Source code for science_jubilee.labware.Labware

import json
import os
import string
from dataclasses import dataclass
from itertools import chain
from math import acos, cos, sin, sqrt
from typing import Dict, Iterable, List, NamedTuple, Tuple, Union

import numpy as np


@dataclass
[docs] class Well: """A class representing a well of a labware. Each Well is associated with a specific name, depth, total liquid volume, shape, diameter, x, y, and z dimension, y-dimension, as well as its coordinates and any applied offset :return: A :class:`Well` object with various information about the geometry of the well and its position in the labware :rtype: :class:`Well` """
[docs] name: str
[docs] depth: float
[docs] totalLiquidVolume: float
[docs] shape: str
[docs] diameter: float = None
[docs] xDimension: float = None
[docs] yDimension: float = None
x: float y: float z: float
[docs] offset: Tuple[float] = None
[docs] slot: int = None
[docs] has_tip: bool = False
[docs] clean_tip: bool = False
[docs] labware_name: str = None
@property
[docs] def x(self): """Offsets the x-position of the each well with respect to the deck-slot coordinates :return: The x-coordinate of the well :rtype: float """ return self._x
@x.setter def x(self, new_x): """Setter for the offsetted x-position of each well with respect to the deck-slot coordinates :param new_x: the new y-coordinate of the well :type new_x: float """ self._x = new_x @property
[docs] def y(self): """Offsets the y-position of the each well with respect to the deck-slot coordinates :return: The y-coordinate of the well :rtype: float """ return self._y
@y.setter def y(self, new_y): """Setter for the offsetted y-position of each well with respect to the deck-slot coordinates :param new_y: The new y-coordinate of the well :type new_y: float """ self._y = new_y @property
[docs] def z(self): """Offsets the z-position of each well with respect to the deck-slot coordinates :return: The z-coordinate of the well :rtype: float """ return self._z
@z.setter def z(self, new_z): """Setter for the offsetted z-position of each well with respect to the deck-slot coordinates :param new_z: The new z-coordinate of the well :type new_z: flaot """ self._z = new_z
[docs] def apply_offset(self, offset: Tuple[float]): """Allows the user to offset the coordinates of the well with respect to the deck-slot coordinates :param offset: A tuple of floats with the new offset of the well :type offset: Tuple[float] """ self._x = self.x + offset[0] self._y = self.y + offset[1] if len(offset) == 3: self._z = self.z + offset[2] self.offset = offset
@property
[docs] def top_(self): """Defines the top-most point of the well :return: The z-coordinate of the top of the well :rtype: float """ return self.z + self.depth
@property
[docs] def bottom_(self): """Defines the bottom-most point of the well :return: The z-coordinate of the bottom of the well :rtype: float """ return self.z
[docs] def bottom(self, z: float, check=False): """Allows the user to dinamically indicate a new Z location relative to the bottom of the well. :param z: the distance in mm to offset the coordinates from the bottom of the well. Should be + :type z: float :param check: the 'z' parameters can either be + or -. If negative, an assert error is raised to avoid collision with the labware. However, there might be instances of custom labware where the bottom of the well is purposely set as higher during the generation of its config .json file., defaults to False :type check: bool, optional :return: A :class:`Location` which contains information about the new coordinates generated and the :class:`Well` object :rtype: :class:`Location` """ from_bottom_z = self.bottom_ + z if check: pass else: assert z >= 0, ( "Indicated location is lower than the bottom of the labware and" " could result in crash. Input a positive 'z' value " ) coord = (self.x, self.y, from_bottom_z) return Location(coord, self)
[docs] def top(self, z: float): """Allows the user to dinamically indicate a new Z location relative to the top of the well. :param z: the distance in mm to offset the coordinates from the top of the well.Can be either + or - :type z: float :return: A :class:`Location` which contains information about the new coordinates generated and the :class:`Well` object. :rtype: :class:`Location` """ from_top_z = self.top_ + z assert ( from_top_z > self.bottom_ ), "Indicated location is lower than the bottom of the labware." coord = (self.x, self.y, from_top_z) return Location(coord, self)
