opentrons 8.6.0a1__py3-none-any.whl

opentrons/hardware_control/modules/utils.py

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+import asyncio
+import logging
+from typing import Dict, Optional, Type
+
+from opentrons.drivers.rpi_drivers.types import USBPort
+
+from ..execution_manager import ExecutionManager
+
+from .types import ModuleDisconnectedCallback, ModuleType, SpeedStatus
+from .mod_abc import AbstractModule
+from .tempdeck import TempDeck
+from .magdeck import MagDeck
+from .thermocycler import Thermocycler
+from .heater_shaker import HeaterShaker
+from .absorbance_reader import AbsorbanceReader
+from .flex_stacker import FlexStacker
+
+
+log = logging.getLogger(__name__)
+
+
+# TODO (lc 05-12-2021) This is pretty gross. We should think
+# of a better way to do this.
+MODULE_TYPE_BY_NAME = {
+    MagDeck.name(): MagDeck.MODULE_TYPE,
+    TempDeck.name(): TempDeck.MODULE_TYPE,
+    Thermocycler.name(): Thermocycler.MODULE_TYPE,
+    HeaterShaker.name(): HeaterShaker.MODULE_TYPE,
+    AbsorbanceReader.name(): AbsorbanceReader.MODULE_TYPE,
+    FlexStacker.name(): FlexStacker.MODULE_TYPE,
+}
+
+_MODULE_CLS_BY_TYPE: Dict[ModuleType, Type[AbstractModule]] = {
+    MagDeck.MODULE_TYPE: MagDeck,
+    TempDeck.MODULE_TYPE: TempDeck,
+    Thermocycler.MODULE_TYPE: Thermocycler,
+    HeaterShaker.MODULE_TYPE: HeaterShaker,
+    AbsorbanceReader.MODULE_TYPE: AbsorbanceReader,
+    FlexStacker.MODULE_TYPE: FlexStacker,
+}
+
+
+async def build(
+    port: str,
+    type: ModuleType,
+    simulating: bool,
+    usb_port: USBPort,
+    hw_control_loop: asyncio.AbstractEventLoop,
+    execution_manager: Optional[ExecutionManager] = None,
+    sim_model: Optional[str] = None,
+    sim_serial_number: Optional[str] = None,
+    disconnected_callback: ModuleDisconnectedCallback = None,
+) -> AbstractModule:
+    return await _MODULE_CLS_BY_TYPE[type].build(
+        port=port,
+        usb_port=usb_port,
+        simulating=simulating,
+        hw_control_loop=hw_control_loop,
+        execution_manager=execution_manager,
+        sim_model=sim_model,
+        sim_serial_number=sim_serial_number,
+        disconnected_callback=disconnected_callback,
+    )
+
+
+async def disable_module(module: AbstractModule) -> None:
+    """Async function to deactivate a module immediately, for error recovery."""
+    if isinstance(module, HeaterShaker):
+        await module.deactivate_heater(must_be_running=False)
+        if module.speed_status != SpeedStatus.IDLE:
+            await module.deactivate_shaker(must_be_running=False)
+    else:
+        await module.deactivate(must_be_running=False)

opentrons/hardware_control/motion_utilities.py

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+"""Utilities for calculating motion correctly."""
+from logging import getLogger
+
+from functools import lru_cache
+from typing import Callable, Dict, Union, Optional, cast
+from collections import OrderedDict
+
+from opentrons_shared_data.robot.types import RobotType
+
+from opentrons.types import Mount, Point
+from opentrons.calibration_storage.types import AttitudeMatrix
+from opentrons.util import linal
+
+from .types import Axis, OT3Mount
+
+log = getLogger(__name__)
+
+# TODO: The offset_for_mount function should be defined with an overload
+# set, as with other functions in this module. Unfortunately, mypy < 0.920
+# has an internal crash when you mix overloads and particular kinds of decorators
+# ( https://github.com/python/mypy/pull/11630 fixes it ) so instead it's defined
+# with unions and therefore requires a bit of casting.
+# @overload
+# def offset_for_mount(
+#     primary_mount: Mount,
+#     left_mount_offset: Point,
+#     right_mount_offset: Point,
+#     gripper_mount_offset: None,
+# ) -> Point:
+#     ...
+
+
+# @overload
+# def offset_for_mount(
+#     primary_mount: OT3Mount,
+#     left_mount_offset: Point,
+#     right_mount_offset: Point,
+#     gripper_mount_offset: Point,
+# ) -> Point:
+#     ...
+
+EMPTY_ORDERED_DICT = OrderedDict(
+    (
+        (Axis.X, 0.0),
+        (Axis.Y, 0.0),
+        (Axis.Z_L, 0.0),
+        (Axis.Z_R, 0.0),
+        (Axis.Z_G, 0.0),
+        (Axis.P_L, 0.0),
+        (Axis.P_R, 0.0),
+        (Axis.Q, 0.0),
+    )
+)
+
+
+@lru_cache(4)
+def offset_for_mount(
+    primary_mount: Union[OT3Mount, Mount],
+    left_mount_offset: Point,
+    right_mount_offset: Point,
+    gripper_mount_offset: Optional[Point] = None,
+) -> Point:
+    offsets = {
+        Mount.LEFT: left_mount_offset,
+        Mount.RIGHT: right_mount_offset,
+        OT3Mount.LEFT: left_mount_offset,
+        OT3Mount.RIGHT: right_mount_offset,
+        OT3Mount.GRIPPER: cast(Point, gripper_mount_offset),
+    }
+    return offsets[primary_mount]
+
+
+def target_position_from_absolute(
+    mount: Union[Mount, OT3Mount],
+    abs_position: Point,
+    get_critical_point: Callable[[Union[Mount, OT3Mount]], Point],
+    left_mount_offset: Point,
+    right_mount_offset: Point,
+    gripper_mount_offset: Optional[Point] = None,
+) -> "OrderedDict[Axis, float]":
+    """Create a target position for all specified machine axes."""
+    offset = offset_for_mount(
+        mount, left_mount_offset, right_mount_offset, gripper_mount_offset
+    )
+    primary_cp = get_critical_point(mount)
+    primary_z = Axis.by_mount(mount)
+
+    target_position = OrderedDict(
+        (
+            (Axis.X, abs_position.x - offset.x - primary_cp.x),
+            (Axis.Y, abs_position.y - offset.y - primary_cp.y),
+            (primary_z, abs_position.z - offset.z - primary_cp.z),
+        )
+    )
+    return target_position
+
+
+def target_position_from_relative(
+    mount: Union[Mount, OT3Mount],
+    delta: Point,
+    current_position: Dict[Axis, float],
+) -> "OrderedDict[Axis, float]":
+    """Create a target position for all specified machine axes."""
+    primary_z = Axis.by_mount(mount)
+    x_ax = Axis.X
+    y_ax = Axis.Y
+    target_position = OrderedDict(
+        (
+            (x_ax, current_position[x_ax] + delta[0]),
+            (y_ax, current_position[y_ax] + delta[1]),
+            (primary_z, current_position[primary_z] + delta[2]),
+        )
+    )
+    return target_position
+
+
+def target_axis_map_from_absolute(
+    primary_mount: Union[OT3Mount, Mount],
+    axis_map: Dict[Axis, float],
+    get_critical_point: Callable[[Union[Mount, OT3Mount]], Point],
+    left_mount_offset: Point,
+    right_mount_offset: Point,
+    gripper_mount_offset: Optional[Point] = None,
+) -> "OrderedDict[Axis, float]":
+    """Create an absolute target position for all specified machine axes."""
+    keys_for_target_position = list(axis_map.keys())
+
+    offset = offset_for_mount(
+        primary_mount, left_mount_offset, right_mount_offset, gripper_mount_offset
+    )
+    primary_cp = get_critical_point(primary_mount)
+    primary_z = Axis.by_mount(primary_mount)
+    target_position = OrderedDict()
+
+    if Axis.X in keys_for_target_position:
+        target_position[Axis.X] = axis_map[Axis.X] - offset.x - primary_cp.x
+    if Axis.Y in keys_for_target_position:
+        target_position[Axis.Y] = axis_map[Axis.Y] - offset.y - primary_cp.y
+    if primary_z in keys_for_target_position:
+        # Since this function is intended to be used in conjunction with `API.move_axes`
+        # we must leave out the carriage offset subtraction from the target position as
+        # `move_axes` already does this calculation.
+        target_position[primary_z] = axis_map[primary_z] - primary_cp.z
+
+    target_position.update(
+        {ax: val for ax, val in axis_map.items() if ax not in Axis.gantry_axes()}
+    )
+    return target_position
+
+
+def target_axis_map_from_relative(
+    axis_map: Dict[Axis, float],
+    current_position: Dict[Axis, float],
+) -> "OrderedDict[Axis, float]":
+    """Create a target position for all specified machine axes."""
+    target_position = OrderedDict(
+        (
+            (ax, current_position[ax] + axis_map[ax])
+            for ax in EMPTY_ORDERED_DICT.keys()
+            if ax in axis_map.keys()
+        )
+    )
+    log.info(f"Current position {current_position} and axis map delta {axis_map}")
+    log.info(f"Relative move target {target_position}")
+    return target_position
+
+
+def target_position_from_plunger(
+    mount: Union[Mount, OT3Mount],
+    delta: float,
+    current_position: Dict[Axis, float],
+) -> "OrderedDict[Axis, float]":
+    """Create a target position for machine axes including plungers.
+
+    Axis positions other than the plunger are identical to current
+    position.
