feat: add plate_row and plate_col fields to PositionBase

Add serialized int fields to PositionBase for annotating which well a
position belongs to, enabling HCS zarr output from plain stage positions
without requiring WellPlatePlan. Also populate these fields in
WellPlatePlan.all_well_positions and selected_well_positions.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: ieivanov

src/useq/_plate.py

@@ -335,19 +335,37 @@ def _transorm_coords(self, coords: np.ndarray) -> np.ndarray:
     def all_well_positions(self) -> Sequence[Position]:
         """Return all wells (centers) as Position objects."""
         return [
-            Position(x=x * 1000, y=y * 1000, name=name)  # convert to µm
-            for (y, x), name in zip(
-                self.all_well_coordinates, self.all_well_names.reshape(-1), strict=False
+            Position(
+                x=x * 1000,
+                y=y * 1000,
+                name=name,
+                plate_row=int(row),
+                plate_col=int(col),
+            )
+            for (y, x), name, (row, col) in zip(
+                self.all_well_coordinates,
+                self.all_well_names.reshape(-1),
+                self.all_well_indices.reshape(-1, 2),
+                strict=False,
             )
         ]
 
     @cached_property
     def selected_well_positions(self) -> Sequence[Position]:
         """Return selected wells (centers) as Position objects."""
         return [
-            Position(x=x * 1000, y=y * 1000, name=name)  # convert to µm
-            for (y, x), name in zip(
-                self.selected_well_coordinates, self.selected_well_names, strict=False
+            Position(
+                x=x * 1000,
+                y=y * 1000,
+                name=name,
+                plate_row=int(row),
+                plate_col=int(col),
+            )
+            for (y, x), name, (row, col) in zip(
+                self.selected_well_coordinates,
+                self.selected_well_names,
+                self.selected_well_indices,
+                strict=False,
             )
         ]
 

src/useq/_position.py

@@ -46,6 +46,8 @@ class PositionBase(MutableModel):
     name: str | None = None
     sequence: Optional["MDASequence"] = None
     properties: list[PropertyTuple] | None = None
+    plate_row: int | None = None
+    plate_col: int | None = None
 
     # excluded from serialization
     row: int | None = Field(default=None, exclude=True)

tests/fixtures/mda.json

@@ -62,15 +62,13 @@
   "stage_positions": [
     {
       "name": null,
-      "properties": null,
       "sequence": null,
       "x": 10.0,
       "y": 20.0,
       "z": null
     },
     {
       "name": "test_name",
-      "properties": null,
       "sequence": {
         "autofocus_plan": null,
         "axis_order": [
@@ -105,7 +103,6 @@
           "step": 1.0
         }
       },
-      "properties": null,
       "x": 10.0,
       "y": 20.0,
       "z": 50.0

tests/fixtures/mda.yaml

@@ -25,17 +25,11 @@ metadata:
 stage_positions:
 - x: 10.0
   y: 20.0
+  z: null
 - name: test_name
   sequence:
-    axis_order:
-    - t
-    - p
-    - g
-    - c
-    - z
     grid_plan:
       columns: 3
-      mode: row_wise_snake
       rows: 2
     z_plan:
       above: 10.0