Swap stream for scan, target_resolution as arg

src/openflexure_microscope_server/things/autofocus.py

@@ -294,7 +294,7 @@ class AutofocusThing(Thing):
         capture: CaptureDep,
         images_dir: str,
         stack_dir: str,
-        capture_method: str = "array",
+        target_resolution: tuple[int, int],
     ) -> None:
         """Run a z stack, saving all images to stack_dir and copying the
         central image to stack_dir"""
@@ -311,21 +311,13 @@ class AutofocusThing(Thing):
                 stack_dir,
                 f"{capture_count}.jpeg",
             )
-            if capture_method == "blob":
+            capture._capture_and_save(
-                capture.capture_jpeg(filename=jpeg_path, cam=cam)
+                jpeg_path=jpeg_path,
-            elif capture_method == "hires_array" or capture_method == "array":
+                cam=cam,
-                stream = "main" if capture_method == "array" else "full"
+                logger=logger,
-                capture._capture_and_save(
+                metadata_getter=metadata_getter,
-                    jpeg_path=jpeg_path,
+                target_resolution=target_resolution,
-                    cam=cam,
+            )
-                    logger=logger,
-                    metadata_getter=metadata_getter,
-                    stream_name=stream,
-                )
-            else:
-                raise ValueError(
-                    'Capture method must be one of "array", "blob" or "hires_array"'
-                )
 
             # If the stack isn't complete yet, move
             if capture_count + 1 < images_to_capture:

src/openflexure_microscope_server/things/camera/__init__.py

@@ -79,14 +79,9 @@ class CameraProtocol(Protocol):
         """Acquire one image from the preview stream and return its size"""
         ...
 
-    def start_highres_streaming(self) -> None:
+    def start_streaming(self, main_resolution) -> None:
-        """Start (or stop and restart) the camera in a configuration for low
+        """Start (or stop and restart) the camera with the given resolution
-        res streaming and instant high res captures"""
+        for the main stream"""
-        ...
-
-    def start_streaming(self) -> None:
-        """Start (or stop and restart) the camera in the default streaming
-        configuration which balances stream and capture quality"""
         ...
 
 
@@ -194,15 +189,9 @@ class CameraStub(BaseCamera):
         raise NotImplementedError("Cameras must not inherit from CameraStub")
 
     @thing_action
-    def start_highres_streaming(self):
+    def start_streaming(self, main_resolution) -> None:
-        """Start (or stop and restart) the camera in a configuration for low
+        """Start (or stop and restart) the camera with the given resolution
-        res streaming and instant high res captures"""
+        for the main stream"""
-        raise NotImplementedError("Cameras must not inherit from CameraStub")
-
-    @thing_action
-    def start_streaming(self) -> None:
-        """Start (or stop and restart) the camera in the default streaming
-        configuration which balances stream and capture quality"""
         raise NotImplementedError("Cameras must not inherit from CameraStub")
 
 

src/openflexure_microscope_server/things/capture.py

@@ -28,7 +28,7 @@ class CaptureThing(Thing):
         cam: CamDep,
         logger: InvocationLogger,
         metadata_getter: GetThingStates,
-        stream_name: str = "main",
+        target_resolution: tuple[int, int],
     ) -> None:
         """Capture an image and save it to disk
 
@@ -39,7 +39,7 @@ class CaptureThing(Thing):
         image, metadata = self._capture_array(
             cam,
             metadata_getter,
-            stream=stream_name,
+            target_resolution=target_resolution,
             logger=logger,
         )
         acquisition_time = time.time()
@@ -81,7 +81,7 @@ class CaptureThing(Thing):
         cam: CamDep,
         metadata_getter: GetThingStates,
         logger: InvocationLogger,
-        stream: str = "main",
+        target_resolution: tuple[int, int] = (1640, 1232),
     ):
         """Capture an image in memory and return it with metadata
         CaptureError raised if the capture fails for any reason
@@ -90,7 +90,13 @@ class CaptureThing(Thing):
         for capture_attempts in range(5):
             try:
                 metadata = metadata_getter()
-                image = cam.capture_array(stream_name=stream, wait=5)[..., :3]
+                image = Image.fromarray(
+                    cam.capture_array(stream_name="main", wait=5)[..., :3].astype(
+                        "uint8"
+                    ),
+                    "RGB",
+                )
+                image = image.resize(target_resolution, Image.LANCZOS)
                 return image, metadata
             except TimeoutError:
                 logger.warning(
@@ -110,9 +116,7 @@ class CaptureThing(Thing):
         IOError is raised if the file cannot be saved
         nothing is returned on success"""
         try:
-            Image.fromarray(image.astype("uint8"), "RGB").save(
+            image.save(jpeg_path, quality=95, subsampling=0)
-                jpeg_path, quality=95, subsampling=0
-            )
             try:
                 exif_dict = piexif.load(jpeg_path)
                 exif_dict["Exif"][piexif.ExifIFD.UserComment] = json.dumps(

src/openflexure_microscope_server/things/smart_scan.py

@@ -182,7 +182,7 @@ class SmartScanThing(Thing):
         self._scan_images_taken = 0
         self._stitch_resize = 1
 
-        self._cam.start_highres_streaming()
+        self._cam.start_streaming(main_resolution=(3280, 2464))
 
         # Don't set self._scan_data dictionary. This is done at the start of _run_scan
 
@@ -692,7 +692,7 @@ class SmartScanThing(Thing):
             self._autofocus.run_z_stack(
                 images_dir=self._ongoing_scan_images_dir,
                 stack_dir=site_folder,
-                capture_method="blob",
+                target_resolution=(1640, 1232),
             )
 
             # increment capure counter as thread has completed