Bug fixes and code cleanup

GUIs/PlotSpec_Integrated.py

@@ -853,7 +853,8 @@ def cellchanged(self):
         except: pass
     def zabs_changed(self):
         try: self.zabs = np.double(self.active_zabs.text())
-        except: self.active_zabs.setText("Please input numerical redshift")
+        except: pass
+        #self.active_zabs.setText("Please input numerical redshift")
 
     def saveCatalog_fn(self,parent):
         self.saving = SaveCatalog(parent)

GUIs/rb_spec.py

@@ -6,6 +6,25 @@
 import os
 import pdb
 
+import json
+
+def load_rb_spec_object(filename):
+    with open(filename, 'r') as f:
+        data = json.load(f)
+    from GUIs.rb_spec import rb_spec as r    
+    sp_n=r.from_data(np.array(data['wave_slice'])*(1.+data['zabs']),np.array(data['flux_slice']),np.array(data['error_slice']))
+    zabs=data['zabs']
+    transition=data['trans_wave']
+    sp_n.shift_spec(zabs)
+    sp_n.slice_spec(transition,data['slice_spec_lam_min'],data['slice_spec_lam_max'],use_vel=data['slice_spec_method'],method=data['line_sel_flag'],linelist=data['linelist'])
+    sp_n.fit_continuum(prefit_cont=np.array(data['cont']))
+    sp_n.compute_EW(transition,vmin=data['vmin'],vmax=data['vmax'],plot=False)
+    print('---Finished loading saved rb_spec object----')
+
+    return sp_n
+
+
+
 # Calculate the confidence bounds
 def calculate_confidence_bounds(x, model, cov_matrix):
     # Evaluate the Legendre basis functions at the given x values
@@ -435,15 +454,17 @@ def fit_continuum(self,mask=False,domain=False,Legendre=False,**kwargs):
         #return self.cont,self.fnorm,self.enorm
 
 
-    def fit_continuum_ransac(self,window=149,mednorm=False):
+    def fit_continuum_ransac(self,window=149,mednorm=False,tweak=False):
         """Alternate continuum fitting method. Does iterative ransac continumm fitting.
 
         """
         from IGM import ransac_contfit as cf 
         #sp=cf.cont_fitter()
         sp=cf.cont_fitter.from_data(self.wave_slice,self.flux_slice,error=self.error_slice,mednorm=mednorm)
         sp.fit_continuum(window=window)
-
+        if tweak:
+            sp.tweak_continuum()
+
         self.cont=sp.cont
         self.fnorm=self.flux_slice/self.cont
         self.enorm=self.error_slice/self.cont
@@ -568,10 +589,4 @@ def vpfit_singlet(self,FWHM=6.5):
         """Test Wrapper to call vpfit GUI
         """
         from GUIs import rb_interactive_vpfit_singlet as vf 
-        vt=vf.rb_interactive_vpfit_singlet(self.wave_slice,self.fnorm,self.enorm,self.transition);    
-
-
-
-
-
-
+        vt=vf.rb_interactive_vpfit_singlet(self.wave_slice,self.fnorm,self.enorm,self.transition)

GUIs/rb_specgui.py

@@ -120,7 +120,16 @@
 
     #sp=XSpectrum1D.from_file('PG0832+251_nbin3_coadd.fits') 
     #r.rb_plot_spec(wave,flux/np.nanmedian(flux),error/np.nanmedian(flux))
-    r.rb_plotspec(wave,flux/np.nanmedian(flux),error/np.nanmedian(flux))
+    if np.nanmedian(flux)==0:
+        cnt=np.nanmean(flux)
+    elif (np.nanmedian(flux)==0) & (np.nanmean(flux)==0):
+        cnt= 1.
+    else:
+        cnt=np.nanmedian(flux)
+
+
+
+    r.rb_plotspec(wave,flux/cnt,error/cnt)
 
     plt.show() # show the window
 

IGM/compute_EW.py

@@ -44,7 +44,7 @@ def compute_EW(lam,flx,wrest,lmts,flx_err,plot=False,**kwargs):
               RB April 28, 2021, changed med_vel to weight be EW & vel_disp
     ------------------------------------------------------------------------------------------
     """
-    defnorm=1.0;
+    defnorm=1.0
     spl=2.9979e5;  #speed of light
     if 'zabs' in kwargs:
         zabs=kwargs['zabs']
@@ -62,18 +62,18 @@ def compute_EW(lam,flx,wrest,lmts,flx_err,plot=False,**kwargs):
 
     norm=defnorm
 
-    norm_flx=flx/norm;
-    flx_err=flx_err/norm;
-    sq=np.isnan(norm_flx);
+    norm_flx=flx/norm
+    flx_err=flx_err/norm
+    sq=np.isnan(norm_flx)
     tmp_flx=flx_err[sq]
     norm_flx[sq]=tmp_flx
     #clip the spectrum. If the flux is less than 0+N*sigma, then we're saturated. Clip the flux array(to avoid inifinite optical depth) and set the saturated flag
-    q=np.where(norm_flx<=sat_limit);
+    q=np.where(norm_flx<=sat_limit)
     tmp_flx=flx_err[q]
     norm_flx[q]=tmp_flx
-    q=np.where(norm_flx<=0.);
+    q=np.where(norm_flx<=0.)
     tmp_flx=flx_err[q]+0.01
-    norm_flx[q]=tmp_flx;
+    norm_flx[q]=tmp_flx
 
 
     del_lam_j=np.diff(lambda_r);