def test_rssmodel():
# load the image and determine its spectrograph parameters
hdu = fits.open(inimage)
# create the header information
grating = hdu[1].header['GRATING'].strip()
grang = hdu[1].header['GR-ANGLE']
arang = hdu[1].header['AR-ANGLE']
slit = float(hdu[1].header['MASKID'])
xbin, ybin = hdu[1].header['CCDSUM'].strip().split()
# create the RSS Model
rss = RSSModel.RSSModel(grating_name=grating, gratang=grang,
camang=arang, slit=slit, xbin=int(xbin),
ybin=int(ybin))
alpha = rss.alpha()
beta = rss.beta()
sigma = 1e7 * rss.calc_resolelement(alpha, beta)
print("SIGMA: ", sigma)
# test to see if giving the wrong name it will raise an error
try:
rss = RSSModel.RSSModel(grating_name="not a grating", gratang=grang,
camang=arang, slit=slit, xbin=int(xbin),
ybin=int(ybin))
except RSSModel.RSSError as e:
pass
def test_Identify():
hdu = fits.open(inimage)
# create the data arra
data = hdu[1].data
# create the header information
instrume = hdu[1].header['INSTRUME'].strip()
grating = hdu[1].header['GRATING'].strip()
grang = hdu[1].header['GR-ANGLE']
arang = hdu[1].header['AR-ANGLE']
filter = hdu[1].header['FILTER'].strip()
slit = float(hdu[1].header['MASKID'])
xbin, ybin = hdu[1].header['CCDSUM'].strip().split()
print(instrume, grating, grang, arang, filter)
print(xbin, ybin)
print(len(data), len(data[0]))
# create the RSS Model
rssmodel = RSSModel.RSSModel(grating_name=grating,
gratang=grang,
camang=arang,
slit=slit,
xbin=int(xbin),
ybin=int(ybin))
def calcsol(xarr, y_i, instrume, grating, grang, arang,
filtername, slit, xbin, ybin, function, order):
rss = RSSModel.RSSModel(grating_name=grating.strip(), gratang=grang,
camang=arang, slit=slit, xbin=xbin, ybin=ybin)
gamma = 180.0 / math.pi * math.atan((y_i * rss.detector.pix_size * rss.detector.ybin
- 0.5 * rss.detector.find_height()) / rss.camera.focallength)
# y_i/rssmodel.detector.height*rssmodel
d = rss.detector.xbin * rss.detector.pix_size * \
(xarr - rss.detector.get_xpixcenter())
alpha = rss.alpha()
beta = -rss.beta()
dbeta = -np.degrees(np.arctan(d / rss.camera.focallength))
w_arr = 1e7 * rss.calc_wavelength(alpha, beta + dbeta, gamma=gamma)
return w_arr
def test_Linefit():
hdu = pyfits.open(inimage)
# create the data arra
data = hdu[1].data
# create the header information
instrume = hdu[1].header['INSTRUME'].strip()
grating = hdu[1].header['GRATING'].strip()
grang = hdu[1].header['GR-ANGLE']
arang = hdu[1].header['AR-ANGLE']
filter = hdu[1].header['FILTER'].strip()
slit = float(hdu[1].header['MASKID'])
xbin, ybin = hdu[1].header['CCDSUM'].strip().split()
# print instrume, grating, grang, arang, filter
# print xbin, ybin
# print len(data), len(data[0])
# create the RSS Model
rssmodel = RSSModel.RSSModel(grating_name=grating,
gratang=grang,
camang=arang,
slit=slit,
xbin=int(xbin),
ybin=int(ybin))
alpha = rssmodel.rss.gratang
beta = rssmodel.rss.gratang - rssmodel.rss.camang
sigma = 1e7 * rssmodel.rss.calc_resolelement(alpha, beta)
# create artificial spectrum
# create the spectrum
stype = 'line'
w, s = np.loadtxt(inspectra, usecols=(0, 1), unpack=True)
spec = Spectrum(w,
s,
wrange=[4000, 5000],
dw=0.1,
stype='line',
sigma=sigma)
spec.flux = spec.set_dispersion(sigma=sigma)
sw_arr, sf_arr = spec.wavelength, spec.flux
def test_ModelSolution():
hdu = fits.open(inimage)
# create the data arra
data = hdu[1].data
# create the header information
instrume = hdu[1].header['INSTRUME'].strip()
grating = hdu[1].header['GRATING'].strip()
grang = hdu[1].header['GR-ANGLE']
arang = hdu[1].header['AR-ANGLE']
filter = hdu[1].header['FILTER'].strip()
slit = float(hdu[1].header['MASKID'])
xbin, ybin = hdu[1].header['CCDSUM'].strip().split()
print(instrume, grating, grang, arang, filter)
print(xbin, ybin)
print(len(data), len(data[0]))
# create the RSS Model
rssmodel = RSSModel.RSSModel(grating_name=grating,
gratang=grang,
camang=arang,
slit=slit,
xbin=int(xbin),
ybin=int(ybin))
err = xp * 0.0 + 0.1
ls = MS.ModelSolution(xp, wp, rssmodel.rss, xlen=len(data[0]), order=4)
ls.fit(cfit='all')
ls.fit(ls.ndcoef)
for c in ls.coef:
print(c(), end=' ')
print()
print(ls.sigma(ls.x, ls.y))
print(ls.chisq(ls.x, ls.y, err))
print(ls.value(2000))
pl.figure()
pl.plot(xp, wp - ls.value(xp), ls='', marker='o')
# pl.plot(ls.x, ls.y-ls(ls.x), ls='', marker='o')
pl.show()
return
def calc_resolution(hdu):
"""Calculate the resolution for a setup"""
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], '')
