Merge pull request #162 from DiamondLightSource/reshape_in_ophyd

Reshape OAV stream in ophyd and switch to using ophyd-async

Author: Tom Willemsen

pyproject.toml

@@ -14,17 +14,18 @@ classifiers = [
 ]
 description = "Ophyd devices and other utils that could be used across DLS beamlines"
 dependencies = [
-    "ophyd@git+https://github.com/DominicOram/ophyd@31a1762435bcb275d2555068233549885eab02e7", # Switch back to just "ophyd" once ophyd#1148, ophyd#1155, ophyd#1140 merged.
+    "ophyd",
+    "ophyd-async",
     "bluesky",
     "pyepics",
     "dataclasses-json",
     "pillow",
     "requests",
     "graypy",
     "pydantic<2.0",
-    "opencv-python-headless",                                                                  # For pin-tip detection.
-    "aioca",                                                                                   # Required for CA support with Ophyd V2.
-    "p4p",                                                                                     # Required for PVA support with Ophyd V2.
+    "opencv-python-headless", # For pin-tip detection.
+    "aioca",                  # Required for CA support with ophyd-async.
+    "p4p",                    # Required for PVA support with ophyd-async.
 ]
 dynamic = ["version"]
 license.file = "LICENSE"

src/dodal/beamlines/beamline_utils.py

@@ -4,8 +4,8 @@
 from bluesky.run_engine import call_in_bluesky_event_loop
 from ophyd import Device as OphydV1Device
 from ophyd.sim import make_fake_device
-from ophyd.v2.core import Device as OphydV2Device
-from ophyd.v2.core import wait_for_connection as v2_device_wait_for_connection
+from ophyd_async.core import Device as OphydV2Device
+from ophyd_async.core import wait_for_connection as v2_device_wait_for_connection
 
 from dodal.utils import AnyDevice, BeamlinePrefix, skip_device
 

src/dodal/devices/oav/pin_image_recognition/__init__.py

@@ -4,10 +4,10 @@
 from typing import Optional, Tuple, Type, TypeVar
 
 import numpy as np
-from bluesky.protocols import Descriptor
+from bluesky.protocols import Descriptor, Readable, Reading
 from numpy.typing import NDArray
-from ophyd.v2.core import Device, Readable, Reading, SimSignalBackend
-from ophyd.v2.epics import SignalR, SignalRW, epics_signal_r
+from ophyd_async.core import Device, SignalR, SignalRW, SimSignalBackend
+from ophyd_async.epics.signal import epics_signal_r
 
 from dodal.devices.oav.pin_image_recognition.utils import (
     ARRAY_PROCESSING_FUNCTIONS_MAP,
@@ -48,13 +48,6 @@ def __init__(self, prefix: str, name: str = ""):
             NDArray[np.uint8], f"pva://{prefix}PVA:ARRAY"
         )
 
-        self.oav_width: SignalR[int] = epics_signal_r(
-            int, f"{prefix}PVA:ArraySize1_RBV"
-        )
-        self.oav_height: SignalR[int] = epics_signal_r(
-            int, f"{prefix}PVA:ArraySize2_RBV"
-        )
-
         # Soft parameters for pin-tip detection.
         self.timeout: SignalRW[float] = _create_soft_signal(float, "timeout")
         self.preprocess: SignalRW[int] = _create_soft_signal(int, "preprocess")
@@ -84,7 +77,6 @@ async def _get_tip_position(
         Returns tuple of:
             ((tip_x, tip_y), timestamp)
         """
-
         preprocess_key = await self.preprocess.get_value()
         preprocess_iter = await self.preprocess_iterations.get_value()
         preprocess_ksize = await self.preprocess_ksize.get_value()
@@ -111,30 +103,9 @@ async def _get_tip_position(
         array_data: NDArray[np.uint8] = array_reading[""]["value"]
         timestamp: float = array_reading[""]["timestamp"]
 
-        height: int = await self.oav_height.get_value()
-        width: int = await self.oav_width.get_value()
-
-        num_pixels: int = height * width  # type: ignore
-        value_len = array_data.shape[0]
-
         try:
-            if value_len == num_pixels * 3:
-                # RGB data
-                value = array_data.reshape(height, width, 3)
-            elif value_len == num_pixels:
-                # Grayscale data
-                value = array_data.reshape(height, width)
-            else:
-                # Something else?
-                raise ValueError(
-                    "Unexpected data array size: expected {} (grayscale data) or {} (rgb data), got {}",
-                    num_pixels,
-                    num_pixels * 3,
-                    value_len,
-                )
-
             start_time = time.time()
-            location = sample_detection.processArray(value)
+            location = sample_detection.processArray(array_data)
             end_time = time.time()
             LOGGER.debug(
                 "Sample location detection took {}ms".format(

src/dodal/devices/oav/pin_image_recognition/manual_test.py

@@ -27,7 +27,7 @@ async def acquire():
     try:
         import matplotlib.pyplot as plt
 
-        plt.imshow(img[""]["value"].reshape(768, 1024, 3))
+        plt.imshow(img[""]["value"])
         plt.show()
     except ImportError:
         print("matplotlib not available; cannot show acquired image")

src/dodal/utils.py

@@ -37,7 +37,7 @@
     WritesExternalAssets,
 )
 from ophyd.device import Device as OphydV1Device
-from ophyd.v2.core import Device as OphydV2Device
+from ophyd_async.core import Device as OphydV2Device
 
 try:
     from typing import TypeAlias

tests/beamlines/unit_tests/test_beamline_utils.py

@@ -5,7 +5,7 @@
 from ophyd import Device
 from ophyd.device import Device as OphydV1Device
 from ophyd.sim import FakeEpicsSignal
-from ophyd.v2.core import Device as OphydV2Device
+from ophyd_async.core import Device as OphydV2Device
 
 from dodal.beamlines import beamline_utils, i03
 from dodal.devices.aperturescatterguard import ApertureScatterguard

tests/devices/unit_tests/oav/image_recognition/test_pin_tip_detect.py

@@ -1,13 +1,10 @@
 import asyncio
-from unittest.mock import MagicMock, patch
+from unittest.mock import patch
 
-import numpy as np
 import pytest
-from numpy.typing import NDArray
-from ophyd.v2.core import set_sim_value
+from ophyd_async.core import set_sim_value
 
 from dodal.devices.oav.pin_image_recognition import MxSampleDetect, PinTipDetection
-from dodal.devices.oav.pin_image_recognition.utils import SampleLocation
 
 EVENT_LOOP = asyncio.new_event_loop()
 
@@ -90,68 +87,3 @@ async def test_invalid_processing_func_uses_identity_function():
     # Assert captured preprocess function is the identitiy function
     arg = object()
     assert arg == captured_func(arg)
-
-
-@pytest.mark.parametrize(
-    "input_array,height,width,reshaped",
-    [
-        (np.zeros(shape=(1,)), 1, 1, np.zeros(shape=(1, 1))),
-        (np.zeros(shape=(3,)), 1, 1, np.zeros(shape=(1, 1, 3))),
-        (np.zeros(shape=(1920 * 1080)), 1080, 1920, np.zeros(shape=(1080, 1920))),
-        (
-            np.zeros(shape=(1920 * 1080 * 3)),
-            1080,
-            1920,
-            np.zeros(shape=(1080, 1920, 3)),
-        ),
-    ],
-)
-def test_when_data_supplied_THEN_reshaped_correctly_before_call_to_process_array(
-    input_array: NDArray, height: int, width: int, reshaped: NDArray
-):
-    device = EVENT_LOOP.run_until_complete(_get_pin_tip_detection_device())
-
-    device.array_data._backend._set_value(input_array)  # type: ignore
-    set_sim_value(device.oav_height, height)
-    set_sim_value(device.oav_width, width)
-
-    MxSampleDetect.processArray = MagicMock(
-        autospec=True,
-        return_value=SampleLocation(
-            tip_x=10, tip_y=20, edge_bottom=np.array([]), edge_top=np.array([])
-        ),
-    )
-
-    result = EVENT_LOOP.run_until_complete(device.read())
-
-    MxSampleDetect.processArray.assert_called_once()
-    np.testing.assert_array_equal(MxSampleDetect.processArray.call_args[0][0], reshaped)
-
-    assert result[""]["value"] == (10, 20)
-
-
-@pytest.mark.parametrize(
-    "input_array,height,width",
-    [
-        (np.zeros(shape=(0,)), 1080, 1920),
-        (np.zeros(shape=(1920 * 1080 * 2)), 1080, 1920),
-    ],
-)
-def test_when_invalid_data_length_supplied_THEN_no_call_to_process_array(
-    input_array: NDArray, height: int, width: int
-):
-    device = EVENT_LOOP.run_until_complete(_get_pin_tip_detection_device())
-
-    set_sim_value(device.array_data, input_array)
-    set_sim_value(device.oav_height, height)
-    set_sim_value(device.oav_width, width)
-
-    MxSampleDetect.processArray = MagicMock(
-        autospec=True,
-    )
-
-    result = EVENT_LOOP.run_until_complete(device.read())
-
-    MxSampleDetect.processArray.assert_not_called()
-
-    assert result[""]["value"] == (None, None)