<commit_before># girguis-isms

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


## Operation of the ISMS Calibration Station
Yeah we need to figure this out...

## File Overview
**calboard_sketch/calboard_sketch.ino** # sketch for the arduino connected to the Calibration Board  
**README.md**  # documentation  
**arduino_comm.py**  # test file for controlling arduino and commanding via python  
**calibrate_isms.py** # main control file for calibrating the mass spec  

## Tech Stack
#### Languages
* Python
   * Modules
      * Tkinter - Graphical Interface (Python interface to the TK GUI toolkit)
      * PySerial - access to serial comm functions
      
### Tested Environment (recommended)
* OSX
* python2

#### Setup
* pip install pyserial
* 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 
      
#### References
* Tkinter
   * https://wiki.python.org/moin/TkInter
   * https://docs.python.org/2/library/tkinter.html
   * http://www.tkdocs.com/tutorial/concepts.html<commit_msg>big updates to readme<commit_after># girguis-isms

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

## 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 simulations 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

## Operation of the ISMS Calibration Station
Yeah we need to figure this out...

## 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


## Tech Stack
* Python27
   * 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
* python27

#### Setup
* On OSX
   * pip install pyserial
   * 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
{'fraction_non_alphanumeric': 0.08721624850657109, 'fraction_numerical': 0.01027479091995221, 'mean_word_length': 3.501075268817204, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 11, 'lorem ipsum': 0, 'www.': 9, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 5, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5718518', 'n_tokens_mistral': 1325, 'n_tokens_neox': 1212, 'n_words': 426}