def initialize_spectrum(self):
# GET WAVELENGTHS INTO RIGHT UNITS
if self.factor:
log.info("Multiplying input wavelengths by factor %s.", self.factor)
wavelengths = self.source_spectrum[0] * self.factor
# REDSHIFT SPECTRA
wavelengths = physics.redshift(self.source_spectrum[0]*1.e-9, self.rv) * 1.e9
flux = self.source_spectrum[1]
# ADD TELLURIC LINES
if self.telluric and self.FITS_SOURCE == "STAR":
flux = wf.convolve_telluric_lines(self.telluric, wavelengths, flux)
# CONVERT FLUX TO NUMBER DENSITY
if self.FITS_SOURCE == "STAR":
pdf = physics.energy2counts(wavelengths, flux)
else:
pdf = flux
# TRUNCATE TO SPECTROGRAPH LIMIT WITH A SMALL BUFFER AS CUSHION
self.source_spectrum = wf.truncate_spectrum(self, wavelengths, pdf)
def main():
# COMMAND LINE ARGUMENTS
args = parse_command_line()
print "\nCARMENES Spectrum Forward Simulator (CSFS v%s)" % __version__
# INITIALIZE SPECTRAL ARM
arm = SpectralArm(args)
# SIMULATION START TIMES
t1 = time.time()
sim_start = time.strftime("%a, %d, %b %Y %H:%M:%S + 0000", time.gmtime())
if arm.fib_simmode[0] not in arm.SIM_LIST or arm.fib_simmode[1] not in arm.SIM_LIST:
raise ValueError
for i in xrange(len(arm.fib_simmode)):
#fiber = i
simmode = arm.fib_simmode[i]
#simmodetype = arm.simmodetypes[i] # seems unnecessary
if simmode is '0':
arm.slittyp = "0D point-source"
arm.add_image(np.zeros(arm.CCD_DIMS, dtype=np.uint16))
elif simmode is 'B':
arm.slittyp = "0D point-source"
arm.fiber_description = 'bias frame'
arm.fib_obstype = ['BIAS', 'BIAS']
arm.fib_src = ['BIAS', 'BIAS']
arm.add_image(np.zeros(arm.CCD_DIMS, dtype=np.uint16))
else:
print "Initializing Fiber %s" % arm.fib_char[i]
wavemap = False
if simmode is 'C':
arm.fiber_description = 'Laser Comb Spectrum'
fn = "MODELS/COMB/comb.npy"
wavelengths, intensities = np.load(fn)
inds = (wavelengths >= arm.wmin) & (wavelengths <= arm.wmax)
wavelengths = wavelengths[inds]
intensities = intensities[inds]
if arm.SAMPLING == "grid":
wf.wavegrid(
arm,
wavelengths=wavelengths,
intensities=intensities,
assign=True,
telluric=False)
elif arm.SAMPLING == "mc":
arm.wavelengths = wavelengths
arm.intensities = intensities
if arm.fib_rv[i]:
arm.wavelengths = redshift(arm.wavelengths, arm.fib_rv[i])
arm.infiles[i] = fn
arm.fib_obstype[i] = 'WAVE'
arm.fib_src[i] = 'COMB'
elif simmode is 'F':
arm.fiber_description = 'flatfield spectrum simulation'
arm.wavelengths = wf.calculate_wavelengths(arm, mode='CCD', nwaves=arm.nw)
arm.intensities = np.ones(arm.wavelengths.size)
arm.fib_obstype[i] = 'FLAT'
arm.fib_src[i] = 'HAL'
elif simmode is 'L':
if len(arm.infiles[i]) is not 1:
raise ValueError
print 'loading %s' % (arm.infiles[i][0])
arm.fiber_description = 'emission line list spectrum simulation'
wavelengths, intensities = np.loadtxt(arm.infiles[i][0], unpack=True)
#wavelengths, intensities = np.load(arm.infiles[i][0])
wavelengths *= 1.0e-7 # convert Ang to mm @MZ
