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import os
import numpy as np
from datetime import datetime
from math import *
# import jdutil
import bisect
import pdb
from taskinit import ms, tb, qa, iatool, rgtool
from astropy.time import Time
from sunpy import sun
import astropy.units as u
import warnings
try:
from astropy.io import fits as pyfits
except:
try:
import pyfits
except ImportError:
raise ImportError('Neither astropy nor pyfits exists in this CASA installation')
def headerfix(header, PC_coor=True):
'''
this code fix the header problem of fits out from CASA 5.4+ which leads to a streched solar image
set PC_coor equal to True will reset the rotation matrix.
'''
keys2remove = []
for k in header:
if k.upper().startswith('PC'):
if not k.upper().startswith('PC0'):
pcidxs = k.upper().replace('PC', '')
hd_ = 'PC0' + pcidxs
keys2remove.append(k)
if PC_coor:
pcidx0, pcidx1 = pcidxs.split('_')
if pcidx0 == pcidx1:
header[hd_] = 1.0
else:
header[hd_] = 0.0
else:
header[hd_] = header[k]
for k in keys2remove:
header.remove(k)
return header
# from astropy.constants import R_sun, au
def msclearhistory(msfile):
from taskinit import tb
tb.open(msfile + '/HISTORY', nomodify=False)
nrows = tb.nrows()
if nrows > 0:
tb.removerows(range(nrows))
tb.close()
def read_horizons(t0=None, dur=None, vis=None, observatory=None, verbose=False):
'''
This function visits JPL Horizons to retrieve J2000 topocentric RA and DEC of the solar disk center
as a function of time.
Keyword arguments:
t0: Referece time in astropy.Time format
dur: duration of the returned coordinates. Default to 2 minutes
vis: CASA visibility dataset (in measurement set format). If provided, use entire duration from
the visibility data
observatory: observatory code (from JPL Horizons). If not provided, use information from visibility.
if no visibility found, use earth center (code=500)
verbose: True to provide extra information
Usage:
>>> from astropy.time import Time
>>> out = read_horizons(t0=Time('2017-09-10 16:00:00'), observatory='-81')
>>> out = read_horizons(vis = 'mydata.ms')
History:
BC (sometime in 2014): function was first wrote, followed by a number of edits by BC and SY
BC (2019-07-16): Added docstring documentation
'''
import urllib2
import ssl
if not t0 and not vis:
t0 = Time.now()
if not dur:
dur = 1. / 60. / 24. # default to 2 minutes
if t0:
try:
btime = Time(t0)
except:
print('input time ' + str(t0) + ' not recognized')
return -1
if vis:
if not os.path.exists(vis):
print('Input ms data ' + vis + ' does not exist! ')
return -1
try:
# ms.open(vis)
# summary = ms.summary()
# ms.close()
# btime = Time(summary['BeginTime'], format='mjd')
# etime = Time(summary['EndTime'], format='mjd')
## alternative way to avoid conflicts with importeovsa, if needed -- more time consuming
if observatory == 'geocentric':
observatory = '500'
else:
ms.open(vis)
metadata = ms.metadata()
if metadata.observatorynames()[0] == 'EVLA':
observatory = '-5'
elif metadata.observatorynames()[0] == 'EOVSA':
observatory = '-81'
elif metadata.observatorynames()[0] == 'ALMA':
observatory = '-7'
ms.close()
tb.open(vis)
btime_vis = Time(tb.getcell('TIME', 0) / 24. / 3600., format='mjd')
etime_vis = Time(tb.getcell('TIME', tb.nrows() - 1) / 24. / 3600., format='mjd')
tb.close()
if verbose:
print("Beginning time of this scan " + btime_vis.iso)
print("End time of this scan " + etime_vis.iso)
# extend the start and end time for jpl horizons by 0.5 hr on each end
btime = Time(btime_vis.mjd - 0.5 / 24., format='mjd')
dur = etime_vis.mjd - btime_vis.mjd + 1.0 / 24.
except:
print('error in reading ms file: ' + vis + ' to obtain the ephemeris!')
