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:
     """

python/tests/test_Transformation.py

@@ -8,10 +8,10 @@ def test_matterhorn10_16bit(test_data_path):
     with CtbRawFile(test_data_path / "raw/Matterhorn10/16bit_master_0.json", transform = transform.Matterhorn10Transform(dynamic_range=16, num_counters=1)) as f:
         headers, frames = f.read_frame()
 
-        assert frames.shape == (256, 256)
+        assert frames.shape == (1, 256, 256)
         assert frames.dtype == np.uint16
 
-        expected_data = np.tile(np.arange(255, -1, -1,dtype=np.uint16), (256, 1)) # TODO: endianess issue ? 
+        expected_data = np.tile(np.arange(255, -1, -1,dtype=np.uint16), (1, 256, 1)) # TODO: endianess issue ? 
 
         assert np.all(frames == expected_data)
 
@@ -22,24 +22,23 @@ def test_matterhorn10_8bit(test_data_path):
     with CtbRawFile(test_data_path / "raw/Matterhorn10/8bit_master_1.json", transform = transform.Matterhorn10Transform(dynamic_range=8, num_counters=1)) as f:
         headers, frames = f.read_frame()
 
-        assert frames.shape == (256, 256)
+        assert frames.shape == (1, 256, 256)
         assert frames.dtype == np.uint8
 
-        expected_data = np.tile(np.arange(255, -1, -1,dtype=np.uint8), (256, 1)) # TODO: endianess issue ? 
+        expected_data = np.tile(np.arange(255, -1, -1,dtype=np.uint8), (1, 256, 1)) # TODO: endianess issue ? 
 
         assert np.all(frames == expected_data)
 
-
 @pytest.mark.withdata
 def test_matterhorn10_4bit(test_data_path): 
     """ Matterhorn10Transform 1 counter 4 bit dynamic range """
     with CtbRawFile(test_data_path / "raw/Matterhorn10/newnewrun_4bit_1counter_master_0.json", transform = transform.Matterhorn10Transform(dynamic_range=4, num_counters=1)) as f:
         headers, frames = f.read_frame()
 
-        assert frames.shape == (256, 256)
+        assert frames.shape == (1, 256, 256)
         assert frames.dtype == np.uint8
 
-        expected_data = np.tile(np.tile(np.arange(15, -1, -1, dtype=np.uint8), 16), (256, 1)) # TODO: endianess issue ? 
+        expected_data = np.tile(np.tile(np.arange(15, -1, -1, dtype=np.uint8), 16), (1, 256, 1)) # TODO: endianess issue ? 
 
         assert np.all(frames == expected_data)
 
@@ -50,9 +49,9 @@ def test_matterhorn10_16bit_4counters(test_data_path):
     with CtbRawFile(test_data_path / "raw/Matterhorn10/4counter_16bit_master_4.json", transform = transform.Matterhorn10Transform(dynamic_range=16, num_counters=4)) as f:
         headers, frames = f.read_frame()
 
-        assert frames.shape == (4*256, 256)
+        assert frames.shape == (4, 256, 256)
         assert frames.dtype == np.uint16
 
-        expected_data = np.tile(np.arange(255, -1, -1,dtype=np.uint16), (4*256, 1)) # TODO: endianess issue ? 
+        expected_data = np.tile(np.arange(255, -1, -1,dtype=np.uint16), (4, 256, 1)) # TODO: endianess issue ? 
 
         assert np.all(frames == expected_data)