girguis-isms

This code allows the Girguis Lab In-Situ Mass Spectrometer to be calibrated automatically before a deployment.

File Overview

README.md # documentation
calboard_sketch/calboard_sketch.ino # sketch for the arduino connected to the Calibration Board
manual_controllers/ # simplified controllers to allow manual commanding and testing of all devices
arduino_comm.py # test file for controlling arduino and commanding via python
calibrate_isms.py # main control file for calibrating the mass spec
calcCRC.py # simple python script to calculate the checksum required for serial comm with the MFCs

Hardware:

• 1x Temp Bath - Thermo Scientific Temperature Bath
• 1x HPLC Pump - ChromTech Dual Piston HPLC Pump
• 1x Arduino - standard Arduino Mega 2560 for controlling the calibration board
• 1x Calibration Board - custom setup with two high pressure loops for and one low pressure loop that simulates the deep sea pressure and gas environment allowing for calibration of the ISMS inlet
• 2x Mass Flow Controllers - Sierra Instruments SmartTrak Series 100 Mass Flow Controller
• 1x Valco 6-Port Valve - Valco Instruments 6-Port Valve Actuators

Tech Stack

• Python
  • Modules
    • Tkinter - Graphical Interface (Python interface to the TK GUI toolkit)
    • PySerial - access to serial comm functions

Tested Environments (recommended)

• OSX or Windows 7

Tested Python Versions

• Python 2.7.x

Setup

• On OSX

  • install Python 2.7.x from https://www.python.org/downloads/mac-osx/
  • from the terminal trype 'pip install pyserial'
  • install git from https://git-scm.com/download/mac
    • from the terminal type ‘git clone https://github.com/patrickcgray/girguis-isms.git’
  • Required Support/Drivers
    • Drivers for serial devices
      • FTDI: http://www.ftdichip.com/FTDrivers.htm
      • Prolific: http://www.prolific.com.tw/US/ShowProduct.aspx?p_id=229&pcid=41

• For clean Windows 7 Setup

  • Install python 2.7.x https://www.python.org/downloads/windows/
    • Open command prompt
    • Navigate to the directory where python is installed (default C:/Python27)
    • Run the command python ‘python -m pip install pyserial’
  • Install git https://git-scm.com/download/win
    • Use all default settings
    • Open Git GUI
      • Clone from https://github.com/patrickcgray/girguis-isms.git
    • OR from git bash
      • Type ‘git clone https://github.com/patrickcgray/girguis-isms.git’
  • Required Drivers
    • For all devices connected using this cable for this cable https://www.sabrent.com/product/SBT-USC1M/usb-serial-cable-adapter/ Type ‘SBT-USC1M’ into this page to get rs232-usb cable drivers https://www.sabrent.com/downloads/?wpdmc=windows-drivers
    • For HPLC Pump
      • Navigate to https://ssihplc.com/manuals/#driver-downloads and download ‘NXP Virtual COM port USB drivers (Micro USB)’

References

• Tkinter
  • https://wiki.python.org/moin/TkInter
  • https://docs.python.org/2/library/tkinter.html
  • http://www.tkdocs.com/tutorial/concepts.html
• PySerial
  • https://pythonhosted.org/pyserial/pyserial.html