def check_polgain(obs_apint_pcal, polcal_field='',):
"""check the solution of amp of polarisation calibrator
This function should be used to for two gain solutions, one with unpolarized source model
another one with polarised model.
The first solution should absorb the polarised single (amp change with parallactic angle or time)
The second solution should have no such signal if the correct model is used
"""
if isinstance(obs_apint_pcal, (list, tuple)):
# ToDo: generate the comparsion bettween this two solutions
pass
plotms(vis=obs_apint_pcal, xaxis='time', yaxis='amp', field=polcal_field,
correlation='/', coloraxis='antenna1', showgui=True)
def check_pol_kcross(vis):
""" check the correction for linear phase variation and select suitable scan
"""
plotms(vis=vis, ydatacolumn='corrected',
xaxis='freq', yaxis='phase',
field= polcal_field,
avgtime='1e9',
correlation='XY,YX',
spw='', antenna='DA48',
iteraxis='baseline',coloraxis='corr',
showgui=True,
plotrange=[0,0,-180,180])
def check_Dterm(Dtermtable, spw='', showgui=False, plotdir='./plots', basename=None,
overwrite=True, gridrows=2, gridcols=3, dpi=600,
**kwargs):
if basename is None:
basename = os.path.basename(Dtermtable)
outdir = os.path.join(plotdir, "Dterm-"+basename)
os.system('mkdir -p {}'.format(outdir))
for yaxis in ['amp', 'real', 'imag']:
subgroups = group_antenna(Dtermtable, subgroup_member=gridrows*gridcols)
for page, subgroup in enumerate(subgroups):
plotms(vis=Dtermtable, xaxis='frequency', yaxis=yaxis, antenna=subgroup,
spw=spw, iteraxis='antenna', coloraxis='corr',
plotfile='{}/freq_{}.page{}.png'.format(outdir, yaxis, page),
showgui=showgui, highres=True, **kwargs)
def check_XYfQU(vis):
"""check the correction for small non-linear absolute phase variation in different antenna
"""
plotms(vis=vis,
ydatacolumn='corrected',
xdatacolumn='corrected',
xaxis='real', yaxis='imag',
field=polcal_field,
avgtime='1e9',
avgchannel='64',
avgbaseline=True,
correlation='XY,YX',
spw='3',
coloraxis='corr',
showgui=True,
plotrange=[-0.06,0.06,-0.06,0.06])
def check_gain(phasecal_int='phase_int.gcal', phasecal_scan='phase_scan.gcal', ampcal_scan='amp_scan.gcal',
dpi=600, gridrows=2, gridcols=2, plotdir='./plots'):
"""check the gain table
In order to use this function, one should follow the same naming
It is designed to plot the phase and amplitude splution from the gain calibrator
Parameters:
phase_int : str
the file of integrated time (or specified short time) solution for phase variation
phase_scan : str
the file of scan based solution for gain calibrator, used for science target
ampcal_scan : str
the file of amplitude solution based on scan integration
gridrows : int
the number of rows
default: 2
gridcols : int
the number of columns
default: 2
dpi : int
the resolution of the saved png files
default: 600
plotdir : str
the root directory to put all the generated plots
"""
os.system('mkdir -p {}/gain_solution/'.format(plotdir))
if os.path.exists(phasecal_int):
print('Plotting {}'.format(phasecal_int))
subgroups = group_antenna(phasecal_int, subgroup_member=gridrows*gridcols)
for page, antenna in enumerate(subgroups):
plotms(vis=phasecal_int, gridrows=gridrows, gridcols=gridcols, xaxis='time',
yaxis='phase', antenna=antenna, iteraxis='antenna', coloraxis='corr',
plotfile='{}/gain_solution/phase_int_page{}.png'.format(plotdir, page),
plotrange=[0,0,-180,180], showgui=False, dpi=dpi, overwrite=True)
else:
print("Warning: you should give the correct integrated phase table! Set the phase_int parameter")
if os.path.exists(phasecal_scan):
print('Plotting {}'.format(phasecal_scan))
subgroups = group_antenna(phasecal_scan, subgroup_member=gridrows*gridcols)
for page, antenna in enumerate(subgroups):
plotms(vis=phasecal_scan, gridrows=gridrows, gridcols=gridcols, xaxis='time',
yaxis='phase', antenna=antenna, iteraxis='antenna', coloraxis='corr',
plotfile='{}/gain_solution/phase_scan_page{}.png'.format(plotdir, page),
plotrange=[0,0,-180,180], showgui=False, dpi=dpi, overwrite=True)
else:
print("Warning: you should give the correct scan averaged phase table! Set the phase_scan parameter")
if os.path.exists(ampcal_scan):
print('Plotting {}'.format(ampcal_scan))
subgroups = group_antenna(ampcal_scan, subgroup_member=gridrows*gridcols)
for page, antenna in enumerate(subgroups):
for yaxis in ['amp', 'phase']:
plotms(vis=ampcal_scan, gridrows=gridrows, gridcols=gridcols, xaxis='time',
yaxis=yaxis, antenna=antenna, iteraxis='antenna', coloraxis='corr',
