def crop_array(opt):
fp_whole = opt.fp[1::3,1::3]
fp_signal_whole = opt.fp_signal[1::3,1::3]
#==============================================================================
#1) Calculate the maximum width (y crop) in pixels and apply crop
#==============================================================================
aa = fp_signal_whole.sum(axis=1).value # sum of profile in x axis
jexosim_plot('y crop selection', opt.diagnostics, ydata=aa, marker='ro-', grid=True)
bb = np.mean(np.vstack((aa[:5],aa[-5:]))) # average of outer 5 pixels
if bb == 0:
aa_ = aa[np.argwhere(aa>0).T[0]]
bb = aa_.min()/np.e
idx_max = np.argmax(aa)
print (bb)
#find where signal falls below b*npe either side
for i in range(int(len(aa)/2)):
s = aa[idx_max-i]
if s < bb*np.e:
# idx0=1+ idx_max-i #+1 so that it starts within the region of > b8npe
idx0=idx_max-i #+1 so that it starts within the region of > b8npe
break
for i in range(int(len(aa)/2)):
s = aa[idx_max+i]
if s < bb*np.e:
# idx1=idx_max+i
idx1=1+idx_max+i
break
#idx0, idx1 #indexs that bound this region
idx1 = int(idx1) ; idx0 = int(idx0)
print (idx0, idx1)
w_crop = idx1- (idx0)
jexosim_msg ("width of crop chosen %s"%(w_crop ) , opt.diagnostics)
jexosim_plot('y crop selection', opt.diagnostics, xdata=np.arange(idx0, idx1,1), ydata=aa[idx0:idx1],
marker='bo-', grid=True)
#==============================================================================
#2) Calculate the maximum length (x crop) in pixels and apply crop
#==============================================================================
wav_sol= opt.x_wav_osr[1::3].value # wav sol in whole pixels
idx = np.argwhere((wav_sol>=opt.channel.pipeline_params.start_wav.val-0.5)& (wav_sol<=opt.channel.pipeline_params.end_wav.val+0.5))
idxA = idx[0].item()
idxB = idx[-1].item()
return idx0, idx1, idxA, idxB
def get_psf(opt):
if os.path.exists('%s/../archive/PSF/%s_psf_stack.npy' %
(opt.__path__, opt.channel.instrument.val)):
psf_stack = np.load('%s/../archive/PSF/%s_psf_stack.npy' %
(opt.__path__, opt.channel.instrument.val))
psf_stack_wl = 1e6 * np.load(
'%s/../archive/PSF/%s_psf_stack_wl.npy' %
(opt.__path__, opt.channel.instrument.val))
psf = interpolate.interp1d(psf_stack_wl,
psf_stack,
axis=2,
bounds_error=False,
fill_value=0.0,
kind='linear')(opt.x_wav_osr.value)
psf = np.rot90(psf)
psf_type = 'wfe'
else: # uses airy if no psf database however this is to be avoided, as pipeline assumes the wfe database psfs.
jexosim_msg('PSF files could not be found. Check psf files location.')
sys.exit()
# psf = jexosim_lib.Psf(opt.x_wav_osr.value, opt.channel.camera.wfno_x.val, opt.channel.camera.wfno_y.val, opt.fp_delta.value, shape='airy')
# psf[np.isnan(psf)] =0
# psf_type = 'airy'
jexosim_msg("PSF shape %s, %s" % (psf.shape[0], psf.shape[1]),
opt.diagnostics)
jexosim_plot('psf check',
opt.diagnostics,
image=True,
image_data=psf[..., int(psf.shape[2] / 2)])
sum1 = []
for i in range(psf.shape[2]):
sum1.append(psf[..., i].sum())
if psf[..., i].sum() != 0:
# psf[...,i] =psf[...,i]/psf[...,i].sum()
if np.round(psf[..., i].sum(), 3) != 1.0:
jexosim_msg(
'error... check PSF normalisation %s %s' %
(psf[..., i].sum(), opt.x_wav_osr[i]), 1)
sys.exit()
jexosim_plot('test7 - psf sum vs subpixel position (should be 1)',
opt.diagnostics,
xdata=opt.x_pix_osr,
ydata=sum1,
marker='bo')
return psf, psf_type
def psf_fp_check(opt):
# Populate focal plane with monochromatic PSFs
j0 = np.arange(opt.fp.shape[1]) - int(opt.psf.shape[1] / 2)
j1 = j0 + opt.psf.shape[1]
idx = np.where((j0 >= 0) & (j1 < opt.fp.shape[1]))[0]
i0 = np.array([opt.fp.shape[0] / 2 - opt.psf.shape[0] / 2 + opt.offs] *
len(j1)).astype(np.int)
i0 += 1
# variable y position (applies only to NIRISS)
if opt.channel.name == 'NIRISS_SOSS_GR700XD':
i0 = (opt.y_pos_osr).astype(np.int)
i1 = i0 + opt.psf.shape[0]
test_fp = np.zeros_like(opt.fp)
# SPECIAL CASE: fix if airy psfs used
if opt.channel.name == 'NIRISS_SOSS_GR700XD':
# fix if airy psfs used
if opt.psf_type == 'airy':
original_fp = copy.deepcopy(test_fp)
if i1.max(
) > test_fp.shape[0]: #psfs will fall outside fp area due to curve
original_fp = copy.deepcopy(test_fp)
test_fp = np.zeros(
(i1.max(), test_fp.shape[1])) # temp increase in fp size
for k in idx: # used for getting sat time, and sizing
test_fp[i0[k]:i1[k], j0[k]:j1[k]] += opt.psf[..., k]
# SPECIAL CASE: fix if airy psfs used
if opt.channel.name == 'NIRISS_SOSS_GR700XD':
if opt.psf_type == 'airy': # now return fp to original size
if i1.max() > original_fp.shape[0]:
diff = i1.max() - original_fp.shape[0]
test_fp = test_fp[diff:]
jexosim_plot('psf fp check', 1, ydata=test_fp.sum(axis=0))
return test_fp
def run(opt):
jexosim_msg('channel check0 : %s' % (opt.star.sed.sed.max()),
opt.diagnostics)
tr_ = np.array([1.] * len(opt.x_wav_osr)) * u.dimensionless_unscaled
opt.channel.transmissions.optical_surface = opt.channel.transmissions.optical_surface if isinstance(opt.channel.transmissions.optical_surface, list) else \
[opt.channel.transmissions.optical_surface]
for op in opt.channel.transmissions.optical_surface:
dtmp = np.loadtxt(op.transmission.replace('__path__', opt.__path__),
delimiter=',')
tr = Sed(dtmp[:, 0] * u.um, dtmp[:, 1] * u.dimensionless_unscaled)
tr.rebin(opt.x_wav_osr)
tr_ *= tr.sed
opt.channel_transmission = Sed(opt.x_wav_osr, tr_)
opt.total_transmission = Sed(
opt.channel_transmission.wl,
opt.telescope_transmission.sed * opt.channel_transmission.sed)
jexosim_lib.sed_propagation(opt.star.sed, opt.channel_transmission)
jexosim_lib.sed_propagation(opt.star.sed_it, opt.channel_transmission)
# apply QE and convert to electrons
dtmp = np.loadtxt(opt.channel.detector_array.qe().replace(
'__path__', opt.__path__),
delimiter=',')
qe = Sed(dtmp[:, 0] * u.um, dtmp[:, 1] * u.dimensionless_unscaled)
qe.rebin(opt.x_wav_osr)
PCE = Sed(opt.total_transmission.wl, opt.total_transmission.sed * qe.sed)
TotTrans = Sed(opt.total_transmission.wl, opt.total_transmission.sed)
opt.PCE = PCE.sed
opt.TotTrans = TotTrans.sed
jexosim_plot('PCE', opt.diagnostics, xdata=PCE.wl, ydata=PCE.sed)
jexosim_plot('Total transmission not including QE',
opt.diagnostics,
xdata=TotTrans.wl,
ydata=TotTrans.sed)
opt.qe_spec = qe
opt.Re = qe.sed * (qe.wl).to(u.m) / (const.c.value * const.h.value * u.m)
opt.star.sed.sed *= opt.Re * u.electron / u.W / u.s
opt.star.sed_it.sed *= opt.Re * u.electron / u.W / u.s
jexosim_plot('channel star sed check',
opt.diagnostics,
xdata=opt.x_wav_osr,
ydata=opt.star.sed.sed,
marker='-')
jexosim_msg('check 1.3 - Star sed max: %s' % (opt.star.sed.sed.max()),
opt.diagnostics)
jexosim_plot('Wavelength solution check -oversampled pixels',
opt.diagnostics,
xdata=opt.x_pix_osr,
ydata=opt.x_wav_osr,
marker='o-')
jexosim_plot('Wavelength solution check -normal pixels',
opt.diagnostics,
xdata=opt.x_pix_osr[1::3],
ydata=opt.x_wav_osr[1::3],
marker='o-')
opt.d_x_wav_osr = np.zeros_like(opt.x_wav_osr)
idx = np.where(opt.x_wav_osr > 0.0)
opt.d_x_wav_osr[idx] = np.gradient(opt.x_wav_osr[idx])
if np.any(opt.d_x_wav_osr < 0): opt.d_x_wav_osr *= -1.0
jexosim_plot('D x wav osr check',
opt.diagnostics,
xdata=opt.x_pix_osr,
ydata=opt.d_x_wav_osr,
marker='o')
jexosim_plot('D x wav osr check 2',
opt.diagnostics,
xdata=opt.x_wav_osr,
ydata=opt.d_x_wav_osr,
marker='o')
jexosim_msg("check 1.4: %s" % (opt.star.sed.sed.max()), opt.diagnostics)
opt.planet_sed_original = copy.deepcopy(opt.planet.sed.sed)
# opt.planet.sed.sed *= opt.star.sed.sed
# opt.planet.sed.sed *= opt.d_x_wav_osr
jexosim_msg("check 1.5: %s" % (opt.star.sed.sed.max()), opt.diagnostics)
opt.star.sed.sed *= opt.d_x_wav_osr
opt.star.sed_it.sed *= opt.d_x_wav_osr
jexosim_msg("check 2: %s" % (opt.star.sed.sed.max()), opt.diagnostics)
jexosim_plot('star sed check 2.0',
opt.diagnostics,
xdata=opt.x_wav_osr,
ydata=opt.star.sed.sed,
marker='-')
return opt
def __init__(self, opt):
output_directory = opt.common.output_directory.val
filename = ""
self.results_dict = {}
self.results_dict['simulation_mode'] = opt.simulation.sim_mode.val
self.results_dict[
'simulation_realisations'] = opt.simulation.sim_realisations.val
self.results_dict['ch'] = opt.observation.obs_channel.val
self.noise_dict = {}
opt.pipeline.useSignal.val = 1
opt.simulation.sim_use_fast.val = 1
opt.pipeline.split = 0
opt.noise.ApplyRandomPRNU.val = 1
opt.timeline.apply_lc.val = 0
opt.timeline.useLDC.val = 0
opt.pipeline.useAllen.val = 1
opt.timeline.use_T14.val = 0
opt.timeline.obs_time.val = 0 * u.hr # 0 means n_exp overides obs_time
opt.timeline.n_exp.val = 1000.0 # uses 1000 exposures
# opt.timeline.n_exp.val = 400
noise_type = int(opt.noise.sim_noise_source.val)
nb_dict = {
'rn': [1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
'sn': [1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0],
'spat': [1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0],
'spec': [1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0],
'emm_switch': [1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1],
'zodi_switch': [1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1],
'dc_switch': [1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0],
'source_switch': [1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1],
'diff': [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0],
'jitter_switch': [1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0],
'fano': [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
'noise_tag': [
'All noise', 'All photon noise', 'Source photon noise',
'Dark current noise', 'Zodi noise', 'Emission noise',
'Read noise', 'Spatial jitter noise', 'Spectral jitter noise',
'Combined jitter noise', 'No noise - no background',
'No noise - all background', 'Fano noise'
],
'color': [
'0.5', 'b', 'b', 'k', 'orange', 'pink', 'y', 'g', 'purple',
'r', '0.8', 'c', 'c'
]
}
opt.noise.EnableReadoutNoise.val = nb_dict['rn'][noise_type]
opt.noise.EnableShotNoise.val = nb_dict['sn'][noise_type]
opt.noise.EnableSpatialJitter.val = nb_dict['spat'][noise_type]
opt.noise.EnableSpectralJitter.val = nb_dict['spec'][noise_type]
opt.noise.EnableFanoNoise.val = nb_dict['fano'][noise_type]
opt.background.EnableEmission.val = nb_dict['emm_switch'][noise_type]
opt.background.EnableZodi.val = nb_dict['zodi_switch'][noise_type]
opt.background.EnableDC.val = nb_dict['dc_switch'][noise_type]
opt.background.EnableSource.val = nb_dict['source_switch'][noise_type]
opt.diff = nb_dict['diff'][noise_type]
opt.noise_tag = nb_dict['noise_tag'][noise_type]
opt.color = nb_dict['color'][noise_type]
self.noise_dict[nb_dict['noise_tag'][noise_type]] = {}
jexosim_msg("Noise type: %s" % (nb_dict['noise_tag'][noise_type]), 1)
start = 0
end = int(start + opt.no_real)
opt = self.run_JexoSimA(opt)
if opt.observation_feasibility == 0:
jexosim_msg("Observation not feasible...", opt.diagnostics)
self.feasibility = 0
else:
self.feasibility = 1
n_ndr0 = opt.n_ndr * 1
ndr_end_frame_number0 = opt.ndr_end_frame_number * 1
frames_per_ndr0 = opt.frames_per_ndr * 1
duration_per_ndr0 = opt.duration_per_ndr * 1
n_exp0 = opt.n_exp
if n_ndr0 > 10000:
opt.pipeline.split = 1
if opt.diagnostics == 1:
jexosim_msg('number of NDRs > 10000: using split protocol',
opt.diagnostics)
else:
opt.pipeline.split = 0
opt.pipeline.split = 0
for j in range(start, end):
if (opt.no_real - start) > 1:
jexosim_msg("", 1)
jexosim_msg("============= REALIZATION %s =============" % (j),
1)
jexosim_msg(opt.lab, 1)
jexosim_msg("", 1)
