Merge branch 'flash-led-sim' into 'v3'

Illumination Thing

See merge request openflexure/openflexure-microscope-server!468

ofm_config_full.json

@@ -10,6 +10,7 @@
         "autofocus": "openflexure_microscope_server.things.autofocus:AutofocusThing",
         "camera_stage_mapping": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
         "system": "openflexure_microscope_server.things.system:OpenFlexureSystem",
+        "illumination": "openflexure_microscope_server.things.illumination:SangaIllumination",
         "smart_scan": {
             "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
             "kwargs": {

ofm_config_simulation.json

@@ -4,6 +4,7 @@
         "stage": "openflexure_microscope_server.things.stage.dummy:DummyStage",
         "autofocus": "openflexure_microscope_server.things.autofocus:AutofocusThing",
         "camera_stage_mapping": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
+        "illumination": "openflexure_microscope_server.things.illumination.SimulatorIllumination",
         "system": "openflexure_microscope_server.things.system:OpenFlexureSystem",
         "smart_scan": {
             "class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",

src/openflexure_microscope_server/things/camera/simulation.py

@@ -140,6 +140,8 @@ class SimulatedCamera(BaseCamera):
         self._capture_thread: Optional[Thread] = None
         self._capture_enabled = False
         self.generate_sprites()
+        # Whether the LED is on
+        self.led_on = True
 
     repeating: bool = lt.property(default=False)
 
@@ -339,8 +341,16 @@ class SimulatedCamera(BaseCamera):
         pl_img = Image.fromarray(np_img.astype("uint8"))
         return pl_img.resize((self.shape[1], self.shape[0]), Image.Resampling.BILINEAR)
 
+    def set_led(self, led_on: bool = True) -> None:
+        """Set the simulated LED to on or off."""
+        self.led_on = led_on
+
     def generate_frame(self) -> Image.Image:
         """Generate a frame with blobs based on the stage coordinates."""
+        # Simulate LED turning off by setting all channels to 0
+        if not self.led_on:
+            return Image.new(mode="RGB", size=(self.shape[1], self.shape[0]), color=0)
+        # Otherwise, generate a frame from current position
         pos = self._stage.instantaneous_position
         return self.generate_image((pos["y"], pos["x"], pos["z"]))
 

src/openflexure_microscope_server/things/illumination.py

@@ -0,0 +1,59 @@
+"""A module to handle the illumination in LabThings."""
+
+import time
+from typing import Literal
+
+import labthings_fastapi as lt
+
+from .camera.simulation import SimulatedCamera
+from .stage.sangaboard import SangaboardThing
+
+
+class Illumination(lt.Thing):
+    """Base class for an illumination controller."""
+
+    @lt.action
+    def set_led(self, led_on: bool = True) -> None:
+        """Set the LED to on or off."""
+        raise NotImplementedError(
+            "Turning the LED on and off should be implemented by child classes."
+        )
+
+    @lt.action
+    def flash(self, number_of_flashes: int = 10, dt: float = 0.5) -> None:
+        """Flash the illumination source.
+
+        :param number_of_flashes: Number of times to flash the LED.
+        :param dt: Flash duration in seconds.
+        """
+        for _ in range(number_of_flashes):
+            self.set_led(False)
+            time.sleep(dt)
+            self.set_led(True)
+            time.sleep(dt)
+
+
+class SangaIllumination(Illumination):
+    """Illumination driven by a Sangaboard."""
+
+    _stage: SangaboardThing = lt.thing_slot()
+
+    @lt.action
+    def set_led(
+        self,
+        led_on: bool = True,
+        led_channel: Literal["cc"] = "cc",
+    ) -> None:
+        """Set the LED to on or off."""
+        self._stage.set_led(led_on, led_channel)
+
+
+class SimulatorIllumination(Illumination):
+    """Illumination control in the simulator."""
+
+    _cam: SimulatedCamera = lt.thing_slot()
+
+    @lt.action
+    def set_led(self, led_on: bool = True) -> None:
+        """Set the LED to on or off."""
+        self._cam.set_led(led_on)

src/openflexure_microscope_server/things/stage/sangaboard.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import threading
-import time
 from contextlib import contextmanager
 from copy import copy
 from types import TracebackType
@@ -174,11 +173,9 @@ class SangaboardThing(BaseStage):
             sb.zero_position()
         self.update_position()
 
-    @lt.action
+    def set_led(
-    def flash_led(
         self,
-        number_of_flashes: int = 10,
+        led_on: bool = True,
-        dt: float = 0.5,
         led_channel: Literal["cc"] = "cc",
     ) -> None:
         """Flash the LED to identify the board.
@@ -196,14 +193,8 @@ class SangaboardThing(BaseStage):
             # Reading and setting LED brightness suffers from repeated reads and writes
             # decreasing the value. Rather than use the value the code warns that the value
             # cannot be used.
-            intended_brightness = float(return_value[7:])
+            if led_on:
-            on_brightness = 0.32
+                on_brightness = 0.32
-            self.logger.warning(
-                "Brightness control is not yet implemented. Desired brightness: "
-                f"{intended_brightness}. Set brightness: {on_brightness}"
-            )
-            for _i in range(number_of_flashes):
-                sb.query(f"{led_command} 0")
-                time.sleep(dt)
                 sb.query(f"{led_command} {on_brightness}")
-                time.sleep(dt)
+            else:
+                sb.query(f"{led_command} 0")

tests/unit_tests/test_illumination.py

@@ -0,0 +1,127 @@
+"""Tests for the Illumination thing."""
+
+from unittest.mock import call, patch
+
+import pytest
+
+from labthings_fastapi.testing import create_thing_without_server
+
+from openflexure_microscope_server.things.illumination import (
+    Illumination,
+    SangaIllumination,
+    SimulatorIllumination,
+)
+
+# Test the BaseClass before testing specific implementation
+
+
+def test_base_illumination_set_led_not_implemented():
+    """Check that calling set_led on the base Illumination raises NotImplementedError."""
+    ill = create_thing_without_server(Illumination)
+    with pytest.raises(
+        NotImplementedError,
+        match="Turning the LED on and off should be implemented by child classes.",
+    ):
+        ill.set_led(led_on=True)
+
+
+def test_flash_calls_set_led_and_raises():
+    """Check that calling flash from Baseclass calls flash with right arguments."""
+    ill = create_thing_without_server(Illumination)
+
+    number_of_flashes = 3  # smaller number for test speed
+    dt = 0  # avoid sleeping
+
+    with pytest.raises(NotImplementedError):
+        ill.flash(number_of_flashes=number_of_flashes, dt=dt)
+
+    # Patch set_led to just record calls without raising
+    with patch.object(ill, "set_led") as mock_set_led:
+        # Call flash normally
+        ill.flash(number_of_flashes=number_of_flashes, dt=dt)
+
+        # Each flash calls set_led twice: False, True
+        expected_sequence = [call(False), call(True)] * number_of_flashes
+        assert mock_set_led.call_args_list == expected_sequence
+
+        # Also check total number of calls
+        assert mock_set_led.call_count == number_of_flashes * 2
+
+
+def test_negative_flash_calls():
+    """Check that calling flash with negative number doesn't call set_led."""
+    ill = create_thing_without_server(Illumination)
+
+    number_of_flashes = -33  # smaller number for test speed
+    dt = 0  # avoid sleeping
+
+    # Patch set_led to just record calls without raising
+    with patch.object(ill, "set_led") as mock_set_led:
+        # Call flash normally
+        ill.flash(number_of_flashes=number_of_flashes, dt=dt)
+
+        # Also check total number of calls
+        assert mock_set_led.call_count == 0
+
+
+def test_negative_flash_dt():
+    """Check that calling flash with negative dt raises ValueError."""
+    ill = create_thing_without_server(Illumination)
+
+    number_of_flashes = 3  # smaller number for test speed
+    dt = -5  # set a negative delay
+
+    # Patch set_led to just record calls without raising
+    with (
+        patch.object(ill, "set_led"),
+        pytest.raises(ValueError, match="sleep length must be non-negative"),
+    ):
+        ill.flash(number_of_flashes=number_of_flashes, dt=dt)
+
+
+@pytest.fixture
+def sanga_mock_stage():
+    """Return a SangaIllumination with a mocked stage."""
+    return create_thing_without_server(SangaIllumination, mock_all_slots=True)
+
+
+@pytest.fixture
+def sim_mock_cam():
+    """Return a SimulatorIllumination with a mocked camera."""
+    return create_thing_without_server(SimulatorIllumination, mock_all_slots=True)
+
+
+def test_sanga_flash_calls_led(sanga_mock_stage):
+    """Test that flashing calls set_led with correct parameters."""
+    number_of_flashes = 3
+    dt = 0.01  # tiny sleep for test speed
+
+    sanga_mock_stage.flash(number_of_flashes=number_of_flashes, dt=dt)
+
+    # Each flash calls set_led False then True
+    assert sanga_mock_stage._stage.set_led.call_count == 2 * number_of_flashes
+
+    # Check that False and True are alternating when sent to _stage.set_led
+    calls = sanga_mock_stage._stage.set_led.call_args_list
+    expected_sequence = [False, True] * number_of_flashes
+    for led_call, expected in zip(calls, expected_sequence, strict=True):
+        args, kwargs = led_call
+        assert args[0] == expected
+
+
+def test_sim_flash_calls_led(sim_mock_cam):
+    """Test that simulator flash calls set_led correctly."""
+    number_of_flashes = 2
+    dt = 0.01
+
+    sim_mock_cam.flash(number_of_flashes=number_of_flashes, dt=dt)
+
+    # Each flash calls set_led False then True
+    assert sim_mock_cam._cam.set_led.call_count == 2 * number_of_flashes
+
+    # Check that False and True are alternating when sent to _cam.set_led
+    calls = sim_mock_cam._cam.set_led.call_args_list
+    expected_sequence = [False, True] * number_of_flashes
+    for led_call, expected in zip(calls, expected_sequence, strict=True):
+        args, kwargs = led_call
+        assert args[0] == expected

tests/unit_tests/test_stage.py

@@ -284,9 +284,6 @@ def test_thing_description_equivalence(dummy_stage, mocker):
     mocker.patch.dict("sys.modules", {"sangaboard": mock_sangaboard})
     from openflexure_microscope_server.things.stage.sangaboard import SangaboardThing
 
-    # Flash LED isn't a standard stage action, most stages do not control illumination.
-    extra_sanga_actions = ["flash_led"]
-
     base_td = create_thing_without_server(BaseStage).thing_description()
     base_actions = set(base_td.actions.keys())
     base_properties = set(base_td.properties.keys())
@@ -298,9 +295,6 @@ def test_thing_description_equivalence(dummy_stage, mocker):
     sanga_td = create_thing_without_server(SangaboardThing).thing_description()
     # Remove known extra actions
     sanga_actions = list(sanga_td.actions.keys())
-    for action in extra_sanga_actions:
-        index = sanga_actions.index(action)
-        sanga_actions.pop(index)
     sanga_actions = set(sanga_actions)
     sanga_properties = set(sanga_td.properties.keys())
 

webapp/src/components/tabContentComponents/aboutComponents/statusPane.vue

@@ -13,9 +13,9 @@
           {{ $store.state.origin }}
         </div>
         <action-button
-          v-if="stageType"
+          v-if="illuminationType"
-          thing="stage"
+          thing="illumination"
-          action="flash_led"
+          action="flash"
           submit-label="Flash Illumination"
           :can-terminate="false"
           :submit-data="{ dt: 0.25 }"
@@ -46,6 +46,13 @@
           {{ stageType }}
         </div>
       </div>
+      <div v-if="illuminationType">
+        <b>Illumination:</b>
+        <br />
+        <div>
+          {{ illuminationType }}
+        </div>
+      </div>
 
       <hr />
     </div>
@@ -77,6 +84,11 @@ export default {
     stageType() {
       return this.thingAvailable("stage") ? this.thingDescription("stage").title : undefined;
     },
+    illuminationType() {
+      return this.thingAvailable("illumination")
+        ? this.thingDescription("illumination").title
+        : undefined;
+    },
   },
 
   async mounted() {