Add transmission in XAS plot and base calibration on 2048 pixels

src/toolbox_scs/detectors/viking.py

@@ -8,8 +8,8 @@ from .hrixs import gauss1d
 __all__ = ['Viking']
 
 
-def plot_viking_xas(xas, plot_errors=True, xas_ylim=(-1, 3)):
-    fig, ax = plt.subplots(3, 1, figsize=(7, 7), sharex=True)
+def plot_viking_xas(xas, plot_errors=True, xas_ylim=(-1, 4)):
+    fig, ax = plt.subplots(4, 1, figsize=(7, 9), sharex=True)
     ax[0].plot(xas.newt_x, xas['I0'])
     ax[0].grid()
     ax[0].set_title('I0 spectra')
@@ -18,10 +18,14 @@ def plot_viking_xas(xas, plot_errors=True, xas_ylim=(-1, 3)):
     ax[1].grid()
     ax[1].set_title('It spectra')
 
-    ax[2].plot(xas.newt_x, xas['absorptionCoef'])
-    ax[2].set_ylim(*xas_ylim)
+    ax[2].plot(xas.newt_x, xas['It'] / xas['I0'])
     ax[2].grid()
-    ax[2].set_title('XAS')
+    ax[2].set_title('Transmission It / I0')
+
+    ax[3].plot(xas.newt_x, xas['absorptionCoef'])
+    ax[3].set_ylim(*xas_ylim)
+    ax[3].grid()
+    ax[3].set_title('XAS -log(It/I0)/thickness')
 
     if plot_errors:
         ax[0].fill_between(xas.newt_x,
@@ -32,7 +36,7 @@ def plot_viking_xas(xas, plot_errors=True, xas_ylim=(-1, 3)):
                            xas['It'] - 1.96*xas['It_stderr'],
                            xas['It'] + 1.96*xas['It_stderr'],
                            alpha=0.2)
-        ax[2].fill_between(xas.newt_x,
+        ax[3].fill_between(xas.newt_x,
                    xas['absorptionCoef'] - 1.96*xas['absorptionCoef_stderr'],
                    xas['absorptionCoef'] + 1.96*xas['absorptionCoef_stderr'],
                    alpha=0.2)
@@ -169,6 +173,7 @@ class Viking:
         roi = {'newton': {'newton': {'roi': (self.Y_RANGE, self.X_RANGE),
                                      'dim': ['newt_y', 'newt_x']}}}
         run, newton = tb.load(self.PROPOSAL, runNB, 'newton', rois=roi)
+        
         newton = newton.shift(trainId=-1).astype(float)
         #load the rest
         fields = [f for f in self.FIELDS if f != 'newton']
@@ -178,8 +183,8 @@ class Viking:
             run, data = tb.load(self.PROPOSAL, runNB,
                             fields=fields)
             data = data.merge(newton, join='inner')
-        data = data.assign_coords(newt_x=np.polyval(self.ENERGY_CALIB,
-                                                    data['newt_x']))
+        calib = np.polyval(self.ENERGY_CALIB, np.arange(0, 2048))
+        data = data.assign_coords(newt_x=calib[self.X_RANGE])
         if add_attrs:
             params = self.get_camera_params(run)
             for k, v in params.items():