return -1
# default the observatory to geocentric, if none provided
if not observatory:
observatory = '500'
etime = Time(btime.mjd + dur, format='mjd')
try:
cmdstr = "https://ssd.jpl.nasa.gov/horizons_batch.cgi?batch=1&TABLE_TYPE='OBSERVER'&QUANTITIES='1,17,20'&CSV_FORMAT='YES'&ANG_FORMAT='DEG'&CAL_FORMAT='BOTH'&SOLAR_ELONG='0,180'&CENTER='{}@399'&COMMAND='10'&START_TIME='".format(
observatory) + btime.iso.replace(' ', ',') + "'&STOP_TIME='" + etime.iso[:-4].replace(' ',
',') + "'&STEP_SIZE='1m'&SKIP_DAYLT='NO'&EXTRA_PREC='YES'&APPARENT='REFRACTED'"
cmdstr = cmdstr.replace("'", "%27")
try:
context = ssl._create_unverified_context()
f = urllib2.urlopen(cmdstr, context=context)
except:
f = urllib2.urlopen(cmdstr)
lines = f.readlines()
f.close()
except:
# todo use geocentric coordinate for the new VLA data
import requests, collections
params = collections.OrderedDict()
params['batch'] = '1'
params['TABLE_TYPE'] = "'OBSERVER'"
params['QUANTITIES'] = "'1,17,20'"
params['CSV_FORMAT'] = "'YES'"
params['ANG_FORMAT'] = "'DEG'"
params['CAL_FORMAT'] = "'BOTH'"
params['SOLAR_ELONG'] = "'0,180'"
if observatory == '500':
params['CENTER'] = "'500'"
else:
params['CENTER'] = "'{}@399'".format(observatory)
params['COMMAND'] = "'10'"
params['START_TIME'] = "'{}'".format(btime.iso[:-4].replace(' ', ','))
params['STOP_TIME'] = "'{}'".format(etime.iso[:-4].replace(' ', ','))
params['STEP_SIZE'] = "'1m'"
params['SKIP_DAYLT'] = "'NO'"
params['EXTRA_PREC'] = "'YES'"
params['APPAENT'] = "'REFRACTED'"
results = requests.get("https://ssd.jpl.nasa.gov/horizons_batch.cgi", params=params)
lines = [ll for ll in results.iter_lines()]
nline = len(lines)
istart = 0
for i in range(nline):
line = lines[i]
if line[0:5] == '$$SOE': # start recording
istart = i + 1
if line[0:5] == '$$EOE': # end recording
iend = i
newlines = lines[istart:iend]
nrec = len(newlines)
ephem_ = []
t = []
ra = []
dec = []
p0 = []
delta = []
for line in newlines:
items = line.split(',')
t.append(Time(float(items[1]), format='jd').mjd)
ra.append(np.radians(float(items[4])))
dec.append(np.radians(float(items[5])))
p0.append(float(items[6]))
delta.append(float(items[8]))
# convert list of dictionary to a dictionary of arrays
ephem = {'time': t, 'ra': ra, 'dec': dec, 'p0': p0, 'delta': delta}
return ephem
def read_msinfo(vis=None, msinfofile=None, use_scan_time=True):
import glob
# read MS information #
msinfo = dict.fromkeys(['vis', 'scans', 'fieldids', 'btimes', 'btimestr', 'inttimes', 'ras', 'decs', 'observatory'])
ms.open(vis)
metadata = ms.metadata()
observatory = metadata.observatorynames()[0]
scans = ms.getscansummary()
scanids = sorted(scans.keys(), key=lambda x: int(x))
nscanid = len(scanids)
btimes = []
btimestr = []
etimes = []
fieldids = []
inttimes = []
dirs = []
ras = []
decs = []
ephem_file = glob.glob(vis + '/FIELD/EPHEM*SUN.tab')
if ephem_file:
print('Loading ephemeris info from {}'.format(ephem_file[0]))
tb.open(ephem_file[0])
col_ra = tb.getcol('RA')
col_dec = tb.getcol('DEC')
col_mjd = tb.getcol('MJD')
if use_scan_time:
from scipy.interpolate import interp1d
f_ra = interp1d(col_mjd, col_ra)
f_dec = interp1d(col_mjd, col_dec)
for idx, scanid in enumerate(scanids):
btimes.append(scans[scanid]['0']['BeginTime'])
etimes.append(scans[scanid]['0']['EndTime'])
fieldid = scans[scanid]['0']['FieldId']
fieldids.append(fieldid)
inttimes.append(scans[scanid]['0']['IntegrationTime'])
ras = f_ra(np.array(btimes))
decs = f_dec(np.array(btimes))
ras = qa.convert(qa.quantity(ras, 'deg'), 'rad')
decs = qa.convert(qa.quantity(decs, 'deg'), 'rad')
else:
ras = qa.convert(qa.quantity(col_ra, 'deg'), 'rad')
decs = qa.convert(qa.quantity(col_dec, 'deg'), 'rad')
else:
for idx, scanid in enumerate(scanids):
btimes.append(scans[scanid]['0']['BeginTime'])
etimes.append(scans[scanid]['0']['EndTime'])
fieldid = scans[scanid]['0']['FieldId']
fieldids.append(fieldid)
inttimes.append(scans[scanid]['0']['IntegrationTime'])
dir = ms.getfielddirmeas('PHASE_DIR', fieldid)
dirs.append(dir)
ras.append(dir['m0'])
decs.append(dir['m1'])
ms.close()
btimestr = [qa.time(qa.quantity(btimes[idx], 'd'), form='fits', prec=10)[0] for idx in range(nscanid)]
msinfo['vis'] = vis
msinfo['scans'] = scans
msinfo['fieldids'] = fieldids
msinfo['btimes'] = btimes
msinfo['btimestr'] = btimestr
msinfo['inttimes'] = inttimes
msinfo['ras'] = ras
msinfo['decs'] = decs
msinfo['observatory'] = observatory
