lambda edge corrected

qsoabsfind/absfinder.py

@@ -69,8 +69,8 @@ def read_single_spectrum_and_find_absorber(fits_file, spec_index, absorber, **kw
     lam_obs = spectra.wavelength
 
     # Define the wavelength range for searching the absorber
-    min_wave, max_wave = lam_obs.min() + kwargs["lam_edge_sep"], lam_obs.max() - kwargs["lam_edge_sep"]  # avoiding edges
-
+    min_wave, max_wave = lam_obs.min(), lam_obs.max()
+    
     # Retrieve flux and error data, ensuring consistent dtype for Numba compatibility
     residual, error = spectra.flux.astype('float64'), spectra.error.astype('float64')
     lam_obs = lam_obs.astype('float64')
@@ -81,7 +81,7 @@ def read_single_spectrum_and_find_absorber(fits_file, spec_index, absorber, **kw
 
     # Identify the wavelength region for searching the specified absorber
     lam_search, unmsk_residual, unmsk_error = absorber_search_window(
-        lam_obs, residual, error, z_qso, absorber, min_wave, max_wave, verbose=kwargs['verbose'])
+        lam_obs, residual, error, z_qso, absorber, min_wave, max_wave, lam_edge_sep= kwargs["lam_edge_sep"], verbose=kwargs['verbose'])
 
     # Verify that the arrays are of equal size
     assert lam_search.size == unmsk_residual.size == unmsk_error.size, "Mismatch in array sizes of lam_search, unmsk_residual, and unmsk_error"

qsoabsfind/absorberutils.py

@@ -534,7 +534,7 @@ def redshift_estimate(fitted_obs_l1, fitted_obs_l2, std_fitted_obs_l1, std_fitte
     return z_corr, z_err
 
 
-def absorber_search_window(wavelength, residual, err_residual, zqso, absorber, min_wave, max_wave, verbose=False):
+def absorber_search_window(wavelength, residual, err_residual, zqso, absorber, min_wave, max_wave, lam_edge_sep=0, verbose=False):
     """
     Wrapper function to return the most basic wavelength window for absorber
     search.
@@ -547,6 +547,7 @@ def absorber_search_window(wavelength, residual, err_residual, zqso, absorber, m
         absorber (str): Options 'CIV', 'MgII'.
         min_wave (float): minimum wavelength edge (in Ang)
         max_wave (float): maximum wavelength edge (in Ang)
+        lam_edge_sep (float): separation from minimum wavelength, i.e. lam_min + lam_edge_sep, this is just to make sure that we avoid the very edge of the spectrum
         verbose (bool, optional): If True will print time info. Default is False.
 
     Returns:
@@ -557,12 +558,12 @@ def absorber_search_window(wavelength, residual, err_residual, zqso, absorber, m
     if absorber == 'MgII':
         lam_CIV = lines['CIV_1549'] * (1 + zqso + lines['dz_start']) #redshifted from CIV emission lines
         lam_MgII = lines['MgI_2799'] * (1 + zqso - lines['dz_end']) #blueshifted MgII emission lines
-        lam_start = max(min_wave, lam_CIV)
+        lam_start = max(min_wave, lam_CIV) + lam_edge_sep
         lam_end = min(max_wave, lam_MgII)
     elif absorber == 'CIV':
         dz = (lines['dv'] / speed_of_light) * (1 + zqso)
         lam_CIV = lines['CIV_1549'] * (1 + zqso + dz)
-        lam_start = max(min_wave, 1310 * (1 + zqso))  # This is from Cooksey et al 2013
+        lam_start = max(min_wave, 1310 * (1 + zqso)) + lam_edge_sep  # This is from Cooksey et al 2013
         lam_end = min(lam_CIV, max_wave)
     else:
         raise ValueError("Absorber must be 'CIV' or 'MgII'")