fix star tests without parameterset

Author: rickwierenga

pylabrobot/liquid_handling/backends/hamilton/STAR.py

@@ -1436,8 +1436,6 @@ async def aspirate(
     self,
     ops: List[Aspiration],
     use_channels: List[int],
-    jet: Optional[List[bool]] = None,
-    blow_out: Optional[List[bool]] = None,
     lld_search_height: Optional[List[float]] = None,
     clot_detection_height: Optional[List[float]] = None,
     pull_out_distance_transport_air: Optional[List[float]] = None,
@@ -1487,9 +1485,6 @@ async def aspirate(
     Args:
       ops: The aspiration operations to perform.
       use_channels: The channels to use for the operations.
-      jet: whether to search for a jet liquid class. Only used on dispense. Default is False.
-      blow_out: whether to blow out air. Only used on dispense. Note that in the VENUS Liquid
-        Editor, this is called "empty". Default is False.
 
       lld_search_height: The height to start searching for the liquid level when using LLD.
       clot_detection_height: Unknown, but probably the height to search for clots when doing LLD.
@@ -1550,11 +1545,6 @@ async def aspirate(
 
     n = len(ops)
 
-    if jet is None:
-      jet = [False] * n
-    if blow_out is None:
-      blow_out = [False] * n
-
     self._assert_valid_resources([op.resource for op in ops])
 
     well_bottoms = [op.resource.get_absolute_location().z + op.offset.z + \
@@ -1934,8 +1924,6 @@ async def drop_tips96(
   async def aspirate96(
     self,
     aspiration: Union[AspirationPlate, AspirationContainer],
-    jet: bool = False,
-    blow_out: bool = False,
 
     use_lld: bool = False,
     liquid_height: float = 0,
@@ -1961,19 +1949,14 @@ async def aspirate96(
     mix_cycles: int = 0,
     mix_position_from_liquid_surface: float = 0,
     surface_following_distance_during_mix: float = 0,
-    speed_of_mix: float = 120.0,
+    mix_speed: float = 120.0,
     limit_curve_index: int = 0,
   ):
     """ Aspirate using the Core96 head.
 
     Args:
       aspiration: The aspiration to perform.
 
-      jet: Whether to search for a jet liquid class. Only used on dispense.
-      blow_out: Whether to use "blow out" dispense mode. Only used on dispense. Note that this is
-        labelled as "empty" in the VENUS liquid editor, but "blow out" in the firmware
-        documentation.
-
       use_lld: If True, use gamma liquid level detection. If False, use liquid height.
       liquid_height: The height of the liquid above the bottom of the well, in millimeters.
       air_transport_retract_dist: The distance to retract after aspirating, in millimeters.
@@ -2002,7 +1985,7 @@ async def aspirate96(
         liquid surface.
       surface_following_distance_during_mix: The distance to follow the liquid surface
         during mix.
-      speed_of_mix: The speed of mix.
+      mix_speed: The speed of mix.
       limit_curve_index: The index of the limit curve to use.
     """
 
@@ -2011,9 +1994,6 @@ async def aspirate96(
 
     assert self.core96_head_installed, "96 head must be installed"
 
-    if jet or blow_out:
-      raise NotImplementedError("jet and blow out are not implemented for aspirate96 yet")
-
     # get the first well and tip as representatives
     if isinstance(aspiration, AspirationPlate):
       top_left_well = aspiration.wells[0]
@@ -2024,28 +2004,25 @@ async def aspirate96(
 
     liquid_height = position.z + liquid_height
 
-    transport_air_volume = transport_air_volume or 0
-    blow_out_air_volume = aspiration.blow_out_air_volume or 0
-    flow_rate = aspiration.flow_rate or 250
-    swap_speed = swap_speed or 100
-    settling_time = settling_time or 0.5
-    speed_of_mix = speed_of_mix or 10.0
+    if transport_air_volume is None:
+      transport_air_volume = 0
+    if aspiration.blow_out_air_volume is None:
+      blow_out_air_volume = 0
+    else:
+      blow_out_air_volume = aspiration.blow_out_air_volume
+    if aspiration.flow_rate is None:
+      flow_rate = 250
+    else:
+      flow_rate = aspiration.flow_rate
+    if swap_speed is None:
+      swap_speed = 100
+    if settling_time is None:
+      settling_time = 0.5
+    if mix_speed is None:
+      mix_speed = 10.0
 
     channel_pattern = [True]*12*8
 
-    # Was this ever true? Just copied it over from pyhamilton. Could have something to do with
-    # the liquid classes and whether blow_out mode is enabled.
-    # # Unfortunately, `blow_out_air_volume` does not work correctly, so instead we aspirate air
-    # # manually.
-    # if blow_out_air_volume is not None and blow_out_air_volume > 0:
-    #   await self.aspirate_core_96(
-    #     x_position=int(position.x * 10),
-    #     y_positions=int(position.y * 10),
-    #     lld_mode=0,
-    #     liquid_surface_at_function_without_lld=int((liquid_height + 30) * 10),
-    #     aspiration_volumes=int(blow_out_air_volume * 10)
-    #   )
-
     return await self.aspirate_core_96(
       x_position=round(position.x * 10),
       x_direction=0,
@@ -2081,7 +2058,7 @@ async def aspirate96(
        round(mix_position_from_liquid_surface * 10),
       surface_following_distance_during_mix=
        round(surface_following_distance_during_mix * 10),
-      speed_of_mix=round(speed_of_mix * 10),
+      mix_speed=round(mix_speed * 10),
       channel_pattern=channel_pattern,
       limit_curve_index=limit_curve_index,
       tadm_algorithm=False,
@@ -2118,7 +2095,7 @@ async def dispense96(
     mixing_cycles: int = 0,
     mixing_position_from_liquid_surface: float = 0,
     surface_following_distance_during_mixing: float = 0,
-    speed_of_mixing: float = 120.0,
+    mix_speed: float = 120.0,
     limit_curve_index: int = 0,
     cut_off_speed: float = 5.0,
     stop_back_volume: float = 0,
@@ -2154,7 +2131,7 @@ async def dispense96(
       mixing_cycles: Mixing cycles.
       mixing_position_from_liquid_surface: Mixing position from liquid surface, in mm.
       surface_following_distance_during_mixing: Surface following distance during mixing, in mm.
-      speed_of_mixing: Speed of mixing, in ul/s.
+      mix_speed: Speed of mixing, in ul/s.
       limit_curve_index: Limit curve index.
       cut_off_speed: Unknown.
       stop_back_volume: Unknown.
@@ -2163,9 +2140,6 @@ async def dispense96(
     if hlc is not None:
       raise NotImplementedError("Hamilton liquid classes are deprecated.")
 
-    if jet or blow_out:
-      raise NotImplementedError("jet and blow out are not implemented for aspirate96 yet")
-
     assert self.core96_head_installed, "96 head must be installed"
 
     # get the first well and tip as representatives
@@ -2180,12 +2154,22 @@ async def dispense96(
 
     dispense_mode = _dispensing_mode_for_op(empty=empty, jet=jet, blow_out=blow_out)
 
-    transport_air_volume = transport_air_volume or 0
-    blow_out_air_volume = dispense.blow_out_air_volume or 0
-    flow_rate = dispense.flow_rate or 120
-    swap_speed = swap_speed or 100
-    settling_time = settling_time or 5
-    speed_of_mixing = speed_of_mixing or 100
+    if transport_air_volume is None:
+      transport_air_volume = 0
+    if dispense.blow_out_air_volume is None:
+      blow_out_air_volume = 0
+    else:
+      blow_out_air_volume = dispense.blow_out_air_volume
+    if dispense.flow_rate is None:
+      flow_rate = 120
+    else:
+      flow_rate = dispense.flow_rate
+    if swap_speed is None:
+      swap_speed = 100
+    if settling_time is None:
+      settling_time = 5
+    if mix_speed is None:
+      mix_speed = 100
 
