def joebvpfit(wave,flux,sig,linepars,flags):
xtol=1e-11
gtol=1e-11
# Only feed to the fitter the parameters that go into the model
partofit=linepars[:5]
parinfo=prepparinfo(partofit,flags)
# Save the velocity windows to add back to the parameter array
vlim1=linepars[5] ; vlim2=linepars[6]
# Get atomic data
lam,fosc,gam=atomicdata.setatomicdata(linepars[0])
cfg.lams=lam ; cfg.fosc=fosc ; cfg.gam=gam
# Set fit regions
cfg.fitidx = fitpix(wave, linepars)
# Prep parameters for fitter
partofit=unfoldpars(partofit)
modelvars={'x':wave,'y':flux,'err':sig}
# Do the fit and translate the parameters back into the received format
m=nmpfit.mpfit(voigterrfunc,partofit,functkw=modelvars,parinfo=parinfo,nprint=1,quiet=0,fastnorm=1,ftol=1e-10,xtol=xtol,gtol=gtol)
if m.status <= 0: print('Fitting error:',m.errmsg)
fitpars=foldpars(m.params)
fiterrors = foldpars(m.perror)
# Add velocity windows back to parameter array
fitpars.append(vlim1) ; fitpars.append(vlim2)
print('\nFit results: \n')
for i in range(len(fitpars[0])):
print(jbg.tabdelimrow([round(fitpars[0][i],2),jbg.decimalplaces(fitpars[3][i],5),jbg.roundto(fitpars[1][i],5),jbg.roundto(fitpars[2][i],5),jbg.roundto(fitpars[4][i],5)])[:-2])
print(jbg.tabdelimrow([' ',' ',' ',round(fiterrors[1][i],3),round(fiterrors[2][i],3),round(fiterrors[4][i],3)]))
return fitpars,fiterrors
def joebvpfit(wave,flux,sig,linepars,flags):
xtol=1e-11
gtol=1e-11
# Only feed to the fitter the parameters that go into the model
partofit=linepars[:5]
parinfo=prepparinfo(partofit,flags)
# Save the velocity windows to add back to the parameter array
vlim1=linepars[5] ; vlim2=linepars[6]
# Get atomic data
lam,fosc,gam=atomicdata.setatomicdata(linepars[0])
cfg.lams=lam ; cfg.fosc=fosc ; cfg.gam=gam
# Set fit regions
cfg.fitidx = fitpix(wave, linepars)
# Prep parameters for fitter
partofit=unfoldpars(partofit)
modelvars={'x':wave,'y':flux,'err':sig}
# Do the fit and translate the parameters back into the received format
m=nmpfit.mpfit(voigterrfunc,partofit,functkw=modelvars,parinfo=parinfo,nprint=1,quiet=0,fastnorm=1,ftol=1e-10,xtol=xtol,gtol=gtol)
if m.status <= 0: print('Fitting error:',m.errmsg)
fitpars=foldpars(m.params)
fiterrors = foldpars(m.perror)
# Add velocity windows back to parameter array
fitpars.append(vlim1) ; fitpars.append(vlim2)
print('\nFit results: \n')
for i in range(len(fitpars[0])):
print(jbg.tabdelimrow([round(fitpars[0][i],2),jbg.decimalplaces(fitpars[3][i],5),jbg.roundto(fitpars[1][i],5),jbg.roundto(fitpars[2][i],5),jbg.roundto(fitpars[4][i],5)])[:-2])
print(jbg.tabdelimrow([' ',' ',' ',round(fiterrors[1][i],3),round(fiterrors[2][i],3),round(fiterrors[4][i],3)]))
return fitpars,fiterrors
def stevebvpfit(wave, flux, sig, flags, linepars=None, xall=None):
if linepars is None:
raise ValueError("Must pass parameters in linepars.")
return
# Only feed to the fitter the parameters that go into the model
partofit = linepars[:5]
parinfo = prepparinfo(linepars, flags)
npar = len(parinfo)
## Be sure that PARINFO is of the right type
if parinfo is not None:
if type(parinfo) != list:
raise ValueError("PARINFO must be a list of dictionaries.")
return
else:
if type(parinfo[0]) != dict:
raise ValueError("PARINFO must be a list of dictionaries.")
return
## If the parameters were not specified at the command line, then
## extract them from PARINFO
if xall is None:
xall = parameterInformationFunction(parinfo, "value")
if xall is None:
raise ValueError(
'either xall or PARINFO(*)["value"] must be supplied.')
xall = np.ravel(np.array(xall).T)
# function that deals with tied and fixed parameters and creates
# indices list to go from non-redundant to redundant array:
indices_and_friends = various_indices(parinfo)
pfixed, ptied, ifree, indices = indices_and_friends
indices = indices.astype(np.int)
ifree = np.squeeze(ifree)
## Compose only VARYING parameters
x = np.squeeze(xall)[np.squeeze(
pfixed == 0)] ## x is the set of free parameters
## LIMITED parameters ?
limited = parameterInformationFunction(parinfo,
"limited",
default=[0, 0],
n=npar)
limits = parameterInformationFunction(parinfo,
"limits",
default=[0.0, 0.0],
n=npar)
if (limited is not None) and (limits is not None):
## Error checking on limits in parinfo
wh = np.nonzero((limited[:, 0] & (xall < limits[:, 0]))
| (limited[:, 1] & (xall > limits[:, 1])))
if len(wh[0]) > 0:
raise ValueError("parameters are not within PARINFO limits")
return
wh = np.nonzero((limited[:, 0] & limited[:, 1])
& (limits[:, 0] >= limits[:, 1])
& (pfixed == 0))
if len(wh[0]) > 0:
raise ValueError("PARINFO parameter limits are not consistent")
return
freeanduntied = np.where(np.squeeze(pfixed == 0))[0]
## Transfer structure values to local variables
qulim = np.take(limited[:, 1], freeanduntied)
ulim = np.take(limits[:, 1], freeanduntied)
qllim = np.take(limited[:, 0], freeanduntied)
llim = np.take(limits[:, 0], freeanduntied)
# Save the velocity windows to add back to the parameter array
vlim1 = linepars[5]
vlim2 = linepars[6]
# Get atomic data
lam, fosc, gam = atomicdata.setatomicdata(linepars[0])
cfg.lams = lam
cfg.fosc = fosc
cfg.gam = gam
# Set fit regions
cfg.fitidx = fitpix(wave, linepars)
# Prep parameters for fitter
partofit = unfoldpars(partofit)
modelvars = {"l": wave, "y": flux, "err": sig}
bnds = (
np.squeeze(np.where(qllim == 1, llim, -np.inf)),
np.squeeze(np.where(qulim == 1, ulim, np.inf)),
)
arg = [
xall, ifree, indices, modelvars["l"], modelvars["y"], modelvars["err"]
]
# here is where fitting happens:
cache = {"x": np.nan, "resid": np.nan, "jac": np.nan}
def cached_resid(x, cache):
if np.all(x == cache["x"]):
return cache["resid"]
cache["x"] = x.copy()
resid, jac = stevevoigterrfunc_w_jac(x, *arg)
cache["resid"] = resid
cache["jac"] = jac.T
return resid
def cached_jac(x, cache):
if np.all(x == cache["x"]):
return cache["jac"]
cache["x"] = x.copy()
resid, jac = stevevoigterrfunc_w_jac(x, *arg)
cache["resid"] = resid
cache["jac"] = jac.T
return jac.T
m = least_squares(
cached_resid,
x,
bounds=bnds,
args=(cache, ),
kwargs={},
verbose=True,
jac=cached_jac,
)
if m.status < 0:
print("Fitting error:", m.message)
done = True
elif m.status == 0:
done = False
else:
done = True
xall_fitted = xall.copy()
xall_fitted[ifree] = m["x"][indices]
fitpars = foldpars(xall_fitted)
# This is a super-hacky fix to the issue of parameters having Jacobians of 0.
# It could obscure other problems and so it would make sense to replace it
# at some point.
badvarmask = np.all(np.isclose(m.jac, 1e-10), axis=0)
if np.any(badvarmask):
try:
(bad_var_ind, ) = np.where(badvarmask)
# Replacing bad columns with value near 0.
m.jac[:, bad_var_ind] = 1e-5
# Giving rest wavelength and redshift of bad lines. Also really janky in and
# of itself so that's fun.
bad_var_indices_mask = np.in1d(indices, bad_var_ind)
bad_ifree = ifree[bad_var_indices_mask]
bad_comp_inds = np.unique(bad_ifree // 5)
for comp in bad_comp_inds:
bad_wav = fitpars[0][comp]
bad_red = fitpars[3][comp]
print("Bad component of {0:.5f} at {1:.5f}.".format(
np.float(bad_wav), np.float(bad_red)))
except IndexError:
pass
perr = calc_perrors(m.jac, freeanduntied, numpars=xall.size)
fitperr = foldpars(perr)
for par in perr:
par = np.ravel(np.array(par))
# Adding in reduced chi-squared bit:
rchi2 = 2 * m.cost / (len(cfg.fitidx) - len(freeanduntied))
# Add velocity windows back to parameter array
fitpars.append(vlim1)
fitpars.append(vlim2)
# prints results in terminal/notebook/whatever thing you have python running from
print("\nFit results: \n")
for i in range(len(fitpars[0])):
print(
jbg.tabdelimrow([
round(fitpars[0][i], 2),
jbg.decimalplaces(fitpars[3][i], 5),
jbg.roundto(fitpars[1][i], 5),
jbg.roundto(fitpars[2][i], 5),
jbg.roundto(fitpars[4][i], 5),
])[:-2])
print(
jbg.tabdelimrow([
" ",
" ",
" ",
round(fitperr[1][i], 3),
round(fitperr[2][i], 3),
round(fitperr[4][i], 3),
]))
print("\nReduced chi-squared: {0:f}".format(rchi2))
return fitpars, fitperr, rchi2, done