def extractSpec(self, inIm, **kwargs):
# remove previous spectra and extract new ones
iraf.imdelete("e" + inIm, verify="yes")
iraf.gfextract(inIm, **kwargs)
return
def extractSpec(self, inIm, **kwargs):
print "\nEXTRACTING SPECTRA FROM", inIm
# destroy previous extracted spectra
iraf.imdelete("e" + inIm)
# extract the spectra and view the result
iraf.gfextract(inIm, **kwargs)
self.viewCube("e" + inIm, frame=1, z1=0., z2=0., extname="SCI", \
version="*")
return
iraf.imdelete('rg@' + ic.lst_flat)
flat0 = iraf.type(ic.lst_flat, Stdout=1)[0]
iraf.gfreduce(flat0,
rawpath=ic.rawdir,
fl_extract='no',
bias=ic.bias,
fl_over='yes',
fl_trim='yes',
mdffile=ic.mdf,
mdfdir='./',
slits='both',
line=1400,
fl_fluxcal='no',
fl_gscrrej='no',
fl_wavtran='no',
fl_skysub='no',
fl_inter='no',
fl_vardq='no')
iraf.imdelete('erg@' + ic.lst_flat)
iraf.gfextract('rg' + flat0, fl_inter='yes', line=1400)
# Writing aperture file
apfile = ['aperg' + flat0 + '_1', 'aperg' + flat0 + '_2']
for i in np.arange(len(apfile)):
os.system('cp -rpv ' + ic.dir_db + apfile[i] + ' ' + ic.dir_db +
apfile[i] + '_old')
# Printing the running time
print('--- %s seconds ---' % (time.time() - start_time))
iraf.unlearn('gfextract')
iraf.unlearn('gfdisplay')
# ---------- QE correction and extraction of the science ---------- #
flat0 = iraf.type(ic.lst_flat, Stdout=1)[0].strip()
response = flat0+'_resp'
ref_flat0 = 'eqbrg'+flat0
arc0 = iraf.type(ic.lst_arc, Stdout=1)[0].strip()
iraf.imdelete('qxbrg@'+ic.lst_sci)
iraf.imdelete('eqxbrg@'+ic.lst_sci)
for sci in iraf.type(ic.lst_sci, Stdout=1):
sci = sci.strip()
iraf.gqecorr('xbrg'+sci, refimage='erg'+arc0, fl_correct='yes',
fl_vardq='yes', verbose='yes')
iraf.gfextract('qxbrg'+sci, response=response, recenter='no',
trace='no', reference=ref_flat0, weights='none',
fl_vardq='yes', line=1400)
os.system('ds9 &')
iraf.sleep(5.0)
for sci in iraf.type(ic.lst_sci, Stdout=1):
sci = sci.strip()
iraf.gfdisplay('eqxbrg'+sci, 1)
# Printing the running time
print('--- %s seconds ---' %(time.time()-start_time))
# Extract a flat
flat = np.loadtxt(ic.lst_flat, dtype=str)
if (flat.size > 1):
raise ValueError("Please check if there is only one flat image for the standard star.")
flat0 = flat.item(0)
iraf.imdelete('g@'+ic.lst_flat)
iraf.imdelete('rg@'+ic.lst_flat)
iraf.gfreduce(flat0, rawpath=ic.rawdir, fl_extract='no', bias=ic.caldir+ic.procbias,
fl_over='yes', fl_trim='yes', mdffile=ic.mdf, mdfdir='./',
slits=ic.cslit, line=pk_line, fl_fluxcal='no', fl_gscrrej='no',
fl_wavtran='no', fl_skysub='no', fl_inter='no', fl_vardq='no')
iraf.imdelete('erg@'+ic.lst_flat)
iraf.gfextract('rg'+flat0, fl_inter='yes', line=pk_line, exslits=ic.eslit)
'''
----- Interactive task after gfextract -----
Extracting slit 1
Find apertures for erg[FLAT]_1? ('yes')
Edit apertures for erg[FLAT]_1? ('yes')
(IRAF graphics displaying... please check the fibers visually.)
- "w" + "e" (left bottom) + "e" (right top) : zoom-in
- "w" + "a" : zoom-out
- "q" : quitting the interactive task
Trace apertures for erg[FLAT]_1? ('yes')
Fit traced positions for erg[FLAT]_1 interactively? ('NO')
Write apertures for erg[FLAT]_1 to database ('yes')
Extract aperture spectra for erg[FLAT]_1? ('yes' (IFU-2 slit) / 'NO' (IFU-1 slit))
--> For the IFU-1 slit, this is the end.
def main():
iraf.set(stdimage='imtgmos')
iraf.gemini()
iraf.gmos()
# set directories
iraf.set(rawdir='/dados/gmos/raw') # raw files
iraf.set(
procdir='/dados/gmos/reduction/products/ngc7213/') # processed files
iraf.gmos.logfile = 'logfile.log'
iraf.gfextract.verbose = 'no'
iraf.cd('procdir')
for task in ['gemini', 'gmos', 'gfextract']:
iraf.unlearn(task)
flat = 'S20110927S0062'
for name in glob.glob('database/apeprg' + flat + '*'):
if os.path.isfile(name):
print('Removing file {:s}'.format(name))
os.remove(name)
if os.path.isfile('eprg' + flat + '.fits'):
os.remove('eprg' + flat + '.fits')
grow_gap = 1
vardq = 'yes'
ap = auto_apertures.AutoApertures('prg' + flat + '.fits')
ap.find_dead_beams()
ap.fix_mdf()
iraf.delete('eprg' + flat + '.fits')
extract_args = {
'inimage': 'prg' + flat,
'exslits': '*',
'trace': 'yes',
'recenter': 'yes',
'order': 9,
't_nsum': 50,
'function': 'chebyshev',
'fl_novl': 'no',
'fl_fulldq': vardq,
'fl_gnsskysub': 'no',
'fl_fixnc': 'no',
'fl_fixgaps': 'yes',
'fl_vardq': 'yes',
'grow': grow_gap,
'fl_inter': 'no',
'verbose': 'no'
}
iraf.gfextract(**extract_args)
sys.exit()
time_out = 0
while (ap.check_iraf('database/apeprg' + flat) != 0) and (time_out < 5):
ap.fix_mdf()
print('Aperture iteration #{:d}.'.format(time_out))
iraf.delete('eprg' + flat + '.fits')
iraf.delete('database/apeprg' + flat + '*')
extract_args['fl_inter'] = 'yes'
iraf.gfextract(**extract_args)
time_out += 1
arc0 = arc.item(0)
std = np.loadtxt(ic.lst_std, dtype=str)
if (std.size > 1):
raise ValueError("Please check if there is only one image for the standard star.")
std0 = std.item(0)
response = flat0+'_resp'
ref_flat0 = 'eqbrg'+flat0
iraf.imdelete('qxbrg@'+ic.lst_std)
iraf.imdelete('eqxbrg@'+ic.lst_std)
iraf.gqecorr('xbrg'+std0, refimage='erg'+arc0, fl_correct='yes',
fl_vardq='yes', verbose='yes')
iraf.gfextract('qxbrg'+std0, response=response, recenter='no',
trace='no', reference=ref_flat0, weights='none',
fl_vardq='yes', line=pk_line, exslits=ic.eslit)
if (ic.nslit == 1):
vkw = '1'
if (ic.nslit == 2):
vkw = '*'
os.system('ds9 &')
iraf.sleep(5.0)
iraf.gfdisplay('eqxbrg'+std0, 1, version=vkw)
# ----- Displaying the extracted data for checking bad columns ----- #
# fits.open('eqxbrg'+std0+'.fits').info()
if (glob.glob("badcol/") == []):