA50@A108,DA46@A034,DA51@A023' combined_spwmap = [0,0,0,0,4,4,4,4,8,8,8,8,12,12,12,12,16,16,16,16] LB1_obs0_timerange = '2017/09/22/00~2017/09/24/00' LB2_obs1_timerange = '2017/10/06/00~2017/10/09/00' """ First round of phase-only self-cal (all data) """ combined_p1 = prefix+'_combined.p1' os.system('rm -rf '+combined_p1) gaincal(vis=combined_cont_p0+'.ms', caltable=combined_p1, gaintype='T', combine='spw,scan', spw=combined_contspws, refant=combined_refant, calmode='p', solint='900s', minsnr=1.5, minblperant=4) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=combined_p1, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB1_obs0_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=combined_p1, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB2_obs1_timerange, plotrange=[0,0,-180,180]) """ Apply the solutions """ applycal(vis=combined_cont_p0+'.ms', spw=combined_contspws, spwmap=combined_spwmap, gaintable=[combined_p1], interp='linearPD', calwt=True, applymode='calonly') """ Split off a corrected MS """ combined_cont_p1 = prefix+'_combined_contp1' os.system('rm -rf %s*' % combined_cont_p1) split(vis=combined_cont_p0+'.ms', outputvis=combined_cont_p1+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=combined_cont_p1+'.ms', imagename=combined_cont_p1, mask=common_mask, scales=LB_scales, threshold='0.03mJy', savemodel='modelcolumn') estimate_SNR(combined_cont_p1+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_combined_contp1.image #Beam 0.040 arcsec x 0.029 arcsec (81.85 deg) #Flux inside disk mask: 104.22 mJy #Peak intensity of source: 3.09 mJy/beam #rms: 1.22e-02 mJy/beam #Peak SNR: 254.38 # ** map SNR improvement negligible, but quality improves ** """ Second round of phase-only self-cal (all data) """ combined_p2 = prefix+'_combined.p2' os.system('rm -rf '+combined_p2) gaincal(vis=combined_cont_p1+'.ms', caltable=combined_p2, gaintype='T', combine='spw,scan', spw=combined_contspws, refant=combined_refant, calmode='p', solint='360s', minsnr=1.5, minblperant=4) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=combined_p2, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB1_obs0_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=combined_p2, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB2_obs1_timerange, plotrange=[0,0,-180,180]) """ Apply the solutions """ applycal(vis=combined_cont_p1+'.ms', spw=combined_contspws, spwmap=combined_spwmap, gaintable=[combined_p2], interp='linearPD', calwt=True, applymode='calonly') """ Split off a corrected MS """ combined_cont_p2 = prefix+'_combined_contp2' os.system('rm -rf %s*' % combined_cont_p2) split(vis=combined_cont_p1+'.ms', outputvis=combined_cont_p2+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=combined_cont_p2+'.ms', imagename=combined_cont_p2, mask=common_mask, scales=LB_scales, threshold='0.03mJy', savemodel='modelcolumn') estimate_SNR(combined_cont_p2+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_combined_contp2.image #Beam 0.040 arcsec x 0.029 arcsec (81.85 deg) #Flux inside disk mask: 104.11 mJy #Peak intensity of source: 3.09 mJy/beam #rms: 1.21e-02 mJy/beam #Peak SNR: 255.77 # ** map quality still improving ** """ Third round of phase-only self-cal (all data) """ combined_p3 = prefix+'_combined.p3' os.system('rm -rf '+combined_p3) gaincal(vis=combined_cont_p2+'.ms', caltable=combined_p3, gaintype='T', combine='spw,scan', spw=combined_contspws, refant=combined_refant, calmode='p', solint='180s', minsnr=1.5, minblperant=4) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=combined_p3, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB1_obs0_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=combined_p3, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB2_obs1_timerange, plotrange=[0,0,-180,180]) """ Apply the solutions """ applycal(vis=combined_cont_p2+'.ms', spw=combined_contspws, spwmap=combined_spwmap, gaintable=[combined_p3], interp='linearPD', calwt=True, applymode='calonly') """ Split off a corrected MS """ combined_cont_p3 = prefix+'_combined_contp3' os.system('rm -rf %s*' % combined_cont_p3) split(vis=combined_cont_p2+'.ms', outputvis=combined_cont_p3+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=combined_cont_p3+'.ms', imagename=combined_cont_p3, mask=common_mask, scales=LB_scales, threshold='0.03mJy', savemodel='modelcolumn') estimate_SNR(combined_cont_p3+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_combined_contp3.image #Beam 0.040 arcsec x 0.029 arcsec (81.85 deg) #Flux inside disk mask: 104.09 mJy #Peak intensity of source: 3.16 mJy/beam #rms: 1.19e-02 mJy/beam #Peak SNR: 265.49 """ Fourth round of phase-only self-cal (all data) """ combined_p4 = prefix+'_combined.p4' os.system('rm -rf '+combined_p4) gaincal(vis=combined_cont_p3+'.ms', caltable=combined_p4, gaintype='T', combine='spw,scan', spw=combined_contspws, refant=combined_refant, calmode='p', solint='60s', minsnr=1.5, minblperant=4) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=combined_p4, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB1_obs0_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=combined_p4, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB2_obs1_timerange, plotrange=[0,0,-180,180]) """ Apply the solutions """ applycal(vis=combined_cont_p3+'.ms', spw=combined_contspws, spwmap=combined_spwmap, gaintable=[combined_p4], interp='linearPD', calwt=True, applymode='calonly') """ Split off a corrected MS """ combined_cont_p4 = prefix+'_combined_contp4' os.system('rm -rf %s*' % combined_cont_p4) split(vis=combined_cont_p3+'.ms', outputvis=combined_cont_p4+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=combined_cont_p4+'.ms', imagename=combined_cont_p4, mask=common_mask, scales=LB_scales, threshold='0.03mJy', savemodel='modelcolumn') estimate_SNR(combined_cont_p4+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_combined_contp4.image #Beam 0.040 arcsec x 0.029 arcsec (81.85 deg) #Flux inside disk mask: 104.24 mJy #Peak intensity of source: 3.29 mJy/beam #rms: 1.18e-02 mJy/beam #Peak SNR: 279.49 """ Fifth round of phase-only self-cal (all data) """ combined_p5 = prefix+'_combined.p5' os.system('rm -rf '+combined_p5) gaincal(vis=combined_cont_p4+'.ms', caltable=combined_p5, gaintype='T', combine='spw,scan', spw=combined_contspws, refant=combined_refant, calmode='p', solint='30s', minsnr=1.5, minblperant=4) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=combined_p5, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB1_obs0_timerange, plotrange=[0,0,-180,180]) plotcal(caltable=combined_p5, xaxis='time', yaxis='phase', subplot=441, iteration='antenna', timerange=LB2_obs1_timerange, plotrange=[0,0,-180,180]) """ Apply the solutions """ applycal(vis=combined_cont_p4+'.ms', spw=combined_contspws, spwmap=combined_spwmap, gaintable=[combined_p5], interp='linearPD', calwt=True, applymode='calonly') """ Split off a corrected MS """ combined_cont_p5 = prefix+'_combined_contp5' os.system('rm -rf %s*' % combined_cont_p5) split(vis=combined_cont_p4+'.ms', outputvis=combined_cont_p5+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=combined_cont_p5+'.ms', imagename=combined_cont_p5, mask=common_mask, scales=LB_scales, threshold='0.03mJy', savemodel='modelcolumn') estimate_SNR(combined_cont_p5+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_combined_contp5.image #Beam 0.040 arcsec x 0.029 arcsec (81.85 deg) #Flux inside disk mask: 104.09 mJy #Peak intensity of source: 3.34 mJy/beam #rms: 1.18e-02 mJy/beam #Peak SNR: 283.50 """ Amplitude self-cal (all data) """ combined_ap = prefix+'_combined.ap' os.system('rm -rf '+combined_ap) gaincal(vis=combined_cont_p5+'.ms', caltable=combined_ap, gaintype='T', combine='spw,scan', spw=combined_contspws, refant=combined_refant, calmode='ap', solint='900s', minsnr=3.0, minblperant=4, solnorm=False) if not skip_plots: """ Inspect gain tables """ plotcal(caltable=combined_ap, xaxis='time', yaxis='amp', subplot=441, iteration='antenna', timerange=LB1_obs0_timerange, plotrange=[0,0,0,2]) plotcal(caltable=combined_ap, xaxis='time', yaxis='amp', subplot=441, iteration='antenna', timerange=LB2_obs1_timerange, plotrange=[0,0,0,2]) """ Apply the solutions """ applycal(vis=combined_cont_p5+'.ms', spw=combined_contspws, spwmap=combined_spwmap, gaintable=[combined_ap], interp='linearPD', calwt=True, applymode='calonly') """ Split off a corrected MS """ combined_cont_ap = prefix+'_combined_contap' os.system('rm -rf %s*' % combined_cont_ap) split(vis=combined_cont_p5+'.ms', outputvis=combined_cont_ap+'.ms', datacolumn='corrected') """ Image the results; check the resulting map """ tclean_wrapper(vis=combined_cont_ap+'.ms', imagename=combined_cont_ap, mask=common_mask, scales=LB_scales, threshold='0.03mJy', savemodel='modelcolumn') estimate_SNR(combined_cont_ap+'.image', disk_mask=common_mask, noise_mask=noise_annulus) #Elias20_combined_contap.image #Beam 0.040 arcsec x 0.029 arcsec (82.29 deg) #Flux inside disk mask: 103.79 mJy #Peak intensity of source: 3.34 mJy/beam #rms: 1.18e-02 mJy/beam #Peak SNR: 282.82 # ** no change in SNR, but map quality definitely improved ** """ Final outputs """ """ Save the final MS """ os.system('cp -r '+combined_cont_ap+'.ms '+prefix+'_continuum.ms') os.system('tar cvzf '+prefix+'_continuum.ms.tgz '+prefix+'_continuum.ms') """ Make a fiducial continuum image (based on experimentation) """ scales = [0, 10, 25, 50, 100] tclean_wrapper(vis=combined_cont_ap+'.ms', imagename=prefix+'_continuum', mask=common_mask, scales=scales, threshold='0.06mJy', robust=0., gain=0.1, cycleniter=100) exportfits(prefix+'_continuum.image', prefix+'_continuum.fits')