slit=st.getslitsize(slitname)
#create RSS Model
rss=RSSModel.RSSModel(grating_name=grating.strip(), gratang=grang, \
camang=arang,slit=slit, xbin=xbin, ybin=ybin, \
)
res=1e7*rss.calc_resolelement(rss.alpha(), -rss.beta())
return res
def test_CreateImage():
# read in the data
hdu = fits.open(inimg)
im_arr = hdu[1].data
hdu.close()
# set up the spectrum
stype = 'line'
w, s = np.loadtxt('Xe.dat', usecols=(0, 1), unpack=True)
spec = Spectrum(w, s, wrange=[4000, 5000], dw=0.1, stype=stype)
# set up the spectrograph
dx = 2 * 0.015 * 8.169
dy = 2 * 0.015 * 0.101
# set up the spectrograph
# rssmodel=RSSModel.RSSModel(grating_name='PG0900', gratang=13.625, camang=27.25, slit=1.0, xbin=2, ybin=2, xpos=dx, ypos=dy)
rssmodel = RSSModel.RSSModel(
grating_name='PG3000',
gratang=43.625,
camang=87.25,
slit=2.0,
xbin=2,
ybin=2,
xpos=dx,
ypos=dy)
rssmodel.set_camera(name='RSS', focallength=330.0)
rss = rssmodel.rss
# set up the outfile
if os.path.isfile(outfile):
os.remove(outfile)
arr = im_arr.copy()
arr = CreateImage(spec, rss)
arr = arr * im_arr.max() / spec.flux.max()
writeout(arr, outfile)
def rssinfo(grating, grang, arang, slitname, xbin, ybin):
"""RSSINFO--Given informtion about the set up of the spectrograph,
return information about the spectrograph
grating--name of the grating used
gratang--angle of the grating in degrees
arang--articulation ange in degrees
slitname--name of the slit being used
xbin--binning in x-direction
ybin--binning in y-direction
returns central wavelength, blue wavelength, red wavelenth, resolution
resolution element
"""
#get the slitsize
slit = getslitsize(slitname)
#set up the rss model
rss=RSSModel.RSSModel(grating_name=grating, gratang=grang, \
camang=arang,slit=slit, xbin=xbin, ybin=ybin)
#calcuation the resolution element
res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
#calculate the central wavelength
wcen = 1e7 * rss.calc_centralwavelength()
#calculate the wavelength edges
w2 = 1e7 * rss.calc_bluewavelength()
w1 = 1e7 * rss.calc_redwavelength()
print w1, w2
#calculate the
R = rss.calc_resolution(wcen / 1e7, rss.alpha(), rss.beta())
return wcen, w1, w2, res, R, slit
def plotarcspectra(arclist='Ne.txt',
grating='PG0900',
gratang=15.0,
camang=30.0,
slit=1.5,
xbin=2,
ybin=2):
"""Plot an Arc Line list for a given RSS set up
arclist--an arc line list in the format of 'wavelength flux' for arc lines
grating--name of the grating
gratang--angle of the grating
camang--angle of the camera (articulation angle)
slit--slit width in arcseconds
xbin--xbinning
ybin--ybinning
"""
rss = RSSModel.RSSModel(grating_name=grating,
gratang=gratang,
camang=camang,
slit=slit,
xbin=xbin,
ybin=ybin)
#print out some basic statistics
print 1e7 * rss.calc_bluewavelength(), 1e7 * rss.calc_centralwavelength(
), 1e7 * rss.calc_redwavelength()
R = rss.calc_resolution(rss.calc_centralwavelength(), rss.alpha(),
-rss.beta())
res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
print R, res
#set up the detector
ycen = rss.detector.get_ypixcenter()
d_arr = rss.detector.make_detector()[ycen, :] #creates 1-D detector map
xarr = np.arange(len(d_arr))
w = 1e7 * rss.get_wavelength(xarr)
#set up the artificial spectrum
sw, sf = pl.loadtxt(arclist, usecols=(0, 1), unpack=True)
wrange = [1e7 * rss.calc_bluewavelength(), 1e7 * rss.calc_redwavelength()]
spec = Spectrum.Spectrum(sw,
sf,
wrange=wrange,
dw=res / 10,
stype='line',
sigma=res)
#interpolate it over the same range as the detector
spec.interp(w)
#plot it
pl.figure()
pl.plot(spec.wavelength, d_arr * ((spec.flux) / spec.flux.max()))
print pl.gca().get_ylim()
for i, f in zip(sw, sf):
if i > spec.wavelength.min() and i < spec.wavelength.max():
print i, f, sf.max(), spec.flux.max()
#pl.text(i, f/sf.max(), i, fontsize='large', rotation=90)
y = max(0.1, f / sf.max())
pl.text(i, y, i, rotation=90)
pl.show()
def test_Linefit():
hdu = fits.open(inimage)
# create the data arra
data = hdu[1].data
# create the header information
grating = hdu[1].header['GRATING'].strip()
grang = hdu[1].header['GR-ANGLE']
arang = hdu[1].header['AR-ANGLE']
slit = float(hdu[1].header['MASKID'])
xbin, ybin = hdu[1].header['CCDSUM'].strip().split()
# print instrume, grating, grang, arang, filter
# print xbin, ybin
# print len(data), len(data[0])
# create the RSS Model
rssmodel = RSSModel.RSSModel(grating_name=grating,
gratang=grang,
camang=arang,
slit=slit,
