clearly differentiate between local and absolute size (#235)

Author: rickwierenga

Diff for: CHANGELOG.md

@@ -32,6 +32,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `material_z_thickness` of a `Container` is used in computing its bottom (https://github.com/PyLabRobot/pylabrobot/pull/205/)
 - Default `pickup_distance_from_top` in `LiquidHandler.{move_plate,move_lid}` were lowered by 3.33 (https://github.com/PyLabRobot/pylabrobot/pull/205/)
 - `PlateCarrierSite` can now take `ResourceStack` as a child, as long as the children are `Plate`s (https://github.com/PyLabRobot/pylabrobot/pull/226)
+- `Resource.get_size_{x,y,z}` now return the size of the resource in local space, not absolute space (https://github.com/PyLabRobot/pylabrobot/pull/235)
+- `Resource.center` now returns the center of the resource in local space, not absolute space (https://github.com/PyLabRobot/pylabrobot/pull/235)
 
 ### Added
 
@@ -57,6 +59,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `size_z` and `nesting_z_height` for `Cor_96_wellplate_360ul_Fb_Lid` (https://github.com/PyLabRobot/pylabrobot/pull/226)
 - `NestedTipRack` (https://github.com/PyLabRobot/pylabrobot/pull/228)
 - `HTF_L_ULTRAWIDE`, `ultrawide_high_volume_tip_with_filter` (https://github.com/PyLabRobot/pylabrobot/pull/229/)
+- `get_absolute_size_x`, `get_absolute_size_y`, `get_absolute_size_z` for `Resource` (https://github.com/PyLabRobot/pylabrobot/pull/235)
 
 ### Deprecated
 

Diff for: pylabrobot/liquid_handling/backends/hamilton/STAR.py

@@ -11,6 +11,7 @@
 import re
 from typing import Callable, Dict, List, Literal, Optional, Sequence, Type, TypeVar, Union, cast
 
+from pylabrobot import audio
 from pylabrobot.liquid_handling.backends.hamilton.base import HamiltonLiquidHandler
 from pylabrobot.liquid_handling.errors import ChannelizedError
 from pylabrobot.liquid_handling.liquid_classes.hamilton import (
@@ -39,7 +40,8 @@
 from pylabrobot.resources.hamilton.hamilton_decks import STAR_SIZE_X, STARLET_SIZE_X
 from pylabrobot.resources.liquid import Liquid
 from pylabrobot.resources.ml_star import HamiltonTip, TipDropMethod, TipPickupMethod, TipSize
-from pylabrobot import audio
+from pylabrobot.resources.utils import get_child_location
+from pylabrobot.utils.linalg import matrix_vector_multiply_3x3
 
 T = TypeVar("T")
 
@@ -1583,7 +1585,7 @@ async def aspirate(
                               for wb, op in zip(well_bottoms, ops)]
     if lld_search_height is None:
       lld_search_height = [
-        (wb + op.resource.get_size_z() + (2.7 if isinstance(op.resource, Well) else 5)) # ?
+        (wb + op.resource.get_absolute_size_z() + (2.7 if isinstance(op.resource, Well) else 5)) # ?
         for wb, op in zip(well_bottoms, ops)
       ]
     else:
@@ -1845,7 +1847,7 @@ async def dispense(
       [ls + (op.liquid_height or 0) for ls, op in zip(well_bottoms, ops)]
     if lld_search_height is None:
       lld_search_height = [
-        (wb + op.resource.get_size_z() + (2.7 if isinstance(op.resource, Well) else 5)) #?
+        (wb + op.resource.get_absolute_size_z() + (2.7 if isinstance(op.resource, Well) else 5)) #?
         for wb, op in zip(well_bottoms, ops)
       ]
     else:
@@ -2378,11 +2380,11 @@ async def iswap_pick_up_resource(
 
     # Get center of source plate. Also gripping height and plate width.
     center = resource.get_absolute_location(x="c", y="c", z="b") + offset
-    grip_height = center.z + resource.get_size_z() - pickup_distance_from_top
+    grip_height = center.z + resource.get_absolute_size_z() - pickup_distance_from_top
     if grip_direction in (GripDirection.FRONT, GripDirection.BACK):
-      plate_width = resource.get_size_x()
+      plate_width = resource.get_absolute_size_x()
     elif grip_direction in (GripDirection.RIGHT, GripDirection.LEFT):
-      plate_width = resource.get_size_y()
+      plate_width = resource.get_absolute_size_y()
     else:
       raise ValueError("Invalid grip direction")
 