if msinfofile:
np.savez(msinfofile, vis=vis, scans=scans, fieldids=fieldids, btimes=btimes, btimestr=btimestr,
inttimes=inttimes, ras=ras, decs=decs,
observatory=observatory)
return msinfo
def ephem_to_helio(vis=None, ephem=None, msinfo=None, reftime=None, polyfit=None, usephacenter=False):
'''1. Take a solar ms database, read the scan and field information, find out the pointings (in RA and DEC)
2. Compare with the ephemeris of the solar disk center (in RA and DEC)
3. Generate VLA pointings in heliocentric coordinates
inputs:
msinfo: CASA MS information, output from read_msinfo
ephem: solar ephem, output from read_horizons
reftime: list of reference times (e.g., used for imaging)
CASA standard time format, either a single time (e.g., '2012/03/03/12:00:00'
or a time range (e.g., '2012/03/03/12:00:00~2012/03/03/13:00:00'. If the latter,
take the midpoint of the timerange for reference. If no date specified, take
the date of the first scan
polyfit: ONLY works for MS database with only one source with continously tracking;
not recommanded unless scan length is too long and want to have very high accuracy
usephacenter: Bool -- if True, correct for the RA and DEC in the ms file based on solar empheris.
Otherwise assume the phasecenter is correctly pointed to the solar disk center
(EOVSA case)
return value:
helio: a list of VLA pointing information
reftimestr: reference time, in FITS format string
reftime: reference time, in mjd format
ra: actual RA of phasecenter in the ms file at the reference time (interpolated)
dec: actual DEC of phasecenter in the ms file at the reference time (interpolated)
# CASA uses only RA and DEC of the closest field (e.g. in clean) #
ra_fld: right ascention of the CASA reference pointing direction
dec_fld: declination of the CASA reference pointing direction
raoff: RA offset of the phasecenter in the ms file to solar center
decoff: DEC offset of the phasecenter in the ms file to solar center
refx: heliocentric X offset of the phasecenter in the ms file to solar center
refy: heliocentric Y offset of the phasecenter in the ms file to solar center
######## Example #########
msfile='sun_C_20140910T221952-222952.10s.cal.ms'
ephemfile='horizons_sun_20140910.radecp'
ephem=vla_prep.read_horizons(ephemfile=ephemfile)
msinfo=vla_prep.read_msinfo(msfile=msfile)
polyfit=0
reftime = '22:25:20~22:25:40'
'''
if not vis or not os.path.exists(vis):
raise ValueError('Please provide information of the MS database!')
if not ephem:
ephem = read_horizons(vis=vis)
if not msinfo:
msinfo0 = read_msinfo(vis)
else:
if isinstance(msinfo, str):
try:
msinfo0 = np.load(msinfo)
except:
raise ValueError('The specified input msinfo file does not exist!')
elif isinstance(msinfo, dict):
msinfo0 = msinfo
else:
raise ValueError('msinfo should be either a numpy npz or a dictionary')
print('msinfo is derived from: {0:s}'.format(msinfo0['vis']))
scans = msinfo0['scans']
fieldids = msinfo0['fieldids']
btimes = msinfo0['btimes']
inttimes = msinfo0['inttimes']
ras = msinfo0['ras']
decs = msinfo0['decs']
if 'observatory' in msinfo0.keys():
if msinfo0['observatory'] == 'EOVSA':
usephacenter = False
if type(ras) is list:
ra_rads = [ra['value'] for ra in ras]
elif type(ras) is dict:
ra_rads = ras['value']
else:
print('Type of msinfo0["ras"] unrecognized.')
return 0
if type(decs) is list:
dec_rads = [dec['value'] for dec in decs]
elif type(decs) is dict:
dec_rads = decs['value']
else:
print('Type of msinfo0["decs"] unrecognized.')
# fit 2nd order polynomial fits to the RAs and DECs #
if polyfit:
cra = np.polyfit(btimes, ra_rads, 2)
cdec = np.polyfit(btimes, dec_rads, 2)
# find out phase center infomation in ms according to the input time or timerange #
if not reftime:
raise ValueError('Please specify a reference time of the image')
if type(reftime) == str:
reftime = [reftime]
if (not isinstance(reftime, list)):
print('input "reftime" is not a valid list. Abort...')
nreftime = len(reftime)
helio = []
for reftime0 in reftime:
helio0 = dict.fromkeys(
['reftimestr', 'reftime', 'ra', 'dec', 'ra_fld', 'dec_fld', 'raoff', 'decoff', 'refx', 'refy', 'p0'])
helio0['reftimestr'] = reftime0
if '~' in reftime0:
# if reftime0 is specified as a timerange
try:
[tbg0, tend0] = reftime0.split('~')
tbg_d = qa.getvalue(qa.convert(qa.totime(tbg0), 'd'))[0]
tend_d = qa.getvalue(qa.convert(qa.totime(tend0), 'd'))[0]
tdur_s = (tend_d - tbg_d) * 3600. * 24.
