[noisereduction] fix getBackground

id06workflow/core/Dataset/__init__.py

@@ -146,5 +146,9 @@ class Dataset(object):
         # TODO: add information if the number of frame is fixed...
         if len(files_list) is 0:
             return None
-        series = FileSeries(files_list)
-        return self._loadSeries(series)
+
+        res = []
+        series = FileSeries(filenames=files_list, single_frame=True)
+        for iframe in range(series.nframes):
+            res.append(series.getframe(iframe).data)
+        return numpy.asarray(res)

id06workflow/core/experiment/__init__.py

@@ -209,18 +209,22 @@ class Experiment(object):
                 steps = (1, 1, 1)
             else:
                 if len(reductionStep) is 1:
-                    steps = reductionStep[0]
+                    steps = reductionStep[0].steps
                 else:
                     raise NotImplementedError(
                         'cannot manage several reduction steps for the moment')
+            # first apply data reduction because roi is applied after data
+            # reduction
             background_img = numpy.median(background, axis=0)
+            background_img = background_img[::steps[1], ::steps[0]]
+
             if self.roi is None:
-                return background_img[::steps[1], ::steps[2]]
+                return background_img
             else:
                 origin, size = self.roi
                 ymin, ymax = int(origin[1]), int(origin[1] + size[1])
                 xmin, xmax = int(origin[0]), int(origin[0] + size[0])
-                return background_img[ymin:ymax:steps[1], xmin:xmax:steps[2]]
+                return background_img[ymin:ymax, xmin:xmax]
 
     def addOperation(self, operation):
         """Add the operation to the stack of operations"""
@@ -250,7 +254,9 @@ class Experiment(object):
     def _getDataReductionOperations(self):
         """
 
-        :return: the list of roi operation
+        :return: the list of roi operation.
+
+        ..note: reduction steps are defined as tuple(x, y, z)
         """
         return self._data_reduction_operations