Merge pull request USNavalResearchLaboratory#87 from MJWeberg/main

Added fit width convenience array
MJWeberg · Mar 5, 2024 · acb6b34 · acb6b34
2 parents 3ee8b49 + 9c237cf
commit acb6b34
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Showing 3 changed files with 17 additions and 6 deletions.
diff --git a/eispac/core/eisfitresult.py b/eispac/core/eisfitresult.py
@@ -757,8 +757,8 @@ def create_fit_dict(n_pxls, n_steps, n_wave, n_gauss, n_poly, data_units='unknow
               # 'err_peak': np.zeros((n_pxls, n_steps, n_gauss)),
               # 'centroid': np.zeros((n_pxls, n_steps, n_gauss)),
               # 'err_centroid': np.zeros((n_pxls, n_steps, n_gauss)),
-              # 'width': np.zeros((n_pxls, n_steps, n_gauss)),
-              # 'err_width': np.zeros((n_pxls, n_steps, n_gauss)),
+              'width': np.zeros((n_pxls, n_steps, n_gauss)),
+              'err_width': np.zeros((n_pxls, n_steps, n_gauss)),
               # 'background': np.zeros((n_pxls, n_steps, n_poly)),
               # 'err_background': np.zeros((n_pxls, n_steps, n_poly)),
               'params': np.zeros((n_pxls, n_steps, n_param)),

diff --git a/eispac/core/fit_spectra.py b/eispac/core/fit_spectra.py
@@ -167,6 +167,8 @@ def fit_with_mpfit(wave_cube, inten_cube, errs_cube, template, parinfo,
                 fit_dict['perror'][ii,jj,:] = out.perror
                 fit_dict['int'][ii,jj,:] = l_inten
                 fit_dict['err_int'][ii,jj,:] = e_inten
+                fit_dict['width'][ii,jj,:] = fwdths
+                fit_dict['err_width'][ii,jj,:] = ewdths
             else:
                 print(' ! fit did not converge!')
                 fit_dict['status'][ii,jj] = out.status
@@ -412,6 +414,8 @@ def fit_spectra(inten, template, parinfo=None, wave=None, errs=None, min_points=
                 fit_res.fit['perror'][:,jj,:] = pool_out[jj]['perror'][:,0,:]
                 fit_res.fit['int'][:,jj,:] = pool_out[jj]['int'][:,0,:]
                 fit_res.fit['err_int'][:,jj,:] = pool_out[jj]['err_int'][:,0,:]
+                fit_res.fit['width'][:,jj,:] = pool_out[jj]['width'][:,0,:]
+                fit_res.fit['err_width'][:,jj,:] = pool_out[jj]['err_width'][:,0,:]
 
         # Calculate the Doppler velocity for each line
         # TODO: revisit error estimation

diff --git a/eispac/core/read_template.py b/eispac/core/read_template.py
@@ -24,11 +24,10 @@ def read_template(filename):
         Object containing the fit template
     """
     # Note: this is just a convience function to avoid breaking the old API
-    #       Please see the code in the class method
+    #       Please see the code in the class method. 
+    #       (coped below for referencce on 2024-03-05)
     return EISFitTemplate.read_template(filename)
 
-    # # TODO: Add loading custom template from a .toml file
-
     # # NOTE: return None here rather than allow h5py to handle
     # # exception so that spectral fitting pipeline can error
     # # more gracefully
@@ -69,6 +68,14 @@ def read_template(filename):
     #                     val = np.char.decode(val) # convert bytes to unicode
     #                 parameter[key] = val
     #             parinfo.append(parameter)
+
+    #         # Fix the datatypes of important keys
+    #         template['n_gauss'] = int(template.get('n_gauss', 1))
+    #         template['n_poly'] = int(template.get('n_poly', 1))
+    #         template['wmin'] = float(template.get('wmin', 100))
+    #         template['wmax'] = float(template.get('wmax', 1000))
+    #         template['component'] = int(template.get('component', 1))
+    #         template['line_ids'] = template['line_ids'].astype('<U24')
     # elif file_type.lower() == '.toml':
     #     # Load a custom template stored in a TOML file
     #     with open(filename, 'rb') as f_temp:
@@ -80,4 +87,4 @@ def read_template(filename):
     #         parinfo = toml_dict.get('parinfo', None)
     #         # note: this parinfo will be an alternative dict of lists
 
-    # return EISFitTemplate(filename, template, parinfo)
+    # return cls(filename, template, parinfo)