Simulation mode

I successfully calibrated and used the camera-stage mapping.

README.md

@@ -67,7 +67,7 @@ To set up a development version of the software (most likely using emulated came
   * `python -m venv .venv`
   * `source .venv/bin/activate` (on Linux) or `.venv/Scripts/activate` (on Windows)
   * `pip install -e .[dev]` (This will install development dependencies.  If you don't need these, there is probably a simpler way to run the server than cloning this repo.)
-* Finally, run the server: currently you can do this with `sudo systemctl start openflexure-microscope-server` if it's pre-installed on a Raspberry Pi, or `uvicorn --port 5000 openflexure_microscope_server.server:app` to run locally.
+* Finally, run the server: currently you can do this with `sudo systemctl start openflexure-microscope-server` if it's pre-installed on a Raspberry Pi, or `openflexure-microscope-server -c ofm_config_stub.json` to run locally.
 
 ### Run the server manually on a Raspberry Pi
 ```

ofm_config_simulation.json

@@ -0,0 +1,20 @@
+{
+    "things": {
+        "/camera/": "openflexure_microscope_server.things.camera.simulation:SimulatedCamera",
+        "/stage/": "openflexure_microscope_server.things.stage.dummy:DummyStage",
+        "/auto_recentre_stage/": "openflexure_microscope_server.things.auto_recentre_stage:RecentringThing",
+        "/autofocus/": "openflexure_microscope_server.things.autofocus:AutofocusThing",
+        "/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
+        "/system_control/": "openflexure_microscope_server.things.system_control:SystemControlThing",
+        "/settings/": "openflexure_microscope_server.things.settings_manager:SettingsManager",
+        "/smart_scan/": {
+            "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
+            "kwargs": {
+                "path_to_openflexure_stitch": "application/openflexure-stitching/.venv/bin/openflexure-stitch"
+            }
+        },
+        "/background_detect/": "openflexure_microscope_server.things.smart_scan:BackgroundDetectThing",
+        "/api_test/": "openflexure_microscope_server.things.test:APITestThing"
+    },
+    "settings_folder": "./openflexure_settings/"
+}

src/openflexure_microscope_server/things/camera/opencv.py

@@ -1,7 +1,7 @@
 """OpenFlexure Microscope OpenCV Camera
 
-This module defines a Thing that is responsible for using the stage and
+This module defines a camera Thing that uses OpenCV's 
-camera together to perform an autofocus routine.
+`VideoCapture`.
 
 See repository root for licensing information.
 """

src/openflexure_microscope_server/things/camera/simulation.py

@@ -0,0 +1,176 @@
+"""OpenFlexure Microscope OpenCV Camera
+
+This module defines a Thing that is responsible for using the stage and
+camera together to perform an autofocus routine.
+
+See repository root for licensing information.
+"""
+from __future__ import annotations
+import io
+import json
+import logging
+from typing import Literal, Optional
+from threading import Thread
+import time
+
+import cv2
+import numpy as np
+import piexif
+
+from labthings_fastapi.utilities import get_blocking_portal
+from labthings_fastapi.decorators import thing_action, thing_property
+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 . import Camera, JPEGBlob
+from ..stage import Stage
+
+
+class SimulatedCamera(Camera):
+    """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):
+        self._capture_thread: Optional[Thread] = None
+        self._capture_enabled = False
+        self.generate_sprites()
+        self.generate_blobs()
+        self.generate_canvas()
+    
+    def generate_sprites(self):
+        """Generate sprites to populate the image"""
+        self.sprites = []
+        black = np.zeros(self.glyph_shape, dtype=np.uint8)
+        x = np.arange(black.shape[0])
+        y = np.arange(black.shape[1])
+        rr = np.sqrt((x[:, None] - np.mean(x))**2 + (y[None, :] - np.mean(y))**2)
+        for i in [5, 7, 9, 11, 13, 15]:
+            sprite = black.copy()
+            sprite[rr < i] = 255
+            self.sprites.append(sprite)
+
+    def generate_blobs(self, N: int = 1000):
+        """Generate coordinates of blobs
+        
+        Blobs are characterised by X, Y, sprite
+        We also generate a KD tree to rapidly find blobs in an image
+        """
+        self.blobs = np.zeros((N, 3))
+        rng = np.random.default_rng()
+        w = np.max(self.glyph_shape)
+        self.blobs[:, 0] = rng.uniform(w/2, self.canvas_shape[0]-w/2, N)
+        self.blobs[:, 1] = rng.uniform(w/2, self.canvas_shape[1]-w/2, N)
+        self.blobs[:, 2] = rng.choice(len(self.sprites), N)
+
+    def generate_canvas(self):
+        """Generate a blank canvas"""
+        self.canvas = np.zeros(self.canvas_shape, dtype=np.uint8)
+        self.canvas[...] = 255
+        w, h, _ = self.glyph_shape
+        for x, y, sprite in self.blobs:
+            self.canvas[
+                int(x) - w//2:int(x) - w//2 + w,
+                int(y) - h//2:int(y) - h//2 + h,
+            ] -= self.sprites[int(sprite)]
+        
+    def generate_image(self, pos: tuple[int, int]):
+        """Generate an image with blobs based on supplied coordinates"""
+        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[
+            tuple(slice(tl[i],tl[i] + self.shape[i]) for i in range(2)) + (slice(None),)
+        ]
+
+    def attach_to_server(self, server: ThingServer, path: str):
+        self._server = server
+        return super().attach_to_server(server, path)