inds = np.where((wavelengths >= arm.wmin) & (wavelengths <= arm.wmax))
arm.wavelengths = wavelengths[inds]
arm.intensities = intensities[inds]
if arm.fib_rv[i]:
arm.wavelengths = redshift(arm.wavelengths, arm.fib_rv[i])
elif simmode is 'P':
arm.fiber_description = """PHOENIX model spectrum simulation: T_eff=3000 K, [Fe/H]=0.0, log(g)=5.0"""
wavelengths = np.load('phx_wavelengths.npy')
intensities = np.load('phx_intensities.npy')
inds = (wavelengths >= arm.wmin) & (wavelengths <= arm.wmax)
wavelengths = wavelengths[inds]
intensities = intensities[inds]
if arm.SAMPLING == 'grid':
wf.wavegrid(
arm,
wavelengths=wavelengths,
intensities=intensities,
assign=True,
telluric=arm.tell)
elif arm.SAMPLING == 'mc':
arm.wavelengths = wavelengths
arm.intensities = intensities
if arm.fib_rv[i]:
arm.wavelengths = redshift(arm.wavelengths, arm.fib_rv[i])
if arm.tell:
arm.intensities = wf.convolve_telluric_lines(
arm,
arm.wavelengths,
arm.intensities)
arm.infiles[i] = ['phx_wavelengths.npy', 'phx_intensities.npy']
arm.catg = 'SCI'
arm.fib_obstype[i] = 'STAR'
arm.fib_src[i] = 'OBJ'
arm.sciobject = 'PHOE_lte03000-5.00-0.0'
elif simmode is 'S':
if len(arm.infiles[i]) == 1:
try:
wavelengths, intensities = pyfits.getdata(arm.infiles[i][0])
except IOError:
wavelengths, intensities = np.loadtxt(arm.infiles[i][0], unpack=True)
elif len(arm.infiles[i]) == 2:
try:
wavelengths = pyfits.getdata(arm.infiles[i][0])
intensities = pyfits.getdata(arm.infiles[i][1])
except IOError:
wavelengths = np.loadtxt(arm.infiles[i][0])
intensities = np.loadtxt(arm.infiles[i][1])
elif len(arm.infiles[i]) not in [1, 2]:
raise AttributeError("Please specify an input wavelength file and input flux/counts file.")
arm.fiber_description = 'object spectrum simulation'
wavelengths *= 1.0e-7 # convert Ang to mm
inds = (wavelengths >= arm.wmin) & (wavelengths <= arm.wmax)
wavelengths = wavelengths[inds]
intensities = intensities[inds]
# wavelength sampling, add telluric lines
if arm.SAMPLING == 'grid':
wf.wavegrid(
arm,
wavelengths=wavelengths,
intensities=intensities,
assign=True,
telluric=arm.tell)
elif arm.SAMPLING == 'mc':
arm.wavelengths = wavelengths
arm.intensities = intensities
if arm.fib_rv[i]:
arm.wavelengths = redshift(arm.wavelengths, arm.fib_rv[i])
if arm.tell:
arm.intensities = wf.convolve_telluric_lines(
arm,
arm.wavelengths,
arm.intensities)
arm.fib_obstype[i] = 'STAR'
arm.fib_src[i] = 'OBJ'
elif simmode is 'T':
from importtharlines import import_thar_lines
arm.fiber_description = 'Thorium Argon line list'
wavelengths, intensities = import_thar_lines()
inds = (wavelengths >= arm.wmin) & (wavelengths <= arm.wmax)
arm.wavelengths = wavelengths[inds]
arm.intensities = intensities[inds]
if arm.fib_rv[i]:
arm.wavelengths = redshift(arm.wavelengths, arm.fib_rv[i])
arm.infiles[i] = "Lovis,2007; Kerber,2008"
arm.fib_obstype[i] = 'WAVE'
arm.fib_src[i] = 'ThAr'
elif simmode is 'U':
arm.fiber_description = 'Uranium Neon calibration lamp'
