Prep pipettes: the container's profile as segments, from its height-volume data, from z_minimum up

pylabrobot/hamilton/prep/driver/features/head8.py

@@ -64,8 +64,8 @@
   PipetteChannel,
   Pipettes,
   _absolute_z_from_well,
-  _build_container_segments,
   _effective_radius,
+  _get_container_segments,
 )
 from .pipettes import (
   default_lld_params as _default_lld_params_fn,
@@ -1115,9 +1115,6 @@ def __init__(self, tip: Tip, volume: float):
       loc = container.get_location_wrt(self._require_deck(), "c", "c", "cavity_bottom")
       ref_x, ref_y = loc.x, loc.y + 3.5 * PROBE_PITCH_MM
       wg = _absolute_z_from_well(container, self._require_deck(), liquid_height)
-      ref_segments = container_segments or (
-        _build_container_segments(container) if auto_container_geometry else []
-      )
       ref_resource = container
     else:
       wells_list = list(wells)  # type: ignore[arg-type]
@@ -1131,14 +1128,20 @@ def __init__(self, tip: Tip, volume: float):
       ref_loc = wells_list[0].get_location_wrt(self._require_deck(), "c", "c", "cavity_bottom")
       ref_x, ref_y = ref_loc.x, ref_loc.y
       wg = _absolute_z_from_well(wells_list[0], self._require_deck(), liquid_height)
-      ref_segments = container_segments or (
-        _build_container_segments(wells_list[0]) if auto_container_geometry else []
-      )
       ref_resource = wells_list[0]
 
     resolved_z_fluid = z_fluid if z_fluid is not None else wg.liquid_surface
     resolved_z_air = z_air if z_air is not None else wg.z_air
     resolved_z_minimum = z_minimum if z_minimum is not None else wg.well_bottom
+    # the firmware counts segment 0 from z_minimum
+    cavity_bottom_z = ref_resource.get_location_wrt(
+      self._require_deck(), "c", "c", "cavity_bottom"
+    ).z
+    ref_segments = container_segments or (
+      _get_container_segments(ref_resource, profile_start=resolved_z_minimum - cavity_bottom_z)
+      if auto_container_geometry
+      else []
+    )
     resolved_z_bottom_search_offset = (
       z_bottom_search_offset if z_bottom_search_offset is not None else 2.0
     )
@@ -1337,9 +1340,6 @@ def __init__(self, tip: Tip, volume: float):
       loc = container.get_location_wrt(self._require_deck(), "c", "c", "cavity_bottom")
       ref_x, ref_y = loc.x, loc.y + 3.5 * PROBE_PITCH_MM
       wg = _absolute_z_from_well(container, self._require_deck(), liquid_height)
-      ref_segments = container_segments or (
-        _build_container_segments(container) if auto_container_geometry else []
-      )
       ref_resource = container
     else:
       wells_list = list(wells)  # type: ignore[arg-type]
@@ -1353,14 +1353,20 @@ def __init__(self, tip: Tip, volume: float):
       ref_loc = wells_list[0].get_location_wrt(self._require_deck(), "c", "c", "cavity_bottom")
       ref_x, ref_y = ref_loc.x, ref_loc.y
       wg = _absolute_z_from_well(wells_list[0], self._require_deck(), liquid_height)
-      ref_segments = container_segments or (
-        _build_container_segments(wells_list[0]) if auto_container_geometry else []
-      )
       ref_resource = wells_list[0]
 
     resolved_z_fluid = z_fluid if z_fluid is not None else wg.liquid_surface
     resolved_z_air = z_air if z_air is not None else wg.z_air
     resolved_z_minimum = z_minimum if z_minimum is not None else wg.well_bottom
+    # the firmware counts segment 0 from z_minimum
+    cavity_bottom_z = ref_resource.get_location_wrt(
+      self._require_deck(), "c", "c", "cavity_bottom"
+    ).z
+    ref_segments = container_segments or (
+      _get_container_segments(ref_resource, profile_start=resolved_z_minimum - cavity_bottom_z)
+      if auto_container_geometry
+      else []
+    )
     resolved_z_bottom_search_offset = (
       z_bottom_search_offset if z_bottom_search_offset is not None else 2.0
     )

pylabrobot/hamilton/prep/driver/features/head8_tests.py

@@ -20,6 +20,7 @@
 from pylabrobot.hamilton.prep.driver.features.pipettes import (
   Pipettes,
   _build_pipettor_gantry_move_parameters,
+  _get_container_segments,
 )
 from pylabrobot.hamilton.prep.driver.simulator import RECORDING_PREP_HEAD8
 from pylabrobot.resources import Coordinate, Resource
@@ -301,6 +302,36 @@ async def _run() -> None:
   asyncio.run(_run())
 
 
+def test_head8_aspirate_container_segments_start_at_z_minimum():
+  """With auto_container_geometry, segment 0 begins at the z_minimum the command sends."""
+
+  async def _run() -> None:
+    deck, tip_rack, src_plate, _ = _make_deck()
+    p = PrepSimulationDriver(deck=deck, declared_configuration_json=RECORDING_PREP_HEAD8)
+    await p.setup()
+    assert p.head8 is not None
+
+    captured, _ = _record_send(p)
+
+    await p.head8.pick_up_tips(tip_rack.column(0))
+    wells = src_plate.column(0)
+    cavity_bottom_z = wells[0].get_location_wrt(deck, "c", "c", "cavity_bottom").z
+    profile_top = sum(s.height for s in _get_container_segments(wells[0]))
+    await p.head8.aspirate(
+      wells=wells, volume=10, z_minimum=cavity_bottom_z + 1.5, auto_container_geometry=True
+    )
+
+    asp = [c for c in captured if isinstance(c, PrepCmd.MphAspirateNoLldMonitoring2)]
+    params = asp[0].aspirate_parameters[0]
+    assert params.common.z_minimum == pytest.approx(cavity_bottom_z + 1.5)
+    sent_height = sum(s.height for s in params.container_description)
+    assert sent_height == pytest.approx(profile_top - 1.5)
+
+    await p.stop()
+
+  asyncio.run(_run())
+
+
 def test_head8_v2_dispense_sends_mphdispensetnolld2():
   """Simulator default (use_v1=False) → V2 dispense command class is sent."""