     channel_pattern = [True]*12*8
 
@@ -2221,7 +2205,7 @@ async def dispense96(
       mixing_cycles=mixing_cycles,
       mixing_position_from_liquid_surface=round(mixing_position_from_liquid_surface*10),
       surface_following_distance_during_mixing=round(surface_following_distance_during_mixing*10),
-      speed_of_mixing=round(speed_of_mixing*10),
+      mix_speed=round(mix_speed*10),
       channel_pattern=channel_pattern,
       limit_curve_index=limit_curve_index,
       tadm_algorithm=False,
@@ -4938,7 +4922,7 @@ async def aspirate_core_96(
     mix_cycles: int = 0,
     mix_position_from_liquid_surface: int = 250,
     surface_following_distance_during_mix: int = 0,
-    speed_of_mix: int = 1000,
+    mix_speed: int = 1000,
     channel_pattern: List[bool] = [True] * 96,
     limit_curve_index: int = 0,
     tadm_algorithm: bool = False,
@@ -4992,7 +4976,7 @@ async def aspirate_core_96(
           liquid surface (LLD or absolute terms) [0.1mm]. Must be between 0 and 990. Default 250.
       surface_following_distance_during_mix: surface following distance during
           mix [0.1mm]. Must be between 0 and 990. Default 0.
-      speed_of_mix: Speed of mix [0.1ul/s]. Must be between 3 and 5000.
+      mix_speed: Speed of mix [0.1ul/s]. Must be between 3 and 5000.
           Default 1000.
       todo: TODO: 24 hex chars. Must be between 4 and 5000.
       limit_curve_index: limit curve index. Must be between 0 and 999. Default 0.
@@ -5038,8 +5022,8 @@ async def aspirate_core_96(
       "mix_position_from_liquid_surface must be between 0 and 990"
     assert 0 <= surface_following_distance_during_mix <= 990, \
       "surface_following_distance_during_mix must be between 0 and 990"
-    assert 3 <= speed_of_mix <= 5000, \
-      "speed_of_mix must be between 3 and 5000"
+    assert 3 <= mix_speed <= 5000, \
+      "mix_speed must be between 3 and 5000"
     assert 0 <= limit_curve_index <= 999, "limit_curve_index must be between 0 and 999"
 
     assert 0 <= recording_mode <= 2, "recording_mode must be between 0 and 2"
@@ -5080,7 +5064,7 @@ async def aspirate_core_96(
       hc=f"{mix_cycles:02}",
       hp=f"{mix_position_from_liquid_surface:03}",
       mj=f"{surface_following_distance_during_mix:03}",
-      hs=f"{speed_of_mix:04}",
+      hs=f"{mix_speed:04}",
       cw=channel_pattern_hex,
       cr=f"{limit_curve_index:03}",
       cj=tadm_algorithm,
@@ -5120,7 +5104,7 @@ async def dispense_core_96(
     mixing_cycles: int = 0,
     mixing_position_from_liquid_surface: int = 250,
     surface_following_distance_during_mixing: int = 0,
-    speed_of_mixing: int = 1000,
+    mix_speed: int = 1000,
     channel_pattern: List[bool] = [True]*12*8,
     limit_curve_index: int = 0,
     tadm_algorithm: bool = False,
@@ -5177,7 +5161,7 @@ async def dispense_core_96(
           surface (LLD or absolute terms) [0.1mm]. Must be between 0 and 990. Default 250.
       surface_following_distance_during_mixing: surface following distance during mixing [0.1mm].
           Must be between 0 and 990. Default 0.
-      speed_of_mixing: Speed of mixing [0.1ul/s]. Must be between 3 and 5000. Default 1000.
+      mix_speed: Speed of mixing [0.1ul/s]. Must be between 3 and 5000. Default 1000.
       channel_pattern: list of 96 boolean values
       limit_curve_index: limit curve index. Must be between 0 and 999. Default 0.
       tadm_algorithm: TADM algorithm. Default False.
@@ -5224,7 +5208,7 @@ async def dispense_core_96(
       "mixing_position_from_liquid_surface must be between 0 and 990"
     assert 0 <= surface_following_distance_during_mixing <= 990, \
       "surface_following_distance_during_mixing must be between 0 and 990"
-    assert 3 <= speed_of_mixing <= 5000, "speed_of_mixing must be between 3 and 5000"
+    assert 3 <= mix_speed <= 5000, "mix_speed must be between 3 and 5000"
     assert 0 <= limit_curve_index <= 999, "limit_curve_index must be between 0 and 999"
     assert 0 <= recording_mode <= 2, "recording_mode must be between 0 and 2"
 
