def run_cube_gen(metadata, prev_suffix, curr_suffix, **args):
# now generate cubes
sci_obs_list = get_primary_sci_obs_list(metadata)
std_obs_list = get_primary_std_obs_list(metadata)
for fn in sci_obs_list+std_obs_list:
in_fn = '%s%s.p%s.fits' % (out_dir, fn, prev_suffix)
out_fn = '%s%s.p%s.fits' % (out_dir, fn, curr_suffix)
if skip_done and os.path.isfile(out_fn):
continue
print 'Generating Data Cube for %s' % in_fn.split('/')[-1]
# decide whether to use global or local wsol and wire files
local_wires = get_associated_calib(metadata,fn, 'wire')
if local_wires :
wire_fn = '%s%s.wire.fits' % (out_dir, local_wires[0])
print '(Note: using %s as wire file)' % wire_fn.split('/')[-1]
else:
wire_fn = wire_out_fn
local_arcs = get_associated_calib(metadata,fn, 'arc')
if local_arcs :
# Do I have two arcs ? Do they surround the Science file ?
# Implement linear interpolation as suggested by Mike I.
if len(local_arcs) ==2:
# First, get the Science time
f = pyfits.open(in_fn)
sci_header = f[0].header
sci_time = sci_header['DATE-OBS']
# Now get the arc times
arc_times = ['','']
for i in range(2):
# Fetch the arc time from the "extra" pkl file
local_wsol_out_fn_extra = '%s%s.wsol.fits_extra.pkl' % (out_dir, local_arcs[i])
f = open(local_wsol_out_fn_extra)
f_pickled = pickle.load(f)
f.close()
arc_times[i] = f_pickled[-1][0]
# Now, make sure the Science is between the arcs:
t0 = datetime.datetime( np.int(arc_times[0].split('-')[0]),
np.int(arc_times[0].split('-')[1]),
np.int(arc_times[0].split('-')[2].split('T')[0]),
np.int(arc_times[0].split('T')[1].split(':')[0]),
np.int(arc_times[0].split(':')[1]),
np.int(arc_times[0].split(':')[2].split('.')[0]),
)
t1 = datetime.datetime( np.int(sci_time.split('-')[0]),
np.int(sci_time.split('-')[1]),
np.int(sci_time.split('-')[2].split('T')[0]),
np.int(sci_time.split('T')[1].split(':')[0]),
np.int(sci_time.split(':')[1]),
np.int(sci_time.split(':')[2].split('.')[0]),
)
t2 = datetime.datetime( np.int(arc_times[01].split('-')[0]),
np.int(arc_times[1].split('-')[1]),
np.int(arc_times[1].split('-')[2].split('T')[0]),
np.int(arc_times[1].split('T')[1].split(':')[0]),
np.int(arc_times[1].split(':')[1]),
np.int(arc_times[1].split(':')[2].split('.')[0]),
)
ds1 = (t1 - t0).total_seconds()
ds2 = (t2 - t1).total_seconds()
if ds1>0 and ds2>0:
# Alright, I need to interpolate betweent the two arcs
w1 = ds1/(ds1+ds2)
w2 = ds2/(ds1+ds2)
# Open the arc solution files
fn0 = '%s%s.wsol.fits' % (out_dir, local_arcs[0])
fn1 = '%s%s.wsol.fits' % (out_dir, local_arcs[1])
fits0 = pyfits.open(fn0)
fits1 = pyfits.open(fn1)
for i in range(1,len(fits0)):
fits0[i].data = w1*fits0[i].data + w2*fits1[i].data
wsol_fn = '%s%s.wsol.fits' % (out_dir, fn)
fits0.writeto(wsol_fn, clobber=True)
print '(2 arcs found)'
print '(Note: using %sx%s.wsol.fits + %sx%s.wsol.fits as wsol file)' % (np.round(w1,2),local_arcs[0],np.round(w2,2),local_arcs[1])
else:
# Arcs do not surround the Science frame
# Revert to using the first one instead
wsol_fn = '%s%s.wsol.fits' % (out_dir, local_arcs[0])
print '(2 arcs found, but they do not bracket the Science frame!)'
print '(Note: using %s as wsol file)' % wsol_fn.split('/')[-1]
else:
# Either 1 or more than two arcs present ... only use the first one !
wsol_fn = '%s%s.wsol.fits' % (out_dir, local_arcs[0])
print '(Note: using %s as wsol file)' % wsol_fn.split('/')[-1]
else:
wsol_fn = wsol_out_fn
# All done, let's generate the cube
pywifes.generate_wifes_cube(
in_fn, out_fn,
wire_fn=wire_fn,
wsol_fn=wsol_fn,
ny_orig=76, offset_orig=2.0, **args)
#print squirrel
return
def run_cube_gen(metadata, prev_suffix, curr_suffix, **args):
# now generate cubes
sci_obs_list = get_primary_sci_obs_list(metadata)
std_obs_list = get_primary_std_obs_list(metadata)
for fn in sci_obs_list+std_obs_list:
in_fn = os.path.join(out_dir, '%s.p%s.fits' % (fn, prev_suffix))
out_fn = os.path.join(out_dir, '%s.p%s.fits' % (fn, curr_suffix))
if skip_done and os.path.isfile(out_fn):
continue
print('Generating Data Cube for %s' % in_fn.split('/')[-1])
# decide whether to use global or local wsol and wire files
local_wires = get_associated_calib(metadata,fn, 'wire')
if local_wires :
wire_fn = os.path.join(out_dir, '%s.wire.fits' % (local_wires[0]))
print('(Note: using %s as wire file)' % wire_fn.split('/')[-1])
else:
wire_fn = wire_out_fn
local_arcs = get_associated_calib(metadata,fn, 'arc')
if local_arcs :
# Do I have two arcs ? Do they surround the Science file ?
# Implement linear interpolation as suggested by Mike I.
if len(local_arcs) ==2:
# First, get the Science time
f = pyfits.open(in_fn)
sci_header = f[0].header
sci_time = sci_header['DATE-OBS']
# Now get the arc times
arc_times = ['','']
for i in range(2):
# Fetch the arc time from the "extra" pkl file
local_wsol_out_fn_extra = os.path.join(out_dir, '%s.wsol.fits_extra.pkl' % (local_arcs[i]))
f = open(local_wsol_out_fn_extra, 'rb')
try:
f_pickled = pickle.load(f, protocol=2) # TODO: see if this works
except:
f_pickled = pickle.load(f) # Python 3
f.close()
arc_times[i] = f_pickled[-1][0]
# Now, make sure the Science is between the arcs:
t0 = datetime.datetime( np.int(arc_times[0].split('-')[0]),
np.int(arc_times[0].split('-')[1]),
np.int(arc_times[0].split('-')[2].split('T')[0]),
np.int(arc_times[0].split('T')[1].split(':')[0]),
np.int(arc_times[0].split(':')[1]),
np.int(arc_times[0].split(':')[2].split('.')[0]),
)
t1 = datetime.datetime( np.int(sci_time.split('-')[0]),
np.int(sci_time.split('-')[1]),
np.int(sci_time.split('-')[2].split('T')[0]),
np.int(sci_time.split('T')[1].split(':')[0]),
np.int(sci_time.split(':')[1]),
np.int(sci_time.split(':')[2].split('.')[0]),
)
t2 = datetime.datetime( np.int(arc_times[1].split('-')[0]),
np.int(arc_times[1].split('-')[1]),
np.int(arc_times[1].split('-')[2].split('T')[0]),
np.int(arc_times[1].split('T')[1].split(':')[0]),
np.int(arc_times[1].split(':')[1]),
np.int(arc_times[1].split(':')[2].split('.')[0]),
)
ds1 = (t1 - t0).total_seconds()
ds2 = (t2 - t1).total_seconds()
if ds1>0 and ds2>0:
# Alright, I need to interpolate betweent the two arcs
w1 = ds1/(ds1+ds2)
w2 = ds2/(ds1+ds2)
# Open the arc solution files
fn0 = os.path.join(out_dir, '%s.wsol.fits' % (local_arcs[0]))
fn1 = os.path.join(out_dir, '%s.wsol.fits' % (local_arcs[1]))
fits0 = pyfits.open(fn0)
fits1 = pyfits.open(fn1)
for i in range(1,len(fits0)):
fits0[i].data = w1*fits0[i].data + w2*fits1[i].data
wsol_fn = os.path.join(out_dir, '%s.wsol.fits' % (fn))
fits0.writeto(wsol_fn, clobber=True)
print('(2 arcs found)')
print('(Note: using %sx%s.wsol.fits + %sx%s.wsol.fits as wsol file)' % (np.round(w1,2),local_arcs[0],np.round(w2,2),local_arcs[1]))
else:
# Arcs do not surround the Science frame
# Revert to using the first one instead
wsol_fn = os.path.join(out_dir, '%s.wsol.fits' % (local_arcs[0]))
print('(2 arcs found, but they do not bracket the Science frame!)')
print('(Note: using %s as wsol file)' % wsol_fn.split('/')[-1])
else:
# Either 1 or more than two arcs present ... only use the first one !
wsol_fn = os.path.join(out_dir, '%s.wsol.fits' % (local_arcs[0]))
print('(Note: using %s as wsol file)' % wsol_fn.split('/')[-1])
else:
wsol_fn = wsol_out_fn
# All done, let's generate the cube
pywifes.generate_wifes_cube(
in_fn, out_fn,
wire_fn=wire_fn,
wsol_fn=wsol_fn,
ny_orig=76, offset_orig=2.0, **args)
#print squirrel
return
wsol_fn = os.path.join(out_dir, '%s.wsol.fits' % (local_arcs[0]))
print('(2 arcs found, but they do not bracket the Science frame!)')
print('(Note: using %s as wsol file)' % wsol_fn.split('/')[-1])
else:
# Either 1 or more than two arcs present ... only use the first one !
wsol_fn = os.path.join(out_dir, '%s.wsol.fits' % (local_arcs[0]))
print('(Note: using %s as wsol file)' % wsol_fn.split('/')[-1])
else:
wsol_fn = wsol_out_fn
# All done, let's generate the cube
pywifes.generate_wifes_cube(
in_fn, out_fn,
wire_fn=wire_fn,
wsol_fn=wsol_fn,
ny_orig=76, offset_orig=2.0, **args)
#print squirrel
return
#------------------------------------------------------
# Standard star extraction
def run_extract_stars(metadata, prev_suffix, curr_suffix, type='all',**args):
# for each std, extract spectrum as desired
std_obs_list = get_primary_std_obs_list(metadata, type=type)
#print std_obs_list
for fn in std_obs_list:
in_fn = os.path.join(out_dir, '%s.p%s.fits' % (fn, prev_suffix))
out_fn = os.path.join(out_dir, '%s.x%s.dat' % (fn, prev_suffix))
print('Extract %s standard star from %s' % (type, in_fn.split('/')[-1]))
