def __init__(self, xcoef, ycoef, wavemin, wavemax, npix_y, xsigcoef = None, ysigcoef = None) :
"""
Lightweight wrapper for trace coordinates and wavelength solution
Args:
xcoef: 2D[ntrace, ncoef] Legendre coefficient of x as a function of wavelength
ycoef: 2D[ntrace, ncoef] Legendre coefficient of y as a function of wavelength
wavemin : float
wavemax : float. wavemin and wavemax are used to define a reduced variable legx(wave,wavemin,wavemax)=2*(wave-wavemin)/(wavemax-wavemin)-1
used to compute the traces, xccd=legval(legx(wave,wavemin,wavemax),xtrace[fiber])
"""
assert(xcoef.shape[0] == ycoef.shape[0])
if xsigcoef is not None :
assert(xcoef.shape[0] == xsigcoef.shape[0])
if ysigcoef is not None :
assert(xcoef.shape[0] == ysigcoef.shape[0])
self.nspec = xcoef.shape[0]
self.wavemin = wavemin
self.wavemax = wavemax
self.npix_y = npix_y
self.x_vs_wave_traceset = TraceSet(xcoef,[wavemin,wavemax])
self.y_vs_wave_traceset = TraceSet(ycoef,[wavemin,wavemax])
self.xsig_vs_wave_traceset = None
self.ysig_vs_wave_traceset = None
if xsigcoef is not None :
self.xsig_vs_wave_traceset = TraceSet(xsigcoef,[wavemin,wavemax])
if ysigcoef is not None :
self.ysig_vs_wave_traceset = TraceSet(ysigcoef,[wavemin,wavemax])
self.wave_vs_y_traceset = None
def write_psffile(infile,
wcoeffs,
wcoeffs_wavemin,
wcoeffs_wavemax,
outfile,
wavestepsize=None):
"""
extract psf file, add wcoeffs, and make a new psf file preserving the traces etc.
psf module will load this
"""
tset = read_xytraceset(infile)
# convert wsigma to ysig ...
nfiber = wcoeffs.shape[0]
ncoef = wcoeffs.shape[1]
nw = 100 # need a larger number than ncoef to get an accurate dydw from the gradients
# wcoeffs and tset do not necessarily have the same wavelength range
wave = np.linspace(tset.wavemin, tset.wavemax, nw)
wsig_set = TraceSet(wcoeffs, [wcoeffs_wavemin, wcoeffs_wavemax])
wsig_vals = np.zeros((nfiber, nw))
for f in range(nfiber):
y_vals = tset.y_vs_wave(f, wave)
dydw = np.gradient(y_vals) / np.gradient(wave)
wsig_vals[f] = wsig_set.eval(f, wave) * dydw
tset.ysig_vs_wave_traceset = fit_traces(wave,
wsig_vals,
deg=ncoef - 1,
domain=(tset.wavemin,
tset.wavemax))
write_xytraceset(outfile, tset)
def write_psffile(infile,wcoeffs,wcoeffs_wavemin,wcoeffs_wavemax,outfile,wavestepsize=None):
"""
extract psf file, add wcoeffs, and make a new psf file preserving the traces etc.
psf module will load this
"""
tset = read_xytraceset(infile)
