Merge changes to code base since Feb/March

AnalyzePDE.py

@@ -323,6 +323,7 @@ def plot_spe(
             }
             df = pd.DataFrame(data)
             df.to_csv(out_file)
+        plt.show()
 
     def plot_CA(self, color: str = "blue", out_file: str = None) -> None:
         """
@@ -343,6 +344,7 @@ def plot_CA(self, color: str = "blue", out_file: str = None) -> None:
         fig = plt.figure()
 
         data_x = self.ov
+        # data_x = self.bias_vals
         data_x_err = self.bias_err
         data_y = self.CA_vals
         data_y_err = self.CA_err
@@ -403,6 +405,8 @@ def plot_CA(self, color: str = "blue", out_file: str = None) -> None:
             }
             df = pd.DataFrame(data)
             df.to_csv(out_file)
+        else:
+            plt.show()
 
     def plot_CA_rms(self, color: str = "blue", out_file: str = None) -> None:
         """
@@ -424,6 +428,8 @@ def plot_CA_rms(self, color: str = "blue", out_file: str = None) -> None:
 
         data_x = self.bias_vals
         data_x_err = self.bias_err
+        # data_x = self.ov
+        # data_x_err = self.ov_err
         data_y = self.CA_rms_vals
         data_y_err = self.CA_rms_err
 
@@ -463,6 +469,8 @@ def plot_CA_rms(self, color: str = "blue", out_file: str = None) -> None:
             }
             df = pd.DataFrame(data)
             df.to_csv(out_file)
+        else:
+            plt.show()
 
     # I HAVE A SECRET TO TELL YOU! (it was reed who wrote that message and thwy are pinning it on me)
 
@@ -760,7 +768,7 @@ def plot_num_det_photons(self, color: str = "purple", out_file: str = None) -> N
         fig = plt.figure()
 
         data_x = self.ov
-        data_x_err = self.bias_err
+        data_x_err = self.bias_err # use error from voltage source, not over correlated error from OV
         data_y = self.num_det_photons
         data_y_err = self.num_det_photons_err
 
@@ -790,6 +798,7 @@ def plot_num_det_photons(self, color: str = "purple", out_file: str = None) -> N
         ylow, yhigh = plt.ylim()
         plt.ylim(-1, yhigh * 1.1)
         plt.tight_layout()
+        plt.show()
 
         if out_file:
             x_label = "Overvoltage [V]"
@@ -872,13 +881,10 @@ def plot_PDE(
             plt.legend(loc="lower left")
         plt.tight_layout()
         if out_file:
-            x_label = "Overvoltage [V]"
-            y_label = "Photon Detection Efficiency"
             data = {
-                x_label: data_x,
-                x_label + " error": data_x_err,
-                y_label: data_y,
-                y_label + " error": data_y_err,
+                'ov': data_x, 'ov error': data_x_err,
+                'amps': self.alpha_vals, 'amps error': self.alpha_err,
+                'bias': self.bias_vals, 'bias err': self.bias_err
             }
             df = pd.DataFrame(data)
             df.to_csv(out_file)