control-lab-ly 0.0.4

Lab Equipment Automation Package

Control.lab.ly

Lab Equipment Automation Package

Description

User-friendly package that enables flexible automation an reconfigurable setups for high-throughput experimentation and machine learning.

Device support

• Make
  • Multi-channel spin-coater [Arduino]
  • Multi-channel LED array [Arduino]
  • Peltier device [Arduino]
• Measure
  • (Keithley) 2450 Source Measure Unit (SMU) Instrument
  • (PiezoRobotics) Dynamic Mechanical Analyser (DMA)
  • Precision mass balance [Arduino]
• Move
  • (Creality) Ender-3
  • (Dobot) M1 Pro
  • (Dobot) MG400
  • Primitiv [Arduino]
• Transfer
  • (Sartorius) rLINE® dispensing modules
  • (TriContinent) C Series syringe pumps
  • Peristaltic pump and syringe system [Arduino]
• View
  • (FLIR) AX8 thermal imaging camera - full functionality in development
  • Web cameras [General]

Installation

$ pip install control-lab-ly

Usage

Import package

import controllably as lab

[Optional] Set safety level for session

lab.set_safety('high')  # Pauses for input before every move action
lab.set_safety('low')   # Waits for countdown before every move action

Import desired class

from controllably.Move.Cartesian import Ender
mover = Ender(...)
mover.safeMoveTo((x,y,z))

More details for each class / module / package can be explored by using the help function.

help(controllably.Move)   # help on package
help(Ender)               # help on class
help(mover)               # help on instance/object

Alternatively, you can use the native pydoc documentation generator.

$ python -m pydoc controllably.Move
$ python -m pydoc controllably.Move.Cartesian.Ender

Tip: when using Interactive Python (IPython) (e.g. Jupyter notebooks), add a exclamation mark (!) in front of the shell command

>>> !python -m pydoc controllably

Create new project

Create a /configs folder in the base folder of your project repository to store all configuration related files from which the package will read from.
This only has to be done once when you first set up the project folder.

lab.create_configs()

A different address may be used by different machines for the same device. To manage the different addresses used by different machines, you first need your machine's unique identifier.

# Get your machine's ID
print(lab.Helper.get_node())

A template of registry.yaml has also been added to the folder to hold the machine-specific addresses of your connected devices (i.e. COM ports).
Populate the YAML file in the format shown below.

### registry.yaml ###
'0123456789ABCDE':              # insert your machine's ID here (from the above step)
    cam_index:                  # camera index of the connected imaging devices
      __cam_01__: 1             # keep the leading and trailing double underscores
      __cam_02__: 0
    port:                       # addresses of serial COM ports
      __device_01__: COM3       # keep the leading and trailing double underscores
      __device_02__: COM16

To find the COM port address(es) of the device(s) that is/are currently connected to your machine, use

lab.Helper.get_ports()

Create new setup

Create a new folder for the configuration files of your new setup. If you had skipped the previous step of creating a project, calling lab.create_setup will also generate the required file structure. However, be sure to populate your machine ID and device addresses in the registry.yaml file.

lab.create_setup(setup_name = "Setup01")
# replace "Setup01" with the desired name for your setup

This creates a /Setup01 folder that holds the configuration files for the setup, which includes config.yaml and layout.json.

config.yaml

Configuration and calibration values for your devices is stored in config.yaml.
Each configuration starts with the name of your device, then its module, class, and settings.

### config.yaml ###
Device01:                                         # name of simple device (user-defined)
  module: __module_name_01__                      # device module
  class: __submodule_1A__.__class_1A__            # device class
  settings:
    port: __device_01__                           # port addresses defined in registry.yaml
    __setting_A__: {'tuple': [300,0,200]}         # use keys to define the type of iterable
    __setting_B__: {'array': [[0,1,0],[-1,0,0]]}  # only tuple and np.array supported

Compound devices are similarly configured. The configuration values for its component devices are defined under the component_config setting. The structure of the configuration values for the component devices are similar to that shown above, except indented to fall under the indentation of the component_config setting.

### config.yaml ###
Device02:                                     # name of 'Compound' device (user-defined)
  module: Compound                            
  class: __submodule_2A__.__class_2A__
  settings:
    __setting_C__: 1                          # other settings for your 'Compound' device
    component_config:                         # nest component configuration settings here
      Component01:                            # name of component
        module: __module_name_03__
        class: __submodule_3A__.__class_3A__
        settings:
          ip_address: '192.0.0.1'             # IP addresses do not vary between machines
      Component02: 
        module: __module_name_04__
        class: __submodule_4A__.__class_4A__
        settings:
          __setting_D__: 2                    # settings for your component device

Lastly, you can define shortcuts to quickly access components of Compound devices.

### config.yaml ###
SHORTCUTS:
  robot_arm: myCompoundDevice.mover
  Nickname1: Device02.Component01
  Nickname2: Device02.Component02

layout.json

Layout configuration of your physical workspace (Deck) will be stored in layout.json. This package uses the same Labware files as those provided by Opentrons, which can be found here, and custom Labware files can be created here. Labware files are JSON files that specifies the external and internal dimensions of a Labware block/module.

This file is optional if your setup does not involve moving objects around in a pre-defined workspace, and hence a layout configuration may not be required.

{
  "reference_points":{
    "1": ["_x01_","_y01_","_z01_"],
    "2": ["_x02_","_y02_","_z02_"]
  },
  "slots":{
    "1": {
      "name": "Labware01",
      "exclusion_height": -1,
      "filepath": "REPO/.../Labware01.json"
    },
    "2": {
      "name": "Labware02",
      "exclusion_height": 0,
      "filepath": "REPO/.../Labware02.json"
    },
    "3": {
      "name": "Labware03",
      "exclusion_height": 10,
      "filepath": "REPO/.../Labware03.json"
    }
  }
}

In reference_points, the bottom-left coordinates of each slot in the workspace are defined. Slots are positions where Labware blocks may be placed.

In slots, the name of each slot and the file reference for Labware block that occupies that slot are defined. The filepath starts with the repository's base folder name.
The exclusion_height is the height (in mm) above the dimensions of the Labware block to steer clear from when performing move actions. Defaults to -1 (i.e. do not avoid).
[Note: only applies to final coordinates. Does not guarantee avoidance when using point-to-point move actions. Use safeMoveTo instead.]

Load setup

The initialisation of the setup occurs during the import SETUP from within configs/Setup01.

# Add repository folder to sys.path
from pathlib import Path
import sys
REPO = 'REPO'
ROOT = str(Path().absolute()).split(REPO)[0]
sys.path.append(f'{ROOT}{REPO}')

# Import the initialised setup
from configs.Setup01 import SETUP
this = SETUP

With this, you can access all the devices that you have defined in configs.yaml.

this.myCompoundDevice
this.robot_arm

Load deck

To load the Deck from the layout file, use the lab.load_deck function.

from configs.Setup01 import LAYOUT_FILE
lab.load_deck(this.DeviceWithDeck, LAYOUT_FILE)

Package Structure

1. Analyse
2. Compound
3. Control
4. Make
5. Measure
6. Move
7. Transfer
8. View

Dependencies

• Dash (>=2.7.1)
• Impedance (>=1.4.1)
• Imutils (>=0.5.4)
• Matplotlib (>=3.3.4)
• Nest-asyncio (>=1.5.1)
• Numpy (>=1.19.5)
• Opencv-python (>=4.5.4.58)
• Pandas (>=1.2.4)
• Plotly (>=5.3.1)
• PyModbusTCP (>=0.2.0)
• Pyserial (>=3.5)
• PySimpleGUI (>=4.60.4)
• PyVISA (>=1.12.0)
• PyYAML (>=6.0)
• Scipy (>=1.6.2)

Contributors

@kylejeanlewis
@mat-fox
@Quijanove
@AniketChitre

How to Contribute

Issues and feature requests are welcome!

License

This project is distributed under the MIT License.

Change Log

Unreleased

Items under development

0.0.4.x

Introduced control for Peltier device and TriContinent Series C syringe pumps. First released 10 Mar 2023.

Added

0.0.4

• Added control for Peltier
  • set and get temperatures
  • hold temperatures for desired duration
  • checks if target temperature has been reached by checking power level lower than a threshold or time passed over a predefined duration, once the temperature is within tolerance
  • ability to record temperatures and timestamps
• Added control for TriContinent and TriContinentEnsemble
  • single actions such as empty, fill, initialise, move actions, set speeds and valves, and wait
  • compound actions such as aspirate, dispense, and prime

Changed

0.0.4

• Update documentation

0.0.3.x

Minor changes to movement robot safety and pipette control. Introduced control for LED array. First released 08 Mar 2023.

Added

0.0.3

• Added safety measures for movement actions
  • In Deck, added exclusion zones when reading the layout.json file and new method is_excluded() to check if target coordinate is within the exclusion zone
  • In Mover, update isFeasible() method to check if target coordinates violates the deck's exclusion zone
  • New function set_safety() defines safety modes when starting a new session to pause for input (in "high" safety setting) and to wait for safety countdown (in "low" safety setting)
• Make.Light.LEDArray for controlling LEDs in the photo-reactor, as well as timing the LED "on" durations

Changed

0.0.3.1

• Update documentation

0.0.3

• Sartorius
  • made the blowout/home optional for the dispense method upon emptying the pipette
• Update documentation

0.0.2.x

Updates in setting up configuration files. First released 24 Feb 2023.

Added

0.0.2.2

• Added import of CompoundSetup class

0.0.2

• Deck.at() method for directly referencing slots using either index numbers or names
• New CompoundSetup class for common methods of Compound devices
• New load_deck() function to load Deck after initialisation

Changed

0.0.2.1

• Changed template files for lab.create_setup()

0.0.2

• Update documentation

0.0.1.x

First release of Control.lab.ly distributed on 23 Feb 2023.

Added

• Make
  • Multi-channel spin-coater [Arduino]
• Measure
  • (Keithley) 2450 Source Measure Unit (SMU) Instrument
  • (PiezoRobotics) Dynamic Mechanical Analyser (DMA)
  • Precision mass balance [Arduino]
• Move
  • (Creality) Ender-3
  • (Dobot) M1 Pro
  • (Dobot) MG400
  • Primitiv [Arduino]
• Transfer
  • (Sartorius) rLINE® dispensing modules
  • Peristaltic pump and syringe system [Arduino]
• View
  • (FLIR) AX8 thermal imaging camera - full functionality in development
  • Web cameras [General]
• misc
  • Helper class for most common actions
  • create_configs: make new directory for configuration files
  • create_setup: make new directory for specific setup-related files
  • load_setup: initialise setup on import during runtime

0.0.0.x

Pre-release packaging checks