config.py modified for user-defined constant file use

data/datamodel.rst

@@ -23,11 +23,13 @@ The input `fits file` must have the following HDU extensions:
 - **FLUX**: Should ideally contain the residual spectra (usually the flux/continuum, i.e., the continuum normalized spectra).
 - **WAVELENGTH**: Observed wavelength (in Angstroms).
 - **ERROR**: Error on residuals.
-- **TGTDETAILS**: Spectral details (such as Z_QSO, RA_QSO, DEC_QSO).
+- **METADATA**: Spectral details (such as Z_QSO, RA_QSO, DEC_QSO).
 
 Constant File (Optional)
 ------------------------
 
+Before using your own constant file, please set an environment variable `QSO_CONSTANTS_FILE` in your `bashrc` or `zshrc` file and point it to the `qsoabsfind.constants` file. As the code loads the constants from new file dynamically, it is important to define this environment variable.
+
 The user-defined **constant-file** must follow the same structure as the `qsoabsfind.constants` file, otherwise, the code will fail. If you want to use the default search parameters, you can run the tool without the `constant-file` option.
 
 Running the Tool
@@ -57,6 +59,6 @@ The **output** `fits file` will have the `ABSORBER` HDU, containing arrays such
 - **${metal}_EW_TOTAL**: Total EW of the lines in Angstroms.
 - **${metal}_EW_TOTAL_ERROR**: Uncertainties in total EW of the lines in Angstroms.
 
-Thanks,  
+Thanks,
 Abhijeet Anand
 Lawrence Berkeley National Lab

docs/fileformat.rst

@@ -14,6 +14,8 @@ The input `fits file` must have the following HDU extensions:
 Constant File (Optional)
 ------------------------
 
+Before using your own constant file, please set an environment variable `QSO_CONSTANTS_FILE` in your bashrc or zshrc file and point it to the qsoabsfind.constants file. As the code loads the constants from new file dynamically, it is important to define this environment variable.
+
 The user-defined **constant-file** must follow the same structure as the `qsoabsfind.constants` file, otherwise, the code will fail. If you want to use the default search parameters, you can run the tool without the `constant-file` option.
 
 Then run `qsoabsfind` with the required FITS file. If using a custom constant file, include it in the command:

qsoabsfind/absfinder.py

@@ -13,10 +13,13 @@
     contiguous_pixel_remover, estimate_snr_for_lines, absorber_search_window
 )
 from .ew import measure_absorber_properties_double_gaussian
-from .config import lines, speed_of_light, oscillator_parameters
+from .config import load_constants
 from .spec import QSOSpecRead
 from numba import jit
 
+constants = load_constants()
+lines, oscillator_parameters, speed_of_light = constants.lines, constants.oscillator_parameters, constants.speed_of_light
+
 @jit(nopython=True)
 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

@@ -3,10 +3,13 @@
 """
 
 import numpy as np
-from .config import speed_of_light, lines
+from .config import load_constants
 from .utils import elapsed
 from numba import jit
 
+constants = load_constants()
+lines, speed_of_light = constants.lines, constants.speed_of_light
+
 @jit(nopython=True)
 def estimate_local_sigma_conv_array(conv_array, pm_pixel):
     """

qsoabsfind/config.py

@@ -12,25 +12,31 @@
 3. Import constants from this module in other parts of the application to use the loaded constants.
 """
 
-import importlib.util
 import os
+import importlib.util
+import qsoabsfind.constants as 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.
+def load_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__)
+    Load constants from the user-provided file if specified, otherwise use the default constants (qsoabsfind.constants).
+    If user provides a constant file, this function will read QSO_CONSTANTS_FILE environment
+    variable, initially set when user provides a constant file.
 
-# 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)
+    Returns:
+        module: The module containing the constants.
+    """
+    constants_file = os.environ.get('QSO_CONSTANTS_FILE')
+
+    # Check if the environment variable for the constants file is set
+    if constants_file and os.path.isfile(constants_file):
+        try:
+            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)
+            return user_constants
+        except Exception as e:
+            print(f"Error loading user constants: {e}. Falling back to default constants.")
+            return default_constants
+    else:
+        print("Using default constants.")
+        return default_constants

qsoabsfind/ew.py

@@ -4,9 +4,12 @@
 
 import numpy as np
 from scipy.optimize import curve_fit
-from .config import lines
 from .utils import double_gaussian
 from .absorberutils import redshift_estimate
+from .config import load_constants
+
+constants = load_constants()
+lines = constants.lines
 
 # Example usage within double_curve_fit
 def double_curve_fit(index, fun_to_run, lam_fit_range, nmf_resi_fit, error_fit, bounds, init_cond, iter_n):

qsoabsfind/parallel_convolution.py

@@ -11,9 +11,7 @@
 import re
 import os
 import pkg_resources
-
-# Ensure config is imported first to set up the environment
-import qsoabsfind.config as config
+from .config import load_constants
 
 def get_package_versions():
     """
@@ -158,7 +156,14 @@ def main():
 
     # Set the environment variable for the constants file
     if args.constant_file:
-        os.environ['QSO_CONSTANTS_FILE'] = args.constant_file
+        if not os.path.isabs(args.constant_file):
+            args.constant_file = os.path.abspath(os.path.join(os.getcwd(), args.constant_file))
+            os.environ['QSO_CONSTANTS_FILE'] = args.constant_file
+            print(f"INFO: Using user-provided constants from: {args.constant_file}")
+
+    print(f"INFO: QSO_CONSTANTS_FILE: {os.environ['QSO_CONSTANTS_FILE']}")
+    # set the new constants
+    constants = load_constants()
 