# if no date is specified, add up the date of the first scan
if tend_d < 1.:
if tend_d >= tbg_d:
tend_d += int(btimes[0])
else:
tend_d += int(btimes[0]) + 1
if tbg_d < 1.:
tbg_d += int(btimes[0])
tref_d = (tbg_d + tend_d) / 2.
except:
print('Error in converting the input reftime: ' + str(reftime0) + '. Aborting...')
else:
# if reftime0 is specified as a single value
try:
tref_d = qa.getvalue(qa.convert(qa.totime(reftime0), 'd'))[0]
# if no date is specified, add up the date of the first scan
if tref_d < 1.:
tref_d += int(btimes[0])
tbg_d = tref_d
# use the intergration time
# ind = bisect.bisect_left(btimes, tref_d)
# if msinfo0['etimes']:
# tdur_s = inttimes[ind - 1]
# else:
# tdur_s = np.mean(inttimes)
tdur_s = 1.
except:
print('Error in converting the input reftime: ' + str(reftime0) + '. Aborting...')
helio0['reftime'] = tref_d
# helio0['date-obs'] = qa.time(qa.quantity(tbg_d, 'd'), form='fits', prec=10)[0]
# helio0['exptime'] = tdur_s
# find out phase center RA and DEC in the measurement set according to the reference time
# if polyfit, then use the 2nd order polynomial coeffs
inttime = np.nanmean(inttimes)
ind = bisect.bisect_left(btimes, tref_d)
if ind > 1:
dt = tref_d - btimes[ind - 1]
if ind < len(btimes):
scanlen = btimes[ind] - btimes[ind - 1]
(ra_b, ra_e) = (ra_rads[ind - 1], ra_rads[ind])
(dec_b, dec_e) = (dec_rads[ind - 1], dec_rads[ind])
if ind >= len(btimes):
scanlen = btimes[ind - 1] - btimes[ind - 2]
(ra_b, ra_e) = (ra_rads[ind - 2], ra_rads[ind - 1])
(dec_b, dec_e) = (dec_rads[ind - 2], dec_rads[ind - 1])
if ind == 1: # only one scan exists (e.g., imported from AIPS)
ra_b = ra_rads[ind - 1]
ra_e = ra_b
dec_b = dec_rads[ind - 1]
dec_e = dec_b
scanlen = 10. # radom value
dt = 0.
if ind < 1:
if np.abs((tref_d - btimes[0]) * 24 * 3600) < inttime / 2.0:
ind = 1
ra_b = ra_rads[ind - 1]
ra_e = ra_b
dec_b = dec_rads[ind - 1]
dec_e = dec_b
scanlen = 10. # radom value
dt = 0.
else:
raise ValueError('Reference time does not fall into the scan list!')
if polyfit:
ra = cra[0] * tref_d ** 2. + cra[1] * tref_d + cra[2]
dec = cdec[0] * tref_d ** 2. + cdec[1] * tref_d + cdec[2]
# if not, use linearly interpolated RA and DEC at the beginning of this scan and next scan
else:
ra = ra_b + (ra_e - ra_b) / scanlen * dt
dec = dec_b + (dec_e - dec_b) / scanlen * dt
if ra < 0:
ra += 2. * np.pi
if ra_b < 0:
ra_b += 2. * np.pi
# compare with ephemeris from JPL Horizons
time0 = ephem['time']
ra0 = ephem['ra']
dec0 = ephem['dec']
p0 = ephem['p0']
delta0 = ephem['delta']
if len(time0) > 1:
ind = bisect.bisect_left(time0, tref_d)
dt0 = time0[ind] - time0[ind - 1]
dt_ref = tref_d - time0[ind - 1]
dra0 = ra0[ind] - ra0[ind - 1]
ddec0 = dec0[ind] - dec0[ind - 1]
dp0 = p0[ind] - p0[ind - 1]
ddelta0 = delta0[ind] - delta0[ind - 1]
ra0 = ra0[ind - 1] + dra0 / dt0 * dt_ref
dec0 = dec0[ind - 1] + ddec0 / dt0 * dt_ref
p0 = p0[ind - 1] + dp0 / dt0 * dt_ref
delta0 = delta0[ind - 1] + ddelta0 / dt0 * dt_ref
else:
try:
ra0 = ra0[0]
dec0 = dec0[0]
p0 = p0[0]
delta0 = delta0[0]
except:
print("Error in retrieving info from ephemeris!")
if ra0 < 0:
ra0 += 2. * np.pi
# RA and DEC offset in arcseconds
decoff = degrees((dec - dec0)) * 3600.
raoff = degrees((ra - ra0) * cos(dec)) * 3600.