[docs] def __repr__(self): """Displayed representation of a :class:`Well` object indicating its name and its coordinates :return: A string representation of the name and coordinates of a well :rtype: str """ if self.slot != None: message = f"Well {self.name} form {self.labware_name} on slot {self.slot}" else: message = f"Well {self.name} at coordinates {self.x, self.y, self.z}" return message
[docs] def set_has_tip(self, value: bool): """Set the value of the `has_tip` attribute. :param value: The new value for the `has_tip` attribute :type value: bool """ self.has_tip = value
[docs] def set_clean_tip(self, value: bool): """Returns the value of the `clean_tip` attribute. :param value: The new value for the `clean_tip` attribute :type value: bool """ self.clean_tip = value
@dataclass(repr=False)
[docs] class WellSet: """A class defining a set of wells expressed as a dictionary in which each keys is the the :attribute:`Well.name` object and the value is the :class:`Well` object itself. """
[docs] wells: Dict[str, Well]
[docs] def __repr__(self): """Displays the wellset as a :list: of wells and the deck-slot nunmber :return: A :list: of :class:`Well` objects diplayed by their :attribute:`Well.name` :rtype: :class:`Row` """ return str(f"{list(self.wells.keys())}")
[docs] def __getitem__(self, id_: Union[str, int]): """Allows the user to select a :class:`Well` object by either their :attribute:`Well.name` or their index in a :list: :param id_: The :attribute:`Well.name` or index representing a :class:`Well` in the labware :type id_: Union[str, int] :return: The :class:`Well` object :rtype: :class:`Well` """ try: if isinstance(id_, slice): well_list = [] start = id_.start stop = id_.stop if id_.step is not None: step = id_.step else: step = 1 for sub_id in range(start, stop, step): well_list.append(self.wells[sub_id]) return well_list else: return self.wells[id_] except KeyError: return list(self.wells.values())[id_]
@dataclass(repr=False)
[docs] class Row(WellSet): """A class representing a row of a labware, for example 'A', 'B', etc :param WellSet: A dictionary of :class:`Well` objects in which each keys is the the :attribute:`Well.name` object and the value is the :class:`Well` object itself. :type WellSet: Dict[str, Well] """
[docs] identifier: str
@dataclass(repr=False)
[docs] class Column(WellSet): """A class representing a column of a labware, for example 1, 2, etc. :param WellSet: A dictionary of :class:`Well` objects in which each keys is the the :attribute:`Well.name` object and the value is the :class:`Well` object itself. :type WellSet: Dict[str, Well] """
[docs] identifier: int
[docs] class Labware(WellSet): """A class representing a basic laboratory labware made up of a set of wells/pipette tips. :param labware_filename: The name of the config `.json` :type labware_filename: str :param offset: Coordinates to use to offset all the wells in a labware for easier handling of coordinates. For example this is called by the :method:`Deck.load_labware` when assignign a labware to a deck slot, defaults to None :type offset: Tuple[float], optional :param order: Option to order the wells of a labware either by `row` or `columns`, defaults to 'rows' :type order: str, optional :param path: Path to the folder containing the configuration `.json` files for the labware, defaults to the 'labware_definition/' in the science_jubilee/labware directory. :type path: str, optional """ def __init__( self, labware_filename: str, offset: Tuple[float] = None, order: str = "rows", path: str = os.path.join(os.path.dirname(__file__), "labware_definition"), ): """Initializes a :class:`Labware` object by loading its configuration file and creating a dictionary of :class:`Well` objects. :param labware_filename: The name of the config `.json` :type labware_filename: str :param offset: Coordinates to use to offset all the wells in a labware for easier handling of coordinates. For example this is called by the :method:`Deck.load_labware` when assignign a labware to a deck slot, defaults to None :type offset: Tuple[float], optional :param order: Option to order the wells of a labware either by `row` or `columns`, defaults to 'rows' :type order: str, optional :param path: Path to the folder containing the configuration `.json` files for the labware, defaults to the 'labware_definition/' in the science_jubilee/labware directory. :type path: str, optional """ # load in the labware configuration file if labware_filename[-4:] != "json": labware_filename = labware_filename + ".json" config_path = os.path.join(path, f"{labware_filename}") with open(config_path, "r") as f: # this will be the raw .json file data and fields should not be modified directly # current exceptions is 'manual_offset' field to allow to save custom data for easier handling # of recurrent slot-labware combinations self.data = json.load(f)
[docs] self.config_path = config_path
[docs] self.wells_data = self.data.get("wells", {})
self.row_data, self.column_data, self.wells = self._create_rows_and_columns() order_options = [ "rows", "row", "Rows", "Row", "R", "cols", "col", "C", "columns", "Columns", ] assert order in order_options, "Order must be one of {}".format(order_options) self.withWellOrder(order) self.offset = offset
[docs] self.slot = None
# check to see if a manual offset was saved for this labware in a specific slot if "manual_offset" in self.data: self.manualOffset = self.data["manual_offset"] else: # otherwise initialize manual_offset instance variable self.manualOffset = {}
[docs] def __repr__(self): """Displayed representation of a :class:`Labware` object indicating the type of labware and its name. Additionally, it will show the :attribute:`Deck.slots` number if the labware has been already assigned to it. """ display = ( self.metadata()["displayCategory"] + ": " + self.parameters()["loadName"] ) if self.slot is not None: display = display + " " + f" on {self.slot}" return display
[docs] def _create_rows_and_columns(self): """Creates a dictionary of :class:`Row` and :class:`Column` and :class:`Well` objects from the data in the config `.json` file. :return: A dictionary of :class:`Row` and :class:`Column` and :class:`Well` objects :rtype: :class:`Row`, :class:`Column`, :class:`Well` """ rows = {} columns = {} wells = {} for row_order, column_data in enumerate(self.ordering): # Assumes the first char is the row identifier, e.g., "A" in "A1" row_id = column_data[0][0] # Extracts column number, e.g., "1" in "A1" col_ids = [int(well[1:]) for well in column_data] if row_id not in rows: rows[row_id] = {} for col_order, well_id in enumerate(column_data): well = Well(name=well_id, **self.wells_data[well_id]) rows[row_id][well_id] = well if col_order + 1 not in columns: # +1 since indexing starts at 0 columns[col_order + 1] = {} columns[col_order + 1][well_id] = well wells[well_id] = well # add tip tracking to the wells if self.is_tip_rack: for well in wells.values(): well.has_tip = True well.clean_tip = True # add labware name to each Well object for well in wells.values(): well.labware_name = self.display_name # Convert dictionary data to Row and Column classes _rows = {k: Row(identifier=k, wells=v) for k, v in rows.items()} _columns = {k: Column(identifier=k, wells=v) for k, v in columns.items()} return _rows, _columns, wells
[docs] def get_row(self, row_id: str) -> Row: """Fucntions to fetch the :class:`Well.name` of the indicated row. :param row_id: The name of a row of the labware, usually indicated by a capital letter (e.g., A, B, etc.) :type row_id: str :return: A list of :class:`Well` objects diplayed by their :attribute:`Well.name` :rtype: :class:`Row` """ return self.row_data.get(row_id)
[docs] def get_column(self, col_id: int) -> Column: """Fucntions to fetch the :class:`Well.name` of the indicated column. :param col_id: The name of a column of the labware, usually indicated by an integer number (e.g., 1, 2, etc.) :type col_id: str :return: A list of :class:`Well` objects diplayed by their :attribute:`Well.name` :rtype: :class:`Column` """ return self.column_data.get(col_id)
@property
[docs] def shape(self): """Returns the shape of the labware as a tuple of (rows, columns) :return: A tuple of (rows, columns) :rtype: Tuple[int, int] """ return (len(self.row_data), len(self.column_data))
@property
[docs] def ordering(self) -> List[List[str]]: """Returns the ordering of the wells in the labware as a list of lists. Each list represents a row of the labware. :return: A list of lists of :class:`Well.name` objects :rtype: List[List[str]] """ return np.array(self.data["ordering"]).T
@property
[docs] def brand(self) -> dict: """Returns the brand of the labware as a strin :return: A string with the brand of the labware :rtype: str """ return self.data.get("brand", {})["brand"]
