Dev/matterhorn decoder (#324)

- reshape image directly in decoder such that first dimension is num
counters
- take into account chip artefact in decoder.

---------

Co-authored-by: Erik Fröjdh <erik.frojdh@psi.ch>

python/aare/transform.py

@@ -81,6 +81,10 @@ class Matterhorn10Transform:
         A matterhorn chip has 256 columns and 256 rows.
         A matterhornchip with dynamic range 16 and 2 counters thus requires 
         256*256*16*2/(2*64) = 1024 transceiver samples. (Per default 2 channels are enabled per transceiver sample, each channel storing 64 bits)
+
+    .. note:: 
+        Due to an artefact in the chip, the transformation only fully supports 2 or 4 counters. Also if you enable 2 counters you can only select counter 1 and 2 or 0, 3 to get reasonable results. 
+        Otherwise only the first half of the image is correct. 
     """
     def __init__(self, dynamic_range : int, num_counters : int):
         self.pixel_map = _aare.GenerateMatterhorn10PixelMap(dynamic_range, num_counters)
@@ -105,7 +109,7 @@ class Matterhorn10Transform:
         checks if data is compatible for transformation 
         
         :param data: data to be transformed, expected to be a 1D numpy array of uint8
-        :type data: np.ndarray
+        :type data: np.ndarray(n_counters, n_rows, n_cols) 
         :raises ValueError: if not compatible
         """
         expected_size = (Matterhorn10.nRows*Matterhorn10.nCols*self.num_counters*self.dynamic_range)//8 # read_frame returns data in uint8_t 
@@ -118,11 +122,11 @@ class Matterhorn10Transform:
     def __call__(self, data):
         self.data_compatibility(data)
         if self.dynamic_range == 16:
-            return np.take(data.view(np.uint16), self.pixel_map)
+            return np.take(data.view(np.uint16), self.pixel_map).reshape(self.num_counters, Matterhorn10.nRows, Matterhorn10.nCols)
         elif self.dynamic_range == 8: 
-            return np.take(data.view(np.uint8), self.pixel_map)
+            return np.take(data.view(np.uint8), self.pixel_map).reshape(self.num_counters, Matterhorn10.nRows, Matterhorn10.nCols)
         else: #dynamic range 4
-            return np.take(_aare.expand4to8bit(data.view(np.uint8)), self.pixel_map)
+            return np.take(_aare.expand4to8bit(data.view(np.uint8)), self.pixel_map).reshape(self.num_counters, Matterhorn10.nRows, Matterhorn10.nCols)
             
 class Mythen302Transform:
     """