# Convert into heliocentric offsets
prad = -radians(p0)
refx = (-raoff) * cos(prad) - decoff * sin(prad)
refy = (-raoff) * sin(prad) + decoff * cos(prad)
helio0['ra'] = ra # ra of the actual pointing
helio0['dec'] = dec # dec of the actual pointing
helio0['ra_fld'] = ra_b # ra of the field, used as the reference in e.g., clean
helio0['dec_fld'] = dec_b # dec of the field, used as the refenrence in e.g., clean
helio0['raoff'] = raoff
helio0['decoff'] = decoff
if usephacenter:
helio0['refx'] = refx
helio0['refy'] = refy
else:
helio0['refx'] = 0.
helio0['refy'] = 0.
helio0['p0'] = p0
# helio['r_sun']=np.degrees(R_sun.value/(au.value*delta0))*3600. #in arcsecs
helio.append(helio0)
return helio
def getbeam(imagefile=None, beamfile=None):
ia = iatool()
if not imagefile:
raise ValueError('Please specify input images')
bmaj = []
bmin = []
bpa = []
beamunit = []
bpaunit = []
chans = []
nimg = len(imagefile)
for n in range(nimg):
img = imagefile[n]
bmaj_ = []
bmin_ = []
bpa_ = []
if not os.path.exists(img):
warnings.warn('{} does not exist!'.format(img))
beamunit_ = []
bpaunit_ = []
chans_ = []
else:
ia.open(img)
sum = ia.summary()
ia.close()
ia.done()
if sum.has_key('perplanebeams'): # beam vary with frequency
nbeams = sum['perplanebeams']['nChannels']
beams = sum['perplanebeams']['beams']
chans_ = [key[1:] for key in beams.keys()]
chans_.sort(key=float)
for chan in chans_:
bmaj0 = beams['*' + chan]['*0']['major']['value']
bmaj_.append(bmaj0)
bmin0 = beams['*' + chan]['*0']['minor']['value']
bmin_.append(bmin0)
bpa0 = beams['*' + chan]['*0']['positionangle']['value']
bpa_.append(bpa0)
beamunit_ = beams['*' + chans_[0]]['*0']['major']['unit']
bpaunit_ = beams['*' + chans_[0]]['*0']['positionangle']['unit']
if sum.has_key('restoringbeam'): # only one beam
bmaj_.append(sum['restoringbeam']['major']['value'])
bmin_.append(sum['restoringbeam']['minor']['value'])
bpa_.append(sum['restoringbeam']['positionangle']['value'])
beamunit_ = sum['restoringbeam']['major']['unit']
bpaunit_ = sum['restoringbeam']['positionangle']['unit']
nbeams = 1
chans_ = [0]
bmaj.append(bmaj_)
bmin.append(bmin_)
bpa.append(bpa_)
beamunit.append(beamunit_)
bpaunit.append(bpaunit_)
chans.append(chans_)
if beamfile: # write beams to ascii file
print('Writing beam info to ascii file...')
f = open(beamfile, 'w')
f.write('CHANNEL No., BMAJ (' + beamunit[0] + '), BMIN (' + beamunit[0] + '), BPA (' + bpaunit[0] + ')')
f.write("\n")
for n in range(nimg):
f.write('----For image: ' + imagefile[n] + '----')
f.write('\n')
chans_ = chans[n]
for i in range(len(chans_)):
f.write(str(chans_[i]) + ', ' + str(bmaj[n][i]) + ', ' + str(bmin[n][i]) + ', ' + str(bpa[n][i]))
f.write("\n")
f.close()
return bmaj, bmin, bpa, beamunit, bpaunit
def imreg(vis=None, ephem=None, msinfo=None, imagefile=None, timerange=None, reftime=None, fitsfile=None, beamfile=None,
offsetfile=None, toTb=None, scl100=None, verbose=False, p_ang=False, overwrite=True, usephacenter=True,
deletehistory=False, subregion=[]):
'''
main routine to register CASA images
Required Inputs:
vis: STRING. CASA measurement set from which the image is derived
imagefile: STRING or LIST. name of the input CASA image
timerange: STRING or LIST. timerange used to generate the CASA image, must have the same length as the input images.
Each element should be in CASA standard time format, e.g., '2012/03/03/12:00:00~2012/03/03/13:00:00'
Optional Inputs:
msinfo: DICTIONARY. CASA MS information, output from read_msinfo. If not provided, generate one from the supplied vis
ephem: DICTIONARY. solar ephem, output from read_horizons.