opt = self.run_JexoSimA1(opt) # set QE grid for this realization
jexosim_msg("QE variations set", 1)
jexosim_msg("Number of exposures %s" % (n_exp0), 1)
# =============================================================================
# split simulation into chunks to permit computation - makes no difference to final results
# =============================================================================
if opt.pipeline.split == 1:
jexosim_msg('Splitting data series into chunks',
opt.diagnostics)
# uses same QE grid and jitter timeline but otherwise randomoses noise
ndrs_per_round = opt.effective_multiaccum * int(
5000 / opt.multiaccum)
# ndrs_per_round = opt.effective_multiaccum*int(50/opt.multiaccum)
total_chunks = len(np.arange(0, n_ndr0, ndrs_per_round))
idx = np.arange(0, n_ndr0,
ndrs_per_round) # list of starting ndrs
for i in range(len(idx)):
jexosim_msg(
'=== Chunk %s / %s=====' % (i + 1, total_chunks),
opt.diagnostics)
if idx[i] == idx[-1]:
opt.n_ndr = n_ndr0 - idx[i]
opt.ndr_end_frame_number = ndr_end_frame_number0[
idx[i]:]
opt.frames_per_ndr = frames_per_ndr0[idx[i]:]
opt.duration_per_ndr = duration_per_ndr0[idx[i]:]
else:
opt.n_ndr = idx[i + 1] - idx[i]
opt.ndr_end_frame_number = ndr_end_frame_number0[
idx[i]:idx[i + 1]]
opt.frames_per_ndr = frames_per_ndr0[idx[i]:idx[i + 1]]
opt.duration_per_ndr = duration_per_ndr0[idx[i]:idx[i +
1]]
opt.n_exp = int(opt.n_ndr / opt.effective_multiaccum)
if i == 0:
opt.use_external_jitter = 0
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
if opt.pipeline.pipeline_auto_ap.val == 1:
opt.pipeline.pipeline_ap_factor.val = opt.AvBest
if (opt.noise.EnableSpatialJitter.val == 1
or opt.noise.EnableSpectralJitter.val == 1
or opt.noise.EnableAll.val
== 1) and opt.noise.DisableAll.val != 1:
opt.input_yaw_jitter, opt.input_pitch_jitter, opt._input_frame_osf = opt.yaw_jitter, opt.pitch_jitter, opt.frame_osf
else:
opt.pipeline.pipeline_auto_ap.val = 0
opt.use_external_jitter = 1 # uses the jitter timeline from the first realization
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
jexosim_msg(
'Aperture used %s' %
(opt.pipeline.pipeline_ap_factor.val), opt.diagnostics)
binnedLC = opt.pipeline_stage_1.binnedLC
data = opt.pipeline_stage_1.opt.data_raw
#After chunks processed, now recombine
if i == 0:
data_stack = data
binnedLC_stack = binnedLC
else:
data_stack = np.dstack((data_stack, data))
binnedLC_stack = np.vstack((binnedLC_stack, binnedLC))
aa = data_stack.sum(axis=0)
bb = aa.sum(axis=0)
jexosim_plot('test_from_sim',
opt.diagnostics,
ydata=bb[opt.effective_multiaccum::opt.
effective_multiaccum])
aa = binnedLC_stack.sum(axis=1)
jexosim_plot('test_from_pipeline', opt.diagnostics, ydata=aa)
opt.n_ndr = n_ndr0
opt.ndr_end_frame_number = ndr_end_frame_number0
opt.frames_per_ndr = frames_per_ndr0
opt.duration_per_ndr = duration_per_ndr0
opt.n_exp = n_exp0
elif opt.pipeline.split == 0:
opt = self.run_JexoSimB(opt)
if j == start: # first realization sets the ap, then the other use the same one
opt.pipeline.pipeline_auto_ap.val = 1
else:
opt.pipeline.pipeline_auto_ap.val = 0
opt = self.run_pipeline_stage_1(opt)
if j == start: # first realization sets the ap, then the other use the same one
if opt.pipeline.pipeline_apply_mask.val == 1:
opt.pipeline.pipeline_ap_factor.val = opt.AvBest
binnedLC_stack = opt.pipeline_stage_1.binnedLC
data_stack = opt.pipeline_stage_1.opt.data_raw
jexosim_plot('testvvv',
opt.diagnostics,
ydata=binnedLC_stack.sum(axis=1))
aa = data_stack.sum(axis=0)
import matplotlib.pyplot as plt
plt.figure('data raw noise')
plt.plot(opt.x_wav_osr[1::3], aa.std(axis=1))
plt.figure('binned lc noise')
std = binnedLC_stack.std(axis=0)
plt.plot(opt.pipeline_stage_1.binnedWav, std)
#take binnedLC_stack and now complete through pipeline stage 2
opt.pipeline_stage_1.binnedLC = binnedLC_stack
opt = self.run_pipeline_stage_2(opt)
self.pipeline = opt.pipeline_stage_2
self.noise_dict[opt.noise_tag]['wl'] = self.pipeline.binnedWav
self.results_dict['input_spec'] = opt.cr
self.results_dict['input_spec_wl'] = opt.cr_wl
if j == start:
self.noise_dict[
opt.noise_tag]['signal_std_stack'] = self.pipeline.ootNoise
self.noise_dict[opt.noise_tag][
'signal_mean_stack'] = self.pipeline.ootSignal
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag][
'fracNoT14_stack'] = self.pipeline.noiseAt1hr
self.noise_dict[
opt.noise_tag]['signal_std_mean'] = self.pipeline.ootNoise
self.noise_dict[opt.noise_tag][
'signal_mean_mean'] = self.pipeline.ootSignal
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag][
'fracNoT14_mean'] = self.pipeline.noiseAt1hr
self.noise_dict[opt.noise_tag]['signal_std_std'] = np.zeros(
len(self.pipeline.binnedWav))
self.noise_dict[opt.noise_tag]['signal_mean_std'] = np.zeros(
len(self.pipeline.binnedWav))
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag]['fracNoT14_std'] = np.zeros(
len(self.pipeline.binnedWav))
else:
self.noise_dict[opt.noise_tag]['signal_std_stack'] = np.vstack(
(self.noise_dict[opt.noise_tag]['signal_std_stack'],
self.pipeline.ootNoise))
self.noise_dict[
opt.noise_tag]['signal_mean_stack'] = np.vstack(
(self.noise_dict[opt.noise_tag]['signal_mean_stack'],
self.pipeline.ootSignal))
if opt.pipeline.useAllen.val == 1:
self.noise_dict[
opt.noise_tag]['fracNoT14_stack'] = np.vstack(
(self.noise_dict[opt.noise_tag]['fracNoT14_stack'],
self.pipeline.noiseAt1hr))
self.noise_dict[
opt.noise_tag]['signal_std_mean'] = self.noise_dict[
opt.noise_tag]['signal_std_stack'].mean(axis=0)
self.noise_dict[
opt.noise_tag]['signal_mean_mean'] = self.noise_dict[
opt.noise_tag]['signal_mean_stack'].mean(axis=0)
if opt.pipeline.useAllen.val == 1:
self.noise_dict[
opt.noise_tag]['fracNoT14_mean'] = self.noise_dict[
opt.noise_tag]['fracNoT14_stack'].mean(axis=0)
self.noise_dict[
opt.noise_tag]['signal_std_std'] = self.noise_dict[
opt.noise_tag]['signal_std_stack'].std(axis=0)
self.noise_dict[
opt.noise_tag]['signal_mean_std'] = self.noise_dict[
opt.noise_tag]['signal_mean_stack'].std(axis=0)
if opt.pipeline.useAllen.val == 1:
self.noise_dict[
opt.noise_tag]['fracNoT14_std'] = self.noise_dict[
opt.noise_tag]['fracNoT14_stack'].std(axis=0)
self.noise_dict[opt.noise_tag]['bad_map'] = opt.bad_map
self.noise_dict[
opt.noise_tag]['example_exposure_image'] = opt.exp_image
self.noise_dict[
opt.noise_tag]['pixel wavelengths'] = opt.x_wav_osr[1::3].value
self.results_dict['noise_dic'] = self.noise_dict
time_tag = (datetime.now().strftime('%Y_%m_%d_%H%M_%S'))
self.results_dict['time_tag'] = time_tag
if j != start:
os.remove(filename) # delete previous temp file
txt_file = '%s.txt' % (filename)
os.remove(txt_file)
filename = '%s/OOT_SNR_%s_%s_TEMP.pickle' % (output_directory,
opt.lab, time_tag)
self.filename = 'OOT_SNR_%s_%s_TEMP.pickle' % (opt.lab, time_tag)
with open(filename, 'wb') as handle:
pickle.dump(self.results_dict,
handle,
protocol=pickle.HIGHEST_PROTOCOL)
if j == end - 1:
os.remove(filename) # delete previous temp file
filename = '%s/OOT_SNR_%s_%s.pickle' % (output_directory,
opt.lab, time_tag)
with open(filename, 'wb') as handle:
pickle.dump(self.results_dict,
handle,
protocol=pickle.HIGHEST_PROTOCOL)
jexosim_msg('Results in %s' % (filename), 1)
self.filename = 'OOT_SNR_%s_%s.pickle' % (opt.lab, time_tag)
write_record(opt, output_directory, self.filename,
opt.params_file_path)
def __init__(self, opt):
output_directory = opt.common.output_directory.val
filename = ""
self.results_dict = {}
self.results_dict['simulation_mode'] = opt.simulation.sim_mode.val
self.results_dict[
'simulation_realisations'] = opt.simulation.sim_realisations.val
self.results_dict['ch'] = opt.observation.obs_channel.val
opt.pipeline.useSignal.val = 0
opt.simulation.sim_use_fast.val = 1
opt.pipeline.split = 0
opt.noise.ApplyRandomPRNU.val = 1
opt.timeline.apply_lc.val = 1
opt.timeline.useLDC.val = 1
opt.pipeline.useAllen.val = 0
opt.pipeline.fit_gamma.val = 0 #keep zero for uncert on p
start = 0
end = int(start + opt.no_real)
if (opt.no_real - start) > 1:
jexosim_msg("Monte Carlo selected", 1)
opt = self.run_JexoSimA(opt)
if opt.observation_feasibility == 0:
jexosim_msg("Observation not feasible...", opt.diagnostics)
self.feasibility = 0
else:
self.feasibility = 1
n_ndr0 = opt.n_ndr * 1
lc0 = opt.lc_original * 1
ndr_end_frame_number0 = opt.ndr_end_frame_number * 1
frames_per_ndr0 = opt.frames_per_ndr * 1
duration_per_ndr0 = opt.duration_per_ndr * 1
n_exp0 = opt.n_exp
if n_ndr0 > 10000:
opt.pipeline.split = 1
if opt.diagnostics == 1:
jexosim_msg('number of NDRs > 10000: using split protocol',
opt.diagnostics)
else:
opt.pipeline.split = 0
for j in range(start, end):
if (opt.no_real - start) > 1:
jexosim_msg("", 1)
jexosim_msg(
"============= REALIZATION %s =============" % (j), 1)
jexosim_msg(opt.lab, 1)
jexosim_msg("", 1)
pp = time.time()
opt = self.run_JexoSimA1(
opt) # set QE grid for this realization
jexosim_msg("QE variations set", 1)
jexosim_msg("Number of exposures %s" % (n_exp0), 1)
lc0 = opt.lc_original * 1
# =============================================================================
# # split simulation into chunks to permit computation - makes no difference to final results
# =============================================================================
if opt.pipeline.split == 1:
jexosim_msg('Splitting data series into chunks',
opt.diagnostics)
# uses same QE grid and jitter timeline but otherwise randomoses noise
ndrs_per_round = opt.effective_multiaccum * int(
5000 / opt.multiaccum)
# ndrs_per_round = opt.effective_multiaccum*int(50/opt.multiaccum)
total_chunks = len(np.arange(0, n_ndr0, ndrs_per_round))
idx = np.arange(0, n_ndr0,
ndrs_per_round) # list of starting ndrs
for i in range(len(idx)):
jexosim_msg(
'=== Chunk %s / %s=====' % (i + 1, total_chunks),
opt.diagnostics)
if idx[i] == idx[-1]:
opt.n_ndr = n_ndr0 - idx[i]
opt.lc_original = lc0[:, idx[i]:]
opt.ndr_end_frame_number = ndr_end_frame_number0[
idx[i]:]
opt.frames_per_ndr = frames_per_ndr0[idx[i]:]
opt.duration_per_ndr = duration_per_ndr0[idx[i]:]
else:
opt.n_ndr = idx[i + 1] - idx[i]
opt.lc_original = lc0[:, idx[i]:idx[i + 1]]
opt.ndr_end_frame_number = ndr_end_frame_number0[
idx[i]:idx[i + 1]]
opt.frames_per_ndr = frames_per_ndr0[idx[i]:idx[i +
1]]
opt.duration_per_ndr = duration_per_ndr0[
idx[i]:idx[i + 1]]
opt.n_exp = int(opt.n_ndr / opt.effective_multiaccum)
if i == 0:
opt.pipeline.pipeline_auto_ap.val = 1
opt.use_external_jitter = 0
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
opt.pipeline.pipeline_ap_factor.val = opt.AvBest
if (opt.noise.EnableSpatialJitter.val == 1
or opt.noise.EnableSpectralJitter.val == 1
or opt.noise.EnableAll.val
== 1) and opt.noise.DisableAll.val != 1:
opt.input_yaw_jitter, opt.input_pitch_jitter, opt._input_frame_osf = opt.yaw_jitter, opt.pitch_jitter, opt.frame_osf
else:
opt.pipeline.pipeline_auto_ap.val = 0
opt.use_external_jitter = 1 # uses the jitter timeline from the first realization
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
jexosim_msg(
'Aperture used %s' %
(opt.pipeline.pipeline_ap_factor.val),
opt.diagnostics)
data0 = opt.pipeline_stage_1.binnedLC
data = opt.pipeline_stage_1.opt.data_raw
if i == 0:
data_stack = data
data_stack0 = data0
else:
data_stack = np.dstack((data_stack, data))
data_stack0 = np.vstack((data_stack0, data0))
aa = data_stack.sum(axis=0)
bb = aa.sum(axis=0)
jexosim_plot('test_from_sim',
opt.diagnostics,
ydata=bb[opt.effective_multiaccum::opt.
