science_jubilee.tools.Loop ========================== .. py:module:: science_jubilee.tools.Loop Classes ------- .. autoapisummary:: science_jubilee.tools.Loop.Well science_jubilee.tools.Loop.Tool science_jubilee.tools.Loop.Loop Functions --------- .. autoapisummary:: science_jubilee.tools.Loop.requires_active_tool Module Contents --------------- .. py: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` .. py:attribute:: name :type: str .. py:attribute:: depth :type: float .. py:attribute:: totalLiquidVolume :type: float .. py:attribute:: shape :type: str .. py:attribute:: diameter :type: float :value: None .. py:attribute:: xDimension :type: float :value: None .. py:attribute:: yDimension :type: float :value: None .. py:attribute:: x :type: float .. py:attribute:: y :type: float .. py:attribute:: z :type: float .. py:attribute:: offset :type: Tuple[float] :value: None .. py:attribute:: slot :type: int :value: None .. py:attribute:: has_tip :type: bool :value: False .. py:attribute:: clean_tip :type: bool :value: False .. py:attribute:: labware_name :type: str :value: None .. py:property:: x Offsets the x-position of the each well with respect to the deck-slot coordinates :return: The x-coordinate of the well :rtype: float .. py:property:: y Offsets the y-position of the each well with respect to the deck-slot coordinates :return: The y-coordinate of the well :rtype: float .. py:property:: z Offsets the z-position of each well with respect to the deck-slot coordinates :return: The z-coordinate of the well :rtype: float .. py:method:: apply_offset(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] .. py:property:: top_ Defines the top-most point of the well :return: The z-coordinate of the top of the well :rtype: float .. py:property:: bottom_ Defines the bottom-most point of the well :return: The z-coordinate of the bottom of the well :rtype: float .. py:method:: bottom(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` .. py:method:: top(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` .. py:method:: __repr__() 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 .. py:method:: set_has_tip(value: bool) Set the value of the `has_tip` attribute. :param value: The new value for the `has_tip` attribute :type value: bool .. py:method:: set_clean_tip(value: bool) Returns the value of the `clean_tip` attribute. :param value: The new value for the `clean_tip` attribute :type value: bool .. py:class:: Tool(index, name, **kwargs) .. py:method:: post_load() Run any code after tool has been associated with the machine. .. py:function:: requires_active_tool(func) Decorator to ensure that a tool cannot complete an action unless it is the current active tool. .. py:class:: Loop(index, name) Bases: :py:obj:`science_jubilee.tools.Tool.Tool` A class representation of an inoculation loop. :param Tool: The base tool class :type Tool: :class:`Tool` .. py:method:: transfer(source: science_jubilee.labware.Labware.Well = None, destination: science_jubilee.labware.Labware.Well = None, s: int = 2000, sweep_x: float = 5, sweep_y: float = 5, sweep_z: float = 10, sweep_speed: float = 100, up_speed: float = 800, randomize_pickup: bool = False) Dip into a number of (source, destination) well pairs. Used for transferring items from source to destination. :param source: Source well, defaults to None :type source: :class:`Well`, optional :param destination: Destination well, defaults to None :type destination: :class:`Well`, optional :param s: Movement speed in mm/min, defaults to 2000 :type s: int, optional :param sweep_x: Distance (in mm) to sweep in the x direction to pick up material, defaults to 5 :type sweep_x: float, optional :param sweep_y: Distance (in mm) to sweep in the y direction to pick up material, defaults to 5 :type sweep_y: float, optional :param sweep_z: Distance (in mm) to move in the z direction to pick up material, defaults to 10 :type sweep_z: float, optional :param sweep_speed: Speed (in mm/min) at which to sweep to pick up material, defaults to 100 :type sweep_speed: float, optional :param up_speed: Speed to move out of well (in mm/min), defaults to 800 :type up_speed: float, optional :param randomize_pickup: Move to a random position in the source well to pick up material, defaults to False :type randomize_pickup: bool, optional .. py:method:: _get_xyz(well: science_jubilee.labware.Labware.Well = None, location: Tuple[float] = None) :staticmethod: Get the (x,y,z) position of a well. :param well: The well to fetch position of, defaults to None :type well: :class:`Well`, optional :param location: Directly specify an (x,y,z) location, defaults to None :type location: Tuple[float], optional :raises ValueError: Must specify either a well or a location :return: The well location :rtype: Tuple[float, float, float] .. py:method:: _get_top_bottom(well: science_jubilee.labware.Labware.Well = None) :staticmethod: Get the top and bottom heights of a well. :param well: The well to fetch position of, defaults to None :type well: Well, optional :return: The z-height of the top and bottom of the well :rtype: Tuple[float, float]