config and datamodel added

README.md

@@ -45,6 +45,11 @@ python -m unittest discover -s tests
 
 ```
 
+Instructions
+-------------
+
+Before you run, please read the `datamodel.md` file. The instructions about the input and output file are provided there.
+
 Running example:
 ----------------
 

qsoabsfind/absfinder.py

@@ -9,7 +9,7 @@
     contiguous_pixel_remover, check_error_on_residual, redshift_estimate, absorber_search_window
 )
 from .ew import measure_absorber_properties_double_gaussian
-from .constants import lines, speed_of_light, oscillator_parameters
+from .config import lines, speed_of_light, oscillator_parameters
 from .spec import QSOSpecRead
 
 def find_valid_indices(our_z, residual_our_z, lam_search, conv_arr, sigma_cr, coeff_sigma, d_pix, beta, line1, line2):

qsoabsfind/absorberutils.py

@@ -5,7 +5,7 @@
 """
 
 import numpy as np
-from .constants import speed_of_light, lines
+from .config import speed_of_light, lines
 from .utils import elapsed
 from numba import jit
 

qsoabsfind/config.py

@@ -0,0 +1,40 @@
+# config.py
+
+"""
+This module handles dynamic loading of constants for the QSO absorber finder.
+It first loads the default constants from the constants module and then optionally
+overwrites them with user-provided constants from a specified file.
+
+If an environment variable 'QSO_CONSTANTS_FILE' is set and points to a valid file, the constants
+from that file will be loaded and used instead of the default ones.
+
+Usage:
+1. Ensure the default constants are defined in the constants module.
+2. Optionally provide a custom constants file path in the environment variable 'QSO_CONSTANTS_FILE'.
+3. Import constants from this module in other parts of the application to use the loaded constants.
+"""
+
+import importlib.util
+import os
+
+# Default constants
+from .constants import *
+
+def load_constants(constants_file):
+    """
+    Dynamically loads constants from a user-provided file.
+
+    Parameters:
+    constants_file (str): Path to the file containing user-defined constants.
+    """
+    spec = importlib.util.spec_from_file_location("user_constants", constants_file)
+    user_constants = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(user_constants)
+
+    # Update the globals dictionary with the user-defined constants
+    globals().update(user_constants.__dict__)
+
+# Check if the environment variable for the constants file is set
+constants_file = os.getenv('QSO_CONSTANTS_FILE')
+if constants_file and os.path.isfile(constants_file):
+    load_constants(constants_file)

qsoabsfind/datamodel.md

@@ -0,0 +1,40 @@
+qsoabsfind
+============
+
+Instructions
+-------------
+
+Please read/perform following details.
+
+`qsoabsfind --help`
+
+Please go through all the functions and their instructions in case you have any doubt.
+
+The **input** `fits file` must have a specific structure with following hdu extensions.
+
+- `FLUX` Should contain ideally the residual spectra (usually the flux/continuum, i.e. the continuum normalized spectra)
+- `WAVELENGTH` observed wavelength (in Ang)
+- `ERROR` error on residuals
+- `TGTDETALS` spectral details (like Z_QSO, RA_QSO, DEC_QSO...)
+
+The user-defined **constant-file** must follow the same structure as the `qsoabsfind.constants`, otherwise the code will fail. In case, users want to use the default search parameters, they can tun without `constant-file` option.
