def panelplot(sd, aipsname, intl_antennas, intl_name, times, refant, ra, dec):
ny, nx = len(intl_antennas), 6
pltsquash = 0.5 * float(sd.shape[3]) / float(sd.shape[2])
for pol in [0, 1]:
for i in range(ny):
wdata = WizAIPSUVData(aipsname, 'FITS', 1, 1)
d, uvw, tjunk = dget(wdata, np.array([intl_antennas[i], refant]))
plt.subplot(nx, ny, i + 1, xticks=[], yticks=[]) # data
if interesting(d):
plt.imshow(np.arctan2(d[0][pol].imag, d[0][pol].real))
if i == 2:
plt.title(aipsname + ' ' + ra + ' ' + dec)
plt.subplot(nx, ny, i + 1 + ny, xticks=[], yticks=[]) #FT of data
if interesting(d):
d_display = np.sqrt(abs(fft.fftshift(fft.fft2(d[0][pol]))))
plt.imshow(d_display, cmap=matplotlib.cm.gray_r)
delays = sd[i, 0, 0, :, pol]
if len(delays[~np.isnan(delays)]):
plt.subplot(nx, ny, i + 1 + 2 * ny, xticks=[],
yticks=[]) # delay plot
plt.plot(times, delays, 'b+')
md = np.nanmedian(delays)
plt.yticks([md - 50, md - 20, md, md + 20, md + 50],
['', '', '', '', ''])
plt.ylim(np.nanmin(delays), np.nanmax(delays))
plt.xlim(times[0], times[-1])
plt.text(times[0], np.nanmin(delays), str(int(md)))
phases = sd[i, 1, 0, :, pol]
if len(phases[~np.isnan(phases)]):
plt.subplot(nx, ny, i + 1 + 3 * ny, xticks=[],
yticks=[]) # phase plot
phx = times[~np.isnan(phases)]
phy = phases[~np.isnan(phases)]
plt.plot(phx, phy, 'b+')
plt.ylim(-np.pi, np.pi)
plt.yticks([-np.pi, 0, np.pi], ['', '', ''])
wdata = WizAIPSUVData(aipsname, 'SPLIT', 1, 1)
d, uvw, tjunk = dget(wdata, np.array([intl_antennas[i], refant]))
plt.subplot(nx, ny, i + 1 + 4 * ny, xticks=[],
yticks=[]) #corr. data
if interesting(d):
plt.imshow(np.arctan2(d[0][pol].imag, d[0][pol].real))
plt.subplot(nx, ny, i + 1 + 5 * ny, xticks=[],
yticks=[]) #FT corr.data
plt.imshow(np.sqrt(abs(fft.fftshift(fft.fft2(d[0][pol])))),
cmap=matplotlib.cm.gray_r)
plt.xlabel(intl_name[i])
# plt.show()
plt.savefig(pngdir + aipsname + ('R' if pol else 'L') + '.png',
bbox_inches='tight')
plt.clf()
def run_load_sort(pwd, data_prefix, delete, disk):
## Load the data into AIPS
fitld = AIPSTask('FITLD')
fitld.datain = pwd + data_prefix + '_1_1.IDI'
fitld.outdisk = disk
fitld.digicor = -1
fitld.doconcat = 1
fitld.outname = data_prefix
fitld.ncount = 3
fitld.go()
#Load the TASAV file which contains the pipelined tables
fitld = AIPSTask('FITLD')
fitld.datain = pwd + data_prefix + '_1.tasav.FITS'
fitld.outdisk = disk
fitld.digicor = -1
fitld.outname = 'pipe_TSAV'
fitld.ncount = 1
fitld.go()
#sort the data into time-baseline order
uvdata = WizAIPSUVData(data_prefix, 'UVDATA', disk, 1)
tasav = WizAIPSUVData('pipe_TSAV', 'TASAV', disk, 1)
uvsrt = AIPSTask('UVSRT')
uvsrt.indata = uvdata
uvsrt.outdata = uvdata
uvsrt.sort = 'TB'
uvsrt.go()
dqual = AIPSTask('DQUAL')
dqual.indata = uvdata
dqual.fqcenter = -1
dqual.go()
if delete == True:
uvdata.zap()
uvdata = WizAIPSUVData(data_prefix, 'DQUAL', disk, 1)
indxr = AIPSTask('INDXR')
uvdata.zap_table('CL', 1)
indxr.indata = uvdata
indxr.cparm[3] = 0.25
indxr.go()
if delete == True:
uvdata.rename(data_prefix, 'UVDATA', 1)
else:
uvdata.rename(data_prefix, 'UVDATA', 2)
def antsortsn(inname='UVSIM', inclass='FITS', indi=1, inseq=1, invers=1):