xbin=int(xbin),
ybin=int(ybin))
alpha = rssmodel.rss.gratang
beta = rssmodel.rss.gratang - rssmodel.rss.camang
sigma = 1e7 * rssmodel.rss.calc_resolelement(alpha, beta)
# create the observed spectrum
midpoint = int(0.5 * len(data))
xarr = np.arange(len(data[0]), dtype='float')
farr = data[midpoint, :]
obs_spec = Spectrum(xarr, farr, stype='continuum')
# create artificial spectrum
stype = 'line'
w, s = np.loadtxt(inspectra, usecols=(0, 1), unpack=True)
cal_spec = Spectrum(w,
s,
wrange=[4000, 5000],
dw=0.1,
stype=stype,
sigma=sigma)
cal_spec.flux = cal_spec.set_dispersion(sigma=sigma)
cal_spec.flux = cal_spec.flux * obs_spec.flux.max() / cal_spec.flux.max(
) + 1
lf = LF.LineFit(obs_spec, cal_spec, function='legendre', order=3)
lf.set_coef(
[4.23180070e+03, 2.45517852e-01, -4.46931562e-06, -2.22067766e-10])
print(lf(2000))
print(lf.obs_spec.get_flux(2000), lf.flux(2000))
print('chisq ', (lf.errfit(lf.coef, xarr, farr)**2).sum() / 1e7)
lf.set_coef(
[4.23280070e+03, 2.45517852e-01, -4.46931562e-06, -2.22067766e-10])
print(lf(2000))
print(lf.obs_spec.get_flux(2000), lf.flux(2000))
print('chisq ', (lf.errfit(lf.coef, xarr, farr)**2).sum() / 1e7)
# print lf.lfit(xarr)
# print lf.coef
# print lf(2000)
# print lf.results
pl.figure()
pl.plot(lf(lf.obs_spec.wavelength), lf.obs_spec.get_flux(xarr))
pl.plot(lf.cal_spec.wavelength, lf.cal_spec.flux)
pl.show()
print 'CHECK RESULTS'
print
return ivec[pk], xcorval[pk]
filename = 'mbxgpP201206140058.fits'
#??data,hdr=pyfits.getdata(filename,extname='sci',header='t')
data = pyfits.getdata(filename)
hdr = pyfits.getheader(filename)
grname = hdr['grating']
camang = hdr['camang']
gratang = hdr['gr-angle']
#create the spectrograph model
rss = RSSModel.RSSModel(grating_name=grname,
gratang=gratang,
camang=camang,
slit=1.50,
xbin=2,
ybin=2)
#print out some basic statistics
print 1e7 * rss.calc_bluewavelength(), 1e7 * rss.calc_centralwavelength(
), 1e7 * rss.calc_redwavelength()
R = rss.calc_resolution(rss.calc_centralwavelength(), rss.alpha(), -rss.beta())
res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
print R, res
#set up the detector
ycen = rss.detector.get_ypixcenter()
d_arr = rss.detector.make_detector()[ycen, :]
xarr = np.arange(len(d_arr))
w = 1e7 * rss.get_wavelength(xarr)
def find_wavelength_solution(filename, line, debug=False):
logger = logging.getLogger("FindWLS")
if (type(filename) == str and os.path.isfile(filename)):
hdulist = fits.open(filename)
elif (type(filename) == fits.hdu.hdulist.HDUList):
hdulist = filename
else:
logger.error("Invalid input, needs to be either HDUList or string, but found %s" % (str(type(filename))))
return None
if (line is None):
line = hdulist['SCI'].data.shape[0] / 2
logger.debug("Picking the central row, # = %d" % (line))
else:
logger.info("Using line %d for wavelength calibration" % (line))
avg_width = 10
spec = extract_arc_spectrum(hdulist, line, avg_width)
if (debug):
numpy.savetxt("findwls.spec", spec)
binx, biny = pysalt.get_binning(hdulist)
logger.debug("Binning: %d x %d" % (binx, biny))
hdr = hdulist[0].header
rss = RSSModel.RSSModel(
grating_name=hdr['GRATING'],
gratang=hdr['GR-ANGLE'], #45,
camang=hdr['CAMANG'], #45,
slit=1.0,
xbin=binx, ybin=biny,
xpos=-0.30659999999999998, ypos=0.0117, wavelength=None)
central_wl = rss.calc_centralwavelength() * mm_to_A
#print central_wl
blue_edge = rss.calc_bluewavelength() * mm_to_A
red_edge = rss.calc_redwavelength() * mm_to_A
wl_range = red_edge - blue_edge
#print "blue:", blue_edge
#print "red:", red_edge
dispersion = (rss.calc_redwavelength()-rss.calc_bluewavelength())*mm_to_A/spec.shape[0]
#print "dispersion: A/px", dispersion
#print "ang.dispersion:", rss.calc_angdisp(rss.beta())
#print "ang.dispersion:", rss.calc_angdisp(-rss.beta())
pixelsize = 15e-6
#print "lin.dispersion:", rss.calc_lindisp(rss.beta())
#print "lin.dispersion:", rss.calc_lindisp(rss.beta()) / (mm_to_A*pixelsize)
#print "resolution @ central w.l.:", rss.calc_resolution(
# w=rss.calc_centralwavelength(),
# alpha=rss.alpha(),
# beta=-rss.beta())
# print "resolution element:", rss.calc_resolelement(rss.alpha(), -rss.beta()) * mm_to_A
logger.info("From RSS model: wl-range: %.1f - %.1f [%.1f], dispersion: %.3f" % (
blue_edge, red_edge, central_wl, dispersion))
#
# Now find a list of strong lines
#
lineinfo = find_list_of_lines(spec, avg_width)
if (debug):
numpy.savetxt("findwls.foundlines", lineinfo)
############################################################################
#
# Now we have a full line-list with signal-to-noise ratios as brightness
# indicators that we can use to select bright and/or faint lines.
#
############################################################################
# based on the wavelength model from RSS translate x-positions into wavelengths
#print dispersion
#print lineinfo[:,0]
# Use Ken's RSS model data here
logger.info("Creating dispersion model")
cols = hdulist['SCI'].data.shape[1]
kens_model = KenRSSModel(hdulist[0].header, cols)
# primhdr = hdulist[0].header
# rbin,cbin = numpy.array(primhdr["CCDSUM"].split(" ")).astype(int)
# grating = primhdr['GRATING'].strip()
# grang = float(primhdr['GR-ANGLE'])
# artic = float(primhdr['CAMANG'])
# logger.info("RSS model: bin: %d,%d - grating: %s - angle: %.2f - artic: %.2f - columns: %d" % (
# rbin,cbin,grating,grang,artic,cols))
# all_wavelength = rssmodelwave(grating,grang,artic,cbin,cols)
# # fit a simple linear interpolation to the curve so we can look up
# # wavelengths for a given pixel more easily
# wl_interpol = scipy.interpolate.interp1d(
# x=numpy.arange(all_wavelength.shape[0]),
# y=all_wavelength
# )
# Now use the wavelength model to translate line position in pixel coordinates
# into wavelength positions
wl = kens_model.compute_wl(lineinfo[:,0])
if (debug):
numpy.savetxt("rss_lines",
numpy.append(wl.reshape((-1,1)),
lineinfo, axis=1))
_x = numpy.arange(hdulist['SCI'].data.shape[1])
_wl = kens_model.compute_wl(_x)
numpy.savetxt("findwls.wl_vs_x", numpy.array([_x,_wl]).T)
# wl = lineinfo[:,0] * dispersion + blue_edge
#lineinfo = numpy.append(lineinfo, wl.reshape((-1,1)), axis=1)
#numpy.savetxt("linecal", lineinfo)
#
# Load linelist
#
lamp=hdulist[0].header['LAMPID'].strip().replace(' ', '')
lampfile=pysalt.get_data_filename("pysalt$data/linelists/%s.txt" % lamp)
#lampfile=pysalt.get_data_filename("pysalt$data/linelists/%s.salt" % lamp)
_, fn_only = os.path.split(lampfile)
logger.info("Reading calibration line wavelengths from data->%s" % (fn_only))
logger.debug("Full path to lamp line list: %s" % (lampfile))
#lampfile=pysalt.get_data_filename("pysalt$data/linelists/%s.wav" % lamp)
#lampfile=pysalt.get_data_filename("pysalt$data/linelists/Ar.salt")
#lampfile="Ar.lines"
if (os.path.isfile(lampfile)):
try:
lines = numpy.loadtxt(lampfile)
except:
lines = manual_loadtxt(lampfile)
else:
return None
#print lines.shape
#print lines
#
# Now select only lines that are in the estimated range of our ARC spectrum
#
in_range = (lines[:,0] > numpy.min(wl)) & (lines[:,0] < numpy.max(wl))
ref_lines = lines #[in_range]
logger.debug("Found these lines for fitting (range: %.2f -- %.2f):\n%s" % (
numpy.min(wl), numpy.max(wl),
"\n".join(["%10.4f" % l for l in ref_lines[:,0]])))
if (debug):
numpy.savetxt("findwls.reflines", ref_lines)
#print ref_lines
############################################################################
#
# Next step for wavelength calibration:
#
# Match lines between ARC spectrum and reference line list,
# allowing for a small uncertainty in dispersion
#
############################################################################
camangle = kens_model.artic
gratingangle = kens_model.grang
max_d_camangle = 1.
max_d_gratingangle = 1.
step_camangle = 0.05
step_gratingangle = 0.1
n_steps_camangle = int(math.ceil(2*max_d_camangle / step_camangle + 1))
n_steps_gratingangle = int(math.ceil(2*max_d_gratingangle / step_gratingangle + 1))
results = numpy.zeros((n_steps_camangle, n_steps_gratingangle))
try_camangles = numpy.linspace(camangle-max_d_camangle,
camangle+max_d_camangle,
n_steps_camangle)
try_gratingangles = numpy.linspace(gratingangle-max_d_gratingangle,
gratingangle+max_d_gratingangle,
n_steps_gratingangle)
ref_kdtree = scipy.spatial.cKDTree(ref_lines[:,0].reshape((-1,1)))
matching_radius=5.0
for idx_camangle, idx_gratingangle in \
itertools.product(range(n_steps_camangle), range(n_steps_gratingangle)):
camangle = try_camangles[idx_camangle]
gratingangle = try_gratingangles[idx_gratingangle]
#print camangle, gratingangle
#match_line_catalogs(arc, ref, matching_radius, verbose=False,
# col_ref=0, col_arc=-1, dumpfile=None):
# compute the wavelength position for all lines using the
# spectrograph parameters of this iteration
wl_lines = kens_model.compute(grang=gratingangle,
artic=camangle,
colpos=lineinfo[:,0])
#print wl_lines, ref_lines.shape
nearest_neighbor, i = ref_kdtree.query(
x=wl_lines.reshape((-1,1)),
k=1, # only find 1 nearest neighbor
p=1, # use linear distance
distance_upper_bound=matching_radius)
# i is the index with the closest match
# good matches have i within legal range
good_match = i < ref_lines.shape[0]
results[idx_camangle, idx_gratingangle] = numpy.sum(good_match)
numpy.savetxt("results", results)
# fig=matplotlib.pyplot.figure()
# ax=fig.add_subplot(111)
# ax.imshow(results, interpolation='none')
# fig.show()
# matplotlib.pyplot.show()
most_matches = numpy.unravel_index(numpy.argmax(results), results.shape)
logger.info("best results: %d matches for camangle=%.3f (%.3f), gratingangle=%.3f (%.3f)" % (
results[most_matches],
try_camangles[most_matches[0]], hdulist[0].header['CAMANG'],
try_gratingangles[most_matches[1]], hdulist[0].header['GR-ANGLE'],
))
best_camangle = try_camangles[most_matches[0]]
best_gratingangle = try_gratingangles[most_matches[1]]
#
# Now write the complete spectrum with the wavelength calibration
#
#print spec.shape
kens_model.compute(artic=best_camangle, grang=best_gratingangle, ncols=spec.shape[0])
spec_wl = kens_model.get_wavelength_list()
numpy.savetxt("spec_precalib", numpy.append(spec_wl.reshape((-1,1)),
spec.reshape((-1,1)), axis=1))
#
# Now cross-identify all lines, and do a least-sq fit to further optimize
# the spectrograph angles and compute the final wavelength calibration fit
#
lineinfo[:,5] = kens_model.compute(
artic=best_camangle,
grang=best_gratingangle,
colpos = lineinfo[:,0],
)
numpy.savetxt("linelist.calib", lineinfo)
# one last time, match the two line lists, using the same matching radius
# as above
nearest_neighbor, i = ref_kdtree.query(
x=lineinfo[:,5].reshape((-1,1)),
k=1, # only find 1 nearest neighbor
p=1, # use linear distance
distance_upper_bound=matching_radius)
good_matches = i < ref_lines.shape[0]
# print "\n-------------"*5
# print nearest_neighbor.shape
# print nearest_neighbor
# print i.shape
# print i
# print good_matches
# print lineinfo.shape
# print ref_lines.shape
# print numpy.sum(good_matches)
n_matches = numpy.sum(good_matches)
# matched_ref = ref_lines[:,0][good_matches]
# matched_line_idx = i[good_matches]
# print "============"
matched_catalog = numpy.zeros((n_matches, lineinfo.shape[1]+ref_lines.shape[1]))
# print matched_catalog.shape
matched_catalog[:,:lineinfo.shape[1]] = lineinfo[good_matches]
matched_catalog[:,lineinfo.shape[1]:] = ref_lines[i[good_matches]]
numpy.savetxt("matched_lines.dat", matched_catalog)
# print "xxxxxxxxxxxxx"
def fit__wavelength(p_fit, line_x, rssmodel):
computed_wl = rssmodel.compute(
grang=p_fit[0],
artic=p_fit[1],
colpos=line_x)
return computed_wl
def fit__wavelength_error(p_fit, matched_lines, rssmodel):
line_wl = fit__wavelength(p_fit, matched_lines[:,0], rssmodel)
ref_wl = matched_lines[:,len(lineinfo_cols)]
delta_wl = line_wl - ref_wl # add some weighting here???
return delta_wl
p_start = [best_gratingangle, best_camangle]
fit_args = (matched_catalog, kens_model)
_fit = scipy.optimize.leastsq(fit__wavelength_error,
p_start,
args=fit_args,
maxfev=500,
full_output=1)
p_final = _fit[0]
logger.info("Fit results: Was: %s --> Now: %s" % (
" ".join(["%.4f" % f for f in p_start]),
" ".join(["%.4f" % f for f in p_final]),
))
# print p_start, " ==> ", p_final
lineinfo[:,lineinfo_colidx['WAVELENGTH']] = fit__wavelength(
p_final, lineinfo[:, lineinfo_colidx["PIXELPOS"]], kens_model)
matched_catalog[:, lineinfo_colidx['WAVELENGTH']] = fit__wavelength(
p_final, matched_catalog[:, lineinfo_colidx["PIXELPOS"]], kens_model)
numpy.savetxt("matched_lines_afterfit.dat", matched_catalog)
#
# compute rms
#
rms = numpy.std(matched_catalog[:, lineinfo_colidx['WAVELENGTH']] - \
matched_catalog[:, len(lineinfo_cols)])
logger.info("Found RMS: %f" % (rms))
wls = compute_wavelength_solution(matched_catalog, max_order=3)
logger.info("Best fit wavelength solution: L = %9.3f %+9.3f * x %+9.3e x^2 %+9.3e x^3" % (
wls[0], wls[1], wls[2], wls[3]))
# # # set the indices for bad matches to a valid value
# # i[~good_matches] = 0
# # matched = numpy.zeros((arc.shape[0], (arc.shape[1]+ref.shape[1])))
# # matched[:,:arc.shape[1]] = arc
# # matched[:,arc.shape[1]:] = ref[i]
# # #print "XXXXXXXXXXXX\n"*3,ref.shape, ref[i].shape, i.shape, bad_matches.shape
# # #print bad_matches
# # numpy.savetxt("matched_raw", matched)
# # numpy.savetxt("matched_bad", bad_matches)
# # #sys.exit(0)
# # #print "XXXX\n"*3
# # matched = matched[~bad_matches]
# return
# i = numpy.array(i)
# bad_matches = (i>=ref.shape[0])
# i[bad_matches] = 0
# return
# reference_pixel_x = 0.5 * spec.shape[0]
# # dispersion was calculated above
# # central wavelength
# central_wavelength = kens_model.central_wavelength() #numpy.median(all_wavelength) # 0.5 * (blue_edge + red_edge)
# max_dispersion_error = 0.00 #10 # +/- 10% should be plenty
# dispersion_search_steps = 0.01 # vary dispersion in 1% steps
# n_dispersion_steps = (max_dispersion_error / dispersion_search_steps) * 2 + 1
# #
# # compute what dispersion factors we are trying
# #
# trial_dispersions = numpy.linspace(1.0-max_dispersion_error,
# 1.0+max_dispersion_error,
# n_dispersion_steps) * dispersion
# n_matches = numpy.zeros((trial_dispersions.shape[0]))
# matched_cats = [None] * trial_dispersions.shape[0]
# #
# # Now try each dispersion, one by one, and compute what wavelength offset
# # we would need to make the maximum number of lines match known lines from
# # the line catalog.
# #
# #
# # New: Assume we know line centers to within a pixel, then we can match
# # lines that lie within a 1-pixel radius
# #
# # Remember: units here are angstroem !!!
# matching_radius = 2 * dispersion
# logger.debug("Considering lines within %.1f A of a known ARC line as matched!" % (
# matching_radius))
# # print "before loop:", lineinfo.shape
# for idx, _dispersion in enumerate(trial_dispersions):
# # compute dispersion including the correction
# #_dispersion = dispersion * disp_factor
# # copy the original line info so we don't accidently overwrite important data
# _lineinfo = numpy.array(lineinfo)
# # find optimal line shifts and match lines
# # consider lines within 5A of each other matches
# # --> this most likely will depend on spectral resolution and binning
# matched_cat = find_matching_lines(ref_lines, _lineinfo,
# rss,
# _dispersion, central_wavelength,
# reference_pixel_x,
# matching_radius = matching_radius,
# )
# # Save results for later picking of the best one
# n_matches[idx] = matched_cat.shape[0]
# matched_cats[idx] = matched_cat
# numpy.savetxt("dispersion_scale_%.3f" % (_dispersion), matched_cat)
# #
# # Find the solution with the most matched lines
# #
# n_max = numpy.argmax(n_matches)
# #print
# #print "most matched lines:", n_matches[n_max],
# #print "best dispersion: %f" % (trial_dispersions[n_max])
# logger.debug("Choosing best solution: %4d for dispersion %8.4f A/px" % (
# n_matches[n_max], trial_dispersions[n_max]))
# numpy.savetxt("matchcount", numpy.append(trial_dispersions.reshape((-1,1)),
# n_matches.reshape((-1,1)),
# axis=1))
# matched = matched_cats[n_max]
# numpy.savetxt("matched.lines.best", matched)
# # print "***************************\n"*5
# # print lineinfo.shape
# logger.info("Computing an analytical wavelength calibration...")
# wls = compute_wavelength_solution(matched, max_order=3)
# spec_x = numpy.polynomial.polynomial.polyval(
# numpy.arange(spec.shape[0]), wls).reshape((-1,1))
# spec_combined = numpy.append(spec_x, spec.reshape((-1,1)), axis=1)
# numpy.savetxt("spec.calib.start", spec_combined)
# #
# # Now we have a best-match solution
# # Match lines again to see what the RMS is - use a small matching radius now
# #
# ############################################################################
# #
# # Since the original matching was done using a simple polynomial form,
# # let's now iterate the rough solution using higher order polynomials to
# # (hopefully) match a larger number of lines
# #
# # Add here:
# # - Keep an eye on r.m.s. of the fit, and the number of matched lines
# # - with every step, reduce the matching radius to make sure we are matching
# # only with the most likely counterpart in case of close line (blends)
# #
# ############################################################################
# #prev_wls = wls
# matching_radius = 2*dispersion
# logger.debug("Refining WLS using all %d lines" % (lineinfo.shape[0]))
# for iteration in range(3):
# #sys.stdout.write("\n\n\n"); sys.stdout.flush()
# _linelist = numpy.array(lineinfo)
# # Now compute the new wavelength for each line
# _linelist[:,lineinfo_colidx['WAVELENGTH']] = numpy.polynomial.polynomial.polyval(
# _linelist[:,lineinfo_colidx['PIXELPOS']], wls)
# numpy.savetxt("lineinfo.iteration=%d" % (iteration+1), _linelist, "%10.4f")
# # compute wl with polyval
# # _wl = lineinfo[:,0]
# # numpy.savetxt("final.1", _wl)
# # numpy.savetxt("final.2", numpy.polynomial.polynomial.polyval(_wl, wls))
# # numpy.savetxt("final.3", _wl*wls[1]+wls[0])
# # With the refined wavelength solution, match lines between the
# # ARC spectrum and the reference line catalog
# new_matches = match_line_catalogs(_linelist, ref_lines,
# matching_radius=1.7, #matching_radius, # wsa 50 XXX
# verbose=False,
# col_arc=lineinfo_colidx['WAVELENGTH'],
# col_ref=0,
# dumpfile="finalmatch.