plotfile='{}/gain_solution/{}_page{}.png'.format(plotdir, yaxis, page),
showgui=False, dpi=dpi, overwrite=True)
else:
print("Warning: you should give the correct amp_scan calibration table! Set the amp_scan parameter")
def extractSpw(self,msName,intent = 'CALIBRATE_BANDPASS', listCal = []):
"Extract the spectra from a spw of a given intent"
es = aU.stuffForScienceDataReduction()
# vm = aU.ValueMapping(msName)
try:
tb.open(msName)
dataColNames = tb.colnames()
tb.close()
except:
print("##")
print("## Error to open : %s"%(msName))
print('## \n\n')
return(False,[], [],[])
if 'CORRECTED_DATA' in dataColNames:
dataCol = 'corrected'
else:
dataCol = 'data'
tb.open(msName+'/FIELD')
sourceIds = tb.getcol('SOURCE_ID')
tb.close()
intentSources = es.getIntentsAndSourceNames(msName)
if intentSources[intent]['name'][0] == '':
return(False, [], [], [])
calIds = intentSources[intent]['sourceid']
calName = intentSources[intent]['name']
calIds = sorted(dict.fromkeys(calIds).keys())
calName = sorted(dict.fromkeys(calName).keys())
### spw info
spwInfo = es.getSpwInfo(msName)
spwIds = sorted(spwInfo.keys())
print spwIds
listFile = []
listCalFile = []
listSuccess = []
listSpw = []
for calNameJ in calName:
found = False
if calNameJ in listCal:
found = True
if not found:
listCal.append(calNameJ)
for spwj in spwIds:
# spwChanFreqs = vm.spwInfo[j]['chanFreqs']
# print spwChanFreqs
spwId = "%s"%(spwj)
msNameWithoutSlash = msName.split('/')[-1]
msNameDat = self.workingDirectory+msNameWithoutSlash
calNameJwithoutmultiplename = calNameJ.split(";")[0]
fileName = "%s-%s-%s-spw%s.dat"%(msNameDat,intent,calNameJwithoutmultiplename,spwj)
print fileName
successSpw = plotms(vis = msName ,xaxis="frequency",xdatacolumn = "",yaxis="amp",ydatacolumn = dataCol ,selectdata=True,field = calNameJ,
spw = spwId ,timerange="",uvrange="",antenna="",scan="",correlation="",array="",observation="",msselect="",averagedata=True,
avgchannel="1",avgtime="1e9",avgscan=True,avgfield=True, avgbaseline=True,avgantenna= False,avgspw=False,scalar=False,
transform=False,freqframe="",restfreq="",veldef="RADIO",shift=[0.0, 0.0],extendflag=False,extcorr=False,extchannel=False,
iteraxis="",plotfile = fileName ,expformat="txt",
highres=False, overwrite=False,showgui=False)
listFile.append(fileName)
listCalFile.append(calNameJwithoutmultiplename)
listSpw.append(spwj)
listSuccess.append(successSpw)
if not successSpw :
print("## Problem with the extraction of %s ..."%(fileName))
print("vvvvvvvvvvvvvvvvvvvvvvvv")
print listFile
print("vvvvvvvvvvvvvvvvvvvvvvv")
return(listSuccess, listFile, listCalFile, listSpw)
def check_info(vis=None, showgui=False, plotdir='./plots', basename=None,
spw='', show_ants=True, show_mosaic=False, show_uvcoverage=True,
show_elevation=True, show_allobs=True, show_uv=True,
refant='1', overwrite=True, avgtime='1e8', avgchannel='1e8',
show_fields=False, fields=None,
show_intents=False, intents=['*BANDPASS*','*PHASE*','*TARGET*'],
**kwargs):
""" plot the basic information of the observation.
Plots include: antenna positions, UV coverage, mosaic coverage(if possible)
Examples:
To give a quick overview
check_info(vis=msfile, spw='')
if you also want to give a glance for the calibrators and science target:
plot_utils.check_info(obs, refant=refant, correlation='XX,YY', avgchannel='64', datacolumn='data')
Args:
vis (str): measurement file
showgui (bool): show the plot window, the plotmosaic does not support yet,
plotdir (str): the base directory for all the info plots.
spw (str): the spectral windows, if unset or empty string all the spws will plot at the same time;
specify the spws in stings can plot them one by one through the loop in spws.split(',')
show_ants (bool): plot the positions of the antennas
show_mosaic (bool): deprecated, it needs analysisUtils. Plot the relative positions of the mosaic
show_uvcoverage (bool): plot the uv coverage of different field. Also depends the field number
show_elevation (bool): plot the elevation with time for all the fields,
show_allobs (bool): plot amplitude vs time for all the fields together
refant (str): the reference antenna, set to '' to plot all the antennas
overwrite (bool): set to True to overwrite all the existing plots
intents (list): all the intents generated by the telescope
fields: all the tageted fields, could be string (the casa style) or list like intents.
Both intents and fields are provided, the fields will be used.
