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 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 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)