missing variables added

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, search_parameters, speed_of_light, oscillator_parameters
+from .constants 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):
@@ -99,9 +99,6 @@ def convolution_method_absorber_finder_in_QSO_spectra(fits_file, spec_index, abs
     line_sep = line2 - line1
     resolution = 69  # km/s for SDSS or DESI
 
-    delta_z_start = lines['dz_start']
-    delta_z_end = lines['dz_end']
-
     del_sigma = line1 * resolution / speed_of_light  # in Ang
 
     bound = ((np.array([2e-2, line1 - d_pix, del_sigma, 2e-2, line2 - d_pix, del_sigma])),

qsoabsfind/ew.py

@@ -1,6 +1,7 @@
 import numpy as np
 from scipy.optimize import curve_fit
 from .constants import lines
+from .utils import double_gaussian
 
 # 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):
@@ -211,7 +212,7 @@ def measure_absorber_properties_double_gaussian(index, wavelength, flux, error,
             init_cond = [amp_first_nmf, line_first, sigma1, 0.54 * amp_first_nmf, line_second, sigma2]
 
             fitting_param_for_spectrum[k], fitting_param_std_for_spectrum[k], EW_first_line[k], EW_second_line[k], EW_total[k] = double_curve_fit(
-                index, gauss, lam_fit, nmf_resi, error_fit=error_flux, bounds=bound, init_cond=init_cond, iter_n=1000)
+                index, double_gaussian, lam_fit, nmf_resi, error_fit=error_flux, bounds=bound, init_cond=init_cond, iter_n=1000)
             #errors on EW
             if not use_covariance:
                 EW_first_line_error[k], EW_second_line_error[k], EW_total_error[k] = calculate_ew_errors(fitting_param_for_spectrum[k], fitting_param_std_for_spectrum[k])

qsoabsfind/io.py

@@ -61,7 +61,7 @@ def save_results_to_fits(results, output_file, headers, absorber):
         fits.Column(name='GAUSS_FIT_STD', format='6D', array=np.array(results['gauss_fit_std'])),
         fits.Column(name=f'{EW_1}', format='D', array=np.array(results['ew_1_mean'])),
         fits.Column(name=f'{EW_2}', format='D', array=np.array(results['ew_2_mean'])),
-        fits.Column(name=ew_total, format='D', array=np.array(results['ew_total_mean'])),
+        fits.Column(name=f'{EW_TOTAL}', format='D', array=np.array(results['ew_total_mean'])),
         fits.Column(name=f'{EW_1}_ERROR', format='D', array=np.array(results['ew_1_error'])),
         fits.Column(name=f'{EW_2}_ERROR', format='D', array=np.array(results['ew_2_error'])),
         fits.Column(name=f'{EW_TOTAL}_ERROR', format='D', array=np.array(results['ew_total_error'])),

qsoabsfind/parallel_convolution.py

@@ -4,7 +4,6 @@
 import argparse
 import time
 from multiprocessing import Pool
-from astropy.io import fits
 from importlib import import_module
 from .absfinder import convolution_method_absorber_finder_in_QSO_spectra
 from .io import save_results_to_fits

qsoabsfind/spec.py

@@ -1,5 +1,3 @@
-import numpy as np
-import argparse
 from .io import read_fits_file
 from .utils import elapsed
 import time