def quickspec(profile, lampid=None, solfile=None, findobj=False, objsection=None, skysection=None, clobber=False, logfile='saltclean.log', verbose=True):
"""From mosaicked data, produce wavelength calibrated files"""
profile = os.path.basename(profile)
#fill in the mosaic
#fillgaps(profile)
#specrectify
caltype='rss'
if solfile:
soldict = entersolution(solfile)
hdu = fits.open(profile)
instrume = hdu[0].header['INSTRUME']
grating = hdu[0].header['GRATING']
grang = hdu[0].header['GRTILT']
arang = hdu[0].header['CAMANG']
filtername = hdu[0].header['FILTER']
slitid=None
for sol in soldict:
if matchobservations( soldict[sol], instrume, grating, grang, arang, filtername, slitid):
caltype='line'
break
specrectify(profile, outimages='', outpref='s', solfile=solfile, caltype=caltype,
function='legendre', order=3, inttype='interp', w1=None, w2=None, dw=None, nw=None,
blank=0.0, clobber=True, logfile=logfile, verbose=True)
y1,y2=quickap('s' + profile, lampid, findobj, objsection, skysection, clobber, logfile, verbose)
if skysection is None:
ylen=100
skysection='[%i:%i]' % (y2+0.1*ylen,y2+0.2*ylen)
specsky('s'+profile, outimages='s'+profile, outpref='', method='normal', section=skysection, function='polynomial', order=3, clobber=clobber, logfile=logfile, verbose=verbose)
return y1,y2
def wavemap(
hdu,
soldict,
caltype="line",
function="poly",
order=3,
blank=0,
nearest=False,
array_only=False,
clobber=True,
log=None,
verbose=True,
):
"""Read in an image and a set of wavlength solutions. Calculate the best
wavelength solution for a given dataset and then apply that data set to the
image
return
"""
# set up the time of the observation
dateobs = saltkey.get("DATE-OBS", hdu[0])
utctime = saltkey.get("TIME-OBS", hdu[0])
exptime = saltkey.get("EXPTIME", hdu[0])
instrume = saltkey.get("INSTRUME", hdu[0]).strip()
grating = saltkey.get("GRATING", hdu[0]).strip()
if caltype == "line":
grang = saltkey.get("GRTILT", hdu[0])
arang = saltkey.get("CAMANG", hdu[0])
else:
grang = saltkey.get("GR-ANGLE", hdu[0])
arang = saltkey.get("AR-ANGLE", hdu[0])
filtername = saltkey.get("FILTER", hdu[0]).strip()
slitname = saltkey.get("MASKID", hdu[0])
slit = st.getslitsize(slitname)
xbin, ybin = saltkey.ccdbin(hdu[0])
timeobs = sr.enterdatetime("%s %s" % (dateobs, utctime))
# check to see if there is more than one solution
if caltype == "line":
if len(soldict) == 1:
sol = soldict.keys()[0]
slitid = None
if not sr.matchobservations(soldict[sol], instrume, grating, grang, arang, filtername, slitid):
msg = "Observations do not match setup for transformation but using the solution anyway"
if log:
log.warning(msg)
for i in range(1, len(hdu)):
if hdu[i].name == "SCI":
if log:
log.message("Correcting extension %i" % i)
istart = int(0.5 * len(hdu[i].data))
# open up the data
# set up the xarr and initial wavlength solution
xarr = np.arange(len(hdu[i].data[istart]), dtype="int64")
# get the slitid
try:
slitid = saltkey.get("SLITNAME", hdu[i])
except:
slitid = None
# check to see if wavext is already there and if so, then check update
# that for the transformation from xshift to wavelength
if saltkey.found("WAVEXT", hdu[i]):
w_ext = saltkey.get("WAVEXT", hdu[i]) - 1
wavemap = hdu[w_ext].data
function, order, coef = sr.findlinesol(
soldict,
istart,
nearest,
timeobs,
exptime,
instrume,
grating,
grang,
arang,
filtername,
slitid,
xarr,
)
ws = WavelengthSolution.WavelengthSolution(xarr, xarr, function=function, order=order)
ws.set_coef(coef)
for j in range(len(hdu[i].data)):
wavemap[j, :] = ws.value(wavemap[j, :])
if array_only:
return wavemap
hdu[w_ext].data = wavemap
continue
# set up a wavelength solution -- still in here for testing MOS data
try:
w_arr = sr.findsol(
xarr,
soldict,
istart,
caltype,
nearest,
timeobs,
exptime,
instrume,
grating,
grang,
arang,
filtername,
slit,
xbin,
ybin,
slitid,
function,
order,
)
except SALTSpecError as e:
if slitid:
msg = "SLITID %s: %s" % (slitid, e)
if log:
log.warning(msg)
continue
else:
raise SALTSpecError(e)
if w_arr is None:
w_arr = sr.findsol(
xarr,
soldict,
istart,
"rss",
nearest,
timeobs,
exptime,
instrume,
grating,
grang,
arang,
filtername,
slit,
xbin,
ybin,
slitid,
function,
order,
)
# for each line in the data, determine the wavelength solution
# for a given line in the image
wavemap = np.zeros_like(hdu[i].data)
for j in range(len(hdu[i].data)):
# find the wavelength solution for the data
w_arr = sr.findsol(
xarr,
soldict,
j,
caltype,
nearest,
timeobs,
exptime,
instrume,
grating,
grang,
arang,
filtername,
slit,
xbin,
ybin,
slitid,
function,
order,
)
if w_arr is not None:
wavemap[j, :] = w_arr
if array_only:
return wavemap
# write out the oimg
hduwav = fits.ImageHDU(data=wavemap, header=hdu[i].header, name="WAV")
hdu.append(hduwav)
saltkey.new("WAVEXT", len(hdu) - 1, "Extension for Wavelength Map", hdu[i])
return hdu
def wavemap(hdu,
soldict,
caltype='line',
function='poly',
order=3,
blank=0,
nearest=False,
array_only=False,
clobber=True,
log=None,
verbose=True):
"""Read in an image and a set of wavlength solutions. Calculate the best
wavelength solution for a given dataset and then apply that data set to the
image
return
"""
# set up the time of the observation
dateobs = saltkey.get('DATE-OBS', hdu[0])
utctime = saltkey.get('TIME-OBS', hdu[0])
exptime = saltkey.get('EXPTIME', hdu[0])
instrume = saltkey.get('INSTRUME', hdu[0]).strip()
grating = saltkey.get('GRATING', hdu[0]).strip()
if caltype == 'line':
grang = saltkey.get('GRTILT', hdu[0])
arang = saltkey.get('CAMANG', hdu[0])
else:
grang = saltkey.get('GR-ANGLE', hdu[0])
arang = saltkey.get('AR-ANGLE', hdu[0])
filtername = saltkey.get('FILTER', hdu[0]).strip()
slitname = saltkey.get('MASKID', hdu[0])
slit = st.getslitsize(slitname)
xbin, ybin = saltkey.ccdbin(hdu[0])
timeobs = sr.enterdatetime('%s %s' % (dateobs, utctime))
# check to see if there is more than one solution
if caltype == 'line':
if len(soldict) == 1:
sol = soldict.keys()[0]
slitid = None
if not sr.matchobservations(soldict[sol], instrume, grating, grang,
arang, filtername, slitid):
msg = 'Observations do not match setup for transformation but using the solution anyway'
if log:
log.warning(msg)
for i in range(1, len(hdu)):
if hdu[i].name == 'SCI':
if log:
log.message('Correcting extension %i' % i)
istart = int(0.5 * len(hdu[i].data))
# open up the data
# set up the xarr and initial wavlength solution
xarr = np.arange(len(hdu[i].data[istart]), dtype='int64')
# get the slitid
try:
slitid = saltkey.get('SLITNAME', hdu[i])
except:
slitid = None
#check to see if wavext is already there and if so, then check update
#that for the transformation from xshift to wavelength
if saltkey.found('WAVEXT', hdu[i]):
w_ext = saltkey.get('WAVEXT', hdu[i]) - 1
wavemap = hdu[w_ext].data
function, order, coef = sr.findlinesol(
soldict, istart, nearest, timeobs, exptime, instrume,
grating, grang, arang, filtername, slitid, xarr)
ws = WavelengthSolution.WavelengthSolution(xarr,
xarr,
function=function,
order=order)
ws.set_coef(coef)
for j in range(len(hdu[i].data)):
wavemap[j, :] = ws.value(wavemap[j, :])
if array_only: return wavemap
hdu[w_ext].data = wavemap
continue
# set up a wavelength solution -- still in here for testing MOS data
try:
w_arr = sr.findsol(xarr, soldict, istart, caltype, nearest,
timeobs, exptime, instrume, grating, grang,
arang, filtername, slit, xbin, ybin, slitid,
function, order)
except SALTSpecError as e:
if slitid:
msg = 'SLITID %s: %s' % (slitid, e)
if log:
log.warning(msg)
continue
else:
raise SALTSpecError(e)
if w_arr is None:
w_arr = sr.findsol(xarr, soldict, istart, 'rss', nearest,
timeobs, exptime, instrume, grating, grang,
arang, filtername, slit, xbin, ybin, slitid,
function, order)
# for each line in the data, determine the wavelength solution
# for a given line in the image
wavemap = np.zeros_like(hdu[i].data)
for j in range(len(hdu[i].data)):
# find the wavelength solution for the data
w_arr = sr.findsol(xarr, soldict, j, caltype, nearest, timeobs,
exptime, instrume, grating, grang, arang,
filtername, slit, xbin, ybin, slitid,
function, order)
if w_arr is not None: wavemap[j, :] = w_arr
if array_only: return wavemap
# write out the oimg
hduwav = fits.ImageHDU(data=wavemap,
header=hdu[i].header,
name='WAV')
hdu.append(hduwav)
saltkey.new('WAVEXT',
len(hdu) - 1, 'Extension for Wavelength Map', hdu[i])
return hdu
