add logger

src/scope/input.txt

@@ -16,6 +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``.
 
 # 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

src/scope/input_output.py

@@ -2,14 +2,18 @@
 Module to handle the input files.
 """
 
+import argparse
 import io
 import os
-import argparse
+import warnings
 from datetime import datetime
 
 import pandas as pd
 
 from scope.calc_quantities import *
+from scope.logger import *
+
+logger = get_logger()
 
 
 class ScopeConfigError(Exception):
@@ -42,14 +46,14 @@ def query_database(
 
     # check whether planet name is in database
     if planet_name not in df["pl_name"].values:
-        print(f"Planet name {planet_name} not found in database.")
+        logger.warning(f"Planet name {planet_name} not found in database.")
     try:
         # Use the mapped parameter name if it exists, otherwise use the original
         db_parameter = parameter_mapping.get(parameter, parameter)
         value = df.loc[df["pl_name"] == planet_name, db_parameter].values[0]
         return float(value)
     except Exception as e:
-        print(f"Error querying database for {planet_name}, {parameter}: {e}")
+        logger.warning(f"Error querying database for {planet_name}, {parameter}: {e}")
 
         return np.nan
 
@@ -88,7 +92,7 @@ def unpack_lines(content):
 def coerce_nulls(data, key, value):
     if value == "NULL":
         data[key] = np.nan
-
+        logger.warning(f" {key} is null on input")
 
     return data
 
@@ -294,51 +298,120 @@ def write_input_file(data, output_file_path="input.txt"):
                     f.write(f"{param:<23} {value}\n")
             f.write("\n")
 
-    print(f"Input file written to {output_file_path}")
-
+    logger.info(f"Input file written to {output_file_path}")
 
 
 def parse_arguments():
-    parser = argparse.ArgumentParser(description='Simulate observation')
-
-    # Input file argument (required)
-    parser.add_argument('--input_file', type=str, default="input.txt", 
-                        help='Input file with parameters (default: input.txt)')
-
-    # All other parameters without default values
-    parser.add_argument('--planet_spectrum_path', type=str, help='Path to planet spectrum')
-    parser.add_argument('--star_spectrum_path', type=str, help='Path to star spectrum')
-    parser.add_argument('--data_cube_path', type=str, help='Path to data cube')
-    parser.add_argument('--phase_start', type=float, help='Start phase')
-    parser.add_argument('--phase_end', type=float, help='End phase')
-    parser.add_argument('--n_exposures', type=int, help='Number of exposures')
-    parser.add_argument('--observation', type=str, help='Observation type')
-    parser.add_argument('--blaze', type=lambda x: x.lower() == 'true', help='Blaze flag')
-    parser.add_argument('--n_princ_comp', type=int, help='Number of principal components')
-    parser.add_argument('--star', type=lambda x: x.lower() == 'true', help='Star flag')
-    parser.add_argument('--SNR', type=float, help='Signal to noise ratio')
-    parser.add_argument('--telluric', type=lambda x: x.lower() == 'true', help='Telluric flag')
-    parser.add_argument('--tell_type', type=str, help='Telluric type')
-    parser.add_argument('--time_dep_tell', type=lambda x: x.lower() == 'true', help='Time dependent telluric')
-    parser.add_argument('--wav_error', type=lambda x: x.lower() == 'true', help='Wavelength error flag')
-    parser.add_argument('--rv_semiamp_orbit', type=float, help='RV semi-amplitude orbit')
-    parser.add_argument('--order_dep_throughput', type=lambda x: x.lower() == 'true', help='Order dependent throughput')
-    parser.add_argument('--Rp', type=float, help='Planet radius (Jupiter radii)')
-    parser.add_argument('--Rstar', type=float, help='Star radius (solar radii)')
-    parser.add_argument('--kp', type=float, help='Planetary orbital velocity (km/s)')
-    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('--modelname', type=str, help='Model name')
-    parser.add_argument('--divide_out_of_transit', type=lambda x: x.lower() == 'true', help='Divide out of transit')
-    parser.add_argument('--out_of_transit_dur', type=float, help='Out of transit duration')
-    parser.add_argument('--include_rm', type=lambda x: x.lower() == 'true', help='Include RM effect')
-    parser.add_argument('--v_rot_star', type=float, help='Star rotation velocity')
-    parser.add_argument('--a', type=float, help='Semi-major axis')
-    parser.add_argument('--lambda_misalign', type=float, help='Misalignment angle')
-    parser.add_argument('--inc', type=float, help='Inclination')
-    parser.add_argument('--seed', type=int, help='Random seed')
-    parser.add_argument('--LD', type=lambda x: x.lower() == 'true', help='Limb darkening')
-    parser.add_argument('--vary_throughput', type=lambda x: x.lower() == 'true', help='Vary throughput')
-
+
+    parser = argparse.ArgumentParser(description="Simulate observation")
+
+    # Required parameters
+    parser.add_argument(
+        "--planet_spectrum_path", type=str, default=".", help="Path to planet spectrum"
+    )
+    parser.add_argument(
+        "--star_spectrum_path", type=str, default=".", help="Path to star spectrum"
+    )
+    parser.add_argument(
+        "--data_cube_path", type=str, default=".", 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"
+    )
+    parser.add_argument(
+        "--observation", type=str, default="emission", help="Observation type"
+    )
+    parser.add_argument("--blaze", type=bool, default=True, help="Blaze flag")
+    parser.add_argument(
+        "--n_princ_comp", type=int, default=4, 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(
+        "--tell_type", type=str, default="data-driven", help="Telluric type"
+    )
+    parser.add_argument(
+        "--time_dep_tell", type=bool, default=False, help="Time dependent telluric"
+    )
+    parser.add_argument(
+        "--wav_error", type=bool, default=False, help="Wavelength error flag"
+    )
+    parser.add_argument(
+        "--rv_semiamp_orbit", type=float, default=0.3229, 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)"
+    )
+    parser.add_argument(
+        "--Rstar", type=float, default=0.955, help="Star radius (solar radii)"
+    )
+    parser.add_argument(
+        "--kp", type=float, default=192.02, 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(
+        "--modelname", type=str, default="yourfirstsimulation", 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"
+    )
+    parser.add_argument(
+        "--include_rm", type=bool, default=False, help="Include RM effect"
+    )
+    parser.add_argument(
+        "--v_rot_star", type=float, default=3.0, help="Star rotation velocity"
+    )
+    parser.add_argument("--a", type=float, default=0.033, help="Semi-major axis")
+    parser.add_argument(
+        "--lambda_misalign", type=float, default=0.0, 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(
+        "--vary_throughput", type=bool, default=True, 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"
+    )
+
+
     return parser.parse_args()

src/scope/logger.py

@@ -0,0 +1,61 @@
+import logging
+
+# Global logger instance
+_logger = None
+
+
+def setup_logging(log_file=None, log_level=logging.INFO):
+    """
+    Configure logging for the entire application
+    """
+    global _logger
+
+    # Create logger
+    _logger = logging.getLogger("simulation")
+    _logger.setLevel(log_level)
+
+    # Clear any existing handlers
+    if _logger.hasHandlers():
+        _logger.handlers.clear()
+
+    # Create formatter
+    formatter = logging.Formatter(
+        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    )
+
+    # Create console handler
+    console_handler = logging.StreamHandler()
+    console_handler.setLevel(log_level)
+    console_handler.setFormatter(formatter)
+    _logger.addHandler(console_handler)
+
+    # Create file handler if log_file is specified
+    if log_file:
+        file_handler = logging.FileHandler(log_file)
+        file_handler.setLevel(log_level)
+        file_handler.setFormatter(formatter)
+        _logger.addHandler(file_handler)
+
+    return _logger
+
+
+def get_logger():
+    """
+    Get the configured logger instance
+    """
+    global _logger
+    if _logger is None:
+        # Configure with defaults if not already configured
+        _logger = logging.getLogger("simulation")
+        _logger.setLevel(logging.INFO)
+
+        # Add a default console handler if no handlers exist
+        if not _logger.handlers:
+            handler = logging.StreamHandler()
+            formatter = logging.Formatter(
+                "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+            )
+            handler.setFormatter(formatter)
+            _logger.addHandler(handler)
+
+    return _logger

src/scope/run_simulation.py

@@ -4,9 +4,19 @@
 calculating the log likelihood and cross-correlation function of the data given the model parameters.
 """
 
+
+import logging
+import os
+
+import numpy as np
+from tqdm import tqdm
+
 from scope.broadening import *
 from scope.ccf import *
 from scope.input_output import *
+from scope.logger import *
+
+
 from scope.noise import *
 from scope.tellurics import *
 from scope.utils import *
@@ -81,13 +91,17 @@ def make_data(
         :just_tellurics: (array) the telluric model that's multiplied to the dataset.
 
     """
-    print(seed)
+
     np.random.seed(seed)
+    logger.info(f"Seed set to {seed}")
 
     rv_planet, rv_star = calc_rvs(
         v_sys, v_sys_measured, Kp, rv_semiamp_orbit, phases
     )  # measured in m/s now
 
+    logger.debug(f"RV planet: {rv_planet}, RV star: {rv_star}")
+
+
     flux_cube = np.zeros(
         (n_order, n_exposure, n_pixel)
     )  # will store planet and star signal
@@ -589,7 +603,7 @@ def simulate_observation(
 
 if __name__ == "__main__":
     args = parse_arguments()
-    
+
     # First, parse the input file to get base parameters
     inputs = parse_input_file(args.input_file)
 
@@ -604,5 +618,12 @@ def simulate_observation(
         if value is not None:
             inputs[key] = value
 
+    logger = setup_logging(log_level=inputs["log_level"])
+    logger.debug(f"Parsed inputs: {inputs}")
+
+
     # Call the simulation function with the merged parameters
-    simulate_observation(**inputs)
+    try:
+        simulate_observation(**inputs)
+    except Exception as e:
+        logger.error(f"An error occurred: {e}", exc_info=True)