Merge pull request #846 from DiamondLightSource/845_gridscan_width

Allow specifying the grid size in microns

live_test_rotation_params.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.1.0",
+    "params_version": "2.2.0",
     "artemis_params": {
         "beamline": "BL03I",
         "insertion_prefix": "SR03I",

live_test_rotation_params_move_xyz.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.1.0",
+    "params_version": "2.2.0",
     "artemis_params": {
         "beamline": "BL03I",
         "insertion_prefix": "SR03I",

src/artemis/experiment_plans/full_grid_scan.py

@@ -137,6 +137,7 @@ def run_grid_detection_plan(
             fgs_params,
             snapshot_template,
             snapshot_dir,
+            grid_width_microns=experiment_params.grid_width_microns,
         )
 
     yield from run_grid_detection_plan(

src/artemis/experiment_plans/oav_grid_detection_plan.py

@@ -34,7 +34,7 @@ def grid_detection_plan(
     out_parameters: GridScanParams,
     snapshot_template: str,
     snapshot_dir: str,
-    width=600,
+    grid_width_microns: float,
     box_size_microns=20,
 ):
     yield from finalize_wrapper(
@@ -43,7 +43,7 @@ def grid_detection_plan(
             out_parameters,
             snapshot_template,
             snapshot_dir,
-            width,
+            grid_width_microns,
             box_size_microns,
         ),
         reset_oav(),
@@ -56,7 +56,7 @@ def grid_detection_main_plan(
     out_parameters: GridScanParams,
     snapshot_template: str,
     snapshot_dir: str,
-    grid_width_px: int,
+    grid_width_microns: int,
     box_size_um: float,
 ):
     """
@@ -68,7 +68,7 @@ def grid_detection_main_plan(
         out_parameters (GridScanParams): The returned parameters for the gridscan
         snapshot_template (str): A template for the name of the snapshots, expected to be filled in with an angle
         snapshot_dir (str): The location to save snapshots
-        grid_width_px (int): The width of the grid to scan in pixels
+        grid_width_microns (int): The width of the grid to scan in microns
         box_size_um (float): The size of each box of the grid in microns
     """
     oav: OAV = i03.oav()
@@ -88,6 +88,8 @@ def grid_detection_main_plan(
     box_size_x_pixels = box_size_um / parameters.micronsPerXPixel
     box_size_y_pixels = box_size_um / parameters.micronsPerYPixel
 
+    grid_width_pixels = int(grid_width_microns / parameters.micronsPerXPixel)
+
     # The FGS uses -90 so we need to match it
     for angle in [0, -90]:
         yield from bps.mv(smargon.omega, angle)
@@ -105,8 +107,8 @@ def grid_detection_main_plan(
         full_image_height_px = yield from bps.rd(oav.cam.array_size.array_size_y)
 
         # only use the area from the start of the pin onwards
-        top_edge = top_edge[tip_x_px : tip_x_px + grid_width_px]
-        bottom_edge = bottom_edge[tip_x_px : tip_x_px + grid_width_px]
+        top_edge = top_edge[tip_x_px : tip_x_px + grid_width_pixels]
+        bottom_edge = bottom_edge[tip_x_px : tip_x_px + grid_width_pixels]
 
         # the edge detection line can jump to the edge of the image sometimes, filter
         # those points out, and if empty after filter use the whole image
@@ -118,10 +120,10 @@ def grid_detection_main_plan(
         max_y = max(filtered_bottom)
         grid_height_px = max_y - min_y
 