+    """
+    x_ax = Axis.X
+    y_ax = Axis.Y
+    all_axes_pos = OrderedDict(
+        (
+            (x_ax, current_position[x_ax]),
+            (y_ax, current_position[y_ax]),
+        )
+    )
+    plunger_pos = OrderedDict()
+    z_ax = Axis.by_mount(mount)
+    plunger = Axis.of_main_tool_actuator(mount)
+    all_axes_pos[z_ax] = current_position[z_ax]
+    plunger_pos[plunger] = delta
+    all_axes_pos.update(plunger_pos)
+    return all_axes_pos
+
+
+def target_positions_from_plunger_tracking(
+    mount: Union[Mount, OT3Mount],
+    plunger_delta: float,
+    z_delta: float,
+    current_position: Dict[Axis, float],
+) -> "OrderedDict[Axis, float]":
+    """Create a target position for machine axes including plungers for dynamic liquid tracking.
+
+    The x/y axes remain constant but the plunger and Z move to create a tracking action.
+
+    plunger_delta: the distance the plunger should move- should be determined based on desired
+    volume to aspirate/dispense.
+    z_delta: the distance to move the z axis- should be determined based on volume and well geometry.
+    """
+    all_axes_pos = target_position_from_plunger(mount, plunger_delta, current_position)
+    z_ax = Axis.by_mount(mount)
+    all_axes_pos[z_ax] = current_position[z_ax] + z_delta
+    return all_axes_pos
+
+
+def deck_point_from_machine_point(
+    machine_point: Point, attitude: AttitudeMatrix, offset: Point
+) -> Point:
+    return Point(
+        *linal.apply_reverse(
+            attitude,
+            machine_point - offset,
+        )
+    )
+
+
+def machine_point_from_deck_point(
+    deck_point: Point, attitude: AttitudeMatrix, offset: Point
+) -> Point:
+    return Point(*linal.apply_transform(attitude, deck_point)) + offset
+
+
+def machine_from_deck(
+    deck_pos: Dict[Axis, float],
+    attitude: AttitudeMatrix,
+    offset: Point,
+    robot_type: RobotType,
+) -> Dict[Axis, float]:
+    """Build a machine-axis position from a deck position"""
+    try:
+        mount_axes = (
+            Axis.ot2_mount_axes()
+            if robot_type == "OT-2 Standard"
+            else Axis.ot3_mount_axes()
+        )
+        point_for_z_axis = {
+            axe: Point(x=deck_pos[type(axe).X], y=deck_pos[type(axe).Y], z=pos)
+            for axe, pos in deck_pos.items()
+            if axe in mount_axes
+        }
+    except KeyError:
+        raise ValueError(
+            "Moves must specify either exactly an x, y, and (z or a) or none of them"
+        )
+
+    # Pre-fill the dict we’ll send to the backend with the axes we don’t
+    # need to transform
+    machine_pos = {
+        ax: pos for ax, pos in deck_pos.items() if ax not in ax.gantry_axes()
+    }
+
+    transformed = {
+        axes: machine_point_from_deck_point(deck_point, attitude, offset)
+        for axes, deck_point in point_for_z_axis.items()
+    }
+
+    to_check = {}
+    for axis, point in transformed.items():
+        to_check[axis] = point.z
+        to_check[type(axis).X] = point.x
+        to_check[type(axis).Y] = point.y
+
+    machine_pos.update({ax: pos for ax, pos in to_check.items()})
+    return machine_pos
+
+
+def deck_from_machine(
+    machine_pos: Dict[Axis, float],
+    attitude: AttitudeMatrix,
+    offset: Point,
+    robot_type: RobotType,
+) -> Dict[Axis, float]:
+    """Build a deck-abs position store from the machine's position"""
+    plunger_axes: Dict[Axis, float] = {
+        k: v for k, v in machine_pos.items() if k not in k.gantry_axes()
+    }
+    mount_axes: Dict[Axis, float]
+    to_mount: Callable[[Axis], Union[Mount, OT3Mount]]
+    if robot_type == "OT-2 Standard":
+        mount_axes = {k: v for k, v in machine_pos.items() if k in k.ot2_mount_axes()}
+        to_mount = Axis.to_ot2_mount
+    else:
+        mount_axes = {k: v for k, v in machine_pos.items() if k in k.ot3_mount_axes()}
+        to_mount = Axis.to_ot3_mount
+    deck_positions_by_mount = {
+        to_mount(axis): deck_point_from_machine_point(
+            Point(machine_pos[Axis.X], machine_pos[Axis.Y], value),
+            attitude,
+            offset,
+        )
+        for axis, value in mount_axes.items()
+    }
+    position_for_gantry = next(iter(deck_positions_by_mount.values()))
+    deck_pos = {
+        Axis.X: position_for_gantry[0],
+        Axis.Y: position_for_gantry[1],
+    }
+    for mount, pos in deck_positions_by_mount.items():
+        deck_pos[Axis.by_mount(mount)] = pos[2]
+
+    deck_pos.update(plunger_axes)
+    return deck_pos
+
+
+def machine_vector_from_deck_vector(
+    machine_vector: Point, attitude: AttitudeMatrix
+) -> Point:
+    """Take a vector and pass it through the attitude matrix."""
+    return machine_point_from_deck_point(machine_vector, attitude, Point(0, 0, 0))