def get_slits(slits):
'''
this function checks whether the detected slits for the left and right
edges are the same length and also that the number of slits detected for
each image section is the same. Additionally it checks whether there is
an unexpecdedly large deviation in the slit curvature.
'''
num_sections = len(slits)
# set up the calculation for the number of slits calculated
# for each section
section = [slits[i] for i in range(0, num_sections)]
lengths = [[len(section[j][0]), len(section[j][1])]
for j in range(0, len(section))]
# first check and see if all the left and right edges are of equal length
for k in range(0, len(lengths)):
if lengths[k][0] != lengths[k][1]:
msg = 'Number of edges for section %i does not match. Try changing your threshold value' % k
raise SALTSpecError(msg)
for m in range(0, len(lengths)):
if lengths[m][0] == 0 or lengths[m][1] == 0:
msg = 'No edges detected for section %i. Try changing your threshold value' % k
raise SALTSpecError(msg)
equal = []
for i in range(0, len(lengths) - 1):
if lengths[i][0] != lengths[i +
1][0] or lengths[i][1] != lengths[i +
1][1]:
equal.append(False)
else:
equal.append(True)
if (not all(equal)):
msg = 'An unequal amount of slits were detected for one of the sections'
raise SALTSpecError(msg)
# write the slit positions into the defined slit positions format
# such that each slit is given by:
# [slitnumber, [bottom slit positions], [top slit positions]]
allslits = []
for j in range(0, len(slits[0][0][:])):
spline_left = [slits[i][0][j] for i in range(0, len(slits))]
spline_right = [slits[i][1][j] for i in range(0, len(slits))]
allslits.append([j, spline_left, spline_right])
return allslits
def specsky(images,
outimages,
outpref,
method='normal',
section=None,
function='polynomial',
order=2,
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
if method not in ['normal', 'fit']:
msg = '%s mode is not supported yet' % method
raise SALTSpecError(msg)
if section is None:
section = saltio.getSection(section)
msg = 'This mode is not supported yet'
raise SALTSpecError(msg)
else:
section = saltio.getSection(section)
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
log.message('Subtracting sky spectrum in image %s into %s' %
(img, ofile))
# open the images
hdu = saltio.openfits(img)
# sky subtract the array
hdu = skysubtract(hdu,
method=method,
section=section,
funct=function,
order=order)
# write out the image
if clobber and os.path.isfile(ofile):
saltio.delete(ofile)
hdu.writeto(ofile)
def which_ext(hdu, ext_name, debug):
'''
this function determines which extension in the fits file is the primary, sci
and binary table. an integer is retunred with the position of the ext in
the fits file.
* hdu is an opened fits file. opened with pyfits.open
* ext_name is the name of the wanted extension
'''
if debug:
print 'determining the fits extension for %s' % ext_name
if ext_name == 'PRIMARY':
for i in range(0, len(hdu)):
if hdu[i].name == 'PRIMARY':
pos = i
return pos
elif ext_name == 'SCI':
for i in range(0, len(hdu)):
if hdu[i].name == 'SCI':
pos = i
return pos
elif ext_name == 'BINTABLE':
for i in range(0, len(hdu)):
if hdu[i].name == 'BINTABLE':
pos = i
return pos
else:
msg = 'the hdu was not found in the fits header'
raise SALTSpecError(msg)
def findsol(xarr, soldict, y_i, caltype, nearest, timeobs, exptime, instrume, grating, grang, arang, filtername,
slit, xbin, ybin, slitid, function, order):
"""Find the wavelength solution. Either from a database containing all the
solutions adn calculate the best one or calculate based on the model
for RSS
"""
if caltype == 'line':
function, order, coef, domain = findlinesol(
soldict, y_i, nearest, timeobs, exptime, instrume, grating, grang, arang, filtername, slitid, xarr)
if function is None:
msg = 'No solution matches for %s, %s, %s, %s, %s, %s' % (
instrume, grating, grang, arang, filtername, slitid)
raise SALTSpecError(msg)
if coef is None:
return None
order = int(order)
ws = WavelengthSolution.WavelengthSolution(
xarr,
xarr,
function=function,
order=order)
ws.func.func.domain = domain
ws.set_coef(coef)
w_arr = ws.value(xarr)