%d" % (iteration+1))
# logger.debug("WLS Refinement step %3d: now %3d matches!" % (
# iteration+1, new_matches.shape[0]))
# # -- for debugging --
# numpy.savetxt("matched.cat.iter%d" % (iteration+1), new_matches)
# #
# # Before fitting, iteratively reject obvious outliers most likely caused
# # by matching wrong lines
# #
# likely_outlier = numpy.isnan(new_matches[:,lineinfo_colidx['WAVELENGTH']])
# for reject in range(3):
# diff_angstroem = new_matches[:,lineinfo_colidx['WAVELENGTH']] - \
# new_matches[:,len(lineinfo_colidx)]
# med = numpy.median(diff_angstroem[~likely_outlier])
# stdx = numpy.std(diff_angstroem[~likely_outlier])
# sigma = scipy.stats.scoreatpercentile(diff_angstroem[~likely_outlier], [16,84])
# std = 0.5*(sigma[1]-sigma[0])
# likely_outlier = (diff_angstroem > med+2*std) | (diff_angstroem < med-2*std)
# logger.debug("Med/Std/StdX= %f / %f / %f" % (med, std, stdx))
# # Now we have a better idea on outliers, so reject them and work with
# # what's left
# new_matches = new_matches[~likely_outlier]
# logger.debug("WLS Refinement step %3d: %3d matches left after outliers!" % (
# iteration+1, new_matches.shape[0]))
# # And with the matched line list, compute a new wavelength solution
# wls = compute_wavelength_solution(new_matches, max_order=4)#+iteration)
# # -- for debugging --
# numpy.savetxt("matched.outlierreject.iter%d" % (iteration+1), new_matches)
# #
# spec_x = numpy.polynomial.polynomial.polyval(
# numpy.arange(spec.shape[0])+1., wls).reshape((-1,1))
# spec_combined = numpy.append(spec_x, spec.reshape((-1,1)), axis=1)
# numpy.savetxt("spec.calib.iteration_%d" % (iteration+1), spec_combined)
# #prev_wls = wls
# #return
# final_match = matched
# numpy.savetxt("matched.cat.final", final_match)
# Also save the original spectrum as text file
spec_x = numpy.polynomial.polynomial.polyval(numpy.arange(spec.shape[0]), wls).reshape((-1,1))
spec_combined = numpy.append(spec_x, spec.reshape((-1,1)), axis=1)
numpy.savetxt("spec.calib", spec_combined)
# print lines
# print _linelist
# print spec.shape
# print spec_combined.shape
# print line
# print wls
return {
'spec': spec,
'spec_combined': spec_combined,
'linelist_ref': lines,
# 'linelist_arc': _linelist,
'linelist_arc': lineinfo,
'line': line,
'wl_fit_coeffs': wls,
}
def test_ModelSolution():
hdu = pyfits.open(inimage)
# create the data arra
data = hdu[1].data
# create the header information
instrume = hdu[1].header['INSTRUME'].strip()
grating = hdu[1].header['GRATING'].strip()
grang = hdu[1].header['GR-ANGLE']
arang = hdu[1].header['AR-ANGLE']
filter = hdu[1].header['FILTER'].strip()
slit = float(hdu[1].header['MASKID'])
xbin, ybin = hdu[1].header['CCDSUM'].strip().split()
# print instrume, grating, grang, arang, filter
# print xbin, ybin
# print len(data), len(data[0])
# create the RSS Model
rssmodel = RSSModel.RSSModel(grating_name=grating,
gratang=grang,
camang=arang,
slit=slit,
xbin=int(xbin),
ybin=int(ybin))
xarr = np.arange(len(data[0]), dtype='int64')
rss = rssmodel.rss
alpha = rss.gratang
beta = rss.gratang - rss.camang
d = rss.detector.xbin * rss.detector.pix_size * (xarr - 0.5 * len(xarr))
dbeta = np.degrees(np.arctan(d / rss.camera.focallength))
y = 1e7 * rss.calc_wavelength(alpha, beta - dbeta)
#ws=WS.WavelengthSolution(xp, wp, function='model', sgraph=rssmodel.rss, xlen=len(data[0]), order=4, cfit='all')
ws = WS.WavelengthSolution(xarr,
y,
function='model',
sgraph=rssmodel.rss,
xlen=len(data[0]),
order=4,
cfit='ndcoef')
#ws=WS.WavelengthSolution(xarr, y, function='poly', order=3)
#ws=WS.WavelengthSolution(xp, wp, function='poly', order=3)
ws.fit()
print ws.coef
print ws.func.result
for c in ws.func.spcoef:
print c()
for c in ws.func.ndcoef:
print c()
print ws.value(2000)
print ws.sigma(xp, wp)
print ws.chisq(xp, wp, ep)
pl.figure()
# pl.plot(xarr,y)
#pl.plot(xarr, ws.value(xarr))
#pl.plot(xp, wp-ws.value(xp), ls='', marker='o')
pl.plot(xarr, y - ws.value(xarr))
#pl.plot(ls.x, ls.y-ls(ls.x), ls='', marker='o')
pl.show()
def arclisfromhdr(hdr, slitwidth=1.50, xbin=2, ybin=2, lamp='Ar.txt'):
# ** some numbers below hardwired for 2x2 binning (~3170 pix) **
grname = hdr['grating']
camang = hdr['camang']
gratang = hdr['gr-angle']
rss = RSSModel.RSSModel(grating_name=grname,
gratang=gratang,
camang=camang,
slit=slitwidth,
xbin=xbin,
ybin=ybin)
# set up the detector
ycen = rss.detector.get_ypixcenter()
d_arr = rss.detector.make_detector()[ycen, :]
xarr = np.arange(len(d_arr))
w = 1e7 * rss.get_wavelength(xarr)
#set up the artificial spectrum
res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
sw, sf = pl.loadtxt(lamp, usecols=(0, 1), unpack=True)
wrange = [1e7 * rss.calc_bluewavelength(), 1e7 * rss.calc_redwavelength()]
spec = Spectrum.Spectrum(sw,
sf,
wrange=wrange,
dw=res / 10,
stype='line',
sigma=res)
#interpolate it over the same range as the detector
spec.interp(w)
if (0):
#plot it
pl.figure()
pl.plot(spec.wavelength, d_arr * ((spec.flux) / spec.flux.max()))
pl.plot(spec.wavelength, d_arr * 0.1)
#yy=np.median(data[1000:1050,3:3173],0)
#pl.plot(spec.wavelength,yy/yy.max())
ymod = d_arr * ((spec.flux) / spec.flux.max())
ydata = yy / yy.max()
off, rval = xcor2(ydata, ymod, 100.)
yyy = np.roll(yy, -int(off)) / yy.max()
pl.plot(spec.wavelength, yyy)
pl.show()
stop()
# We need to return
# - a matched list of wavelength(of each pixel),flux for the arc
# - a list of the arc lines
modarclam = spec.wavelength
modarcspec = d_arr * ((spec.flux) / spec.flux.max())
# extract pixel positions for lines of wavelength sw:
xpix = np.arange(np.size(modarclam))
ixp = np.interp(sw, modarclam, xpix, left=0, right=0)
ok = np.reshape(((ixp > 0.) & (ixp < 3170)).nonzero(), -1)
np.savetxt('_tmparc.lis', np.transpose((ixp[ok], sw[ok], sw[ok])))
return modarclam, modarcspec
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)
import pylab as pl
import numpy as np
import PySpectrograph
from PySpectrograph.Models import RSSModel
from PySpectrograph.Spectra import Spectrum
# create the spectrograph model
rss = RSSModel.RSSModel(grating_name="PG0900",
gratang=15.875,
camang=31.76496,
slit=1.50,
xbin=2,
ybin=2)
# print out some basic statistics
print 1e7 * rss.calc_bluewavelength(), 1e7 * rss.calc_centralwavelength(
), 1e7 * rss.calc_redwavelength()
R = rss.calc_resolution(rss.calc_centralwavelength(), rss.alpha(), -rss.beta())
res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
print R, res
# set up the detector
ycen = rss.detector.get_ypixcenter()
d_arr = rss.detector.make_detector()[ycen, :]
w = 1e7 * rss.get_wavelength(xarr)
# set up the artificial spectrum
sw, sf = pl.loadtxt('Ne.txt', usecols=(0, 1), unpack=True)
wrange = [1e7 * rss.calc_bluewavelength(), 1e7 * rss.calc_redwavelength()]
spec = Spectrum.Spectrum(sw,