348 replaced point 3d and point 2d to support arithmetic, using numpy arrays

setup.cfg

@@ -36,7 +36,7 @@ install_requires =
     xarray
     doct
     databroker
-    dodal @ git+https://github.com/DiamondLightSource/python-dodal.git
+    dodal @ git+https://github.com/DiamondLightSource/python-dodal.git@0570e5e6e5e134fd0697cadccc5bd6d2c6ed77d1
 
 
 [options.extras_require]

src/artemis/experiment_plans/fast_grid_scan_plan.py

@@ -5,6 +5,7 @@
 
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
+import numpy as np
 from bluesky import RunEngine
 from bluesky.utils import ProgressBarManager
 from dodal.beamlines import i03
@@ -36,7 +37,6 @@
 )
 from artemis.parameters.constants import ISPYB_PLAN_NAME, SIM_BEAMLINE
 from artemis.tracing import TRACER
-from artemis.utils.utils import Point3D
 
 if TYPE_CHECKING:
     from artemis.external_interaction.callbacks.fgs.fgs_callback_collection import (
@@ -146,7 +146,7 @@ def read_hardware_for_ispyb(
 @bpp.run_decorator(md={"subplan_name": "move_xyz"})
 def move_xyz(
     sample_motors,
-    xray_centre_motor_position: Point3D,
+    xray_centre_motor_position: np.ndarray,
     md={
         "plan_name": "move_xyz",
     },
@@ -156,11 +156,11 @@ def move_xyz(
     artemis.log.LOGGER.info(f"Moving Smargon x, y, z to: {xray_centre_motor_position}")
     yield from bps.mv(
         sample_motors.x,
-        xray_centre_motor_position.x,
+        xray_centre_motor_position[0],
         sample_motors.y,
-        xray_centre_motor_position.y,
+        xray_centre_motor_position[1],
         sample_motors.z,
-        xray_centre_motor_position.z,
+        xray_centre_motor_position[2],
     )
 
 
@@ -242,10 +242,12 @@ def run_gridscan_and_move(
     and moves to the centre of mass determined by zocalo"""
 
     # We get the initial motor positions so we can return to them on zocalo failure
-    initial_xyz = Point3D(
-        (yield from bps.rd(fgs_composite.sample_motors.x)),
-        (yield from bps.rd(fgs_composite.sample_motors.y)),
-        (yield from bps.rd(fgs_composite.sample_motors.z)),
+    initial_xyz = np.array(
+        [
+            (yield from bps.rd(fgs_composite.sample_motors.x)),
+            (yield from bps.rd(fgs_composite.sample_motors.y)),
+            (yield from bps.rd(fgs_composite.sample_motors.z)),
+        ]
     )
 
     yield from setup_zebra_for_fgs(fgs_composite.zebra)

src/artemis/experiment_plans/full_grid_scan.py

@@ -23,7 +23,6 @@
 from artemis.log import LOGGER
 from artemis.parameters.beamline_parameters import get_beamline_parameters
 from artemis.parameters.plan_specific.fgs_internal_params import GridScanParams
-from artemis.utils.utils import Point3D
 
 if TYPE_CHECKING:
     from artemis.parameters.plan_specific.grid_scan_with_edge_detect_params import (
@@ -102,7 +101,7 @@ def detect_grid_and_do_gridscan():
         parameters.artemis_params.ispyb_params.xtal_snapshots_omega_end = (
             out_snapshot_filenames[1]
         )
-        parameters.artemis_params.ispyb_params.upper_left = Point3D(**out_upper_left)
+        parameters.artemis_params.ispyb_params.upper_left = out_upper_left
 
         fgs_params.__post_init__()
 

src/artemis/experiment_plans/oav_grid_detection_plan.py

@@ -2,7 +2,7 @@
 
 import math
 from os.path import join as path_join
-from typing import TYPE_CHECKING, Dict, List
+from typing import TYPE_CHECKING, List
 
 import bluesky.plan_stubs as bps
 import numpy as np
@@ -32,7 +32,7 @@ def grid_detection_plan(
     snapshot_template: str,
     snapshot_dir: str,
     out_snapshot_filenames: List[List[str]],
-    out_upper_left: Dict,
+    out_upper_left: list[float] | np.ndarray,
     width=600,
     box_size_microns=20,
 ):
@@ -57,7 +57,7 @@ def grid_detection_main_plan(
     snapshot_template: str,
     snapshot_dir: str,
     out_snapshot_filenames: List[List[str]],
-    out_upper_left: Dict,
+    out_upper_left: list[float] | np.ndarray,
     grid_width_px: int,
     box_size_um: float,
 ):
@@ -133,10 +133,10 @@ def grid_detection_main_plan(
 
         upper_left = (tip_x_px, min_y)
         if angle == 0:
-            out_upper_left["x"] = int(tip_x_px)
-            out_upper_left["y"] = int(min_y)
+            out_upper_left[0] = int(tip_x_px)
+            out_upper_left[1] = int(min_y)
         else:
-            out_upper_left["z"] = int(min_y)
+            out_upper_left[2] = int(min_y)
 
         yield from bps.abs_set(oav.snapshot.top_left_x, upper_left[0])
         yield from bps.abs_set(oav.snapshot.top_left_y, upper_left[1])

src/artemis/experiment_plans/tests/test_fast_grid_scan_plan.py

@@ -2,6 +2,7 @@
 from unittest.mock import ANY, MagicMock, call, patch
 
 import bluesky.plan_stubs as bps
+import numpy as np
 import pytest
 from bluesky.run_engine import RunEngine
 from dodal.devices.det_dim_constants import (
@@ -38,7 +39,6 @@
 from artemis.log import set_up_logging_handlers
 from artemis.parameters import external_parameters
 from artemis.parameters.plan_specific.fgs_internal_params import FGSInternalParameters
-from artemis.utils.utils import Point3D
 
 
 def test_given_full_parameters_dict_when_detector_name_used_and_converted_then_detector_constants_correct(
@@ -177,11 +177,11 @@ def test_results_passed_to_move_motors(
     set_up_logging_handlers(logging_level="INFO", dev_mode=True)
     RE.subscribe(VerbosePlanExecutionLoggingCallback())
     motor_position = test_params.experiment_params.grid_position_to_motor_position(
-        Point3D(1, 2, 3)
+        np.array([1, 2, 3])
     )
     RE(move_xyz(fake_fgs_composite.sample_motors, motor_position))
     bps_mv.assert_called_once_with(
-        ANY, motor_position.x, ANY, motor_position.y, ANY, motor_position.z
+        ANY, motor_position[0], ANY, motor_position[1], ANY, motor_position[2]
     )
 
 
@@ -215,9 +215,9 @@ def test_individual_plans_triggered_once_and_only_once_in_composite_run(
     )
 
     run_gridscan.assert_called_once_with(fake_fgs_composite, test_params)
-    move_xyz.assert_called_once_with(
-        ANY, Point3D(x=-0.05, y=0.05, z=0.15000000000000002)
-    )
+    array_arg = move_xyz.call_args.args[1]
+    np.testing.assert_allclose(array_arg, np.array([-0.05, 0.05, 0.15]))
+    move_xyz.assert_called_once()
 
 
 @patch(
@@ -250,9 +250,9 @@ def test_logging_within_plan(
     )
 
     run_gridscan.assert_called_once_with(fake_fgs_composite, test_params)
-    move_xyz.assert_called_once_with(
-        ANY, Point3D(x=-0.05, y=0.05, z=0.15000000000000002)
-    )
+    array_arg = move_xyz.call_args.args[1]
+    np.testing.assert_array_almost_equal(array_arg, np.array([-0.05, 0.05, 0.15]))
+    move_xyz.assert_called_once()
 
 
 @patch("artemis.experiment_plans.fast_grid_scan_plan.bps.sleep")

src/artemis/external_interaction/callbacks/fgs/tests/test_fgs_callback_collection.py

@@ -1,5 +1,6 @@
 from unittest.mock import MagicMock
 
+import numpy as np
 import pytest
 from bluesky.run_engine import RunEngine
 from dodal.devices.eiger import DetectorParams, EigerDetector
@@ -14,7 +15,6 @@
 from artemis.parameters.constants import SIM_BEAMLINE
 from artemis.parameters.external_parameters import from_file as default_raw_params
 from artemis.parameters.plan_specific.fgs_internal_params import FGSInternalParameters
-from artemis.utils.utils import Point3D
 
 
 def test_callback_collection_init():
@@ -90,7 +90,7 @@ def test_communicator_in_composite_run(
     callbacks.zocalo_handler._wait_for_result = MagicMock()
     callbacks.zocalo_handler._run_end = MagicMock()
     callbacks.zocalo_handler._run_start = MagicMock()
-    callbacks.zocalo_handler.xray_centre_motor_position = Point3D(1, 2, 3)
+    callbacks.zocalo_handler.xray_centre_motor_position = np.array([1, 2, 3])
 
