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Merged
arjunsavel merged 2 commits into from
Mar 5, 2025
Merged

make those local changes! #114

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24d08fc
make those local changes!
Mar 5, 2025
57cb679
Merge branch 'main' into local_changes
arjunsavel Mar 5, 2025
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2 changes: 1 addition & 1 deletion src/scope/calc_quantities.py
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Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,7 @@ def calc_crossing_time(
n_exp: number of exposures you can take during transit.

"""

print(mstar, rstar, period, e, b, peri, mplanet)
orbit = KeplerianOrbit(
m_star=mstar, # solar masses!
r_star=rstar, # solar radii!
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12 changes: 6 additions & 6 deletions src/scope/input.txt
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Expand Up @@ -16,7 +16,7 @@ Planet name: WASP-166 b

modelname wasp_166_150seed_ld # name of the model. used for saving the output files.
seed 150 # seed for the random number generator when generating noisy data. set to None for a random seed.
log_level INFO # logging level above which statements are printed. Supported levels are ``DEBUG``, ``INFO``, ``WARNING``, ``ERROR``, and ``CRITICAL``.
log_level DEBUG # logging level above which statements are printed. Supported levels are ``DEBUG``, ``INFO``, ``WARNING``, ``ERROR``, and ``CRITICAL``.

# Filepaths
planet_spectrum_path /home/asavel/scratch/retrieval_stuff/fm_wasp_77ab_noisy/fm_wasp_77ab_noisy/spectrum_tran_WASP-166b_0.3_c_to_o.pic
Expand All @@ -28,7 +28,7 @@ snr_path /home/asavel/scratch/scope/src/scope/data/snr_IGRINS_LTT-
Rp DATABASE # planetary radius in Jupiter radii. [DB]
Mp DATABASE # planetary mass in Jupiter masses. [DB]
e DATABASE # eccentricity of the planet's orbit. [DB]
omega DATABASE # argument of periastron of the planet's orbit, in degrees. [DB]
omega 0 # argument of periastron of the planet's orbit, in degrees. [DB]
b DATABASE # impact parameter of the planet's orbit. [DB]
Rstar DATABASE # stellar radius, in solar radii. [DB]
Mstar DATABASE # stellar mass, in solar masses. [DB]
Expand All @@ -47,7 +47,7 @@ lambda_misalign 0 # misalignment angle of the planet's or
inc 90.0 # inclination of the planet's orbit with respect to the line of sight, in degrees. only matters if include_rm is set to True. and observation is set to transmission.

# Instrument Parameters
spectrograph IGRINS # name of the spectrograph to simulate. currently spectrographs are ``IGRINS`` and ``CRIRES+``.
instrument IGRINS # name of the spectrograph to simulate. currently spectrographs are ``IGRINS`` and ``CRIRES+``.
blaze True # whether to include a blaze function or not.
wav_error False # whether to include wavelength solution errors or not.
order_dep_throughput True # whether to include order-dependent throughput variations.
Expand All @@ -56,9 +56,9 @@ vary_throughput True # whether to include throughput variations.