w = WizAIPSUVData(inname, inclass, indisk, inseq)
sn = w.table('SN', invers)
anno = 8
### starting no of international station
print 'i[refant]', i['refant_1']
for i in sn:
#print 'i[refant]', i['refant_1'];
#print 'i[antenna_no]', i['antenna_no'];
#print 'anno: ', anno
i['refant_1'] = 16
i['refant_2'] = 16
i['antenna_no'] = anno
if anno == 16:
anno = 8
else:
anno = anno + 1
i.update()
def find_difmap_chan(inna, incl, indisk=1, inseq=1):
INCR = 1
if incl == '':
output = inna.split('/')[-1] if '/' in inna else inna
try:
AIPSUVData('DIFMAP', 'UVDATA', indisk, inseq).zap()
print 'Removed DIFMAP.UVDATA.%d disk %d' % (inseq, indisk)
except:
pass
fitld = AIPSTask('fitld')
fitld.datain = inna if '/' in inna else './' + inna
fitld.outname = 'DIFMAP'
fitld.outclass = 'UVDATA'
fitld.outdisk = indisk
fitld.outseq = inseq
fitld.go()
inna, incl = 'DIFMAP', 'UVDATA'
else:
output = '%s_%s' % (inna, incl)
data = WizAIPSUVData(inna, incl, indisk, inseq)
for i in data:
v = i.visibility
na = np.asarray(np.ravel(v[:, :, 0, 0]), dtype='bool')
try:
a = na | a
except:
a = np.copy(na)
bstart, bend = [], []
for i in range(len(a)):
if (i == 0 and a[i]) or (i != 0 and a[i] and not a[i - 1]):
bstart.append(i + 1)
if (i != 0 and not a[i] and a[i - 1]):
bend.append(i)
if (a[i] and i == len(a) - 1):
bend.append(len(a))
fo = open('dchan_%s' % (output), 'w')
fo.write('select I,')
for i in range(len(bstart)):
fo.write('%d,%d' % (bstart[i], bend[i]))
if i != len(bstart) - 1:
fo.write(',')
fo.write('\n')
fo.close()
def find_chan_fits(infile, indisk=1, inseq=1):
try:
AIPSUVData('DIFMAP', 'UVDATA', indisk, inseq).zap()
print('Removed DIFMAP.UVDATA.%d disk %d' % (inseq, indisk))
except:
pass
fitld = AIPSTask('fitld')
fitld.datain = infile if '/' in infile else './' + infile
fitld.outname = 'DIFMAP'
fitld.outclass = 'UVDATA'
fitld.outdisk = indisk
fitld.outseq = inseq
fitld.go()
data = WizAIPSUVData('DIFMAP', 'UVDATA', indisk, inseq)
for i in data:
v = i.visibility
na = np.asarray(np.ravel(v[:, :, 0, 0]), dtype='bool')
try:
a = na | a
except:
a = np.copy(na)
return a
def closure_aips(aipsno,
triangle,
inna,
incl,
indisk=1,
inseq=1,
minmatch=5,
ipol=0,
dt=0.5,
spw=0):
AIPS.userno = aipsno
data = WizAIPSUVData(inna, incl, indisk, inseq)
antnum = np.array([], dtype='int')
for i in range(3):
foundit = False
for j in range(len(data.antennas)):
tellen = min(len(data.antennas[j]), len(triangle[i]))
if tellen < minmatch:
if triangle[i][:tellen] == data.antennas[j][:tellen]:
foundit = True
antnum = np.append(antnum, j + 1)
break
else:
if triangle[i][:minmatch] == data.antennas[j][:minmatch]:
foundit = True
antnum = np.append(antnum, j + 1)
break
antnum = np.sort(antnum)
print '***', antnum
isbase = [[antnum[0], antnum[1]], [antnum[1], antnum[2]],
[antnum[0], antnum[2]]]
icou, nvis = 0, len(data)
d = [np.array([]), np.array([]), np.array([])]
t = [np.array([]), np.array([]), np.array([])]
for v in data:
if v.baseline in isbase:
vwhich = isbase.index(v.baseline)
else:
continue
print '***uuu', v.visibility
vvis = v.visibility
vv = vvis.reshape(vvis.shape[0] * vvis.shape[1], vvis.shape[2],
vvis.shape[3])
vphas = np.arctan2(vv[:, ipol, 1], vv[:, ipol, 0])
