Get images as a PIL image from camera, use resizing and saving as settling time in stack

src/openflexure_microscope_server/things/autofocus.py

@@ -14,13 +14,11 @@ from typing import Annotated, Mapping, Optional, Sequence
 import os
 import shutil
 import glob
-import os
-import shutil
-import glob
 
 from fastapi import Depends
 import numpy as np
 from pydantic import BaseModel
+from PIL import Image
 
 from labthings_fastapi.thing import Thing
 from labthings_fastapi.dependencies.blocking_portal import BlockingPortal
@@ -34,13 +32,12 @@ from .camera import RawCameraDependency as Camera
 from .camera import CameraDependency as WrappedCamera
 from .stage import StageDependency as Stage
 from .capture import CaptureThing
-import numpy as np
-from pydantic import BaseModel
 
 
 CaptureDep = direct_thing_client_dependency(CaptureThing, "/capture/")
 
 SETTLING_TIME = 0.3
+STACK_OVERSHOOT = 200
 
 
 class JPEGSharpnessMonitor:
@@ -302,7 +299,8 @@ class AutofocusThing(Thing):
         images_to_capture = self.stack_images_to_capture
 
         stack_z_range = stack_dz * (images_to_capture - 1)
-        stage.move_relative(z=-stack_z_range / 2)
+        stage.move_relative(z=-(STACK_OVERSHOOT + stack_z_range / 2))
+        stage.move_relative(z=STACK_OVERSHOOT)
 
         for capture_count in range(images_to_capture):
             time.sleep(SETTLING_TIME)
@@ -311,17 +309,29 @@ class AutofocusThing(Thing):
                 stack_dir,
                 f"{capture_count}.jpeg",
             )
-            capture._capture_and_save(
-                jpeg_path=jpeg_path,
+            start = time.time()
+            image, metadata = capture._capture_image(
                 cam=cam,
-                logger=logger,
                 metadata_getter=metadata_getter,
-                target_resolution=target_resolution,
+                logger=logger,
             )
-
-            # If the stack isn't complete yet, move
-            if capture_count + 1 < images_to_capture:
-                stage.move_relative(z=stack_dz)
+            captured = time.time()
+            # There's an unnecessary move up at the end of the stack
+            stage.move_relative(z=stack_dz)
+            moved = time.time()
+            image = image.resize(target_resolution, Image.LANCZOS)
+            downsampled = time.time()
+            capture._save_capture(
+                jpeg_path=jpeg_path,
+                image=image,
+                metadata=metadata,
+                logger=logger,
+            )
+            saved = time.time()
+            logger.info(f"Capturing took {round(captured - start, 2)} s")
+            logger.info(f"Resizing took {round(downsampled - moved, 2)} s")
+            logger.info(f"Saving took {round(saved - downsampled, 2)} s")
+            logger.info(f"Effective settling time was {round(saved - moved, 2)} s")
 
         self.copy_central_image_from_stack(images_dir, stack_dir)
 

src/openflexure_microscope_server/things/camera/__init__.py

@@ -84,6 +84,11 @@ class CameraProtocol(Protocol):
         for the main stream"""
         ...
 
+    @thing_action
+    def capture_image(self, stream_name, wait):
+        """Capture a PIL image from stream stream_name with timeout wait"""
+        ...
+
 
 class BaseCamera(Thing):
     """A Thing representing a camera
@@ -194,6 +199,11 @@ class CameraStub(BaseCamera):
         for the main stream"""
         raise NotImplementedError("Cameras must not inherit from CameraStub")
 
+    @thing_action
+    def capture_image(self, stream_name, wait):
+        """Capture a PIL image from stream stream_name with timeout wait"""
+        raise Exception
+
 
 CameraDependency = direct_thing_client_dependency(CameraStub, "/camera/")
 RawCameraDependency = raw_thing_dependency(CameraProtocol)

src/openflexure_microscope_server/things/capture.py

@@ -1,5 +1,3 @@
-import numpy as np
-from PIL import Image
 import time
 import piexif
 import json
@@ -28,7 +26,6 @@ class CaptureThing(Thing):
         cam: CamDep,
         logger: InvocationLogger,
         metadata_getter: GetThingStates,
-        target_resolution: tuple[int, int],
     ) -> None:
         """Capture an image and save it to disk
 
@@ -36,14 +33,18 @@ class CaptureThing(Thing):
         that the stage may be moved while it's saved.
         """
         capture_start = time.time()
-        image, metadata = self._capture_array(
+        image, metadata = self._capture_image(
             cam,
             metadata_getter,
-            target_resolution=target_resolution,
             logger=logger,
         )
         acquisition_time = time.time()
-        self._save_capture(jpeg_path, image, metadata, logger)
+        self._save_capture(
+            jpeg_path,
+            image,
+            metadata,
+            logger,
+        )
         save_time = time.time()
         acquisition_duration = round(acquisition_time - capture_start, 1)
         saving_duration = round(save_time - acquisition_time, 1)
@@ -56,7 +57,7 @@ class CaptureThing(Thing):
         """Capture a JPEG (from a JPEGBlob) to disk"""
         for capture_attempts in range(5):
             try:
-                jpeg = cam.capture_jpeg(resolution="full", wait=5)
+                jpeg = cam.capture_jpeg(resolution="main", wait=5)
                 jpeg.save(filename)
                 return
             except TimeoutError:
@@ -76,12 +77,11 @@ class CaptureThing(Thing):
         cam.restart_stream()
 
     @thing_action
-    def _capture_array(
+    def _capture_image(
         self,
         cam: CamDep,
         metadata_getter: GetThingStates,
         logger: InvocationLogger,
-        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
@@ -90,13 +90,7 @@ class CaptureThing(Thing):
         for capture_attempts in range(5):
             try:
                 metadata = metadata_getter()
-                image = Image.fromarray(
-                    cam.capture_array(stream_name="main", wait=5)[..., :3].astype(
-                        "uint8"
-                    ),
-                    "RGB",
-                )
-                image = image.resize(target_resolution, Image.LANCZOS)
+                image = cam.capture_image(stream_name="main", wait=5)
                 return image, metadata
             except TimeoutError:
                 logger.warning(
@@ -104,10 +98,11 @@ class CaptureThing(Thing):
                 )
         raise CaptureError("An error occurred while capturing after 5 attempts")
 
+    @thing_action
     def _save_capture(
         self,
         jpeg_path: str,
-        image: np.ndarray,
+        image,
         metadata: dict,
         logger: InvocationLogger,
     ) -> None: