add cytomat (#332)

.vscode/settings.json

@@ -5,6 +5,7 @@
     "agrow",
     "agrowpumps",
     "coro",
+    "cytomat",
     "decalibrate",
     "Defaultable",
     "Deprecated",

CHANGELOG.md

@@ -116,6 +116,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `LiquidHandler{Backend}.{pick_up_resource,move_picked_up_resource,drop_resource}` (https://github.com/PyLabRobot/pylabrobot/pull/328)
 - `Access2` loader for vspin (https://github.com/PyLabRobot/pylabrobot/pull/308)
 - `CentrifugeChatterboxBackend` and `LoaderChatterboxBackend` (https://github.com/PyLabRobot/pylabrobot/pull/335)
+- Add support for TF cytomat `C6000`, `C2C_50`, `C2C_425`, `C2C_450_SHAKE`, `C5C` (https://github.com/PyLabRobot/pylabrobot/pull/332)
 
 ### Deprecated
 

pylabrobot/incubators/__init__.py

@@ -0,0 +1,4 @@
+from .backend import IncubatorBackend
+from .chatterbox import IncubatorChatterboxBackend
+from .cytomat import Cytomat
+from .incubator import Incubator

pylabrobot/incubators/backend.py

@@ -0,0 +1,51 @@
+from abc import ABCMeta, abstractmethod
+from typing import List, Optional
+
+from pylabrobot.machines.backends import MachineBackend
+from pylabrobot.resources import Plate, PlateCarrier, PlateHolder
+
+
+class IncubatorBackend(MachineBackend, metaclass=ABCMeta):
+  def __init__(self):
+    self._racks: Optional[List[PlateCarrier]] = None
+
+  @property
+  def racks(self) -> List[PlateCarrier]:
+    assert self._racks is not None, "Backend not set up?"
+    return self._racks
+
+  async def set_racks(self, racks: List[PlateCarrier]):
+    self._racks = racks
+
+  @abstractmethod
+  async def open_door(self):
+    pass
+
+  @abstractmethod
+  async def close_door(self):
+    pass
+
+  @abstractmethod
+  async def fetch_plate_to_loading_tray(self, plate: Plate):
+    pass
+
+  @abstractmethod
+  async def take_in_plate(self, plate: Plate, site: PlateHolder):
+    pass
+
+  @abstractmethod
+  async def set_temperature(self, temperature: float):
+    """Set the temperature of the incubator in degrees Celsius."""
+
+  @abstractmethod
+  async def get_temperature(self) -> float:
+    """Get the temperature of the incubator in degrees Celsius."""
+
+  @abstractmethod
+  async def start_shaking(self, frequency: float):
+    """Start shaking the incubator at the given frequency in Hz."""
+    pass
+
+  @abstractmethod
+  async def stop_shaking(self):
+    pass

pylabrobot/incubators/chatterbox.py

@@ -0,0 +1,39 @@
+from pylabrobot.incubators.backend import IncubatorBackend
+from pylabrobot.resources.carrier import PlateHolder
+from pylabrobot.resources.plate import Plate
+
+
+class IncubatorChatterboxBackend(IncubatorBackend):
+  def __init__(self):
+    self._dummy_temperature = 37.0
+
+  async def setup(self):
+    print("Setting up incubator backend")
+
+  async def stop(self):
+    print("Stopping incubator backend")
+
+  async def open_door(self):
+    print("Opening door")
+
+  async def close_door(self):
+    print("Closing door")
+
+  async def fetch_plate_to_loading_tray(self, plate: Plate):
+    print(f"Fetching plate {plate} to loading tray")
+
+  async def take_in_plate(self, plate: Plate, site: PlateHolder):
+    print(f"Taking in plate {plate} at site {site}")
+
+  async def set_temperature(self, temperature: float):
+    print(f"Setting temperature to {temperature}")
+
+  async def get_temperature(self) -> float:
+    print("Getting temperature")
+    return self._dummy_temperature
+
+  async def start_shaking(self, frequency: float):
+    print(f"Starting shaking at {frequency} Hz")
+
+  async def stop_shaking(self):
+    print("Stopping shaking")

