Wait params in captures, multiple attempts to capture

src/openflexure_microscope_server/things/camera/__init__.py

@@ -8,7 +8,7 @@ See repository root for licensing information.
 
 from __future__ import annotations
 import logging
-from typing import Literal, Protocol, runtime_checkable
+from typing import Literal, Protocol, runtime_checkable, Optional
 
 from labthings_fastapi.thing import Thing
 from labthings_fastapi.decorators import thing_action, thing_property
@@ -45,12 +45,14 @@ class CameraProtocol(Protocol):
     def capture_array(
         self,
         stream_name: Literal["main", "lores", "raw", "full"] = "main",
+        wait: Optional[float] = 5,
     ) -> NDArray: ...
 
     def capture_jpeg(
         self,
         metadata_getter: GetThingStates,
         resolution: Literal["lores", "main", "full"] = "main",
+        wait: Optional[float] = 5,
     ) -> JPEGBlob:
         """Acquire one image from the camera and return as a JPEG blob"""
         ...
@@ -166,6 +168,7 @@ class CameraStub(BaseCamera):
     def capture_array(
         self,
         stream_name: Literal["main", "lores", "raw", "full"] = "main",
+        wait: Optional[float] = 5,
     ) -> NDArray:
         raise NotImplementedError("Cameras must not inherit from CameraStub")
 
@@ -174,6 +177,7 @@ class CameraStub(BaseCamera):
         self,
         metadata_getter: GetThingStates,
         resolution: Literal["lores", "main", "full"] = "main",
+        wait: Optional[float] = 5,
     ) -> JPEGBlob:
         """Acquire one image from the camera and return as a JPEG blob"""
         raise NotImplementedError("Cameras must not inherit from CameraStub")

src/openflexure_microscope_server/things/capture.py

@@ -40,6 +40,7 @@ class CaptureThing(Thing):
             cam,
             metadata_getter,
             stream=stream_name,
+            logger=logger,
         )
         acquisition_time = time.time()
         self._save_capture(jpeg_path, image, metadata, logger)
@@ -51,23 +52,33 @@ class CaptureThing(Thing):
         )
 
     @thing_action
-    def capture_jpeg(self, filename: str, cam: CamDep):
+    def capture_jpeg(self, filename: str, cam: CamDep, logger: InvocationLogger):
         """Capture a JPEG (from a JPEGBlob) to disk"""
-        jpeg = cam.capture_jpeg(resolution="full")
-        jpeg.save(filename)
+        for capture_attempts in range(5):
+            try:
+                jpeg = cam.capture_jpeg(resolution="full", wait=5)
+                jpeg.save(filename)
+                return
+            except TimeoutError:
+                logger.warning(f'Attempt {capture_attempts+1} to capture image timed out. Do you have enough RAM?')
+            except Exception as e:
+                logger.warning(e)
+        raise CaptureError("An error occurred while capturing after 5 attempts")
 
     @thing_action
-    def _capture_array(self, cam: CamDep, metadata_getter: GetThingStates, stream: str = 'main'):
+    def _capture_array(self, cam: CamDep, metadata_getter: GetThingStates, logger: InvocationLogger, stream: str = 'main'):
         """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
         """
-        try:
-            metadata = metadata_getter()
-            image = cam.capture_array(stream_name=stream)[..., :3]
-        except Exception as e:
-            raise CaptureError("An error occurred while capturing") from e
-        return image, metadata
+        for capture_attempts in range(5):
+            try:
+                metadata = metadata_getter()
+                image = cam.capture_array(stream_name=stream, wait=5)[..., :3]
+                return image, metadata
+            except TimeoutError:
+                logger.warning(f'Attempt {capture_attempts+1} to capture image timed out. Do you have enough RAM?')
+        raise CaptureError("An error occurred while capturing after 5 attempts")
 
     def _save_capture(
         self,

src/openflexure_microscope_server/things/smart_scan.py

@@ -694,7 +694,7 @@ class SmartScanThing(Thing):
             self._autofocus.run_z_stack(
                 images_dir=self._ongoing_scan_images_dir,
                 stack_dir=site_folder,
-                capture_method="hires_array",
+                capture_method="blob",
             )
 
             # increment capure counter as thread has completed