Merge pull request #51 from machineagency/sonicator

Added Sonicator tool module and documentation. Also, fixed issue #50

science_jubilee/labware/Labware.py

@@ -1,9 +1,11 @@
+import os
+import json
+
 import numpy as np
+
 from dataclasses import dataclass
 from itertools import chain
 from typing import List, Dict, Tuple, Union, Iterable, NamedTuple
-import os
-import json
 
 
 @dataclass
@@ -509,6 +511,28 @@ def withWellOrder(self, order) -> list:
 
         self.wells = ordered_wells
 
+    @staticmethod
+    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
+
 ## Adapted from Opentrons API  opentrons.types##        
 class Point(NamedTuple):
     """A point in the Jubilee 3D coordinate system.

science_jubilee/tools/Camera.py

@@ -1,14 +1,16 @@
-from .Tool import Tool, ToolStateError, requires_active_tool
-from science_jubilee.labware.Labware import Labware, Well
-from typing import Tuple, Union
 import cv2
 import matplotlib
+import platform
+import time
+
+import numpy as np
 
 matplotlib.use("TkAgg")
 from matplotlib import pyplot as plt
-import numpy as np
-import time
-import platform
+from science_jubilee.labware.Labware import Well
+from science_jubilee.tools.Tool import Tool,  requires_active_tool
+from typing import Tuple
+
 
 if platform.system() == "Linux":
     import picamera  # Note that this can only be installed on raspbery pi.

science_jubilee/tools/Loop.py

@@ -1,11 +1,13 @@
-from science_jubilee.tools.Tool import Tool, ToolStateError, ToolConfigurationError, requires_active_tool
-from science_jubilee.labware.Labware import Labware, Well
-from typing import Tuple, Union
-import warnings
-import numpy as np
-import os
 import json
+import os
 import random
+import warnings
+
+import numpy as np
+
+from science_jubilee.labware.Labware import  Well
+from science_jubilee.tools.Tool import Tool,  requires_active_tool
+from typing import Tuple
 
 
 class Loop(Tool):

science_jubilee/tools/PeristalticPumps.py

@@ -2,8 +2,8 @@
 import logging
 import os
 
-from science_jubilee.tools.Tool import Tool, ToolStateError, ToolConfigurationError
-from typing import Tuple, Union
+from science_jubilee.tools.Tool import Tool 
+from typing import Union
 
 class PeristalticPumps(Tool):
     """

science_jubilee/tools/Pipette.py

@@ -4,7 +4,6 @@
 
 from science_jubilee.labware.Labware import Labware, Well, Location
 from science_jubilee.tools.Tool import Tool, ToolStateError, ToolConfigurationError, requires_active_tool
-from science_jubilee import utils
 from typing import Tuple, Union
 
 
@@ -23,7 +22,7 @@ def wrapper(self, *args, **kwargs):
 class Pipette(Tool):
     """ A class representation of an Opentrons OT2 pipette.
     """
-    def __init__(self, machine, index, name, brand, model, max_volume,
+    def __init__(self,  index, name, brand, model, max_volume,
                   min_volume, zero_position, blowout_position, 
                   drop_tip_position, mm_to_ul):
         """ Initialize the pipette object
@@ -49,14 +48,11 @@ def __init__(self, machine, index, name, brand, model, max_volume,
         :param mm_to_ul: The conversion factor for converting motor microsteps in mm to uL
         :type mm_to_ul: float
         """        
-        #TODO:Removed machine from init, check if this should be asigned here or is added later
         super().__init__(index, name, brand = brand, 
                          model = model, max_volume = max_volume, min_volume = min_volume,
                          zero_position = zero_position, blowout_position = blowout_position,
                          drop_tip_position = drop_tip_position, mm_to_ul = mm_to_ul)
-        self._machine = machine
         self.has_tip = False
-        # TODO: add a way to change this to True/False and check before performing action with tool
         self.first_available_tip = None
         self.tool_offset = self._machine.tool_z_offsets[self.index]
         self.is_primed = False 
@@ -68,8 +64,6 @@ def from_config(cls, index, name, config_file: str,
 
