debug

Analyser/ImagingAnalyser.py

@@ -296,11 +296,13 @@ class ImageAnalyser():
 
         if fringeRemoval:
             
+            dataSetAtoms = dataSet[self._image_name['atoms']] - dataSet[self._image_name['dark']]
+            
             scanAxis = list(get_scanAxis(dataSet))
             if not scanAxis[1] is None:
-                OptimumRef = self._fringeRemoval.fringe_removal(dataSet[self._image_name['atoms']].stack(_imgIdx=scanAxis))
+                OptimumRef = self._fringeRemoval.fringe_removal(dataSetAtoms.stack(_imgIdx=scanAxis))
             else:
-                OptimumRef = self._fringeRemoval.fringe_removal(dataSet[self._image_name['atoms']])
+                OptimumRef = self._fringeRemoval.fringe_removal(dataSetAtoms)
             
             dataSet = dataSet.assign(
                 {
@@ -310,7 +312,7 @@ class ImageAnalyser():
             
             dataSet = dataSet.assign(
                 {
-                    self._image_name['OD']: xr.apply_ufunc(self.get_OD_no_dark, dataSet[self._image_name['atoms']], dataSet[self._image_name['optimumBackground']], **kwargs)
+                    self._image_name['OD']: xr.apply_ufunc(self.get_OD_no_dark, dataSetAtoms, dataSet[self._image_name['optimumBackground']], **kwargs)
                 }
             )
         else:
@@ -395,7 +397,7 @@ class ImageAnalyser():
         dataSet = read_hdf5_file(filePath, group, **kwargs)
         scanAxis = dataSet.scanAxis
         
-        dataSet = dataSet[self._image_name['background']]
+        dataSet = dataSet[self._image_name['background']] - dataSet[self._image_name['dark']]
         dataSet.attrs['scanAxis'] = scanAxis
         
         if crop: