More logging, and yell about tellurics and blaze correctly

src/scope/input_output.py

@@ -241,7 +241,11 @@ def parse_input_file(
 
     data = calculate_derived_parameters(data)
 
-    if data["tell_type"] == "data-driven" and data["blaze"] == False:
+    if (
+        data["tell_type"] == "data-driven"
+        and data["blaze"] == False
+        and data["telluric"] == True
+    ):
         raise ScopeConfigError("Data-driven tellurics requires blaze set to True.")
 
     return data

src/scope/noise.py

@@ -3,8 +3,11 @@
 """
 import numpy as np
 
+from scope.logger import get_logger
 from scope.utils import *
 
+logger = get_logger()
+
 test_data_path = os.path.join(os.path.dirname(__file__), "data")
 
 
@@ -92,7 +95,8 @@ def add_quadratic_noise(flux_cube_model, wl_grid, SNR, IGRINS=False, **kwargs):
 
     else:
         raise NotImplementedError("Only IGRINS data is currently supported.")
-
+    logger.debug("Added quadratic IGRINS noise to the flux cube model.")
+    logger.debug("mean noisy flux: {}".format(np.mean(noisy_flux)))
     return noisy_flux
 
 
@@ -130,6 +134,9 @@ def add_crires_plus_noise(flux_cube_model, wl_grid, SNR):
             # a few quick checks to make sure that nothing has gone wrong with adding noise
             noisy_flux[order][exposure][noisy_flux[order][exposure] < 0.0] = 0.0
             noisy_flux[order][exposure][~np.isfinite(noisy_flux[order][exposure])] = 0.0
+    logger.debug("Added CRIRES+ noise to the flux cube model.")
+    logger.debug("mean SNR: {}".format(np.mean(SNR)))
+    logger.debug("mean noisy flux: {}".format(np.mean(noisy_flux)))
     return noisy_flux
 
 

src/scope/run_simulation.py

@@ -93,6 +93,7 @@ def make_data(
 
     np.random.seed(seed)
     logger.info(f"Seed set to {seed}")
+    logger.debug(f"Mean stellar flux: {np.mean(Fstar_conv)}")
 
     rv_planet, rv_star = calc_rvs(
         v_sys, v_sys_measured, Kp, rv_semiamp_orbit, phases
@@ -143,7 +144,7 @@ def make_data(
                 flux_cube[:, i, :], 90
             )
             flux_cube[:, i, :] *= throughput_factor
-
+    logger.debug(f"Mean flux post-throughput variation: {np.mean(flux_cube)}")
     if tellurics:
         if instrument != "IGRINS":
             raise NotImplementedError(
@@ -174,8 +175,11 @@ def make_data(
         just_tellurics[just_tellurics < 0.0] = 0.0
     flux_cube = detrend_cube(flux_cube, n_order, n_exposure)
     if blaze:
-        flux_cube = add_blaze_function(wlgrid, flux_cube, n_order, n_exposure)
+        flux_cube = add_blaze_function(
+            wlgrid, flux_cube, n_order, n_exposure, instrument=instrument
+        )
         flux_cube[flux_cube < 0.0] = 0.0
+        logger.debug(f"Mean flux post-blaze: {np.mean(flux_cube)}")
     flux_cube[np.isnan(flux_cube)] = 0.0
 
     flux_cube = detrend_cube(flux_cube, n_order, n_exposure)
@@ -255,13 +259,14 @@ def make_data(
         flux_cube /= median_out_of_transit  # todo: check axes work out
 
     if do_pca:
+        logger.debug("mean flux pre-pca: ", np.mean(flux_cube))
         for j in range(n_order):
             flux_cube[j] -= np.mean(flux_cube[j])
             flux_cube[j] /= np.std(flux_cube[j])
             flux_cube[j], pca_noise_matrix[j] = perform_pca(
                 flux_cube[j], n_princ_comp, pca_removal=pca_removal
             )
-
+        logger.debug("mean flux post-pca: ", np.mean(flux_cube))
     else:
         for j in range(n_order):
             for i in range(n_exposure):
@@ -523,7 +528,6 @@ def simulate_observation(
             star_flux, star_wave, v_rot_star, phases, Rstar, inc, lambda_misalign, a, Rp
         )
 
-    # todo: swap out
     Fstar_conv = get_star_spline(
         star_wave, star_flux, wl_model, instrument_kernel, smooth=False
     )

src/scope/tellurics.py

@@ -9,6 +9,10 @@
 import pandas as pd
 from scipy import interpolate
 
+from scope.logger import get_logger
+
+logger = get_logger()
+
 abs_path = os.path.dirname(__file__)
 
 
@@ -230,4 +234,6 @@ def add_tellurics(
         flux_cube_model = add_tellurics_atran(
             wl_cube_model, flux_cube_model, n_order, n_exp, vary_airmass=vary_airmass
         )
+    logger.debug("Tellurics added.")
+    logger.debug("mean flux post-tellurics: ", np.mean(flux_cube_model))
     return flux_cube_model

src/scope/utils.py

@@ -191,11 +191,6 @@ def calc_limb_darkening(u1, u2, a, b, Rstar, ph, LD):
     return I
 
 
-# todo: download atran scripts
-# todo: fit wavelength solution stuff
-# todo: plot the maps
-
-
 @njit
 def perform_pca(input_matrix, n_princ_comp, pca_removal="subtract"):
     """