np.putmask(vphas, vv[:, ipol, 2] == 0.0, np.nan)
try:
d[vwhich] = np.vstack((d[vwhich], vphas))
t[vwhich] = np.append(t[vwhich], 86400. * v.time)
except:
d[vwhich] = np.copy(vphas)
t[vwhich] = np.append(t[vwhich], 86400. * v.time)
icou += 1
if icou % 100000 == 0:
print 'Visibility %d/%d' % (icou, nvis)
tu = np.sort(np.unique(np.append(t[0], np.append(t[1], t[2]))))
print tu
for i in range(2):
tu_diff = np.append(np.array([1.0E9]), np.diff(tu))
tu = tu[tu_diff > dt]
# print len(t[0]),len(t[1]),len(t[2]),'********'
for i in range(3):
if len(t[i]) == len(tu):
continue
j = 0
k = 0
kmiss = []
dummy = np.ones_like(d[i][0]) * np.nan
while j < len(tu) and k < len(t[i]):
if abs(tu[j] - t[i][k]) < dt:
j += 1
k += 1
else:
kmiss.append(k)
d[i] = np.insert(d[i], j + 1, dummy, axis=0)
j += 1
while len(d[i]) < len(tu): # missing data at the end
d[i] = np.insert(d[i], len(d[i]), dummy, axis=0)
np.save('d0_aips', d[0])
np.save('d1_aips', d[1])
np.save('d2_aips', d[2])
from scipy.fftpack import *
p = np.asarray(d[0] + d[1] - d[2], dtype='float')
np.putmask(p, p > np.pi, p - 2. * np.pi) # no need to worry about nans
np.putmask(p, p < -np.pi, p + 2. * np.pi)
prand = np.random.random(p.shape[0] * p.shape[1]).reshape(
p.shape) * 2 * np.pi - np.pi
np.putmask(p, np.isnan(p), prand)
pp = np.cos(p) + 1j * np.sin(p)
pprand = np.cos(prand) + 1j * np.sin(prand)
qbig = fftshift(fft2(pp))
qbigrand = fftshift(fft2(pprand))
yr = (qbig.shape[0] / 2 - 30, qbig.shape[0] / 2 + 30)
xr = (qbig.shape[1] / 2 - 30, qbig.shape[1] / 2 + 30)
q = qbig[yr[0]:yr[1], xr[0]:xr[1]]
qrand = qbigrand[yr[0]:yr[1], xr[0]:xr[1]]
qq = np.sort(np.ravel(abs(q)))
qqrand = np.sort(np.ravel(abs(qrand)))
x, y = np.arange(-30, 30), np.arange(-30, 30)
xx, yy = np.meshgrid(x, y)
z = np.hypot(xx, yy)
maxsig = 0.0
for i in range(3, 30):
zz = np.zeros_like(z)
np.putmask(zz, z < i, 1.0)
sig = ((zz*abs(q)).sum()-(zz*abs(qrand)).sum()) \
/(np.std(abs(qrand))*np.sqrt(zz.sum()))
maxsig = max(maxsig, sig)
# plt.subplot(121);plt.imshow(abs(qrand));plt.subplot(122);plt.imshow(abs(q));plt.show()
return maxsig, q, p
def panelplot(sd, aipsname, intl_antennas, intl_name, times, refant, ra, dec):
ny, nx = len(intl_antennas), 6
fftsn = np.zeros((ny, 2))
pltsquash = 0.5 * float(sd.shape[3]) / float(sd.shape[2])
for pol in [0, 1]:
for i in range(ny):
wdata = WizAIPSUVData(aipsname, 'FITS', 1, 1)
d, uvw, tjunk = dget(wdata, np.array([intl_antennas[i], refant]))
plt.subplot(nx, ny, i + 1, xticks=[], yticks=[])
if d != []:
dq, val = dqual(d[0], clip=True)
if dq == 'A':
np.putmask(d[0][pol],
abs(d[0][pol]) > CLIP * val, val + 0.0j)
plt.imshow(np.arctan2(d[0][pol].imag, d[0][pol].real))
# plt.imshow(abs(d[0][pol]))
if i == 2:
plt.title(aipsname + ' ' + ra + ' ' + dec)
plt.subplot(nx, ny, i + 1 + ny, xticks=[], yticks=[])
if d != []:
dfft = abs(fft.fftshift(fft.fft2(d[0][pol])))
fftsn[i, pol] = get_fftsn(dfft)
plt.imshow(np.sqrt(dfft), cmap=matplotlib.cm.gray_r)
plt.subplot(nx, ny, i + 1 + 2 * ny, xticks=[], yticks=[])
plt.plot(times, sd[i, 0, 0, :, pol], 'b+')
meddelay = np.nanmedian(sd[i, 0, 0, :, pol])
meddelay = meddelay if meddelay < 3.e6 else 0
if meddelay:
plt.text(times[0], meddelay - 50, str(int(meddelay)))
plt.ylim(meddelay - 50., meddelay + 50)
plt.subplot(nx, ny, i + 1 + 3 * ny, xticks=[], yticks=[])
phx = times[~np.isnan(sd[i, 1, 0, :, pol])]
phy = sd[i, 1, 0, :, pol][~np.isnan(sd[i, 1, 0, :, pol])]
medphase = np.median(np.unwrap(phy))
plt.plot(phx, phy, 'b+')
# plt.ylim(medphase-2.0,medphase+2.0)
wdata = WizAIPSUVData(aipsname, 'SPLIT', 1, 1)
d, uvw, tjunk = dget(wdata, np.array([intl_antennas[i], refant]))
if d != []:
dq, val = dqual(d[0], clip=True)
if dq == 'A':
np.putmask(d[0][pol],
abs(d[0][pol]) > CLIP * val, val + 0.0j)
plt.subplot(nx, ny, i + 1 + 4 * ny, xticks=[], yticks=[])
try:
plt.imshow(np.arctan2(d[0][pol].imag, d[0][pol].real))
except:
print 'No calibrated data on ', intl_antennas[i]
flog = open(FLOG, 'a')
flog.write('No calibrated data on %s\n' %
str(intl_antennas[i]))
flog.close()
plt.subplot(nx, ny, i + 1 + 5 * ny, xticks=[], yticks=[])
try:
plt.imshow(np.sqrt(abs(fft.fftshift(fft.fft2(d[0][pol])))),
cmap=matplotlib.cm.gray_r)
except:
pass
plt.xlabel(intl_name[i])
plt.savefig(pngdir + aipsname + ('R' if pol else 'L') + '.png',
bbox_inches='tight')
plt.clf()
return 0.5 * (fftsn[:, 0] + fftsn[:, 1])
try:
nif = len(fq[0]['if_freq'])
except:
nif = 1
source = su[0]['source'].rstrip()
pfring_antennas,pfring_name,pfring_qual,intl_antennas,intl_name,\
refant = [],[],[],[],[],-1
for i in an: # Find the reference antenna
annew = i['anname'].strip('HBA').strip('LBA')[:5]
if annew in SUPERTERP:
refant = i['nosta']
refant_name = annew
if refant == -1: # No reference antenna
print 'Aborting; no reference antenna found'
sys.exit()
wdata = WizAIPSUVData(aipsname, 'FITS', 1, 1)
for i in an:
annew = i['anname'].strip('HBA').strip('LBA')[:5]
if annew in fring_antennas:
if i['nosta'] != refant:
d, uvw, tjunk = dget(wdata, np.array([i['nosta'], refant]))
if not d[0].sum(): # No data on this antenna
print 'No data on antenna', i['nosta']
flog = open(FLOG, 'a')
flog.write('No data on antenna %s\n' % str(i['nosta']))
flog.close()
continue
intl_antennas.append(i['nosta'])
intl_name.append(annew)
pfring_antennas.append(i['nosta'])
pfring_name.append(annew)
uvsub.in2data = imagedatacl
uvsub.inver = 1
uvsub.outdisk = indisk
uvsub.ncomp[1] = -1000000
uvsub.opcode = 'DIV'
uvsub.go()
uvdata = AIPSUVData(uvname[i], 'UVSUB', indisk, 1)
#wtmod = AIPSTask('WTMOD') #change weight relative to amplitude adjustments
#wtmod.indata = uvdata
#wtmod.aparm[1] = (maxamplitude(uvname[i])**2)*(10**10)
#wtmod.outdisk = indisk
#wtmod.go()
#uvdata = AIPSUVData(uvname[i],'WTMOD',2,1)
uvdata2 = WizAIPSUVData(uvname[i], 'UVSUB', indisk, 1)
uvdata2.header['crval'][4] = pointcenRA
uvdata2.header.update()
uvdata2.header['crval'][5] = pointcenDEC
uvdata2.header.update()
uvdata.rename(name='COMBO', klass='UV', seq=0)
if len(uvname) > 1:
dbapp = AIPSTask('DBAPP')
uvdata = AIPSUVData('COMBO', 'UV', indisk, 1)
dbapp.inname = 'COMBO'
dbapp.inclass = 'UV'
dbapp.indisk = indisk
dbapp.inseq = 2
dbapp.in2seq = len(uvname)
dbapp.outdata = uvdata
dbapp.outdisk = indisk
imean.indisk = indisk
imean.doprint = 1
imean.outtext = 'PWD:IMEAN_%s.txt' % UV_files[i]
imean()
uvsub = AIPSTask('UVSUB') #Divide visibilites by clean model!
uvsub.indata = uvdata
uvsub.nmaps = 1
uvsub.in2data = imagedatacl
uvsub.inver = 1
uvsub.outdisk = indisk
uvsub.ncomp[1] = -1000000
uvsub.opcode = 'DIV'
uvsub.go()
uvdata = WizAIPSUVData('A%s' % i, 'UVSUB',indisk,1)
uvdata.header['crval'][4] = pointcenRA
uvdata.header.update()
uvdata.header['crval'][5] = pointcenDEC
uvdata.header.update()
uvdata.rename(name='COMBO',klass='UV', seq=0)
os.system('rm %s' % UV_files[i])
update_progress(total/total_progress)
if use_DBAPP == 'True':
dbapp = AIPSTask('DBAPP')
uvdata = WizAIPSUVData('COMBO','UV',indisk,1)
dbapp.inname = 'COMBO'
dbapp.inclass = 'UV'
dbapp.indisk = indisk
dbapp.inseq = 2
mystep = 1
## e.g. this step will load data in directory /Users/jackradcliffe/Documents/EG078E_calibration/calibration/ called eg078e_1_1.IDI'
if (mystep in thesteps):
print 'Step ', mystep, step_title[mystep]
## FITLD loads data
fitld = AIPSTask('FITLD') ## initilise task first (same name as in AIPS)
fitld.datain = pwd + data_prefix + '_1_1.IDI' ## set inputs, same as in AIPS!
fitld.outdisk = disk
fitld.digicor = -1
fitld.doconcat = 1
fitld.outname = data_prefix
fitld.ncount = 3
fitld.go() ## <taskname>.go() will run task with inputs above
#sort the data into time-baseline order
uvdata = WizAIPSUVData(data_prefix, 'UVDATA', disk,
1) ## Parseltongue has these special variables
### which hold the names of data. It is of the form WizAIPSUVData(name,class,disk,seq) look at AIPS catalogue using command pcat
## Uvsrt sorts it in time-baseline order
uvsrt = AIPSTask('UVSRT')
uvsrt.indata = uvdata ##special input of <taskname>.indata is equivalent to the AIPS getn <num> command but you use the WizAIPSUVData type i.e. uvdata in this case
uvsrt.outdata = uvdata ## same as above but AIPS command geton <num>
uvsrt.sort = 'TB'
uvsrt.go()
## dont worry about this
dqual = AIPSTask('DQUAL')
dqual.indata = uvdata
dqual.fqcenter = -1
dqual.go()
if delete == True:
break
if s == 'no' or s=='n':
sys.exit('Please restate the mysteps parameter')
if (thesteps==[]):
thesteps = range(0,len(step_title))
print 'Executing all steps: ', thesteps
mystep = 1
if(mystep in thesteps):
print 'Step ', mystep, step_title[mystep]
eg.run_load_sort(pwd=pwd,data_prefix=data_prefix,delete=True,disk=disk)
mystep = 2
uvdata = WizAIPSUVData(data_prefix,'UVDATA',disk,1)
tasav = WizAIPSUVData('pipe_TSAV','TASAV',disk,1)
if(mystep in thesteps):
print 'Step ', mystep, step_title[mystep]
eg.amplitude_calibration_EVN(uvdata,tasav,disk,refant,sources,snedt_amp)
mystep = 3
if(mystep in thesteps):
print 'Step ', mystep, step_title[mystep]
#eg.initial_flag(uvdata,tasav,disk,refant)
eg.eg078e_specific_flagging(uvdata,tasav,disk,refant)
mystep = 4
if(mystep in thesteps):
print 'Step ', mystep, step_title[mystep]
uvsub.inver = 1
uvsub.outdisk = 2
uvsub.ncomp[1] = -1000000
uvsub.opcode = 'DIV'
uvsub.go()
uvdata = AIPSUVData(uvname[i], 'UVSUB', 2, 1)
wtmod = AIPSTask(
'WTMOD') #change weight relative to amplitude adjustments
wtmod.indata = uvdata
wtmod.aparm[1] = (maxamplitude(uvname[i])**2) * (10**10)
wtmod.outdisk = 2
wtmod.go()
uvdata = AIPSUVData(uvname[i], 'WTMOD', 2, 1)
uvdata2 = WizAIPSUVData(uvname[i], 'WTMOD', 2, 1)
