From 17f3bbe646f4bd26919a0dbd270bb0b5c94e78e6 Mon Sep 17 00:00:00 2001
From: jaknapper <jaknapper@hotmail.com>
Date: Wed, 7 May 2025 10:39:05 +0100
Subject: [PATCH] Low res stream during scanning for instant high res captures

---
 .../things/camera/__init__.py                 | 21 +++++++++++++++++++
 .../things/capture.py                         |  8 +++++++
 .../things/smart_scan.py                      | 19 +++++++++--------
 3 files changed, 39 insertions(+), 9 deletions(-)

diff --git a/src/openflexure_microscope_server/things/camera/__init__.py b/src/openflexure_microscope_server/things/camera/__init__.py
index 8e095e75..cf765e99 100644
--- a/src/openflexure_microscope_server/things/camera/__init__.py
+++ b/src/openflexure_microscope_server/things/camera/__init__.py
@@ -79,6 +79,16 @@ class CameraProtocol(Protocol):
         """Acquire one image from the preview stream and return its size"""
         ...
 
+    def start_highres_streaming(self) -> None:
+        """Start (or stop and restart) the camera in a configuration for low
+        res streaming and instant high res captures"""
+        ...
+    
+    def start_streaming(self) -> None:
+        """Start (or stop and restart) the camera in the default streaming
+        configuration which balances stream and capture quality"""
+        ...
+
 class BaseCamera(Thing):
     """A Thing representing a camera
 
@@ -182,6 +192,17 @@ class CameraStub(BaseCamera):
         """Acquire one image from the camera and return as a JPEG blob"""
         raise NotImplementedError("Cameras must not inherit from CameraStub")
 
+    @thing_action
+    def start_highres_streaming(self):
+        """Start (or stop and restart) the camera in a configuration for low
+        res streaming and instant high res captures"""
+        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")
 
 CameraDependency = direct_thing_client_dependency(CameraStub, "/camera/")
 RawCameraDependency = raw_thing_dependency(CameraProtocol)
diff --git a/src/openflexure_microscope_server/things/capture.py b/src/openflexure_microscope_server/things/capture.py
index 8d3dc413..7b8d260e 100644
--- a/src/openflexure_microscope_server/things/capture.py
+++ b/src/openflexure_microscope_server/things/capture.py
@@ -65,6 +65,14 @@ class CaptureThing(Thing):
                 logger.warning(e)
         raise CaptureError("An error occurred while capturing after 5 attempts")
 
+    @thing_action
+    def stop_streaming(self, cam: CamDep):
+        cam.stop_streaming()
+
+    @thing_action
+    def restart_stream(self, cam:CamDep):
+        cam.restart_stream()
+
     @thing_action
     def _capture_array(self, cam: CamDep, metadata_getter: GetThingStates, logger: InvocationLogger, stream: str = 'main'):
         """Capture an image in memory and return it with metadata
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 46799104..61cc00c2 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -182,6 +182,8 @@ class SmartScanThing(Thing):
         self._scan_images_taken = 0
         self._stitch_resize = 1
 
+        self._cam.start_highres_streaming()
+
         # Don't set self._scan_data dictionary. This is done at the start of _run_scan
 
         try:
@@ -202,6 +204,7 @@ class SmartScanThing(Thing):
             # Error must be raised so UI gives correct output
             raise e
         finally:
+            self._cam.start_streaming()
             # However the scan finishes, unset all variables and release lock
             self._cancel = None
             self._scan_logger = None
@@ -404,19 +407,17 @@ class SmartScanThing(Thing):
         test_jpg = self._cam.grab_jpeg()
         test_image = np.array(Image.open(test_jpg.open()))
 
-        test_image_res = list(test_image.shape[:2])
+        test_image_res = list(test_image.shape)
         csm_image_res = [int(i) for i in self._csm.image_resolution]
 
-        if test_image_res != csm_image_res:
-            raise RuntimeError(
-                "Cannot start scan as it is set up to capture with a resolution that "
-                "has not been mapped.\n"
-                f"Scan resolution: {test_image_res}\n"
-                f"camera-stage-mapping resolution {csm_image_res}."
-            )
+
+        # If current stream width is different to csm calibration width,
+        # perform the conversion here
+        res_ratio = csm_image_res[0] / test_image_res[0]
 
         # get displacement matrix. note it is for (y, x) not (x, y) coordinates
-        csm_disp_matrix = self._csm.image_to_stage_displacement_matrix
+        csm_disp_matrix = np.array(self._csm.image_to_stage_displacement_matrix)
+        csm_disp_matrix *= res_ratio
 
         # Calculate displacements in image coordinates
         dx_img = test_image.shape[1] * (1 - overlap)