elif caltype == 'rss':
w_arr = calcsol(
xarr,
y_i,
instrume,
grating,
grang,
arang,
filtername,
slit,
xbin,
ybin,
function,
order)
else:
message = 'SALTRECTIFY--Invalid caltype'
raise SALTSpecError(message)
return w_arr
def specextract(images,
outfile,
method='normal',
section=None,
thresh=3.0,
minsize=3.0,
outformat='ascii',
ext=1,
convert=True,
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.argunpack('outfile', outfile)
if method is 'weighted':
msg = 'This mode is not supported yet'
raise SALTSpecError(msg)
section = saltio.checkfornone(section)
if section is not None:
sections = saltio.getSection(section, iraf_format=False)
section = []
for i in range(0, len(sections), 2):
section.append((sections[i], sections[i + 1]))
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
log.message('\nExtracting spectrum in image %s to %s' %
(img, ofile),
with_header=False,
with_stdout=verbose)
# open the images
hdu = saltio.openfits(img)
ap_list = extract(hdu,
ext=ext,
method=method,
section=section,
minsize=minsize,
thresh=thresh,
convert=convert)
# write the spectra out
if ap_list:
write_extract(ofile.strip(),
ap_list,
outformat=outformat,
clobber=clobber)
log.message('', with_header=False, with_stdout=verbose)
def speccal(specfile, outfile, calfile, extfile, airmass=None, exptime=None,
clobber=True, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# read in the specfile and create a spectrum object
obs_spectra = st.readspectrum(specfile, error=True, ftype='ascii')
# read in the std file and convert from magnitudes to fnu
# then convert it to fwave (ergs/s/cm2/A)
cal_spectra = st.readspectrum(calfile, error=False, ftype='ascii')
# read in the extinction file (leave in magnitudes)
ext_spectra = st.readspectrum(extfile, error=False, ftype='ascii')
# determine the airmass if not specified
if saltio.checkfornone(airmass) is None:
message = 'Airmass was not supplied'
raise SALTSpecError(message)
# determine the exptime if not specified
if saltio.checkfornone(airmass) is None:
message = 'Exposure Time was not supplied'
raise SALTSpecError(message)
# calculate the calibrated spectra
log.message('Calculating the calibration curve for %s' % specfile)
error = False
try:
if obs_spectra.var is not None:
error = True
except:
error = False
flux_spectra = calfunc(
obs_spectra,
cal_spectra,
ext_spectra,
airmass,
exptime,
error)
# write the spectra out
st.writespectrum(flux_spectra, outfile, ftype='ascii', error=error)
def createoutputxaxis(wstart, wend, nw):
"""Create the output array for the axis for the data to be transformed onto.
"""
try:
warr = np.linspace(wstart, wend, num=nw)
except Exception as e:
msg = 'No output array was create because %s' % e
raise SALTSpecError(msg)
return warr
def write_extract(ofile, ap_list, outformat='ascii', fvar=None, clobber=False):
"""Write out to either a txt file or fits file depending on the extension
of ofile
"""
if outformat == 'FITS':
write_extract_fits(ofile, ap_list, clobber)
elif outformat == 'ascii':
write_extract_text(ofile, ap_list, clobber)
else:
msg = '%s is not a supported output format' % outformat
raise SALTSpecError(msg)
return
def createbadpixel(inhdu, bphdu, sci_ext, bp_ext):
"""Create the bad pixel hdu from a bad pixel hdu"""
if bphdu is None:
data = inhdu[sci_ext].data * 0.0
else:
infile = inhdu._HDUList__file.name
bpfile = bphdu._HDUList__file.name
for k in ['INSTRUME', 'CCDSUM', 'NAXIS1', 'NAXIS2']:
if not saltkey.compare(
inhdu[sci_ext], bphdu[sci_ext], k, infile, bpfile):
message = '%s and %s are not the same %s' % (infile, bpfile, k)
raise SALTSpecError(message)
data = bphdu[sci_ext].data.copy()
header = inhdu[sci_ext].header.copy()
header['EXTVER'] = bp_ext
header.update('SCIEXT', sci_ext, comment='Extension of science frame')
return pyfits.ImageHDU(data=data, header=header, name='BPM')
def read_slits_from_ds9(simg, order=1):
'''
This function reads the input from an outputslitfile if it specified as a
ds9 region file. It will read the slit positions return an array that resembles
the split_pos array that is passed to the extract_slits function and the
order of the spline to be fitted.