effective_multiaccum])
aa = data_stack0.sum(axis=1)
jexosim_plot('test_from_pipeline',
opt.diagnostics,
ydata=aa)
opt.n_ndr = n_ndr0
opt.ndr_end_frame_number = ndr_end_frame_number0
opt.frames_per_ndr = frames_per_ndr0
opt.duration_per_ndr = duration_per_ndr0
opt.n_exp = n_exp0
elif opt.pipeline.split == 0:
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
if j == start: # first realization sets the ap, then the other use the same one
opt.use_auto_Ap = 1
opt.pipeline.pipeline_ap_factor.val = opt.AvBest
else:
opt.use_auto_Ap = 0
data_stack0 = opt.pipeline_stage_1.binnedLC
jexosim_plot('testvvv',
opt.diagnostics,
ydata=data_stack0.sum(axis=1))
opt.pipeline_stage_1.binnedLC = data_stack0
opt = self.run_pipeline_stage_2(opt)
pipeline = opt.pipeline_stage_2
p = pipeline.transitDepths
if j == start:
p_stack = p
else:
p_stack = np.vstack((p_stack, p))
jexosim_msg(
"time to complete realization %s %s" %
(j, time.time() - pp), opt.diagnostics)
self.results_dict['wl'] = pipeline.binnedWav
self.results_dict['input_spec'] = opt.cr
self.results_dict['input_spec_wl'] = opt.cr_wl
if j == start: # if only one realisation slightly different format
self.results_dict['p_stack'] = np.array(p)
self.results_dict['p_std'] = np.zeros(len(p))
self.results_dict['p_mean'] = np.array(p)
else:
self.results_dict['p_stack'] = np.vstack(
(self.results_dict['p_stack'], p))
self.results_dict['p_std'] = self.results_dict[
'p_stack'].std(axis=0)
self.results_dict['p_mean'] = self.results_dict[
'p_stack'].mean(axis=0)
time_tag = (datetime.now().strftime('%Y_%m_%d_%H%M_%S'))
self.results_dict['time_tag'] = time_tag
self.results_dict['bad_map'] = opt.bad_map
self.results_dict['example_exposure_image'] = opt.exp_image
self.results_dict['pixel wavelengths'] = opt.x_wav_osr[
1::3].value
if j != start:
os.remove(filename) # delete previous temp file
filename = '%s/Full_transit_%s_TEMP.pickle' % (
output_directory, opt.lab)
with open(filename, 'wb') as handle:
pickle.dump(self.results_dict,
handle,
protocol=pickle.HIGHEST_PROTOCOL)
os.remove(filename) # delete previous temp file
# write final file
filename = '%s/Full_transit_%s_%s.pickle' % (output_directory,
opt.lab, time_tag)
with open(filename, 'wb') as handle:
pickle.dump(self.results_dict,
handle,
protocol=pickle.HIGHEST_PROTOCOL)
jexosim_msg('Results in %s' % (filename), 1)
self.filename = 'Full_transit_%s_%s.pickle' % (opt.lab, time_tag)
write_record(opt, output_directory, self.filename,
opt.params_file_path)
def run(opt):
opt.observation_feasibility = 1 # this variable is currently not changed to zero under any circumstances
opt.psf, opt.psf_type = instrument_lib.get_psf(opt)
opt.fp, opt.fp_signal = instrument_lib.get_focal_plane(opt)
opt.fp_it, opt.fp_signal_it = instrument_lib.get_focal_plane_it(opt)
mask_fp = np.where(opt.fp > 0, 1, 0)
mask_fp_it = np.where(opt.fp_it > 0, 1, 0)
mask_fp_signal = np.where(opt.fp_signal > 0, 1, 0)
mask_fp_signal_it = np.where(opt.fp_signal_it > 0, 1, 0)
opt.fp, opt.fp_signal = instrument_lib.convolve_prf(
opt, opt.fp,
opt.fp_signal) #this step can gen some small negative values on fp
opt.fp = np.where(opt.fp < 0, 0, opt.fp)
opt.fp_signal = np.where(opt.fp_signal < 0, 0, opt.fp_signal)
opt.fp_it, opt.fp_signal_it = instrument_lib.convolve_prf(
opt, opt.fp_it,
opt.fp_signal_it) #this step can gen some small negative values on fp
opt.fp_it = np.where(opt.fp_it < 0, 0, opt.fp_it)
opt.fp_signal_it = np.where(opt.fp_signal_it < 0, 0, opt.fp_signal_it)
# mask out small values arising from the PRF convolution where there was originally zero signal
opt.fp *= mask_fp
opt.fp_it *= mask_fp_it
opt.fp_signal *= mask_fp_signal
opt.fp_signal_it *= mask_fp_signal_it
opt.planet.sed = instrument_lib.get_planet_spectrum(opt)
jexosim_plot(
'planet sed',
opt.diagnostics,
xdata=opt.planet.sed.wl,
ydata=opt.planet.sed.sed,
)
opt = instrument_lib.user_subarray(opt)
opt = instrument_lib.crop_to_subarray(opt)
opt = instrument_lib.exposure_timing(opt)
jexosim_msg("Integration time - zeroth read %s" % (opt.t_int),
opt.diagnostics)
jexosim_msg(
"Estimated integration time incl. zeroth read %s" %
(opt.t_int + opt.zero_time), opt.diagnostics)
jexosim_msg("Estimated TOTAL CYCLE TIME %s" % (opt.exposure_time),
opt.diagnostics)
jexosim_msg("CDS time estimate %s" % (opt.t_int), opt.diagnostics)
jexosim_msg("FP max %s" % (opt.fp[1::3, 1::3].max()), opt.diagnostics)
jexosim_msg("DC SWITCH.......%s" % (opt.background.EnableDC.val),
opt.diagnostics)
jexosim_msg(
"DISABLE ALL SWITCH.......%s" % (opt.background.DisableAll.val),
opt.diagnostics)
jexosim_msg("DARK CURRENT %s" % (opt.channel.detector_pixel.Idc.val),
opt.diagnostics)
jexosim_plot('focal plane check',
opt.diagnostics,
image=True,
image_data=opt.fp[1::3, 1::3],
aspect='auto',
interpolation=None,
xlabel='x \'spectral\' pixel',
ylabel='y \'spatial\' pixel')
if opt.diagnostics == 1:
plt.figure('focal plane check')
cbar = plt.colorbar()
cbar.set_label(('Count (e$^-$/s)'), rotation=270, size=15, labelpad=20)
cbar.ax.tick_params(labelsize=15)
ax = plt.gca()
for item in ([ax.title, ax.xaxis.label, ax.yaxis.label] +
ax.get_xticklabels() + ax.get_yticklabels()):
item.set_fontsize(15)
opt.fp_original = copy.deepcopy(opt.fp)
opt.fp_signal_original = copy.deepcopy(opt.fp_signal)
opt.x_wav_osr_original = copy.deepcopy(opt.x_wav_osr)
opt.x_pix_osr_original = copy.deepcopy(opt.x_pix_osr)
opt.quantum_yield_original = copy.deepcopy(opt.quantum_yield)
opt.qy_zodi_original = copy.deepcopy(opt.qy_zodi)
opt.qy_sunshield_original = copy.deepcopy(opt.qy_sunshield)
opt.qy_emission_original = copy.deepcopy(opt.qy_emission)
opt.zodi_sed_original = copy.deepcopy(
opt.zodi.sed
) # needed here due to possible cropping above for subarrays
opt.sunshield_sed_original = copy.deepcopy(opt.sunshield.sed)
opt.emission_sed_original = copy.deepcopy(opt.emission.sed)
if opt.channel.instrument.val == 'NIRSpec':
opt.channel.pipeline_params.wavrange_hi.val = opt.gap[3]
opt.channel.pipeline_params.wavrange_lo.val = opt.gap[2]
opt.channel.pipeline_params.end_wav.val = opt.gap[3] + 0.1
opt.channel.pipeline_params.start_wav.val = opt.gap[2] - 0.1
jexosim_plot('final wl solution on subarray',
opt.diagnostics,
ydata=opt.x_wav_osr[1::3],
xlabel='x \'spectral\' pixel',
ylabel='y \'spatial\' pixel',
grid=True)
if opt.diagnostics == 1:
wl = opt.x_wav_osr
wav = opt.x_wav_osr[1::3]
if opt.channel.name == 'NIRSpec_BOTS_G140H_F100LP' or \
opt.channel.name == 'NIRSpec_BOTS_G235H_F170LP'\
or opt.channel.name == 'NIRSpec_BOTS_G395H_F290LP':
idx0 = np.argwhere(wav == opt.wav_gap_start)[0].item(
) #recover the start of the gap
idx1 = idx0 + opt.gap_len # gap of 172 pix works well for G1H and G2H, but a little off (by 0.01 microns for the other in some cases from published values)
fp_1d = opt.fp_signal[1::3, 1::3].sum(axis=0)
fp_1d[idx0:idx1] = 0
idx0 = np.argwhere(wl == opt.wav_gap_start)[0].item(
) #recover the start of the gap
idx1 = idx0 + opt.gap_len * 3 # gap of 172 p
opt.PCE[idx0:idx1] = 0
opt.TotTrans[idx0:idx1] = 0
opt.R.sed[idx0:idx1] = 0
else:
fp_1d = opt.fp_signal[1::3, 1::3].sum(axis=0)
plt.figure('Focal plane pixel count rate')
plt.plot(wav, fp_1d, 'r-')
plt.grid()
plt.figure('Final PCE and transmission on subarray')
plt.plot(wl, opt.PCE, '-')
plt.plot(wl, opt.TotTrans, '--')
plt.figure('R power')
plt.plot(wl, opt.R.sed, '-')
instrument_lib.sanity_check(opt)
return opt
def __init__(self, opt):
output_directory = opt.common.output_directory.val
filename=""
self.results_dict ={}
self.results_dict['simulation_mode'] = opt.simulation.sim_mode.val
self.results_dict['simulation_realisations'] = opt.simulation.sim_realisations.val
self.results_dict['ch'] = opt.observation.obs_channel.val
self.noise_dict ={}
self.feasibility =1
opt.pipeline.useSignal.val=1
opt.simulation.sim_use_fast.val =1
opt.pipeline.split = 0
opt.noise.ApplyRandomPRNU.val=1
opt.timeline.apply_lc.val = 0
opt.timeline.useLDC.val = 0
opt.pipeline.useAllen.val =1
opt.pipeline.pipeline_auto_ap.val = 0 # for noise budget keep this to a fixed value (i.e. choose 0) so same for all sims
opt.timeline.obs_time.val = 0*u.hr
opt.timeline.n_exp.val = 1000.0
noise_list = [0,2,3,4,5,6,7,8,9,12,13]
# noise_list = [0,2,3,4,5,6,7,8,9]
# noise_list = [2,9,12]
start = 0
end = int(start + opt.no_real)
nb_dict = {'rn' :[1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
'sn' :[1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1],
'spat' :[1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0],
'spec' :[1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0],
'emm_switch' :[1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0],
'zodi_switch' :[1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0],
'dc_switch' :[1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
'source_switch' :[1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0],
'diff' :[0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1],
'jitter_switch' :[1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
'fano' :[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
'sunshield_switch' :[1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
'noise_tag': [ 'All noise','All photon noise','Source photon noise','Dark current noise',
'Zodi noise','Emission noise','Read noise','Spatial jitter noise',
'Spectral jitter noise','Combined jitter noise','No noise - no background','No noise - all background', 'Fano noise', 'Sunshield noise'],
'color': ['0.5','b', 'b','k','orange','pink', 'y','g','purple','r', '0.8','c', 'c','brown']
}
for i in noise_list:
self.noise_dict[nb_dict['noise_tag'][i]] ={}
for j in range(start,end):
seed = np.random.randint(100000000)
for i in noise_list:
opt.noise.EnableReadoutNoise.val = nb_dict['rn'][i]
opt.noise.EnableShotNoise.val = nb_dict['sn'][i]
opt.noise.EnableSpatialJitter.val= nb_dict['spat'][i]
opt.noise.EnableSpectralJitter.val= nb_dict['spec'][i]
opt.noise.EnableFanoNoise.val= nb_dict['fano'][i]
opt.background.EnableEmission.val = nb_dict['emm_switch'][i]
opt.background.EnableZodi.val = nb_dict['zodi_switch'][i]
opt.background.EnableSunshield.val = nb_dict['sunshield_switch'][i]
opt.background.EnableDC.val = nb_dict['dc_switch'][i]
