can now fit and plot spectra in eV, user bound inputs are still in nm but converted to eV in the backend

Author: SarthakJariwala

PythonGUI_apps/Spectrum_analysis/Spectra_fit_funcs.py

@@ -40,7 +40,9 @@ def background_correction(self):
             y = y/wlref
 
         if self.fit_in_eV is True:
-            x = 1240/x
+            x = np.sort(1240/self.data[:, 0]) # converting to eV and sorting in ascending order
+            y = [y[i] for i in np.argsort(1240/x)] # sorting argument of y acc to x sorting index
+            # need to do this because data is collected in wavelength
 
         return [x,y]
 
@@ -69,12 +71,16 @@ def gaussian_model(self):
     #     return result #770 760 780   sigma 15 
     def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range):
         x,y = self.background_correction()
+        if self.fit_in_eV is True:
+            peak_pos = 1240/peak_pos
+            sigma = 1240/sigma
+            min_max_range = np.sort(1240/np.asarray(min_max_range))
         gmodel = GaussianModel(prefix = 'g1_') # calling gaussian model
         pars = gmodel.guess(y, x=x) # parameters - center, width, height
         pars['g1_center'].set(peak_pos, min=min_max_range[0], max=min_max_range[1])
         pars['g1_sigma'].set(sigma)
         result = gmodel.fit(y, pars, x=x, nan_policy='propagate')
-        return result #770 760 780   sigma 15 
+        return result 
 
 class Single_Lorentzian(Spectra_Fit):
     """Fit a single Lorentzian to the spectrum
@@ -93,6 +99,10 @@ def lorentzian_model(self):
 
     def lorentzian_model_w_lims(self, peak_pos, sigma, min_max_range):
         x,y = self.background_correction()
+        if self.fit_in_eV is True:
+            peak_pos = 1240/peak_pos
+            sigma = 1240/sigma
+            min_max_range = np.sort(1240/np.asarray(min_max_range))
         lmodel = LorentzianModel(prefix = 'l1_') # calling lorentzian model
         pars = lmodel.guess(y, x=x) # parameters - center, width, height
         pars['l1_center'].set(peak_pos, min = min_max_range[0], max = min_max_range[1])
@@ -127,6 +137,10 @@ def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range):
         #min_max_range - list containing lists of min and max for peak center. [ [min1, max1], [min2, max2] ] 
 
         x,y = self.background_correction()
+        if self.fit_in_eV is True:
+            peak_pos = 1240/np.asarray(peak_pos)
+            sigma = 1240/np.asarray(sigma)
+            min_max_range = np.sort(1240/np.asarray(min_max_range))
         gmodel_1 = GaussianModel(prefix='g1_') # calling gaussian model
         pars = gmodel_1.guess(y, x=x) # parameters - center, width, height
         pars['g1_center'].set(peak_pos[0], min = min_max_range[0][0], max = min_max_range[0][1])
@@ -136,7 +150,7 @@ def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range):
         gmodel_2 = GaussianModel(prefix='g2_')
         pars.update(gmodel_2.make_params()) # update parameters - center, width, height
         pars['g2_center'].set(peak_pos[1], min = min_max_range[1][0], max = min_max_range[1][1])
-        pars['g2_sigma'].set(sigma[1],  min = composite_pars['g1_sigma'].value)
+        pars['g2_sigma'].set(sigma[1],  min = pars['g1_sigma'].value)
         pars['g2_amplitude'].set(min = 0)
 
         gmodel = gmodel_1 + gmodel_2
@@ -192,6 +206,11 @@ def gaussian_model_w_lims(self, peak_pos, sigma, min_max_range):
         assert self.num_of_gaussians == len(self.peak_pos), ("Number of gaussians must be equal to the number of peak positions")
         assert len(self.min_max_range) == len(self.peak_pos), ("Number of bounds on the range must be equal to the number of peak positions")
 