@@ -5266,7 +5250,7 @@ async def dispense_core_96(
       hc=f"{mixing_cycles:02}",
       hp=f"{mixing_position_from_liquid_surface:03}",
       mj=f"{surface_following_distance_during_mixing:03}",
-      hs=f"{speed_of_mixing:04}",
+      hs=f"{mix_speed:04}",
       cw=channel_pattern_hex,
       cr=f"{limit_curve_index:03}",
       cj=tadm_algorithm,

pylabrobot/liquid_handling/backends/hamilton/STAR_tests.py

@@ -406,8 +406,8 @@ async def test_single_channel_aspiration(self):
     self.plate.lid.unassign()
     well = self.plate.get_item("A1")
     well.tracker.set_liquids([(None, 100 * 1.072)]) # liquid class correction
-    ps = STARParameterSet.from_hamilton_liquid_class(self.hlc, num_channels=1)
-    await self.lh.aspirate([well], vols=[self.hlc.compute_corrected_volume(100)], **ps.make_asp_kwargs())
+    await self.lh.aspirate([well], vols=[self.hlc.compute_corrected_volume(100)],
+                           **self.hlc.make_asp_kwargs(1))
 
     # This passes the test, but is not the real command.
     self._assert_command_sent_once(
@@ -426,9 +426,8 @@ async def test_single_channel_aspiration_liquid_height(self):
     self.plate.lid.unassign()
     well = self.plate.get_item("A1")
     well.tracker.set_liquids([(None, 100 * 1.072)]) # liquid class correction
-    ps = STARParameterSet.from_hamilton_liquid_class(self.hlc, num_channels=1)
     await self.lh.aspirate([well], vols=[self.hlc.compute_corrected_volume(100)],
-                           liquid_height=[10], **ps.make_asp_kwargs())
+                           liquid_height=[10], **self.hlc.make_asp_kwargs(1))
 
     # This passes the test, but is not the real command.
     self._assert_command_sent_once(
@@ -448,9 +447,9 @@ async def test_multi_channel_aspiration(self):
     wells = self.plate.get_items("A1:B1")
     for well in wells:
       well.tracker.set_liquids([(None, 100 * 1.072)]) # liquid class correction
-    ps = STARParameterSet.from_hamilton_liquid_class(self.hlc, num_channels=2)
     corrected_vol = self.hlc.compute_corrected_volume(100)
-    await self.lh.aspirate(self.plate["A1:B1"], vols=[corrected_vol]*2, **ps.make_asp_kwargs())
+    await self.lh.aspirate(self.plate["A1:B1"], vols=[corrected_vol]*2,
+                           **self.hlc.make_asp_kwargs(2))
 
     # This passes the test, but is not the real command.
     self._assert_command_sent_once(
@@ -466,11 +465,10 @@ async def test_multi_channel_aspiration(self):
 
   async def test_aspirate_single_resource(self):
     self.lh.update_head_state({i: self.tip_rack.get_tip(i) for i in range(5)})
-    ps = STARParameterSet.from_hamilton_liquid_class(self.hlc, num_channels=5)
     corrected_vol = self.hlc.compute_corrected_volume(10)
     with no_volume_tracking():
       await self.lh.aspirate([self.bb]*5,vols=[corrected_vol]*5, use_channels=[0,1,2,3,4],
-                             liquid_height=[1]*5, **ps.make_asp_kwargs())
+                             liquid_height=[1]*5, **self.hlc.make_asp_kwargs(5))
     self._assert_command_sent_once(
       "C0ASid0002at0 0 0 0 0 0&tm1 1 1 1 1 0&xp04865 04865 04865 04865 04865 00000&yp2098 1962 "
       "1825 1688 1552 0000&th2450te2450lp2000 2000 2000 2000 2000 2000&ch000 000 000 000 000 000&"
@@ -490,12 +488,10 @@ async def test_aspirate_single_resource(self):
   async def test_dispense_single_resource(self):
     self.lh.update_head_state({i: self.tip_rack.get_tip(i) for i in range(5)})
     hlc = StandardVolumeFilter_Water_DispenseJet_Empty
-    ps = STARParameterSet.from_hamilton_liquid_class(hlc, num_channels=5,
-                                                     jet=[True]*5, blow_out=[True]*5)
     corrected_vol = hlc.compute_corrected_volume(10)
     with no_volume_tracking():
       await self.lh.dispense([self.bb]*5, vols=[corrected_vol]*5, liquid_height=[1]*5,
-                             **ps.make_disp_kwargs())
+                             jet=[True]*5, blow_out=[True]*5, **hlc.make_disp_kwargs(5))
     self._assert_command_sent_once(
       "C0DSid0002dm1 1 1 1 1 1&tm1 1 1 1 1 0&xp04865 04865 04865 04865 04865 00000&yp2098 1962 "
       "1825 1688 1552 0000&zx1200 1200 1200 1200 1200 1200&lp2000 2000 2000 2000 2000 2000&zl1210 "
@@ -514,11 +510,10 @@ async def test_single_channel_dispense(self):
     assert self.plate.lid is not None
     self.plate.lid.unassign()
     hlc = StandardVolumeFilter_Water_DispenseJet_Empty
-    ps = STARParameterSet.from_hamilton_liquid_class(hlc, num_channels=1,
-                                                      jet=[True]*1, blow_out=[True]*1)
     corrected_vol = hlc.compute_corrected_volume(100)
     with no_volume_tracking():
-      await self.lh.dispense(self.plate["A1"], vols=[corrected_vol], **ps.make_disp_kwargs())
+      await self.lh.dispense(self.plate["A1"], vols=[corrected_vol], jet=[True], blow_out=[True],
+                             **hlc.make_disp_kwargs(1))
     self._assert_command_sent_once(
       "C0DSid0002dm1 1&tm1 0&xp02983 00000&yp1457 0000&zx1866 1866&lp2000 2000&zl1866 1866&"
       "po0100 0100&ip0000 0000&it0 0&fp0000 0000&zu0032 0032&zr06180 06180&th2450te2450"
@@ -533,11 +528,10 @@ async def test_multi_channel_dispense(self):
     assert self.plate.lid is not None
     self.plate.lid.unassign()
     hlc = StandardVolumeFilter_Water_DispenseJet_Empty
-    ps = STARParameterSet.from_hamilton_liquid_class(hlc, num_channels=2,
-                                                      jet=[True]*2, blow_out=[True]*2)
     corrected_vol = hlc.compute_corrected_volume(100)
     with no_volume_tracking():
-      await self.lh.dispense(self.plate["A1:B1"], vols=[corrected_vol]*2, **ps.make_disp_kwargs())
+      await self.lh.dispense(self.plate["A1:B1"], vols=[corrected_vol]*2, jet=[True]*2,
+                             blow_out=[True]*2, **hlc.make_disp_kwargs(2))
 