         """Initialize the pipette object from a config file
 
-        :param machine: The :class:`Machine` object that the pipette is loaded on
-        :type machine: :class:`Machine`
         :param index: The tool index of the pipette on the machine
         :type index: int
         :param name: The tool name
@@ -144,7 +138,7 @@ def aspirate(self, vol: float, location : Union[Well, Tuple, Location], s:int =
         :type s: int, optional
         :raises ToolStateError: If the pipette does not have a tip attached
         """
-        x, y, z = utils.getxyz(location)
+        x, y, z = Labware._getxyz(location)
 
         if type(location) == Well:
             self.current_well = location
@@ -194,7 +188,7 @@ def dispense(self, vol: float, location :Union[Well, Tuple, Location], s:int = 2
         :type s: int, optional
         :raises ToolStateError: If the pipette does not have a tip attached
         """
-        x, y, z = utils.getxyz(location)
+        x, y, z = Labware._getxyz(location)
 
         if type(location) == Well:
             self.current_well = location
@@ -245,7 +239,7 @@ def transfer(self, vol: float, source_well: Union[Well, Tuple, Location],
 
         vol_ = self.vol2move(vol)
         # get locations
-        xs, ys, zs = utils.getxyz(source_well)
+        xs, ys, zs = Labware._getxyz(source_well)
 
         if self.is_primed == True:
             pass
@@ -258,7 +252,7 @@ def transfer(self, vol: float, source_well: Union[Well, Tuple, Location],
 
         if isinstance(destination_well, list):
             for well in destination_well:
-                xd, yd, zd = utils.getxyz(well)
+                xd, yd, zd = Labware._getxyz(well)
 
                 self._machine.safe_z_movement()
                 self._machine.move_to(x= xs, y=ys)
@@ -459,7 +453,7 @@ def pickup_tip(self, tip_ : Union[Well, Tuple] = None):
         else:
             tip = tip_
 
-        x, y, z = utils.getxyz(tip)
+        x, y, z = Labware._getxyz(tip)
         self._machine.safe_z_movement()
         self._machine.move_to(x=x, y=y)
         self._pickup_tip(z)
@@ -480,9 +474,9 @@ def return_tip(self, location: Well = None):
         :type location: :class:`Well`, optional
         """
         if location is None:
-            x, y, z = utils.getxyz(self.first_available_tip)
+            x, y, z = Labware._getxyz(self.first_available_tip)
         else:
-            x, y, z = utils.getxyz(location)
+            x, y, z = Labware._getxyz(location)
         self._machine.safe_z_movement()
         self._machine.move_to(x=x, y=y)
         # z moves up/down to make sure tip actually makes it into rack 
@@ -517,7 +511,7 @@ def drop_tip(self, location: Union[Well, Tuple]):
         :param location: The location to drop the tip into
         :type location: Union[:class:`Well`, tuple]
         """        
-        x, y, z = utils.getxyz(location)
+        x, y, z = Labware._getxyz(location)
 
         self._machine.safe_z_movement()
         if x is not None or y is not None:

science_jubilee/tools/PumpDispenser.py

@@ -3,9 +3,9 @@
 import os
 
 from science_jubilee.labware.Labware import Labware, Well, Location
-from science_jubilee.tools.Tool import Tool, ToolStateError, ToolConfigurationError, requires_active_tool
+from science_jubilee.tools.Tool import Tool
 from typing import Tuple, Union
-from science_jubilee import utils
+
 
 class PumpDispenser(Tool):
     """
@@ -116,7 +116,7 @@ def dispense(self, vol: Union[float, int, list], location:Union[Well, Tuple, Loc
 
 
         # calculate XY location for each dispense head
-        x, y, z = utils.getxyz(location)
+        x, y, z = Labware._getxyz(location)
 
         if type(location) == Well:
             if z == location.z:
@@ -171,7 +171,7 @@ def prime_lines(self, volume: Union[int, float] = None, location:Union[Well, Tup
             location = self.waste
 
         # calculate XY location for each dispense head
-        x, y, z = utils.getxyz(location)
+        x, y, z = Labware._getxyz(location)
 
         if type(location) == Well:
             if z == location.z: