def get_fits(no):
seq = 1
if no<1000:
n = str(no)
n = n.zfill(3)
imtype = 'IIM'+n
else:
imtype = 'II'+str(no)
dat = AIPSImage('J0528+2200',imtype,1,seq)
if not dat.exists():
print imtype+' failed!!!!'
fittp = AIPSTask('FITTP')
fittp.indata = dat
fittp.dataout = '/jop87_2/scratch/huang/rp024c/grid_trial/p0beam/beam'+str(no)+'.fits'
fittp.go()
import math
import os
import urllib
AIPS.userno = 1999
# Download a smallish FITS file from the EVN archive.
url = 'http://archive.jive.nl/exp/N05L1_050301/pipe/n05l1_4C39.25_ICLN.FITS'
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('_')[1].upper()
image = AIPSImage(name, 'ICLN', 1, 1)
if image.exists():
image.zap()
pass
assert (not image.exists())
fitld = AIPSTask('fitld')
fitld.datain = file
fitld.outdata = image
fitld.go()
assert (image.exists())
try:
image = WizAIPSImage(image)
def __init__(self, iterNum, **args):
self.iterNum = iterNum
self.args = args
AIPS.userno=self.args["user"]#username
snInit = 0
clInit = 1
AIPSTask.msgkill = -5 #makes the output less verbose
uvdata = AIPSUVData(self.args["name"], 'UVDATA', 1, self.args["inseq"])
cleaninseq = iterNum
imageClean = AIPSImage(self.args["name"], 'ICL001', 1, cleaninseq)
imageDirty = AIPSImage(self.args["name"], 'IBM001', 1, cleaninseq)
imageCleanSC = AIPSImage(self.args["source"], 'ICL001', 1, 1)
imageDirtySC = AIPSImage(self.args["source"], 'IBM001', 1, 1)
flag = AIPSUVData(self.args["name"], 'TASAV', 1, 100)
if uvdata.exists() and iterNum == 1:
print("Data is already present")
ans1 = raw_input('\033[33mDo you want to zap the data (yes/no)? \033[0m').upper()
if ans1 == 'YES':
print("Zapping data and reloading.")
uvdata.clrstat()
uvdata.zap()
fitld = AIPSTask('fitld')
fitld.datain = self.args["dataPath"]
fitld.outname = self.args["name"]
fitld.outseq = self.args["inseq"]
fitld.ncount = self.args["fileCount"]
fitld.doconcat = 1
#fitldFL = AIPSTask("FITLD")
#fitldFL.datain = args["flagPath"]
#fitldFL.outname = self.args["name"]
#fitldFL.outseq = 100
#fitldFL.ncount = 1
#fitldFL.go()
snVers = 0
clVers = 1
fitld.go()
else:
ans2 = raw_input('\033[33mDo you want to zap the tables and images(yes/no)? \033[0m').upper()
if ans2 == 'YES':
print("Zapping tables/images.")
uvdata.clrstat()
uvdata.zap_table('SN', -1)
uvdata.zap_table('FL', -1)
tablesToDelete = 0
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>tablesToDelete:
tablesToDelete = i[0]
for k in range(tablesToDelete,1,-1):
uvdata.zap_table('CL', k)
snVers = 0
clVers = 1
else:
print("Going direclty to imaging.")
"""
snVers = 0
clVers = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0] > snVers:
snVers = i[0]
if i[1] == 'AIPS CL' and i[0] > clVers:
clVers = i[0]
"""
clVers = int(raw_input("What cl table would you like to use? "))
loc = location_finder.Location_finder(clVers, **self.args)
sys.exit()
elif not uvdata.exists():
print("Loading data")
fitld = AIPSTask('fitld')
fitld.datain = self.args["dataPath"]
fitld.outname = self.args["name"]
fitld.outseq = self.args["inseq"]
fitld.ncount = self.args["fileCount"]
fitld.doconcat = 1
fitld.go()
#fitldFL = AIPSTask("FITLD")
#fitldFL.datain = args["flagPath"]
#fitldFL.outname = self.args["name"]
#fitldFL.outseq = 100
#fitldFL.ncount = 1
#fitldFL.go()
snVers = 0
clVers = 1
else:
snVers = 0
clVers = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0] > snVers:
snVers = i[0]
if i[1] == 'AIPS CL' and i[0] > clVers:
clVers = i[0]
print("Deleting tables.")
uvdata.zap_table('SN', -1)
for k in range(clVers,1,-1):
uvdata.zap_table('CL', k)
snVers = 0
clVers = 1
if imageClean.exists():
imageClean.clrstat()
imageClean.zap()
if imageDirty.exists():
imageDirty.clrstat()
imageDirty.zap()
if flag.exists():
flag.clrstat()
flag.zap()
fitldFL = AIPSTask("FITLD")
fitldFL.datain = args["flagPath"]
fitldFL.outname = self.args["name"]
fitldFL.outseq = 100
fitldFL.ncount = 1
fitldFL.go()
print("Copying flagging")
tacop = AIPSTask("TACOP")
tacop.indata = flag
tacop.invers = 3
tacop.ncount = 1
tacop.outname = self.args["name"]
tacop.outseq = self.args["inseq"]
tacop.outclass = 'UVDATA'
tacop.outdisk = 1
tacop.outver = 0
tacop.inext = 'FG'
tacop.go()
if self.args["doBP"]:
uvdata.zap_table('BP', -1) #create a new bp table for each reftelly
print("Running bandpass")
bpass = AIPSTask('BPASS')
bpass.indata = uvdata
bpass.calsour[1] = self.args["bandPassCal"]
bpass.timer = self.args["time"]
bpass.refant = self.args["refTelly"]
if self.args["excludeTelly"]:
bpass.antennas[1:] = self.args["excludedTellys"]
bpass.go()
"""
uvdata.zap_table('TY', -1)
uvdata.zap_table('GC', -1)
print("Running antab")
antab = AIPSTask('ANTAB')
antab.indata = uvdata
antab.calin = self.args["antPath"]
antab.go()
print("Running apcal")
apcal = AIPSTask('APCAL')
apcal.indata = uvdata
apcal.timer = self.args["time"]
apcal.tyver = 1
apcal.gcver = 1
apcal.go()
snVers = snVers + 1
print("apcal made snVers {0}".format(snVers))
#applies new SN table to CL
print("Running clcal.")
clcal = AIPSTask('clcal')
clcal.indata = uvdata
clcal.calsour[1] = self.args["cal"]
clcal.timerang = self.args["time"]
clcal.snver = snVers
clcal.inver = snVers
clcal.gainver = clInit #apply to original cl
clcal.timer = self.args["time"]
clcal.interpol = "ambg"
clcal.opcode = "calp"
clcal.refant = self.args["refTelly"]
clcal.go()
clVers = clVers + 1
print("clcal made cl table {0}".format(clVers))
"""
print("Running Fring.")
fring = AIPSTask('fring') #finds fringes
fring.indata = uvdata
fring.docalib = 1
fring.gainuse = clVers
if self.args["excludeTelly"]:
fring.antennas[1:] = self.args["excludedTellys"]
fring.calsour[1] = self.args["cal"]
fring.bchan = self.args["bchan"]
fring.echan = self.args["echan"]
fring.timer = self.args["time"]
fring.refant = self.args["refTelly"]
if self.args["doBP"]:
fring.doband = 1
fring.bpver = 1
fring.go()
snVers = snVers + 1
SN = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0]>SN:
SN = i[0]
if not SN == snVers:
sys.exit("SN table number missmatch")
print("Fring created SN table {0}".\
format(snVers))
#applies new SN table to CL
print("Running clcal.")
clcal = AIPSTask('clcal')
clcal.indata = uvdata
clcal.calsour[1] = self.args["cal"]
clcal.timerang = self.args["time"]
if self.args["excludeTelly"]:
clcal.antennas[1:] = self.args["excludedTellys"]
clcal.snver = snVers
clcal.inver = snVers
clcal.gainver = clInit #apply to original cl
clcal.timer = self.args["time"]
clcal.interpol = "ambg"
clcal.opcode = "calp"
clcal.refant = self.args["refTelly"]
clcal.go()
"""
clcal.snver = snVers
clcal.inver = snVers
clcal.gainver = clVers
clcal.go()
"""
CL = 0
clVers = clVers + 1
clFring = clVers
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>CL:
CL = i[0]
if not CL == clVers:
sys.exit("CL table number missmatch")
print("Clcal created CL table {0}".\
format(clVers))
#determines calibration, creates new SN
print("Running calib")
calib = AIPSTask('calib')
calib.indata = uvdata
calib.calsour[1] = self.args["cal"]
calib.docalib = 1
calib.gainuse = clVers
if self.args["excludeTelly"]:
calib.antennas[1:] = self.args["excludedTellys"]
calib.smodel[1] = 1
calib.solint = 0.2
calib.soltype = 'L1'
calib.solmode = 'P'
if self.args["doBP"]:
calib.doband = 1
calib.bpver = 1
calib.timer = self.args["time"]
calib.refant = self.args["refTelly"]
calib.go()
snVers = snVers + 1
SN = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0]>SN:
SN = i[0]
if not SN == snVers:
sys.exit("SN table number missmatch")
print("Calib created SN table {0}".\
format(snVers))
#takes SN table created by calib and applies to CL
print("Running clcal")
clcal.sources[1] = self.args["cal"]
clcal.snver = snVers
clcal.inver = snVers
clcal.gainver = clVers
clcal.go() #Apply only to cal
clVers = clVers + 1
CL = 0
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>CL:
CL = i[0]
if not CL == clVers:
sys.exit("CL table number missmatch")
print("Clcal created CL table {0}".format(clVers))
#cleans the image
print("Running imagr")
imagr = AIPSTask('IMAGR')
imagr.indata = uvdata
imagr.sources[1] = self.args["cal"]
imagr.timerang = self.args["time"]
imagr.docalib = 1
imagr.outseq = iterNum #test to force it to make file
imagr.gainuse = clVers
imagr.bchan = self.args["bchan"]
imagr.echan = self.args["echan"]
imagr.nchav = (self.args["echan"]-self.args["bchan"] + 1)
if self.args["doBP"]:
imagr.doband = 1
imagr.bpver = 1
if self.args["excludeTelly"]:
imagr.antennas[1:] = self.args["excludedTellys"]
imagr.cellsize = AIPSList([0.0001,0.0001])
imagr.imsize = AIPSList([256,256])
imagr.nboxes = len(self.args["CalCleanBox"])
imagr.clbox[1:] = self.args["CalCleanBox"]
imagr.niter = 1000
imagr.go()
print("Done with imagr")
#to get last positive row
latestImgTable = 0
for j in imageClean.tables:
if j[1] == 'AIPS CC' and j[0]>latestImgTable:
latestImgTable = j[0]
ccTable = imageClean.table('CC', latestImgTable)
for row, i in enumerate(ccTable, start=2): #start @ 2 to get last positive
if i['flux']<0:
lastPositive = row
break
print("The last positive component number is: {0}".\
format(lastPositive))
print("Running Calib")
calibSelf = AIPSTask('calib')
calibSelf.in2data = imageClean
calibSelf.indata = uvdata
calibSelf.calsour[1] = self.args["cal"]
calibSelf.docalib = 1
calibSelf.gainuse = clFring
calibSelf.solint = 0.2
calibSelf.soltype = 'L1'
calibSelf.solmode = 'A&P'
if self.args["excludeTelly"]:
calibSelf.antennas[1:] = self.args["excludedTellys"]
calibSelf.ncomp[1] = lastPositive
calibSelf.timer = self.args["time"]
if self.args["doBP"]:
calibSelf.doband = 1
calibSelf.bpver = 1
calibSelf.go()
snVers = snVers + 1
SN = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0]>SN:
SN = i[0]
if not SN == snVers:
print("SN = {0} , snVers = {1}".format(SN, snVers))
sys.exit("SN table number missmatch")
print("calibSelf created SN table {0}".format(snVers))
#makes contour plot
kntr = AIPSTask('KNTR')
kntr.indata = imageClean
kntr.levs = AIPSList([-1,1,2,3,4,5,7,10])
kntr.dogrey = -1
kntr.dotv = -1
kntr.dovect = - 1
#kntr.blc[1] = .80*self.args["fitBox"][1]
#kntr.blc[2] = .80*self.args["fitBox"][2]
#kntr.trc[1] = 1.20*self.args["fitBox"][3]
#kntr.trc[2] = 1.20*self.args["fitBox"][4]
kntr.go()
lwmp = AIPSTask('LWPLA')
lwmp.indata = imageClean
lwmp.plver = 1
lwmp.invers = 1
lwmp.outfile = os.getcwd() + '/images_{0}/{1}_time{2}'.format(self.args["date"],self.args["cal"],self.iterNum) + '.ps'
lwmp.go()
print("Running clcal")
clcal.snver = snVers
clcal.inver = snVers
clcal.sources[1] = self.args["cal"]
clcal.calsour[1] = self.args["cal"]
clcal.gainver = clVers
print("clVers = {0}".format(clVers))
clcal.go() #Apply only to cal
clVers = clVers + 1
CL = 0
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>CL:
CL = i[0]
if not CL == clVers:
sys.exit("CL table number missmatch")
print("clcal created CL table {0}".format(clVers))
print("Running clcal.")
clcalFinal = AIPSTask('clcal')
clcalFinal.indata = uvdata
clcalFinal.sources[1] = self.args["source"]
clcalFinal.calsour[1] = self.args["cal"]
clcalFinal.timerang = self.args["time"]
clcalFinal.snver = snVers
clcalFinal.inver = snVers
clcalFinal.gainver = clFring
if self.args["excludeTelly"]:
clcalFinal.antennas[1:] = self.args["excludedTellys"]
clcalFinal.timer = self.args["time"]
clcalFinal.refant = self.args["refTelly"]
print("clFring = {0}".format(clFring))
clcalFinal.go()
clVers = clVers +1
CL = 0
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>CL:
CL = i[0]
if not CL == clVers:
sys.exit("CL table number missmatch")
print("clcalFinal created CL table {0}".format(clVers))
print("Running imagr")
imagrSC = AIPSTask('IMAGR')
imagrSC.indata = uvdata
imagrSC.sources[1] = self.args["source"]
imagrSC.timerang = self.args["time"]
imagrSC.docalib = 1
imagrSC.outseq = 1
imagrSC.outname = self.args["source"]
imagrSC.gainuse = clVers
imagrSC.bchan = self.args["SCbchan"]
imagrSC.echan = self.args["SCechan"]
imagrSC.nchav = (self.args["SCechan"]-self.args["SCbchan"] + 1)
if self.args["doBP"]:
imagrSC.doband = 1
imagrSC.bpver = 1
if self.args["excludeTelly"]:
imagrSC.antennas[1:] = self.args["excludedTellys"]
imagrSC.cellsize = AIPSList([0.0001,0.0001])
imagrSC.imsize = AIPSList([256,256])
imagrSC.nboxes = 1
imagrSC.clbox[1] = self.args["fitBox"]
imagrSC.niter = 1000
imagrSC.go()
print("Done with imagr")
#makes contour plot
kntrSC = AIPSTask('KNTR')
kntrSC.indata = imageCleanSC
kntrSC.levs = AIPSList([2,3,4,5,7,10,13,17])
kntrSC.dogrey = -1
kntrSC.dotv = -1
kntrSC.dovect = - 1
#kntr.blc[1] = .80*self.args["fitBox"][1]
#kntr.blc[2] = .80*self.args["fitBox"][2]
#kntr.trc[1] = 1.20*self.args["fitBox"][3]
#kntr.trc[2] = 1.20*self.args["fitBox"][4]
kntrSC.go()
lwmpSC = AIPSTask('LWPLA')
lwmpSC.indata = imageCleanSC
lwmpSC.plver = 1
lwmpSC.invers = 1
lwmpSC.outfile = os.getcwd() + '/images_{0}/{1}_time{2}'.format(self.args["date"],self.args["source"],self.iterNum) + '.ps'
lwmpSC.go()
loc = location_finder.Location_finder(clVers, **self.args)
imageClean.zap()
imageDirty.zap()
imageCleanSC.zap()
imageDirtySC.zap()
flag.zap()
with open(os.getcwd() + '/images_{0}/params{1}.txt'.format(self.args["date"],self.iterNum),'w') as f:
for l in self.args:
f.write("\n{0}".format(l))
from AIPS import AIPS
from AIPSTask import AIPSTask
from AIPSData import AIPSImage
AIPS.userno = 1999
image = AIPSImage('MANDELBROT', 'MANDL', 1, 1)
if image.exists():
image.zap()
mandl = AIPSTask('mandl')
mandl.outdata = image
mandl.imsize[1:] = [ 512, 512 ]
mandl.go()
try:
header = image.header
print 'Dimension: %dx%d' % (header.naxis[0], header.naxis[1])
print image.tables
finally:
image.zap()
from AIPS import AIPS
from AIPSTask import AIPSTask
from AIPSData import AIPSImage
AIPS.userno = 1999
image = AIPSImage('MANDELBROT', 'MANDL', 1, 1)
if image.exists():
image.zap()
mandl = AIPSTask('mandl')
mandl.outdata = image
mandl.imsize[1:] = [64, 64]
mandl.go()
try:
jmfit = AIPSTask('jmfit')
jmfit.indata = image
jmfit.ngauss = 4
jmfit.domax[1:] = [1, 0, 0, 0]
jmfit.go()
print 'Peak values:', jmfit.fmax[1:]
for fmax in jmfit.fmax[1:]:
assert (fmax)
finally:
image.zap()
import os
import urllib
AIPS.userno = 1999
# Download a smallish FITS file from the EVN archive.
url = 'http://archive.jive.nl/exp/N05L1_050301/pipe/n05l1_4C39.25_ICLN.FITS'
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('_')[1].upper()
image = AIPSImage(name, 'ICLN', 1, 1)
if image.exists():
image.zap()
pass
assert(not image.exists())
fitld = AIPSTask('fitld')
fitld.datain = file
fitld.outdata = image
fitld.go()
assert(image.exists())
try:
image = WizAIPSImage(image)
refant=OP.st_refant[i],
gainu=cl_hv,
plotname=OP.st_plotname[i])
if OP.global_fring:
for clv in range(40, uvdata.table_highver('CL')):
uvdata.zap_table('CL', clv)
for snv in range(45, uvdata.table_highver('SN')):
uvdata.zap_table('SN', snv)
if OP.gf_scan:
OP.gf_timer = []
for i in OP.gf_scan:
OP.gf_timer = AF.scantime(uvdata, i)
if OP.get2n:
imfile = AIPSImage(OP.cmap_name, 'CMAP', uvdata.disk, 1)
if imfile.exists():
image = [OP.cmap_name, 'CMAP', uvdata.disk, 1]
logger.info('Using clean image')
if OP.use_bp:
cl_hv_af = AF.do_global_fring(uvdata,
cals=OP.gf_cals,
sources=OP.gf_sources,
bpv=1,
doband=2,
timer=OP.gf_timer,
dofit=OP.gf_dofit,
antennas=OP.gf_antennas,
aparm=OP.gf_aparm,
dparm=OP.gf_dparm,
refant=OP.gf_refant,
interpol=OP.gf_interpol,
vlbatasks.applysntable(targetdata, snversion, "SELN", clversion, refant)
snversion += 1
clversion += 1
# Correct for leakage if needed
#leakagedopol = 0
if xpolmodelfile != "":
# First the xpoldelays
if not options.targetonly:
xpolscan = 1
if not os.path.exists(xpolmodelfile):
print "Can't find xpol delay model " + xpolmodelfile
print "Aborting!!"
sys.exit(1)
xpolmodel = AIPSImage("LKGSRC", "CLEAN", 1, 1)
if xpolmodel.exists():
xpolmodel.zap()
vlbatasks.fitld_image(xpolmodelfile, xpolmodel)
xpolsolintmins = 1
inttimesecs = 0.5 # Doesn't matter if this is wrong
if os.path.exists(xpolsnfilename):
os.remove(xpolsnfilename)
vlbatasks.xpoldelaycal(caldata, clversion, refant, options.sourcename,
xpolscan, xpolmodel, xpolsolintmins,
inttimesecs, xpolsnfilename, delaywindow,
ratewindow)
vlbatasks.loadtable(caldata, xpolsnfilename, snversion)
vlbatasks.applysntable(caldata, snversion, '2PT', clversion, refant)
if not options.calibrateonly:
vlbatasks.loadtable(targetdata, xpolsnfilename, snversion)
vlbatasks.applysntable(targetdata, snversion, '2PT', clversion, refant)
def makeslices(imfile, source=False, freq=False, outdisk=1, **kwargs):
logger = logging.getLogger('__name__')
'''
imfile: location to the image
source: source name to use for naming of catalog in aips, if not set the imfile name will be used
freq: frequency string to use for naming of catalog in aips, if not set the imfile name will be used
'''
args = {
'ang': 0,
'blc': False,
'trc': False,
'nfit': 0,
'gmax': 1,
'gwidth': 9,
'gpos': 0,
'step1': True, #rotate image
'step2': True, #make slices
'step3': True, #fit slices
'step4': True, #plot slices with fit and write output data table
'ang_step': False,
'image_fraction': 1,
'del_imcat': True, # delete image files after program is finished
'plot_slice': False
}
args.update(kwargs)
if not args['blc']:
blc, trc = get_blc_trc(imfile, args['image_fraction'])
else:
blc = args['blc']
trc = args['trc']
nfit = args['nfit']
gmax = args['gmax']
gwidth = args['gwidth']
gpos = args['gpos']
fitdir = 'SLFIT_{}degree'.format(args['ang'])
if source:
if freq:
imname = source + '_' + freq
else:
imname = source
else:
imname = imfile.split('/')[-1].split('.')[0]
if len(imname) > 12:
imname = imname[:12]
logger.info('Image name too long, will use \'{}\'\n'.format(imname))
imdata = AIPSImage(*[imname, 'FITS', outdisk, 1])
if imdata.exists() == True:
imdata.zap()
imcat = AT.imlod(imname, outdisk, imfile, 'FITS')
imdata = AIPSImage(*AT.getndata(outdisk, imcat))
if imdata.exists() == True:
logger.info('Successfully loaded new image file.\n')
logger.info('Data Loaded: (%s, %s, %d, %d)\n', imdata.name,
imdata.klass, imdata.disk, imdata.seq)
else:
logger.info('Image file not loeaded. Check input.\n')
return
if args['ang_step']:
raw_input("Press Enter to continue...")
rotname = imname[:10] + '_R'
####
if args['step1']:
rotdata = AIPSImage(*[rotname, 'FITS', outdisk, 1])
if rotdata.exists() == True:
rotdata.zap()
rotcat = AT.lgeom(imdata,
rotname,
outdisk,
outseq=1,
aparm=[0, 0, args['ang'], 0, 0, 0, 0, 0, 0])
rotdata = AIPSImage(*AT.getndata(outdisk, rotcat))
if rotdata.exists() == True:
logger.info('Rotated image exists.\n')
else:
logger.error('Rotated image not loaded.\n')
sys.exit()
else:
rotdata = AIPSImage(*[rotname, 'FITS', outdisk, 1])
sys.stdout.write('data that will be used {}'.format(rotdata))
###########3####
if args['step2']:
AT.extd(rotdata, 'SL', -1)
j = 1
for i in range(blc[0], trc[0]):
AT.slices(rotdata, blc=[i, blc[1], 1], trc=[i, trc[1], 1])
if args['plot_slice']:
AT.sl2pl(rotdata, inv=j)
j += 1
if args['plot_slice']:
outfile = '%s_slice.pdf' % rotdata.name
AT.lwpla(rotdata, outfile)
#############
if args['step3']:
if os.path.isdir(fitdir):
for f in glob(fitdir + '/*'):
os.remove(f)
else:
os.makedirs(fitdir)
if type(gmax) != list:
if type(nfit) == int:
nn = np.arange(nfit, rotdata.table_highver('SL') + 1)
else:
nn = np.concatenate([np.arange(n[0], n[1] + 1) for n in nfit])
for ii in nn:
gmax1 = gmax
gwidth1 = gwidth
saveLog = fitdir + '/SLFIT_{}_{}.log'.format(rotdata.name, ii)
AT.slfit(rotdata,
inv=int(ii),
gmax=gmax,
gwidth=gwidth,
gpos=gpos,
savelog=saveLog)
lines = []
with open(saveLog, 'r') as f:
for line in f:
if line.find('LOGFILE') == -1:
lines.append(line)
# automatically get the fitting results from this slice to use as starting values for the next one
jj = 0
for line in lines:
if line.find('Results in physical units') != -1:
gmax = float(lines[jj + 2].split()[3])
peakunit = lines[jj + 2].split()[5]
gwidth = float(lines[jj + 4].split()[3])
gwidthEr = float(lines[jj + 4].split()[4])
if peakunit == 'MicroJy/BEAM':
gmax *= 1e-3 #convert everything to MilliJy/beam
# elif peakunit == 'MilliJy/BEAM':
# gmax *= 1
break
jj += 1
if np.logical_or.reduce(
(gwidth < gwidthEr, gmax < gmax1 / 5., gmax > 5 * gmax1)):
gmax = gmax1
gwidth = gwidth1
else:
for gma, gwi, nf in zip(gmax, gwidth, nfit):
for ii in range(nf[0], nf[1] + 1):
AT.slfit(rotdata,
inv=ii,
gmax=gma,
gwidth=gwi,
savelog=fitdir +
'/SLFIT_{}_{}.log'.format(rotdata.name, ii))
###########
if args['step4']:
AT.extd(rotdata, 'PL', -1)
for i in range(0, trc[0] - blc[0]):
AT.sl2pl(rotdata, inv=i + 1, domod=1, dores=1)
outfile = '{}_fit_{}degree'.format(rotdata.name, args['ang'])
AT.lwpla(rotdata,
outfile + '.pdf',
docol=1,
plcolors=[[0, 0, 0], [0, 0, 0], [0, 0, 1], [0, 1,
0], [0, 0, 0],
[0, 0, 0], [0, 0, 0], [0, 0, 0], [0, 0, 0],
[1, 1, 1]])
AT.slcol(rotdata,
outfile + '.txt',
inv=1,
nfiles=rotdata.table_highver('SL'))
#################
if args['del_imcat']:
sys.stdout.write('Deleting loaded map catalog and rotated catalog.\n')
rotdata.zap()
imdata.zap()