"""
if basename is None:
basename = os.path.basename(vis)
outdir = os.path.join(plotdir, "info-"+basename)
os.system('mkdir -p {}'.format(outdir))
if show_ants and not os.path.exists('{}/antpos.png'.format(outdir)):
# Checking antenna position, choosing the reference antenna
print('Plotting antenna positions...')
plotants(vis=vis, figfile='{}/antpos.png'.format(outdir))
if show_mosaic:
# TODO, adapt the function from analysisUtils
print("Warning, mosaic plot deprecated!")
pass
# if show_uvcoverage and not os.path.exists('{}/uvcoverage.png'.format(outdir)):
# print("Plotting u-v coverage...")
# plotms(vis=vis, xaxis='U', yaxis='V', coloraxis='field',
# spw=spw, showgui=showgui, avgchannel=avgchannel,
# plotfile='{}/all_uvcoverage.png'.format(outdir),
# overwrite=overwrite)
if show_elevation and not os.path.exists('{}/elevation.png'.format(outdir)):
print("Plotting elevation with time...")
# Checking the evevation, determine the need of elivation calibration
plotms(vis=vis, xaxis='time', yaxis='elevation', spw=spw,
avgchannel=avgchannel, coloraxis='field', highres=True,
plotfile='{}/elevation.png'.format(outdir),
showgui=showgui, overwrite=overwrite)
if show_allobs and not os.path.exists('{}/all_observations.png'.format(outdir)):
print("Plotting amplitude with time for all obs...")
plotms(vis=vis, xaxis='time', yaxis='amp', spw=spw, highres=True,
avgchannel=avgchannel, avgtime='60', coloraxis='field',
plotfile='{}/all_observations.png'.format(outdir),
showgui=showgui, overwrite=overwrite, **kwargs)
if show_uv and not os.path.isfile('{}/uvcoverage.png'.format(outdir)):
plotms(vis=vis, xaxis='U', yaxis='V', coloraxis='field', highres=True,
spw=spw, showgui=showgui, avgchannel=avgchannel,
plotfile='{}/uvcoverage.png'.format(outdir),
overwrite=overwrite)
if show_fields:
if fields is None:
print("Warning: plot all the fields togeather!")
fields_list = ['',]
elif isinstance(fields, (list, tuple)):
fields_list = fields
elif isinstance(fields, str):
fields_list = fields.split(',')
for myfield in fields_list:
# amp change with time
plotms(vis=vis, field=myfield, xaxis='time', yaxis='amp', antenna=refant,
avgchannel=avgchannel, spw=spw, coloraxis='spw',
plotfile='{}/field{}_amp_time.png'.format(outdir, myfield),
highres=True, showgui=showgui, overwrite=overwrite, **kwargs)
# amplitude change with freq
plotms(vis=vis, field=myfield, xaxis='freq', yaxis='amp', antenna=refant,
avgtime=avgtime,spw=spw, coloraxis='scan',
plotfile='{}/field{}_amp_freq.png'.format(outdir, myfield),
highres=True, showgui=showgui, overwrite=overwrite, **kwargs)
# amp change with uvdist
plotms(vis=vis, field=myfield, xaxis='uvdist', yaxis='amp', antenna=refant,
avgchannel=avgchannel, spw=spw, coloraxis='spw',
plotfile='{}/field{}_amp_uvdist.png'.format(outdir, myfield),
highres=True, showgui=showgui, overwrite=overwrite, **kwargs)
if show_intents:
for myintent in intents:
myintent_name = myintent[1:-1]
# amp change with time
plotms(vis=vis, intent=myintent, xaxis='time', yaxis='amp', antenna=refant,
avgchannel=avgchannel, spw=spw, coloraxis='spw',
plotfile='{}/{}_amp_time.png'.format(outdir, myintent_name),
highres=True, showgui=showgui, overwrite=overwrite, **kwargs)
# amplitude change with freq
plotms(vis=vis, intent=myintent, xaxis='freq', yaxis='amp', antenna=refant,
avgtime=avgtime,spw=spw, coloraxis='scan',
plotfile='{}/{}_amp__freq.png'.format(outdir, myintent_name),
highres=True, showgui=showgui, overwrite=overwrite, **kwargs)
# amp change with uvdist
plotms(vis=vis, intent=myintent, xaxis='uvdist', yaxis='amp', antenna=refant,
avgchannel=avgchannel, spw=spw, coloraxis='spw',
plotfile='{}/{}_amp_uvdist.png'.format(outdir, myintent_name),
highres=True, showgui=showgui, overwrite=overwrite, **kwargs)
def check_bandpass(phaseint_cal='bpphase.gcal', bandpass_cal='bandpass.bcal', basename=None,
dpi=600, gridrows=2, gridcols=2, plotdir='./plots/bandpass'):
"""check the data quality of bandpass calibrator and the calibration
it can plot two solution: the short time gain (fgcal) and the bandpass solution (fbcal)
Parameters
----------
phasecal_int : str
the file of gain solution for bandpass calibrator
bpcal : str
the file of the bandpass solution
gridrows : int
the number of rows
default: 2
gridcols : int
the number of columns
default: 2
dpi : int
the resolution of the saved png files
default: 600
plotdir : str
the root directory to put all the generated plots
"""
if os.path.exists(phaseint_cal):
if basename is None:
outname = os.path.basename(phaseint_cal)
else:
outname = basename+'phaseint'
outdir = os.path.join(plotdir, outname)
os.system('mkdir -p {}'.format(outdir))
print('Plotting {}'.format(phaseint_cal))
subgroups = group_antenna(phaseint_cal, subgroup_member=gridrows*gridcols)
for page, antenna in enumerate(subgroups):
# after casa 6, consider using pathlib
plotms(vis=phaseint_cal, gridrows=gridrows, gridcols=gridcols, xaxis='time',