+        if self.fit_in_eV is True:
+            peak_pos = 1240/np.asarray(peak_pos)
+            sigma = 1240/np.asarray(sigma)
+            min_max_range = np.sort(1240/np.asarray(min_max_range))
+
 
         for i in range(self.num_of_gaussians):
 

PythonGUI_apps/Spectrum_analysis/Spectra_plot_fit.py

@@ -347,7 +347,6 @@ def plot(self):
                 self.y = self.file[:,1]
 
             self.check_loaded_files()
-            self.check_eV_state()
 
             if self.check_loaded_files() == True: #check the following conditions if all required files have been provided
                 if self.ui.subtract_bck_radioButton.isChecked() == True and self.ui.WLRef_checkBox.isChecked() == False:
@@ -365,6 +364,8 @@ def plot(self):
 
             if self.ui.norm_checkBox.isChecked():
                 self.normalize()
+            
+            self.check_eV_state()
 
             self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
 
@@ -384,9 +385,11 @@ def normalize(self):
 
     def check_eV_state(self):
         if self.ui.fit_in_eV.isChecked():
-            self.x = 1240/self.file[:,0]
+            self.x = np.sort(1240/self.file[:,0])
+            self.y = [self.y[i] for i in np.argsort(1240/self.file[:,0])]
         else:
             self.x = self.file[:,0]
+            self.y = self.file[:,1]
 
     def clear_plot(self):
         self.ui.plot.clear()
@@ -430,7 +433,7 @@ def fit_and_plot(self):
                 pass
             else:
                 self.check_eV_state()
-                if fit_func == "Single Gaussian": #and self.ui.subtract_bck_radioButton.isChecked() == True:
+                if fit_func == "Single Gaussian":
                     single_gauss = Single_Gaussian(self.file, self.bck_file, wlref=self.wlref_file, fit_in_eV=self.ui.fit_in_eV.isChecked())
                     if self.ui.adjust_param_checkBox.isChecked():
                         center1_min = self.ui.single_peakcenter1_min_spinBox.value()
@@ -441,7 +444,8 @@ def fit_and_plot(self):
                             [center1_min, center1_max])
                     else:
                         self.result = single_gauss.gaussian_model()
-                    self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
+                    #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
+                    self.plot()
                     self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k')
                     self.ui.result_textBrowser.setText(self.result.fit_report())
 
@@ -457,7 +461,8 @@ def fit_and_plot(self):
                                 [center1_min, center1_max])
                     else:
                         self.result = single_lorentzian.lorentzian_model()
-                    self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
+                    #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
+                    self.plot()
                     self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k')
                     self.ui.result_textBrowser.setText(self.result.fit_report())
 
@@ -481,7 +486,8 @@ def fit_and_plot(self):
                     else:
                         self.result = double_gauss.gaussian_model()
 
-                    self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
+                    #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
+                    self.plot()
                     self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k')
                     if self.ui.plot_components_checkBox.isChecked():
                         comps = self.result.eval_components(x=self.x)
@@ -515,7 +521,8 @@ def fit_and_plot(self):
                     else:
                         self.result = multiple_gauss.gaussian_model()
 
-                    self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
+                    #self.ui.plot.plot(self.x, self.y, clear=self.clear_check(), pen='r')
+                    self.plot()
                     self.ui.plot.plot(self.x, self.result.best_fit, clear=False, pen='k')
                     if self.ui.plot_components_checkBox.isChecked():
                         comps = self.result.eval_components(x=self.x)

PythonGUI_apps/Spectrum_analysis/Spectra_plot_fit_gui.ui

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>2284</width>
-    <height>1434</height>
+    <height>1476</height>
    </rect>
   </property>
   <property name="minimumSize">
@@ -620,7 +620,7 @@
          </font>
         </property>
         <property name="text">
-         <string>Fit in eV</string>
+         <string>Fit/Plot in eV</string>
         </property>
         <property name="checked">
          <bool>true</bool>