+
+The **output** `fits file` will have the hdu `ABSORBER`, that will arrays such as
+
+- `INDEX_SPEC` index of quasar (can be used to read the RA, DEC ans Z of QSOs)
+- `Z_ABS`: redshift of absorber
+- `${METAL}_${line}_EW`: Rest-frame EWs of absorber lines (like MgII 2796, 2803 or CIV 1548, 1550) (in Ang)
+- `${METAL}_${line}_EW_ERROR`: uncertainities in rest-frame EWs of absorber lines (like MgII 2796, 2803 or CIV 1548, 1550) (in Ang)
+- `Z_ABS_ERR`: measured error in redshift of absorber
+- `GAUSS_FIT`: rest-frame fitting parameters of double gaussian to the absorber doublet (the width can be used to measure the velocity dispersion)
+- `GAUSS_FIT_STD`: uncertainities in  rest-frame fitting parameters of double gaussian to the absorber doublet (the width can be used to measure the velocity dispersion)
+- `SN_${METAL}_${line}`: S/N of the lines
+- `${metal}_EW_TOTAL`: Total EW of the lines (in Ang)
+- `${metal}_EW_TOTAL_ERROR`: uncertainities in total EW of the lines (in Ang)
+
+
+Thanks,  
+Abhijeet Anand  
+Lawrence Berkeley National Lab  
+
+If you have any questions/suggestions, please feel free to write to [email protected]

qsoabsfind/ew.py

@@ -1,6 +1,6 @@
 import numpy as np
 from scipy.optimize import curve_fit
-from .constants import lines
+from .config import lines
 from .utils import double_gaussian
 
 # Example usage within double_curve_fit

qsoabsfind/parallel_convolution.py

@@ -7,10 +7,14 @@
 from .absfinder import convolution_method_absorber_finder_in_QSO_spectra
 from .io import save_results_to_fits
 import re
-from .constants import search_parameters
 
-def run_convolution_method_absorber_finder_QSO_spectra(fits_file, spec_index, absorber, ker_width_pix, coeff_sigma, mult_resi, d_pix, pm_pixel, sn_line1, sn_line2, use_covariance):
-    return convolution_method_absorber_finder_in_QSO_spectra(fits_file, spec_index, absorber, ker_width_pix, coeff_sigma, mult_resi, d_pix, pm_pixel, sn_line1, sn_line2, use_covariance)
+from importlib import import_module
+
+# Ensure config is imported first to set up the environment
+import config
+
+def run_convolution_method_absorber_finder_QSO_spectra(params):
+    return convolution_method_absorber_finder_in_QSO_spectra(*params)
 
 
 def parse_qso_sequence(qso_sequence):
@@ -107,12 +111,18 @@ def main():
     parser.add_argument('--input-fits-file', type=str, required=True, help='Path to the input FITS file.')
     parser.add_argument('--n-qso', required=True, help="Number of QSO spectra to process, or a bash-like sequence (e.g., '1-1000', '1-1000:10').")
     parser.add_argument('--absorber', type=str, required=True, help='Absorber name for searching doublets (MgII, CIV).')
+    parser.add_argument('--constant-file', type=str, help='Path to the constants .py file, please follow the exact same strcuture as qsoabsfind.constants, i.e the default parameter that the code uses')
     parser.add_argument('--output', type=str, required=True, help='Path to the output FITS file.')
     parser.add_argument('--headers', type=str, nargs='+', help='Headers for the output FITS file in the format NAME=VALUE.')
     parser.add_argument('--n-tasks', type=int, required=True, help='Number of tasks.')
     parser.add_argument('--ncpus', type=int, required=True, help='Number of CPUs per task.')
 
     args = parser.parse_args()
+
+    # Set the environment variable for the constants file
+    if args.constant_file:
+        os.environ['QSO_CONSTANTS_FILE'] = args.constant_file
+
     # Prepare headers
     headers = {}
     if args.headers:
@@ -129,13 +139,13 @@ def main():
     # Run the convolution method in parallel
     results = parallel_convolution_method_absorber_finder_QSO_spectra(
         args.input_fits_file, spec_indices, absorber=args.absorber,
-        ker_width_pix=search_parameters[args.absorber]["ker_width_pixels"],
-        coeff_sigma=search_parameters[args.absorber]["coeff_sigma"],
-        mult_resi=search_parameters[args.absorber]["mult_resi"],
-        d_pix=search_parameters[args.absorber]["d_pix"],
-        pm_pixel=search_parameters[args.absorber]["pm_pixel"],
-        sn_line1=search_parameters[args.absorber]["sn1_thresh"],
-        sn_line2=search_parameters[args.absorber]["sn2_thresh"],
+        ker_width_pix=config.search_parameters[args.absorber]["ker_width_pixels"],
+        coeff_sigma=config.search_parameters[args.absorber]["coeff_sigma"],
+        mult_resi=config.search_parameters[args.absorber]["mult_resi"],
+        d_pix=config.search_parameters[args.absorber]["d_pix"],
+        pm_pixel=config.search_parameters[args.absorber]["pm_pixel"],
+        sn_line1=config.search_parameters[args.absorber]["sn1_thresh"],
+        sn_line2=config.search_parameters[args.absorber]["sn2_thresh"],
         use_covariance=False, n_jobs=args.n_tasks * args.ncpus
     )
 

qsoabsfind/utils.py

@@ -1,6 +1,6 @@
 import time
 import numpy as np
-from .constants import lines, amplitude_dict
+from .config import lines, amplitude_dict
 
 def elapsed(start, msg):
     """

tests/test_constants.py

@@ -1,5 +1,5 @@
 import unittest
-from qsoabsfind.constants import lines, search_parameters, speed_of_light
+from qsoabsfind.config import lines, search_parameters, speed_of_light
 
 class TestConstants(unittest.TestCase):
     def test_line_data(self):