def initialpars(self,parfilename):
### Deal with initial parameters from line input file
self.fitpars,self.fiterrors,self.parinfo,self.linecmts = joebvpfit.readpars(parfilename)
cfg.fitidx=joebvpfit.fitpix(self.wave, self.fitpars) #Set pixels for fit
cfg.wavegroups=[]
self.datamodel = LineParTableModel(self.fitpars,self.fiterrors,self.parinfo,linecmts=self.linecmts)
self.tableView.setModel(self.datamodel)
self.datamodel.updatedata(self.fitpars,self.fitpars,self.parinfo,self.linecmts)
def initialpars(self,parfilename):
### Deal with initial parameters from line input file
self.fitpars,self.fiterrors,self.parinfo,self.linecmts = joebvpfit.readpars(parfilename)
cfg.fitidx=joebvpfit.fitpix(self.wave, self.fitpars) #Set pixels for fit
cfg.wavegroups=[]
self.datamodel = LineParTableModel(self.fitpars,self.fiterrors,self.parinfo,linecmts=self.linecmts)
self.tableView.setModel(self.datamodel)
self.datamodel.updatedata(self.fitpars,self.fitpars,self.parinfo,self.linecmts)
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 compose_model(spec,filelist,outfile):
'''
Generates full-model spectrum (XSpectrum1D) from a set of joebvp output files and writes out a file with the spectrum.
Parameters
----------
spec : string or XSpectrum1D
The spectrum to be fitted with the input lines
filelist : list of strings or str
This should be a list containing the names of VP input files or a string referring to a file simply
listing the input files.
See joebvpfit.readpars for details of file format
outfile : str
Name of model spectrum output file
'''
from joebvp import joebvpfit
### Deal with alternate input types
if isinstance(spec,str):
specobj = readspec(spec)
else:
specobj = spec
### Load essentials from spectrum
wave = specobj.wavelength.value
normsig=specobj.sig.value/specobj.co.value
cfg.wave = wave
### Concatenate all the parameter tables
concatenate_line_tables(filelist,outtablefile='compiledVPinputs.dat')
### Make the model!
fitpars, fiterrors, parinfo, linecmts = joebvpfit.readpars('compiledVPinputs.dat') # read this back in to load params
cfg.fitidx = joebvpfit.fitpix(wave, fitpars) # set the pixels in the line regions
model = joebvpfit.voigtfunc(wave,fitpars) # generate the Voigt profiles of all lines
### Instantiate XSpectrum1D object and write it out
outspec=XSpectrum1D.from_tuple((wave,model,normsig))
outspec.write_to_fits(outfile)
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=[]
