def importeovsa(idbfiles=None,
ncpu=None,
timebin=None,
width=None,
visprefix=None,
udb_corr=True,
nocreatms=None,
doconcat=None,
modelms=None,
doscaling=False,
keep_nsclms=False):
casalog.origin('importeovsa')
# if type(idbfiles) == Time:
# filelist = ri.get_trange_files(idbfiles)
# else:
# # If input type is not Time, assume that it is the list of files to read
filelist = idbfiles
if type(filelist) == str:
filelist = [filelist]
filelist_tmp = []
for ll in filelist:
if not os.path.exists(ll):
casalog.post("Warning: {} not exist.".format(ll))
else:
filelist_tmp.append(ll)
filelist = filelist_tmp
if not filelist:
casalog.post("No file in idbfiles list exists. Abort.")
return False
for idx, ll in enumerate(filelist):
if ll[-1] == '/':
filelist[idx] = ll[:-1]
if not visprefix:
visprefix = './'
if not timebin:
timebin = '0s'
if not width:
width = 1
import sys
print 10
sys.stdout.flush()
if udb_corr:
udbcorr_path = visprefix + '/tmp_UDBcorr/'
print 0
sys.stdout.flush()
if not os.path.exists(udbcorr_path):
os.makedirs(udbcorr_path)
print 1
sys.stdout.flush()
from eovsapy import pipeline_cal as pc
print 2
sys.stdout.flush()
filelist_tmp = []
for ll in filelist:
filelist_tmp.append(
pc.udb_corr(ll, outpath=udbcorr_path, calibrate=True))
filelist = filelist_tmp
print 3
sys.stdout.flush()
print 4
sys.stdout.flush()
if not modelms:
if nocreatms:
filename = filelist[0]
modelms = ipe.creatms(filename, visprefix)
else:
if not os.path.exists(modelms):
if nocreatms:
filename = filelist[0]
modelms = ipe.creatms(filename, visprefix)
iterable = range(len(filelist))
t0 = time.time()
casalog.post(
'Perform importeovsa in parallel with {} CPUs...'.format(ncpu))
if ncpu == 1:
res = []
for fidx, ll in enumerate(filelist):
res.append(
importeovsa_iter(filelist, timebin, width, visprefix,
nocreatms, modelms, doscaling, keep_nsclms,
fidx))
if ncpu > 1:
import multiprocessing as mprocs
from functools import partial
imppart = partial(importeovsa_iter, filelist, timebin, width,
visprefix, nocreatms, modelms, doscaling,
keep_nsclms)
pool = mprocs.Pool(ncpu)
res = pool.map(imppart, iterable)
pool.close()
pool.join()
# print res
t1 = time.time()
timelapse = t1 - t0
print 'It took %f secs to complete' % timelapse
# results = pd.DataFrame({'succeeded': [], 'msfile': [], 'durtim': []})
# for r in res:
# results = results.append(pd.DataFrame({'succeeded': [r[0]], 'msfile': [r[1]], 'durtim': [r[2]]}))
# try:
succeeded = []
msfile = []
durtim = []
if doscaling:
msfile_scl = []
for r in res:
succeeded.append(r[0])
msfile.append(r[1])
msfile_scl.append(r[2])
durtim.append(r[3])
results = {
'succeeded': succeeded,
'msfile': msfile,
'msfile_scl': msfile_scl,
'durtim': durtim
}
else:
for r in res:
succeeded.append(r[0])
msfile.append(r[1])
durtim.append(r[2])
results = {'succeeded': succeeded, 'msfile': msfile, 'durtim': durtim}
# except:
# print 'errors occurred when creating the output summary.'
if doconcat:
from suncasa.tasks import concateovsa_cli as ce
msname = os.path.basename(filelist[0])
durtim = int(np.array(results['durtim']).sum())
if doscaling:
msfiles = list(
np.array(results['msfile_scl'])[np.where(
np.array(results['succeeded']) == True)])
if keep_nsclms:
concatvis = visprefix + msname + '-{:d}m{}.ms'.format(
durtim, '_scl')
else:
concatvis = visprefix + msname + '-{:d}m{}.ms'.format(
durtim, '')
else:
msfiles = list(
np.array(results['msfile'])[np.where(
np.array(results['succeeded']) == True)])
concatvis = visprefix + msname + '-{:d}m{}.ms'.format(durtim, '')
ce.concateovsa(msfiles,
concatvis,
datacolumn='data',
keep_orig_ms=True,
cols2rm="model,corrected")
return True
if udb_corr:
os.system('rm -rf {}'.format(udbcorr_path))
def calibeovsa(vis=None,
caltype=None,
interp=None,
docalib=True,
doflag=True,
flagant=None,
doimage=False,
imagedir=None,
antenna=None,
timerange=None,
spw=None,
stokes=None,
doconcat=False,
msoutdir=None,
keep_orig_ms=True):
'''
:param vis: EOVSA visibility dataset(s) to be calibrated
:param caltype:
:param interp:
:param docalib:
:param qlookimage:
:param flagant:
:param stokes:
:param doconcat:
:return:
'''
if type(vis) == str:
vis = [vis]
for idx, f in enumerate(vis):
if f[-1] == '/':
vis[idx] = f[:-1]
for msfile in vis:
casalog.origin('calibeovsa')
if not caltype:
casalog.post(
"Caltype not provided. Perform reference phase calibration and daily phase calibration."