yaxis='phase', antenna=antenna, iteraxis='antenna', coloraxis='corr',
plotfile='{}/phase_page{}.png'.format(outdir, page),
plotrange=[0,0,-180,180],
showgui=False, dpi=dpi, overwrite=True, highres=True)
else:
print("Warning: you should give the correct bandpass gain table! Set the fgcal parameter")
if os.path.exists(bandpass_cal):
if basename is None:
outname = os.path.basename(bandpass_cal)
else:
outname = basename+'bandpass'
outdir = os.path.join(plotdir, outname)
os.system('mkdir -p {}'.format(outdir))
print('Plotting {}'.format(bandpass_cal))
subgroups = group_antenna(bandpass_cal, subgroup_member=gridrows*gridcols)
for page, antenna in enumerate(subgroups):
for yaxis in ['amp', 'phase']:
plotms(vis=bandpass_cal, gridrows=gridrows, gridcols=gridcols, xaxis='freq',
yaxis=yaxis, antenna=antenna, iteraxis='antenna', coloraxis='corr',
plotfile='{}/{}_page{}.png'.format(outdir, yaxis, page),
showgui=False, dpi=dpi, overwrite=True, highres=True)
else:
print("Warning: you should give the correct bandpass calibration table! Set the fbcal parameter")
def check_cal(vis='', spw='', refant='', ydatacolumn='corrected', basename=None,
field='', yaxis=['amplitude', 'phase'],
plot_freq=True, plot_time=True, plot_uvdist=True,
overwrite=True, showgui=False,
avgtime='1e8', avgchannel='1e8',
gridrows=2, gridcols=3, dpi=600, plotdir='./plots',
**kwargs):
"""
Check the calibrated data after `applycal`
The wrapped tools based on `plotms` for manual calibration.
Examples
--------
check the amplitude and phase of calibrator change with time and frequency:
(set refant to plot with baseline, which is much faster)
# to iterate the baseline of refant
check_cal(vis=msfile, spw='', field='bcal,gcal', refant='ea01')
# to include all the antenna
check_cal(vis=msfile, spw='', field='bcal,gcal')
for the science target:
check_cal(vis=msfile, spw='', field='science_field')
Parameters
----------
vis : str
measurements file
spw : str
same as casa
default: ''
refant : str
the reference antenna, like 'CM03', 'DV48', 'ea01'
if the refant is specified, the iteration axis will change to baseline, otherwise it will iterate through antennas
default: ''
ydatacolumn : str
the ydatacolumn of `plotms`
default: 'corrected'
field : str
the field or fileds to be plotted
example: '0,2,3' or 'J1427-4260,Mars', not support '~'
plot_freq : bool
Plot the amplitude-vs-frequency, phase-vs-frequency for both data.
default: True
plot_time : bool
plot the amplitude-vs-time, phase-vs-time for both data column
default: True
plot_uvdist : bool
plot amplitude vs uvdist
default: True
overwrite : bool
default: True
showgui : bool
default: True
gridrows : int
the number of rows
default: gridrows=2
gridcols : int
the number of columns
default: gridcols=3
dpi : int
the resolution of the saved png files
default: 600
plotdir : str
the root directory to put all the generated plots
"""
# checking the validation of parameters
if vis == '':
raise ValueError("You must give the measurements file name `vis`!")
if basename is None:
basename = os.path.basename(vis)
outdir = os.path.join(plotdir, "checkcal-"+basename)
os.system('mkdir -p {}'.format(outdir))
tb = tbtool()
if field == '':
# read all the fields
tb.open(vis)
field_list = np.unique(tb.getcol('FIELD_ID'))
field = list2str(field_list)
tb.close()
# plot the frequency related scatter
if plot_freq:
print("Plot frequency related calibration for field: {} ...".format(field))
os.system('mkdir -p {}/freq_{}/'.format(outdir, ydatacolumn))
for field_single in field.split(','):
print(">> field: {}".format(field_single))
for yx in yaxis:
if refant == 'all':
for spw_single in spw.split(','):
plotms(vis=vis, field=field_single, xaxis='frequency', yaxis=yx,
spw=spw_single, avgtime=avgtime, avgscan=False, coloraxis='corr',
ydatacolumn=ydatacolumn, showgui=showgui,
dpi = dpi, overwrite=overwrite, verbose=False,
plotfile='{}/freq_{}/field{}-spw{}-{}_vs_freq.all.png'.format(
outdir, ydatacolumn, field_single, spw_single, yx))
else:
if refant == '':
iteraxis = 'antenna'
else:
iteraxis = 'baseline'
# generate all the antenna firstly
subgroups = group_antenna(vis, refant=refant, subgroup_member=gridrows*gridcols)
# print(subgroups)
for page, subgroup in enumerate(subgroups):
for spw_single in spw.split(','):
if spw == '':
mycoloraxis = 'spw'
else:
mycoloraxis = 'corr'
plotms(vis=vis, field=field_single, xaxis='frequency', yaxis=yx,
spw=spw_single, avgtime=avgtime, avgscan=False,
coloraxis=mycoloraxis,
antenna=subgroup, iteraxis=iteraxis, ydatacolumn=ydatacolumn,
showgui=showgui, gridrows=gridrows, gridcols=gridcols,
dpi = dpi, overwrite=overwrite, verbose=False, highres=True,
plotfile='{}/freq_{}/field{}-spw{}-{}_vs_freq.page{}.png'.format(
outdir, ydatacolumn, field_single, spw_single, yx, page),
**kwargs)
# the phase should be significantly improved after bandpass calibration
# especially for the phase calibrator
if plot_time:
print("Plot time related calibration for field: {} ...".format(field))
