def fitpars_from_abslines(abslinelist):
'''Builds veeper parameter array from list of linetools AbsLines
Parameters
----------
abslinelist: list
List of AbsLine objects
Returns
-------
fitpars : list of lists
The joebvp parameter array that includes line measurements
'''
from joebvp import joebvpfit
restwaves = [al.wrest.value for al in abslinelist]
linecol = [al.attrib['logN'] for al in abslinelist]
lineb = [al.attrib['b'].value for al in abslinelist]
linevel = [al.attrib['vel'].value for al in abslinelist]
linevlim1 = [al.limits.vlim[0].value for al in abslinelist]
linevlim2 = [al.limits.vlim[1].value for al in abslinelist]
zs = [al.z for al in abslinelist]
initpars = [restwaves, linecol, lineb, zs, linevel, linevlim1, linevlim2]
initinfo = [[1]*len(abslinelist)]*len(initpars)
fitpars, parinfo = joebvpfit.initlinepars(zs, restwaves, initpars,
initinfo=initinfo)
return fitpars
def cosvoigt_cont(vwave,cont,vpars):
from joebvp import joebvpfit
pars,info=joebvpfit.initlinepars(vpars[3],vpars[0],vpars,initinfo=[0,0,0])
cfg.fitidx=joebvpfit.fitpix(vwave, pars,find_bad_pixels=False)
cfg.wave=vwave
vflux=np.zeros(len(vwave))+1.
factor=voigt(vwave,vpars[0],vpars[1],vpars[2],vpars[3],vpars[4])
convfactor=convolvecos(vwave,factor*cont,vpars[0],vpars[3])
vflux*=convfactor
return vflux
def addLine(self,wave,newrestwave,newz,newcol,newb,newvel,newvel1,newvel2,newrely=None,newcmt=None):
### Setup new parameters and append them to main arrays of the data model
newpars=[[newrestwave],[newcol],[newb],[newz],[newvel],[newvel1],[newvel2]]
fitpars=np.hstack((self.fitpars,newpars))
newerrors=[[-99],[-99],[-99],[-99],[-99]]
fiterrors=np.hstack((self.fiterrors,newerrors))
newindex=np.max(self.parinfo[1])+1
newinfo=[[1],[newindex],[newindex],[1],[newindex]]
parinfo=np.hstack((self.parinfo,newinfo))
newcmts=[newrely,newcmt]
linecmts=np.hstack((self.linecmts,newcmts))
### Call initlinepars to set atomic data in cfg.fosc, etc.
junk,junk=joebvpfit.initlinepars(fitpars[3],fitpars[0],initvals=fitpars,initinfo=parinfo)
### Do the update
midx=QModelIndex() # Needed for 'beginInsertRows'
self.beginInsertRows(midx,len(self.fitpars[0]),len(self.fitpars[0]))
self.updatedata(fitpars,fiterrors,parinfo,linecmts)
self.endInsertRows()
### Reset pixels for fit and wavegroups for convolution
cfg.fitidx=joebvpfit.fitpix(wave, fitpars) #Reset pixels for fit
cfg.wavegroups=[]
def addLine(self,wave,newrestwave,newz,newcol,newb,newvel,newvel1,newvel2,newrely=None,newcmt=None):
### Setup new parameters and append them to main arrays of the data model
newpars=[[newrestwave],[newcol],[newb],[newz],[newvel],[newvel1],[newvel2]]
fitpars=np.hstack((self.fitpars,newpars))
newerrors=[[-99],[-99],[-99],[-99],[-99]]
fiterrors=np.hstack((self.fiterrors,newerrors))
newindex=np.max(self.parinfo[1])+1
newinfo=[[1],[newindex],[newindex],[1],[newindex]]
parinfo=np.hstack((self.parinfo,newinfo))
newcmts=[newrely,newcmt]
linecmts=np.hstack((self.linecmts,newcmts))
### Call initlinepars to set atomic data in cfg.fosc, etc.
junk,junk=joebvpfit.initlinepars(fitpars[3],fitpars[0],initvals=fitpars,initinfo=parinfo)
### Do the update
midx=QModelIndex() # Needed for 'beginInsertRows'
self.beginInsertRows(midx,len(self.fitpars[0]),len(self.fitpars[0]))
self.updatedata(fitpars,fiterrors,parinfo,linecmts)
self.endInsertRows()
### Reset pixels for fit and wavegroups for convolution
cfg.fitidx=joebvpfit.fitpix(wave, fitpars) #Reset pixels for fit
cfg.wavegroups=[]