)
caltype = [
'refpha', 'phacal', 'fluxcal'
] ## use this line after the phacal is applied # caltype = ['refcal']
if not os.path.exists(msfile):
casalog.post("Input visibility does not exist. Aborting...")
continue
if msfile.endswith('/'):
msfile = msfile[:-1]
if not msfile[-3:] in ['.ms', '.MS']:
casalog.post(
"Invalid visibility. Please provide a proper visibility file ending with .ms"
)
# if not caltable:
# caltable=[os.path.basename(vis).replace('.ms','.'+c) for c in caltype]
# get band information
tb.open(msfile + '/SPECTRAL_WINDOW')
nspw = tb.nrows()
bdname = tb.getcol('NAME')
bd_nchan = tb.getcol('NUM_CHAN')
bd = [int(b[4:]) - 1 for b in bdname] # band index from 0 to 33
# nchans = tb.getcol('NUM_CHAN')
# reffreqs = tb.getcol('REF_FREQUENCY')
# cenfreqs = np.zeros((nspw))
tb.close()
tb.open(msfile + '/ANTENNA')
nant = tb.nrows()
antname = tb.getcol('NAME')
antlist = [str(ll) for ll in range(len(antname) - 1)]
antennas = ','.join(antlist)
tb.close()
# get time stamp, use the beginning of the file
tb.open(msfile + '/OBSERVATION')
trs = {'BegTime': [], 'EndTime': []}
for ll in range(tb.nrows()):
tim0, tim1 = Time(tb.getcell('TIME_RANGE', ll) / 24 / 3600,
format='mjd')
trs['BegTime'].append(tim0)
trs['EndTime'].append(tim1)
tb.close()
trs['BegTime'] = Time(trs['BegTime'])
trs['EndTime'] = Time(trs['EndTime'])
btime = np.min(trs['BegTime'])
etime = np.max(trs['EndTime'])
# ms.open(vis)
# summary = ms.summary()
# ms.close()
# btime = Time(summary['BeginTime'], format='mjd')
# etime = Time(summary['EndTime'], format='mjd')
## stop using ms.summary to avoid conflicts with importeovsa
t_mid = Time((btime.mjd + etime.mjd) / 2., format='mjd')
print "This scan observed from {} to {} UTC".format(
btime.iso, etime.iso)
gaintables = []
if ('refpha' in caltype) or ('refamp' in caltype) or ('refcal'
in caltype):
refcal = ra.sql2refcalX(btime)
pha = refcal['pha'] # shape is 15 (nant) x 2 (npol) x 34 (nband)
pha[np.where(refcal['flag'] == 1)] = 0.
amp = refcal['amp']
amp[np.where(refcal['flag'] == 1)] = 1.
t_ref = refcal['timestamp']
# find the start and end time of the local day when refcal is registered
try:
dhr = t_ref.LocalTime.utcoffset().total_seconds() / 60. / 60.
except:
dhr = -7.
bt = Time(np.fix(t_ref.mjd + dhr / 24.) - dhr / 24., format='mjd')
et = Time(bt.mjd + 1., format='mjd')
(yr, mon, day) = (bt.datetime.year, bt.datetime.month,
bt.datetime.day)
dirname = caltbdir + str(yr) + str(mon).zfill(2) + '/'
if not os.path.exists(dirname):
os.mkdir(dirname)
# check if there is any ROACH reboot between the reference calibration found and the current data
t_rbts = db.get_reboot(Time([t_ref, btime]))
if not t_rbts:
casalog.post(
"Reference calibration is derived from observation at " +
t_ref.iso)
print "Reference calibration is derived from observation at " + t_ref.iso
else:
casalog.post(
"Oh crap! Roach reboot detected between the reference calibration time "
+ t_ref.iso + ' and the current observation at ' +
btime.iso)
casalog.post("Aborting...")
