def writelinepars(fitpars,
fiterrors,
parinfo,
specfile,
outfilename,
linecmts=None):
'''
Write fit parameters out to file.
Parameters
----------
fitpars : list of lists
Parameters for fit ready for fitter!
fiterrors : array of numpy vectors
Error array for the fitting initialized to '0' for each param
parinfo : array of arrays
Flags to be used in fit
specfile : str
Name of the input file containing the spectrum
outfilename : str
Parameter output filename
linecmts : list of lists, optional
Reliability flags and comments, e.g., from igmguesses
'''
import os
### Set outputs and open files
bigfiletowrite = cfg.largeVPparfile
filetowrite = outfilename
if os.path.isfile(filetowrite):
VPparfile = open(filetowrite, 'wb')
bigparfile = open(bigfiletowrite, 'ab') # Append to the running list
else:
VPparfile = open(filetowrite, 'wb')
bigparfile = open(bigfiletowrite, 'wb')
### Prep header of line parameter file
if linecmts is not None:
header = b'specfile|restwave|zsys|col|sigcol|bval|sigbval|vel|sigvel|nflag|bflag|vflag|vlim1|vlim2|wobs1|wobs2|pix1|pix2|z_comp|trans|rely|comment \n'
else:
header = b'specfile|restwave|zsys|col|sigcol|bval|sigbval|vel|sigvel|nflag|bflag|vflag|vlim1|vlim2|wobs1|wobs2|pix1|pix2|z_comp|trans \n'
VPparfile.write(header)
bigparfile.write(header)
### Grab parameters/info for each line
for i in range(len(fitpars[0])):
zline = fitpars[3][i]
vlim1 = fitpars[5][i]
vlim2 = fitpars[6][i]
restwave = fitpars[0][i]
wobs1 = restwave * (1 + zline + vlim1 / 299792.458)
wobs2 = restwave * (1 + zline + vlim2 / 299792.458)
pix1 = jbg.closest(cfg.wave, wobs1)
pix2 = jbg.closest(cfg.wave, wobs2)
trans = atomicdata.lam2ion(fitpars[0][i])
z_comp = ltu.z_from_dv(fitpars[4][i] * u.km / u.s, zline)
if linecmts is not None:
towrite = jbg.pipedelimrow([
specfile, restwave,
round(zline, 5),
round(fitpars[1][i], 3),
round(fiterrors[1][i], 3),
round(fitpars[2][i], 3),
round(fiterrors[2][i], 3),
round(fitpars[4][i], 3),
round(fiterrors[4][i], 3), parinfo[1][i], parinfo[2][i],
parinfo[4][i], vlim1, vlim2, wobs1, wobs2, pix1, pix2,
round(z_comp, 5), trans, linecmts[0][i], linecmts[1][i]
])
else:
towrite = jbg.pipedelimrow([
specfile, restwave,
round(zline, 5),
round(fitpars[1][i], 3),
round(fiterrors[1][i], 3),
round(fitpars[2][i], 3),
round(fiterrors[2][i], 3),
round(fitpars[4][i], 3),
round(fiterrors[4][i], 3), parinfo[1][i], parinfo[2][i],
parinfo[4][i], vlim1, vlim2, wobs1, wobs2, pix1, pix2,
round(z_comp, 5), trans
])
VPparfile.write(towrite.encode())
bigparfile.write(towrite.encode())
VPparfile.close()
bigparfile.close()
print('Line parameters written to:')
print(filetowrite)
def writelinepars(fitpars,fiterrors,parinfo, specfile, outfilename, linecmts=None):
'''
Write fit parameters out to file.
Parameters
----------
fitpars : list of lists
Parameters for fit ready for fitter!
fiterrors : array of numpy vectors
Error array for the fitting initialized to '0' for each param
parinfo : array of arrays
Flags to be used in fit
specfile : str
Name of the input file containing the spectrum
outfilename : str
Parameter output filename
linecmts : list of lists, optional
Reliability flags and comments, e.g., from igmguesses
'''
import os
### Set outputs and open files
bigfiletowrite = cfg.largeVPparfile
filetowrite = outfilename
if os.path.isfile(filetowrite):
VPparfile = open(filetowrite, 'wb')
bigparfile = open(bigfiletowrite, 'ab') # Append to the running list
else:
VPparfile = open(filetowrite, 'wb')
bigparfile = open(bigfiletowrite, 'wb')
### Prep header of line parameter file
if linecmts is not None:
header = 'specfile|restwave|zsys|col|sigcol|bval|sigbval|vel|sigvel|nflag|bflag|vflag|vlim1|vlim2|wobs1|wobs2|pix1|pix2|z_comp|trans|rely|comment \n'
else:
header = 'specfile|restwave|zsys|col|sigcol|bval|sigbval|vel|sigvel|nflag|bflag|vflag|vlim1|vlim2|wobs1|wobs2|pix1|pix2|z_comp|trans \n'
VPparfile.write(header)
bigparfile.write(header)
### Grab parameters/info for each line
for i in range(len(fitpars[0])):
zline = fitpars[3][i]
vlim1 = fitpars[5][i]
vlim2 = fitpars[6][i]
restwave = fitpars[0][i]
wobs1 = restwave * (1 + zline + vlim1 / 299792.458)
wobs2 = restwave * (1 + zline + vlim2 / 299792.458)
pix1 = jbg.closest(cfg.wave, wobs1)
pix2 = jbg.closest(cfg.wave, wobs2)
trans = atomicdata.lam2ion(fitpars[0][i])
z_comp = ltu.z_from_dv(fitpars[4][i]*u.km/u.s, zline)
if linecmts is not None:
towrite = jbg.pipedelimrow(
[specfile, restwave, round(zline, 5), round(fitpars[1][i], 3), round(fiterrors[1][i], 3),
round(fitpars[2][i], 3), round(fiterrors[2][i], 3), round(fitpars[4][i], 3), round(fiterrors[4][i], 3),
parinfo[1][i], parinfo[2][i], parinfo[4][i], vlim1, vlim2, wobs1, wobs2, pix1, pix2,round(z_comp, 5), trans,
linecmts[0][i],linecmts[1][i]])
else:
towrite = jbg.pipedelimrow(
[specfile, restwave, round(zline, 5), round(fitpars[1][i], 3), round(fiterrors[1][i], 3),
round(fitpars[2][i], 3), round(fiterrors[2][i], 3), round(fitpars[4][i], 3), round(fiterrors[4][i], 3),
parinfo[1][i], parinfo[2][i], parinfo[4][i], vlim1, vlim2, wobs1, wobs2, pix1, pix2, round(z_comp, 5),trans])
VPparfile.write(towrite)
bigparfile.write(towrite)
VPparfile.close()
bigparfile.close()
print('Line parameters written to:')
print(filetowrite)