     # Prepare headers
     headers = {}
@@ -169,15 +174,15 @@ def main():
     # Add search parameters and package versions to headers
     headers.update({
         'ABSORBER': {"value": args.absorber, "comment": 'Absorber name'},
-        'KERWIDTH': {"value": str(config.search_parameters[args.absorber]["ker_width_pixels"]), "comment": 'Kernel width in pixels'},
-        'COEFFSIG': {"value": config.search_parameters[args.absorber]["coeff_sigma"], "comment": 'Coefficient for sigma threshold'},
-        'MULTRE': {"value": config.search_parameters[args.absorber]["mult_resi"], "comment": 'Multiplicative factor for residuals'},
-        'D_PIX': {"value": config.search_parameters[args.absorber]["d_pix"], "comment": 'toloerance for line separation (in Ang)'},
-        'PM_PIXEL': {"value": config.search_parameters[args.absorber]["pm_pixel"], "comment": 'Pixel parameter for local noise estimation'},
-        'SN_LINE1': {"value": config.search_parameters[args.absorber]["sn_line1"], "comment": 'S/N threshold for first line'},
-        'SN_LINE2': {"value": config.search_parameters[args.absorber]["sn_line2"], "comment": 'S/N threshold for second line'},
-        'EWCOVAR': {"value": config.search_parameters[args.absorber]["use_covariance"], "comment": 'Use covariance for EW error calculation'},
-        'LOGWAVE': {"value": config.search_parameters[args.absorber]["logwave"], "comment": 'Use log wavelength scaling'}
+        'KERWIDTH': {"value": str(constants.search_parameters[args.absorber]["ker_width_pixels"]), "comment": 'Kernel width in pixels'},
+        'COEFFSIG': {"value": constants.search_parameters[args.absorber]["coeff_sigma"], "comment": 'Coefficient for sigma threshold'},
+        'MULTRE': {"value": constants.search_parameters[args.absorber]["mult_resi"], "comment": 'Multiplicative factor for residuals'},
+        'D_PIX': {"value": constants.search_parameters[args.absorber]["d_pix"], "comment": 'toloerance for line separation (in Ang)'},
+        'PM_PIXEL': {"value": constants.search_parameters[args.absorber]["pm_pixel"], "comment": 'Pixel parameter for local noise estimation'},
+        'SN_LINE1': {"value": constants.search_parameters[args.absorber]["sn_line1"], "comment": 'S/N threshold for first line'},
+        'SN_LINE2': {"value": constants.search_parameters[args.absorber]["sn_line2"], "comment": 'S/N threshold for second line'},
+        'EWCOVAR': {"value": constants.search_parameters[args.absorber]["use_covariance"], "comment": 'Use covariance for EW error calculation'},
+        'LOGWAVE': {"value": constants.search_parameters[args.absorber]["logwave"], "comment": 'Use log wavelength scaling'}
     })
 
     package_versions = get_package_versions()
@@ -195,15 +200,15 @@ 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_pixels=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]["sn_line1"],
-        sn_line2=config.search_parameters[args.absorber]["sn_line2"],
-        use_covariance=config.search_parameters[args.absorber]["use_covariance"],
-        logwave=config.search_parameters[args.absorber]["logwave"], verbose=config.search_parameters[args.absorber]["verbose"], n_jobs=args.n_tasks * args.ncpus
+        ker_width_pixels=constants.search_parameters[args.absorber]["ker_width_pixels"],
+        coeff_sigma=constants.search_parameters[args.absorber]["coeff_sigma"],
+        mult_resi=constants.search_parameters[args.absorber]["mult_resi"],
+        d_pix=constants.search_parameters[args.absorber]["d_pix"],
+        pm_pixel=constants.search_parameters[args.absorber]["pm_pixel"],
+        sn_line1=constants.search_parameters[args.absorber]["sn_line1"],
+        sn_line2=constants.search_parameters[args.absorber]["sn_line2"],
+        use_covariance=constants.search_parameters[args.absorber]["use_covariance"],
+        logwave=constants.search_parameters[args.absorber]["logwave"], verbose=constants.search_parameters[args.absorber]["verbose"], n_jobs=args.n_tasks * args.ncpus
     )
 
     # Save the results to a FITS file

qsoabsfind/utils.py

@@ -5,7 +5,7 @@
 import time
 #import logging
 import numpy as np
-from .config import lines, amplitude_dict, speed_of_light
+from .config import load_constants
 import matplotlib.pyplot as plt
 import os
 
@@ -15,6 +15,9 @@
 # Set the logging level for Matplotlib to WARNING to suppress DEBUG messages
 #logging.getLogger('matplotlib').setLevel(logging.WARNING)
 
+constants = load_constants()
+lines, amplitude_dict, speed_of_light = constants.lines, constants.amplitude_dict, constants.speed_of_light
+
 def elapsed(start, msg):
     """
     Prints the elapsed time since `start`.

tests/test_constants.py

@@ -1,5 +1,8 @@
 import unittest
-from qsoabsfind.config import lines, search_parameters, speed_of_light
+from qsoabsfind.config import load_constants
+constants = load_constants()
+
+lines, search_parameters, speed_of_light = constants.lines, constants.search_parameters, constants.speed_of_light
 
 class TestConstants(unittest.TestCase):
     def test_line_data(self):