uvdata2.header['crval'][4] = pointcenRA
uvdata2.header.update()
uvdata2.header['crval'][5] = pointcenDEC
uvdata2.header.update()
uvdata.rename(name='COMBO', klass='UV', seq=0)
if len(uvname) > 1:
dbapp = AIPSTask('DBAPP')
uvdata = AIPSUVData('COMBO', 'UV', 2, 1)
dbapp.inname = 'COMBO'
dbapp.inclass = 'UV'
dbapp.indisk = 2
dbapp.inseq = 2
dbapp.in2seq = len(uvname)
dbapp.outdata = uvdata
dbapp.outdisk = 2
tumin -= 60
if tlsec < 0:
tlmin -= 1
tlsec += 60
if tlmin < 0:
tlhr -= 1
tlmin += 60
return np.array([tday, tlhr, tlmin, tlsec, tday, tuhr, tumin, tusec])
# syntax: checkregular userno inna incl indisk inseq
inna = sys.argv[2]
incl = sys.argv[3]
indisk = 1 if len(sys.argv) < 5 else int(sys.argv[4])
inseq = 1 if len(sys.argv) < 6 else int(sys.argv[5])
w = WizAIPSUVData(inna, incl, indisk, inseq)
times = []
nant = float(len(w.antennas))
nbas = int((nant - 1.) * 0.5 * nant)
for wi in w:
times.append(wi.time)
# Get array of times from the data
utime = np.unique(np.asarray(times, dtype='f'))
for u in utime:
if times.count(u) != nbas:
print u, times.count(u)
new = time2timera(u)
try:
flg = np.vstack((flg, new))
urlretrieve(url, file)
assert (os.path.isfile(file))
name = os.path.basename(url).split('_')[0].upper()
uvdata = AIPSUVData(name, 'UVDATA', 1, 1)
if uvdata.exists():
uvdata.zap()
fitld = AIPSTask('fitld')
fitld.datain = file
fitld.outdata = uvdata
fitld.msgkill = 2
fitld.go()
try:
uvdata = WizAIPSUVData(name, 'UVDATA', 1, 1)
antable = uvdata.table('AN', 0)
arrnam = antable.keywords['ARRNAM']
assert (arrnam.strip() == 'EVN')
assert (antable.keywords['FREQID'] == -1)
assert (antable.keywords['FREQ'] == 1642490000.0)
assert (antable.keywords['IATUTC'] != 33.0)
antable.keywords['ARRNAM'] = 'VLBA'
antable.keywords['FREQID'] = 1
antable.keywords['FREQ'] = 4974990000.0
antable.keywords['IATUTC'] = 33.0
antable.keywords['E'] = math.e
antable.keywords['OPERATOR'] = 'NRAO'
antable.close()
def fringemap(aipsno, aipsname, intl_name, refant, imaxoff=0.0, \
aipsclass= 'FITS', utstart=0, utstop=0, utinc=0, fsiz=256, \
dofilt = False, indisk=1, fridir='./', w_max=1000., zap=True, logdir='./'):
AIPS.userno = aipsno
#if zap:
# print 'Removing all files beginning FR_ from directory '+fridir
# os.system('rm '+fridir+'FR_*')
wdata = WizAIPSUVData(aipsname, aipsclass, indisk, 1)
intl_antennas, status = procants(intl_name, AIPSUVData(wdata))
refant, status = procants([refant], AIPSUVData(wdata))
if status:
return
h = wdata.header
ra = h['crval'][h['ctype'].index('RA')]
dec = h['crval'][h['ctype'].index('DEC')]
npol = min(h['naxis'][h['ctype'].index('STOKES')], 2) # only ll,rr
#nc = h['naxis'][h['ctype'].index('FREQ')]*h['naxis'][h['ctype'].index('IF')
nc = h['naxis'][h['ctype'].index('FREQ')]
f0 = h['crval'][h['ctype'].index('FREQ')]
chw = h['cdelt'][h['ctype'].index('FREQ')]
uvfac = 1.0 + 0.5 * chw * (nc - 1) / f0 # converts uvw to centre of band
baseline = np.dstack((intl_antennas, list(refant) * len(intl_antennas)))[0]
baseline = np.array([baseline]) if baseline.ndim == 1 else baseline
for i in range(len(baseline)):
baseline[i] = np.sort(baseline[i])
utstart = wdata[0].time - 0.0001 if utstart == 0.0 else utstart
if utstop == 0.0:
try: # quicker if NX table exists
nx = AIPSUVData(wdata).table('NX', 0)
utstop = nx[len(nx) -
1].time + 0.5 * nx[len(nx) - 1].time_interval + 0.0001
except: # find time of last visibility, can be slow
print 'No NX table, so checking for end time manually....'
utstop = wdata[len(wdata) - 1].time
if utinc == 0.0: # doing the whole file
Utstart, Utstop = [utstart], [utstop]
else: # setup array of start and stop times for each chunk
Utstart = np.arange(utstart, utstop, utinc)
Utstop = Utstart + utinc
if Utstop[-1] > utstop: # avoid truncated one at the end
Utstart, Utstop = Utstart[:-1], Utstop[:-1]
print 'Time range: %.4f %.4f, intervals %d' % (utstart, utstop,
len(Utstart))
# v0,v1 = visstart (wdata, u0, -1), visstart (wdata, u1, +1)
# ------------------
ui = -1
amap = np.array([])
for visibility in wdata:
vtime = visibility.time
if vtime < Utstart[0]:
continue
elif vtime >= Utstart[0] and vtime < Utstop[-1]:
for j in range(len(Utstart)):
if Utstart[j] <= vtime < Utstop[j]:
this_ui = j
if this_ui != ui:
ui = this_ui
if ui:
amap,maxoff = proc_chunk (d,u,times,baseline,Utstart[ui],\
Utstop[ui],uvfac,npol,intl_antennas,h,imaxoff,\
fsiz,dofilt,fridir,aipsname,intl_name,\
logdir,ra,dec,amap)
d = [np.array([])] * len(baseline)
u = [np.array([])] * len(baseline)
times = [np.array([])] * len(baseline)
else:
continue_chunk(visibility, baseline, nc, npol, d, u, times)
# elif vtime > Utstop[-1]:
# amap,maxoff = proc_chunk (d,u,times,baseline,Utstart[-1],Utstop[-1],uvfac,\
# npol,intl_antennas,h,imaxoff,fsiz,dofilt,\
# fridir,aipsname,intl_name,logdir,ra,dec,amap)
# break
else:
print 'WTF?'
amap,maxoff = proc_chunk (d,u,times,baseline,Utstart[-1],Utstop[-1],uvfac,\
npol,intl_antennas,h,imaxoff,fsiz,dofilt,\
fridir,aipsname,intl_name,logdir,ra,dec,amap)
np.save('amap', amap)
if imaxoff != 0.0:
amap = np.rollaxis(amap, 2, 0)
acomb = imcomb(amap)
writeit(acomb, ra, dec, fsiz, maxoff, 'fring.fits')
pload('./fring.fits',
aipsname,
indisk,
'IMAP',
logdir=logdir,
doindxr=False)
b = np.ravel(acomb)
b = np.sort(b[~np.isnan(b)])
bmin, bmax = b[len(b) / 10], b[99 * len(b) / 100]
addwenss (aipsname,indisk,ra,dec,maxoff,bmin,bmax,w_max=w_max,\
fridir=fridir,logdir=logdir)
for name in intl_name:
nlist, ncube = np.sort(glob.glob(fridir + 'FR_*' + name +
'_*.fits')), np.array([])
for nfile in nlist:
try:
ncube = np.dstack((ncube, getdata(nfile)))
except:
ncube = np.copy(getdata(nfile))
h = getheader(nfile)
ncube = np.rollaxis(ncube, 2, 0)
ncomb = imcomb(ncube)
thisname = fridir + 'FR_' + aipsname + '_' + name + '.fits'
writeit (ncomb,h['CRVAL1'],h['CRVAL2'],h['NAXIS1'],\
h['NAXIS1']*h['CDELT2'],thisname)
pload (thisname,aipsname[:7]+name[:5],indisk,'IMAP',\
logdir=logdir,doindxr=False)
b = np.ravel(ncomb)
b = np.sort(b[~np.isnan(b)])
bmin, bmax = b[len(b) / 10], b[99 * len(b) / 100]
fitld.msgkill = 2
fitld.go()
assert (uvdata.exists())
try:
count = 0
for record in uvdata.history:
print(record)
if record[0:5] == 'FITLD':
count += 1
pass
continue
assert (count > 5)
uvdata = WizAIPSUVData(uvdata)
history = uvdata.history
history.append('Something new!')
