Sped up camera and got CSM passing

Using lower resolution helps speed it up, and skipping CSM settling time makes a big difference.

src/openflexure_microscope_server/things/camera/simulation.py

@@ -23,21 +23,31 @@ from labthings_fastapi.dependencies.metadata import GetThingStates
 from labthings_fastapi.outputs.mjpeg_stream import MJPEGStreamDescriptor
 from labthings_fastapi.types.numpy import NDArray
 from labthings_fastapi.server import ThingServer
+from pydantic import RootModel
 
 from . import BaseCamera, JPEGBlob
 from ..stage import StageProtocol as Stage
 
+class ArrayModel(RootModel):
+    """A model for an array"""
+    root: NDArray
 
 class SimulatedCamera(BaseCamera):
     """A Thing representing an OpenCV camera"""
-    shape = (600, 800, 3)
-    glyph_shape = (51, 51, 3)
-    canvas_shape = (3000, 4000, 3)
-    frame_interval = 0.1
     _stage: Optional[Stage] = None
     _server: Optional[ThingServer] = None
 
-    def __init__(self):
+    def __init__(
+            self,
+            shape: tuple[int, int, int] = (600, 800, 3),
+            glyph_shape: tuple[int, int, int] = (51, 51, 3),
+            canvas_shape: tuple[int, int, int] = (3000, 4000, 3),
+            frame_interval: float = 0.1,
+        ):
+        self.shape = shape
+        self.glyph_shape = glyph_shape
+        self.canvas_shape = canvas_shape
+        self.frame_interval = frame_interval
         self._capture_thread: Optional[Thread] = None
         self._capture_enabled = False
         self.generate_sprites()
@@ -85,9 +95,12 @@ class SimulatedCamera(BaseCamera):
         cw, ch, _ = self.canvas_shape
         w, h, _ = self.shape
         tl = (int(pos[0]) - w//2 - cw//2, int(pos[1]) - h//2 - ch//2)
-        return self.canvas[
+        image = self.canvas[
             tuple(slice(tl[i],tl[i] + self.shape[i]) for i in range(2)) + (slice(None),)
         ]
+        if image.shape != self.shape:
+            raise ValueError(f"Image shape {image.shape} does not match intended shape {self.shape}")
+        return image
 
     def attach_to_server(self, server: ThingServer, path: str):
         self._server = server
@@ -131,17 +144,20 @@ class SimulatedCamera(BaseCamera):
         portal = get_blocking_portal(self)
         while self._capture_enabled:
             time.sleep(self.frame_interval)
-            frame = self.generate_frame()
+            try:
-            jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
+                frame = self.generate_frame()
-            self.mjpeg_stream.add_frame(jpeg, portal)
+                jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
-            jpeg_lores = cv2.imencode(".jpg", cv2.resize(frame, (320, 240)))[1].tobytes()
+                self.mjpeg_stream.add_frame(jpeg, portal)
-            self.lores_mjpeg_stream.add_frame(jpeg_lores, portal)
+                jpeg_lores = cv2.imencode(".jpg", cv2.resize(frame, (320, 240)))[1].tobytes()
+                self.lores_mjpeg_stream.add_frame(jpeg_lores, portal)
+            except Exception as e:
+                logging.error(f"Failed to capture frame: {e}, retrying...")
 
     @thing_action
     def capture_array(
         self,
         resolution: Literal["main", "full"] = "full",
-    ) -> NDArray:
+    ) -> ArrayModel:
         """Acquire one image from the camera and return as an array
 
         This function will produce a nested list containing an uncompressed RGB image.

src/openflexure_microscope_server/things/camera_stage_mapping.py

@@ -61,6 +61,9 @@ def downsample(factor: int, image: np.ndarray) -> np.ndarray:
     return reshaped.mean(axis=(1,3))
 
 
+DEFAULT_SETTLING_TIME = 0.2
+
+
 def make_hardware_interface(
         stage: Stage, camera: Camera, downsample_factor: int = 2
     ) -> HardwareInterfaceModel:
@@ -81,7 +84,7 @@ def make_hardware_interface(
         img = camera.capture_array()
         return downsample(downsample_factor, img)
     def settle() -> None:
-        time.sleep(0.2)
+        time.sleep(DEFAULT_SETTLING_TIME)
         try:
             camera.capture_metadata  # This discards frames on a picamera
         except AttributeError:

tests/test_dummy_server.py

@@ -6,6 +6,7 @@ from fastapi import Depends, FastAPI
 from fastapi.testclient import TestClient
 from labthings_fastapi.client import ThingClient
 from PIL import Image
+import numpy as np
 import piexif
 import pytest
 
@@ -14,12 +15,15 @@ from openflexure_microscope_server.things.camera.simulation import SimulatedCame
 from openflexure_microscope_server.things.stage.dummy import DummyStage
 from openflexure_microscope_server.things.autofocus import AutofocusThing
 from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
+from openflexure_microscope_server.things import camera_stage_mapping
+
+camera_stage_mapping.DEFAULT_SETTLING_TIME = 0 # skip the settling time for tests
 
 @pytest.fixture
 def thing_server():
     temp_folder = tempfile.TemporaryDirectory()
     server = ThingServer(settings_folder=temp_folder.name)
-    server.add_thing(SimulatedCamera(), "/camera/")
+    server.add_thing(SimulatedCamera(shape=(240, 320, 3), canvas_shape=(960, 1240, 3), frame_interval=0.01), "/camera/")
     server.add_thing(DummyStage(step_time=0.000001), "/stage/")
     server.add_thing(AutofocusThing(), "/autofocus/")
     server.add_thing(CameraStageMapper(), "/camera_stage_mapping/")
@@ -34,7 +38,7 @@ def client(thing_server):
 
 @pytest.fixture
 def slower_client(thing_server):
-    thing_server.things["/stage/"].step_time = 0.0002
+    thing_server.things["/stage/"].step_time = 0.0001
     with TestClient(thing_server.app) as client:
         yield client
 
@@ -70,7 +74,12 @@ def test_stage(client):
     for s, p in zip(start.values(), pos.values()):
         assert s == p
 
+def test_capture_array(client):
+    camera = ThingClient.from_url("/camera/", client)
+    array = np.asarray(camera.capture_array())
+    assert array.shape == (240, 320, 3)
+
 # Currently this fails, not yet sure why.
-#def test_camera_stage_mapping_calibration(client):
+def test_camera_stage_mapping_calibration(client):
-#    camera_stage_mapping = ThingClient.from_url("/camera_stage_mapping/", client)
+    camera_stage_mapping = ThingClient.from_url("/camera_stage_mapping/", client)
-#    camera_stage_mapping.calibrate_xy()
+    camera_stage_mapping.calibrate_xy()