Added a new way to capture full res JPEGs, need to do a comparison of results

src/openflexure_microscope_server/things/autofocus.py

@@ -33,7 +33,7 @@ from labthings_fastapi.dependencies.invocation import InvocationLogger
 from .camera import RawCameraDependency as Camera
 from .camera import CameraDependency as WrappedCamera
 from .stage import StageDependency as Stage
-from .capture import CaptureThing
+from .capture import CaptureThing, _save_capture
 import numpy as np
 from pydantic import BaseModel
 
@@ -310,7 +310,27 @@ class AutofocusThing(Thing):
                 stack_dir,
                 f"{capture_count}.jpeg",
             )
-            capture.capture_jpeg(filename=jpeg_path, cam=cam)
+            # The pre-existing capture_jpeg
+            # capture.capture_jpeg(filename=jpeg_path, cam=cam)
+            
+            # A new way to get the full array
+            img = capture.capture_jpeg_array()
+            
+            metadata = metadata_getter()
+            _save_capture(
+                jpeg_path,
+                img,
+                metadata,
+                logger
+            )
+            
+            # The old capture and save a "main" res image
+            # capture._capture_and_save(
+            #     jpeg_path=jpeg_path,
+            #     cam=cam,
+            #     logger=logger,
+            #     metadata_getter=metadata_getter,
+            # )
 
             # If the stack isn't complete yet, move
             if capture_count + 1 < images_to_capture:

src/openflexure_microscope_server/things/camera/__init__.py

@@ -77,6 +77,11 @@ class CameraProtocol(Protocol):
         """Acquire one image from the preview stream and return its size"""
         ...
 
+    def capture_jpeg_array(
+        self,
+        ):
+        ...
+
 
 class BaseCamera(Thing):
     """A Thing representing a camera
@@ -170,6 +175,12 @@ class CameraStub(BaseCamera):
     ) -> NDArray:
         raise NotImplementedError("Cameras must not inherit from CameraStub")
 
+    @thing_action
+    def capture_jpeg_array(
+        self,
+        ):
+        raise NotImplementedError("Cameras must not inherit from CameraStub")
+
     @thing_action
     def capture_jpeg(
         self,

src/openflexure_microscope_server/things/capture.py

@@ -54,6 +54,11 @@ class CaptureThing(Thing):
         jpeg = cam.capture_jpeg(resolution="full")
         jpeg.save(filename)
 
+    @thing_action
+    def capture_jpeg_array(self, cam: CamDep):
+        """Return a full resolution stream array"""
+        return cam.capture_jpeg_array()
+
     @thing_action
     def _capture_array(self, cam: CamDep, metadata_getter: GetThingStates):
         """Capture an image in memory and return it with metadata
@@ -94,3 +99,30 @@ class CaptureThing(Thing):
                 logger.warning(f"Failed to add metadata to {jpeg_path}")
         except Exception as e:
             raise IOError(f"An error occurred while saving {jpeg_path}") from e
+        
+def _save_capture(
+    jpeg_path: str,
+    image: np.ndarray,
+    metadata: dict,
+    logger: InvocationLogger,
+) -> None:
+    """Saving the captured image and metadata to disk
+    logger warning (via InvocationLogger) is raised if metadata is failed to be added
+    IOError is raised if the file cannot be saved
+    nothing is returned on success"""
+    try:
+        Image.fromarray(image.astype("uint8"), "RGB").save(
+            jpeg_path, quality=95, subsampling=0
+        )
+        try:
+            exif_dict = piexif.load(jpeg_path)
+            exif_dict["Exif"][piexif.ExifIFD.UserComment] = json.dumps(
+                metadata
+            ).encode("utf-8")
+            piexif.insert(piexif.dump(exif_dict), jpeg_path)
+        except:  # noqa: E722
+            # We need to capture any exception as there are many reasons metadata
+            # might not be added. We warn rather than log the error.
+            logger.warning(f"Failed to add metadata to {jpeg_path}")
+    except Exception as e:
+        raise IOError(f"An error occurred while saving {jpeg_path}") from e