def run_fitradecsp(ra, dec, step, nstep, w_center, w_range, ifit1, starobs,
specfiles, wdir):
"""
Setup and call fitradecsp. This creates a file called spec.out
Parameters
----------
starobs : list
List of StarObservation structures one for each fiber
specfiles : list
List of filename of the different spec files
"""
with open(os.path.join(wdir, 'list'), 'w') as f:
for st, sp in zip(starobs, specfiles):
f.write('%s %.7f %.7f %.6f %s\n' %
(sp, st.ra, st.dec, st.structaz, st.expname))
input = '{ra:.7f} {dec:.7f} {step:d} {nstep:d} {wcen:f} {wr:f} {ifit1:d}\n'
run_command(_vdrp_bindir + '/fitradecsp',
input.format(ra=ra,
dec=dec,
step=step,
nstep=nstep,
wcen=w_center,
wr=w_range,
ifit1=ifit1),
wdir=wdir)
def call_fitonevp(wave, outname, wdir):
"""
Call fitonevp
Requires fitghsp.in created by apply_factor_spline
Parameters
----------
wave : float
Wavelength
outname : str
Output filename
wdir : str
Name of the work directory
"""
input = '0 0\n{wave:f}\n/vcps\n'
run_command(_vdrp_bindir + '/fitonevp', input.format(wave=wave), wdir=wdir)
shutil.move(os.path.join(wdir, 'pgplot.ps'),
os.path.join(wdir, outname + 'tot.ps'))
shutil.move(os.path.join(wdir, 'out'),
os.path.join(wdir, outname + 'spec.dat'))
shutil.move(os.path.join(wdir, 'lines.out'),
os.path.join(wdir, outname + 'spec.res'))
splinedata = np.loadtxt(os.path.join(wdir, 'splines.out'))
with open(os.path.join(wdir, outname + 'spece.dat'), 'w') as f:
for d in splinedata:
f.write('%.4f\t%.7f\t%.8e\t%.7f\t%.8e\n' %
(d[0], d[1], d[3], d[2] * 1e17, d[4] * 1e17))
def call_fit2d(ra, dec, outname, wdir):
"""
Call fit2d. Calculate the 2D spatial fit based on fwhm, fiber locations,
and ADC. This convolves the PSF over each fiber, for a given input
position. It fits the ampltiude, minimizing to a chi^2.
Requires input files generated by run_fit2d
Parameters
----------
ra : float
Right Ascension of the star.
dec : float
Declination of the star.
outname : str
Output filename.
wdir : str
Name of the work directory
"""
input = '{ra:f} {dec:f}\n/vcps\n'
run_command(_vdrp_bindir + '/fit2d',
input.format(ra=ra, dec=dec),
wdir=wdir)
shutil.move(os.path.join(wdir, 'pgplot.ps'), os.path.join(wdir, outname))
shutil.move(os.path.join(wdir, 'out'), os.path.join(wdir, 'out2d'))
def call_getnormexp(nightshot, normdir, fwhmdir, wdir):
"""
Call getnormexp. Get fwhm and relative normalizations for the frames.
Parameters
----------
name : str
Observation name
"""
input = '{name:s}\n'
fwhm_file = fwhmdir + '/' + nightshot + '/fwhm.out'
try:
shutil.copy2(normdir + '/' + nightshot + '/norm.dat', wdir)
except FileNotFoundError:
_logger.warn('norm.dat is missing for %s' % nightshot)
try:
shutil.copy2(fwhm_file, wdir)
except FileNotFoundError:
_logger.warn('fwhm.out is missing for %s' % nightshot)
_logger.info('Grabbing FWHM file from' + fwhm_file)
run_command(_vdrp_bindir + '/getnormexp',
input.format(name=nightshot),
wdir=wdir)
def call_mkimage3d(wdir):
"""
Run the mkimage3d command, creating an output file called image3d.fits
"""
if os.path.exists(os.path.join(wdir, './image3d.fits')):
os.remove(os.path.join(wdir, './image3d.fits'))
print(os.path.exists(os.path.join(wdir, './image3d.fits')))
run_command(_vdrp_bindir + '/mkimage3d', wdir=wdir)
def run_combsed(sedlist, sigmacut, rmscut, outfile, wdir, plotfile=None):
"""
Parameters
----------
sedlist : list
List of filenames of SED fits
sigmacut : float
Cut value for sigma
rmscut : float
Cut value for rms
outfile : str
Output filename
plotfile : str (optional)
Optional plot output filename
Returns
-------
n, biwt, error
"""
with open(os.path.join(wdir, 'list'), 'w') as f:
for l in sedlist:
f.write('%s\n' % l)
input = '{:f} {:f}\n'
run_command(vp._vdrp_bindir + '/combsed',
input.format(sigmacut, rmscut), wdir=wdir)
shutil.move(os.path.join(wdir, 'comb.out'), os.path.join(wdir, outfile))
if plotfile is not None:
fdata = np.loadtxt(os.path.join(wdir, 'out'), dtype=float,
usecols=[1, 2, 4, 5])
idata = np.loadtxt(os.path.join(wdir, 'out'), dtype=int,
usecols=[0, 3])
f_in = os.path.join(wdir, 'in')
f_in2 = os.path.join(wdir, 'in2')
with open(f_in, 'w') as f, open(f_in2, 'w') as f2:
for di, df, sf in zip(idata, fdata, sedlist):
if di[1] == 0:
f.write('%s %d %f %f %d %f %f\n'
% (sf, di[0], df[0], df[1],
di[1], df[2], df[3]))
f2.write('%s %d %f %f %d %f %f\n'
% (sf, di[0], df[0], df[1],
di[1], df[2], df[3]))
f2.write('%s\n' % outfile)
run_command(vp._vdrp_bindir + '/plotseda', '/vcps\n', wdir=wdir)
shutil.move(os.path.join(wdir, 'pgplot.ps'),
os.path.join(wdir, plotfile))
def call_imextsp(filename, ifuslot, wl, wlw, tpavg, norm, outfile, wdir):
"""
Equivalent of the rextsp script,
a wrapper around the imextsp fortran routine.
Extracts the spectrum from the multi fits files and writes the tmp*dat.
This also calculates the appropriate photon errors, using counting and
sky residual errors. This applies the throughput and fiber to fiber.
Parameters
----------
filename : str
The filename to process
ifuslot : str
The ifuslot name
wl : float
The central extraction wavelength
wlw : float
The width of the extraction window around wl
tpavg : float
Throughput average for the spectrum
norm : str
File with fiber to fiber normaliztion for the spectrum
outfile : str
Name of the output filename
wdir : str
Name of the work directory
"""
input = '"{filename:s}"\n{ifuslot} {wl} {wlw}\n"{tpavg}"\n"{norm}"\n'
try:
os.remove(os.path.join(wdir, 'out.sp'))
except OSError:
pass
try:
os.remove(os.path.join(wdir, outfile))
except OSError:
pass
s = input.format(filename=os.path.join(wdir, filename),
ifuslot=ifuslot,
wl=wl,
wlw=wlw,
tpavg=tpavg,
norm=norm)
run_command(_vdrp_bindir + '/imextsp', s, wdir=wdir)
shutil.move(os.path.join(wdir, 'out.sp'), os.path.join(wdir, 'specin'))
run_command(_vdrp_bindir + '/specclean', wdir=wdir)
shutil.move(os.path.join(wdir, 'out'), os.path.join(wdir, outfile))
def call_fitem(wl, wdir):
"""
Call fitem requires input files created by run_fitem
The line fitter. It fits a gauss-hermite. input is fitghsp.in.
Parameters
----------
wl : float
Wavelength
"""
input = '{wl:f}\n/vcps\n'
run_command(_vdrp_bindir + '/fitem', input.format(wl=wl), wdir=wdir)
def call_sumspec(starname, wdir):
"""
Call sumpspec. Sums a set of spectra, and then bins to 100AA bins.
Used for SED fitting.
Parameters
----------
starname : str
Star name used to create the outputn filename (adds specf.dat)
"""
if os.path.exists(os.path.join(wdir, 'sumspec.out')):
os.remove(os.path.join(wdir, 'sumspec.out'))
with open(os.path.join(wdir, 'list'), 'w') as f:
f.write(starname + 'specf.dat')
run_command(_vdrp_bindir + '/sumspec', wdir=wdir)
def call_sumsplines(nspec, wdir):
"""
Call sumsplines, calculate a straight sum of the spectra in a list,
including errors. Expects the spectra to be called tmp101 to
tmp100+nspec.