fn = "MODELS/UNE/une.npy"
arm.infiles[i] = fn
wavelengths, intensities = np.load(fn)
inds = (wavelengths >= arm.wmin) & (wavelengths <= arm.wmax)
wavelengths = wavelengths[inds]
intensities = intensities[inds]
if arm.fib_rv[i]:
wavelengths = redshift(wavelengths, arm.fib_rv[i])
if arm.SAMPLING == "grid":
wf.wavegrid(
arm,
wavelengths=wavelengths,
intensities=intensities,
assign=True,
telluric=False)
elif arm.SAMPLING == "mc":
arm.wavelengths = wavelengths
arm.intensities = intensities
arm.fib_obstype[i] = 'WAVE'
arm.fib_src[i] = 'UNe'
elif simmode is 'W':
arm.fiber_description = 'wavelength mapping'
arm.wavelengths = wf.calculate_wavelengths(arm, mode='CCD', nwaves=arm.nw)
arm.intensities = arm.wavelengths
if arm.fib_rv[i]:
arm.wavelengths = redshift(arm.wavelengths, arm.fib_rv[i])
arm.wavemap = True
arm.fib_obstype[i] = 'WAVE'
arm.fib_src[i] = 'WAVE'
elif simmode is 'X':
arm.fiber_description = 'Fabry-Perot spectrum simulation'
# arm.wavelengths = np.load('phx_wavelengths.npy')
# print arm.wavelengths
arm.wavelengths = wf.calculate_wavelengths(arm, mode='CCD', nwaves=arm.nw)
arm.intensities = fabry_perot(arm.wavelengths)
if arm.fib_rv[i]:
arm.wavelengths = redshift(arm.wavelengths, arm.fib_rv[i])
arm.fib_obstype[i] = 'WAVE'
arm.fib_src[i] = 'FP'
## APPLY RV SHIFT TO WAVELENGTHS
#if arm.fib_rv[i]:
#arm.wavelengths = redshift(arm.wavelengths, arm.fib_rv[i]) # @MZ arm.fib_rv[fiber] not fiber
# RUN SIMULATION
sim_general(arm, i)
print "Fiber %s simulation finished\n" % arm.fib_char[i]
# PROCESS ARRAYS INTO A SINGLE IMAGE / ADD NOISE
arm.add_full_sim_time(sim_start) # start time
arm.add_full_sim_time(time.time() - t1) # finish time
arm.image = arm.images[0] + arm.images[1] # final image array
# ADD NOISE
# if arm.noise:
add_noise(arm)
# prevents value overflow wraparound
arm.image[arm.image > np.iinfo(np.uint16).max] = np.iinfo(np.uint16).max
arm.image = np.array(arm.image, dtype=np.uint16) # noise converts array to int64 at some step - let's bring it back to uint16
print "Converting image array to %s" % arm.image.dtype
# WRITE FITS FILE
write_to_fits(arm)
# WAVELENGTH SOLUTIONS; CREATE WAVETRACE REGION FILES
for i in xrange(len(arm.wt)):
if arm.wt[i]:
wlt.wavelength_trace(arm, i)
# SPAWN FITS OUTPUT IMAGE IN SAO-DS9
if args.ds9 or args.ds9_mosaic:
if args.ds9_mosaic:
ds9_param = '-mosaicimage iraf'
else:
ds9_param = '-mecube'
if arm.WT_FLAG:
if args.no_compress:
call = 'ds9 %s.fits %s -region %s.reg' % (ds9_param, rm.outfile, arm.outfile)
else:
call = 'ds9 %s.fits.gz %s -region %s.reg' % (ds9_param, arm.outfile, arm.outfile)
else:
if args.no_compress:
call = 'ds9 %s %s.fits' % (ds9_param, arm.outfile)
else:
call = 'ds9 %s %s.fits.gz' % (ds9_param, arm.outfile)
print "Executing '%s'" % call
try:
subprocess.check_call(call.split())
except OSError, e:
print e
print "Shell call failed. You can just run the following line in the shell:"
print call
