Apply suggestions from code review of branch jpeg-capture-in-stacking

Co-authored-by: Beth Probert <beth_probert@outlook.com>

src/openflexure_microscope_server/things/camera/__init__.py

@@ -250,6 +250,7 @@ class BaseCamera(Thing):
         try:
             image.save(jpeg_path, quality=95, subsampling=0)
             try:
+                # Load EXIF metadata from image so it can be added to.
                 exif_dict = piexif.load(jpeg_path)
                 exif_dict["Exif"][piexif.ExifIFD.UserComment] = json.dumps(
                     metadata

src/openflexure_microscope_server/things/camera/picamera.py

@@ -152,7 +152,7 @@ class StreamingPiCamera2(BaseCamera):
         tolerance of current value. This allows ignoring small changes
         """
         if key not in self.persistent_control_tolerances:
-            # Not tolerance range set, so it is not within tollerance
+            # Not tolerance range set, so it is not within tolerance
             return False
 
         difference = np.abs(self.persistent_controls[key] - value)
@@ -419,7 +419,7 @@ class StreamingPiCamera2(BaseCamera):
                 )
 
     @thing_action
-    def stop_streaming(self, stop_web_stream=True) -> None:
+    def stop_streaming(self, stop_web_stream: bool = True) -> None:
         """
         Stop the MJPEG stream
         """
@@ -617,7 +617,7 @@ class StreamingPiCamera2(BaseCamera):
             self.update_persistent_controls()
 
     @thing_action
-    def calibrate_lens_shading(self):
+    def calibrate_lens_shading(self) -> None:
         """Take an image and use it for flat-field correction.
 
         This method requires an empty (i.e. bright) field of view. It will take
@@ -643,7 +643,7 @@ class StreamingPiCamera2(BaseCamera):
         )
 
     @colour_correction_matrix.setter  # type: ignore
-    def colour_correction_matrix(self, value):
+    def colour_correction_matrix(self, value) -> None:
         self.thing_settings["colour_correction_matrix"] = value
         self.calibrate_colour_correction(value)
 
@@ -664,14 +664,14 @@ class StreamingPiCamera2(BaseCamera):
         self.colour_correction_matrix = c
 
     @thing_action
-    def calibrate_colour_correction(self, c: tuple):
+    def calibrate_colour_correction(self, c: tuple) -> None:
         """Overwrite the colour correction matrix in camera tuning"""
         with self.picamera(pause_stream=True):
             recalibrate_utils.set_static_ccm(self.tuning, c)
             self.initialise_picamera()
 
     @thing_action
-    def set_static_green_equalisation(self, offset: int = 65535):
+    def set_static_green_equalisation(self, offset: int = 65535) -> None:
         """Set the green equalisation to a static value.
 
         Green equalisation avoids the debayering algorithm becoming confused
@@ -686,7 +686,7 @@ class StreamingPiCamera2(BaseCamera):
             self.initialise_picamera()
 
     @thing_action
-    def full_auto_calibrate(self):
+    def full_auto_calibrate(self) -> None:
         """Perform a full auto-calibration
 
         This function will call the other calibration actions in sequence:
@@ -704,7 +704,7 @@ class StreamingPiCamera2(BaseCamera):
         self.calibrate_white_balance()
 
     @thing_action
-    def flat_lens_shading(self):
+    def flat_lens_shading(self) -> None:
         """Disable flat-field correction
 
         This method will set a completely flat lens shading table. It is not the
@@ -786,7 +786,7 @@ class StreamingPiCamera2(BaseCamera):
         )
 
     @thing_action
-    def flat_lens_shading_chrominance(self):
+    def flat_lens_shading_chrominance(self) -> None:
         """Disable flat-field correction
 
         This method will set the chrominance of the lens shading table to be
@@ -801,7 +801,7 @@ class StreamingPiCamera2(BaseCamera):
             self.initialise_picamera()
 
     @thing_action
-    def reset_lens_shading(self):
+    def reset_lens_shading(self) -> None:
         """Revert to default lens shading settings
 
         This method will restore the default "adaptive" lens shading method used

src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py

@@ -69,13 +69,13 @@ def load_default_tuning(cam: Picamera2) -> dict:
         tuning_dir = "/usr/share/libcamera/ipa/raspberrypi"
         # from picamera2 v0.3.9
         # The directory above has been removed from the search path seems
-        # find odd - as that's where the files currently are on a default
+        # odd - as that's where the files currently are on a default
         # Raspbian image. This may need updating if the files have moved
         # in future updates to the system libcamera package
         return cam.load_tuning_file(fname, dir=tuning_dir)
 
 
-def set_minimum_exposure(camera: Picamera2):
+def set_minimum_exposure(camera: Picamera2) -> None:
     """Enable manual exposure, with low gain and shutter speed
 
     We set exposure mode to manual, analog and digital gain
@@ -135,7 +135,7 @@ def test_exposure_settings(camera: Picamera2, percentile: float) -> ExposureTest
     return result
 
 
-def check_convergence(test: ExposureTest, target: int, tolerance: float):
+def check_convergence(test: ExposureTest, target: int, tolerance: float) -> bool:
     """Check whether the brightness is within the specified target range"""
     return abs(test.level - target) < target * tolerance
 
@@ -222,7 +222,7 @@ def adjust_shutter_and_gain_from_raw(
 
         # Check the gain is still changing - if not, we have probably hit the maximum
         if camera.capture_metadata()["AnalogueGain"] == test.analog_gain:
-            logging.info(f"Gain has maxed out. at {test.analog_gain}")
+            logging.info(f"Gain has maxed out at {test.analog_gain}")
             break
 
     if check_convergence(test, target_white_level, tolerance):
@@ -504,7 +504,7 @@ def index_of_algorithm(algorithms: list[dict], algorithm: str) -> int:
     raise ValueError(f"Algorithm {algorithm} is not available.")
 
 
-def copy_alsc_section(from_tuning: dict, to_tuning: dict):
+def copy_alsc_section(from_tuning: dict, to_tuning: dict) -> None:
     """Copy the `rpi.alsc` algorithm from one tuning to another.
 
     This is done in-place, i.e. modifying to_tuning.
@@ -544,7 +544,7 @@ def raw_channels_from_camera(camera: Picamera2) -> LensShadingTables:
     return channels_from_bayer_array(raw_image)
 
 
-def recreate_camera_manager():
+def recreate_camera_manager() -> None:
     """Delete and recreate the camera manager.
 
     This is necessary to ensure the tuning file is re-read.