# Observation Parameters
observation transmission # type of observation to perform. supported observations are ``emission`` and ``transmission``.
phase_start 0.986222200994206 # phase of the beginning of the observations. 0 is center of transit, 0.5 is secondary eclipse. If DATABASE, just the transit duration. [DB]
phase_end 1.0137777990057941 # phase of the end of the observations. 0 is center of transit, 0.5 is secondary eclipse. If DATABASE, just the transit duration. [DB]
n_exposures 0 # number of exposures to simulate. sets the phases of the exposures. if set to 0, the minimum number of exposures that prevent pixel crossing for the provided instrument is used.
phase_start DATABASE # phase of the beginning of the observations. 0 is center of transit, 0.5 is secondary eclipse. If DATABASE, just the transit duration. [DB]
phase_end DATABASE # phase of the end of the observations. 0 is center of transit, 0.5 is secondary eclipse. If DATABASE, just the transit duration. [DB]
n_exposures 17 # number of exposures to simulate. sets the phases of the exposures. if set to 0, the minimum number of exposures that prevent pixel crossing for the provided instrument is used.
star True # whether to include the star in the simulation. In general, you'd like to!
telluric True # whether to include tellurics in the simulation. In general, you'd like to!
SNR 250 # signal-to-noise ratio of the observations, per pixel. I.e., what sets the photon counts at the detector.
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79 changes: 42 additions & 37 deletions src/scope/input_output.py
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Expand Up @@ -41,6 +41,7 @@ def __init__(self, message="scope input file error:"):
"e": "pl_orbeccen",
"peri": "pl_orblper",
"v_rot_star": "st_vsin",
"b": "pl_imppar",
"Kmag": "sy_kmag",
}

Expand Down Expand Up @@ -120,8 +121,10 @@ def coerce_integers(data, key, value):


def coerce_database(data, key, value, astrophysical_params, planet_name, database_path):

if value == "DATABASE" and key in astrophysical_params:
data[key] = query_database(planet_name, key, database_path)

elif value == "DATABASE" and key in ["phase_start", "phase_end"]:
tdur = query_database(planet_name, "pl_trandur", database_path)
period = query_database(planet_name, "pl_orbper", database_path)
Expand Down Expand Up @@ -206,6 +209,8 @@ def parse_input_file(
"P_rot",
"a",
"u1",
"e",
"b",
"u2",
"Mstar",
"Mp",
Expand Down Expand Up @@ -318,113 +323,113 @@ def parse_arguments():

# Required parameters
parser.add_argument(
"--planet_spectrum_path", type=str, default=".", help="Path to planet spectrum"
"--planet_spectrum_path", type=str, help="Path to planet spectrum"
)
parser.add_argument(
"--star_spectrum_path", type=str, default=".", help="Path to star spectrum"
"--star_spectrum_path", type=str, help="Path to star spectrum"
)
parser.add_argument(
"--data_cube_path", type=str, default=".", help="Path to data cube"
"--data_cube_path", type=str, help="Path to data cube"
)

# Optional parameters with their defaults matching your function
parser.add_argument(
"--phase_start",
type=float,
default=0,

help="Start phase of the simulated observations",
)
parser.add_argument(
"--phase_end",
type=float,
default=1,

help="End phase of the simulated observations",
)
parser.add_argument(
"--n_exposures", type=int, default=10, help="Number of exposures"
"--n_exposures", type=int, help="Number of exposures"
)
parser.add_argument(
"--observation", type=str, default="emission", help="Observation type"
"--observation", type=str, help="Observation type"
)
parser.add_argument("--blaze", type=bool, default=True, help="Blaze flag")
parser.add_argument("--blaze", type=bool, help="Blaze flag")
parser.add_argument(
"--n_princ_comp", type=int, default=4, help="Number of principal components"
"--n_princ_comp", type=int, help="Number of principal components"
)
parser.add_argument("--star", type=bool, default=True, help="Star flag")
parser.add_argument("--SNR", type=float, default=250, help="Signal to noise ratio")
parser.add_argument("--telluric", type=bool, default=True, help="Telluric flag")
parser.add_argument("--star", type=bool, help="Star flag")
parser.add_argument("--SNR", type=float, help="Signal to noise ratio")
parser.add_argument("--telluric", type=bool, help="Telluric flag")
parser.add_argument(
"--tell_type", type=str, default="data-driven", help="Telluric type"
"--tell_type", type=str, help="Telluric type"
)
parser.add_argument(
"--time_dep_tell", type=bool, default=False, help="Time dependent telluric"
"--time_dep_tell", type=bool, help="Time dependent telluric"
)
parser.add_argument(
"--wav_error", type=bool, default=False, help="Wavelength error flag"
"--wav_error", type=bool, help="Wavelength error flag"
)
parser.add_argument(
"--rv_semiamp_orbit", type=float, default=0.3229, help="RV semi-amplitude orbit"
"--rv_semiamp_orbit", type=float, help="RV semi-amplitude orbit"
)
parser.add_argument(
"--order_dep_throughput",
type=bool,
default=True,