print "Oh crap! Roach reboot detected between the reference calibration time " + t_ref.iso + ' and the current observation at ' + btime.iso
print "Aborting..."
para_pha = []
para_amp = []
calpha = np.zeros((nspw, 15, 2))
calamp = np.zeros((nspw, 15, 2))
for s in range(nspw):
for n in range(15):
for p in range(2):
calpha[s, n, p] = pha[n, p, bd[s]]
calamp[s, n, p] = amp[n, p, bd[s]]
para_pha.append(np.degrees(pha[n, p, bd[s]]))
para_amp.append(amp[n, p, bd[s]])
if 'fluxcal' in caltype:
calfac = pc.get_calfac(Time(t_mid.iso.split(' ')[0] + 'T23:59:59'))
t_bp = Time(calfac['timestamp'], format='lv')
if int(t_mid.mjd) == int(t_bp.mjd):
accalfac = calfac['accalfac'] # (ant x pol x freq)
# tpcalfac = calfac['tpcalfac'] # (ant x pol x freq)
caltb_autoamp = dirname + t_bp.isot[:-4].replace(
':', '').replace('-', '') + '.bandpass'
if not os.path.exists(caltb_autoamp):
bandpass(vis=msfile,
caltable=caltb_autoamp,
solint='inf',
refant='eo01',
minblperant=0,
minsnr=0,
bandtype='B',
docallib=False)
tb.open(caltb_autoamp, nomodify=False) # (ant x spw)
bd_chanidx = np.hstack([[0], bd_nchan.cumsum()])
for ll in range(nspw):
antfac = np.sqrt(
accalfac[:, :, bd_chanidx[ll]:bd_chanidx[ll + 1]])
# # antfac *= tpcalfac[:, :,bd_chanidx[ll]:bd_chanidx[ll + 1]]
antfac = np.moveaxis(antfac, 0, 2)
cparam = np.zeros((2, bd_nchan[ll], nant))
cparam[:, :, :-3] = 1.0 / antfac
tb.putcol('CPARAM', cparam + 0j, ll * nant, nant)
paramerr = tb.getcol('PARAMERR', ll * nant, nant)
paramerr = paramerr * 0
tb.putcol('PARAMERR', paramerr, ll * nant, nant)
bpflag = tb.getcol('FLAG', ll * nant, nant)
bpant1 = tb.getcol('ANTENNA1', ll * nant, nant)
bpflagidx, = np.where(bpant1 >= 13)
bpflag[:] = False
bpflag[:, :, bpflagidx] = True
tb.putcol('FLAG', bpflag, ll * nant, nant)
bpsnr = tb.getcol('SNR', ll * nant, nant)
bpsnr[:] = 100.0
bpsnr[:, :, bpflagidx] = 0.0
tb.putcol('SNR', bpsnr, ll * nant, nant)
tb.close()
msg_prompt = "Scaling calibration is derived for {}.".format(
msfile)
casalog.post(msg_prompt)
print msg_prompt
gaintables.append(caltb_autoamp)
else:
msg_prompt = "Caution: No TPCAL is available on {}. No scaling calibration is derived for {}.".format(
t_mid.datetime.strftime('%b %d, %Y'), msfile)
casalog.post(msg_prompt)
print msg_prompt
if ('refpha' in caltype) or ('refcal' in caltype):
# caltb_pha = os.path.basename(vis).replace('.ms', '.refpha')
# check if the calibration table already exists
caltb_pha = dirname + t_ref.isot[:-4].replace(':', '').replace(
'-', '') + '.refpha'
if not os.path.exists(caltb_pha):
gencal(vis=msfile,
caltable=caltb_pha,
caltype='ph',
antenna=antennas,
pol='X,Y',
spw='0~' + str(nspw - 1),
parameter=para_pha)
gaintables.append(caltb_pha)
if ('refamp' in caltype) or ('refcal' in caltype):
# caltb_amp = os.path.basename(vis).replace('.ms', '.refamp')
caltb_amp = dirname + t_ref.isot[:-4].replace(':', '').replace(
'-', '') + '.refamp'
if not os.path.exists(caltb_amp):
gencal(vis=msfile,
caltable=caltb_amp,
caltype='amp',
antenna=antennas,
pol='X,Y',
spw='0~' + str(nspw - 1),
parameter=para_amp)
gaintables.append(caltb_amp)
