def do_mstransform(infile, outdir, min_freq, max_freq, bottom_edge, width_freq=15.625):
"""
Perform the MS_TRANSFORM step
:param infile:
:param outdir:
:param min_freq:
:param max_freq:
:param bottom_edge:
:param width_freq:
:return:
"""
if not os.path.exists(outdir):
os.makedirs(outdir)
spw_range = freq_map(min_freq, max_freq, bottom_edge)
LOG.info('spw_range: {0}'.format(spw_range))
if spw_range.startswith('-1') or spw_range.endswith('-1'):
LOG.info('The spw_range is {0} which is outside the spectral window '.format(spw_range))
else:
step_freq = max_freq - min_freq
no_chan = int(step_freq * 1000.0 / width_freq) # MHz/kHz!!
outfile = os.path.join(outdir, 'vis_{0}~{1}'.format(min_freq, max_freq))
LOG.info('working on: {0}'.format(outfile))
if os.path.exists(outfile):
shutil.rmtree(outfile)
try:
# dump_all()
mstransform(
vis=infile,
outputvis=outfile,
regridms=True,
restfreq='1420.405752MHz',
mode='frequency',
nchan=no_chan,
outframe='lsrk',
interpolation='linear',
veltype='radio',
start='{0}MHz'.format(min_freq),
width='{0}kHz'.format(width_freq),
spw=spw_range,
combinespws=True,
nspw=1,
createmms=False,
datacolumn="data"
)
except Exception:
LOG.exception('*********\nmstransform exception:\n***********')
def do_cvel(infile, outdir, backup_dir, min_freq, max_freq, step_freq, width_freq, spec_window, obsId):
"""
Adapted from loop.split.py with changes
(1) deal with (max_freq - min_freq) % step_freq > 0
(2) some debug info
(3) obsId parameter for marking split_done
If spec_window is blank ('') then freq_map is called to define the spw selection
"""
if not os.path.exists(outdir):
os.system('mkdir ' + outdir)
if not os.path.exists(backup_dir):
os.system('mkdir ' + backup_dir)
steps = (max_freq - min_freq) / step_freq
rem = (max_freq - min_freq) % step_freq
if rem:
steps += 1
freq1 = min_freq
freq2 = min_freq + step_freq
bottom_edge = re.search('_[0-9]{3}_',infile)
if bottom_edge:
bedge = bottom_edge.group(0)
bedge = int(bedge[1:4])
if not sel_freq:
steps = 1
for i in range(steps):
if sel_freq:
#if (rem and (i == steps - 1)):
# freq_range = '%d~%d' % (min_freq + i * step_freq, max_freq)
#else:
# freq_range = str(freq1) + '~' + str(freq2)
if rem and i == steps - 1:
freq_range = '%d~%d' % (min_freq + i * step_freq, max_freq)
cvel_freq_range = '%f~%f' % (min_freq - 2 + i * step_freq, max_freq + 2)
else:
freq_range = str(freq1) + '~' + str(freq2)
cvel_freq_range = str(int(freq1-2)) + '~' + str(int(freq2+2))
spw_range = spec_window + ':' + freq_range + 'MHz'
cvel_spw_range = spec_window + ':' + cvel_freq_range + 'MHz'
# spanning spectral windows and selecting freq fails
# so use freq_map
# THEREFORE ~10 lines above are IGNORED!!
cvel_spw_range = freq_map(freq1, freq2, bedge)
else:
freq_range = 'min~max'
spw_range = spec_window
# If no spw is given then calculate from the max and min range
if spec_window == '':
spw_range = freq_map(freq1, freq2)
no_chan = int(step_freq * 1000.0 / width_freq) # MHz/kHz!!
# I think I always want this with cvel.
outfile = outdir + 'vis_' + freq_range
backupfile = backup_dir + 'vis_' + freq_range
if not debug:
if os.path.exists(outfile):
shutil.rmtree(outfile)
if os.path.exists(backupfile):
shutil.rmtree(backupfile)
print 'working on: ' + outfile
try:
# dump_all()
mstransform(
vis=infile,
outputvis=outfile,
regridms=True,
restfreq='1420.405752MHz',
mode='frequency',
nchan=no_chan,
outframe='lsrk',
interpolation='linear',
veltype='radio',
start=str(freq1) + 'MHz',
width=str(width_freq) + 'kHz',
spw=cvel_spw_range,
combinespws=True,
nspw=1,
createmms=False,
datacolumn="data")
# cvel(vis=infile,
# outputvis=outfile,
# restfreq='1420.405752MHz',
# mode='frequency',
# nchan=no_chan,
# outframe='lsrk',
# interpolation='linear',
# veltype='radio',
# start=str(freq1)+'MHz',
# width=str(width_freq)+'kHz',
# spw=spw_range)
except Exception, spEx:
print '*********\nSplit exception: %s\n***********' % str(spEx)
else:
msg = '''
mstransform(vis=%s,
outputvis=%s,
start=%s,
width=%s,
spw=%s,
nchan=%d)'''.format(infile, outfile, str(freq1)+'MHz', width_freq, cvel_spw_range, no_chan)
print msg
freq1 = freq1 + step_freq
freq2 = freq2 + step_freq
def extract_continuum(in_file=None,
out_file=None,
lines_to_flag=None,
gal='',
spw='',
vsys=0.0,
vwidth=500.,
do_statwt=True,
do_collapse=True,
quiet=False,
collapse_width=10000):
"""
Extract a continuum measurement set, flagging any specified lines,
reweighting using statwt, and then binning the continuum channels.
"""
sol_kms = 2.99e5
# Set up the input file
if os.path.isdir(in_file) == False:
if quiet == False:
print("Input file not found: " + in_file)
return
# pull the parameters from the galaxy in the mosaic file
# if gal != None:
# mosaic_parms = read_mosaic_key()
# if mosaic_parms.has_key(gal):
# vsys = mosaic_parms[gal]['vsys']
# vwidth = mosaic_parms[gal]['vwidth']
#
# set the list of lines to flag
if lines_to_flag == None:
lines_to_flag = line_list.lines_co + line_list.lines_13co + line_list.lines_c18o + line_list.lines_cn
# Make a continuum copy of the science data
os.system('rm -rf ' + out_file)
os.system('rm -rf ' + out_file + '.flagversions')
# command = 'cp -r -H '+in_file+' '+out_file
# print command
# var = os.system(command)
# print var
#
split(vis=in_file,
outputvis=out_file,
datacolumn='DATA',
keepflags=False,
field=gal,
spw=spw)
os.system('rm -rf ' + out_file + '.temp_copy')
command = 'mv ' + out_file + ' ' + out_file + '.temp_copy'
print command
var = os.system(command)
mstransform(vis=out_file + '.temp_copy',
outputvis=out_file,
outframe='Bary',
datacolumn='DATA')
# Figure out the line channels and flag them
vm = au.ValueMapping(out_file)
spw_flagging_string = ''
first = True
for spw in vm.spwInfo.keys():
this_spw_string = str(spw) + ':0'
if first:
spw_flagging_string += this_spw_string
first = False
else:
spw_flagging_string += ',' + this_spw_string
for line in lines_to_flag:
rest_linefreq_ghz = line_list.line_list[line]
shifted_linefreq_hz = rest_linefreq_ghz * (1. - vsys / sol_kms) * 1e9
hi_linefreq_hz = rest_linefreq_ghz * (
1. - (vsys - vwidth / 2.0) / sol_kms) * 1e9
lo_linefreq_hz = rest_linefreq_ghz * (
1. - (vsys + vwidth / 2.0) / sol_kms) * 1e9
spw_list = au.getScienceSpwsForFrequency(out_file, shifted_linefreq_hz)
if spw_list == []:
continue
print "Found overlap for " + line
for this_spw in spw_list:
freq_ra = vm.spwInfo[this_spw]['chanFreqs']
chan_ra = np.arange(len(freq_ra))
to_flag = (freq_ra >= lo_linefreq_hz) * (freq_ra <= hi_linefreq_hz)
to_flag[np.argmin(np.abs(freq_ra - shifted_linefreq_hz))]
low_chan = np.min(chan_ra[to_flag])
hi_chan = np.max(chan_ra[to_flag])
this_spw_string = str(this_spw) + ':' + str(low_chan) + '~' + str(
hi_chan)
if first:
spw_flagging_string += this_spw_string
first = False
else:
spw_flagging_string += ',' + this_spw_string
print "... proposed flagging " + spw_flagging_string
if spw_flagging_string != '':
flagdata(
vis=out_file,
spw=spw_flagging_string,
)
# Here - this comman needs to be examined and refined in CASA
# 5.6.1 to see if it can be sped up. Right now things are
# devastatingly slow.
if do_statwt:
print "... deriving empirical weights using STATWT."