# convert wsigma to ysig ...
nfiber = wcoeffs.shape[0]
ncoef = wcoeffs.shape[1]
nw = 100 # need a larger number than ncoef to get an accurate dydw from the gradients
# wcoeffs and tset do not necessarily have the same wavelength range
wave = np.linspace(tset.wavemin,tset.wavemax,nw)
wsig_set = TraceSet(wcoeffs,[wcoeffs_wavemin,wcoeffs_wavemax])
wsig_vals = np.zeros((nfiber,nw))
for f in range(nfiber) :
y_vals = tset.y_vs_wave(f,wave)
dydw = np.gradient(y_vals)/np.gradient(wave)
wsig_vals[f]=wsig_set.eval(f,wave)*dydw
tset.ysig_vs_wave_traceset = fit_traces(wave, wsig_vals, deg=ncoef-1, domain=(tset.wavemin,tset.wavemax))
write_xytraceset(outfile,tset)
def __init__(self,
xcoef,
ycoef,
wavemin,
wavemax,
npix_y,
xsigcoef=None,
ysigcoef=None,
meta=None):
"""
Lightweight wrapper for trace coordinates and wavelength solution
Args:
xcoef: 2D[ntrace, ncoef] Legendre coefficient of x as a function of wavelength
ycoef: 2D[ntrace, ncoef] Legendre coefficient of y as a function of wavelength
wavemin : float
wavemax : float. wavemin and wavemax are used to define a reduced variable legx(wave,wavemin,wavemax)=2*(wave-wavemin)/(wavemax-wavemin)-1
used to compute the traces, xccd=legval(legx(wave,wavemin,wavemax),xtrace[fiber])
"""
from specter.util.traceset import TraceSet
assert (xcoef.shape[0] == ycoef.shape[0])
if xsigcoef is not None:
assert (xcoef.shape[0] == xsigcoef.shape[0])
if ysigcoef is not None:
assert (xcoef.shape[0] == ysigcoef.shape[0])
self.nspec = xcoef.shape[0]
self.wavemin = wavemin
self.wavemax = wavemax
self.npix_y = npix_y
self.x_vs_wave_traceset = TraceSet(xcoef, [wavemin, wavemax])
self.y_vs_wave_traceset = TraceSet(ycoef, [wavemin, wavemax])
self.xsig_vs_wave_traceset = None
self.ysig_vs_wave_traceset = None
if xsigcoef is not None:
self.xsig_vs_wave_traceset = TraceSet(xsigcoef, [wavemin, wavemax])
if ysigcoef is not None:
self.ysig_vs_wave_traceset = TraceSet(ysigcoef, [wavemin, wavemax])
self.wave_vs_y_traceset = None
self.meta = meta
def read_xytraceset(filename) :
"""
Reads traces in PSF fits file
Args:
filename : Path to input fits file which has to contain XTRACE and YTRACE HDUs
Returns:
XYTraceSet object
"""
log=get_logger()
xcoef=None
ycoef=None
xsigcoef=None
ysigcoef=None
wsigmacoef=None
wavemin=None
wavemax=None
log.info("reading traces in '%s'"%filename)
fits_file = fits.open(filename)
# npix_y, needed for boxcar extractions
npix_y=0
for hdu in [0,"XTRACE","PSF"] :
if npix_y > 0 : break
if hdu in fits_file :
head = fits_file[hdu].header
if "NPIX_Y" in head :
npix_y=int(head["NPIX_Y"])
if npix_y == 0 :
raise KeyError("Didn't find head entry NPIX_Y in hdu 0, XTRACE or PSF")
log.info("npix_y={}".format(npix_y))
try :
psftype=fits_file[0].header["PSFTYPE"]
except KeyError :
psftype=""
# now read trace coefficients
log.info("psf is a '%s'"%psftype)
if psftype == "bootcalib" :
xcoef,wavemin,wavemax =_traceset_from_image(wavemin,wavemax,fits_file[0],"xcoef")
ycoef,wavemin,wavemax =_traceset_from_image(wavemin,wavemax,fits_file[1],"ycoef")
else :
for k in ["XTRACE","XCOEF","XCOEFF"] :
