def specidentify(images, linelist, outfile, guesstype='rss', guessfile='',
automethod='Matchlines', function='poly', order=3, rstep=100,
rstart='middlerow', mdiff=5, thresh=3, niter=5, smooth=0,
subback=0, inter=True, startext=0, clobber=False,
textcolor='black', logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# set up the variables
infiles = []
outfiles = []
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.argunpack('Output', outfile)
# open the line lists
slines, sfluxes = st.readlinelist(linelist)
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
# open the image
hdu = saltio.openfits(img)
# get the basic information about the spectrograph
dateobs = saltkey.get('DATE-OBS', hdu[0])
try:
utctime = saltkey.get('UTC-OBS', hdu[0])
except SaltError:
utctime = saltkey.get('TIME-OBS', hdu[0])
instrume = saltkey.get('INSTRUME', hdu[0]).strip()
grating = saltkey.get('GRATING', hdu[0]).strip()
grang = saltkey.get('GR-ANGLE', hdu[0])
grasteps = saltkey.get('GRTILT', hdu[0])
arang = saltkey.get('AR-ANGLE', hdu[0])
arsteps = saltkey.get('CAMANG', hdu[0])
rssfilter = saltkey.get('FILTER', hdu[0])
specmode = saltkey.get('OBSMODE', hdu[0])
masktype = saltkey.get('MASKTYP', hdu[0]).strip().upper()
slitname = saltkey.get('MASKID', hdu[0])
xbin, ybin = saltkey.ccdbin(hdu[0], img)
for i in range(startext, len(hdu)):
if hdu[i].name == 'SCI':
log.message('Proccessing extension %i in %s' % (i, img))
# things that will change for each slit
if masktype == 'LONGSLIT':
slit = st.getslitsize(slitname)
xpos = -0.2666
ypos = 0.0117
objid = None
elif masktype == 'MOS':
slit = 1.5
#slit=saltkey.get('SLIT', hdu[i])
# set up the x and y positions
miny = hdu[i].header['MINY']
maxy = hdu[i].header['MAXY']
ras = hdu[i].header['SLIT_RA']
des = hdu[i].header['SLIT_DEC']
objid = hdu[i].header['SLITNAME']
# TODO: Check the perfomance of masks at different PA
rac = hdu[0].header['MASK_RA']
dec = hdu[0].header['MASK_DEC']
pac = hdu[0].header['PA']
# these are hard wired at the moment
xpixscale = 0.1267 * xbin
ypixscale = 0.1267 * ybin
cx = int(3162 / xbin)
cy = int(2050 / ybin)
x, y = mt.convert_fromsky(ras, des, rac, dec, xpixscale=xpixscale, ypixscale=ypixscale,
position_angle=-pac, ccd_cx=cx, ccd_cy=cy)
xpos = 0.015 * 2 * (cx - x[0])
ypos = 0.0117
else:
msg = '%s is not a currently supported masktype' % masktype
raise SALTSpecError(msg)
if instrume not in ['PFIS', 'RSS']:
msg = '%s is not a currently supported instrument' % instrume
raise SALTSpecError(msg)
# create RSS Model
rss = RSSModel.RSSModel(grating_name=grating.strip(), gratang=grang,
camang=arang, slit=slit, xbin=xbin, ybin=ybin,
xpos=xpos, ypos=ypos)
res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
dres = res / 10.0
wcen = 1e7 * rss.calc_centralwavelength()
R = rss.calc_resolution(
wcen / 1e7, rss.alpha(), -rss.beta())
logmsg = '\nGrating\tGR-ANGLE\tAR-ANGLE\tSlit\tWCEN\tR\n'
logmsg += '%s\t%8.3f\t%8.3f\t%4.2f\t%6.2f\t%4f\n' % (
grating, grang, arang, slit, wcen, R)
if log:
log.message(logmsg, with_header=False)
# set up the data for the source
try:
data = hdu[i].data
except Exception as e:
message = 'Unable to read in data array in %s because %s' % (
img, e)
raise SALTSpecError(message)
# set up the center row
if rstart == 'middlerow':
ystart = int(0.5 * len(data))
else:
ystart = int(rstart)
rss.gamma = 0.0
if masktype == 'MOS':
rss.gamma = 180.0 / math.pi * math.atan((y * rss.detector.pix_size * rss.detector.ybin
- 0.5 * rss.detector.find_height()) / rss.camera.focallength)
# set up the xarr array based on the image
xarr = np.arange(len(data[ystart]), dtype='int64')
# get the guess for the wavelength solution
if guesstype == 'rss':
# set up the rss model
ws = st.useRSSModel(
xarr, rss, function=function, order=order, gamma=rss.gamma)
elif guesstype == 'file':
soldict = {}
soldict = readsolascii(guessfile, soldict)
timeobs = enterdatetime('%s %s' % (dateobs, utctime))
exptime = saltkey.get('EXPTIME', hdu[0])
filtername = saltkey.get('FILTER', hdu[0]).strip()
try:
slitid = saltkey.get('SLITNAME', hdu[i])
except:
slitid = None
function, order, coef = findlinesol(
soldict, ystart, True, timeobs, exptime, instrume, grating, grang, arang, filtername, slitid, xarr=xarr)
ws = WavelengthSolution.WavelengthSolution(
xarr, xarr, function=function, order=order)
ws.set_coef(coef)
else:
raise SALTSpecError(
'This guesstype is not currently supported')
# identify the spectral lines
ImageSolution = identify(data, slines, sfluxes, xarr, ystart, ws=ws, function=function,
order=order, rstep=rstep, mdiff=mdiff, thresh=thresh, niter=niter,
method=automethod, res=res, dres=dres, smooth=smooth, inter=inter, filename=img,
subback=0, textcolor=textcolor, log=log, verbose=verbose)
if outfile and len(ImageSolution):
writeIS(ImageSolution, outfile, dateobs=dateobs, utctime=utctime, instrume=instrume,
grating=grating, grang=grang, grasteps=grasteps, arsteps=arsteps,
arang=arang, rfilter=rssfilter, slit=slit, xbin=xbin,
ybin=ybin, objid=objid,
filename=img, log=log, verbose=verbose)
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
def specidentify(images,
linelist,
outfile,
guesstype='rss',
guessfile='',
automethod='Matchlines',
function='poly',
order=3,
rstep=100,
rstart='middlerow',
mdiff=5,
thresh=3,
niter=5,
smooth=0,
subback=0,
inter=True,
startext=0,
clobber=False,
textcolor='black',
preprocess=False,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# set up the variables
infiles = []
outfiles = []
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.argunpack('Output', outfile)
# open the line lists
slines, sfluxes = st.readlinelist(linelist)
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
# open the image
hdu = saltio.openfits(img)
# get the basic information about the spectrograph
dateobs = saltkey.get('DATE-OBS', hdu[0])
try:
utctime = saltkey.get('UTC-OBS', hdu[0])
except SaltError:
utctime = saltkey.get('TIME-OBS', hdu[0])
instrume = saltkey.get('INSTRUME', hdu[0]).strip()
grating = saltkey.get('GRATING', hdu[0]).strip()
grang = saltkey.get('GR-ANGLE', hdu[0])
grasteps = saltkey.get('GRTILT', hdu[0])
arang = saltkey.get('AR-ANGLE', hdu[0])
arsteps = saltkey.get('CAMANG', hdu[0])
rssfilter = saltkey.get('FILTER', hdu[0])
specmode = saltkey.get('OBSMODE', hdu[0])
masktype = saltkey.get('MASKTYP', hdu[0]).strip().upper()
slitname = saltkey.get('MASKID', hdu[0])
xbin, ybin = saltkey.ccdbin(hdu[0], img)
for i in range(startext, len(hdu)):
if hdu[i].name == 'SCI':
log.message('Proccessing extension %i in %s' % (i, img))
# things that will change for each slit
if masktype == 'LONGSLIT':
slit = st.getslitsize(slitname)
xpos = -0.2666
ypos = 0.0117
objid = None
elif masktype == 'MOS':
slit = 1.
#slit=saltkey.get('SLIT', hdu[i])
# set up the x and y positions
miny = hdu[i].header['MINY']
maxy = hdu[i].header['MAXY']
ras = hdu[i].header['SLIT_RA']
des = hdu[i].header['SLIT_DEC']
objid = hdu[i].header['SLITNAME']
# TODO: Check the perfomance of masks at different PA
rac = hdu[0].header['MASK_RA']
dec = hdu[0].header['MASK_DEC']
pac = hdu[0].header['PA']
# these are hard wired at the moment
xpixscale = 0.1267 * xbin
ypixscale = 0.1267 * ybin
cx = int(3162 / xbin)
cy = int(2050 / ybin)
x, y = mt.convert_fromsky(ras,
des,
rac,
dec,
xpixscale=xpixscale,
ypixscale=ypixscale,
position_angle=-pac,
ccd_cx=cx,
ccd_cy=cy)
xpos = 0.015 * 2 * (cx - x[0])
ypos = 0.0117
else:
msg = '%s is not a currently supported masktype' % masktype
raise SALTSpecError(msg)
if instrume not in ['PFIS', 'RSS']:
msg = '%s is not a currently supported instrument' % instrume
raise SALTSpecError(msg)
# create RSS Model
rss = RSSModel.RSSModel(grating_name=grating.strip(),
gratang=grang,
camang=arang,
slit=slit,
xbin=xbin,
ybin=ybin,
xpos=xpos,
ypos=ypos)
res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
dres = res / 10.0
wcen = 1e7 * rss.calc_centralwavelength()
R = rss.calc_resolution(wcen / 1e7, rss.alpha(),
-rss.beta())
logmsg = '\nGrating\tGR-ANGLE\tAR-ANGLE\tSlit\tWCEN\tR\n'
logmsg += '%s\t%8.3f\t%8.3f\t%4.2f\t%6.2f\t%4f\n' % (
grating, grang, arang, slit, wcen, R)
if log:
log.message(logmsg, with_header=False)
# set up the data for the source
try:
data = hdu[i].data
except Exception, e:
message = 'Unable to read in data array in %s because %s' % (
img, e)
raise SALTSpecError(message)
# set up the center row
if rstart == 'middlerow':
ystart = int(0.5 * len(data))
else:
ystart = int(rstart)
rss.gamma = 0.0
if masktype == 'MOS':
rss.gamma = 180.0 / math.pi * math.atan(
(y * rss.detector.pix_size * rss.detector.ybin -
0.5 * rss.detector.find_height()) /
rss.camera.focallength)
# set up the xarr array based on the image
xarr = np.arange(len(data[ystart]), dtype='int64')
# get the guess for the wavelength solution
if guesstype == 'rss':
# set up the rss model
ws = st.useRSSModel(xarr,
rss,
function=function,
order=order,
gamma=rss.gamma)
if function in ['legendre', 'chebyshev']:
ws.func.func.domain = [xarr.min(), xarr.max()]
elif guesstype == 'file':
soldict = {}
soldict = readsolascii(guessfile, soldict)
timeobs = enterdatetime('%s %s' % (dateobs, utctime))
exptime = saltkey.get('EXPTIME', hdu[0])
filtername = saltkey.get('FILTER', hdu[0]).strip()
try:
slitid = saltkey.get('SLITNAME', hdu[i])
except:
slitid = None
function, order, coef, domain = findlinesol(soldict,
ystart,
True,
timeobs,
exptime,
instrume,
grating,
grang,
arang,
filtername,
slitid,
xarr=xarr)
ws = WavelengthSolution.WavelengthSolution(
xarr, xarr, function=function, order=order)
ws.func.func.domain = domain
ws.set_coef(coef)
else:
raise SALTSpecError(
'This guesstype is not currently supported')
# identify the spectral lines
ImageSolution = identify(data,
slines,
sfluxes,
xarr,
ystart,
ws=ws,
function=function,
order=order,
rstep=rstep,
mdiff=mdiff,
thresh=thresh,
niter=niter,
method=automethod,
res=res,
dres=dres,
smooth=smooth,
inter=inter,
filename=img,
subback=0,
textcolor=textcolor,
preprocess=preprocess,
log=log,
verbose=verbose)
if outfile and len(ImageSolution):
writeIS(ImageSolution,
outfile,
dateobs=dateobs,
utctime=utctime,
instrume=instrume,
grating=grating,
grang=grang,
grasteps=grasteps,
arsteps=arsteps,
arang=arang,
rfilter=rssfilter,
slit=slit,
xbin=xbin,
ybin=ybin,
objid=objid,
filename=img,
log=log,
verbose=verbose)