'''
# read in the slit file
slitfile = open(simg, 'r')
slits = slitfile.read()
slitfile.close()
# throw an error if the positions aren't in image format
if slits.count('image') == 0:
msg = "Please use 'image' for format when saving ds9 region file"
raise SALTSpecError(msg)
slits = slits.split('\n')
# loop through and create all slits
allslits = []
alltext = []
i = 0
for line in slits:
if line.startswith('#') or line.startswith('global'):
pass
elif line.count('box'):
line = line.split('#')
if len(line) == 2:
rtext = line[1].replace(' text={', '')
rtext = rtext.replace('}', '')
alltext.append(rtext.split(','))
line = line[0].replace('box(', '')
line = line.replace(')', '')
col = line.split(',')
slitnum = i
left_edge = [int(float(col[1]) - 0.5 * float(col[3]))]
right_edge = [int(float(col[1]) + 0.5 * float(col[3]))]
allslits.append([slitnum, left_edge, right_edge])
i += 1
return order, allslits, alltext
def specprepare(images, outimages, outpref, badpixelimage='',
clobber=True, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
# verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# open the badpixel image
if saltio.checkfornone(badpixelimage) is None:
badpixelstruct = None
else:
try:
badpixelstruct = saltio.openfits(badpixelimage)
except saltio.SaltIOError as e:
msg = 'badpixel image must be specificied\n %s' % e
raise SALTSpecError(msg)
# open each raw image file
for img, oimg, in zip(infiles, outfiles):
# open the fits file
struct = saltio.openfits(img)
# prepare file
struct = prepare(struct, badpixelstruct)
# write FITS file
saltio.writefits(struct, oimg, clobber=clobber)
saltio.closefits(struct)
message = 'SPECPREPARE -- %s => %s' % (img, oimg)
log.message(message)
def specarcstraighten(images, outfile, function='poly', order=3, rstep=1,
rstart='middlerow', nrows=1,
y1=None, y2=None, sigma=5, sections=3, niter=5,
startext=0, clobber=False, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.argunpack('Output', outfile)
# 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)
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']
# 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']
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)
# 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 = rstart
# set up the xarr array based on the image
xarr = np.arange(len(data[ystart]), dtype='int64')
# calculate the transformation
ImageSolution = arcstraight(data, xarr, ystart, function=function, order=order,
rstep=rstep, y1=y1, y2=y2, sigma=sigma, sections=sections,
niter=niter, 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 extract(hdu,
ext=1,
method='normal',
section=[],
minsize=3.0,
thresh=3.0,
convert=True):
"""For a given image, extract a 1D spectra from the image
and write the spectra to the output file
"""
ap_list = []
i = ext
if hdu[i].name == 'SCI':
# set up the data, variance, and bad pixel frames
# first step is to find the region to extract
data_arr = hdu[i].data
try:
var_arr = hdu[hdu[i].header['VAREXT']].data
except:
var_arr = None
try:
bpm_arr = hdu[hdu[i].header['BPMEXT']].data
except:
bpm_arr = None
var_arr = None
bpm_arr = None
xarr = np.arange(len(data_arr[0]))
# convert using the WCS information
try:
w0 = saltkey.get('CRVAL1', hdu[i])
dw = saltkey.get('CD1_1', hdu[i])
except Exception as e:
msg = 'Error on Ext %i: %s' % (i, e)
raise SALTSpecError(msg)
warr = w0 + dw * xarr
# convert from air to vacuum
if convert:
warr = Spectrum.air2vac(warr)
# set up the sections in case of findobj
if section is None:
section = findobj.findObjects(data_arr,
method='median',
specaxis=1,
minsize=minsize,
thresh=thresh,
niter=5)
# extract all of the regions
for sec in section:
ap = apext.apext(warr, data_arr, ivar=var_arr)
y1, y2 = sec
ap.flatten(y1, y2)
ap_list.append(ap)
return ap_list
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 rectify(hdu, soldict, caltype='line', function='poly', order=3, inttype='interp',
w1=None, w2=None, dw=None, nw=None, blank=0, pixscale=0.0, time_interp=False,
conserve=False, nearest=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 the basic values
set_w1 = (w1 is None)
set_w2 = (w2 is None)
set_dw = (dw is None)
set_nw = (nw is None)
# 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 = 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 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
# set up a wavelength solution
try:
w_arr = 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 = findsol(xarr, soldict, istart, 'rss', nearest, timeobs, exptime, instrume, grating, grang, arang, filtername,
slit, xbin, ybin, slitid, function, order)
# set up the output x-axis
if set_w1:
w1 = w_arr.min()
if set_w2:
w2 = w_arr.max()
if set_nw:
nw = len(xarr)
if set_dw:
dw = float(w2 - w1) / nw
nw_arr = createoutputxaxis(w1, w2, nw)
# setup the VARIANCE and BPM frames
if saltkey.found('VAREXT', hdu[i]):
varext = saltkey.get('VAREXT', hdu[i])
else:
varext = None
# setup the BPM frames
if saltkey.found('BPMEXT', hdu[i]):
bpmext = saltkey.get('BPMEXT', hdu[i])
else:
bpmext = None
# for each line in the data, determine the wavelength solution
# for a given line in the image
for j in range(len(hdu[i].data)):
# find the wavelength solution for the data
w_arr = findsol(xarr, soldict, j, caltype, nearest, timeobs, exptime, instrume, grating, grang, arang, filtername,
slit, xbin, ybin, slitid, function, order)
# apply that wavelength solution to the data
if w_arr is not None:
try:
hdu[i].data[
j,
:] = st.interpolate(
nw_arr,
w_arr,
hdu[i].data[
j,
:],
inttype,
left=blank,
right=blank)
except Exception as e:
hdu[i].data[j, :] = hdu[i].data[j, :] * 0.0 + blank
msg = 'In row %i, solution cannot be found due to %s' % (
i, e)
# correct the variance frame
if varext:
try:
hdu[varext].data[
j,
:] = st.interpolate(
nw_arr,
w_arr,
hdu[varext].data[
j,
:],
inttype,
left=blank,
right=blank)
except Exception as e:
msg = 'In row %i, solution cannot be found due to %s' % (
i, e)
# correct the BPM frame
if bpmext:
try:
hdu[bpmext].data[
j,
:] = st.interpolate(