os.system('mkdir -p {}/time_{}/'.format(outdir, ydatacolumn))
for field_single in field.split(','):
print(">> field: {}".format(field_single))
for yx in yaxis:
# plot the general consistency of each field
if refant == 'all':
for spw_single in spw.split(','):
plotms(vis=vis, field=field_single, xaxis='time', yaxis=yx, spw=spw_single,
avgchannel=avgchannel, coloraxis='corr', ydatacolumn=ydatacolumn,
plotfile='{}/time_{}/field{}-spw{}-{}_vs_time.png'.format(
outdir, ydatacolumn, field_single, spw_single, yx),
showgui=showgui, dpi = dpi, overwrite=overwrite)
else:
if refant == '':
iteraxis = 'antenna'
else:
iteraxis = 'baseline'
subgroups = group_antenna(vis, refant=refant, subgroup_member=gridrows*gridcols)
for page, subgroup in enumerate(subgroups):
for spw_single in spw.split(','):
if spw == '':
mycoloraxis = 'spw'
else:
mycoloraxis = 'corr'
plotms(vis=vis, field=field_single, xaxis='time', yaxis=yx,
spw=spw_single, avgchannel=avgchannel, coloraxis=mycoloraxis,
antenna=subgroup, iteraxis=iteraxis, ydatacolumn=ydatacolumn,
showgui=showgui, gridrows=gridrows, gridcols=gridcols,
plotfile='{}/time_{}/field{}_spw{}_{}_vs_time.page{}.png'.format(
outdir, ydatacolumn, field_single, spw_single, yx, page),
dpi = dpi, overwrite=overwrite, highres=True, **kwargs)
if plot_uvdist:
# well behaved point source should show flat amplitude with uvdist
print("Plot uvdist related calibration for {} ...".format(field))
os.system('mkdir -p {}/uvdist/'.format(outdir))
for field_single in field.split(','):
print('>> field: {}'.format(field_single))
for spw_single in spw.split(','):
if spw == '':
mycoloraxis = 'spw'
else:
mycoloraxis = 'corr'
plotms(vis=vis, field=field_single, xaxis='uvdist', yaxis='amp', spw=spw_single,
avgchannel=avgchannel, coloraxis='corr', ydatacolumn=ydatacolumn,
plotfile='{}/uvdist/field{}_spw{}_amp_vs_uvdist.png'.format(outdir, field_single, spw_single),
dpi=dpi, overwrite=overwrite, showgui=showgui, highres=True, **kwargs)
plotms(vis=vis, field=field_single, xaxis='U', yaxis='V', spw=spw_single,
avgchannel=avgchannel, coloraxis=mycoloraxis, ydatacolumn=ydatacolumn,
plotfile='{}/uvdist/field{}_spw{}_uvcoverage.png'.format(outdir, field_single, spw_single),
dpi=dpi, overwrite=overwrite, showgui=showgui, highres=True, **kwargs)
def check_tsys(tsystable=None, spws=None, ants_subgroups=None, gridcols=2, gridrows=3,
basename=None, basedir='./', plotdir='./plots', showgui=False,
dpi=400):
"""the stand alone plot function for tsys
Example
-------
check_tsys(tsystable='msfile1.tsys')
check_tsys(tsystable='msfile1.tsys', spws='13,15,17,19')
Parameters
----------
vis : str
visibility of the measurement file
tdmspws : str
time domain mode spws, seperated with comma
ants_subgroups (list): the list contains the subgroups to be plot into one figure
spws : str
time domain mode spws, for example: '2,3,4' or '2~3'
gridrows : int
the rows for subplots
gridcols : int
the columns for subplots
plotdir : str
the directory where to generate the plots
showgui : bool
set to "True" to open the gui window
"""
if basename is None:
basename = os.path.basename(tsystable)
if ants_subgroups is None:
ants_subgroups = group_antenna(vis=tsystable, subgroup_member=gridrows*gridcols)
outdir = '{}/tsys-{}'.format(plotdir, basename)
os.system('mkdir -p {}'.format(outdir))
# plot tsys vs time, to pick out bad antenna
for page,antenna in enumerate(ants_subgroups):
plotms(vis=tsystable, xaxis='time', yaxis='Tsys',
coloraxis='spw', antenna=antenna,
gridcols=2, gridrows=gridrows, iteraxis='antenna',
showgui=showgui, dpi=dpi, highres=True,
plotfile='{}/Tsys_vs_time.page{}.png'.format(outdir, page))
# plot tsys vs frequency
if spws is not None:
for spw in spw_expand(spws):
plotms(vis=tsystable, xaxis='channel', yaxis='Tsys', spw=spw,
gridcols=2, gridrows=gridrows, iteraxis='antenna',
coloraxis='corr', antenna=antenna, showgui=showgui,
plotfile='{}/spw{}_tsys_vs_freq.page{}.png'.format(outdir, spw, page),
dpi=dpi, highres=True)
else:
plotms(vis=tsystable, xaxis='freq', yaxis='Tsys', spw='',
gridcols=2, gridrows=gridrows, iteraxis='antenna',
coloraxis='corr', antenna=antenna, showgui=showgui,
plotfile='{}/tsys_vs_freq.page{}.png'.format(outdir, page),
dpi=dpi, highres=True)
def check_cal(vis=None,
fdmspw=None,
tdmspws=None,
calibrator_fields=None,
ants=None,
refant=None,
detail=1,
ydatacolumn='corrected',
bandpass_calibrator=None,
phase_calibrator=None,
science_field=None,
flux_calibrator=None,
plot_tsys=False,
plot_freq=False,
plot_time=False,
plot_bandpass=False,
plot_solutions=False,
plot_target=False,
plot_uvdist=False,
overwrite=True,
showgui=False,
dpi=600,
plotdir='./plots'):
"""check the calibrated data after applycal
the wrapped plotms for self calibration
Parameters
----------
vis : str
measurements file
fdmspw : str
the spw of frequency domain mode
tdmspws : str
the spws of time domain mode, the spws used for tsys calibration
usually 128 channels.
example: '1,3,4', '1~3'
calibrator_fields : list
a list contains all the fields of calibrators
example: ['0', '2', '3'] or ['J1427-4206', 'Mars']
science_field : str
the fields of the science target
example: 'Cen*' or '4~22'
ydatacolumn : str
the ydatacolumn of `plotms`
detail : str
what detail the plot generates
0: gather all the antenna based information without set the `interation`
1: generates all the plots with `interation`='antenna'
2: generates all the plots with `interation`='baseline', require `refant`
ants : list
all the antennas to be included
refant : str
the reference antenna, like 'CM03', 'DV48'
bandpass_calibrator : str
the field of bandpass calibrator
example: '0' or 'J1427-4206'
phase_calibrator : str
the same as bandpass_calibrator but for bandpass
flux_calibrator : str
the same as bandpass_calibrator but for flux calibrator
plot_tsys : bool
plot the tsys calibration table, the filename should be vis+'.tsys'
require: `tdmspws`
plot_freq : bool
plot the amplitude-vs-frequency, phase-vs-frequency for both data
column and corrected data column
require: `fdmspw`, `refant`, `calibrator_fields`
plot_time : bool
plot the amplitude-vs-time, phase-vs-time for both data column
and corrected data column
require: `fdmspw`, `refant`, `calibrator_fields`
plot_uvdist : bool
plot amplitude-vs-uvdist
require: `calibrator_fields`
plot_solutions : bool
plot bandpass calibration and gain calibration
require: `flux_calibrator`, and with vis+'.banpass.cal',
vis+'.phase_inf.cal', vis+'flux.cal' availabe in current
directory
plot_target : bool
plot the amplitude-vs-amplitude and amplitude-vs-frequency for the
science target
require: `science_field`
plot_bandpass : bool
the plot option to control the plotbandpass task. The default value is
false since plotbandpass always make casa crash
overwrite, showgui, dpi
the same option for plotms, see casa document for more detail
plotdir : str
the root directory to put all the generated plots
"""
# Extract the antenna list from ms
if ants is None:
tb = tbtool()
tb.open(vis + '/ANTENNA', nomodify=True)
ants = tb.getcol('NAME')
tb.close()
# generates the antenna or baseline subgroups
gridcols = 2 # default
subgroup_member = 6 # default
gridrows = subgroup_member / gridcols # default column number is 2
if detail >= 1:
ants_subgroups = group_antenna(ants, subgroup_member=subgroup_member)
if detail >= 2:
if refant is None:
refant = random.choice(ants)
print('Warning: No refant specified, choose a random one!')