Creates a file called splines.out
Parameters
----------
nspec : int
Number of spectra to read.
wdir : str
Name of the work directory
"""
with open(os.path.join(wdir, 'list'), 'w') as f:
for i in range(0, nspec):
f.write('tmp{c}.dat\n'.format(c=i + 101))
run_command(_vdrp_bindir + '/sumsplines', wdir=wdir)
def run_biwt(data, outfile, wdir):
"""
Calculate biweight of the supplied data.
Parameters
----------
data : list
List of the data to be run through biwt.
Returns
-------
n, biwt, error
"""
with open(os.path.join(wdir, 'tp.dat'), 'w') as f:
for d in data:
f.write('%f\n' % d)
run_command(vp._vdrp_bindir + '/biwt', 'tp.dat\n1\n', wdir=wdir)
os.remove(os.path.join(wdir, 'tp.dat'))
shutil.move(os.path.join(wdir, 'biwt.out'), os.path.join(wdir, outfile))
def run_getsdss(filename, sdss_file, wdir):
"""
Run getsdss on filename. Equivalent to rsdss file.
Parameters
----------
filename : str
Filename with spectral data
sdss_file : str
Full path and filename to the sdss g-band filter curve.
Returns
-------
The flux in the g-Band.
"""
shutil.copy2(os.path.join(wdir, sdss_file),
os.path.join(wdir, 'sdssg.dat'))
shutil.copy2(os.path.join(wdir, filename), os.path.join(wdir, 's1'))
run_command(vp._vdrp_bindir + '/getsdssg', wdir=wdir)
return float(np.loadtxt(os.path.join(wdir, 'out')))
def run_sumlineserr(specfiles, wdir):
"""
Prepare input and run sumlineserr. It sums a set of spectra, and then bins
to 100AA bins. Used for SED fitting.
Parameters
----------
specfiles : list
List of spectrum filenames.
"""
indata = np.loadtxt(os.path.join(wdir, 'out2d'),
dtype='U50',
ndmin=2,
usecols=[8, 9, 10, 11, 12, 13, 14])
with open(os.path.join(wdir, 'list2'), 'w') as f:
for spf, d in zip(specfiles, indata):
f.write('%s %s %s %s %s %s %s %s\n' %
(spf, d[0], d[1], d[2], d[3], d[4], d[5], d[6]))
run_command(vp._vdrp_bindir + '/sumlineserr', wdir=wdir)
def call_mkimage(ra, dec, starobs, wdir):
"""
Call mkimage, equivalent of rmkim
Reads the out2d file and creates three images of the
emission line data, best fit model and residuals, called
im[123].fits.
Parameters
----------
ra : float
Right Ascension of the star.
dec : float
Declination of the star.
starobs : list
List of StarObservation objects for the star
"""
gausa = np.loadtxt(os.path.join(wdir, 'out2d'), ndmin=1, usecols=[9])
# First write the first j4 input file
with open(os.path.join(wdir, 'j4'), 'w') as f:
for obs in starobs:
f.write('%f %f %f\n' %
(3600. * (obs.ra - ra) * np.cos(dec / 57.3), 3600 *
(obs.dec - dec), obs.avg))
run_command(_vdrp_bindir + '/mkimage', wdir=wdir)
shutil.move(os.path.join(wdir, 'image.fits'),
os.path.join(wdir, 'im1.fits'))
with open(os.path.join(wdir, 'j4'), 'w') as f:
for i in range(0, len(starobs)):
f.write('%f %f %f\n' %
(3600. * (starobs[i].ra - ra) * np.cos(dec / 57.3), 3600 *
(starobs[i].dec - dec), starobs[i].avg - gausa[i]))
run_command(_vdrp_bindir + '/mkimage', wdir=wdir)
shutil.move(os.path.join(wdir, 'image.fits'),
os.path.join(wdir, 'im2.fits'))
with open(os.path.join(wdir, 'j4'), 'w') as f:
for i in range(0, len(starobs)):
f.write('%f %f %f\n' %
(3600. * (starobs[i].ra - ra) * np.cos(dec / 57.3), 3600 *
(starobs[i].dec - dec), gausa[i]))
run_command(_vdrp_bindir + '/mkimage', wdir=wdir)
shutil.move(os.path.join(wdir, 'image.fits'),
os.path.join(wdir, 'im3.fits'))