if k in fits_file :
xcoef,wavemin,wavemax =_traceset_from_image(wavemin,wavemax,fits_file[k],"xcoef")
for k in ["YTRACE","YCOEF","YCOEFF"] :
if k in fits_file :
ycoef,wavemin,wavemax =_traceset_from_image(wavemin,wavemax,fits_file[k],"ycoef")
for k in ["XSIG"] :
if k in fits_file :
xsigcoef,wavemin,wavemax =_traceset_from_image(wavemin,wavemax,fits_file[k],"xsigcoef")
for k in ["YSIG"] :
if k in fits_file :
ysigcoef,wavemin,wavemax =_traceset_from_image(wavemin,wavemax,fits_file[k],"ysigcoef")
if "WSIGMA" in fits_file :
wsigmacoef = fits_file["WSIGMA"].data
if psftype == "GAUSS-HERMITE" : # older version where XTRACE and YTRACE are not saved in separate HDUs
hdu=fits_file["PSF"]
if xcoef is None : xcoef,wavemin,wavemax =_traceset_from_table(wavemin,wavemax,hdu,"X")
if ycoef is None : ycoef,wavemin,wavemax =_traceset_from_table(wavemin,wavemax,hdu,"Y")
if xsigcoef is None : xsigcoef,wavemin,wavemax =_traceset_from_table(wavemin,wavemax,hdu,"GHSIGX")
if ysigcoef is None : ysigcoef,wavemin,wavemax =_traceset_from_table(wavemin,wavemax,hdu,"GHSIGY")
log.info("wavemin={} wavemax={}".format(wavemin,wavemax))
if xcoef is None or ycoef is None :
raise ValueError("could not find xcoef and ycoef in psf file %s"%filename)
if xcoef.shape[0] != ycoef.shape[0] :
raise ValueError("XCOEF and YCOEF don't have same number of fibers %d %d"%(xcoef.shape[0],ycoef.shape[0]))
fits_file.close()
if wsigmacoef is not None :
log.warning("Converting deprecated WSIGMA coefficents (in Ang.) into YSIG (in CCD pixels)")
nfiber = wsigmacoef.shape[0]
ncoef = wsigmacoef.shape[1]
nw = 100 # to get accurate dydw
wave = np.linspace(wavemin,wavemax,nw)
wsig_set = TraceSet(wsigmacoef,[wavemin,wavemax])
y_set = TraceSet(ycoef,[wavemin,wavemax])
wsig_vals = np.zeros((nfiber,nw))
for f in range(nfiber) :
y_vals = y_set.eval(f,wave)
dydw = np.gradient(y_vals)/np.gradient(wave)
wsig_vals[f]=wsig_set.eval(f,wave)*dydw
tset = fit_traces(wave, wsig_vals, deg=ncoef-1, domain=(wavemin,wavemax))
ysigcoef = tset._coeff
return XYTraceSet(xcoef,ycoef,wavemin,wavemax,npix_y,xsigcoef=xsigcoef,ysigcoef=ysigcoef)
def process_arc(qframe, xytraceset, linelist=None, npoly=2, nbins=2):
"""
qframe: desispec.qframe.QFrame object
xytraceset : desispec.xytraceset.XYTraceSet object
linelist: line list to fit
npoly: polynomial order for sigma expansion
nbins: no of bins for the half of the fitting window
return: xytraceset (with ysig vs wave)
"""
log = get_logger()
if linelist is None:
if qframe.meta is None or "CAMERA" not in qframe.meta:
log.error(
"no information about camera in qframe so I don't know which lines to use"
)
raise RuntimeError(
"no information about camera in qframe so I don't know which lines to use"
)
camera = qframe.meta["CAMERA"]
#- load arc lines
from desispec.bootcalib import load_arcline_list, load_gdarc_lines, find_arc_lines
llist = load_arcline_list(camera)
dlamb, gd_lines = load_gdarc_lines(camera, llist)
linelist = gd_lines
log.info(
"No line list configured. Fitting for lines {}".format(linelist))
tset = xytraceset