If not provided, query JPL Horizons based on time info of the vis (internet connection required)
fitsfile: STRING or LIST. name of the output registered fits files
reftime: STRING or LIST. Each element should be in CASA standard time format, e.g., '2012/03/03/12:00:00'
offsetfile: optionally provide an offset with a series of solar x and y offsets with timestamps
toTb: Bool. Convert the default Jy/beam to brightness temperature?
scl100: Bool. If True, scale the image values up by 100 (to compensate VLA 20 dB attenuator)
verbose: Bool. Show more diagnostic info if True.
usephacenter: Bool -- if True, correct for the RA and DEC in the ms file based on solar empheris.
Otherwise assume the phasecenter is correctly pointed to the solar disk center
(EOVSA case)
subregion: Region selection. See 'help par.region' for details.
Usage:
>>> from suncasa.utils import helioimage2fits as hf
>>> hf.imreg(vis='mydata.ms', imagefile='myimage.image', fitsfile='myimage.fits',
timerange='2017/08/21/20:21:10~2017/08/21/20:21:18')
The output fits file is 'myimage.fits'
History:
BC (sometime in 2014): function was first wrote, followed by a number of edits by BC and SY
BC (2019-07-16): Added checks for stokes parameter. Verified that for converting from Jy/beam to brightness temperature,
the convention of 2*k_b*T should always be used. I.e., for unpolarized source, stokes I, RR, LL, XX, YY,
etc. in the output CASA images from (t)clean should all have same values of radio intensity
(in Jy/beam) and brightness temperature (in K).
'''
ia = iatool()
if deletehistory:
msclearhistory(vis)
if not imagefile:
raise ValueError('Please specify input image')
if not timerange:
raise ValueError('Please specify timerange of the input image')
if type(imagefile) == str:
imagefile = [imagefile]
if type(timerange) == str:
timerange = [timerange]
if not fitsfile:
fitsfile = [img + '.fits' for img in imagefile]
if type(fitsfile) == str:
fitsfile = [fitsfile]
nimg = len(imagefile)
if len(timerange) != nimg:
raise ValueError('Number of input images does not equal to number of timeranges!')
if len(fitsfile) != nimg:
raise ValueError('Number of input images does not equal to number of output fits files!')
nimg = len(imagefile)
if verbose:
print(str(nimg) + ' images to process...')
if reftime: # use as reference time to find solar disk RA and DEC to register the image, but not the actual timerange associated with the image
if type(reftime) == str:
reftime = [reftime] * nimg
if len(reftime) != nimg:
raise ValueError('Number of reference times does not match that of input images!')
helio = ephem_to_helio(vis, ephem=ephem, msinfo=msinfo, reftime=reftime, usephacenter=usephacenter)
else:
# use the supplied timerange to register the image
helio = ephem_to_helio(vis, ephem=ephem, msinfo=msinfo, reftime=timerange, usephacenter=usephacenter)
if toTb:
(bmajs, bmins, bpas, beamunits, bpaunits) = getbeam(imagefile=imagefile, beamfile=beamfile)
for n, img in enumerate(imagefile):
if verbose:
print('processing image #' + str(n) + ' ' + img)
fitsf = fitsfile[n]
timeran = timerange[n]
# obtain duration of the image as FITS header exptime
try:
[tbg0, tend0] = timeran.split('~')
tbg_d = qa.getvalue(qa.convert(qa.totime(tbg0), 'd'))[0]
tend_d = qa.getvalue(qa.convert(qa.totime(tend0), 'd'))[0]
tdur_s = (tend_d - tbg_d) * 3600. * 24.
dateobs = qa.time(qa.quantity(tbg_d, 'd'), form='fits', prec=10)[0]
except:
print('Error in converting the input timerange: ' + str(timeran) + '. Proceeding to the next image...')
continue
hel = helio[n]
if not os.path.exists(img):
warnings.warn('{} does not existed!'.format(img))
else:
if os.path.exists(fitsf) and not overwrite:
raise ValueError('Specified fits file already exists and overwrite is set to False. Aborting...')
else:
p0 = hel['p0']
tb.open(img + '/logtable', nomodify=False)
nobs = tb.nrows()
tb.removerows([i + 1 for i in range(nobs - 1)])
tb.close()
ia.open(img)
imr = ia.rotate(pa=str(-p0) + 'deg')
if subregion is not []:
imr = imr.subimage(region=subregion)
imr.tofits(fitsf, history=False, overwrite=overwrite)
imr.close()
imsum = ia.summary()
ia.close()
ia.done()
# construct the standard fits header
# RA and DEC of the reference pixel crpix1 and crpix2
(imra, imdec) = (imsum['refval'][0], imsum['refval'][1])
# find out the difference of the image center to the CASA phase center
# RA and DEC difference in arcseconds
ddec = degrees((imdec - hel['dec_fld'])) * 3600.
dra = degrees((imra - hel['ra_fld']) * cos(hel['dec_fld'])) * 3600.