[docs] def metadata(self) -> dict: """Returns the metadata of the labware as a dictionary The metadata of a labware will generally contain the display name, the type of labware, and the units of volume. These can also be found as attributes of the :class:`Labware` object. :return: A dictionary with the metadata of the labware :rtype: dict """ return self.data.get("metadata", {})
@property
[docs] def display_name(self): """Returns the display name of the labware as a string :return: A string with the display name of the labware :rtype: str """ return self.metadata()["displayName"]
@property
[docs] def labware_type(self): """Returns the type of labware as a string The type fo labware will generally either be a tiprack, wellplate, reservoir, etc. :return: A string with the type of labware :rtype: str """ return self.metadata()["displayCategory"]
@property
[docs] def volume_units(self): """Returns the units of volume of the labware as a string The volume units will be either uL or mL. :return: A string with the units of volume of the labware :rtype: str """ return self.metadata()["displayVolumeUnits"]
@property
[docs] def dimensions(self) -> dict: """Returns the dimensions of the labware as a dictionary :return: A dictionary with the x,y, and z dimensions of the labware :rtype: dict """ return self.data.get("dimensions", {})
[docs] def parameters(self) -> dict: """Returns the parameters describing certain features of the labware as a dictionary The parameters genereally include whether the shape of the labware is regular or irregular, if it is a tiprack, and other Opentrons specific parameters as we are using their 'Custom Labware Page' to generate the .json config files. :return: A dictionary with the parameters of the labware :rtype: dict """ return self.data.get("parameters", {})
@property
[docs] def is_tip_rack(self): """Returns a boolean indicating if the labware is a tiprack :return: True if the labware is a tiprack, False otherwise :rtype: bool """ return self.parameters()["isTiprack"]
@property
[docs] def load_name(self): """Returns the name of the labware as a string :return: A string with the name of the labware :rtype: str """ return self.parameters()["loadName"]
@property
[docs] def tip_length(self): """Returns the length of the tip of the labware as a float if the labware is a tiprack, otherwise returns None :return: A float with the length of the tip of the labware or None otherwise :rtype: float """ try: return self.parameters()["tipLength"] except: pass
@property
[docs] def tip_overlap(self): """Returns the overlap of the tip of the labware as a float if the labware is a tiprack, otherwise returns None :return: A float with the overlap of the tip of the labware or None otherwise :rtype: float """ try: return self.parameters()["tipOverlap"] except: pass
@property
[docs] def offset(self): """Returns the offset of the labware as a tuple of floats :return: A tuple of floats with the offset of the labware :rtype: Tuple[float] """ return self._offset
@offset.setter def offset(self, new_offset): """Sets the offset of the labware to the indicated values and updates the offset of each well in the labware :param new_offset: A tuple of floats with the new offset of the labware :type new_offset: Tuple[float] """ self._offset = new_offset if new_offset is not None: for w in self: w.apply_offset(new_offset)
[docs] def add_slot(self, slot_): """Add name of deck slot after labware has been loaded :param slot_: The name of the deck slot :type slot_: str """ self.slot = slot_ for w in self: w.slot = slot_
[docs] def withWellOrder(self, order) -> list: """Reorders the wells by rows or by columns. Automatically updates the :attribute:`Labware.wells` :param order: The order in which to reorder the wells. Can be either 'rows' or 'columns' :type order: str :return: A list of :class:`Well` objects diplayed by their :attribute:`Well.name` :rtype: list """ ordered_wells = {} if order in ["rows", "row", "Rows", "Row", "R"]: for well in list(chain(*self.row_data.values())): ordered_wells[well.name] = well elif order in ["cols", "col", "C", "columns", "Columns"]: for well in list(chain(*self.column_data.values())): ordered_wells[well.name] = well else: print("Order needs to be either rows or columns") self.wells = ordered_wells
# @staticmethod
[docs] def _translate_point( self, well: Well, theta: float, x_space: float, y_space: float, upper_left: Tuple[float], ): """ Helper function to translate the coordinates of a well by a given angle theta. :param well: A :class:`Well` object :type well: :class:`Well` :param theta: The angle by which to translate the coordinates of the well :type theta: float :return: The new x and y coordinates of the well :rtype: float, float """ x_nom, y_nom = self._nominal_coordinates(well, x_space, y_space) x_translated = upper_left[0] + x_nom * cos(theta) - y_nom * sin(theta) y_translated = upper_left[1] - (x_nom * sin(theta) + y_nom * cos(theta)) return x_translated, y_translated