nw_arr,
w_arr,
hdu[bpmext].data[
j,
:],
inttype,
left=blank,
right=blank)
except Exception as e:
msg = 'In row %i, solution cannot be found due to %s' % (
i, e)
else:
hdu[i].data[j, :] = hdu[i].data[j, :] * 0.0 + blank
if conserve:
hdu[i].data = hdu[i].data / dw
if varext:
hdu[varext].data = hdu[varext].data / dw
# Add WCS information
saltkey.new('CTYPE1', 'LAMBDA', 'Coordinate Type', hdu[i])
saltkey.new('CTYPE2', 'PIXEL', 'Coordinate Type', hdu[i])
saltkey.new(
'CD1_1',
dw,
'WCS: Wavelength Dispersion in angstrom/pixel',
hdu[i])
saltkey.new('CD2_1', 0.0, 'WCS: ', hdu[i])
saltkey.new('CD1_2', 0.0, 'WCS: ', hdu[i])
saltkey.new('CD2_2', ybin * pixscale, 'WCS: ', hdu[i])
saltkey.new('CRPIX1', 0.0, 'WCS: X Reference pixel', hdu[i])
saltkey.new('CRPIX2', 0.0, 'WCS: Y Reference pixel', hdu[i])
saltkey.new('CRVAL1', w1, 'WCS: X Reference pixel', hdu[i])
saltkey.new('CRVAL2', 0.0, 'WCS: Y Reference pixel', hdu[i])
saltkey.new('CDELT1', 1.0, 'WCS: X pixel size', hdu[i])
saltkey.new('CDELT2', 1.0, 'WCS: Y pixel size', hdu[i])
saltkey.new('DC-FLAG', 0, 'Dispesion Corrected image', hdu[i])
return hdu
def specsens(specfile,
outfile,
stdfile,
extfile,
airmass=None,
exptime=None,
stdzp=3.68e-20,
function='polynomial',
order=3,
thresh=3,
niter=5,
fitter='gaussian',
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# read in the specfile and create a spectrum object
obs_spectra = st.readspectrum(specfile.strip(),
error=True,
ftype='ascii')
# smooth the observed spectrum
# read in the std file and convert from magnitudes to fnu
# then convert it to fwave (ergs/s/cm2/A)
std_spectra = st.readspectrum(stdfile.strip(),
error=False,
ftype='ascii')
std_spectra.flux = Spectrum.magtoflux(std_spectra.flux, stdzp)
std_spectra.flux = Spectrum.fnutofwave(std_spectra.wavelength,
std_spectra.flux)
# Get the typical bandpass of the standard star,
std_bandpass = np.diff(std_spectra.wavelength).mean()
# Smooth the observed spectrum to that bandpass
obs_spectra.flux = st.boxcar_smooth(obs_spectra, std_bandpass)
# read in the extinction file (leave in magnitudes)
ext_spectra = st.readspectrum(extfile.strip(),
error=False,
ftype='ascii')
# determine the airmass if not specified
if saltio.checkfornone(airmass) is None:
message = 'Airmass was not supplied'
raise SALTSpecError(message)
# determine the exptime if not specified
if saltio.checkfornone(exptime) is None:
message = 'Exposure Time was not supplied'
raise SALTSpecError(message)
# calculate the calibrated spectra
log.message('Calculating the calibration curve for %s' % specfile)
cal_spectra = sensfunc(obs_spectra, std_spectra, ext_spectra, airmass,
exptime)
# plot(cal_spectra.wavelength, cal_spectra.flux * std_spectra.flux)
# fit the spectra--first take a first cut of the spectra
# using the median absolute deviation to throw away bad points
cmed = np.median(cal_spectra.flux)
cmad = saltstat.mad(cal_spectra.flux)
mask = (abs(cal_spectra.flux - cmed) < thresh * cmad)
mask = np.logical_and(mask, (cal_spectra.flux > 0))
