Merge branch 'main' into 684_serial-detector-params

.gitignore

@@ -172,3 +172,6 @@ edm_serial/
 **/parameters/fixed_target/*/*.map
 # idea project files
 .idea/
+
+# Generated PlantUML diagrams
+docs/developer/hyperion/reference/param_hierarchy.puml

docs/conf.py

@@ -49,6 +49,8 @@
     "sphinx_design",
     # For markdown
     "myst_parser",
+    # For plantUML diagrams
+    "plantweb.directive",
 ]
 
 myst_enable_extensions = [

docs/developer/hyperion/reference/gridscan.puml

@@ -0,0 +1,109 @@
+@startuml
+title Gridscan Parameter Relationships
+
+class DiffractionExperiment
+class DiffractionExperimentWithSample
+class GridCommon {
+    grid_width_um
+    exposure_time_s
+}
+class GridScanWithEdgeDetect {
+    box_size_um
+}
+class HyperionGridCommon {
+    enable_dev_shm
+}
+class HyperionThreeDGridScan {
+    x_step_size_um
+    y_step_size_um
+    z_step_size_um
+    y2_start_um
+    z2_start_um
+    --
+    grid_1_spec
+    grid_2_spec
+    scan_indices
+    scan_spec
+    scan_points
+    scan_points_first_grid
+    scan_points_second_grid
+    num_images
+    FGS_Params
+    panda_FGS_Params
+}
+class MxBlueSkyParameters
+class SpecifiedGrid
+class XyzStarts {
+    x_start_um
+    y_start_um
+    z_start_um
+}
+class OptionalXYZStarts {
+    x_start_um
+    y_start_um
+    z_start_um
+}
+class RotationScanPerSweep
+
+MxBlueSkyParameters <|-- DiffractionExperiment
+DiffractionExperiment <|-- DiffractionExperimentWithSample
+DiffractionExperimentWithSample <|-- GridCommon
+GridCommon <|-- GridScanWithEdgeDetect
+GridCommon <|-- HyperionGridCommon
+HyperionGridCommon <|-- HyperionThreeDGridScan
+SpecifiedGrid <|-- HyperionThreeDGridScan
+XyzStarts <|-- SpecifiedGrid
+OptionalXYZStarts <|-- RotationScanPerSweep
+class GridParamUpdate {
+    x_start_um
+    y_start_um
+    y2_start_um
+    z_start_um
+    z2_start_um
+    x_steps
+    y_steps
+    z_steps
+    x_step_size_um
+    y_step_size_um
+    z_step_size_um
+}
+
+class GridDetectionCallback {
+    get_grid_parameters() -> GridParamUpdate
+}
+
+GridDetectionCallback --> GridParamUpdate : generates from event. Adds 0.5 to get box-centres
+GridParamUpdate --> HyperionThreeDGridScan : combines with GridScanWithEdgeDetect
+
+class experiment_plans {
+    grid_detect_then_xray_centre()
+    flyscan_xray_centre_no_move()
+    create_parameters_for_flyscan_xray_centre(GridScanWithEdgeDetect, GridParamUpdate) -> HyperionThreeDGridScan
+}
+
+class AbstractExperimentBase
+class AbstractExperimentWithBeamParams
+class GridScanParamsCommon {
+    x_steps
+    y_steps
+    z_steps
+    x_step_size_mm
+    y_step_size_mm
+    z_step_size_mm
+    x_start_mm
+    y1_start_mm
+    y2_start_mm
+    z1_start_mm
+    z2_start_mm
+}
+class PandAGridScanParams
+class ZebraGridScanParams
+
+AbstractExperimentBase <|-- AbstractExperimentWithBeamParams
+AbstractExperimentWithBeamParams <|-- GridScanParamsCommon
+GridScanParamsCommon <|-- PandAGridScanParams
+GridScanParamsCommon <|-- ZebraGridScanParams
+
+HyperionThreeDGridScan --> ZebraGridScanParams : generates
+HyperionThreeDGridScan --> PandAGridScanParams : generates
+@enduml

docs/developer/hyperion/reference/param-hierarchy.rst

@@ -1,4 +1,4 @@
 Hyperion Parameter class hierarchy
 ==================================
 
-TODO: automate including the param hierarchy here
+.. uml:: param_hierarchy.puml

pyproject.toml

@@ -46,7 +46,7 @@ dependencies = [
     "ophyd == 1.9.0",
     "ophyd-async >= 0.8a5",
     "bluesky >= 1.13.0a4",
-    "dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@6295feafb43acd158ed80b30f06de2bf29fe4b16",
+    "dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@e6ad77ee5aa489d0035918e45a28a0d6f72b19ed",
 ]
 