opt.background.EnableSource.val = nb_dict['source_switch'][i]
opt.diff = nb_dict['diff'][i]
opt.noise_tag = nb_dict['noise_tag'][i]
opt.color = nb_dict['color'][i]
jexosim_msg('==========================================', 1)
jexosim_msg('Noise source:%s'%(opt.noise_tag), 1)
np.random.seed(seed)
opt = self.run_JexoSimA(opt)
opt = self.run_JexoSimA1(opt)
n_ndr0 = opt.n_ndr*1
ndr_end_frame_number0 = opt.ndr_end_frame_number*1
frames_per_ndr0 = opt.frames_per_ndr*1
duration_per_ndr0 = opt.duration_per_ndr*1
n_exp0 = opt.n_exp
if n_ndr0 > 10000:
opt.pipeline.split = 1
if opt.diagnostics ==1 :
jexosim_msg ('number of NDRs > 10000: using split protocol', opt.diagnostics)
else:
opt.pipeline.split = 0
opt.pipeline.split = 1
# =============================================================================
# split simulation into chunks to permit computation - makes no difference to final results
# =============================================================================
if opt.pipeline.split ==1:
jexosim_msg('Splitting data series into chunks', opt.diagnostics)
# uses same QE grid and jitter timeline but otherwise randomoses noise
ndrs_per_round = opt.effective_multiaccum*int(5000/opt.multiaccum)
ndrs_per_round = opt.effective_multiaccum*int(50/opt.multiaccum)
total_chunks = len(np.arange(0, n_ndr0, ndrs_per_round))
idx = np.arange(0, n_ndr0, ndrs_per_round) # list of starting ndrs
for i in range(len(idx)):
jexosim_msg('=== Chunk %s / %s====='%(i+1, total_chunks), opt.diagnostics)
if idx[i] == idx[-1]:
opt.n_ndr = n_ndr0 - idx[i]
opt.ndr_end_frame_number = ndr_end_frame_number0[idx[i]:]
opt.frames_per_ndr= frames_per_ndr0[idx[i]:]
opt.duration_per_ndr = duration_per_ndr0[idx[i]:]
else:
opt.n_ndr = idx[i+1]- idx[i]
opt.ndr_end_frame_number = ndr_end_frame_number0[idx[i]: idx[i+1]]
opt.frames_per_ndr= frames_per_ndr0[idx[i]: idx[i+1]]
opt.duration_per_ndr = duration_per_ndr0[idx[i]: idx[i+1]]
opt.n_exp = int(opt.n_ndr/opt.effective_multiaccum)
if i == 0:
opt.use_external_jitter = 0
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
if opt.pipeline.pipeline_auto_ap.val == 1:
opt.pipeline.pipeline_ap_factor.val= opt.AvBest
if (opt.noise.EnableSpatialJitter.val ==1 or opt.noise.EnableSpectralJitter.val ==1 or opt.noise.EnableAll.val == 1) and opt.noise.DisableAll.val != 1:
opt.input_yaw_jitter, opt.input_pitch_jitter, opt._input_frame_osf = opt.yaw_jitter, opt.pitch_jitter, opt.frame_osf
else:
opt.pipeline.pipeline_auto_ap.val = 0
opt.use_external_jitter = 1 # uses the jitter timeline from the first realization
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
jexosim_msg('Aperture used %s'%(opt.pipeline.pipeline_ap_factor.val), opt.diagnostics)
binnedLC = opt.pipeline_stage_1.binnedLC
data = opt.pipeline_stage_1.opt.data_raw
#After chunks processed, now recombine
if i ==0:
data_stack = data
binnedLC_stack = binnedLC
else:
data_stack = np.dstack((data_stack,data))
binnedLC_stack = np.vstack((binnedLC_stack, binnedLC))
aa = data_stack.sum(axis=0)
bb = aa.sum(axis=0)
jexosim_plot('test_from_sim', opt.diagnostics,
ydata=bb[opt.effective_multiaccum::opt.effective_multiaccum] )
aa = binnedLC_stack.sum(axis=1)
jexosim_plot('test_from_pipeline', opt.diagnostics,
ydata=aa)
opt.n_ndr = n_ndr0
opt.ndr_end_frame_number = ndr_end_frame_number0
opt.frames_per_ndr = frames_per_ndr0
opt.duration_per_ndr = duration_per_ndr0
opt.n_exp = n_exp0
elif opt.pipeline.split ==0:
opt = self.run_JexoSimB(opt)
if j==start: # first realization sets the ap, then the other use the same one
opt.pipeline.pipeline_auto_ap.val= 1
else:
opt.pipeline.pipeline_auto_ap.val= 0
opt = self.run_pipeline_stage_1(opt)
if j==start: # first realization sets the ap, then the other use the same one
if opt.pipeline.pipeline_apply_mask.val == 1:
opt.pipeline.pipeline_ap_factor.val= opt.AvBest
binnedLC_stack = opt.pipeline_stage_1.binnedLC
data_stack = opt.pipeline_stage_1.opt.data_raw
jexosim_plot('testvvv', opt.diagnostics,
ydata=binnedLC_stack.sum(axis=1) )
#take binnedLC_stack and now complete through pipeline stage 2
opt.pipeline_stage_1.binnedLC = binnedLC_stack
opt = self.run_pipeline_stage_2(opt)
self.pipeline = opt.pipeline_stage_2
self.opt = opt
self.noise_dict[opt.noise_tag]['wl'] = self.pipeline.binnedWav
if j == start:
self.noise_dict[opt.noise_tag]['signal_std_stack'] = self.pipeline.ootNoise
self.noise_dict[opt.noise_tag]['signal_mean_stack'] = self.pipeline.ootSignal
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag]['fracNoT14_stack'] = self.pipeline.noiseAt1hr
self.noise_dict[opt.noise_tag]['signal_std_mean'] = self.pipeline.ootNoise
self.noise_dict[opt.noise_tag]['signal_mean_mean'] = self.pipeline.ootSignal
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag]['fracNoT14_mean'] = self.pipeline.noiseAt1hr
self.noise_dict[opt.noise_tag]['signal_std_std'] = np.zeros(len(self.pipeline.binnedWav))
self.noise_dict[opt.noise_tag]['signal_mean_std'] = np.zeros(len(self.pipeline.binnedWav))
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag]['fracNoT14_std'] = np.zeros(len(self.pipeline.binnedWav))
self.noise_dict[opt.noise_tag]['bad_map'] = opt.bad_map
self.noise_dict[opt.noise_tag]['example_exposure_image'] = opt.exp_image
self.noise_dict[opt.noise_tag]['pixel wavelengths'] = opt.x_wav_osr[1::3].value
else:
self.noise_dict[opt.noise_tag]['signal_std_stack'] = np.vstack((self.noise_dict[opt.noise_tag]['signal_std_stack'], self.pipeline.ootNoise))
self.noise_dict[opt.noise_tag]['signal_mean_stack'] = np.vstack((self.noise_dict[opt.noise_tag]['signal_mean_stack'], self.pipeline.ootSignal))
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag]['fracNoT14_stack'] = np.vstack((self.noise_dict[opt.noise_tag]['fracNoT14_stack'], self.pipeline.noiseAt1hr))
self.noise_dict[opt.noise_tag]['signal_std_mean'] = self.noise_dict[opt.noise_tag]['signal_std_stack'].mean(axis=0)
self.noise_dict[opt.noise_tag]['signal_mean_mean'] = self.noise_dict[opt.noise_tag]['signal_mean_stack'].mean(axis=0)
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag]['fracNoT14_mean'] = self.noise_dict[opt.noise_tag]['fracNoT14_stack'].mean(axis=0)
self.noise_dict[opt.noise_tag]['signal_std_std'] = self.noise_dict[opt.noise_tag]['signal_std_stack'].std(axis=0)
self.noise_dict[opt.noise_tag]['signal_mean_std'] = self.noise_dict[opt.noise_tag]['signal_mean_stack'].std(axis=0)
if opt.pipeline.useAllen.val == 1:
self.noise_dict[opt.noise_tag]['fracNoT14_std'] = self.noise_dict[opt.noise_tag]['fracNoT14_stack'].std(axis=0)
self.noise_dict[opt.noise_tag]['bad_map'] = opt.bad_map
self.noise_dict[opt.noise_tag]['example_exposure_image'] = opt.exp_image
self.noise_dict[opt.noise_tag]['pixel wavelengths'] = opt.x_wav_osr[1::3].value
self.results_dict['noise_dic'] = self.noise_dict
# dump pickle file at end of each cycle of noise sims
if opt.simulation.sim_output_type.val == 1:
time_tag = (datetime.now().strftime('%Y_%m_%d_%H%M_%S'))
self.results_dict['time_tag'] = time_tag
# if j != start:
# os.remove(filename) # delete previous temp file
# filename = '%s/Noise_budget_%s_TEMP.pickle'%(output_directory, opt.lab)
# with open(filename, 'wb') as handle:
# pickle.dump(self.results_dict , handle, protocol=pickle.HIGHEST_PROTOCOL)
if j == end-1:
# os.remove(filename) # delete previous temp file
filename = '%s/Noise_budget_%s_%s.pickle'%(output_directory, opt.lab, time_tag)
with open(filename, 'wb') as handle:
pickle.dump(self.results_dict , handle, protocol=pickle.HIGHEST_PROTOCOL)
jexosim_msg('Results in %s'%(filename), 1)
self.filename = 'Noise_budget_%s_%s.pickle'%(opt.lab, time_tag)
write_record(opt, output_directory, self.filename, opt.params_file_path)
def getLDC_interp(opt, planet, wl):
jexosim_msg('Calculating LDC from pre-installed files', 1)
T = planet.star.T.value
if T < 3000.0: # temp fix as LDCs not available for T< 3000 K
T = 3000.0
logg = planet.star.logg
jexosim_msg("T_s, logg>>>> %s %s" % (T, logg), opt.diagnostics)
folder = '%s/archive/LDC' % (opt.jexosim_path)
t_base = np.int(T / 100.) * 100
if T >= t_base + 100:
t1 = t_base + 100
t2 = t_base + 200
else:
t1 = t_base
t2 = t_base + 100
logg_base = np.int(logg)
if logg >= logg_base + 0.5:
logg1 = logg_base + 0.5
logg2 = logg_base + 1.0
else:
logg1 = logg_base
logg2 = logg_base + 0.5
logg1 = np.float(logg1)
logg2 = np.float(logg2)
#==============================================================================
# interpolate between temperatures assuming logg1
#==============================================================================
u0_a = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t1, logg1))[:, 1]
u0_b = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t2, logg1))[:, 1]
w2 = 1.0 - abs(t2 - T) / 100.
w1 = 1.0 - abs(t1 - T) / 100.
u0_1 = w1 * u0_a + w2 * u0_b
u1_a = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t1, logg1))[:, 2]
u1_b = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t2, logg1))[:, 2]
w2 = 1.0 - abs(t2 - T) / 100.
w1 = 1.0 - abs(t1 - T) / 100.
u1_1 = w1 * u1_a + w2 * u1_b
jexosim_plot('ldc interp logg1', opt.diagnostics, ydata=u0_a, marker='b-')
jexosim_plot('ldc interp logg1', opt.diagnostics, ydata=u0_b, marker='r-')
jexosim_plot('ldc interp logg1', opt.diagnostics, ydata=u0_1, marker='g-')
jexosim_plot('ldc interp logg1', opt.diagnostics, ydata=u1_a, marker='b-')
jexosim_plot('ldc interp logg1', opt.diagnostics, ydata=u1_b, marker='r-')
jexosim_plot('ldc interp logg1', opt.diagnostics, ydata=u1_1, marker='g-')
ldc_wl = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t1, logg1))[:, 0]
#==============================================================================
# interpolate between temperatures assuming logg2
#==============================================================================
u0_a = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t1, logg2))[:, 1]
u0_b = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t2, logg2))[:, 1]
w2 = 1.0 - abs(t2 - T) / 100.
w1 = 1.0 - abs(t1 - T) / 100.
u0_2 = w1 * u0_a + w2 * u0_b
u1_a = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t1, logg2))[:, 2]
u1_b = np.loadtxt('%s/T=%s_logg=%s_z=0.txt' % (folder, t2, logg2))[:, 2]
w2 = 1.0 - abs(t2 - T) / 100.
w1 = 1.0 - abs(t1 - T) / 100.