@@ -2435,7 +2437,7 @@ async def iswap_move_picked_up_resource(
       x_direction=0,
       y_position=round(center.y * 10),
       y_direction=0,
-      z_position=round((location.z + resource.get_size_z() / 2) * 10),
+      z_position=round((location.z + resource.get_absolute_size_z() / 2) * 10),
       z_direction=0,
       grip_direction={
         GripDirection.FRONT: 1,
@@ -2476,15 +2478,24 @@ async def iswap_release_picked_up_resource(
 
     assert self.iswap_installed, "iswap must be installed"
 
-    # Get center of source plate. Also gripping height and plate width.
-    center = location + resource.rotated(z=rotation).center() + offset
-    grip_height = center.z + resource.get_size_z() - pickup_distance_from_top
+    # Get center of source plate in absolute space.
+    # The computation of the center has to be rotated so that the offset is in absolute space.
+    center_in_absolute_space = Coordinate(*matrix_vector_multiply_3x3(
+      resource.rotated(z=rotation).get_absolute_rotation().get_rotation_matrix(),
+      resource.center().vector()
+    ))
+    # This is when the resource is rotated (around its origin), but we also need to translate
+    # so that the left front bottom corner of the plate is lfb in absolute space, not local.
+    center_in_absolute_space += get_child_location(resource.rotated(z=rotation))
+
+    center = location + center_in_absolute_space + offset
+    grip_height = center.z + resource.get_absolute_size_z() - pickup_distance_from_top
     # grip_direction here is the put_direction. We use `rotation` to cancel it out and get the
     # original grip direction. Hack.
     if grip_direction in (GripDirection.FRONT, GripDirection.BACK):
-      plate_width = resource.rotated(z=rotation).get_size_x()
+      plate_width = resource.rotated(z=rotation).get_absolute_size_x()
     elif grip_direction in (GripDirection.RIGHT, GripDirection.LEFT):
-      plate_width = resource.rotated(z=rotation).get_size_y()
+      plate_width = resource.rotated(z=rotation).get_absolute_size_y()
     else:
       raise ValueError("Invalid grip direction")
 
@@ -2540,8 +2551,8 @@ async def core_pick_up_resource(
 
     # Get center of source plate. Also gripping height and plate width.
     center = resource.get_absolute_location(x="c", y="c", z="b") + offset
-    grip_height = center.z + resource.get_size_z() - pickup_distance_from_top
-    grip_width = resource.get_size_y() #grip width is y size of resource
+    grip_height = center.z + resource.get_absolute_size_z() - pickup_distance_from_top
+    grip_width = resource.get_absolute_size_y() #grip width is y size of resource
 
     if self.core_parked:
       await self.get_core(p1=channel_1, p2=channel_2)
@@ -2625,8 +2636,8 @@ async def core_release_picked_up_resource(
 
     # Get center of destination location. Also gripping height and plate width.
     center = location + resource.center() + offset
-    grip_height = center.z + resource.get_size_z() - pickup_distance_from_top
-    grip_width = resource.get_size_y()
+    grip_height = center.z + resource.get_absolute_size_z() - pickup_distance_from_top
+    grip_width = resource.get_absolute_size_y()
 
     await self.core_put_plate(
       x_position=round(center.x * 10),
@@ -2691,7 +2702,7 @@ async def move_resource(
 
     previous_location = move.resource.get_absolute_location() + move.resource_offset
     minimum_traverse_height = 284.0
-    previous_location.z = minimum_traverse_height - move.resource.get_size_z() / 2
+    previous_location.z = minimum_traverse_height - move.resource.get_absolute_size_z() / 2
 
     for location in move.intermediate_locations:
       if use_arm == "iswap":
@@ -2793,9 +2804,9 @@ async def core_check_resource_exists_at_location_center(
       """
 
     center = location + resource.centers()[0] + offset
-    y_width_to_gripper_bump = resource.get_size_y() - gripper_y_margin*2
-    assert 9 <= y_width_to_gripper_bump <= round(resource.get_size_y()), \
-      f"width between channels must be between 9 and {resource.get_size_y()} mm" \
+    y_width_to_gripper_bump = resource.get_absolute_size_y() - gripper_y_margin*2
+    assert 9 <= y_width_to_gripper_bump <= round(resource.get_absolute_size_y()), \
+      f"width between channels must be between 9 and {resource.get_absolute_size_y()} mm" \
       " (i.e. the minimal distance between channels and the max y size of the resource"
 
