remove z_travel from tecan resources (#553)

Author: rickwierenga

pylabrobot/liquid_handling/backends/tecan/EVO_backend.py

@@ -212,6 +212,11 @@ def __init__(
     self._pnp_connected: Optional[bool] = None
     self._mca_connected: Optional[bool] = None
 
+    self._z_traversal_height = 210  # mm, the default value for SHZ command
+    self._z_roma_traversal_height = (
+      68.7  # mm, is what was used to develop this but possibly too low
+    )
+
   @property
   def num_channels(self) -> int:
     """The number of pipette channels present on the robot."""
@@ -412,7 +417,7 @@ async def aspirate(
       await self.liha.set_search_z_start(z_positions["start"])
       await self.liha.set_search_z_max(list(z if z else self._z_range for z in z_positions["max"]))
       await self.liha.set_search_submerge(sbl)
-      shz = [min(z for z in z_positions["travel"] if z)] * self.num_channels
+      shz = [min(z for z in z_positions["travel"] if z)] * self.num_channels  # TODO: max?
       await self.liha.set_z_travel_height(shz)
       await self.liha.move_detect_liquid(self._bin_use_channels(use_channels), zadd)
       await self.liha.set_z_travel_height([self._z_range] * self.num_channels)
@@ -686,9 +691,9 @@ def get_z_position(z, z_off, tip_length):
         raise ValueError(f"Operation is not supported by resource {par}.")
       # TODO: calculate defaults when z-attribs are not specified
       tip_length = int(ops[i].tip.total_tip_length * 10)
-      z_positions["travel"][channel] = get_z_position(
-        par.z_travel, par.get_absolute_location().z + op.offset.z, tip_length
-      )
+      # z travel seems to only be used for aspiration and dispense right now
+      if isinstance(op, (SingleChannelAspiration, SingleChannelDispense)):
+        z_positions["travel"][channel] = round(self._z_traversal_height * 10)
       z_positions["start"][channel] = get_z_position(
         par.z_start, par.get_absolute_location().z + op.offset.z, tip_length
       )
@@ -850,27 +855,28 @@ def _roma_positions(
   ) -> Tuple[int, int, Dict[str, int]]:
     """Creates x, y, and z positions used by RoMa ops."""
 
-    par = resource.parent
-    if par is None:
+    parent = resource.parent  # PlateHolder
+    if parent is None:
       raise ValueError(f"Operation is not supported by resource {resource}.")
-    par = par.parent
-    if not isinstance(par, TecanPlateCarrier):
-      raise ValueError(f"Operation is not supported by resource {par}.")
+    parent = parent.parent  # PlateCarrier
+    # TODO: this is probably the current plate carrier, not the destination.
+    # Also, we should just support any coordinate as the destination.
+    if not isinstance(parent, TecanPlateCarrier):
+      raise ValueError(f"Operation is not supported by resource {parent}.")
 
     if (
-      par.roma_x is None
-      or par.roma_y is None
-      or par.roma_z_safe is None
-      or par.roma_z_travel is None
-      or par.roma_z_end is None
+      parent.roma_x is None
+      or parent.roma_y is None
+      or parent.roma_z_safe is None
+      or parent.roma_z_end is None
     ):
-      raise ValueError(f"Operation is not supported by resource {par}.")
-    x_position = int((offset.x - 100) * 10 + par.roma_x)
-    y_position = int((347.1 - (offset.y + resource.get_absolute_size_y())) * 10 + par.roma_y)
+      raise ValueError(f"Operation is not supported by resource {parent}.")
+    x_position = int((offset.x - 100) * 10 + parent.roma_x)
+    y_position = int((347.1 - (offset.y + resource.get_absolute_size_y())) * 10 + parent.roma_y)
     z_positions = {
-      "safe": z_range - int(par.roma_z_safe),
-      "travel": z_range - int(par.roma_z_travel - offset.z * 10),
-      "end": z_range - int(par.roma_z_end - offset.z * 10),
+      "safe": z_range - int(parent.roma_z_safe),
+      "travel": int(self._z_roma_traversal_height * 10),
+      "end": z_range - int(parent.roma_z_end - offset.z * 10),
     }
 
     return x_position, y_position, z_positions
@@ -933,8 +939,20 @@ async def initialize_plunger(self, tips):
   async def report_z_param(self, param: int) -> List[int]:
     """Report current parameters for z-axis.
 
-    Args:
-      param: 0 - current position, 5 - actual machine range
+    Param:
+    0   Report current position in 1/10 mm.
+    1   Report acceleration in 1/10 mm/s².
+    2   Report fast speed in 1/10 mm/s.
+    3   Report initialization speed in 1/10 mm.
+    4   Report initialization offset in 1/10 mm.
+    5   Report actual machine range in 1/10 mm.
+    6   Report deviation in encoder increments.
+    7   Report every time 0.
+    8   Report scale adjust factor.
+    9   Report slow speed in 1/10 mm/s.
+    10  Report axis scale factor.
+    11  Report target position in 1/10 mm.
+    12  Report travel position in 1/10 mm.
     """
 
     resp: List[int] = (

pylabrobot/liquid_handling/backends/tecan/EVO_tests.py

@@ -160,7 +160,7 @@ async def test_aspirate(self):
             3829,
             2051,
             90,
-            1455,
+            2100,
             2000,
             2000,
             2000,
@@ -214,7 +214,7 @@ async def test_aspirate(self):
         call(
           module="C5",
           command="SHZ",
-          params=[1455, 1455, 1455, 1455, 1455, 1455, 1455, 1455],
+          params=[2100, 2100, 2100, 2100, 2100, 2100, 2100, 2100],
         ),
         call(
           module="C5",

pylabrobot/resources/tecan/plate_carriers.py

@@ -23,7 +23,6 @@ def __init__(
     roma_x: Optional[float] = None,
     roma_y: Optional[float] = None,
     roma_z_safe: Optional[float] = None,
-    roma_z_travel: Optional[float] = None,
     roma_z_end: Optional[float] = None,
     sites: Optional[Dict[int, PlateHolder]] = None,
     category="tecan_plate_carrier",
@@ -44,7 +43,6 @@ def __init__(
     self.roma_x = roma_x
     self.roma_y = roma_y
     self.roma_z_safe = roma_z_safe
-    self.roma_z_travel = roma_z_travel
     self.roma_z_end = roma_z_end
 
 
@@ -106,7 +104,6 @@ def MP_3Pos_PCR(name: str) -> TecanPlateCarrier:
     roma_x=1876,
     roma_y=423,
     roma_z_safe=946,
-    roma_z_travel=1938,
     roma_z_end=2566,
     sites=create_homogeneous_resources(
       klass=PlateHolder,
@@ -136,7 +133,6 @@ def MP_3Pos_TePS(name: str) -> TecanPlateCarrier:
     roma_x=1876,
     roma_y=405,
     roma_z_safe=780,
-    roma_z_travel=2012,
     roma_z_end=2543,
     sites=create_homogeneous_resources(
       klass=PlateHolder,
@@ -166,7 +162,6 @@ def LI___MP_3Pos(name: str) -> TecanPlateCarrier:
     roma_x=1878,
     roma_y=423,
     roma_z_safe=946,
-    roma_z_travel=1938,
     roma_z_end=2537,
     sites=create_homogeneous_resources(
       klass=PlateHolder,
@@ -359,7 +354,6 @@ def MP_3Pos(name: str) -> TecanPlateCarrier:
     roma_x=1878,
     roma_y=423,
     roma_z_safe=946,
-    roma_z_travel=1938,
     roma_z_end=2537,
     sites=create_homogeneous_resources(
       klass=PlateHolder,
@@ -389,7 +383,6 @@ def MP_3Pos_Cooled(name: str) -> TecanPlateCarrier:
     roma_x=1810,
     roma_y=421,
     roma_z_safe=946,
-    roma_z_travel=1853,
     roma_z_end=2534,
     sites=create_homogeneous_resources(
       klass=PlateHolder,
@@ -418,7 +411,6 @@ def MP_3Pos_Fixed(name: str) -> TecanPlateCarrier:
     roma_x=1870,
     roma_y=420,
     roma_z_safe=946,
-    roma_z_travel=1938,
     roma_z_end=2537,
     sites=create_homogeneous_resources(
       klass=PlateHolder,
@@ -472,7 +464,6 @@ def MP_3Pos_Flat(name: str) -> TecanPlateCarrier:
     roma_x=2056,
     roma_y=441,
     roma_z_safe=610,
-    roma_z_travel=2418,
     roma_z_end=2503,
     sites=create_homogeneous_resources(
       klass=PlateHolder,
@@ -527,7 +518,6 @@ def MP_4Pos(name: str) -> TecanPlateCarrier:
     roma_x=1840,
     roma_y=386,
     roma_z_safe=946,
-    roma_z_travel=1938,
     roma_z_end=2476,
     sites=create_homogeneous_resources(
       klass=PlateHolder,
@@ -558,7 +548,6 @@ def MP_4Pos_flat(name: str) -> TecanPlateCarrier:
     roma_x=1835,
     roma_y=388,
     roma_z_safe=946,
-    roma_z_travel=1938,
     roma_z_end=2475,
     sites=create_homogeneous_resources(
       klass=PlateHolder,