u1_2 = w1 * u1_a + w2 * u1_b
jexosim_plot('ldc interp logg2', opt.diagnostics, ydata=u0_a, marker='b-')
jexosim_plot('ldc interp logg2', opt.diagnostics, ydata=u0_b, marker='r-')
jexosim_plot('ldc interp logg2', opt.diagnostics, ydata=u0_2, marker='g-')
jexosim_plot('ldc interp logg2', opt.diagnostics, ydata=u1_a, marker='b-')
jexosim_plot('ldc interp logg2', opt.diagnostics, ydata=u1_b, marker='r-')
jexosim_plot('ldc interp logg2', opt.diagnostics, ydata=u1_2, marker='g-')
#==============================================================================
# interpolate between logg
#==============================================================================
w2 = 1.0 - abs(logg2 - logg) / .5
w1 = 1.0 - abs(logg1 - logg) / .5
u0 = w1 * u0_1 + w2 * u0_2
u1 = w1 * u1_1 + w2 * u1_2
jexosim_plot('ldc interp', opt.diagnostics, ydata=u0_1, marker='b-')
jexosim_plot('ldc interp', opt.diagnostics, ydata=u0_2, marker='r-')
jexosim_plot('ldc interp', opt.diagnostics, ydata=u0, marker='g-')
jexosim_plot('ldc interp', opt.diagnostics, ydata=u1_1, marker='b-')
jexosim_plot('ldc interp', opt.diagnostics, ydata=u1_2, marker='r-')
jexosim_plot('ldc interp', opt.diagnostics, ydata=u1, marker='g-')
#==============================================================================
# interpolate to new wl grid
#==============================================================================
u0_final = np.interp(wl, ldc_wl, u0)
u1_final = np.interp(wl, ldc_wl, u1)
jexosim_plot('ldc final',
opt.diagnostics,
xdata=ldc_wl,
ydata=u0,
marker='ro',
alpha=0.1)
jexosim_plot('ldc final',
opt.diagnostics,
xdata=ldc_wl,
ydata=u1,
marker='bo',
alpha=0.1)
jexosim_plot('ldc final',
opt.diagnostics,
xdata=wl,
ydata=u0_final,
marker='rx')
jexosim_plot('ldc final',
opt.diagnostics,
xdata=wl,
ydata=u1_final,
marker='bx')
return u0_final, u1_final
def read_phoenix_spectrum_interp(self):
jexosim_msg ("Star... star_temperature %s, star_logg %s, star_f_h %s"%(self.star_temperature, self.star_logg, self.star_f_h) , self.opt.diagnostics)
if self.star_temperature.value >= 2400:
t0 = np.round(self.star_temperature,-2)/100.
else:
t0= np.round(np.round(self.star_temperature,-1)/100./0.5)*0.5
t0 = t0.value
if t0*100 != self.star_temperature.value:
cond_1 = 1
if t0*100 > self.star_temperature.value:
if self.star_temperature.value >= 2400:
t1 = t0-1
else:
t1 = t0-0.5
elif t0*100 < self.star_temperature.value:
if self.star_temperature.value >= 2400:
t1= t0+1
else:
t1 = t0+0.5
print (t0,t1, self.star_temperature)
else:
cond_1 = 0 # do not interp for temp
logg0 = np.round(np.round(self.star_logg,1)/0.5)*0.5
if logg0 <= 2.5:
logg0 = 2.5
cond_2 = 0 # do not interp for logg
elif logg0 >= 5.5:
logg0 = 5.5
cond_2 = 0
elif logg0 == self.star_logg:
cond_2 = 0
else:
cond_2 = 1
if logg0 < self.star_logg:
logg1 = logg0 + 0.5
if logg0 > self.star_logg:
logg1 = logg0 - 0.5
if cond_1 == 1 and cond_2 == 0:
jexosim_msg ("interpolating spectra by temperature only", self.opt.diagnostics)
wav_t0_logg0, flux_t0_logg0 = self.open_Phoenix(t0,logg0, self.star_f_h, self.sed_folder)
wav_t1_logg0, flux_t1_logg0 = self.open_Phoenix(t1,logg0, self.star_f_h, self.sed_folder)
sed_t0_logg0 = sed.Sed(wav_t0_logg0, flux_t0_logg0)
sed_t1_logg0 = sed.Sed(wav_t1_logg0, flux_t1_logg0)
# bin to same wav grid
sed_t1_logg0.rebin(wav_t0_logg0)
wt0 = 1 - abs(t0*100 - self.star_temperature.value)/abs(t0*100 - t1*100)
wt1 = 1 - abs(self.star_temperature.value - t1*100)/abs(t0*100 - t1*100)
sed_final = wt0*sed_t0_logg0.sed + wt1*sed_t1_logg0.sed
star_final_sed = sed_final
star_final_wl = sed_t0_logg0.wl
jexosim_plot('temperature interpolation', self.opt.diagnostics, xdata = wav_t0_logg0, ydata = flux_t0_logg0, marker ='r-')
jexosim_plot('temperature interpolation', self.opt.diagnostics, xdata = wav_t1_logg0, ydata = flux_t1_logg0, marker ='b-')
jexosim_plot('temperature interpolation', self.opt.diagnostics, xdata = star_final_wl, ydata = star_final_sed, marker ='g-')
if cond_1 == 1 and cond_2 == 1:
jexosim_msg ("interpolating spectra by temperature and logg", self.opt.diagnostics)
#interp temp at logg0
wav_t0_logg0, flux_t0_logg0 = self.open_Phoenix(t0,logg0, self.star_f_h, self.sed_folder)
wav_t1_logg0, flux_t1_logg0 = self.open_Phoenix(t1,logg0, self.star_f_h, self.sed_folder)
sed_t0_logg0 = sed.Sed(wav_t0_logg0, flux_t0_logg0)
sed_t1_logg0 = sed.Sed(wav_t1_logg0, flux_t1_logg0)
# bin to same wav grid
sed_t1_logg0.rebin(wav_t0_logg0)
wt0 = 1 - abs(t0*100 - self.star_temperature.value)/abs(t0*100 - t1*100)
wt1 = 1 - abs(self.star_temperature.value - t1*100)/abs(t0*100 - t1*100)
sed_ = wt0*sed_t0_logg0.sed + wt1*sed_t1_logg0.sed
sed_logg0 = sed.Sed(wav_t0_logg0, sed_)
print (t0,t1)
print (wt0,wt1)
box = 1000
bbox = np.ones(box)/box
jexosim_plot('temperature interpolation logg0', self.opt.diagnostics, xdata = wav_t0_logg0, \
ydata = np.convolve(flux_t0_logg0, bbox,'same'), marker ='r-')
jexosim_plot('temperature interpolation logg0', self.opt.diagnostics, xdata = wav_t1_logg0, \
ydata = np.convolve(flux_t1_logg0, bbox,'same'), marker ='b-')
jexosim_plot('temperature interpolation logg0', self.opt.diagnostics, xdata = sed_logg0.wl, \
ydata = np.convolve(sed_logg0.sed, bbox,'same'), marker ='g-')
#interp temp at logg1
wav_t0_logg1, flux_t0_logg1 = self.open_Phoenix(t0,logg1, self.star_f_h, self.sed_folder)
wav_t1_logg1, flux_t1_logg1 = self.open_Phoenix(t1,logg1, self.star_f_h, self.sed_folder)
sed_t0_logg1 = sed.Sed(wav_t0_logg1, flux_t0_logg1)
sed_t1_logg1 = sed.Sed(wav_t1_logg1, flux_t1_logg1)
# bin to same wav grid
sed_t1_logg1.rebin(wav_t0_logg1)
wt0 = 1 - abs(t0*100 - self.star_temperature.value)/abs(t0*100 - t1*100)
wt1 = 1 - abs(self.star_temperature.value - t1*100)/abs(t0*100 - t1*100)
sed_ = wt0*sed_t0_logg1.sed + wt1*sed_t1_logg1.sed
sed_logg1 = sed.Sed(wav_t0_logg1, sed_)
box = 100
bbox = np.ones(box)/box
jexosim_plot('temperature interpolation logg1', self.opt.diagnostics, xdata = wav_t0_logg1, \
ydata = np.convolve(flux_t0_logg1, bbox,'same'), marker ='r-')
jexosim_plot('temperature interpolation logg1', self.opt.diagnostics, xdata = wav_t1_logg1, \
ydata = np.convolve(flux_t1_logg1, bbox,'same'), marker ='b-')
jexosim_plot('temperature interpolation logg1', self.opt.diagnostics, xdata = sed_logg1.wl, \
ydata = np.convolve(sed_logg1.sed, bbox,'same'), marker ='g-')
# now interp logg
sed_logg1.rebin(sed_logg0.wl)
wt0 = 1 - abs(logg0 - self.star_logg)/abs(logg0 - logg1)
wt1 = 1 - abs(self.star_logg - logg1)/abs(logg0 - logg1)
print (wt0,wt1)
print (logg0,logg1)
sed_final = wt0*sed_logg0.sed + wt1*sed_logg1.sed
star_final_sed = sed_final
star_final_wl = sed_logg0.wl
box = 100
bbox = np.ones(box)/box
jexosim_plot('interpolation between logg', self.opt.diagnostics, xdata = sed_logg0.wl, \
ydata = np.convolve(sed_logg0.sed, bbox,'same'), marker ='r-')
jexosim_plot('interpolation between logg', self.opt.diagnostics, xdata = sed_logg1.wl, \
ydata = np.convolve(sed_logg1.sed, bbox,'same'), marker ='b-')
jexosim_plot('interpolation between logg', self.opt.diagnostics, xdata = star_final_wl, \
ydata = np.convolve(star_final_sed, bbox,'same'), marker ='g-')
if cond_1 == 0 and cond_2 == 1:
jexosim_msg ("interpolating spectra by logg only", self.opt.diagnostics)
#interp logg at t0
wav_t0_logg0, flux_t0_logg0 = self.open_Phoenix(t0,logg0, self.star_f_h, self.sed_folder)
wav_t0_logg1, flux_t0_logg1 = self.open_Phoenix(t0,logg1, self.star_f_h, self.sed_folder)
sed_t0_logg0 = sed.Sed(wav_t0_logg0, flux_t0_logg0)
sed_t0_logg1 = sed.Sed(wav_t0_logg1, flux_t0_logg1)
# bin to same wav grid
sed_t0_logg1.rebin(wav_t0_logg0)
wt0 = 1 - abs(logg0 - self.star_logg)/abs(logg0 - logg1)
wt1 = 1 - abs(self.star_logg - logg1)/abs(logg0 - logg1)
sed_final = wt0*sed_logg0.sed + wt1*sed_logg1.sed
star_final_sed = sed_final
star_final_wl = sed_t0_logg0.wl
box = 100
bbox = np.ones(box)/box
jexosim_plot('interpolation between logg', self.opt.diagnostics, xdata = sed_t0_logg0.wl, \
ydata = np.convolve(sed_t0_logg0.sed, bbox,'same'), marker ='r-')
jexosim_plot('interpolation between logg', self.opt.diagnostics, xdata = sed_t0_logg1.wl, \
ydata = np.convolve(sed_t0_logg1.sed, bbox,'same'), marker ='b-')
jexosim_plot('interpolation between logg', self.opt.diagnostics, xdata = star_final_wl, \
ydata = np.convolve(star_final_sed, bbox,'same'), marker ='g-')
if cond_1 == 0 and cond_2 == 0:
star_final_wl, star_final_sed = self.open_Phoenix(t0,logg0, self.star_f_h, self.sed_folder)
return star_final_wl, star_final_sed
def extractSpec(self):
jexosim_msg("extracting 1 D spectra....", self.opt.diagnostics)
#==============================================================================
# 1) initialise class objects a) noisy data, b) noiseless data if used, c) extraction of n_pix per bin
#==============================================================================
self.extractSpec = binning.extractSpec(self.opt.data, self.opt,
self.opt.diff, self.ApFactor, 1)