statwt(
vis=out_file,
timebin='0.001s',
slidetimebin=False,
chanbin='spw',
statalg='classic',
datacolumn='DATA',
)
if do_collapse:
print "... Binning the continuum channels"
os.system('rm -rf ' + out_file + '.temp_copy')
os.system('rm -rf ' + out_file + '.temp_copy.flagversions')
command = 'mv ' + out_file + ' ' + out_file + '.temp_copy'
print command
var = os.system(command)
print var
command = 'mv ' + out_file + '.flagversions ' + out_file + '.temp_copy.flagversions'
print command
var = os.system(command)
print var
split(vis=out_file + '.temp_copy',
outputvis=out_file,
width=collapse_width,
datacolumn='DATA',
keepflags=False)
os.system('rm -rf ' + out_file + '.temp_copy')
os.system('rm -rf ' + out_file + '.temp_copy.flagversions')
os.system('rm -rf ' + out_file + '.temp_copy')
os.system('rm -rf ' + out_file + '.flagversions')
return
timestr = dt.strftime('%Y-%m-%dT%H-%M-%S')
ms_dir = '/mnt/Data/data1/20131122_941_6_FINAL_PRODUCTS/13B-266.sb27261805.eb28549602.56618.334173599535_calibrated_deepfield.ms'
output_vis = '/mnt/output/Chiles/split_vis/{0}'.format(timestr)
os.makedirs(output_vis)
gap = 4
start_time = datetime.datetime.now()
for i in range(1):
mstransform(vis=ms_dir,
outputvis='{0}/vis_{1}~{2}'.format(output_vis, 1020 + i * gap, 1024 + i * gap),
start='{0}MHz'.format(1020 + i * gap),
width='15.625kHz',
spw='2~2',
nchan=256,
regridms=True,
restfreq='1420.405752MHz',
mode='frequency',
outframe='lsrk',
interpolation='linear',
veltype='radio',
combinespws=True,
nspw=1,
createmms=False,
datacolumn="data")
end_time = datetime.datetime.now()
print 'Time taken:', end_time, start_time, end_time - start_time
ms_dir = '/mnt/Data/data1/20131122_941_6_FINAL_PRODUCTS/13B-266.sb27261805.eb28549602.56618.334173599535_calibrated_deepfield.ms'
output_vis = '/mnt/output/Chiles/split_vis/{0}'.format(timestr)
os.makedirs(output_vis)
gap = 4
start_time = datetime.datetime.now()
for i in range(1):
mstransform(vis=ms_dir,
outputvis='{0}/vis_{1}~{2}'.format(output_vis, 1020 + i * gap,
1024 + i * gap),
start='{0}MHz'.format(1020 + i * gap),
width='15.625kHz',
spw='2~2',
nchan=256,
regridms=True,
restfreq='1420.405752MHz',
mode='frequency',
outframe='lsrk',
interpolation='linear',
veltype='radio',
combinespws=True,
nspw=1,
createmms=False,
datacolumn="data")
end_time = datetime.datetime.now()
print 'Time taken:', end_time, start_time, end_time - start_time
nu_0=nu_0,
nterms_angle=1,
nterms_frac=1,
nu_min=min_freqs,
nu_max=max_freqs)
fluxtable = polcal_obj.setModelFluxScale(pol_source_object=p_source2,
field=leakagefield,
gaintable=complexgaintable,
referencefield=polanglefield,
transferfield=leakagefield,
nu_0=nu_0)
kcrosstable = polcal_obj.solveCrossHandDelays(refantmode="strict",
channels="13~115")
leakagetable = polcal_obj.calibrateLeakage(solint='inf,0.5MHz', minsnr=3.0)
polcal_obj.plotLeakage(plotdir="./")
polangletable = polcal_obj.calibratePolAngle(solint='inf,0.5MHz',
minsnr=3.0)
polcal_obj.applySolutions()
polcal_obj.finalPlots()
mstransform(vis=inputvis,
outputvis='A1314.ms',
datacolumn='corrected',
field=target)