# Convert into image heliocentric offsets
prad = -radians(hel['p0'])
dx = (-dra) * cos(prad) - ddec * sin(prad)
dy = (-dra) * sin(prad) + ddec * cos(prad)
if offsetfile:
try:
offset = np.load(offsetfile)
except:
raise ValueError('The specified offsetfile does not exist!')
reftimes_d = offset['reftimes_d']
xoffs = offset['xoffs']
yoffs = offset['yoffs']
timg_d = hel['reftime']
ind = bisect.bisect_left(reftimes_d, timg_d)
xoff = xoffs[ind - 1]
yoff = yoffs[ind - 1]
else:
xoff = hel['refx']
yoff = hel['refy']
if verbose:
print('offset of image phase center to visibility phase center (arcsec): dx={0:.2f}, dy={1:.2f}'.format(
dx, dy))
print('offset of visibility phase center to solar disk center (arcsec): dx={0:.2f}, dy={1:.2f}'.format(
xoff, yoff))
(crval1, crval2) = (xoff + dx, yoff + dy)
# update the fits header to heliocentric coordinates
hdu = pyfits.open(fitsf, mode='update')
hdu[0].verify('fix')
header = hdu[0].header
(cdelt1, cdelt2) = (
-header['cdelt1'] * 3600., header['cdelt2'] * 3600.) # Original CDELT1, 2 are for RA and DEC in degrees
header['cdelt1'] = cdelt1
header['cdelt2'] = cdelt2
header['cunit1'] = 'arcsec'
header['cunit2'] = 'arcsec'
header['crval1'] = crval1
header['crval2'] = crval2
header['ctype1'] = 'HPLN-TAN'
header['ctype2'] = 'HPLT-TAN'
header['date-obs'] = dateobs # begin time of the image
if not p_ang:
hel['p0'] = 0
try:
# this works for pyfits version of CASA 4.7.0 but not CASA 4.6.0
if tdur_s:
header.set('exptime', tdur_s)
else:
header.set('exptime', 1.)
header.set('p_angle', hel['p0'])
header.set('dsun_obs', sun.sunearth_distance(Time(dateobs)).to(u.meter).value)
header.set('rsun_obs', sun.solar_semidiameter_angular_size(Time(dateobs)).value)
header.set('rsun_ref', sun.constants.radius.value)
header.set('hgln_obs', 0.)
header.set('hglt_obs', sun.heliographic_solar_center(Time(dateobs))[1].value)
except:
# this works for astropy.io.fits
if tdur_s:
header.append(('exptime', tdur_s))
else:
header.append(('exptime', 1.))
header.append(('p_angle', hel['p0']))
header.append(('dsun_obs', sun.sunearth_distance(Time(dateobs)).to(u.meter).value))
header.append(('rsun_obs', sun.solar_semidiameter_angular_size(Time(dateobs)).value))
header.append(('rsun_ref', sun.constants.radius.value))
header.append(('hgln_obs', 0.))
header.append(('hglt_obs', sun.heliographic_solar_center(Time(dateobs))[1].value))
# check if stokes parameter exist
exist_stokes = False
stokes_mapper = {'I': 1, 'Q': 2, 'U': 3, 'V': 4, 'RR': -1, 'LL': -2,
'RL': -3, 'LR': -4, 'XX': -5, 'YY': -6, 'XY': -7, 'YX': -8}
if 'CRVAL3' in header.keys():
if header['CTYPE3'] == 'STOKES':
stokenum = header['CRVAL3']
exist_stokes = True
if 'CRVAL4' in header.keys():
if header['CTYPE4'] == 'STOKES':
stokenum = header['CRVAL4']
exist_stokes = True
if exist_stokes:
stokesstr = stokes_mapper.keys()[stokes_mapper.values().index(stokenum)]
if verbose:
print('This image is in Stokes ' + stokesstr)
else:
print('STOKES Information does not seem to exist! Assuming Stokes I')
stokenum = 1
# update intensity units, i.e. to brightness temperature?
if toTb:
# get restoring beam info
bmaj = bmajs[n]
bmin = bmins[n]
beamunit = beamunits[n]
data = hdu[0].data # remember the data order is reversed due to the FITS convension
dim = data.ndim
sz = data.shape
keys = header.keys()
values = header.values()
# which axis is frequency?
faxis = keys[values.index('FREQ')][-1]
faxis_ind = dim - int(faxis)
# find out the polarization of this image
k_b = qa.constants('k')['value']
c_l = qa.constants('c')['value']
# Always use 2*kb for all polarizations
const = 2. * k_b / c_l ** 2
if header['BUNIT'].lower() == 'jy/beam':
header['BUNIT'] = 'K'
header['BTYPE'] = 'Brightness Temperature'
for i in range(sz[faxis_ind]):
nu = header['CRVAL' + faxis] + header['CDELT' + faxis] * (i + 1 - header['CRPIX' + faxis])
if header['CUNIT' + faxis] == 'KHz':
nu *= 1e3
if header['CUNIT' + faxis] == 'MHz':
nu *= 1e6
if header['CUNIT' + faxis] == 'GHz':
nu *= 1e9
if len(bmaj) > 1: # multiple (per-plane) beams
bmajtmp = bmaj[i]
bmintmp = bmin[i]
else: # one single beam
bmajtmp = bmaj[0]
bmintmp = bmin[0]
if beamunit == 'arcsec':
bmaj0 = np.radians(bmajtmp / 3600.)
bmin0 = np.radians(bmintmp / 3600.)
if beamunit == 'arcmin':
bmaj0 = np.radians(bmajtmp / 60.)
bmin0 = np.radians(bmintmp / 60.)
if beamunit == 'deg':
bmaj0 = np.radians(bmajtmp)
bmin0 = np.radians(bmintmp)
if beamunit == 'rad':
bmaj0 = bmajtmp
bmin0 = bmintmp
beam_area = bmaj0 * bmin0 * np.pi / (4. * log(2.))
factor = const * nu ** 2 # SI unit
jy_to_si = 1e-26
# print(nu/1e9, beam_area, factor)
factor2 = 1.
if scl100:
factor2 = 100.
if faxis == '3':
data[:, i, :, :] *= jy_to_si / beam_area / factor * factor2
if faxis == '4':
data[i, :, :, :] *= jy_to_si / beam_area / factor * factor2
header = headerfix(header)
hdu.flush()
hdu.close()
def calc_phasecenter_from_solxy(vis, timerange='', xycen=None, usemsphacenter=True):
'''
return the phase center in RA and DEC of a given solar coordinates
:param vis: input measurement sets file
:param timerange: can be a string or astropy.time.core.Time object, or a 2-element list of string or Time object
:param xycen: solar x-pos and y-pos in arcsec
:param usemsphacenter:
:return:
phasecenter
midtim: mid time of the given timerange
'''
tb.open(vis + '/POINTING')
tst = Time(tb.getcell('TIME_ORIGIN', 0) / 24. / 3600., format='mjd')
ted = Time(tb.getcell('TIME_ORIGIN', tb.nrows() - 1) / 24. / 3600., format='mjd')
tb.close()
datstr = tst.iso[:10]
if isinstance(timerange, Time):
try:
(sttim, edtim) = timerange
except:
sttim = timerange
edtim = sttim
else:
if timerange == '':
sttim = tst
edtim = ted
else:
try:
(tstart, tend) = timerange.split('~')
if tstart[2] == ':':
sttim = Time(datstr + 'T' + tstart)
edtim = Time(datstr + 'T' + tend)
# timerange = '{0}/{1}~{0}/{2}'.format(datstr.replace('-', '/'), tstart, tend)
else:
sttim = Time(qa.quantity(tstart, 'd')['value'], format='mjd')
edtim = Time(qa.quantity(tend, 'd')['value'], format='mjd')
except:
try:
if timerange[2] == ':':
sttim = Time(datstr + 'T' + timerange)
edtim = sttim
else:
sttim = Time(qa.quantity(timerange, 'd')['value'], format='mjd')
edtim = sttim
except ValueError:
print("keyword 'timerange' in wrong format")
ms.open(vis)
metadata = ms.metadata()
observatory = metadata.observatorynames()[0]
ms.close()
midtim_mjd = (sttim.mjd + edtim.mjd) / 2.
midtim = Time(midtim_mjd, format='mjd')
eph = read_horizons(t0=midtim)
if observatory == 'EOVSA' or (not usemsphacenter):
print('This is EOVSA data')
# use RA and DEC from FIELD ID 0
tb.open(vis + '/FIELD')
phadir = tb.getcol('PHASE_DIR').flatten()
tb.close()
ra0 = phadir[0]
dec0 = phadir[1]
else:
ra0 = eph['ra'][0]
dec0 = eph['dec'][0]
if not xycen:
# use solar disk center as default
phasecenter = 'J2000 ' + str(ra0) + 'rad ' + str(dec0) + 'rad'
else:
x0 = np.radians(xycen[0] / 3600.)
y0 = np.radians(xycen[1] / 3600.)
p0 = np.radians(eph['p0'][0]) # p angle in radians
raoff = -((x0) * np.cos(p0) - y0 * np.sin(p0)) / np.cos(eph['dec'][0])
decoff = (x0) * np.sin(p0) + y0 * np.cos(p0)
newra = ra0 + raoff
newdec = dec0 + decoff
phasecenter = 'J2000 ' + str(newra) + 'rad ' + str(newdec) + 'rad'
return phasecenter, midtim
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