science_jubilee.tools.SyringeExtruder ===================================== .. py:module:: science_jubilee.tools.SyringeExtruder Exceptions ---------- .. autoapisummary:: science_jubilee.tools.SyringeExtruder.ToolConfigurationError science_jubilee.tools.SyringeExtruder.ToolStateError Classes ------- .. autoapisummary:: science_jubilee.tools.SyringeExtruder.Labware science_jubilee.tools.SyringeExtruder.Location science_jubilee.tools.SyringeExtruder.Well science_jubilee.tools.SyringeExtruder.Tool science_jubilee.tools.SyringeExtruder.SyringeExtruder Functions --------- .. autoapisummary:: science_jubilee.tools.SyringeExtruder.requires_active_tool Module Contents --------------- .. py:class:: Labware(labware_filename: str, offset: Tuple[float] = None, order: str = 'rows', path: str = os.path.join(os.path.dirname(__file__), 'labware_definition')) Bases: :py:obj:`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 .. py:method:: __repr__() 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. .. py:method:: _create_rows_and_columns() 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` .. py:method:: get_row(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` .. py:method:: get_column(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` .. py:property:: shape Returns the shape of the labware as a tuple of (rows, columns) :return: A tuple of (rows, columns) :rtype: Tuple[int, int] .. py:property:: ordering :type: 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]] .. py:property:: brand :type: dict Returns the brand of the labware as a strin :return: A string with the brand of the labware :rtype: str .. py:method:: metadata() -> 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 .. py:property:: display_name Returns the display name of the labware as a string :return: A string with the display name of the labware :rtype: str .. py:property:: labware_type 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 .. py:property:: volume_units 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 .. py:property:: dimensions :type: 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 .. py:method:: parameters() -> 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 .. py:property:: is_tip_rack Returns a boolean indicating if the labware is a tiprack :return: True if the labware is a tiprack, False otherwise :rtype: bool .. py:property:: load_name Returns the name of the labware as a string :return: A string with the name of the labware :rtype: str .. py:property:: tip_length 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 .. py:property:: tip_overlap 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 .. py:property:: offset 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] .. py:method:: add_slot(slot_) Add name of deck slot after labware has been loaded :param slot_: The name of the deck slot :type slot_: str .. py:method:: withWellOrder(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 .. py:method:: _translate_point(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 .. py:method:: _nominal_coordinates(well: Well, x_space: float, y_space: float) :staticmethod: Helper function to calculate the nominal coordinates of a well in a labware based on its row and column index. .. py:method:: manual_offset(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` .. py:method:: load_manualOffset(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]] .. py:method:: _getxyz(location: Union[Well, Tuple, Location]) :staticmethod: 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 .. py:class:: Location(point: Point, labware: Union[Well, Labware]) A location to target as a motion. The location contains a :class:`Point` and possibly an associated :class:`Labware` or :class:`Well` instance. .. py:property:: point :type: Point The coordinates (x,y,z) of a Well or a Labware :return: A tuple of coordinates (x,y,z) :rtype: :class:`Point` .. py:property:: labware The :class:`Well` object associated with the coordinates (x,y,z) :return: A :class:`Well` object :rtype: :class:`Well` .. py:method:: __iter__() -> 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]] .. py:method:: __eq__(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 .. py:method:: __repr__() -> str Returns a string representation of the :class:`Location` object. :return: A string representation of the :class:`Location` object :rtype: str .. 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:exception:: ToolConfigurationError Bases: :py:obj:`Exception` Raise this error if there is something wrong with how the tool is configured .. py:exception:: ToolStateError Bases: :py:obj:`Exception` Raise this error if the tool is in the wrong state to perform such a command. .. 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:: SyringeExtruder(index, name, config) Bases: :py:obj:`science_jubilee.tools.Tool.Tool` A class representation of a syringe for extrusion 3D printing. :param Tool: The base tool class :type Tool: :class:`Tool` .. py:method:: load_config(config) Loads the confirguration file for the syringe tool :param config: Name of the config file for your syringe. Expects the file to be in /tools/configs :type config: str .. py:method:: post_load() Query the object model after loading the tool to find the extruder number of this syringe. .. py:method:: check_bounds(pos) Disallow commands outside of the syringe's configured range :param pos: The E position to check :type pos: float .. py:method:: make_e(x, y, z) .. py:method:: dist(start, end) .. py:method:: wipe_nozzle(x=285, y=250, z=0.2) .. py:method:: wipe_tower(x=285, y=250, z=0.2) .. py:method:: move_extrude(x=None, y=None, z=None, s=180, multiplier=1, e=None) .. py:method:: _aspirate(vol: float, s: int = 2000) Aspirate a certain volume in milliliters. Used only to move the syringe; to aspirate from a particular well, see aspirate() :param vol: Volume to aspirate, in milliliters :type vol: float :param s: Speed at which to aspirate in mm/min, defaults to 2000 :type s: int, optional .. py:method:: _dispense(vol, s: int = 2000) Dispense a certain volume in milliliters. Used only to move the syringe; to dispense into a particular well, see dispense() :param vol: Volume to dispense, in milliliters :type vol: float :param s: Speed at which to dispense in mm/min, defaults to 2000 :type s: int, optional .. py:method:: aspirate(vol: float, location: Union[science_jubilee.labware.Labware.Well, Tuple, science_jubilee.labware.Labware.Location], s: int = 2000) Aspirate a certain volume from a given well. :param vol: Volume to aspirate, in milliliters :type vol: float :param location: The location (e.g. a `Well` object) from where to aspirate the liquid from. :type location: Union[Well, Tuple, Location] :param s: Speed at which to aspirate in mm/min, defaults to 2000 :type s: int, optional .. py:method:: dispense(vol: float, location: Union[science_jubilee.labware.Labware.Well, Tuple, science_jubilee.labware.Labware.Location], s: int = 2000) Dispense a certain volume into a given well. :param vol: Volume to dispense, in milliliters :type vol: float :param location: The location to dispense the liquid into. :type location: Union[Well, Tuple, Location] :param s: Speed at which to dispense in mm/min, defaults to 2000 :type s: int, optional