spec = slitlet[mid-3:mid+3, :]
spec = np.median(spec, axis=0)
continuum = median_filter(spec, 250)
if fiducial_spec.shape == (0,):
fiducial_spec = spec
fiducial_spec /= continuum
fiducial_spec /= fiducial_spec.max()
soc = spec/continuum
soc /= soc.max()
as_per_pix = .18/1.4
shift = -np.median(loc)/as_per_pix
lags = np.arange(shift-300,shift+300,dtype=np.int)
xc = Fit.xcor(soc[800:1300], fiducial_spec[800:1300], lags)
#start_shell()
shift = lags[np.argmax(xc)]
center = width/2 - shift
print center, write_pos
xs = np.arange(len(spec))
pl.plot(xs - shift, spec/continuum)
try:
out[(write_pos - dy):write_pos, center-1024:center+1024] = slitlet
if minl > center-1024: minl = center-1024
if maxl < center+1024: maxl = center+1024