# calibration for the change of delay center between refcal time and beginning of scan -- hopefully none!
xml, buf = ch.read_calX(4, t=[t_ref, btime], verbose=False)
if buf:
dly_t2 = Time(stf.extract(buf[0], xml['Timestamp']), format='lv')
dlycen_ns2 = stf.extract(buf[0], xml['Delaycen_ns'])[:15]
xml, buf = ch.read_calX(4, t=t_ref)
dly_t1 = Time(stf.extract(buf, xml['Timestamp']), format='lv')
dlycen_ns1 = stf.extract(buf, xml['Delaycen_ns'])[:15]
dlycen_ns_diff = dlycen_ns2 - dlycen_ns1
for n in range(2):
dlycen_ns_diff[:, n] -= dlycen_ns_diff[0, n]
print 'Multi-band delay is derived from delay center difference at {} & {}'.format(
dly_t1.iso, dly_t2.iso)
# print '=====Delays relative to Ant 14====='
# for i, dl in enumerate(dlacen_ns_diff[:, 0] - dlacen_ns_diff[13, 0]):
# ant = antlist[i]
# print 'Ant eo{0:02d}: x {1:.2f} ns & y {2:.2f} ns'.format(int(ant) + 1, dl
# dlacen_ns_diff[i, 1] - dlacen_ns_diff[13, 1])
# caltb_mbd0 = os.path.basename(vis).replace('.ms', '.mbd0')
caltb_dlycen = dirname + dly_t2.isot[:-4].replace(':', '').replace(
'-', '') + '.dlycen'
if not os.path.exists(caltb_dlycen):
gencal(vis=msfile,
caltable=caltb_dlycen,
caltype='mbd',
pol='X,Y',
antenna=antennas,
parameter=dlycen_ns_diff.flatten().tolist())
gaintables.append(caltb_dlycen)
if 'phacal' in caltype:
phacals = np.array(
ra.sql2phacalX([bt, et], neat=True, verbose=False))
if not phacals.any() or len(phacals) == 0:
print "Found no phacal records in SQL database, will skip phase calibration"
else:
# first generate all phacal calibration tables if not already exist
t_phas = Time([phacal['t_pha'] for phacal in phacals])
# sort the array in ascending order by t_pha
sinds = t_phas.mjd.argsort()
t_phas = t_phas[sinds]
phacals = phacals[sinds]
caltbs_phambd = []
for i, phacal in enumerate(phacals):
# filter out phase cals with reference time stamp >30 min away from the provided refcal time
if (phacal['t_ref'].jd -
refcal['timestamp'].jd) > 30. / 1440.:
del phacals[i]
del t_phas[i]
continue
else:
t_pha = phacal['t_pha']
phambd_ns = phacal['pslope']
for n in range(2):
phambd_ns[:, n] -= phambd_ns[0, n]
# set all flagged values to be zero
phambd_ns[np.where(phacal['flag'] == 1)] = 0.
caltb_phambd = dirname + t_pha.isot[:-4].replace(
':', '').replace('-', '') + '.phambd'
caltbs_phambd.append(caltb_phambd)
if not os.path.exists(caltb_phambd):
gencal(vis=msfile,
caltable=caltb_phambd,
caltype='mbd',
pol='X,Y',
antenna=antennas,
parameter=phambd_ns.flatten().tolist())
# now decides which table to apply depending on the interpolation method ("neatest" or "linear")
if interp == 'nearest':
tbind = np.argmin(np.abs(t_phas.mjd - t_mid.mjd))
dt = np.min(np.abs(t_phas.mjd - t_mid.mjd)) * 24.
print "Selected nearest phase calibration table at " + t_phas[
tbind].iso
gaintables.append(caltbs_phambd[tbind])
if interp == 'linear':
# bphacal = ra.sql2phacalX(btime)
# ephacal = ra.sql2phacalX(etime,reverse=True)
bt_ind, = np.where(t_phas.mjd < btime.mjd)
et_ind, = np.where(t_phas.mjd > etime.mjd)
if len(bt_ind) == 0 and len(et_ind) == 0:
print "No phacal found before or after the ms data within the day of observation"
print "Skipping daily phase calibration"
elif len(bt_ind) > 0 and len(et_ind) == 0:
gaintables.append(caltbs_phambd[bt_ind[-1]])
elif len(bt_ind) == 0 and len(et_ind) > 0:
gaintables.append(caltbs_phambd[et_ind[0]])
elif len(bt_ind) > 0 and len(et_ind) > 0:
bphacal = phacals[bt_ind[-1]]
ephacal = phacals[et_ind[0]]
# generate a new table interpolating between two daily phase calibrations
t_pha_mean = Time(np.mean(
[bphacal['t_pha'].mjd, ephacal['t_pha'].mjd]),
format='mjd')
phambd_ns = (bphacal['pslope'] +
ephacal['pslope']) / 2.