# now fit the data
# Fit using a gaussian process.
if fitter == 'gaussian':
from sklearn.gaussian_process import GaussianProcess
#Instanciate a Gaussian Process model
dy = obs_spectra.var[mask]**0.5
dy /= obs_spectra.flux[mask] / cal_spectra.flux[mask]
y = cal_spectra.flux[mask]
gp = GaussianProcess(corr='squared_exponential',
theta0=1e-2,
thetaL=1e-4,
thetaU=0.1,
nugget=(dy / y)**2.0)
X = np.atleast_2d(cal_spectra.wavelength[mask]).T
# Fit to data using Maximum Likelihood Estimation of the parameters
gp.fit(X, y)
x = np.atleast_2d(cal_spectra.wavelength).T
# Make the prediction on the meshed x-axis (ask for MSE as well)
y_pred = gp.predict(x)
cal_spectra.flux = y_pred
else:
fit = interfit(cal_spectra.wavelength[mask],
cal_spectra.flux[mask],
function=function,
order=order,
thresh=thresh,
niter=niter)
fit.interfit()
cal_spectra.flux = fit(cal_spectra.wavelength)
# write the spectra out
st.writespectrum(cal_spectra, outfile, ftype='ascii')
def specslitnormalize(images,
outimages,
outpref,
response=None,
response_output=None,
order=2,
conv=1e-2,
niter=20,
startext=0,
clobber=False,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
# read in the response function
response = saltio.checkfornone(response)
if response:
log.message('Loading response from %s' % response)
response = readresponse(response)
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
# open the image
hdu = saltio.openfits(img)
for i in range(startext, len(hdu)):
if hdu[i].name == 'SCI':
log.message('Normalizing extension %i in %s' % (i, img))
# things that will change for each slit
# 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)
if response is None:
response = create_response(data,
spatial_axis=1,
order=order,
conv=conv,
niter=niter)
if response_output:
write_response(response, clobber=clobber)
else:
# add a check that the response is the same shape as
# the data
if len(response) != data.shape[0]:
raise SALTSpecError(
'Length of response function does not equal size of image array'
)
# correct the data
data = data / response
# correct the variance frame
if saltkey.found('VAREXT', hdu[i]):
vhdu = saltkey.get('VAREXT', hdu[i])
hdu[vhdu].data = hdu[vhdu].data / response
saltio.writefits(hdu, ofile, clobber=clobber)
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)
def prepare(struct, badpixelstruct):
"""Prepare a structure for spectroscopic processing
"""
# identify instrument
infile = struct._HDUList__file.name
nextend = len(struct)
if badpixelstruct is not None:
bpfile = badpixelstruct._HDUList__file.name
# Check that the image is the same number of extensions as the
# badpixelmap
if len(struct) != len(badpixelstruct):
message = '%s and %s are not the same length' % (infile, bpfile)
raise SALTSpecError(message)
# Add variance frames and bad pixel maps
# If no variance frame exists, add the file at the end of the
# extensions. If a variance file does exist, do nothing
# Add a keyword to the Science extension indication what
# extension the variance from is on
j = 0
for i in range(nextend):
if struct[i].size() > 0 and struct[i].name == 'SCI':
# Check to see if the variance frame exists
try:
key = struct[i].header['VAREXT']
except:
try:
hdu = createvariance(struct[i], i, nextend + j)
struct[i].header.update(
'VAREXT',
nextend + j,
comment='Extension for Variance Frame')
struct.append(hdu)
j = j + 1
except Exception as e:
message = 'Could not create variance extension in ext %i of %s because %s' \
% (i, infile, e)
raise SALTSpecError(message)
# Check to see if the BPM frame exists
try:
key = struct[1].header['BPMEXT']
except:
try:
hdu = createbadpixel(
struct,
badpixelstruct,
i,
nextend +
j)
except Exception as e:
message = 'Could not create bad pixel extension in ext %i of %s because %s' \
% (i, infile, e)
raise SALTSpecError(message)
if (1):
struct[i].header.update(
'BPMEXT',
nextend + j,
comment='Extension for Bad Pixel Mask')
struct.append(hdu)
j = j + 1
return struct
def specslit(image,
outimage,
outpref,
exttype='auto',
slitfile='',
outputslitfile='',
regprefix='',
sections=3,
width=25,
sigma=2.2,
thres=6,
order=3,
padding=5,
yoffset=0,
inter=False,
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# check all the input and make sure that all the input needed is provided
# by the user
# read the image or image list and check if each in the list exist
infiles = saltio.argunpack('Input', image)
# unpack the outfiles
outfiles = saltio.listparse('Outimages', outimage, outpref, infiles,
'')
# from the extraction type, check whether the input file is specified.
# if the slitfile parameter is specified then use the slit files for
# the extraction. if the extraction type is auto then use image for the
# detection and the slit extraction
if exttype == 'rsmt' or exttype == 'fits' or exttype == 'ascii' or exttype == 'ds9':
slitfiles = saltio.argunpack('Slitfile', slitfile)
if len(slitfiles) == 1:
slitfiles = slitfiles * len(infiles)
saltio.comparelists(infiles, slitfiles, 'image', 'slitfile')
elif exttype == 'auto':
slitfiles = infiles
log.message(
'Extraction type is AUTO. Slit detection will be done from image'
)
# read in if an optional ascii file is requested
if len(outputslitfile) > 0:
outslitfiles = saltio.argunpack('Outslitfiles', outputslitfile)
saltio.comparelists(infiles, outslitfiles, 'image',
'outputslitfile')
else:
outslitfiles = [''] * len(infiles)
# check if the width and sigma parameters were specified.
# default is 25 and 2.2
if width < 10.:
msg = 'The width parameter needs be a value larger than 10'
raise SALTSpecError(msg)
if sigma < 0.0:
msg = 'Sigma must be greater than zero'
raise SaltSpecError(msg)
# check the treshold parameter. this needs to be specified by the user
if thres <= 0.0:
msg = 'Threshold must be greater than zero'
raise SaltSpecError(msg)
# check to make sure that the sections are greater than the order
if sections <= order:
msg = 'Number of sections must be greater than the order for the spline fit'
raise SaltSpecError(msg)
# run through each of the images and extract the slits
for img, oimg, sfile, oslit in zip(infiles, outfiles, slitfiles,
outslitfiles):
log.message('Proccessing image %s' % img)
# open the image
struct = saltio.openfits(img)
ylen, xlen = struct[1].data.shape
xbin, ybin = saltkey.ccdbin(struct[0], img)
# setup the VARIANCE and BPM frames
if saltkey.found('VAREXT', struct[1]):
varext = saltkey.get('VAREXT', struct[1])
varlist = []
else:
varext = None
# setup the BPM frames
if saltkey.found('BPMEXT', struct[1]):
bpmext = saltkey.get('BPMEXT', struct[1])
bpmlist = []
else:
bpmext = None
# open the slit definition file or identify the slits in the image
slitmask = None
ycheck = False
if exttype == 'rsmt':
log.message('Using slits from %s' % sfile)
if yoffset is None:
yoffset = 0
ycheck = True
slitmask = mt.read_slitmask_from_xml(sfile)
xpos = -0.3066
ypos = 0.0117
cx = int(xlen / 2.0)
cy = int(ylen / 2.0) + ypos / 0.015 / ybin + yoffset
order, slit_positions = mt.convert_slits_from_mask(
slitmask,
order=1,
xbin=xbin,
ybin=ybin,
pix_scale=0.1267,
cx=cx,
cy=cy)
sections = 1
elif exttype == 'fits':
log.message('Using slits from %s' % sfile)
order, slit_positions = read_slits_from_fits(sfile)
elif exttype == 'ascii':
log.message('Using slits from %s' % sfile)
order, slit_positions = mt.read_slits_from_ascii(sfile)
elif exttype == 'ds9':
log.message('Using slits from %s' % sfile)
order, slit_positions, slitmask = mt.read_slits_from_ds9(
sfile, order=order)
slitmask = None
sections = 1
elif exttype == 'auto':
log.message('Identifying slits in %s' % img)
# identify the slits in the image
order, slit_positions = identify_slits(struct[1].data, order,
sections, width, sigma,
thres)
# write out the slit identifications if ofile has been supplied
if oslit:
log.message('Writing slit positions to %s' % oslit)
mt.write_outputslitfile(slit_positions, oslit, order)
if ycheck:
slit_positions, dy = check_ypos(slit_positions, struct[1].data)
log.message('Using an offset of {}'.format(dy))