     fast_grid_scan_composite = FGSComposite()
     # this is where it's currently getting stuck:

src/artemis/external_interaction/callbacks/fgs/tests/test_zocalo_handler.py

@@ -1,6 +1,6 @@
-import operator
 from unittest.mock import MagicMock, call
 
+import numpy as np
 import pytest
 
 from artemis.external_interaction.callbacks.fgs.fgs_callback_collection import (
@@ -11,7 +11,6 @@
 from artemis.external_interaction.zocalo.zocalo_interaction import NoDiffractionFound
 from artemis.parameters.external_parameters import from_file as default_raw_params
 from artemis.parameters.plan_specific.fgs_internal_params import FGSInternalParameters
-from artemis.utils.utils import Point3D
 
 EXPECTED_DCID = 100
 EXPECTED_RUN_START_MESSAGE = {"event": "start", "ispyb_dcid": EXPECTED_DCID}
@@ -82,7 +81,7 @@ def test_zocalo_called_to_wait_on_results_when_communicator_wait_for_results_cal
     callbacks = FGSCallbackCollection.from_params(dummy_params)
     mock_zocalo_functions(callbacks)
     callbacks.ispyb_handler.ispyb_ids = (0, 0, 100)
-    expected_centre_grid_coords = Point3D(1, 2, 3)
+    expected_centre_grid_coords = np.array([1, 2, 3])
     single_crystal_result = [
         {
             "max_voxel": [1, 2, 3],
@@ -95,20 +94,16 @@ def test_zocalo_called_to_wait_on_results_when_communicator_wait_for_results_cal
         single_crystal_result
     )
 
-    found_centre = callbacks.zocalo_handler.wait_for_results(Point3D(0, 0, 0))[0]
+    found_centre = callbacks.zocalo_handler.wait_for_results(np.array([0, 0, 0]))[0]
     callbacks.zocalo_handler.zocalo_interactor.wait_for_result.assert_called_once_with(
         100
     )
     expected_centre_motor_coords = (
         dummy_params.experiment_params.grid_position_to_motor_position(
-            Point3D(
-                expected_centre_grid_coords.x - 0.5,
-                expected_centre_grid_coords.y - 0.5,
-                expected_centre_grid_coords.z - 0.5,
-            )
+            expected_centre_grid_coords - 0.5
         )
     )
-    assert found_centre == expected_centre_motor_coords
+    np.testing.assert_array_equal(found_centre, expected_centre_motor_coords)
 
 
 def test_GIVEN_no_results_from_zocalo_WHEN_communicator_wait_for_results_called_THEN_fallback_centre_used(
@@ -121,13 +116,13 @@ def test_GIVEN_no_results_from_zocalo_WHEN_communicator_wait_for_results_called_
         NoDiffractionFound()
     )
 
-    fallback_position = Point3D(1, 2, 3)
+    fallback_position = np.array([1, 2, 3])
 
     found_centre = callbacks.zocalo_handler.wait_for_results(fallback_position)[0]
     callbacks.zocalo_handler.zocalo_interactor.wait_for_result.assert_called_once_with(
         100
     )
-    assert found_centre == fallback_position
+    np.testing.assert_array_equal(found_centre, fallback_position)
 
 
 def test_GIVEN_ispyb_not_started_WHEN_trigger_zocalo_handler_THEN_raises_exception(
@@ -146,11 +141,11 @@ def test_multiple_results_from_zocalo_sorted_by_total_count_returns_centre_and_b
     callbacks = FGSCallbackCollection.from_params(dummy_params)
     mock_zocalo_functions(callbacks)
     callbacks.ispyb_handler.ispyb_ids = (0, 0, 100)
-    expected_centre_grid_coords = Point3D(4, 6, 2)
+    expected_centre_grid_coords = np.array([4, 6, 2])
     multi_crystal_result = [
         {
             "max_voxel": [1, 2, 3],
-            "centre_of_mass": Point3D(3, 11, 11),
+            "centre_of_mass": np.array([3, 11, 11]),
             "bounding_box": [[1, 1, 1], [3, 3, 3]],
             "n_voxels": 2,
             "total_count": 192512.0,
@@ -167,21 +162,23 @@ def test_multiple_results_from_zocalo_sorted_by_total_count_returns_centre_and_b
         multi_crystal_result
     )
     found_centre, found_bbox = callbacks.zocalo_handler.wait_for_results(
-        Point3D(0, 0, 0)
+        np.array([0, 0, 0])
     )
     callbacks.zocalo_handler.zocalo_interactor.wait_for_result.assert_called_once_with(
         100
     )
     expected_centre_motor_coords = (
         dummy_params.experiment_params.grid_position_to_motor_position(
-            Point3D(
-                expected_centre_grid_coords.x - 0.5,
-                expected_centre_grid_coords.y - 0.5,
-                expected_centre_grid_coords.z - 0.5,
+            np.array(
+                [
+                    expected_centre_grid_coords[0] - 0.5,
+                    expected_centre_grid_coords[1] - 0.5,
+                    expected_centre_grid_coords[2] - 0.5,
+                ]
             )
         )
     )
-    assert found_centre == expected_centre_motor_coords
+    np.testing.assert_array_equal(found_centre, expected_centre_motor_coords)
 