-        LOGGER.info(f"Drawing snapshot {grid_width_px} by {grid_height_px}")
+        LOGGER.info(f"Drawing snapshot {grid_width_pixels} by {grid_height_px}")
 
         boxes = (
-            math.ceil(grid_width_px / box_size_x_pixels),
+            math.ceil(grid_width_pixels / box_size_x_pixels),
             math.ceil(grid_height_px / box_size_y_pixels),
         )
         box_numbers.append(boxes)

src/artemis/experiment_plans/tests/test_full_grid_scan_plan.py

@@ -32,7 +32,7 @@ def _fake_grid_detection(
     out_parameters,
     snapshot_template: str,
     snapshot_dir: str,
-    grid_width_px: int = 0,
+    grid_width_microns: float = 0,
     box_size_um: float = 0.0,
 ):
     out_parameters.x_start = 0

src/artemis/experiment_plans/tests/test_grid_detection_plan.py

@@ -67,6 +67,7 @@ def test_grid_detection_plan_runs_and_triggers_snapshots(
             out_parameters=gridscan_params,
             snapshot_dir="tmp",
             snapshot_template="test_{angle}",
+            grid_width_microns=161.2,
         )
     )
     assert fake_devices[3].save.call_count == 6
@@ -99,6 +100,7 @@ def test_grid_detection_plan_gives_warningerror_if_tip_not_found(
                 out_parameters=gridscan_params,
                 snapshot_dir="tmp",
                 snapshot_template="test_{angle}",
+                grid_width_microns=161.2,
             )
         )
     assert "No pin found" in excinfo.value.args[0]
@@ -148,6 +150,7 @@ def test_given_when_grid_detect_then_upper_left_and_start_position_as_expected(
             snapshot_dir="tmp",
             snapshot_template="test_{angle}",
             box_size_microns=0.2,
+            grid_width_microns=161.2,
         )
     )
 
@@ -181,6 +184,7 @@ def test_when_grid_detection_plan_run_twice_then_values_do_not_persist_in_callba
                 out_parameters=gridscan_params,
                 snapshot_dir="tmp",
                 snapshot_template="test_{angle}",
+                grid_width_microns=161.2,
             )
         )
     assert len(cb.snapshot_filenames) == 2

src/artemis/parameters/plan_specific/grid_scan_with_edge_detect_params.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Any
+from typing import Any, Optional
 
 import numpy as np
 from dodal.devices.detector import TriggerMode
@@ -31,6 +31,9 @@ class GridScanWithEdgeDetectParams(AbstractExperimentParameterBase):
     detector_distance: float
     omega_start: float
 
+    # This is the correct grid size for single pin
+    grid_width_microns: Optional[float] = 161
+
     def get_num_images(self):
         return 0
 

src/artemis/parameters/schemas/experiment_schemas/grid_scan_with_edge_detect_params_schema.json

@@ -13,6 +13,9 @@
         },
         "omega_start": {
             "type": "number"
+        },
+        "grid_width_microns": {
+            "type": "number"
         }
     },
     "required": [

src/artemis/parameters/schemas/full_external_parameters_schema.json

@@ -3,7 +3,7 @@
     "type": "object",
     "properties": {
         "params_version": {
-            "const": "2.1.0"
+            "const": "2.2.0"
         },
         "artemis_params": {
             "type": "object",

src/artemis/parameters/tests/test_data/good_test_grid_with_edge_detect_parameters.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.1.0",
+    "params_version": "2.2.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -41,6 +41,7 @@
         "snapshot_dir": "/tmp",
         "exposure_time": 0.1,
         "detector_distance": 100.0,
-        "omega_start": 0.0
+        "omega_start": 0.0,
+        "grid_width_microns": 151
     }
 }

src/artemis/parameters/tests/test_data/good_test_parameters.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.1.0",
+    "params_version": "2.2.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

src/artemis/parameters/tests/test_data/good_test_rotation_scan_parameters.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.1.0",
+    "params_version": "2.2.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

src/artemis/parameters/tests/test_data/good_test_rotation_scan_parameters_nomove.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.1.0",
+    "params_version": "2.2.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

test_parameter_defaults.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.1.0",
+    "params_version": "2.2.0",
     "artemis_params": {
         "zocalo_environment": "dev_artemis",
         "beamline": "BL03S",

test_parameters.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.1.0",
+    "params_version": "2.2.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",