diff --git a/src/scope/run_simulation.py b/src/scope/run_simulation.py index 1826708..f236d23 100644 --- a/src/scope/run_simulation.py +++ b/src/scope/run_simulation.py @@ -4,14 +4,9 @@ calculating the log likelihood and cross-correlation function of the data given the model parameters. """ -import os - -import numpy as np -from tqdm import tqdm - from scope.broadening import * from scope.ccf import * -from scope.input_output import parse_input_file, write_input_file, parse_arguments +from scope.input_output import * from scope.noise import * from scope.tellurics import * from scope.utils import * @@ -92,7 +87,7 @@ def make_data( rv_planet, rv_star = calc_rvs( v_sys, v_sys_measured, Kp, rv_semiamp_orbit, phases ) # measured in m/s now - + flux_cube = np.zeros( (n_order, n_exposure, n_pixel) ) # will store planet and star signal @@ -120,7 +115,7 @@ def make_data( star, observation, ) - + throughput_baselines = np.loadtxt(abs_path + "/data/throughputs.txt") flux_cube = detrend_cube(flux_cube, n_order, n_exposure) @@ -275,7 +270,7 @@ def make_data( ) # returning CCF and logL values -#@njit +# @njit def calc_log_likelihood( v_sys, Kp, @@ -432,7 +427,7 @@ def simulate_observation( lambda_misalign=0.0, inc=90.0, seed=42, - LD=True, + LD=True, vary_throughput=True, instrument="IGRINS", snr_path=None, @@ -502,7 +497,7 @@ def simulate_observation( # instrument profile convolution instrument_kernel = get_instrument_kernel(instrument) Fp_conv = np.convolve(Fp_conv_rot, instrument_kernel, mode="same") - print('here spectrum') + print("here spectrum") print(Fp_conv) star_wave, star_flux = np.loadtxt( star_spectrum_path @@ -555,7 +550,7 @@ def simulate_observation( instrument=instrument, ) - run_name = f"{n_princ_comp}_NPC_{blaze}_blaze_{star}_star_{telluric}_telluric_{SNR}_SNR_{tell_type}_{time_dep_tell}_{wav_error}_{order_dep_throughput}" + run_name = f"{n_princ_comp}_NPC_{blaze}_blaze_{star}_star_{telluric}_telluric_{SNR}_SNR_{tell_type}_{time_dep_tell}_{wav_error}_{order_dep_throughput}_{seed}" save_data(outdir, run_name, flux_cube, flux_cube_nopca, A_noplanet, just_tellurics) @@ -585,7 +580,7 @@ def simulate_observation( star=star, observation=observation, v_sys_measured=v_sys, - LD=LD + LD=LD, ) lls[l, k], ccfs[l, k] = res @@ -596,17 +591,17 @@ def simulate_observation( args = parse_arguments() # First, parse the input file to get base parameters inputs = parse_input_file(args.input_file) - + # Then override with any command line arguments that were explicitly provided args_dict = vars(args) for key, value in args_dict.items(): # Skip the input_file parameter - if key == 'input_file': + if key == "input_file": continue - + # Only override if the argument was explicitly provided (not None) if value is not None: inputs[key] = value - + # Call the simulation function with the merged parameters simulate_observation(**inputs)