# extract the slits
spline_x = mt.divide_image(struct[1].data, sections)
spline_x = 0.5 * (np.array(spline_x[:-1]) + np.array(spline_x[1:]))
extracted_spectra, spline_positions = mt.extract_slits(
slit_positions,
spline_x,
struct[1].data,
order=order,
padding=padding)
if varext:
extracted_var, var_positions = mt.extract_slits(
slit_positions,
spline_x,
struct[varext].data,
order=order,
padding=padding)
if bpmext:
extracted_bpm, bpm_positions = mt.extract_slits(
slit_positions,
spline_x,
struct[bpmext].data,
order=order,
padding=padding)
# write out the data to the new array
# create the new file
hdulist = fits.HDUList([struct[0]])
# log the extracted spectra if needed
log.message('', with_stdout=verbose)
# setup output ds9 file
if regprefix:
regout = open(
regprefix + os.path.basename(img).strip('.fits') + '.reg',
'w')
regout.write('# Region file format: DS9 version 4.1\n')
regout.write('# Filename: %s\n' % img)
regout.write(
'global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1\nphysical\n'
)
# add each
imglist = []
nslits = len(spline_positions)
for i in range(nslits):
y1 = spline_positions[i][0].min()
y2 = spline_positions[i][1].max()
msg = 'Extracted Spectra %i between %i to %i' % (i + 1, y1, y2)
# log.message(msg, with_header=False, with_stdout=verbose)
sdu = fits.ImageHDU(extracted_spectra[i],
header=struct[1].header)
if varext:
vdu = fits.ImageHDU(extracted_var[i],
header=struct[varext].header)
sdu.header['VAREXT'] = i + nslits + 1
varlist.append(vdu)
if bpmext:
bdu = fits.ImageHDU(extracted_bpm[i],
header=struct[bpmext].header)
sdu.header['BPMEXT'] = i + 2 * nslits + 1
bpmlist.append(bdu)
imglist.append(sdu)
# add in some additional keywords
imglist[i].header['MINY'] = (y1,
'Lower Y value in original image')
imglist[i].header['MAXY'] = (y2,
'Upper Y value in original image')
if regprefix:
xsize = struct[1].data.shape[1]
xsize = int(0.5 * xsize)
rtext = ''
if slitmask:
# rtext='%s, %8.7f, %8.7f, %3.2f' % (slitmask.slitlets.data[i]['name'], slitmask.slitlets.data[i]['targ_ra'], slitmask.slitlets.data[i]['targ_dec'], slitmask.slitlets.data[i]['slit_width'])
pass
regout.write('box(%i,%i, %i, %i) #text={%s}\n' %
(xsize, 0.5 *
(y1 + y2), 2 * xsize, y2 - y1, rtext))
# add slit information
if slitmask:
imglist[i].header['SLITNAME'] = (
slitmask.slitlets.data[i]['name'], 'Slit Name')
imglist[i].header['SLIT_RA'] = (
slitmask.slitlets.data[i]['targ_ra'], 'Slit RA')
imglist[i].header['SLIT_DEC'] = (
slitmask.slitlets.data[i]['targ_dec'], 'Slit DEC')
imglist[i].header['SLIT'] = (
slitmask.slitlets.data[i]['slit_width'], 'Slit Width')
# add to the hdulist
hdulist += imglist
if varext:
hdulist += varlist
if bpmext:
hdulist += bpmlist
# write the slit positions to the header
# create the binary table HDU that contains the split positions
tbhdu = mt.slits_HDUtable(slit_positions, order)
bintable_hdr = tbhdu.header
# add the extname parameter to the extension
tbhdu.header['EXTNAME'] = 'BINTABLE'
# add the extname parameter to the extension
hdulist[0].header['SLITEXT'] = len(hdulist)
hdulist.append(tbhdu)
# add addition header information about the mask
if slitmask:
hdulist[0].header['MASKNAME'] = (slitmask.mask_name,
'SlitMask Name')
hdulist[0].header['MASK_RA'] = (slitmask.center_ra,
'SlitMask RA')
hdulist[0].header['MASK_DEC'] = (slitmask.center_dec,
'SlitMask DEC')
hdulist[0].header['MASK_PA'] = (slitmask.position_angle,
'SlitMask Position Angle')
# write out the image
saltio.writefits(hdulist, oimg, clobber)