     self._assert_command_sent_once(
       "C0DSid0002dm1 1 1&tm1 1 0&xp02983 02983 00000&yp1457 1367 0000&zx1866 1866 1866&lp2000 2000 "
@@ -586,9 +580,8 @@ async def test_core_96_aspirate(self):
     assert self.plate.lid is not None
     self.plate.lid.unassign()
     hlc = HighVolumeFilter_96COREHead1000ul_Water_DispenseSurface_Empty
-    ps = STARParameterSet.from_hamilton_liquid_class(hlc)
-    corrected_volume = hlc.compute_corrected_volume(100) # need different liquid class
-    await self.lh.aspirate96(self.plate, volume=corrected_volume, **ps.make_asp96_kwargs())
+    corrected_volume = hlc.compute_corrected_volume(100)
+    await self.lh.aspirate96(self.plate, volume=corrected_volume, **hlc.make_asp96_kwargs())
 
     # volume used to be 01072, but that was generated using a non-core liquid class.
     self._assert_command_sent_once(
@@ -603,13 +596,13 @@ async def test_core_96_dispense(self):
     await self.lh.pick_up_tips96(self.tip_rack2) # pick up high volume tips
     if self.plate.lid is not None:
       self.plate.lid.unassign()
-    corrected_volume = self.hlc.compute_corrected_volume(100) # need different liquid class
-    await self.lh.aspirate96(self.plate, corrected_volume) # aspirate first
+    hlc = HighVolumeFilter_96COREHead1000ul_Water_DispenseSurface_Empty
+    corrected_volume = hlc.compute_corrected_volume(100)
+    await self.lh.aspirate96(self.plate, corrected_volume, **hlc.make_asp96_kwargs())
 
     with no_volume_tracking():
-      await self.lh.dispense96(self.plate, corrected_volume)
+      await self.lh.dispense96(self.plate, corrected_volume, **hlc.make_disp96_kwargs(), blow_out=True)
 
-    # volume used to be 01072, but that was generated using a non-core liquid class.
     self._assert_command_sent_once(
       "C0EDid0001da3xs02983xd0yh1457zh2450ze2450lz1999zt1866zm1866iw000ix0fh000df01083dg1200vt050"
       "bv00000cm0cs1bs0020wh00hv00000hc00hp000hs1200es0050ev000zv0032ej00zq06180mj000cj0cx0cr000"