A stack that tests whether the sharpest image is towards the middle

src/openflexure_microscope_server/things/autofocus.py

@@ -266,6 +266,16 @@ class AutofocusThing(Thing):
     def stack_images_to_capture(self, value: int) -> None:
         self.thing_settings["stack_images_to_capture"] = value
 
+    @thing_property
+    def stack_images_to_test(self) -> int:
+        """The number of images to test for successful focusing in a stack
+        Defaults to 9, which balances reliability and speed"""
+        return self.thing_settings.get("stack_images_to_test", 9)
+
+    @stack_images_to_test.setter
+    def stack_images_to_test(self, value: int) -> None:
+        self.thing_settings["stack_images_to_test"] = value
+
     @thing_property
     def stack_dz(self) -> int:
         """Space in steps between images in a z-stack
@@ -287,35 +297,78 @@ class AutofocusThing(Thing):
         metadata_getter: GetThingStates,
         capture: CaptureDep,
         images_dir: str,
-        stack_dir: str,
     ) -> None:
         """Run a z stack, saving all images to stack_dir and copying the
         central image to stack_dir"""
         stack_dz = self.stack_dz
         images_to_capture = self.stack_images_to_capture
+        images_to_test = self.stack_images_to_test
 
-        stack_z_range = stack_dz * (images_to_capture - 1)
+        if images_to_test < images_to_capture:
-        stage.move_relative(z=-stack_z_range / 2)
+            raise RuntimeError(
+                "Can't capture more images than are tested. Please increase number to test, or decrease number to capture"
+            )
+        if images_to_test % 2 == 0:
+            raise RuntimeError("Images to test should be odd")
 
-        for capture_count in range(images_to_capture):
+        stack_z_range = stack_dz * (images_to_test - 1)
+        overshoot = stack_dz * 5
+        backlash_correction = 250
+
+        stage.move_relative(z=-(overshoot + backlash_correction + stack_z_range / 2))
+        stage.move_relative(z=backlash_correction)
+
+        continue_stack = True
+        captures = []
+        sharpnesses = []
+        heights = []
+        capture_count = 0
+        starting_height = stage.position["z"]
+
+        while continue_stack:
             time.sleep(SETTLING_TIME)
 
+            stage_location = stage.position
+
             jpeg_path = os.path.join(
-                stack_dir,
+                images_dir,
-                f"{capture_count}.jpeg",
+                f"{stage_location['x']}_{stage_location['y']}_{stage_location['z']}.jpeg",
             )
-            capture._capture_and_save(
+            image, metadata = capture._capture_image(
-                jpeg_path=jpeg_path,
                 cam=cam,
-                logger=logger,
                 metadata_getter=metadata_getter,
             )
+            captures.append([jpeg_path, image, metadata])
+            sharpnesses.append(cam.grab_jpeg_size(stream_name="lores"))
+            heights.append(stage.position["z"])
+            capture_count += 1
 
             # If the stack isn't complete yet, move
-            if capture_count + 1 < images_to_capture:
+            if capture_count >= images_to_test:
-                stage.move_relative(z=stack_dz)
+                logger.info(sharpnesses[-images_to_test:])
+                stack_result = self.test_stack(sharpnesses[-images_to_test:])
 
-        self.copy_central_image_from_stack(images_dir, stack_dir)
+                if stack_result == "success":
+                    continue_stack = False
+                elif stack_result == "restart" or capture_count > 20:
+                    captures = []
+                    sharpnesses = []
+                    heights = []
+                    capture_count = 0
+                    stage.move_absolute(
+                        z=starting_height - stack_dz * (images_to_test - 1)
+                    )
+            stage.move_relative(z=stack_dz)
+
+        sharpest_index = np.argmax(sharpnesses[-images_to_test:])
+        capture._save_capture(
+            jpeg_path=captures[-images_to_test:][sharpest_index][0],
+            image=captures[-images_to_test:][sharpest_index][1],
+            metadata=captures[-images_to_test:][sharpest_index][2],
+            logger=logger,
+        )
+
+        return heights[-images_to_test:][sharpest_index]
 
     def copy_central_image_from_stack(
         self,
@@ -331,3 +384,22 @@ class AutofocusThing(Thing):
         xy_location = os.path.basename(stack_dir)
 
         shutil.copy(central_image, os.path.join(images_dir, f"{xy_location}.jpeg"))
+
+    def test_stack(self, sharpnesses: list):
+        """Test a list of sharpnesses, to decide whether the focal plane is within them"""
+        sharpest_index = np.argmax(sharpnesses)
+        sharpness_length = len(sharpnesses)
+
+        if sharpness_length == 1:
+            return "success"
+        if sharpness_length == 3:
+            if sharpest_index == 1:
+                return "success"
+
+        exclusion_range = 3
+
+        if sharpest_index < exclusion_range:
+            return "restart"
+        if sharpest_index >= len(sharpnesses) - exclusion_range:
+            return "continue"
+        return "success"

src/openflexure_microscope_server/things/capture.py

@@ -1,4 +1,3 @@
-import numpy as np
 from PIL import Image
 import time
 import piexif
@@ -48,7 +47,8 @@ class CaptureThing(Thing):
             f"Acquired {jpeg_path} in {acquisition_duration}s then {saving_duration}s saving to disk"
         )
 
-    def _capture_image(self, cam, metadata_getter) -> tuple[np.ndarray, dict]:
+    @thing_action
+    def _capture_image(self, cam, metadata_getter):
         """Capture an image in memory and return it with metadata
         CaptureError raised if the capture fails for any reason
         returns tuple with numpy array of image data, and dict of metadata
@@ -60,10 +60,11 @@ class CaptureThing(Thing):
             raise CaptureError("An error occurred while capturing") from e
         return image, metadata
 
+    @thing_action
     def _save_capture(
         self,
         jpeg_path: str,
-        image: np.ndarray,
+        image,
         metadata: dict,
         logger: InvocationLogger,
     ) -> None:

src/openflexure_microscope_server/things/smart_scan.py

@@ -620,6 +620,8 @@ class SmartScanThing(Thing):
             self._manage_stitching_threads()
 
             next_pos_xy, z_est = route_planner.get_next_location_and_z_estimate()
+            self._scan_logger.info(z_est)
+            self._scan_logger.info(self._stage.position["z"])
             new_pos_xyz = self._move_to_next_point(next_pos_xy, z_est)
             current_pos_xyz = (
                 new_pos_xyz[0],
@@ -642,32 +644,18 @@ class SmartScanThing(Thing):
                 self._scan_logger.info(msg)
                 continue
 
-            focused = False
+            focused_height = self._autofocus.run_z_stack(
-            if self._scan_data["autofocus_on"]:
+                images_dir=self._ongoing_scan_images_dir,
-                self._autofocus.looping_autofocus(
+            )
-                    dz=self._scan_data["autofocus_dz"], start="centre"
+
-                )
+            current_pos_xyz = (
-                current_pos_xyz = (
+                new_pos_xyz[0],
-                    new_pos_xyz[0],
+                new_pos_xyz[1],
-                    new_pos_xyz[1],
+                focused_height,
-                    self._stage.position["z"],
+            )
-                )
-                # Without a test for autofocus success, assume it worked
-                focused = True
 
             route_planner.mark_location_visited(
-                current_pos_xyz, imaged=True, focused=focused
+                current_pos_xyz, imaged=True, focused=True
-            )
-
-            site_folder = os.path.join(
-                self._ongoing_scan_images_dir,
-                "stacks",
-                f"{new_pos_xyz[0]}_{new_pos_xyz[1]}",
-            )
-            os.makedirs(site_folder, exist_ok=True)
-            self._autofocus.run_z_stack(
-                images_dir=self._ongoing_scan_images_dir,
-                stack_dir=site_folder,
             )
 
             # increment capure counter as thread has completed