# 1 = final ap : means code knows this is the ap factor to use on noisy data and plots
# final ap 0 = signal only or n_pix evals, so no figures for aperture on image plotted.
if self.opt.pipeline.useSignal.val == 1:
self.extractSpec_signal = binning.extractSpec(
self.opt.data_signal_only, self.opt, 0, self.ApFactor,
0) #diff always 0 for signal
# use a set of 3 images with 1 value for all pixels to find out no of pixels per bin
self.extractSpec_nPix = binning.extractSpec(
self.opt.data[..., 0:3] * 0 + 1, self.opt, 1, self.ApFactor, 0)
#==============================================================================
# 2) apply mask and extract 1D spectrum if apply mask selected # special case for NIRISS
#==============================================================================
if self.opt.pipeline.pipeline_apply_mask.val == 1:
# a) noisy data
jexosim_msg(
"applying mask and extracting 1D spectrum from noisy data",
self.opt.diagnostics)
if self.opt.channel.instrument.val == 'NIRISS':
self.extractSpec.applyMask_extract_1D_NIRISS()
else:
self.extractSpec.applyMask_extract_1D()
# b) noiseless data if selected
if self.opt.pipeline.useSignal.val == 1:
jexosim_msg(
"applying mask and extracting 1D spectrum from signal only data",
self.opt.diagnostics)
if self.opt.channel.instrument.val == 'NIRISS':
self.extractSpec_signal.applyMask_extract_1D_NIRISS()
else:
self.extractSpec_signal.applyMask_extract_1D()
# c) sample data to find n_pix per bin
jexosim_msg(
"applying mask and extracting 1D spectrum to find n_pix per bin",
self.opt.diagnostics)
if self.opt.channel.instrument.val == 'NIRISS':
self.extractSpec_nPix.applyMask_extract_1D_NIRISS()
else:
jexosim_msg("extracting 1 D spectra for pixel in bin test",
self.opt.diagnostics)
self.extractSpec_nPix.applyMask_extract_1D()
#==============================================================================
# 3) extract 1D spectrum only if no mask selected
#==============================================================================
else:
# a) noisy data
jexosim_msg(
"NOT applying mask and extracting 1D spectrum from noisy data",
self.opt.diagnostics)
self.extractSpec.extract1DSpectra()
# b) noiseless data if selected
if self.opt.pipeline.useSignal.val == 1:
jexosim_msg(
"NOT applying mask and extracting 1D spectrum from signal only data",
self.opt.diagnostics)
self.extractSpec_signal.extract1DSpectra()
# c) sample data to find n_pix per bin
jexosim_msg(
"NOT applying mask and extracting 1D spectrum to find n_pix per bin",
self.opt.diagnostics)
self.extractSpec_nPix.extract1DSpectra()
self.nPix_1 = self.extractSpec_nPix.spectra[0]
jexosim_plot('n_pix per pixel column',
self.opt.diagnostics,
xdata=self.opt.cr_wl.value,
ydata=self.nPix_1,
marker='bo')
#==============================================================================
# 4) Now bin into spectral bins
#==============================================================================
# a) noisy data
jexosim_msg("binning 1D spectra into spectral bins... from noisy data",
self.opt.diagnostics)
self.extractSpec.binSpectra()
# b) noiseless data if selected
if self.opt.pipeline.useSignal.val == 1:
jexosim_msg(
"binning 1D spectra into spectral bins... from signal only data",
self.opt.diagnostics)
self.extractSpec_signal.binSpectra()
# c) sample data to find n_pix per bin
jexosim_msg(
"binning 1D spectra into spectral bins... to find n_pix per bin",
self.opt.diagnostics)
self.extractSpec_nPix.binSpectra()
#==============================================================================
# 5) Define objects from binning process
#==============================================================================
self.binnedLC = self.extractSpec.binnedLC
self.binnedWav = self.extractSpec.binnedWav
if self.opt.pipeline.useSignal.val == 1:
self.binnedLC_signal = self.extractSpec_signal.binnedLC
self.binnedWav_signal = self.extractSpec_signal.binnedWav
else:
self.binnedLC_signal = self.binnedLC
self.binnedWav_signal = self.binnedWav
if self.opt.timeline.apply_lc.val == 1:
self.extractSpec.binGamma()
self.binnedGamma = self.extractSpec.binnedGamma
self.nPix_2 = self.extractSpec_nPix.binnedLC[0]
jexosim_plot('n_pix per bin',
self.opt.diagnostics,
xdata=self.binnedWav,
ydata=self.nPix_2,
marker='ro')
def __init__(self, opt):
self.opt = opt
self.exp_end_time_grid = self.opt.ndr_end_time[
self.opt.effective_multiaccum - 1::self.opt.effective_multiaccum]
self.ndr_end_time_grid = self.opt.ndr_end_time
self.opt.data_raw = opt.data * 1
self.ApFactor = opt.pipeline.pipeline_ap_factor.val
if opt.background.EnableSource.val == 1:
self.opt.diff = 0
else:
self.opt.diff = 1
self.loadData()
opt.init_pix = np.zeros(opt.data[
..., 0].shape) # placeholder - replace with initial bad pixel map
self.dqInit()
self.satFlag()
if (opt.background.EnableDC.val == 1 or opt.background.EnableAll.val
== 1) and opt.background.DisableAll.val != 1:
if opt.diff == 0:
self.subDark()
if (opt.noise.ApplyPRNU.val == 1 or opt.noise.EnableAll.val
== 1) and opt.noise.DisableAll.val != 1:
jexosim_msg(
"mean and standard deviation of qe grid %s %s" %
(opt.qe_grid.mean(), opt.qe_grid.std()), opt.diagnostics)
self.flatField()
if (opt.background.EnableZodi.val == 1
or opt.background.EnableSunshield.val == 1
or opt.background.EnableEmission.val == 1
or opt.background.EnableAll.val
== 1) and opt.background.DisableAll.val != 1:
if opt.diff == 0:
self.subBackground()
jexosim_plot('sample NDR image',
opt.diagnostics,
image=True,
image_data=self.opt.data[..., 1])
self.doUTR() # lose astropy units at this step
jexosim_plot('sample exposure image',
opt.diagnostics,
image=True,
image_data=self.opt.data[..., 1])
# currently this applies zero values to saturated pixels
self.badCorr() # exp image obtained here
if (opt.noise.EnableSpatialJitter.val == 1
or opt.noise.EnableSpectralJitter.val == 1
or opt.noise.EnableAll.val
== 1) and opt.noise.DisableAll.val != 1:
jexosim_msg("Decorrelating pointing jitter...", opt.diagnostics)
self.jitterDecorr()
if opt.pipeline.pipeline_apply_mask.val == 1:
if opt.pipeline.pipeline_auto_ap.val == 1:
self.autoSizeAp()
self.extractSpec()
def autoSizeAp(self):
F = self.opt.channel.camera.wfno_x.val
wl_max = self.opt.channel.pipeline_params.wavrange_hi.val
wl_min = self.opt.channel.pipeline_params.wavrange_lo.val
wl = self.opt.cr_wl.value
if self.opt.timeline.apply_lc.val == 0:
x = 100
if self.opt.data.shape[2] < x: # has to use the noisy data
x = self.opt.data.shape[2]
sample = self.opt.data[..., 0:x]
elif self.opt.timeline.apply_lc.val == 1: # must use OOT portions else the transit will contribute falsely to the stand dev
if self.opt.pipeline.split == 0: # can only use the pre-transit values
total_obs_time = self.opt.exposure_time * self.opt.n_exp
pre_transit_time = self.opt.observation.obs_frac_t14_pre_transit.val * self.opt.T14
post_transit_time = self.opt.observation.obs_frac_t14_post_transit.val * self.opt.T14
pre_transit_exp = self.opt.n_exp * pre_transit_time / total_obs_time
post_transit_exp = self.opt.n_exp * post_transit_time / total_obs_time
x0 = int(pre_transit_exp * 0.75)
if x0 > 20:
x0 = 20
x1 = int(post_transit_exp * 0.75)
if x1 > 20:
x1 = 20
sample1 = self.opt.data[..., 0:x0]
sample2 = self.opt.data[..., -x1:]
sample = np.dstack((sample1, sample2))
if self.opt.pipeline.split == 1: # can only use the pre-transit values
total_obs_time = self.opt.exposure_time * self.opt.n_exp
pre_transit_time = self.opt.observation.obs_frac_t14_pre_transit.val * self.opt.T14
pre_transit_exp = pre_transit_time / self.opt.exposure_time
if self.opt.n_exp < pre_transit_exp:
x0 = int(self.opt.n_exp * 0.75)
else:
x0 = int(pre_transit_exp * 0.75)
if x0 > 40:
x0 = 40
sample = self.opt.data[..., 0:x0]
# print (sample.shape)
# zero_check = sample.sum(axis=0)
# zero_check = zero_check.sum(axis=1)
# idx_zero = np.argwhere(zero_check==0)
# sample = np.delete(sample, idx_zero, axis=1)
# print (sample.shape)
# print (idx_zero)
# idx_zero_0 = idx_zero[0].item()
# idx_zero_1 = idx_zero[-1].item()
# print (idx_zero_0, idx_zero_1)
# print (zero_check[idx_zero_0], zero_check[idx_zero_1])
# import matplotlib.pyplot as plt
# plt.figure('zero_check')
# plt.plot(zero_check)
# xxxx
jexosim_msg("SAMPLE SHAPE %s %s %s" % (sample.shape),
self.opt.diagnostics)
pix_size = (self.opt.channel.detector_pixel.pixel_size.val).to(
u.um).value
y_width = self.opt.data.shape[0] * pix_size
testApFactorMax = int(int(y_width / 2.) / (F * wl_max))
if (testApFactorMax * F * wl_max /
pix_size) + 1 >= self.opt.data.shape[0] / 2:
testApFactorMax = int(
((self.opt.data.shape[0] / 2) - 1) * pix_size / (F * wl_max))
ApList = np.arange(1.0, testApFactorMax + 1, 1.0)
if self.opt.channel.instrument.val == 'NIRISS':
testApFactorMax = 18.0 # set empirically
ApList = np.arange(7.0, testApFactorMax + 1, 1.0)
jexosim_msg("maximum test ap factor %s" % (testApFactorMax),
self.opt.diagnostics)
for i in ApList:
testApFactor = 1.0 * i
jexosim_msg("test ApFactor %s" % (testApFactor),
self.opt.diagnostics)
self.extractSample = binning.extractSpec(sample, self.opt,
self.opt.diff,
testApFactor, 2)
if self.opt.channel.instrument.val == 'NIRISS':
self.extractSample.applyMask_extract_1D_NIRISS()
else:
self.extractSample.applyMask_extract_1D()
spectra = self.extractSample.spectra
self.extractSample.binSpectra()
binnedLC = self.extractSample.binnedLC
wl = self.extractSample.binnedWav
SNR = binnedLC.mean(axis=0) / binnedLC.std(axis=0)
if i == ApList[0]:
SNR_stack = SNR
else:
SNR_stack = np.vstack((SNR_stack, SNR))
jexosim_plot('test aperture SNR',
self.opt.diagnostics,
xdata=wl,
ydata=SNR,
label=testApFactor)
idx = np.argwhere((wl >= wl_min) & (wl <= wl_max))
SNR_stack = SNR_stack[:, idx][..., 0]
wl = wl[idx].T[0]
wl0 = wl
nan_check = SNR_stack.sum(axis=0)
nan_idx = np.argwhere(np.isnan(nan_check))
SNR_stack = np.delete(SNR_stack, nan_idx, axis=1)
wl0 = np.delete(wl, nan_idx)
zero_check = SNR_stack.sum(axis=0)
zero_idx = np.argwhere(zero_check == 0)
SNR_stack = np.delete(SNR_stack, zero_idx, axis=1)
wl0 = np.delete(wl0, zero_idx)
best = []
for i in range(SNR_stack.shape[1]):
aa = SNR_stack[:, i]
# jexosim_msg i, np.argmax(aa), ApList[np.argmax(aa)]
best.append(ApList[np.argmax(aa)])
jexosim_plot('highest SNR aperture vs wavelength',
self.opt.diagnostics,
xdata=wl0,
ydata=best,
marker='bo-')
AvBest = np.round(np.mean(best), 0)
jexosim_msg("average best aperture factor %s" % (AvBest),
self.opt.diagnostics)
self.opt.AvBest = AvBest
self.ApFactor = AvBest
self.opt.pipeline.pipeline_ap_factor.val = self.ApFactor
def __init__(self, opt):
output_directory = opt.common.output_directory.val
filename = ""
runtag = int(np.random.uniform(0, 100000))
self.results_dict = {}
self.results_dict['simulation_mode'] = opt.simulation.sim_mode.val
self.results_dict[
'simulation_realisations'] = opt.simulation.sim_realisations.val
self.results_dict['ch'] = opt.observation.obs_channel.val
opt.pipeline.useSignal.val = 0
opt.simulation.sim_use_fast.val = 1
opt.pipeline.split = 0
opt.noise.ApplyRandomPRNU.val = 1
opt.timeline.apply_lc.val = 1
opt.timeline.useLDC.val = 1
opt.pipeline.useAllen.val = 0
opt.pipeline.fit_gamma.val = 0 #keep zero for uncert on p
start = 0
end = int(start + opt.no_real)
if (opt.no_real - start) > 1:
jexosim_msg("Monte Carlo selected", 1)
opt = self.run_JexoSimA(opt)
# np.save('/Users/user1/Desktop/fp_signal.npy', opt.fp_signal[1::3,1::3].value)
# np.save('/Users/user1/Desktop/fp_wav.npy', opt.x_wav_osr[1::3].value)
# xxxx
if opt.observation_feasibility == 0:
jexosim_msg("Observation not feasible...", opt.diagnostics)
self.feasibility = 0
else:
self.feasibility = 1
n_ndr0 = opt.n_ndr * 1
ndr_end_frame_number0 = opt.ndr_end_frame_number * 1
frames_per_ndr0 = opt.frames_per_ndr * 1
duration_per_ndr0 = opt.duration_per_ndr * 1
n_exp0 = opt.n_exp
lc0 = opt.lc_original * 1 # important this happens at this stage
if n_ndr0 > 10000:
opt.pipeline.split = 1
if opt.diagnostics == 1:
jexosim_msg('number of NDRs > 10000: using split protocol',
opt.diagnostics)
else:
opt.pipeline.split = 0
# #delete
# opt.pipeline.split = 1
for j in range(start, end):
if (opt.no_real - start) > 1:
jexosim_msg("", 1)
jexosim_msg(
"============= REALIZATION %s =============" % (j), 1)
jexosim_msg(opt.lab, 1)
jexosim_msg("", 1)
pp = time.time()
opt = self.run_JexoSimA1(
opt) # set QE grid for this realization
jexosim_msg("QE variations set", 1)
jexosim_msg("Number of exposures %s" % (n_exp0), 1)
print(opt.diagnostics)
# =============================================================================
# # split simulation into chunks to permit computation - makes no difference to final results
# =============================================================================
if opt.pipeline.split == 1:
jexosim_msg('Splitting data series into chunks',
opt.diagnostics)
# uses same QE grid and jitter timeline but otherwise randomoses noise
ndrs_per_round = opt.effective_multiaccum * int(
5000 / opt.multiaccum)
# ndrs_per_round = opt.effective_multiaccum*int(500/opt.multiaccum)
total_chunks = len(np.arange(0, n_ndr0, ndrs_per_round))
idx = np.arange(0, n_ndr0,
ndrs_per_round) # list of starting ndrs
for i in range(len(idx)):
jexosim_msg(
'=== Realisation %s Chunk %s / %s=====' %
(j, i + 1, total_chunks), 1)
jexosim_msg(opt.lab, 1)
if idx[i] == idx[-1]:
opt.n_ndr = n_ndr0 - idx[i]
opt.lc_original = lc0[:, idx[i]:]
opt.ndr_end_frame_number = ndr_end_frame_number0[
idx[i]:]
opt.frames_per_ndr = frames_per_ndr0[idx[i]:]
opt.duration_per_ndr = duration_per_ndr0[idx[i]:]
else:
opt.n_ndr = idx[i + 1] - idx[i]
opt.lc_original = lc0[:, idx[i]:idx[i + 1]]
print('idx start......', idx[i])
opt.ndr_end_frame_number = ndr_end_frame_number0[
idx[i]:idx[i + 1]]
opt.frames_per_ndr = frames_per_ndr0[idx[i]:idx[i +
1]]
opt.duration_per_ndr = duration_per_ndr0[
idx[i]:idx[i + 1]]
opt.n_exp = int(opt.n_ndr / opt.effective_multiaccum)
if i == 0:
opt.pipeline.pipeline_auto_ap.val = 1
opt.use_external_jitter = 0
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
opt.pipeline.pipeline_ap_factor.val = opt.AvBest
if (opt.noise.EnableSpatialJitter.val == 1
or opt.noise.EnableSpectralJitter.val == 1
or opt.noise.EnableAll.val
== 1) and opt.noise.DisableAll.val != 1:
opt.input_yaw_jitter, opt.input_pitch_jitter, opt._input_frame_osf = opt.yaw_jitter, opt.pitch_jitter, opt.frame_osf
else:
opt.pipeline.pipeline_auto_ap.val = 0
opt.use_external_jitter = 1 # uses the jitter timeline from the first realization
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
jexosim_msg(
'Aperture used %s' %
(opt.pipeline.pipeline_ap_factor.val),
opt.diagnostics)
binnedLC = opt.pipeline_stage_1.binnedLC
data = opt.pipeline_stage_1.opt.data_raw
if i == 0:
data_stack = data * 1
binnedLC_stack = binnedLC * 1
else:
data_stack = np.dstack((data_stack, data))
binnedLC_stack = np.vstack(
(binnedLC_stack, binnedLC))
del data
del binnedLC
aa = data_stack.sum(axis=0)
bb = aa.sum(axis=0)
jexosim_plot('test_from_sim',
opt.diagnostics,
ydata=bb[opt.effective_multiaccum::opt.