pylabrobot/incubators/cytomat/__init__.py

@@ -0,0 +1 @@
+from .cytomat import Cytomat, CytomatChatterbox

pylabrobot/incubators/cytomat/constants.py

@@ -0,0 +1,174 @@
+from dataclasses import dataclass
+from enum import Enum, IntEnum
+
+
+class OverviewRegister(Enum):
+  """
+  This is returned by:
+    the check_register command f"ch:{OverviewRegister.value}"
+    any of the `mv` commands
+  """
+
+  TRANSFER_STATION_OCCUPIED = 0
+  DEVICE_DOOR_OPEN = 1
+  AUTOMATIC_GATE_OPEN = 2
+  HANDLER_OCCUPIED = 3
+  ERROR_REGISTER_SET = 4
+  WARNING_REGISTER_SET = 5
+  READY_BIT_SET = 6
+  BUSY_BIT_SET = 7
+
+
+class WarningRegister(Enum):
+  NO_WARNING = "00"
+  COMMUNICATION_WITH_MOTOR_CONTROLLERS_INTERRUPTED = "01"
+  MTP_NOT_LOADED_ON_HANDLER_SHOVEL = "02"
+  MTP_NOT_UNLOADED_FROM_HANDLER_SHOVEL = "03"
+  SHOVEL_NOT_EXTENDED_HANDLER_MOVEMENT_ERROR = "04"
+  PROCESS_TIMEOUT = "05"
+  AUTOMATIC_LIFT_DOOR_NOT_OPEN = "06"
+  AUTOMATIC_LIFT_DOOR_NOT_CLOSED = "07"
+  SHOVEL_NOT_RETRACTED = "08"
+  INITIALIZATION_DUE_TO_OPEN_DEVICE_DOOR = "09"
+  TRANSFER_STATION_NOT_ROTATED = "0C"
+  OTHER_MOTOR_FAULT_INIT_PHYTRON = "0D"
+  REINITIALIZATION_CAROUSEL = "0E"
+
+
+class ErrorRegister(Enum):
+  NO_ERROR = "00"
+  COMMUNICATION_WITH_MOTOR_CONTROLLERS_INTERRUPTED = "01"
+  NO_MTP_LOADED_ON_HANDLER_SHOVEL = "02"
+  NO_MTP_UNLOADED_FROM_HANDLER_SHOVEL = "03"
+  SHOVEL_NOT_EXTENDED_AUTOMATIC_UNIT_POSITION_ERROR = "04"
+  PROCESS_TIMEOUT = "05"
+  AUTOMATIC_LIFT_DOOR_NOT_OPEN = "06"
+  AUTOMATIC_LIFT_DOOR_NOT_CLOSED = "07"
+  SHOVEL_NOT_RETRACTED = "08"
+  STEPPER_MOTOR_CONTROLLER_TEMPERATURE_TOO_HIGH = "0A"
+  OTHER_STEPPER_MOTOR_CONTROLLER_ERROR = "0B"
+  TRANSFER_STATION_NOT_ROTATED = "0C"
+  COMMUNICATION_WITH_HEATING_CONTROLLERS_AND_GAS_SUPPLY_DISTURBED = "0D"
+  FATAL_ERROR_OCCURRED_DURING_ERROR_ROUTINE = "FF"
+
+
+class ActionRegister(Enum):
+  MOVEMENT_HEIGHT_MOTOR_TO_STORAGE_MINUS_OFFSET = "01"
+  QUERY_HEIGHT_POSITION_REACHED_MINUS_OFFSET = "02"
+  MOVEMENT_HEIGHT_MOTOR_TO_STORAGE_PLUS_OFFSET = "03"
+  QUERY_HEIGHT_POSITION_REACHED_PLUS_OFFSET = "04"
+  MOVEMENT_ROTATION_MOTOR_TO_STORAGE_LOCATION = "05"
+  QUERY_ROTATION_POSITION_REACHED = "06"
+  MOVEMENT_EXTEND_SHOVEL = "07"
+  QUERY_SHOVEL_EXTENDED = "08"
+  QUERY_SHOVEL_EXTENSION_LIMIT_SWITCH = "09"
+  MOVEMENT_RETRACT_SHOVEL = "0A"
+  QUERY_SHOVEL_RETRACTED = "0B"
+  CLOSE_AUTOMATIC_LIFT_DOOR = "0C"
+  QUERY_AUTOMATIC_LIFT_DOOR_CLOSED = "0D"
+  OPEN_AUTOMATIC_LIFT_DOOR = "0E"
+  QUERY_AUTOMATIC_LIFT_DOOR_OPEN = "0F"
+  TRANSFER_STATION_IN_POSITION_1 = "10"
+  QUERY_TRANSFER_STATION_IN_POSITION_1 = "11"
+  TRANSFER_STATION_IN_POSITION_2 = "12"
+  QUERY_TRANSFER_STATION_IN_POSITION_2 = "13"
+  CHECK_MTP_ON_SHOVEL = "14"