assert (qframe.nspec == tset.nspec)
tset.ysig_vs_wave_traceset = TraceSet(np.zeros((tset.nspec, npoly + 1)),
[tset.wavemin, tset.wavemax])
for spec in range(tset.nspec):
spec_wave = qframe.wave[spec]
spec_linelist = linelist[(linelist > spec_wave[0])
& (linelist < spec_wave[-1])]
meanwaves, emeanwaves, sigmas, esigmas = sigmas_from_arc(
spec_wave,
qframe.flux[spec],
qframe.ivar[spec],
spec_linelist,
n=nbins)
# convert from wavelength A unit to CCD pixel for consistency with specex PSF
y = tset.y_vs_wave(spec, spec_wave)
dydw = np.interp(meanwaves, spec_wave,
np.gradient(y) / np.gradient(spec_wave))
sigmas *= dydw # A -> pixels
esigmas *= dydw # A -> pixels
ok = (sigmas > 0) & (esigmas > 0)
try:
thislegfit = Legendre.fit(meanwaves[ok],
sigmas[ok],
npoly,
domain=[tset.wavemin, tset.wavemax],
w=1. / esigmas[ok]**2)
tset.ysig_vs_wave_traceset._coeff[spec] = thislegfit.coef
except:
log.error("legfit of psf width failed for spec {}".format(spec))
wave = np.linspace(tset.wavemin, tset.wavemax, 20)
#plt.plot(wave,tset.ysig_vs_wave(spec,wave))
#plt.show()
return xytraceset
def read_xytraceset(filename):
"""
Reads traces in PSF fits file
Args:
filename : Path to input fits file which has to contain XTRACE and YTRACE HDUs
Returns:
XYTraceSet object
"""
#- specter import isolated within function so specter only loaded if
#- really needed
from specter.util.traceset import TraceSet, fit_traces
log = get_logger()
xcoef = None
ycoef = None
xsigcoef = None
ysigcoef = None
wsigmacoef = None
wavemin = None
wavemax = None
log.info("reading traces in '%s'" % filename)
fits_file = fits.open(filename)
# npix_y, needed for boxcar extractions
npix_y = 0
for hdu in [0, "XTRACE", "PSF"]:
if npix_y > 0: break
if hdu in fits_file:
head = fits_file[hdu].header
if "NPIX_Y" in head:
npix_y = int(head["NPIX_Y"])
if npix_y == 0:
raise KeyError("Didn't find head entry NPIX_Y in hdu 0, XTRACE or PSF")
log.debug("npix_y={}".format(npix_y))
try:
psftype = fits_file[0].header["PSFTYPE"]
except KeyError:
psftype = ""
# now read trace coefficients
log.debug("psf is a '%s'" % psftype)
if psftype == "bootcalib":
xcoef, wavemin, wavemax = _traceset_from_image(wavemin, wavemax,
fits_file[0], "xcoef")
ycoef, wavemin, wavemax = _traceset_from_image(wavemin, wavemax,
fits_file[1], "ycoef")
else:
for k in ["XTRACE", "XCOEF", "XCOEFF"]:
if k in fits_file:
xcoef, wavemin, wavemax = _traceset_from_image(
wavemin, wavemax, fits_file[k], "xcoef")
for k in ["YTRACE", "YCOEF", "YCOEFF"]:
if k in fits_file:
ycoef, wavemin, wavemax = _traceset_from_image(
wavemin, wavemax, fits_file[k], "ycoef")
for k in ["XSIG"]:
if k in fits_file:
xsigcoef, wavemin, wavemax = _traceset_from_image(
wavemin, wavemax, fits_file[k], "xsigcoef")
for k in ["YSIG"]:
if k in fits_file:
ysigcoef, wavemin, wavemax = _traceset_from_image(
wavemin, wavemax, fits_file[k], "ysigcoef")
if "WSIGMA" in fits_file:
wsigmacoef = fits_file["WSIGMA"].data
if psftype == "GAUSS-HERMITE": # older version where XTRACE and YTRACE are not saved in separate HDUs
hdu = fits_file["PSF"]
if xcoef is None:
xcoef, wavemin, wavemax = _traceset_from_table(
wavemin, wavemax, hdu, "X")
if ycoef is None:
ycoef, wavemin, wavemax = _traceset_from_table(
wavemin, wavemax, hdu, "Y")
if xsigcoef is None:
xsigcoef, wavemin, wavemax = _traceset_from_table(
wavemin, wavemax, hdu, "GHSIGX")
if ysigcoef is None:
ysigcoef, wavemin, wavemax = _traceset_from_table(
wavemin, wavemax, hdu, "GHSIGY")
log.debug("wavemin={} wavemax={}".format(wavemin, wavemax))
if xcoef is None or ycoef is None:
raise ValueError("could not find xcoef and ycoef in psf file %s" %
filename)
if xcoef.shape[0] != ycoef.shape[0]:
raise ValueError(
"XCOEF and YCOEF don't have same number of fibers %d %d" %
(xcoef.shape[0], ycoef.shape[0]))
fits_file.close()
if wsigmacoef is not None:
log.warning(
"Converting deprecated WSIGMA coefficents (in Ang.) into YSIG (in CCD pixels)"
)
nfiber = wsigmacoef.shape[0]
ncoef = wsigmacoef.shape[1]
nw = 100 # to get accurate dydw
wave = np.linspace(wavemin, wavemax, nw)
wsig_set = TraceSet(wsigmacoef, [wavemin, wavemax])
y_set = TraceSet(ycoef, [wavemin, wavemax])
wsig_vals = np.zeros((nfiber, nw))
for f in range(nfiber):
y_vals = y_set.eval(f, wave)
dydw = np.gradient(y_vals) / np.gradient(wave)
wsig_vals[f] = wsig_set.eval(f, wave) * dydw
tset = fit_traces(wave,
wsig_vals,
deg=ncoef - 1,
domain=(wavemin, wavemax))
ysigcoef = tset._coeff
return XYTraceSet(xcoef,
ycoef,
wavemin,
wavemax,
npix_y,
xsigcoef=xsigcoef,
ysigcoef=ysigcoef)
class XYTraceSet(object):
def __init__(self, xcoef, ycoef, wavemin, wavemax, npix_y, xsigcoef = None, ysigcoef = None) :
"""
Lightweight wrapper for trace coordinates and wavelength solution
Args:
xcoef: 2D[ntrace, ncoef] Legendre coefficient of x as a function of wavelength
ycoef: 2D[ntrace, ncoef] Legendre coefficient of y as a function of wavelength
wavemin : float
wavemax : float. wavemin and wavemax are used to define a reduced variable legx(wave,wavemin,wavemax)=2*(wave-wavemin)/(wavemax-wavemin)-1
used to compute the traces, xccd=legval(legx(wave,wavemin,wavemax),xtrace[fiber])
"""
assert(xcoef.shape[0] == ycoef.shape[0])
if xsigcoef is not None :
assert(xcoef.shape[0] == xsigcoef.shape[0])
if ysigcoef is not None :
assert(xcoef.shape[0] == ysigcoef.shape[0])
self.nspec = xcoef.shape[0]
self.wavemin = wavemin
self.wavemax = wavemax
self.npix_y = npix_y
self.x_vs_wave_traceset = TraceSet(xcoef,[wavemin,wavemax])
self.y_vs_wave_traceset = TraceSet(ycoef,[wavemin,wavemax])
self.xsig_vs_wave_traceset = None
self.ysig_vs_wave_traceset = None
if xsigcoef is not None :
self.xsig_vs_wave_traceset = TraceSet(xsigcoef,[wavemin,wavemax])
if ysigcoef is not None :
self.ysig_vs_wave_traceset = TraceSet(ysigcoef,[wavemin,wavemax])
self.wave_vs_y_traceset = None
def x_vs_wave(self,fiber,wavelength) :
return self.x_vs_wave_traceset.eval(fiber,wavelength)
def y_vs_wave(self,fiber,wavelength) :
return self.y_vs_wave_traceset.eval(fiber,wavelength)
def xsig_vs_wave(self,fiber,wavelength) :
if self.xsig_vs_wave_traceset is None :
raise RuntimeError("no xsig coefficents were read in the PSF")
return self.xsig_vs_wave_traceset.eval(fiber,wavelength)
def ysig_vs_wave(self,fiber,wavelength) :
if self.ysig_vs_wave_traceset is None :
raise RuntimeError("no ysig coefficents were read in the PSF")
return self.ysig_vs_wave_traceset.eval(fiber,wavelength)
def wave_vs_y(self,fiber,y) :
if self.wave_vs_y_traceset is None :
self.wave_vs_y_traceset = self.y_vs_wave_traceset.invert()
return self.wave_vs_y_traceset.eval(fiber,y)
def x_vs_y(self,fiber,y) :
return self.x_vs_wave(fiber,self.wave_vs_y(fiber,y))
def xsig_vs_y(self,fiber,y) :
return self.xsig_vs_wave(fiber,self.wave_vs_y(fiber,y))
def ysig_vs_y(self,fiber,y) :
return self.ysig_vs_wave(fiber,self.wave_vs_y(fiber,y))
"""
class XYTraceSet(object):
def __init__(self, xcoef, ycoef, wavemin, wavemax, npix_y, xsigcoef = None, ysigcoef = None, meta = None) :
"""
Lightweight wrapper for trace coordinates and wavelength solution
Args:
xcoef: 2D[ntrace, ncoef] Legendre coefficient of x as a function of wavelength
ycoef: 2D[ntrace, ncoef] Legendre coefficient of y as a function of wavelength
wavemin : float
wavemax : float. wavemin and wavemax are used to define a reduced variable legx(wave,wavemin,wavemax)=2*(wave-wavemin)/(wavemax-wavemin)-1
used to compute the traces, xccd=legval(legx(wave,wavemin,wavemax),xtrace[fiber])
"""
assert(xcoef.shape[0] == ycoef.shape[0])
if xsigcoef is not None :
assert(xcoef.shape[0] == xsigcoef.shape[0])
if ysigcoef is not None :
assert(xcoef.shape[0] == ysigcoef.shape[0])
self.nspec = xcoef.shape[0]
self.wavemin = wavemin
self.wavemax = wavemax
self.npix_y = npix_y
self.x_vs_wave_traceset = TraceSet(xcoef,[wavemin,wavemax])
self.y_vs_wave_traceset = TraceSet(ycoef,[wavemin,wavemax])
self.xsig_vs_wave_traceset = None
self.ysig_vs_wave_traceset = None
if xsigcoef is not None :
self.xsig_vs_wave_traceset = TraceSet(xsigcoef,[wavemin,wavemax])
if ysigcoef is not None :
self.ysig_vs_wave_traceset = TraceSet(ysigcoef,[wavemin,wavemax])
self.wave_vs_y_traceset = None
self.meta = meta
def x_vs_wave(self,fiber,wavelength) :
return self.x_vs_wave_traceset.eval(fiber,wavelength)
def y_vs_wave(self,fiber,wavelength) :
return self.y_vs_wave_traceset.eval(fiber,wavelength)
def xsig_vs_wave(self,fiber,wavelength) :
if self.xsig_vs_wave_traceset is None :
raise RuntimeError("no xsig coefficents were read in the PSF")
return self.xsig_vs_wave_traceset.eval(fiber,wavelength)
def ysig_vs_wave(self,fiber,wavelength) :
if self.ysig_vs_wave_traceset is None :
raise RuntimeError("no ysig coefficents were read in the PSF")
return self.ysig_vs_wave_traceset.eval(fiber,wavelength)
def wave_vs_y(self,fiber,y) :
if self.wave_vs_y_traceset is None :
self.wave_vs_y_traceset = self.y_vs_wave_traceset.invert()
return self.wave_vs_y_traceset.eval(fiber,y)
def x_vs_y(self,fiber,y) :
return self.x_vs_wave(fiber,self.wave_vs_y(fiber,y))
def xsig_vs_y(self,fiber,y) :
return self.xsig_vs_wave(fiber,self.wave_vs_y(fiber,y))
def ysig_vs_y(self,fiber,y) :
return self.ysig_vs_wave(fiber,self.wave_vs_y(fiber,y))
"""