 
@@ -68,6 +68,7 @@ dev = [
     "mypy",
     "myst-parser",
     "pipdeptree",
+    "plantweb",
     "pre-commit",
     "pydata-sphinx-theme>=0.12",
     "pyright",
@@ -78,7 +79,6 @@ dev = [
     "ruff",
     "sphinx-autobuild",
     "sphinx-copybutton",
-    "sphinxcontrib-plantuml",
     "sphinx-design",
     "tox-direct",
     "tox",
@@ -180,6 +180,9 @@ commands =
     type-checking: pyright src tests {posargs}
     tests: pytest --cov=mx_bluesky --cov-report term --cov-report xml:cov.xml {posargs}
     docs: sphinx-{posargs:build -EW --keep-going} -T docs build/html
+commands_pre =
+    docs: /usr/bin/bash -c "{toxinidir}/utility_scripts/generate_plantuml.py > \
+        docs/developer/hyperion/reference/param_hierarchy.puml"
 """
 
 [tool.ruff]

src/mx_bluesky/beamlines/i24/serial/extruder/i24ssx_Extruder_Collect_py3v2.py

@@ -16,7 +16,7 @@
 import bluesky.preprocessors as bpp
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
-from dodal.devices.attenuator import ReadOnlyAttenuator
+from dodal.devices.attenuator.attenuator import ReadOnlyAttenuator
 from dodal.devices.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
 from dodal.devices.i24.beam_center import DetectorBeamCenter

src/mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_Chip_Collect_py3v1.py

@@ -10,7 +10,7 @@
 import bluesky.preprocessors as bpp
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
-from dodal.devices.attenuator import ReadOnlyAttenuator
+from dodal.devices.attenuator.attenuator import ReadOnlyAttenuator
 from dodal.devices.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
 from dodal.devices.i24.beam_center import DetectorBeamCenter

src/mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_Chip_Manager_py3v1.py

@@ -15,7 +15,7 @@
 import numpy as np
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
-from dodal.devices.attenuator import ReadOnlyAttenuator
+from dodal.devices.attenuator.attenuator import ReadOnlyAttenuator
 from dodal.devices.i24.beamstop import Beamstop, BeamstopPositions
 from dodal.devices.i24.dual_backlight import BacklightPositions, DualBacklight
 from dodal.devices.i24.i24_detector_motion import DetectorMotion

src/mx_bluesky/hyperion/external_interaction/callbacks/aperture_change_callback.py → src/mx_bluesky/common/external_interaction/callbacks/common/aperture_change_callback.py

@@ -1,7 +1,7 @@
 from bluesky.callbacks import CallbackBase
 from event_model.documents.run_start import RunStart
 
-from mx_bluesky.hyperion.log import LOGGER
+from mx_bluesky.common.utils.log import LOGGER
 
 from .logging_callback import format_doc_for_log
 

src/mx_bluesky/hyperion/external_interaction/callbacks/grid_detection_callback.py → src/mx_bluesky/common/external_interaction/callbacks/common/grid_detection_callback.py

@@ -5,10 +5,28 @@
 from dodal.devices.oav.utils import calculate_x_y_z_of_pixel
 from event_model.documents import Event
 
-from mx_bluesky.hyperion.log import LOGGER
+from mx_bluesky.common.utils.log import LOGGER
 
 
 class GridParamUpdate(TypedDict):
+    """
+    Grid parameters extracted from the grid detection.
+    Positions are in motor-space.
+
+    Attributes:
+        x_start_um: x position of the centre of the first xy-gridscan box in microns
+        y_start_um: y position of the centre of the first xy-gridscan box in microns
+        y2_start_um: y position of the centre of the first xz-gridscan box in microns
+        z_start_um: z position of the centre of the first xy-gridscan box in microns
+        z2_start_um: z position of the centre of the first xz-gridscan box in microns
+        x_steps: Number of grid boxes in x-direction for xy- and xz- gridscans
+        y_steps: Number of grid boxes in y-direction for xy-gridscan
+        z_steps: Number of grid boxes in z-direction for xz-gridscan
+        x_step_size_um: x-dimension of the grid box
+        y_step_size_um: y-dimension of the grid box
+        z_step_size_um: z-dimension of the grid box
+    """
+
     x_start_um: float
     y_start_um: float
     y2_start_um: float