pylabrobot/resources/tecan/plates.py

@@ -21,7 +21,6 @@ def __init__(
     size_x: float,
     size_y: float,
     size_z: float,
-    z_travel: float,
     z_start: float,
     z_dispense: float,
     z_max: float,
@@ -42,7 +41,6 @@ def __init__(
       model=model,
     )
 
-    self.z_travel = z_travel
     self.z_start = z_start
     self.z_dispense = z_dispense
     self.z_max = z_max
@@ -77,7 +75,6 @@ def Microplate_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
         with_lid=with_lid,
         lid_height=8,
         model="Microplate_96_Well",
-        z_travel=1750.0,
         z_start=1800.0,
         z_dispense=1970.0,
         z_max=2026.0,
@@ -104,7 +101,6 @@ def Microplate_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=7.6,
     lid=Microplate_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Microplate_96_Well",
-    z_travel=1900.0,
     z_start=1957.0,
     z_dispense=1975.0,
     z_max=2005.0,
@@ -146,7 +142,6 @@ def Microplate_portrait_96_Well(name: str, with_lid: bool = False) -> TecanPlate
     size_z=11.0,
     lid=Microplate_portrait_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Microplate_portrait_96_Well",
-    z_travel=1900.0,
     z_start=1940.0,
     z_dispense=1960.0,
     z_max=2050.0,
@@ -188,7 +183,6 @@ def DeepWell_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=39.0,
     lid=DeepWell_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="DeepWell_96_Well",
-    z_travel=1590.0,
     z_start=1670.0,
     z_dispense=1690.0,
     z_max=2060.0,
@@ -230,7 +224,6 @@ def HalfDeepWell_384_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=18.8,
     lid=HalfDeepWell_384_Well_Lid(name=name + "_lid") if with_lid else None,
     model="HalfDeepWell_384_Well",
-    z_travel=1789.0,
     z_start=1869.0,
     z_dispense=1889.0,
     z_max=2057.0,
@@ -272,7 +265,6 @@ def DeepWell_portait_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=38.0,
     lid=DeepWell_portait_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="DeepWell_portait_96_Well",
-    z_travel=1625.0,
     z_start=1670.0,
     z_dispense=1690.0,
     z_max=2050.0,
@@ -314,7 +306,6 @@ def Plate_portrait_384_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=11.0,
     lid=Plate_portrait_384_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Plate_portrait_384_Well",
-    z_travel=1900.0,
     z_start=1940.0,
     z_dispense=1960.0,
     z_max=2050.0,
@@ -356,7 +347,6 @@ def Macherey_Nagel_Plate_96_Well(name: str, with_lid: bool = False) -> TecanPlat
     size_z=29.9,
     lid=Macherey_Nagel_Plate_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Macherey_Nagel_Plate_96_Well",
-    z_travel=1514.0,
     z_start=1532.0,
     z_dispense=1578.0,
     z_max=1831.0,
@@ -398,7 +388,6 @@ def Qiagen_Plate_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=26.6,
     lid=Qiagen_Plate_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Qiagen_Plate_96_Well",
-    z_travel=1493.0,
     z_start=1541.0,
     z_dispense=1549.0,
     z_max=1807.0,
@@ -440,7 +429,6 @@ def AB_Plate_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=19.5,
     lid=AB_Plate_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="AB_Plate_96_Well",
-    z_travel=1772.0,
     z_start=1822.0,
     z_dispense=1837.0,