help="Order dependent throughput",
)
parser.add_argument(
"--Rp", type=float, default=1.21, help="Planet radius (Jupiter radii)"
"--Rp", type=float, help="Planet radius (Jupiter radii)"
)
parser.add_argument(
"--Rstar", type=float, default=0.955, help="Star radius (solar radii)"
"--Rstar", type=float, help="Star radius (solar radii)"
)
parser.add_argument(
"--kp", type=float, default=192.02, help="Planetary orbital velocity (km/s)"
"--kp", type=float, help="Planetary orbital velocity (km/s)"
)
parser.add_argument("--v_rot", type=float, default=4.5, help="Rotation velocity")
parser.add_argument("--scale", type=float, default=1.0, help="Scale factor")
parser.add_argument("--v_sys", type=float, default=0.0, help="Systemic velocity")
parser.add_argument("--v_rot", type=float, help="Rotation velocity")
parser.add_argument("--scale", type=float, help="Scale factor")
parser.add_argument("--v_sys", type=float, help="Systemic velocity")
parser.add_argument(
"--pca_rmeove", type=str, default="subtract", help="PCA removal scheme"
"--pca_rmeove", type=str, help="PCA removal scheme"
)
parser.add_argument(
"--modelname", type=str, default="yourfirstsimulation", help="Model name"
"--modelname", type=str, help="Model name"
)
parser.add_argument(
"--divide_out_of_transit",
type=bool,
default=False,

help="Divide out of transit",
)
parser.add_argument(
"--out_of_transit_dur", type=float, default=0.1, help="Out of transit duration"
"--out_of_transit_dur", type=float, help="Out of transit duration"
)
parser.add_argument(
"--include_rm", type=bool, default=False, help="Include RM effect"
"--include_rm", type=bool, help="Include RM effect"
)
parser.add_argument(
"--v_rot_star", type=float, default=3.0, help="Star rotation velocity"
"--v_rot_star", type=float, help="Star rotation velocity"
)
parser.add_argument("--a", type=float, default=0.033, help="Semi-major axis")
parser.add_argument("--a", type=float, help="Semi-major axis")
parser.add_argument(
"--lambda_misalign", type=float, default=0.0, help="Misalignment angle"
"--lambda_misalign", type=float, help="Misalignment angle"
)
parser.add_argument("--inc", type=float, default=90.0, help="Inclination")
parser.add_argument("--seed", type=int, default=42, help="Random seed")
parser.add_argument("--LD", type=bool, default=True, help="Limb darkening")
parser.add_argument("--inc", type=float, help="Inclination")
parser.add_argument("--seed", type=int, help="Random seed")
parser.add_argument("--LD", type=bool, help="Limb darkening")
parser.add_argument(
"--vary_throughput", type=bool, default=True, help="Vary throughput"
"--vary_throughput", type=bool, help="Vary throughput"
)
parser.add_argument(
"--log_level",
type=str,
default="INFO",

choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
help="Logging level (default: INFO)",
)

# For file input option
parser.add_argument(
"--input_file", type=str, default="input.txt", help="Input file with parameters"
"--input_file", type=str, default='input.txt',help="Input file with parameters"
)

return parser.parse_args()
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2 changes: 1 addition & 1 deletion src/scope/run_simulation.py
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Expand Up @@ -625,7 +625,7 @@ def simulate_observation(

logger = setup_logging(log_level=inputs["log_level"])
logger.debug(f"Parsed inputs: {inputs}")

print(inputs)
# Call the simulation function with the merged parameters
try:
simulate_observation(**inputs)
Expand Down
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