     # Check if CoRe gripper currently in use
@@ -4325,7 +4336,7 @@ async def get_core(self, p1: int, p2: int):
     # This appears to be deck.get_size_x() - 562.5, but let's keep an explicit check so that we
     # can catch unknown deck sizes. Can the grippers exist at another location? If so, define it as
     # a resource on the robot deck and use deck.get_resource().get_absolute_location().
-    deck_size = self.deck.get_size_x()
+    deck_size = self.deck.get_absolute_size_x()
     if deck_size == STARLET_SIZE_X:
       xs = 7975 # 1360-797.5 = 562.5
     elif deck_size == STAR_SIZE_X:
@@ -4354,7 +4365,7 @@ async def get_core(self, p1: int, p2: int):
   async def put_core(self):
     """ Put CoRe gripper tool at wasteblock mount. """
     assert self.deck is not None, "must have deck defined to access CoRe grippers"
-    deck_size = self.deck.get_size_x()
+    deck_size = self.deck.get_absolute_size_x()
     if deck_size == STARLET_SIZE_X:
       xs = 7975
     elif deck_size == STAR_SIZE_X:
@@ -5591,7 +5602,7 @@ async def unload_carrier(self, carrier: Carrier):
     """ Use autoload to unload carrier. """
     # Identify carrier end rail
     track_width = 22.5
-    carrier_width = carrier.get_absolute_location().x - 100  + carrier.get_size_x()
+    carrier_width = carrier.get_absolute_location().x - 100  + carrier.get_absolute_size_x()
     carrier_end_rail = int(carrier_width / track_width)
     assert 1 <= carrier_end_rail <= 54, "carrier loading rail must be between 1 and 54"
 
@@ -5655,7 +5666,7 @@ async def load_carrier(
     }
     # Identify carrier end rail
     track_width = 22.5
-    carrier_width = carrier.get_absolute_location().x - 100  + carrier.get_size_x()
+    carrier_width = carrier.get_absolute_location().x - 100  + carrier.get_absolute_size_x()
     carrier_end_rail = int(carrier_width / track_width)
     assert 1 <= carrier_end_rail <= 54, "carrier loading rail must be between 1 and 54"
 

Diff for: pylabrobot/liquid_handling/backends/hamilton/STAR_tests.py

@@ -637,8 +637,8 @@ async def test_iswap_plate_reader(self):
                 "xs#####xd#yj####yd#zj####zd#th####te####go####gr#ga#")
 
     assert self.plate.rotation.z == 270
-    self.assertAlmostEqual(self.plate.get_size_x(), 85.48, places=2)
-    self.assertAlmostEqual(self.plate.get_size_y(), 127.76, places=2)
+    self.assertAlmostEqual(self.plate.get_absolute_size_x(), 85.48, places=2)
+    self.assertAlmostEqual(self.plate.get_absolute_size_y(), 127.76, places=2)
 
     await self.lh.move_plate(plate_reader.get_plate(), self.plt_car[0],
       pickup_distance_from_top=8.2-3.33, get_direction=GripDirection.LEFT,

Diff for: pylabrobot/liquid_handling/backends/hamilton/vantage.py

@@ -628,7 +628,7 @@ async def aspirate(
     liquid_surfaces_no_lld = liquid_surface_at_function_without_lld or [wb + (op.liquid_height or 0)
                               for wb, op in zip(well_bottoms, ops)]
     # -1 compared to STAR?
-    lld_search_heights = lld_search_height or [wb + op.resource.get_size_z() + \
+    lld_search_heights = lld_search_height or [wb + op.resource.get_absolute_size_z() + \
                           (2.7-1 if isinstance(op.resource, Well) else 5) #?
                           for wb, op in zip(well_bottoms, ops)]
 
@@ -793,7 +793,7 @@ async def dispense(
     liquid_surfaces_no_lld = [wb + (op.liquid_height or 0)
                               for wb, op in zip(well_bottoms, ops)]
     # -1 compared to STAR?
-    lld_search_heights = lld_search_height or [wb + op.resource.get_size_z() + \
+    lld_search_heights = lld_search_height or [wb + op.resource.get_absolute_size_z() + \
                           (2.7-1 if isinstance(op.resource, Well) else 5) #?
                           for wb, op in zip(well_bottoms, ops)]
 
@@ -964,12 +964,12 @@ async def aspirate96(
         aspiration.offset + Coordinate(z=top_left_well.material_z_thickness)
       # -1 compared to STAR?
       well_bottoms = position.z
-      lld_search_height = well_bottoms + top_left_well.get_size_z() + 2.7-1
+      lld_search_height = well_bottoms + top_left_well.get_absolute_size_z() + 2.7-1
     else:
       position = aspiration.container.get_absolute_location(y="b") + aspiration.offset + \
         Coordinate(z=aspiration.container.material_z_thickness)
       bottom = position.z
-      lld_search_height = bottom + aspiration.container.get_size_z() + 2.7-1
+      lld_search_height = bottom + aspiration.container.get_absolute_size_z() + 2.7-1
 
     liquid_height = position.z + (aspiration.liquid_height or 0)
 
@@ -1095,12 +1095,12 @@ async def dispense96(
         dispense.offset + Coordinate(z=top_left_well.material_z_thickness)
       # -1 compared to STAR?
       well_bottoms = position.z
-      lld_search_height = well_bottoms + top_left_well.get_size_z() + 2.7-1
+      lld_search_height = well_bottoms + top_left_well.get_absolute_size_z() + 2.7-1
     else:
       position = dispense.container.get_absolute_location(y="b") + dispense.offset + \
         Coordinate(z=dispense.container.material_z_thickness)
       bottom = position.z
-      lld_search_height = bottom + dispense.container.get_size_z() + 2.7-1
+      lld_search_height = bottom + dispense.container.get_absolute_size_z() + 2.7-1
 
     liquid_height = position.z + (dispense.liquid_height or 0) + 10
 
@@ -1202,8 +1202,8 @@ async def pick_up_resource(
     allows you to pick up and move a resource with a single command. """
 
     center = resource.get_absolute_location() + resource.center() + offset
-    grip_height = center.z + resource.get_size_z() - pickup_distance_from_top
-    plate_width = resource.get_size_x()
+    grip_height = center.z + resource.get_absolute_size_z() - pickup_distance_from_top
+    plate_width = resource.get_absolute_size_x()
 
     await self.ipg_grip_plate(
       x_position=round(center.x * 10),
@@ -1247,8 +1247,8 @@ async def release_picked_up_resource(
     """
 
     center = destination + resource.center() + offset
-    grip_height = center.z + resource.get_size_z() - pickup_distance_from_top
-    plate_width = resource.get_size_x()
+    grip_height = center.z + resource.get_absolute_size_z() - pickup_distance_from_top
+    plate_width = resource.get_absolute_size_x()
 
     await self.ipg_put_plate(
       x_position=round(center.x * 10),

Diff for: pylabrobot/liquid_handling/backends/opentrons_backend.py

@@ -191,14 +191,14 @@ def _get_volume(well: Resource) -> float:
 
     well_definitions = {
       child.name: {
-        "depth": child.get_size_z(),
-        "x": cast(Coordinate, child.location).x + child.get_size_x() / 2,
-        "y": cast(Coordinate, child.location).y + child.get_size_y() / 2,
+        "depth": child.get_absolute_size_z(),
+        "x": cast(Coordinate, child.location).x + child.get_absolute_size_x() / 2,
+        "y": cast(Coordinate, child.location).y + child.get_absolute_size_y() / 2,
         "z": cast(Coordinate, child.location).z,
         "shape": "circular",
 
         # inscribed circle has diameter equal to the width of the well
-        "diameter": child.get_size_x(),
+        "diameter": child.get_absolute_size_x(),
 
         # Opentrons requires `totalLiquidVolume`, even for tip racks!
         "totalLiquidVolume": _get_volume(child),
@@ -247,9 +247,9 @@ def _get_volume(well: Resource) -> float:
         "z": 0
       },
       "dimensions":{
-        "xDimension": resource.get_size_x(),
-        "yDimension": resource.get_size_y(),
-        "zDimension": resource.get_size_z(),
+        "xDimension": resource.get_absolute_size_x(),
+        "yDimension": resource.get_absolute_size_y(),
+        "zDimension": resource.get_absolute_size_z(),
       },
       "wells": well_definitions,
       "groups": [

Diff for: pylabrobot/liquid_handling/backends/tecan/EVO.py

@@ -320,7 +320,7 @@ async def aspirate(
     for op, tlc in zip(ops, tecan_liquid_classes):
       op.volume = tlc.compute_corrected_volume(op.volume) if tlc is not None else op.volume
 
-    ys = int(ops[0].resource.get_size_y() * 10)
+    ys = int(ops[0].resource.get_absolute_size_y() * 10)
     zadd: List[Optional[int]] = [0] * self.num_channels
     for i, channel in enumerate(use_channels):
       par = ops[i].resource.parent
@@ -397,7 +397,7 @@ async def dispense(
     """
 
     x_positions, y_positions, z_positions = self._liha_positions(ops, use_channels)
-    ys = int(ops[0].resource.get_size_y() * 10)
+    ys = int(ops[0].resource.get_absolute_size_y() * 10)
 
     tecan_liquid_classes = [
       get_liquid_class(
@@ -443,7 +443,7 @@ async def pick_up_tips(
     x_positions, y_positions, _ = self._liha_positions(ops, use_channels)
 
     # move channels
-    ys = int(ops[0].resource.get_size_y() * 10)
+    ys = int(ops[0].resource.get_absolute_size_y() * 10)
     x, _ = self._first_valid(x_positions)
     y, yi = self._first_valid(y_positions)
     assert x is not None and y is not None
@@ -517,7 +517,7 @@ async def move_resource(self, move: Move):
 
     z_range = await self.roma.report_z_param(5)
     x, y, z = self._roma_positions(move.resource, move.resource.get_absolute_location(), z_range)
-    h = int(move.resource.get_size_y() * 10)
+    h = int(move.resource.get_absolute_size_y() * 10)
     xt, yt, zt = self._roma_positions(move.resource, move.destination, z_range)
 
     # move to resource
@@ -778,7 +778,7 @@ def _roma_positions(
       or par.roma_z_travel is None or par.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_size_y())) * 10 + par.roma_y)
+    y_position = int((347.1 - (offset.y + resource.get_absolute_size_y())) * 10 + par.roma_y)
     z_positions = {
       "safe": z_range - int(par.roma_z_safe),
       "travel": z_range - int(par.roma_z_travel - offset.z * 10),

Diff for: pylabrobot/liquid_handling/liquid_handler.py

@@ -1378,7 +1378,8 @@ async def aspirate96(
     blow_out_air_volume = float(blow_out_air_volume) if blow_out_air_volume is not None else None
 
     if isinstance(resource, Container):
-      if resource.get_size_x() < 108.0 or resource.get_size_y() < 70.0:  # TODO: analyze as attr
+      if resource.get_absolute_size_x() < 108.0 or \
+        resource.get_absolute_size_y() < 70.0:  # TODO: analyze as attr
         raise ValueError("Container too small to accommodate 96 head")
 
       for channel in self.head96.values():
@@ -1519,7 +1520,8 @@ async def dispense96(
     blow_out_air_volume = float(blow_out_air_volume) if blow_out_air_volume is not None else None
 
     if isinstance(resource, Container):
-      if resource.get_size_x() < 108.0 or resource.get_size_y() < 70.0:  # TODO: analyze as attr
+      if resource.get_absolute_size_x() < 108.0 or \
+        resource.get_absolute_size_y() < 70.0:  # TODO: analyze as attr
         raise ValueError("Container too small to accommodate 96 head")
 
       for channel in self.head96.values():
@@ -1753,7 +1755,7 @@ async def move_lid(
       to_location = Coordinate(
         x=to_location.x,
         y=to_location.y,
-        z=to_location.z  + to.get_size_z() - lid.nesting_z_height)
+        z=to_location.z  + to.get_absolute_size_z() - lid.nesting_z_height)
     elif isinstance(to, ResourceStack):
       assert to.direction == "z", "Only ResourceStacks with direction 'z' are currently supported"
       to_location = to.get_absolute_location(z="top")