+    
+    def get_stage_position(self):
+        if not self._stage and self._server:
+            self._stage = self._server.things["/stage/"]
+        return self._stage.instantaneous_position
+    
+    def generate_frame(self):
+        """Generate a frame with blobs based on the stage coordinates"""
+        try:
+            pos = self.get_stage_position()
+        except Exception as e:
+            print(f"Failed to get stage position: {e}")
+            pos = {"x": 0, "y": 0}
+        return self.generate_image((pos["x"]/10, pos["y"]/10))
+
+    def __enter__(self):
+        self._capture_enabled = True
+        self._capture_thread = Thread(target=self._capture_frames)
+        self._capture_thread.start()
+        return self
+    
+    def __exit__(self, _exc_type, _exc_value, _traceback):
+        if self.stream_active:
+            self._capture_enabled = False
+            self._capture_thread.join()
+
+    @thing_property
+    def stream_active(self) -> bool:
+        "Whether the MJPEG stream is active"
+        if self._capture_enabled and self._capture_thread:
+            return self._capture_thread.is_alive()
+        return False
+    mjpeg_stream = MJPEGStreamDescriptor()
+    lores_mjpeg_stream = MJPEGStreamDescriptor()
+
+    def _capture_frames(self):
+        portal = get_blocking_portal(self)
+        while self._capture_enabled:
+            time.sleep(self.frame_interval)
+            frame = self.generate_frame()
+            jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
+            self.mjpeg_stream.add_frame(jpeg, portal)
+            jpeg_lores = cv2.imencode(".jpg", cv2.resize(frame, (320, 240)))[1].tobytes()
+            self.lores_mjpeg_stream.add_frame(jpeg_lores, portal)
+
+    @thing_action
+    def capture_array(
+        self,
+        resolution: Literal["main", "full"] = "full",
+    ) -> NDArray:
+        """Acquire one image from the camera and return as an array
+
+        This function will produce a nested list containing an uncompressed RGB image.
+        It's likely to be highly inefficient - raw and/or uncompressed captures using
+        binary image formats will be added in due course.
+        """
+        return self.generate_frame()
+    
+    @thing_action
+    def capture_jpeg(
+        self,
+        metadata_getter: GetThingStates,
+        resolution: Literal["main", "full"] = "main",
+    ) -> JPEGBlob:
+        """Acquire one image from the camera and return as a JPEG blob
+
+        This function will produce a JPEG image.
+        """
+        frame = self.capture_array()
+        jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
+        exif_dict = {
+            "Exif": {
+                piexif.ExifIFD.UserComment: json.dumps(metadata_getter()).encode("utf-8")
+            },
+            "GPS": {},
+            "Interop": {},
+            "1st": {},
+            "thumbnail": None,
+        }
+        output = io.BytesIO()
+        piexif.insert(piexif.dump(exif_dict), jpeg, output)
+        return JPEGBlob.from_bytes(output.getvalue())

src/openflexure_microscope_server/things/stage/dummy.py

@@ -13,8 +13,9 @@ class DummyStage(Stage):
     This stage should work similarly to a Sangaboard stage, but without any
     hardware attached.
     """
+
     def __enter__(self):
-        pass
+        self.instantaneous_position = self.position
 
     def __exit__(self, _exc_type, _exc_value, _traceback):
         pass
@@ -26,19 +27,24 @@ class DummyStage(Stage):
         self.moving = True
         try:
             fraction_complete = 0.0
+            dt = 0.001
             max_displacement = max(abs(v) for v in displacement)
-            if block_cancellation:
+            start_time = time.time()
-                time.sleep(0.001 * max_displacement)
+            while time.time() - start_time < dt * max_displacement:
-            else:
+                if block_cancellation:
-                start_time = time.time()
+                    time.sleep(dt)
-                while time.time() - start_time < 0.001 * max_displacement:
+                else:
-                    cancel.sleep(0.1)
+                    cancel.sleep(dt)
+                fraction_complete = (time.time() - start_time) / (dt * max_displacement)
+                self.instantaneous_position = {
+                    k: self.position[k] + int(fraction_complete * v)
+                    for k, v in zip(self.axis_names, displacement)
+                }
             fraction_complete = 1.0
         except InvocationCancelledError as e:
             # If the move has been cancelled, stop it but don't handle the exception.
             # We need the exception to propagate in order to stop any calling tasks,
             # and to mark the invocation as "cancelled" rather than stopped.
-            fraction_complete = (time.time() - start_time) / (0.001 * max_displacement)
             raise e
         finally:
             self.moving=False
@@ -46,6 +52,7 @@ class DummyStage(Stage):
                 k: self.position[k] + int(fraction_complete * v)
                 for k, v in zip(self.axis_names, displacement)
             }
+            self.instantaneous_position = self.position
 
     @thing_action
     def move_absolute(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
@@ -66,3 +73,4 @@ class DummyStage(Stage):
         stage.
         """
         self.position = {k: 0 for k in self.axis_names}
+        self.instantaneous_position = self.position