def plotCalibrations(flatsol, wvlCalFile, pixel):
"""
Plot weights of each wavelength bin for every single pixel
Makes a plot of wavelength vs weights, twilight spectrum, and wavecal solution for each pixel
"""
wavesol = wavecal.load_solution(wvlCalFile)
assert os.path.exists(flatsol), "{0} does not exist".format(flatsol)
flat_cal = tables.open_file(flatsol, mode='r')
calsoln = flat_cal.root.flatcal.calsoln.read()
wavelengths = flat_cal.root.flatcal.wavelengthBins.read()
beamImage = flat_cal.root.header.beamMap.read()
matplotlib.rcParams['font.size'] = 10
res_id = beamImage[pixel[0], pixel[1]]
index = np.where(res_id == np.array(calsoln['resid']))
weights = calsoln['weight'][index].flatten()
spectrum = calsoln['spectrum'][index].flatten()
errors = calsoln['err'][index].flatten()
if not calsoln['bad'][index]:
fig = plt.figure(figsize=(20, 10), dpi=100)
ax = fig.add_subplot(1, 3, 1)
ax.scatter(wavelengths,
weights,
label='weights',
alpha=.7,
color='red')
ax.errorbar(wavelengths,
weights,
yerr=errors,
label='weights',
color='green',
fmt='o')
ax.set_title('p %d,%d' % (pixel[0], pixel[1]))
ax.set_ylabel('weight')
ax.set_xlabel(r'$\lambda$ ($\AA$)')
ax.set_ylim(
min(weights) - 2 * np.nanstd(weights),
max(weights) + 2 * np.nanstd(weights))
plt.plot(wavelengths,
np.poly1d(calsoln[index]['coeff'][0])(wavelengths))
# Put a plot of twilight spectrums for this pixel
ax = fig.add_subplot(1, 3, 2)
ax.scatter(wavelengths,
spectrum,
label='spectrum',
alpha=.7,
color='blue')
ax.set_title('p %d,%d' % (pixel[0], pixel[1]))
ax.set_ylim(
min(spectrum) - 2 * np.nanstd(spectrum),
max(spectrum) + 2 * np.nanstd(spectrum))
ax.set_ylabel('spectrum')
ax.set_xlabel(r'$\lambda$ ($\AA$)')
# Plot wavecal solution
ax = fig.add_subplot(1, 3, 3)
my_pixel = [pixel[0], pixel[1]]
wavesol.plot_calibration(pixel=my_pixel, axes=ax)
ax.set_title('p %d,%d' % (pixel[0], pixel[1]))
plt.show()
else:
print('Pixel Failed Wavecal')
def wavecal_apply(o):
if o.wavecal is None:
getLogger(__name__).info('No wavecal to apply for {}'.format(o.h5))
return
try:
of = mkidpipeline.hdf.photontable.Photontable(o.h5, mode='a')
of.applyWaveCal(wavecal.load_solution(o.wavecal.path))
of.file.close()
except Exception as e:
getLogger(__name__).critical(
'Caught exception during run of {}'.format(o.h5), exc_info=True)
def flatcal_apply(o):
of = mkidpipeline.hdf.photontable.Photontable(o.h5, mode='a')
of.applyFlatCal(wavecal.load_solution(o.flatcal))
of.file.close()
time.time())
args = parser.parse_args()
flattner = WhiteCalibrator(args.cfgfile,
cal_file_name='calsol_{}.h5'.format(timestamp))
if not os.path.isfile(flattner.cfg.h5file):
raise RuntimeError('Not up to date')
b2h_config = bin2hdf.Bin2HdfConfig(datadir=flattner.cfg.paths.data,
beamfile=flattner.cfg.beammap.file,
outdir=flattner.paths.out,
starttime=flattner.cfg.start_time,
inttime=flattner.cfg.expTime,
x=flattner.cfg.beammap.ncols,
y=flattner.cfg.beammap.ncols)
bin2hdf.makehdf(b2h_config, maxprocs=1)
getLogger(__name__).info('Made h5 file at {}.h5'.format(
flattner.cfg.start_time))
obsfile = Photontable(flattner.h5file, mode='write')
if not obsfile.wavelength_calibrated:
obsfile.applyWaveCal(wavecal.load_solution(flattner.cfg.wavesol))
getLogger(__name__).info('Applied Wavecal {} to {}.h5'.format(
flattner.cfg.wavesol, flattner.h5file))
if args.h5only:
exit()
flattner.makeCalibration()