effective_multiaccum])
aa = binnedLC_stack.sum(axis=1)
jexosim_plot('test_from_pipeline',
opt.diagnostics,
ydata=aa)
opt.n_ndr = n_ndr0
opt.ndr_end_frame_number = ndr_end_frame_number0
opt.frames_per_ndr = frames_per_ndr0
opt.duration_per_ndr = duration_per_ndr0
opt.n_exp = n_exp0
elif opt.pipeline.split == 0:
opt = self.run_JexoSimB(opt)
if j == start: # first realization sets the ap, then the other use the same one
opt.pipeline.pipeline_auto_ap.val = 1
else:
opt.pipeline.pipeline_auto_ap.val = 0
opt = self.run_pipeline_stage_1(opt)
if j == start: # first realization sets the ap, then the other use the same one
opt.pipeline.pipeline_ap_factor.val = opt.AvBest
binnedLC_stack = opt.pipeline_stage_1.binnedLC
jexosim_plot('testvvv',
opt.diagnostics,
ydata=binnedLC_stack.sum(axis=1))
opt.pipeline_stage_1.binnedLC = binnedLC_stack
opt = self.run_pipeline_stage_2(opt)
pipeline = opt.pipeline_stage_2
p = pipeline.transitDepths
if j == start:
p_stack = p
else:
p_stack = np.vstack((p_stack, p))
jexosim_msg(
"time to complete realization %s %s" %
(j, time.time() - pp), opt.diagnostics)
self.results_dict['wl'] = pipeline.binnedWav
self.results_dict['input_spec'] = opt.cr
self.results_dict['input_spec_wl'] = opt.cr_wl
if j == start: # if only one realisation slightly different format
self.results_dict['p_stack'] = np.array(p)
self.results_dict['p_std'] = np.zeros(len(p))
self.results_dict['p_mean'] = np.array(p)
else:
self.results_dict['p_stack'] = np.vstack(
(self.results_dict['p_stack'], p))
self.results_dict['p_std'] = self.results_dict[
'p_stack'].std(axis=0)
self.results_dict['p_mean'] = self.results_dict[
'p_stack'].mean(axis=0)
time_tag = (datetime.now().strftime('%Y_%m_%d_%H%M_%S'))
self.results_dict['time_tag'] = time_tag
self.results_dict['bad_map'] = opt.bad_map
self.results_dict['example_exposure_image'] = opt.exp_image
self.results_dict['pixel wavelengths'] = opt.x_wav_osr[
1::3].value
self.results_dict['focal_plane_star_signal'] = opt.fp_signal[
1::3, 1::3].value
# fq = '/Users/user1/Desktop/tempGit/JexoSim_A/output/Full_eclipse_MIRI_LRS_slitless_SLITLESSPRISM_FAST_HD_209458_b_2021_07_18_0852_28.pickle'
# with open(fq, 'rb') as handle:
# rd = pickle.load(handle)
# rd['focal_plane_star_signal'] = opt.fp_signal[1::3,1::3]
# rd['pixel wavelengths'] = opt.x_wav_osr[1::3].value
# with open(fq, 'wb') as handle:
# pickle.dump(rd , handle, protocol=pickle.HIGHEST_PROTOCOL)
# run('Full_transit_NIRSpec_BOTS_G140M_F100LP_SUB2048_NRSRAPID_K2-18_b_2021_07_18_1402_38.pickle',0)
# run('Full_transit_NIRSpec_BOTS_G235M_F170LP_SUB2048_NRSRAPID_K2-18_b_2021_07_18_0709_24.pickle', 2)
# run('Full_transit_NIRSpec_BOTS_G395M_F290LP_SUB2048_NRSRAPID_K2-18_b_2021_07_17_2339_51.pickle',4)
# run('Full_eclipse_NIRCam_TSGRISM_F444W_SUBGRISM64_4_output_RAPID_HD_209458_b_2021_07_19_0654_29.pickle',0)
# run('Full_eclipse_NIRCam_TSGRISM_F322W2_SUBGRISM64_4_output_RAPID_HD_209458_b_2021_07_19_0359_08.pickle',1)
# run('Full_eclipse_MIRI_LRS_slitless_SLITLESSPRISM_FAST_HD_209458_b_2021_07_18_0852_28.pickle', 2)
if j != start:
os.remove(filename) # delete previous temp file
filename = '%s/Full_transit_%s_TEMP%s.pickle' % (
output_directory, opt.lab, runtag)
if opt.observation.obs_type.val == 2:
filename = '%s/Full_eclipse_%s_TEMP%s.pickle' % (
output_directory, opt.lab, runtag)
with open(filename, 'wb') as handle:
pickle.dump(self.results_dict,
handle,
protocol=pickle.HIGHEST_PROTOCOL)
del pipeline
del binnedLC_stack
gc.collect()
os.remove(filename) # delete previous temp file
# write final file
filename = '%s/Full_transit_%s_%s.pickle' % (output_directory,
opt.lab, time_tag)
if opt.observation.obs_type.val == 2:
filename = '%s/Full_eclipse_%s_%s.pickle' % (output_directory,
opt.lab, time_tag)
with open(filename, 'wb') as handle:
pickle.dump(self.results_dict,
handle,
protocol=pickle.HIGHEST_PROTOCOL)
jexosim_msg('Results in %s' % (filename), 1)
self.filename = 'Full_transit_%s_%s.pickle' % (opt.lab, time_tag)
if opt.observation.obs_type.val == 2:
self.filename = 'Full_eclipse_%s_%s.pickle' % (opt.lab,
time_tag)
write_record(opt, output_directory, self.filename,
opt.params_file_path)
def run(opt):
jexosim_msg('Running backgrounds module ...\n ', opt.diagnostics)
opt.zodi, zodi_transmission = backgrounds_lib.zodical_light(opt)
opt.emission = backgrounds_lib.optical_emission(opt)
opt.sunshield = backgrounds_lib.sunshield_emission(opt)
# import matplotlib.pyplot as plt
# plt.figure ('backgrounds 1')
# plt.plot(opt.sunshield.wl, opt.sunshield.sed, 'r', label='sunshield before transmission')
# plt.plot(opt.zodi.wl, opt.zodi.sed, 'g--', label='zodi before transmission')
# plt.plot(opt.emission.wl, opt.emission.sed ,'bx', label = 'optical after transmission')
# plt.grid()
# plt.legend()
# propagate star through zodi transmission
jexosim_lib.sed_propagation(opt.star.sed, zodi_transmission)
ch = opt.channel
Omega_pix = 2.0 * np.pi * (
1.0 - np.cos(np.arctan(0.5 / ch.camera.wfno_x()))) * u.sr
Apix = ((ch.detector_pixel.pixel_size.val).to(u.m))**2
opt.zodi.sed *= Apix * Omega_pix * opt.Re * u.electron / u.W / u.s
opt.sunshield.sed *= Apix * Omega_pix * opt.Re * u.electron / u.W / u.s
opt.emission.sed *= Apix * Omega_pix * opt.Re * u.electron / u.W / u.s
# apply transmission to zodi and sunshield (not to optical emission -alreay applied)
jexosim_lib.sed_propagation(opt.zodi, opt.total_transmission)
jexosim_lib.sed_propagation(opt.sunshield, opt.total_transmission)
opt.zodi.sed[np.isnan(opt.zodi.sed)] = 0
opt.sunshield.sed[np.isnan(opt.sunshield.sed)] = 0
opt.emission.sed[np.isnan(opt.emission.sed)] = 0
opt.zodi.sed *= opt.d_x_wav_osr
opt.sunshield.sed *= opt.d_x_wav_osr
opt.emission.sed *= opt.d_x_wav_osr
zodi_photons_sed = copy.deepcopy(opt.zodi.sed)
sunshield_photons_sed = copy.deepcopy(opt.sunshield.sed)
emission_photons_sed = copy.deepcopy(opt.emission.sed)
if ch.camera.slit_width.val == 0:
slit_size = opt.fpn[
1] * 2 # to ensure all wavelengths convolved onto all pixels in slitless case
else:
slit_size = ch.camera.slit_width.val
# import matplotlib.pyplot as plt
# plt.figure ('backgrounds 2')
# plt.plot(opt.zodi.wl, opt.zodi.sed, 'bo-')
# print (opt.zodi.sed)
# need to work on this to make more accurate : filter wavelength range might not correspond to wl sol on the detector, i.e. some wavelengths not being included that should be
opt.zodi.sed = scipy.signal.convolve(
opt.zodi.sed, np.ones(np.int(slit_size * ch.simulation_factors.osf())),
'same') * opt.zodi.sed.unit
opt.sunshield.sed = scipy.signal.convolve(
opt.sunshield.sed,
np.ones(np.int(slit_size * ch.simulation_factors.osf())),
'same') * opt.sunshield.sed.unit
opt.emission.sed = scipy.signal.convolve(
opt.emission.sed.value,
np.ones(np.int(slit_size * ch.simulation_factors.osf())),
'same') * opt.emission.sed.unit
# print (opt.zodi.sed)
# import matplotlib.pyplot as plt
# plt.figure ('backgrounds 2')
# plt.plot(opt.zodi.wl, opt.zodi.sed, 'ro-')
# xxxx
opt.zodi_sed_original = copy.deepcopy(opt.zodi.sed)
opt.sunshield_sed_original = copy.deepcopy(opt.sunshield.sed)
opt.emission_sed_original = copy.deepcopy(opt.emission.sed)
jexosim_plot('zodi spectrum',
opt.diagnostics,
xdata=opt.zodi.wl,
ydata=opt.zodi.sed)
jexosim_plot('sunshield spectrum',
opt.diagnostics,
xdata=opt.sunshield.wl,
ydata=opt.sunshield.sed)
jexosim_plot('emission spectrum',
opt.diagnostics,
xdata=opt.emission.wl,
ydata=opt.emission.sed)
