def voigtfunc_and_jac(vwave, vpars, convolve_jac=True):
### Check to see if cfg variables are set
if isinstance(cfg.fitidx, int) | isinstance(cfg.wave, int):
cfg.fitidx = fitpix(vwave, vpars)
cfg.wave = vwave
if len(cfg.lsfs) == 0:
makevoigt.get_lsfs()
g, dg_dcol, dg_dv, dg_db = makevoigt.voigt_and_jac(vwave[cfg.fitidx],
vpars[0], vpars[1],
vpars[2], vpars[3],
vpars[4])
g_full = np.ones(len(vwave))
g_full[cfg.fitidx] = g
convfactor = makevoigt.convolvecos(vwave, g_full, vpars[0], vpars[3])
jac = np.vstack([dg_dcol, dg_db, dg_dv])
jac_full = np.zeros([jac.shape[0], len(vwave)])
jac_full[:, cfg.fitidx] = jac
# might be better to wait to do the convolution until after things are agglomerated
if convolve_jac:
for e, row in enumerate(jac_full):
# minus 1 plus 1 because convolvecos pads with 1s
jac_full[e] = makevoigt.convolvecos(vwave, 1 + row, vpars[0],
vpars[3]) - 1
return convfactor, jac_full
def model_profile(spec,
fitpars,
instr=None,
gratings=None,
lsfranges=None,
cen_wave=None,
lps=None,
slits=None):
'''Produce Voigt profile model from parameters and instrumental setup for
convolving proper line spread function. Note
Parameters
----------
spec : string or XSpectrum1D
The spectrum to be fitted with the input lines
fitpars : list of lists
The joebvp parameter array that includes line measurements
instr : list of str, optional
Instruments used to observe the spectral regions defined in lsfranges
gratings : list of str, optional
Gratings used for each spectral region defined in lsfranges
lsfranges : array of size len(instr)x2
Beginning and ending wavelengths of spectral ranges for each setup
cen_wave : list of str, optional
Central wavelength setting for each spectral region defined in lsfranges
lps : list of str, optional
Lifetime positions of detector (particularly for COS)
slits : list of str, optional
Slit setting for each spectral region defined in lsfranges
Returns
-------
wavelength : Quantity
Wavelength array from spec
profile : array
Voigt profile model
'''
### Setup LSF parameters if provided
if instr is not None:
cfg.instr = instr
cfg.lsfranges = lsfranges
cfg.gratings = gratings
cfg.cen_wave = cen_wave
cfg.lps = lps
cfg.slits = slits
### Deal with alternate input types
if isinstance(spec, str):
specobj = readspec(spec)
else:
specobj = spec
makevoigt.get_lsfs()
#import pdb; pdb.set_trace()
cfg.wave = specobj.wavelength.value
cfg.spectrum = specobj
profile = makevoigt.cosvoigt(cfg.wave, fitpars)
return specobj.wavelength, profile
def voigtfunc(vwave,vpars): ### Check to see if cfg variables are set if isinstance(cfg.fitidx, int)|isinstance(cfg.wave, int): cfg.fitidx = fitpix(vwave, vpars) cfg.wave = vwave if len(cfg.lsfs) == 0: makevoigt.get_lsfs() vflux=np.zeros(len(vwave))+1. factor=makevoigt.voigt(vwave,vpars[0],vpars[1],vpars[2],vpars[3],vpars[4]) convfactor=makevoigt.convolvecos(vwave,factor,vpars[0],vpars[3]) vflux*=convfactor return vflux