Fix issue #138 (#139)

* moved activation noise subtraction

* fixed type for mock frames

* implemented check for matching size

sashimi/hardware/cameras/mock.py

@@ -79,7 +79,7 @@ def get_frames(self):
             self.elapsed = (self.current_time - self.previous_frame_time) * 1e-9
             if self.elapsed >= self._exposure_time * 1e-3:
                 multiplier = np.random.randint(1, 5, 1)
-                frames.append(self.current_mock_image * multiplier)
+                frames.append(np.uint16(self.current_mock_image * multiplier))
                 self.previous_frame_time = self.current_time
         else:
             self.previous_frame_time = self.current_time

sashimi/processes/dispatcher.py

@@ -64,7 +64,8 @@ def run(self):
 
     def process_frame(self, current_frame):
         if self.calibration_ref is not None and self.noise_subtraction_active.is_set():
-            current_frame = neg_dif(current_frame, self.calibration_ref)
+            if np.shape(current_frame) == np.shape(self.calibration_ref):
+                current_frame = neg_dif(current_frame, self.calibration_ref)
 
         if self.first_volume or self.volume_buffer.shape[1:3] != current_frame.shape:
             self.volume_buffer = np.empty(

sashimi/state.py

@@ -597,12 +597,13 @@ def obtain_noise_average(self, n_images=50):
                 calibration_set[n_image, :, :] = current_image
                 n_image += 1
 
-        self.noise_subtraction_active.set()
         self.calibration_ref = np.mean(calibration_set, axis=0).astype(
             dtype=current_volume.dtype
         )
         self.light_source.intensity = light_intensity
 
+        self.noise_subtraction_active.set()
+
         self.dispatcher.calibration_ref_queue.put(self.calibration_ref)
 
     def reset_noise_subtraction(self):