# ====Now work out quantum yield ==============================================
# weight the qy by relative number of photons
zodi_w_qy = zodi_photons_sed * opt.quantum_yield.sed
# convolve this with slit
zodi_w_qy = scipy.signal.convolve(
zodi_w_qy, np.ones(np.int(slit_size * ch.simulation_factors.osf())),
'same') * opt.zodi.sed.unit
# divide by convolved spectrum.... thus this factor will return the expected qy
opt.qy_zodi = zodi_w_qy / opt.zodi.sed
# (Ph conv. slit )x Qy' = (Ph x Qy) conv. slit
# thus Qy' is the needed Qy per pixel applied to the convolve Ph spectrum.
sunshield_w_qy = sunshield_photons_sed * opt.quantum_yield.sed
sunshield_w_qy = scipy.signal.convolve(
sunshield_w_qy, np.ones(np.int(
slit_size * ch.simulation_factors.osf())),
'same') * opt.sunshield.sed.unit
opt.qy_sunshield = sunshield_w_qy / opt.sunshield.sed
emission_w_qy = emission_photons_sed * opt.quantum_yield.sed
emission_w_qy = scipy.signal.convolve(
emission_w_qy, np.ones(np.int(
slit_size * ch.simulation_factors.osf())),
'same') * opt.emission.sed.unit
opt.qy_emission = emission_w_qy / opt.emission.sed
opt.qy_zodi[np.isnan(opt.qy_zodi)] = 1
opt.qy_sunshield[np.isnan(opt.qy_sunshield)] = 1
opt.qy_emission[np.isnan(opt.qy_emission)] = 1
return opt
def run(opt):
opt.fp = copy.deepcopy(
opt.fp_original
) # needed to reuse if cropped fp is used and monte carlo mode used
opt.fp_signal = copy.deepcopy(opt.fp_signal_original) # "
opt.zodi.sed = copy.deepcopy(opt.zodi_sed_original) # "
opt.sunshield.sed = copy.deepcopy(opt.sunshield_sed_original) # "
opt.emission.sed = copy.deepcopy(opt.emission_sed_original) # "
opt.lc = copy.deepcopy(opt.lc_original)
opt.ldc = copy.deepcopy(opt.ldc_original)
opt.cr_wl = copy.deepcopy(opt.cr_wl_original)
opt.cr = copy.deepcopy(opt.cr_original)
opt.x_wav_osr = copy.deepcopy(opt.x_wav_osr_original)
opt.x_pix_osr = copy.deepcopy(opt.x_pix_osr_original)
opt.qe = copy.deepcopy(opt.qe_original)
opt.qe_uncert = copy.deepcopy(opt.qe_uncert_original)
opt.quantum_yield = copy.deepcopy(opt.quantum_yield_original)
opt.qy_zodi = copy.deepcopy(opt.qy_zodi_original)
opt.qy_sunshield = copy.deepcopy(opt.qy_sunshield_original)
opt.qy_emission = copy.deepcopy(opt.qy_emission_original)
opt.syst_grid = copy.deepcopy(opt.syst_grid_original)
opt = signal_lib.initiate_signal(opt)
opt = signal_lib.apply_jitter(opt) # opt.signal iniatated here
opt = signal_lib.apply_lc(opt)
opt = signal_lib.initiate_noise(opt)
opt = signal_lib.apply_non_stellar_photons(opt)
opt = signal_lib.apply_prnu(opt)
opt = signal_lib.apply_dc(opt)
opt = signal_lib.apply_poisson_noise(opt)
opt = signal_lib.apply_quantum_yield(opt)
opt = signal_lib.apply_fano(opt)
opt = signal_lib.apply_utr_correction(opt)
opt = signal_lib.apply_combined_noise(opt)
opt = signal_lib.make_ramps(opt)
opt = signal_lib.apply_ipc(opt)
opt = signal_lib.apply_read_noise(opt)
opt = signal_lib.apply_gaps(opt)
opt.data = opt.signal
opt.data_signal_only = opt.signal_only
jexosim_plot('focal plane check1',
opt.diagnostics,
image=True,
image_data=opt.fp_signal[1::3, 1::3],
aspect='auto',
interpolation=None,
xlabel='x \'spectral\' pixel',
ylabel='y \'spatial\' pixel')
jexosim_plot('test - check NDR0',
opt.diagnostics,
image=True,
image_data=opt.data[..., 0])
jexosim_plot('test - check NDR1',
opt.diagnostics,
image=True,
image_data=opt.data[..., 1])
return opt
def get_light_curve(opt, planet_sed, wavelength, obs_type):
wavelength = wavelength.value
timegrid = opt.z_params[0]
t0 = opt.z_params[1]
per = opt.z_params[2]
ars = opt.z_params[3]
inc = opt.z_params[4]
ecc = opt.z_params[5]
omega = opt.z_params[6]
if opt.observation.obs_type.val == 2:
opt.timeline.useLDC.val = 0
if opt.timeline.useLDC.val == 0: # linear ldc
jexosim_msg('LDCs set to zero', 1)
u0 = np.zeros(len(wavelength))
u1 = np.zeros(len(wavelength))
ldc = np.vstack((wavelength, u0, u1))
elif opt.timeline.useLDC.val == 1: # use to get ldc from filed values
u0, u1 = getLDC_interp(opt, opt.planet.planet, wavelength)
ldc = np.vstack((wavelength, u0, u1))
gamma = np.zeros((ldc.shape[1], 2))
gamma[:, 0] = ldc[1]
gamma[:, 1] = ldc[2]
jexosim_plot('ldc', opt.diagnostics, ydata=ldc[1])
jexosim_plot('ldc', opt.diagnostics, ydata=ldc[2])
tm = QuadraticModel(interpolate=False)
tm.set_data(timegrid)
lc = np.zeros((len(planet_sed), len(timegrid)))
if obs_type == 1: #primary transit
for i in range(len(planet_sed)):
k = np.sqrt(planet_sed[i]).value
lc[i, ...] = tm.evaluate(k=k,
ldc=gamma[i, ...],
t0=t0,
p=per,
a=ars,
i=inc,
e=ecc,
w=omega)
jexosim_plot('light curve check',
opt.diagnostics,
ydata=lc[i, ...])
elif obs_type == 2: # secondary eclipse
for i in range(len(planet_sed)):
k = np.sqrt(planet_sed[i]) # planet star radius ratio
lc_base = tm.evaluate(k=k,
ldc=[0, 0],
t0=t0,
p=per,
a=ars,
i=inc,
e=ecc,
w=omega)
jexosim_plot('light curve check', opt.diagnostics, ydata=lc_base)
# f_e = (planet_sed[i] + ( lc_base -1.0))/planet_sed[i]
# lc[i, ...] = 1.0 + f_e*(planet_sed[i])
lc[i, ...] = lc_base + planet_sed[i]
jexosim_plot('light curve check',
opt.diagnostics,
ydata=lc[i, ...])
return lc, ldc
def __init__(self, opt):
output_directory = opt.common.output_directory.val
filename = ""
self.results_dict = {}
self.results_dict['simulation_mode'] = opt.simulation.sim_mode.val
self.results_dict[
'simulation_realisations'] = opt.simulation.sim_realisations.val
self.results_dict['ch'] = opt.observation.obs_channel.val
opt.pipeline.useSignal.val = 0
opt.simulation.sim_use_fast.val = 1
opt.pipeline.split = 0
opt.noise.ApplyRandomPRNU.val = 1
opt.timeline.apply_lc.val = 1
opt.timeline.useLDC.val = 1
opt.pipeline.useAllen.val = 0
opt.pipeline.fit_gamma.val = 0 #keep zero for uncert on p
start = 0
end = int(start + opt.no_real)
if (opt.no_real - start) > 1:
jexosim_msg("Monte Carlo selected", 1)
opt = self.run_JexoSimA(opt)
if opt.observation_feasibility == 0:
jexosim_msg("Observation not feasible...", opt.diagnostics)
self.feasibility = 0
else:
self.feasibility = 1
n_ndr0 = opt.n_ndr * 1
ndr_end_frame_number0 = opt.ndr_end_frame_number * 1
frames_per_ndr0 = opt.frames_per_ndr * 1
duration_per_ndr0 = opt.duration_per_ndr * 1
n_exp0 = opt.n_exp
lc0 = opt.lc_original * 1 # important this happens at this stage
if n_ndr0 > 10000:
opt.pipeline.split = 1
if opt.diagnostics == 1:
jexosim_msg('number of NDRs > 10000: using split protocol',
opt.diagnostics)
else:
opt.pipeline.split = 0
# #delete
# opt.pipeline.split = 1
for j in range(start, end):
if (opt.no_real - start) > 1:
jexosim_msg("", 1)
jexosim_msg(
"============= REALIZATION %s =============" % (j), 1)
jexosim_msg(opt.lab, 1)
jexosim_msg("", 1)
pp = time.time()
opt = self.run_JexoSimA1(
opt) # set QE grid for this realization
jexosim_msg("QE variations set", 1)
jexosim_msg("Number of exposures %s" % (n_exp0), 1)
# =============================================================================
# # split simulation into chunks to permit computation - makes no difference to final results
# =============================================================================
if opt.pipeline.split == 1:
jexosim_msg('Splitting data series into chunks',
opt.diagnostics)
# uses same QE grid and jitter timeline but otherwise randomoses noise
ndrs_per_round = opt.effective_multiaccum * int(
5000 / opt.multiaccum)
# ndrs_per_round = opt.effective_multiaccum*int(500/opt.multiaccum)
total_chunks = len(np.arange(0, n_ndr0, ndrs_per_round))
idx = np.arange(0, n_ndr0,
ndrs_per_round) # list of starting ndrs
for i in range(len(idx)):
jexosim_msg(
'=== Realisation %s Chunk %s / %s=====' %
(j, i + 1, total_chunks), opt.diagnostics)
if idx[i] == idx[-1]:
opt.n_ndr = n_ndr0 - idx[i]
opt.lc_original = lc0[:, idx[i]:]
opt.ndr_end_frame_number = ndr_end_frame_number0[
idx[i]:]
opt.frames_per_ndr = frames_per_ndr0[idx[i]:]
opt.duration_per_ndr = duration_per_ndr0[idx[i]:]
else:
opt.n_ndr = idx[i + 1] - idx[i]
opt.lc_original = lc0[:, idx[i]:idx[i + 1]]
print('idx start......', idx[i])
opt.ndr_end_frame_number = ndr_end_frame_number0[
idx[i]:idx[i + 1]]
opt.frames_per_ndr = frames_per_ndr0[idx[i]:idx[i +
1]]
opt.duration_per_ndr = duration_per_ndr0[
idx[i]:idx[i + 1]]
opt.n_exp = int(opt.n_ndr / opt.effective_multiaccum)
if i == 0:
opt.pipeline.pipeline_auto_ap.val = 1
opt.use_external_jitter = 0
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
opt.pipeline.pipeline_ap_factor.val = opt.AvBest
if (opt.noise.EnableSpatialJitter.val == 1
or opt.noise.EnableSpectralJitter.val == 1
or opt.noise.EnableAll.val
== 1) and opt.noise.DisableAll.val != 1:
opt.input_yaw_jitter, opt.input_pitch_jitter, opt._input_frame_osf = opt.yaw_jitter, opt.pitch_jitter, opt.frame_osf
else:
opt.pipeline.pipeline_auto_ap.val = 0
opt.use_external_jitter = 1 # uses the jitter timeline from the first realization
opt = self.run_JexoSimB(opt)
opt = self.run_pipeline_stage_1(opt)
jexosim_msg(
'Aperture used %s' %
(opt.pipeline.pipeline_ap_factor.val),
opt.diagnostics)
binnedLC = opt.pipeline_stage_1.binnedLC
data = opt.pipeline_stage_1.opt.data_raw
if i == 0:
data_stack = data
binnedLC_stack = binnedLC
else:
data_stack = np.dstack((data_stack, data))
binnedLC_stack = np.vstack(
(binnedLC_stack, binnedLC))
aa = data_stack.sum(axis=0)
bb = aa.sum(axis=0)
jexosim_plot('test_from_sim',
opt.diagnostics,
ydata=bb[opt.effective_multiaccum::opt.
effective_multiaccum])
aa = binnedLC_stack.sum(axis=1)
jexosim_plot('test_from_pipeline',
opt.diagnostics,
ydata=aa)
opt.n_ndr = n_ndr0
opt.ndr_end_frame_number = ndr_end_frame_number0
opt.frames_per_ndr = frames_per_ndr0
opt.duration_per_ndr = duration_per_ndr0
opt.n_exp = n_exp0
elif opt.pipeline.split == 0:
opt = self.run_JexoSimB(opt)
if j == start: # first realization sets the ap, then the other use the same one
opt.pipeline.pipeline_auto_ap.val = 1
else:
opt.pipeline.pipeline_auto_ap.val = 0
opt = self.run_pipeline_stage_1(opt)
if j == start: # first realization sets the ap, then the other use the same one
opt.pipeline.pipeline_ap_factor.val = opt.AvBest
binnedLC_stack = opt.pipeline_stage_1.binnedLC
jexosim_plot('testvvv',
opt.diagnostics,
ydata=binnedLC_stack.sum(axis=1))
# =============================================================================
# Now put intermediate data (binned light curves) into FITS files
# =============================================================================
opt.pipeline_stage_1.binnedLC *= u.electron
opt.pipeline_stage_1.binnedWav *= u.um
self.filename = output.run(opt)
write_record(opt, output_directory, self.filename,
opt.params_file_path)
jexosim_msg(
'File saved as %s/%s' % (output_directory, self.filename),
1)