-    expected_bbox_size = list(map(operator.sub, [8, 8, 7], [2, 2, 2]))
-    assert found_bbox == expected_bbox_size
+    expected_bbox_size = np.array([8, 8, 7]) - np.array([2, 2, 2])
+    np.testing.assert_array_equal(found_bbox, expected_bbox_size)

src/artemis/external_interaction/callbacks/fgs/zocalo_callback.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 
-import operator
 import time
 from typing import Callable, Optional
 
+import numpy as np
 from bluesky.callbacks import CallbackBase
+from numpy import ndarray
 
 from artemis.external_interaction.callbacks.fgs.ispyb_callback import (
     FGSISPyBHandlerCallback,
@@ -16,7 +17,6 @@
 )
 from artemis.log import LOGGER
 from artemis.parameters.plan_specific.fgs_internal_params import FGSInternalParameters
-from artemis.utils.utils import Point3D
 
 
 class FGSZocaloCallback(CallbackBase):
@@ -43,7 +43,7 @@ def __init__(
         self, parameters: FGSInternalParameters, ispyb_handler: FGSISPyBHandlerCallback
     ):
         self.grid_position_to_motor_position: Callable[
-            [Point3D], Point3D
+            [ndarray], ndarray
         ] = parameters.experiment_params.grid_position_to_motor_position
         self.processing_start_time = 0.0
         self.processing_time = 0.0
@@ -76,14 +76,14 @@ def stop(self, doc: dict):
                 self.zocalo_interactor.run_end(id)
             self.processing_start_time = time.time()
 
-    def wait_for_results(self, fallback_xyz: Point3D) -> Point3D:
+    def wait_for_results(self, fallback_xyz: ndarray) -> tuple[ndarray, Optional[list]]:
         """Blocks until a centre has been received from Zocalo
 
         Args:
-            fallback_xyz (Point3D): The position to fallback to if no centre is found
+            fallback_xyz (ndarray): The position to fallback to if no centre is found
 
         Returns:
-            Point3D: The xray centre position to move to
+            ndarray: The xray centre position to move to
         """
         datacollection_group_id = self.ispyb.ispyb_ids[2]
 
@@ -102,13 +102,12 @@ def wait_for_results(self, fallback_xyz: Point3D) -> Point3D:
             bboxes = []
             for n, res in enumerate(raw_results):
                 bboxes.append(
-                    list(
-                        map(
-                            operator.sub, res["bounding_box"][1], res["bounding_box"][0]
-                        )
-                    )
+                    np.array(res["bounding_box"][1]) - np.array(res["bounding_box"][0])
                 )
-                nicely_formatted_com = [f"{com:.2f}" for com in res["centre_of_mass"]]
+
+                nicely_formatted_com = [
+                    f"{np.round(com,2)}" for com in res["centre_of_mass"]
+                ]
                 crystal_summary += (
                     f"Crystal {n+1}: "
                     f"Strength {res['total_count']}; "
@@ -117,11 +116,11 @@ def wait_for_results(self, fallback_xyz: Point3D) -> Point3D:
                 )
             self.ispyb.append_to_comment(crystal_summary)
 
-            raw_centre = Point3D(*(raw_results[0]["centre_of_mass"]))
+            raw_centre = np.array([*(raw_results[0]["centre_of_mass"])])
 
             # _wait_for_result returns the centre of the grid box, but we want the corner
-            results = Point3D(
-                raw_centre.x - 0.5, raw_centre.y - 0.5, raw_centre.z - 0.5
+            results = np.array(
+                [raw_centre[0] - 0.5, raw_centre[1] - 0.5, raw_centre[2] - 0.5]
             )
             xray_centre = self.grid_position_to_motor_position(results)