science_jubilee.tools.Spectrometer ================================== .. py:module:: science_jubilee.tools.Spectrometer Classes ------- .. autoapisummary:: science_jubilee.tools.Spectrometer.Labware science_jubilee.tools.Spectrometer.Location science_jubilee.tools.Spectrometer.Well science_jubilee.tools.Spectrometer.Tool science_jubilee.tools.Spectrometer.SpectroscopyTool science_jubilee.tools.Spectrometer.MeasurementManager Functions --------- .. autoapisummary:: science_jubilee.tools.Spectrometer.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:function:: requires_active_tool(func) Decorator to ensure that a tool cannot complete an action unless it is the current active tool. .. py:class:: SpectroscopyTool(index, name) Bases: :py:obj:`science_jubilee.tools.Tool.Tool`, :py:obj:`oceandirect.OceanDirectAPI.OceanDirectAPI` A class representation for an Ocean Optics Spectrometer, Light source, and Probe For that we wil be unfortunately using their own SDK package, which is NOT open-source. .. py:property:: _api_version The version of the Ocean Insight SDK .. py:property:: _usb_device .. py:property:: _device_id The ID of the spectrometer .. py:method:: _open_device() Connects to the spectrometer device .. py:property:: _model The spectrometer model .. py:property:: _serial_number The spectrometer serial number .. py:property:: _integration_time .. py:method:: integration_time(t: float, units: str = 'ms') Sets the integration time for the spectrometer. :param t: integration time :type t: float :param units: units of integration time, defaults to 'ms' :type units: str, optional .. py:property:: wavelengths Return list containing the wavelengths of the spectrometer. :return: A list of wavelengths :rtype: list .. py:method:: scans_to_average(n: int) Set the number of scans to average together to compose a single spectrum. :param n: number of scans to average :type n:int .. py:method:: boxcar_width(w: int = None) Unit used to smooth the spectrum. The boxcar width is the number of adjacent pixels that are averaged together to smooth the spectrum. Pixel average = 2* boxcar_width + 1 :param w: boxcar width :type w: int .. py:method:: lamp_shutter(open=True) Opens or closes light source shutter, if feature is available on light source.) :param open: True opens the shutter/False closes it, defaults to False :type state: bool, optional .. py:method:: _take_spectrum(open=True) Collect a spectrum with the specified experimental parameters .. py:method:: dark_spectrum(int_time: float, scan_num: int, boxcar_w: int = None, save: bool = False, path: str = None, filename: str = None) Collect a dark spectrum with the specified experimental parameters. A dark spectrum is collected when no light is incident on the detector. This shuold later be used to correct the actual spectrum for dark counts (i.e. thermal noise). Note: these shuold be the same as the ones used for the actual spectrum. :param int_time: integration time .. py:method:: _collect_raw_spectrum(int_time: float, scan_num: int, boxcar_w: int, int_time_units: str = 'ms') Collect a spectrum with the specified experimental parameters :param int_time: integration time :type int_time: float :param scan_num: number of scans to average :type scan_num: int :param boxcar_w: boxcar width for smoothing the spectrum, defaults to None :type boxcar_w: int, optional :param int_time_units: units of integration time, defaults to 'ms' :type int_time_units: str, optional :return: spectrum :rtype: numpy array .. py:method:: collect_spectrum(location: Union[science_jubilee.labware.Labware.Well, Tuple, science_jubilee.labware.Labware.Location], int_time, scan_num, boxcar_w, int_time_units='ms', save: bool = False, filename: str = None, path: str = None) Collect spectrum at the specified location on the labware .. py:method:: save_to_file(data, dark: bool = False, path: str = None, filename: str = None) Save the spectrum to a file .. py:method:: read_from_file(filepath, scale=True, reference_spectrum=None) .. py:method:: scale_intensity(data: list, reference_spectrum: list) :staticmethod: .. py:class:: MeasurementManager(metadata, raw_data) A class to manage the measurements taken by the SpectroscopyTool .. py:method:: pretty_print() .. py:method:: generate_file(filename, path) .. py:method:: read_file()