#mstransform(vis=inputvis, outputvis='A1314_statwt.ms', datacolumn='corrected', field=target)
#statwt(vis='A1314_statwt.ms', datacolumn='data', timebin='0.001s')
def do_cvel(infile, outdir, backup_dir, min_freq, max_freq, step_freq,
width_freq, spec_window, obsId):
"""
Adapted from loop.split.py with changes
(1) deal with (max_freq - min_freq) % step_freq > 0
(2) some debug info
(3) obsId parameter for marking split_done
If spec_window is blank ('') then freq_map is called to define the spw selection
"""
if not os.path.exists(outdir):
os.system('mkdir ' + outdir)
if not os.path.exists(backup_dir):
os.system('mkdir ' + backup_dir)
steps = (max_freq - min_freq) / step_freq
rem = (max_freq - min_freq) % step_freq
if rem:
steps += 1
freq1 = min_freq
freq2 = min_freq + step_freq
bottom_edge = re.search('_[0-9]{3}_', infile)
if bottom_edge:
bedge = bottom_edge.group(0)
bedge = int(bedge[1:4])
if not sel_freq:
steps = 1
for i in range(steps):
if sel_freq:
#if (rem and (i == steps - 1)):
# freq_range = '%d~%d' % (min_freq + i * step_freq, max_freq)
#else:
# freq_range = str(freq1) + '~' + str(freq2)
if rem and i == steps - 1:
freq_range = '%d~%d' % (min_freq + i * step_freq, max_freq)
cvel_freq_range = '%f~%f' % (min_freq - 2 + i * step_freq,
max_freq + 2)
else:
freq_range = str(freq1) + '~' + str(freq2)
cvel_freq_range = str(int(freq1 - 2)) + '~' + str(
int(freq2 + 2))
spw_range = spec_window + ':' + freq_range + 'MHz'
cvel_spw_range = spec_window + ':' + cvel_freq_range + 'MHz'
# spanning spectral windows and selecting freq fails
# so use freq_map
# THEREFORE ~10 lines above are IGNORED!!
cvel_spw_range = freq_map(freq1, freq2, bedge)
else:
freq_range = 'min~max'
spw_range = spec_window
# If no spw is given then calculate from the max and min range
if spec_window == '':
spw_range = freq_map(freq1, freq2)
no_chan = int(step_freq * 1000.0 / width_freq) # MHz/kHz!!
# I think I always want this with cvel.
outfile = outdir + 'vis_' + freq_range
backupfile = backup_dir + 'vis_' + freq_range
if not debug:
if os.path.exists(outfile):
shutil.rmtree(outfile)
if os.path.exists(backupfile):
shutil.rmtree(backupfile)
print 'working on: ' + outfile
try:
# dump_all()
mstransform(vis=infile,
outputvis=outfile,
regridms=True,
restfreq='1420.405752MHz',
mode='frequency',
nchan=no_chan,
outframe='lsrk',
interpolation='linear',
veltype='radio',
start=str(freq1) + 'MHz',
width=str(width_freq) + 'kHz',
spw=cvel_spw_range,
combinespws=True,
nspw=1,
createmms=False,
datacolumn="data")
# cvel(vis=infile,
# outputvis=outfile,
# restfreq='1420.405752MHz',
# mode='frequency',
# nchan=no_chan,
# outframe='lsrk',
# interpolation='linear',
# veltype='radio',
# start=str(freq1)+'MHz',
# width=str(width_freq)+'kHz',
# spw=spw_range)
except Exception, spEx:
print '*********\nSplit exception: %s\n***********' % str(spEx)
else:
msg = '''
mstransform(vis=%s,
outputvis=%s,
start=%s,
width=%s,
spw=%s,
nchan=%d)'''.format(infile, outfile,
str(freq1) + 'MHz', width_freq, cvel_spw_range, no_chan)
print msg
freq1 = freq1 + step_freq
freq2 = freq2 + step_freq