icarus_v2 0.1.0

Monitoring software for the Icarus Pressure Jump apparatus

icarus v2

Monitoring software for the Icarus NMR pressure jump apparatus

Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Roadmap
5. Contributing
6. License
7. Contact
8. Acknowledgments

About The Project

The Icarus NMR Pressure Jump Apparatus is a novel device used to rapidly switch the pressure within an NMR sample cell. This enables study of the unfolded protein under native conditions and, vice versa, study of the native protein under denaturing conditions. This project is the second version of a monitoring software for the pressure sensors and digital controls. It is responsible for displaying device readings, controlling and testing hardware, and detecting faults.

Once a DATAQ DI-4108 USB device is detected by the monitoring software, it establishes a connection and begins reading data from the USB device at 4000Hz. The analog and digital channels monitored are as follows:

• Analog:
  CH0: target pressure sensor
  CH1: depressurization valve lower sensor
  CH2: depressurization valve upper sensor
  CH3: pressurization valve lower sensor
  CH4: pressurization valve upper sensor
  CH5: high pressure sensor at the origin
  CH6: high pressure sensor at the sample
• Digital:
  CH0: high pressure pump control
  CH1: depressurize valve control
  CH2: pressurize valve control
  CH4: log control

The data is stored in a circular buffer with a default length of 2 minutes. The data is read by many event handlers which each detect certain features in the readings. They then signal events containing their respective data which may be read by the GUI. The event handlers are as follows:

1. Depressurize: detects high to low state transitions in digital CH0
2. Pressurize: detects high to low state transitions in digital CH1
3. Period: detects consecutive high to low state transitions in digital CH1
4. Pressure: detects current pressure of analog CH5
5. Pump: detects drops in analog CH0, signifying the pump stroking
6. Log: detects state changes in digital CH4

The digital channels may be controlled by the software by sending commands to the DATAQ DI-4108. This is used for the following:

1. Toggling the high pressure pump
2. Hardware tests under manual device operation
3. Shutdowns, either manual or when a fatal error is detected by the Sentry

All events are transmitted to the GUI and are rendered in dedicated event plots, history plots, and status indicators. They are also transmitted to a Sentry module which analyzes them to detect leaks and abnormal behavior. In the event of a serious leak, the device will automatically shut down. Pressurize, depressurize, and period events are also transmitted to a logger, which generates LZMA compressed log files. These files may be opened by the GUI for later viewing.

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Built With

Python >=3.10, <=3.12

PySide6

PyQtDarkTheme

poetry

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Getting Started

Prerequisites

System Requirements

These instructions are tailored for Ubuntu 24, which is the only operating system tested and supported for this setup.

Installing Python

Ensure you have Python 3.10-3.12 installed on your system. If you do not have Python installed, you can install it using the following commands:

sudo apt update
sudo apt install python3.12

Cloning the Repository

Before you can start setting up your environment, you'll need to clone the repository containing the project. Open your terminal and execute the following command:

git clone https://github.com/SeanIFitch/icarus_v2
cd icarus_v2

Installation

Setting Up Your Environment

1. Create a Virtual Environment: Use a virtual environment to manage dependencies effectively and avoid conflicts between package versions. Run the following command in your project directory to create a virtual environment:

   python3.12 -m venv icarus_venv
   

2. Activate the Virtual Environment: Once the virtual environment is created, activate it with:

   source icarus_venv/bin/activate
   

Installing Dependencies

With the virtual environment activated, you can now install all required packages from required-packages.txt. Install these packages by running:

pip install -r requirements.txt

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Usage

To start the application, ensure you have activated the virtual environment:

source icarus_venv/bin/activate

And then, launch the application using:

python3 src/__main__.py

Note: the first time the application is run with a DATAQ connected, it will attempt to install a udev rule to allow access to the USB device. This requires admin permissions. If the application fails to connect to the device after a few seconds, reboot your computer to ensure the udev rules are fully reloaded.

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Roadmap

See the open issues for a full list of proposed features (and known issues).

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Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

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License

Distributed under the MIT License. See LICENSE.txt for more information.

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Contact

Sean Fitch - [e-mail]

Project Link: https://github.com/SeanIFitch/icarus_v2

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Acknowledgments

• Dr. Philip Anfinrud - Software specification
• icarus-nmr by Valentyn Stadnytskyi

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