history.close()
uvdata = AIPSUVData(uvdata)
seen = 0
for record in uvdata.history:
print(record)
if record[0:5] == 'Somet':
seen = 1
pass
continue
assert (seen)
finally:
import os
import urllib
AIPS.userno = 1999
# Download a smallish FITS file from the EVN archive.
url = 'http://archive.jive.nl/exp/N03L1_030225/fits/n03l1_1_1.IDI1'
file = '/tmp/' + os.path.basename(url)
if not os.path.isfile(file):
urllib.urlretrieve(url, file)
assert (os.path.isfile(file))
name = os.path.basename(url).split('_')[0].upper()
uvdata = AIPSUVData(name, 'UVDATA', 1, 1)
if uvdata.exists():
uvdata.zap()
fitld = AIPSTask('fitld')
fitld.datain = file
fitld.outdata = uvdata
fitld.douvcomp = 0
fitld.msgkill = 2
fitld.go()
uvdata = WizAIPSUVData(name, 'UVDATA', 1, 1, AIPS.userno)
for vis in uvdata:
vis.visibility[0][0][0][2] = 1.234
vis.update()
continue
def dfluxpy(freq, uvdata):
"Function to calculate 3C286 values, modified from Danielle's dfluxpy.py."
"Updated 20140506 to include new coefficients and a calculation for projected"
"baseline length from inspecting the u's and v's."
data = WizAIPSUVData(uvdata.name, uvdata.klass, uvdata.disk, uvdata.seq)
antab = data.table('AN', 1)
numLO = 10
numM2 = 10
for row in antab: # Ignore the Lovell baselines
if 'Lo' in row.anname:
numLO = row.nosta
if 'Mk2' in row.anname:
numM2 = row.nosta
u = []
v = []
proj = []
basel = []
baseline = 10000000
for visibility in data:
if (visibility.baseline != [numLO, numM2]) and (visibility.baseline !=
[numM2, numLO]):
u.append(visibility.uvw[0])
v.append(visibility.uvw[1])
newbasel = (299792458.0 / data.header.crval[2]) * math.sqrt(
(visibility.uvw[0]**2) + (visibility.uvw[1]**2))
proj.append(newbasel)
if newbasel < baseline:
baseline = newbasel
basel = visibility.baseline
antab = data.table('AN', 1)
for row in antab:
if row.nosta == basel[0]:
ant1 = row.anname
for row in antab:
if row.nosta == basel[1]:
ant2 = row.anname
print "For projected baseline", baseline / 1000, "km, between", ant1, "and", ant2
# Perley & Butler 2012 values
A = 1.2515
B = -0.4605
C = -0.1715
D = 0.0336
log10f = (math.log(freq) / 2.3025851) - 3.0
# Why the -3? Because freq has to be GHz for the formula to work.
log_flux = A + B * log10f + C * log10f * log10f + D * log10f * log10f * log10f
vlaflux = math.pow(10.0, log_flux)
ref_bl_length = 11236.79 # MK-TA separation in metres.
ref_freq = 5000.0
ref_rho = 0.04
bl_length = baseline
frac = (freq / ref_freq) * (bl_length / ref_bl_length)
rho = frac * frac * ref_rho
merlinflux = vlaflux / (1.0 + rho)
print "\tfor IF with freq =", freq, ", e-MERLIN flux =", merlinflux
return merlinflux