@staticmethod
[docs] def _nominal_coordinates(well: Well, x_space: float, y_space: float): """ Helper function to calculate the nominal coordinates of a well in a labware based on its row and column index. """ col_index = int(well.name[1:]) - 1 row_index = list(string.ascii_uppercase).index(well.name[0]) x_nominal = col_index * x_space y_nominal = row_index * y_space return x_nominal, y_nominal
[docs] def manual_offset(self, corner_wells: List[Tuple[float]], save: bool = False): """Allows the user to manually offset the coordinates of the labware based on three corner wells. Adapted from `https://github.com/machineagency/sonication_station` labware calibration procedure. :param offset: A list containing tuples of floats :type offset: Tuple[float] :param save: Option to save the manual offset to the original config `.json` file, defaults to False :type save: bool, optional :return: An updated :class:`Labware` object with the new coordinates of the wells :rtype: :class:`Labware` """ assert ( self.slot is not None ), "Labware has not been assigned to a slot yet. Use the 'add_slot' method to assign a slot" assert len(corner_wells) == 3, "Three points needed to apply manual offset" assert all( [len(o) == 2 for o in corner_wells] ), "Each point should have three coordinates (x,y)" # Get the coordinates of the three corner wells (e.g., A1, A12, H12) upper_left = corner_wells[0] upper_right = corner_wells[1] bottom_right = corner_wells[2] # Get the coordinates of the three corner wells # calculate total spacing between wells in each row (width) and column (height) plate_width = sqrt( (upper_right[0] - upper_left[0]) ** 2 + (upper_right[1] - upper_left[1]) ** 2 ) plate_height = sqrt( (bottom_right[0] - upper_right[0]) ** 2 + (bottom_right[1] - upper_right[1]) ** 2 ) # Assume evenly spaced wells, but possible to have different spacing in rows and columns x_space = plate_width / (len(self.column_data) - 1) y_space = plate_height / (len(self.row_data) - 1) # Define and average the offset angles for the plate theta1 = acos((upper_right[1] - bottom_right[1]) / plate_height) theta2 = acos((upper_right[0] - upper_left[0]) / plate_width) theta = (theta1 + theta2) / 2.0 # Apply direction correction to theta if (upper_right[1] < upper_left[1]) and (bottom_right[0] < upper_right[0]): # in this case, plate is rotated down theta = -1 * theta # apply offset to all wells in the labware object for well in self: new_x, new_y = self._translate_point( well, theta, x_space, y_space, upper_left ) well.x = new_x well.y = new_y print(f'New manual offset applied to {self.parameters()["loadName"]}') if save: if str(self.slot) in self.manualOffset.keys(): k = input( "Are you sure you want to overwrite the manual offset for this labware? Press 'y' key to continue" ) if k == "y": self.manualOffset[str(self.slot)] = corner_wells with open(self.config_path, "w") as f: self.data["manual_offset"] = {str(self.slot): corner_wells} json.dump(self.data, f) print("Manual offset saved") else: print("Manual offset applied, but not saved") else: self.manualOffset[str(self.slot)] = corner_wells with open(self.config_path, "w") as f: self.data["manual_offset"] = {str(self.slot): corner_wells} f.seek(0) json.dump(self.data, f, indent=4) print("Manual offset saved") else: self.manualOffset[str(self.slot)] = corner_wells
[docs] def load_manualOffset(self, apply: bool = True): """Loads the manual offset of a labware from its config `.json` file for a specific slot :param apply: Option to apply the manual offset to the labware or return values, defaults to False :type apply: bool, optional :return: A list of tuples containing the manual offset of the labware :rtype: List[Tuple[float]] """ assert ( self.slot is not None ), "Labware has not been assigned to a slot yet. Use the 'add_slot' method to assign a slot" if self.manualOffset[str(self.slot)]: if apply: self.manual_offset(self.manualOffset[str(self.slot)]) return else: return self.manualOffset[str(self.slot)] else: return self.data["manual_offset"][self.slot]
@staticmethod
[docs] def _getxyz(location: Union[Well, Tuple, "Location"]): """Helper function to extract the x, y, z coordinates of a location object. :param location: The location object to extract the coordinates from. This can either be a :class:`Well`, a :tuple: of x, y, z coordinates, or a :class:`Location` object :type location: Union[Well, Tuple, Location] :raises ValueError: If the location is not a :class:`Well`, a :class:`tuple`, or a :class:`Location` object :return: The x, y, z coordinates of the location :rtype: float, float, float """ if type(location) == Well: x, y, z = location.x, location.y, location.z elif type(location) == tuple: x, y, z = location elif type(location) == Location: x, y, z = location._point else: raise ValueError("Location should be of type Well or Tuple") return x, y, z
@staticmethod
[docs] def list_labware_definitions(): """Returns a list of all the labware definitions available in the labware_definition folder. :return: A list of all the labware definitions available :rtype: List[str] """ path = os.path.join(os.path.dirname(__file__), "labware_definition") return os.listdir(path)
## Adapted from Opentrons API opentrons.types##
[docs] class Point(NamedTuple): """A point in the Jubilee 3D coordinate system. :param NamedTuple: A list-like container with a fixed number of elements :type NamedTuple: :class:`NamedTuple` :return: A tuple of coordinates (x,y,z) :rtype: :class:`Point` """
[docs] x: float = 0.0
[docs] y: float = 0.0
[docs] z: float = 0.0
[docs] def add(self, other): """Adds the coordinates of two points :param other: A tuple of coordinates (x,y,z) :type other: :class:`Point` :return: A new :class:`Point` object :rtype: :class:`Point` """ if not isinstance(other, Point): return NotImplemented return Point(self.x + other.x, self.y + other.y, self.z + other.z)
[docs] def substract(self, other): """Substracts the coordinates of two points :param other: A tuple of coordinates (x,y,z) :type other: :class:`Point` :return: A new :class:`Point` object :rtype: :class:`Point` """ if not isinstance(other, Point): return NotImplemented return Point(self.x - other.x, self.y - other.y, self.z - other.z)
[docs] def multiply(self, other: Union[int, float]): """Multiplies the coordinates of a point by a scalar :param other: A scalar to multiply the coordinates of a point :type other: Union[int, float] :return: A new :class:`Point` object scaled by the value indicated as the function parameter :rtype: :class:`Point` """ if not isinstance(other, (float, int)): return NotImplemented return Point(self.x * other, self.y * other, self.z * other)
[docs] def absolute(self): """Returns the absolute value of the coordinates of a point. :return: The absolute values of a :class:`Point` object :rtype: :class:`Point` """ return Point(abs(self.x), abs(self.y), abs(self.z))
[docs] def __repr__(self) -> str: """Returns a string representation of the coordinates of a point. :return: A string representation of the coordinates of a point :rtype: str """ display = "x:{}, y: {}, z:{}".format(self.x, self.y, self.z) return display
[docs] class Location: """A location to target as a motion. The location contains a :class:`Point` and possibly an associated :class:`Labware` or :class:`Well` instance. """ def __init__(self, point: Point, labware: Union[Well, Labware]):
[docs] self._point = point
[docs] self._labware = labware
@property
[docs] def point(self) -> Point: """The coordinates (x,y,z) of a Well or a Labware :return: A tuple of coordinates (x,y,z) :rtype: :class:`Point` """ return self._point
@property
[docs] def labware(self): """The :class:`Well` object associated with the coordinates (x,y,z) :return: A :class:`Well` object :rtype: :class:`Well` """ return self._labware
[docs] def __iter__(self) -> Iterable[Union[Point, Well, Labware]]: """Iterable interface to support unpacking of :class:`Location` objects. :return: An interable of :class:`Location` objects :rtype: Iterable[Union[Point, Well, Labware]] """ return iter((self._point, self._labware))
[docs] def __eq__(self, other: object) -> bool: """Comparison between two :class:`Location` objects. :param other: A :class:`Location` object :type other: :class:`Location` :return: True if the two :class:`Location` objects are equal, False otherwise :rtype: bool """ return ( isinstance(other, Location) and other._point == self._point and other._labware == self._labware )
[docs] def __repr__(self) -> str: """Returns a string representation of the :class:`Location` object. :return: A string representation of the :class:`Location` object :rtype: str """ return f"Location(point={repr(self._point)}, labware={self._labware})"