for n in range(2):
phambd_ns[:, n] -= phambd_ns[0, n]
# set all flagged values to be zero
phambd_ns[np.where(bphacal['flag'] == 1)] = 0.
phambd_ns[np.where(ephacal['flag'] == 1)] = 0.
caltb_phambd_interp = dirname + t_pha_mean.isot[:-4].replace(
':', '').replace('-', '') + '.phambd'
if not os.path.exists(caltb_phambd_interp):
gencal(vis=msfile,
caltable=caltb_phambd_interp,
caltype='mbd',
pol='X,Y',
antenna=antennas,
parameter=phambd_ns.flatten().tolist())
print "Using phase calibration table interpolated between records at " + bphacal[
't_pha'].iso + ' and ' + ephacal['t_pha'].iso
gaintables.append(caltb_phambd_interp)
if docalib:
clearcal(msfile)
applycal(vis=msfile,
gaintable=gaintables,
applymode='calflag',
calwt=False)
# delete the interpolated phase calibration table
try:
caltb_phambd_interp
except:
pass
else:
if os.path.exists(caltb_phambd_interp):
shutil.rmtree(caltb_phambd_interp)
if doflag:
# flag zeros and NaNs
flagdata(vis=msfile, mode='clip', clipzeros=True)
if flagant:
try:
flagdata(vis=msfile, antenna=flagant)
except:
print "Something wrong with flagant. Abort..."
if doimage:
from matplotlib import pyplot as plt
from suncasa.utils import helioimage2fits as hf
from sunpy import map as smap
if not antenna:
antenna = '0~12'
if not stokes:
stokes = 'XX'
if not timerange:
timerange = ''
if not spw:
spw = '1~3'
if not imagedir:
imagedir = '.'
#(yr, mon, day) = (bt.datetime.year, bt.datetime.month, bt.datetime.day)
#dirname = imagedir + str(yr) + '/' + str(mon).zfill(2) + '/' + str(day).zfill(2) + '/'
#if not os.path.exists(dirname):
# os.makedirs(dirname)
bds = [spw]
nbd = len(bds)
imgs = []
for bd in bds:
if '~' in bd:
bdstr = bd.replace('~', '-')
else:
bdstr = str(bd).zfill(2)
imname = imagedir + '/' + os.path.basename(msfile).replace(
'.ms', '.bd' + bdstr)
print 'Cleaning image: ' + imname
try:
clean(vis=msfile,
imagename=imname,
antenna=antenna,
spw=bd,
timerange=timerange,
imsize=[512],
cell=['5.0arcsec'],
stokes=stokes,
niter=500)
except:
print 'clean not successfull for band ' + str(bd)
else:
imgs.append(imname + '.image')
junks = ['.flux', '.mask', '.model', '.psf', '.residual']
for junk in junks:
if os.path.exists(imname + junk):
shutil.rmtree(imname + junk)
tranges = [btime.iso + '~' + etime.iso] * nbd
fitsfiles = [img.replace('.image', '.fits') for img in imgs]
hf.imreg(vis=msfile,
timerange=tranges,
imagefile=imgs,
fitsfile=fitsfiles,
usephacenter=False)
plt.figure(figsize=(6, 6))
for i, fitsfile in enumerate(fitsfiles):
plt.subplot(1, nbd, i + 1)
eomap = smap.Map(fitsfile)
sz = eomap.data.shape
if len(sz) == 4:
eomap.data = eomap.data.reshape((sz[2], sz[3]))
eomap.plot_settings['cmap'] = plt.get_cmap('jet')
eomap.plot()
eomap.draw_limb()
eomap.draw_grid()
plt.show()
if doconcat:
if len(vis) > 1:
# from suncasa.eovsa import concateovsa as ce
from suncasa.tasks import concateovsa_cli as ce
if msoutdir is None:
msoutdir = './'
concatvis = os.path.basename(vis[0])
concatvis = msoutdir + '/' + concatvis.split('.')[0] + '_concat.ms'
ce.concateovsa(vis,
concatvis,
datacolumn='corrected',
keep_orig_ms=keep_orig_ms,
cols2rm="model,corrected")
return [concatvis]
else:
return vis