Merge pull request #151 from portugueslab/add_crop_param

Add crop parameter to the save parameters

sashimi/hardware/cameras/hamamatsu/interface.py

@@ -242,7 +242,6 @@ def get_property_value(self, property_name):
     def set_property_value(self, property_name, property_value, *args, **kwargs):
         # Check if the property exists.
         if not (property_name in self.properties):
-
             raise CameraException(f"Unknown property name {property_name}")
 
         # If the value is text, figure out what the

sashimi/hardware/cameras/hamamatsu/sdk.py

@@ -44,6 +44,7 @@
 
 # Hamamatsu structures.
 
+
 ## DCAMAPI_INIT
 #
 # The dcam initialization structure

sashimi/hardware/scanning/scanloops.py

@@ -110,7 +110,6 @@ def __init__(
         logger: ConcurrenceLogger,
         trigger_exp_from_scanner,
     ):
-
         self.sample_rate = sample_rate
         self.n_samples = n_samples
 

sashimi/processes/camera.py

@@ -178,7 +178,6 @@ def camera_loop(self):
             # if no frames are received (either this loop is in between frames
             # or we are in the waining period)
             if frames:
-
                 for frame in frames:
                     self.logger.log_message(
                         "received frame of shape " + str(frame.shape)

sashimi/processes/streaming_save.py

@@ -28,6 +28,7 @@ class SavingParameters:
     notification_email: str = "None"
     volumerate: float = 1
     voxel_size: tuple = (1, 1, 1)
+    crop: tuple = (0, 0, None, None)
 
 
 @dataclass
@@ -175,8 +176,7 @@ def finalize_dataset(self):
                         self.save_parameters.chunk_size,
                         *self.current_data.shape[1:],
                     ),
-                    "crop_start": [0, 0, 0, 0],
-                    "crop_end": [0, 0, 0, 0],
+                    "crop": self.save_parameters.crop,  # order of params here is [hpos, vpos, hsize, vsize,]
                     "padding": [0, 0, 0, 0],
                     "voxel_size": self.save_parameters.voxel_size,
                 },

sashimi/state.py

@@ -228,7 +228,6 @@ def get_voxel_size(
     scanning_settings: Union[ZRecordingSettings, SinglePlaneSettings],
     camera_settings: CameraSettings,
 ):
-
     binning = int(camera_settings.binning)
 
     if isinstance(scanning_settings, SinglePlaneSettings):
@@ -266,6 +265,9 @@ def convert_save_params(
         notification_email=str(save_settings.notification_email),
         volumerate=scanning_settings.frequency,
         voxel_size=get_voxel_size(scanning_settings, camera_settings),
+        crop=[
+            int(item) for item in camera_settings.roi
+        ],  # int conversion makes it json serializable
     )
 
 
@@ -669,7 +671,6 @@ def obtain_noise_average(self, n_images=50):
         self.dispatcher.calibration_ref_queue.put(self.calibration_ref)
 
     def reset_noise_subtraction(self):
-
         self.calibration_ref = None
         self.noise_subtraction_active.clear()