baselines = refant + '&*' # all the related baseline
baselines_subgroups = group_antenna(ants,
refant,
subgroup_member=subgroup_member)
if bandpass_calibrator:
calibrator_fields = [bandpass_calibrator]
# plot the frequency related scatter
if plot_freq:
print("Plot frequency related calibration for fields: {} ...".format(
calibrator_fields))
os.system('mkdir -p {}/freq_{}/'.format(plotdir, ydatacolumn))
for yaxis in ['amplitude', 'phase']:
for field in calibrator_fields:
if detail >= 0:
for spw_single in spw_expand(fdmspw):
plotms(
vis=vis,
field=field,
xaxis='frequency',
yaxis=yaxis,
spw=spw_single,
avgtime='1e8',
avgscan=True,
coloraxis='corr',
ydatacolumn=ydatacolumn,
showgui=showgui,
dpi=dpi,
overwrite=overwrite,
verbose=False,
plotfile='{}/freq_{}/field{}-spw{}-amp_vs_{}.all.png'
.format(plotdir, ydatacolumn, field, spw_single,
yaxis))
if detail >= 1: # antenna based plots
for page, antenna in enumerate(ants_subgroups):
for spw_single in spw_expand(fdmspw):
plotms(
vis=vis,
field=field,
xaxis='frequency',
yaxis=yaxis,
spw=spw_single,
avgtime='1e8',
avgscan=True,
coloraxis='corr',
antenna=antenna,
iteraxis='antenna',
ydatacolumn=ydatacolumn,
showgui=showgui,
gridrows=gridrows,
gridcols=2,
dpi=dpi,
overwrite=overwrite,
verbose=False,
plotfile=
'{}/freq_{}/field{}-spw{}-amp_vs_{}.page{}.png'
.format(plotdir, ydatacolumn, field,
spw_single, yaxis, page))
if detail >= 2: #baseline based plots
for page, baselines in enumerate(baselines_subgroups):
for spw_single in spw_expand(fdmspw):
plotms(
vis=vis,
field=field,
xaxis='frequency',
yaxis=yaxis,
spw=spw_single,
avgtime='1e8',
avgscan=True,
coloraxis='corr',
antenna=baselines,
iteraxis='baseline',
ydatacolumn=ydatacolumn,
showgui=showgui,
gridrows=gridrows,
gridcols=2,
dpi=dpi,
overwrite=overwrite,
verbose=False,
plotfile=
'{}/freq_{}/field{}-spw{}-amp_vs_{}.page{}.png'
.format(plotdir, ydatacolumn, field,
spw_single, yaxis, page))
# the phase should be significantly improved after bandpass calibration
# especially for the phase calibrator
if plot_time:
print("Plot time related calibration for fields: {} ...".format(
calibrator_fields))
os.system('mkdir -p {}/time_{}/'.format(plotdir, ydatacolumn))
for yaxis in ['amplitude', 'phase']:
# plot the general consistency of each field
for field in calibrator_fields:
if detail >= 0:
for spw_single in spw_expand(fdmspw):
plotms(vis=vis,
field=field,
xaxis='time',
yaxis=yaxis,
spw=spw_single,
avgchannel='1e8',
coloraxis='corr',
ydatacolumn=ydatacolumn,
showgui=showgui,
dpi=dpi,
overwrite=overwrite,
plotfile='{}/time_{}/field{}_{}_vs_time.png'.
format(plotdir, ydatacolumn, field, yaxis))
if detail >= 1: # antenna based plots
for page, antenna in enumerate(ants_subgroups):
for spw_single in spw_expand(fdmspw):
plotms(vis=vis,
field=field,
xaxis='time',
yaxis=yaxis,
spw=spw_single,
avgchannel='1e8',
coloraxis='corr',
antenna=antenna,
iteraxis='antenna',
ydatacolumn=ydatacolumn,
showgui=showgui,
gridrows=gridrows,
gridcols=2,
dpi=dpi,
overwrite=overwrite,
plotfile=
'{}/time_{}/field{}_{}_vs_time.page{}.png'.
format(plotdir, ydatacolumn, field, yaxis,
page))
if detail >= 2: # baseline based plots
for page, baselines in enumerate(baselines_subgroups):
for spw_single in spw_expand(fdmspw):
plotms(vis=vis,
field=field,
xaxis='time',
yaxis=yaxis,
spw=spw_single,
avgchannel='1e8',
coloraxis='corr',
antenna=baselines,
iteraxis='baseline',
ydatacolumn=ydatacolumn,
showgui=showgui,
gridrows=gridrows,
gridcols=2,
dpi=dpi,
overwrite=overwrite,
plotfile=
'{}/time_{}/field{}_{}_vs_time.page{}.png'.
format(plotdir, ydatacolumn, field, yaxis,
page))
if plot_tsys:
# plot tsys vs time, to pick out bad antenna
check_tsys(vis=vis,
ants_subgroups=ants_subgroups,
plotdir=plotdir,
tdmspws=tdmspws,
gridrows=gridrows,
gridcols=gridcols,
showgui=showgui)
if plot_uvdist:
# well behaved point source should show flat amplitude with uvdist
print("Plot uvdist related calibration for {} ...".format(
calibrator_fields))
os.system('mkdir -p {}/uvdist/'.format(plotdir))
for field in calibrator_fields:
plotms(vis=vis,
field=field,
xaxis='uvdist',
yaxis='amp',
avgchannel='1e8',
coloraxis='corr',
showgui=showgui,
dpi=dpi,
overwrite=overwrite,
plotfile='{}/uvdist/field{}_amp_vs_uvdist.png'.format(
plotdir, field))
if plot_solutions:
print("Plot calibration solutions ...".format(calibrator_fields))
os.system('mkdir -p {}/solutions/'.format(plotdir))
# bandpass
if plot_bandpass:
aU.plotbandpass(
caltable=vis + '.bandpass.cal',
xaxis='freq',
yaxis='both',
showatm=True,
interactive=showgui,
subplot=42,
figfile='{}/solutions/bandpasscal.png'.format(plotdir))
# flux calibrator model
plotms(vis=vis,
xaxis='uvdist',
yaxis='amp',
ydatacolumn='model',
field=flux_calibrator,
avgtime='1e8',
coloraxis='corr',
showgui=showgui,
dpi=dpi,
overwrite=overwrite,
plotfile='{}/solutions/flux_model_amp.png'.format(plotdir))
plotms(vis=vis,
xaxis='uvdist',
yaxis='phase',
ydatacolumn='model',
field=flux_calibrator,
avgtime='1e8',
coloraxis='corr',
showgui=showgui,
dpi=dpi,
overwrite=overwrite,
plotfile='{}/solutions/flux_model_phase.png'.format(plotdir))
# phase calibration table
for page, antenna in enumerate(ants_subgroups):
plotms(vis=vis + '.phase_inf.cal',
xaxis='time',
yaxis='phase',
coloraxis='corr',
iteraxis='antenna',
gridcols=2,
gridrows=gridrows,
showgui=showgui,
dpi=dpi,
overwrite=overwrite,
plotfile='{}/solutions/phase_inf_cal_page{}.png'.format(
plotdir, page))
# flux calibration table
plotms(vis=vis + '.flux.cal',
xaxis='time',
yaxis='amp',
coloraxis='corr',
iteraxis='antenna',
gridcols=2,
gridrows=gridrows,
showgui=showgui,
dpi=dpi,
overwrite=overwrite,
plotfile='{}/solutions/flux_cal_page{}.png'.format(
plotdir, page))
if plot_target:
print("Giving the science target a glance ...")
os.system('mkdir -p {}/target/'.format(plotdir))
if science_field is None:
raise ValueError("Science field is not specified!")
plotms(vis=vis,
xaxis='uvdist',
yaxis='amp',
ydatacolumn=ydatacolumn,
field=science_field,
avgchannel='1e8',
coloraxis='corr',
plotfile='{}/target/target_amp_vs_uvdist.png'.format(plotdir),
showgui=showgui,
dpi=dpi,
overwrite=overwrite)
for spw in spw_expand(fdmspw):
plotms(vis=vis,
xaxis='freq',
yaxis='amp',
spw=spw,
ydatacolumn=ydatacolumn,
field=science_field,
avgtime='1e8',
avgscan=True,
coloraxis='corr',
plotfile='{}/target/target_amp_vs_freq.png'.format(plotdir),
showgui=showgui,
dpi=dpi,
overwrite=overwrite)
def check_tsys(vis=None,
tdmspws=None,
ants_subgroups=None,
gridcols=2,
gridrows=3,
plotdir='./plots',
showgui=False):
"""the stand alone plot function for tsys
Parameters
----------
vis : str
visibility of the measurement file
tdmspws : str
time domain mode spws
ants_subgroups : list
the list contains the subgroups to be plot into one figure
tdmspws : str
time domain mode spws
for example: '2,3,4' or '2~3'
gridrows : int
the rows for subplots
gridcols : int
the columns for subplots
plotdir : str
the directory where to generate the plots
showgui : bool
set to "True" to open the gui window
"""
if ants_subgroups is None:
# Extract the antenna list from ms
tb = tbtool()
tb.open(vis + '/ANTENNA', nomodify=True)
ants = tb.getcol('NAME')
tb.close()
ants_subgroups = group_antenna(ants,
subgroup_member=gridrows * gridcols)
os.system('mkdir -p {}/tsys/'.format(plotdir))
# plot tsys vs time, to pick out bad antenna
for page, antenna in enumerate(ants_subgroups):
plotms(vis=vis + '.tsys',
xaxis='time',
yaxis='Tsys',
coloraxis='spw',
antenna=antenna,
gridcols=2,
gridrows=gridrows,
iteraxis='antenna',
showgui=showgui,
plotfile='{}/tsys/Tsys_vs_time.page{}.png'.format(
plotdir, page))
# plot tsys vs frequency
if tdmspws is None:
raise ValueError("No tdmspws founded!")
for spw in spw_expand(tdmspws):
plotms(vis=vis + '.tsys',
xaxis='freq',
yaxis='Tsys',
spw=spw,
gridcols=2,
gridrows=gridrows,
iteraxis='antenna',
coloraxis='corr',
antenna=antenna,
showgui=showgui,
plotfile='{}/tsys/spw{}_tsys_vs_freq.page{}.png'.format(
plotdir, spw, page))
def check_info(vis=None,
showgui=False,
plotdir='./plots',
sciencespws='',
show_ants=True,
show_mosaic=True,
show_uvcoverage=True,
show_allobs=True):
""" plot the basic information of the observation.
Plots include: antenna positions, UV coverage, mosaic coverage(if possible)
Parameters
----------
vis : str
measurement file
showgui : bool
show the plot window, (the plotmosaic does not support yet)
info_dir : str
the base directory for all the info plots
sciencespws : str
the spw related to the science target
show_mosaic : bool
plot the relative positions of the mosaic
show_ants : bool
plot the positions of the antennae
show_uvcoverage : bool
plot the uv coverage of different field, or only the science target if
sciencespws is specified
show_allobs : bool
plot the all the amp vs time
"""
os.system('mkdir -p {}/info'.format(plotdir))
plotdir = plotdir + '/info'
if show_ants:
plotants(vis=vis, figfile='{}/antenna_position.png'.format(plotdir))
if show_mosaic:
aU.plotmosaic(vis, figfile='{}/mosaic.png'.format(plotdir))
if show_uvcoverage:
plotms(vis=vis,
xaxis='U',
yaxis='V',
coloraxis='field',
spw=sciencespws,
showgui=showgui,
plotfile='{}/uvcoverage.png'.format(plotdir),
overwrite=True)
if show_allobs:
plotms(vis=vis,
xaxis='time',
yaxis='amp',
avgchannel='1e8',
avgtime='100',
coloraxis='field',
showgui=showgui,
plotfile='{}/all_observations.png'.format(plotdir),
overwrite=True)