support non-full tip racks with 96 head pickup (#548)

Author: rickwierenga

pylabrobot/liquid_handling/backends/hamilton/STAR_backend.py

@@ -2181,9 +2181,15 @@ async def pick_up_tips96(
     """Pick up tips using the 96 head."""
     assert self.core96_head_installed, "96 head must be installed"
     tip_spot_a1 = pickup.resource.get_item("A1")
-    tip_a1 = tip_spot_a1.get_tip()
-    assert isinstance(tip_a1, HamiltonTip), "Tip type must be HamiltonTip."
-    ttti = await self.get_or_assign_tip_type_index(tip_a1)
+    prototypical_tip = None
+    for tip_spot in pickup.resource.get_all_items():
+      if tip_spot.has_tip():
+        prototypical_tip = tip_spot.get_tip()
+        break
+    if prototypical_tip is None:
+      raise ValueError("No tips found in the tip rack.")
+    assert isinstance(prototypical_tip, HamiltonTip), "Tip type must be HamiltonTip."
+    ttti = await self.get_or_assign_tip_type_index(prototypical_tip)
     position = tip_spot_a1.get_absolute_location() + tip_spot_a1.center() + pickup.offset
     z_deposit_position += round(pickup.offset.z * 10)
 
@@ -2213,8 +2219,8 @@ async def drop_tips96(
     """Drop tips from the 96 head."""
     assert self.core96_head_installed, "96 head must be installed"
     if isinstance(drop.resource, TipRack):
-      tip_a1 = drop.resource.get_item("A1")
-      position = tip_a1.get_absolute_location() + tip_a1.center() + drop.offset
+      tip_spot_a1 = drop.resource.get_item("A1")
+      position = tip_spot_a1.get_absolute_location() + tip_spot_a1.center() + drop.offset
     else:
       position = self._position_96_head_in_resource(drop.resource) + drop.offset
 

pylabrobot/liquid_handling/backends/hamilton/STAR_tests.py

@@ -24,6 +24,7 @@
   Lid,
   ResourceStack,
   no_volume_tracking,
+  set_tip_tracking,
 )
 from pylabrobot.resources.hamilton import STF, STARLetDeck
 
@@ -264,6 +265,8 @@ def __init__(self, name: str):
     self.STAR._iswap_parked = True
     await self.lh.setup()
 
+    set_tip_tracking(enabled=False)
+
   async def asyncTearDown(self):
     await self.lh.stop()
 

pylabrobot/liquid_handling/backends/hamilton/vantage_backend.py

@@ -946,9 +946,15 @@ async def pick_up_tips96(
   ):
     # assert self.core96_head_installed, "96 head must be installed"
     tip_spot_a1 = pickup.resource.get_item("A1")
-    tip_a1 = tip_spot_a1.get_tip()
-    assert isinstance(tip_a1, HamiltonTip), "Tip type must be HamiltonTip."
-    ttti = await self.get_or_assign_tip_type_index(tip_a1)
+    prototypical_tip = None
+    for tip_spot in pickup.resource.get_all_items():
+      if tip_spot.has_tip():
+        prototypical_tip = tip_spot.get_tip()
+        break
+    if prototypical_tip is None:
+      raise ValueError("No tips found in the tip rack.")
+    assert isinstance(prototypical_tip, HamiltonTip), "Tip type must be HamiltonTip."
+    ttti = await self.get_or_assign_tip_type_index(prototypical_tip)
     position = tip_spot_a1.get_absolute_location() + tip_spot_a1.center() + pickup.offset
     offset_z = pickup.offset.z
 

pylabrobot/liquid_handling/backends/hamilton/vantage_tests.py

@@ -10,6 +10,7 @@
   TIP_CAR_480_A00,
   Coordinate,
   Cor_96_wellplate_360ul_Fb,
+  set_tip_tracking,
 )
 from pylabrobot.resources.hamilton import VantageDeck
 
@@ -259,6 +260,8 @@ async def asyncSetUp(self):
 
     await self.lh.setup()
 
+    set_tip_tracking(enabled=False)
+
   async def asyncTearDown(self):
     await self.lh.stop()
 

pylabrobot/liquid_handling/liquid_handler.py

@@ -1243,8 +1243,11 @@ async def pick_up_tips96(
     for i, tip_spot in enumerate(tip_rack.get_all_items()):
       if not does_tip_tracking() and self.head96[i].has_tip:
         self.head96[i].remove_tip()
-      self.head96[i].add_tip(tip_spot.get_tip(), origin=tip_spot, commit=False)
-      if does_tip_tracking() and not tip_spot.tracker.is_disabled:
+      # only add tips where there is one present.
+      # it's possible only some tips are present in the tip rack.
+      if tip_spot.has_tip():
+        self.head96[i].add_tip(tip_spot.get_tip(), origin=tip_spot, commit=False)
+      if does_tip_tracking() and not tip_spot.tracker.is_disabled and tip_spot.has_tip():
         tip_spot.tracker.remove_tip()
 
     pickup_operation = PickupTipRack(resource=tip_rack, offset=offset)
@@ -1302,6 +1305,9 @@ async def drop_tips96(
 
     # queue operation on all tip trackers
     for i in range(96):
+      # it's possible not every channel on this head has a tip.
+      if not self.head96[i].has_tip:
+        continue
       tip = self.head96[i].get_tip()
       if tip.tracker.get_used_volume() > 0 and not allow_nonzero_volume:
         error = f"Cannot drop tip with volume {tip.tracker.get_used_volume()} on channel {i}"

pylabrobot/liquid_handling/liquid_handler_tests.py

@@ -1016,6 +1016,22 @@ async def test_aspirate_single_reservoir(self):
     await self.lh.pick_up_tips96(self.tip_rack)
     await self.lh.aspirate96(reagent_reservoir.get_item("A1"), volume=100)
 
+  async def test_pick_up_tips96_incomplete_rack(self):
+    set_tip_tracking(enabled=True)
+
+    # Test that picking up tips from an incomplete rack works
+    self.tip_rack.fill()
+    self.tip_rack.get_item("A1").tracker.remove_tip()
+
+    await self.lh.pick_up_tips96(self.tip_rack)
+
+    # Check that the tips were picked up correctly
+    self.assertFalse(self.lh.head96[0].has_tip)
+    for i in range(1, 96):
+      self.assertTrue(self.lh.head96[i].has_tip)
+
+    set_tip_tracking(enabled=False)
+
 
 class TestLiquidHandlerVolumeTracking(unittest.IsolatedAsyncioTestCase):
   async def asyncSetUp(self):