     z_max=2017.0,
@@ -482,7 +470,6 @@ def PCR_Plate_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=19.5,
     lid=PCR_Plate_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="PCR_Plate_96_Well",
-    z_travel=1857.0,
     z_start=1900.0,
     z_dispense=1915.0,
     z_max=2095.0,
@@ -524,7 +511,6 @@ def DeepWell_Greiner_1536_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=8.6,
     lid=DeepWell_Greiner_1536_Well_Lid(name=name + "_lid") if with_lid else None,
     model="DeepWell_Greiner_1536_Well",
-    z_travel=1946.0,
     z_start=1984.0,
     z_dispense=2004.0,
     z_max=2070.0,
@@ -566,7 +552,6 @@ def Hibase_Greiner_1536_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=5.4,
     lid=Hibase_Greiner_1536_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Hibase_Greiner_1536_Well",
-    z_travel=1946.0,
     z_start=1984.0,
     z_dispense=2004.0,
     z_max=2038.0,
@@ -608,7 +593,6 @@ def Lowbase_Greiner_1536_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=6.2,
     lid=Lowbase_Greiner_1536_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Lowbase_Greiner_1536_Well",
-    z_travel=1946.0,
     z_start=2024.0,
     z_dispense=2034.0,
     z_max=2086.0,
@@ -650,7 +634,6 @@ def Separation_Plate_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=26.6,
     lid=Separation_Plate_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Separation_Plate_96_Well",
-    z_travel=1493.0,
     z_start=1541.0,
     z_dispense=1549.0,
     z_max=1807.0,
@@ -692,7 +675,6 @@ def DeepWell_square_96_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=39.0,
     lid=DeepWell_square_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="DeepWell_square_96_Well",
-    z_travel=1590.0,
     z_start=1670.0,
     z_dispense=1690.0,
     z_max=2060.0,
@@ -734,7 +716,6 @@ def CaCo2_Plate_24_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=6.5,
     lid=CaCo2_Plate_24_Well_Lid(name=name + "_lid") if with_lid else None,
     model="CaCo2_Plate_24_Well",
-    z_travel=1774.0,
     z_start=1960.0,
     z_dispense=2007.0,
     z_max=2025.0,
@@ -777,7 +758,6 @@ def Plate_384_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=12.1,
     lid=Plate_384_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Plate_384_Well",
-    z_travel=1900.0,
     z_start=1940.0,
     z_dispense=1960.0,
     z_max=2061.0,
@@ -820,7 +800,6 @@ def Microplate_24_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=17.6,
     lid=Microplate_24_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Microplate_24_Well",
-    z_travel=1841.0,
     z_start=1885.0,
     z_dispense=1917.0,
     z_max=2061.0,
@@ -862,7 +841,6 @@ def TecanExtractionPlate_96_Well(name: str, with_lid: bool = False) -> TecanPlat
     size_z=23.0,
     lid=TecanExtractionPlate_96_Well_Lid(name=name + "_lid") if with_lid else None,
     model="TecanExtractionPlate_96_Well",
-    z_travel=1793.0,
     z_start=1831.0,
     z_dispense=1910.0,
     z_max=2061.0,
@@ -905,7 +883,6 @@ def Microplate_48_Well(name: str, with_lid: bool = False) -> TecanPlate:
     size_z=17.3,
     lid=Microplate_48_Well_Lid(name=name + "_lid") if with_lid else None,
     model="Microplate_48_Well",
-    z_travel=1839.0,
     z_start=1887.0,
     z_dispense=1921.0,
     z_max=2060.0,