+  CHECK_MTP_ON_TRANSFER_STATION = "15"
+  MOVEMENT_TURNTABLE = "19"
+  TURNTABLE_POSITION_QUERY = "1A"
+  TURNTABLE_INIT_MOVEMENT = "1B"
+  TURNTABLE_INIT_POSITION_QUERY = "1C"
+  PARAMETER_SET_FOR_MOTOR_CONTROLLER_CHANGED = "1D"
+
+
+class ActionType(Enum):
+  INIT_POSITION = "01"
+  WAIT_POSITION = "02"
+  STACKER = "03"
+  TRANSFER_STATION = "04"
+
+
+class SwapStationPosition(IntEnum):
+  PLATE_1_IN_FRONT_OF_AUTOMATIC_GATE = 1
+  PLATE_2_IN_FRONT_OF_AUTOMATIC_GATE = 2
+
+
+class LoadStatusFrontOfGate(IntEnum):
+  EMPTY = 0
+  OCCUPIED = 1  # Occupied (microtiter plate loaded)
+
+
+class LoadStatusAtProcessor(IntEnum):
+  EMPTY = 0
+  OCCUPIED = 1  # Occupied (microtiter plate loaded)
+
+
+class SensorRegister(IntEnum):
+  INIT_SENSOR_HEIGHT_MOTOR = 0
+  INIT_SENSOR_CAROUSEL = 1
+  SHOVEL_RETRACTED = 2
+  SHOVEL_EXTENDED = 3
+  SHOVEL_OCCUPIED = 4
+  GATE_OPENED = 5
+  GATE_CLOSED = 6
+  TRANSFER_STATION_OCCUPIED = 7
+  TRANSFER_STATION_POSITION_1 = 8
+  TRANSFER_STATION_POSITION_2 = 9
+  INNER_DOOR_OPENED = 10
+  CAROUSEL_POSITION = 11
+  HANDLER_POSITIONED_TOWARDS_STACKER = 12
+  HANDLER_POSITIONED_TOWARDS_GATE = 13
+  TRANSFER_STATION_SECOND_PLATE_OCCUPIED = 14
+
+
+@dataclass(frozen=True)
+class CytomatIncupationResponse:
+  nominal_value: float
+  actual_value: float
+
+
+class CytomatActionResponse(Enum):
+  OK = "ok"
+  ERROR = "er"
+
+
+@dataclass(frozen=True)
+class CytomatRack:
+  num_slots: int  # number of plate locations in rack
+  pitch: int  # distance between 2 plate locations
+
+  @classmethod
+  def deserialize(cls, data: dict):
+    return cls(num_slots=data["num_slots"], pitch=data["pitch"])
+
+
+class CytomatType(Enum):
+  C6000 = "C6000"
+  C6002 = "C6002"
+  C2C_50 = "C2C_50"
+  C2C_425 = "C2C_425"
+  C2C_450_SHAKE = "C2C_450_SHAKE"
+  C5C = "C5C"  # Cytomat 5C
+
+
+@dataclass(frozen=True)
+class CytomatCapability:  # to enhance protocol modularity across cytomats, here we define instrument capabilities
+  incubate: bool
+  cool: bool
+  shake: bool
+
+
+CytomatCapabilities = {
+  CytomatType.C6000: CytomatCapability(incubate=True, cool=False, shake=False),
+  CytomatType.C6002: CytomatCapability(incubate=False, cool=True, shake=False),
+  CytomatType.C2C_50: CytomatCapability(
+    incubate=True, cool=False, shake=False
+  ),  # Refers to cytomat with temp range 25-50 (incubator-only)
+  CytomatType.C2C_425: CytomatCapability(
+    incubate=False, cool=True, shake=False
+  ),  # Refers to cytomat with temp range 4-25 (fridge-only)
+  CytomatType.C2C_450_SHAKE: CytomatCapability(
+    incubate=True, cool=True, shake=True
+  ),  # Refers to cytomat with temp range 4-50 & shaker plugs
+  CytomatType.C5C: CytomatCapability(incubate=True, cool=True, shake=False),
+}