NMR Machine Simulator

Purpose

To demonstrate the macroscopic behavior of M in an NMR machine and to make clear the workflow of NMR analysis, I constructed a simulator of Bloch Equations. The user can configure all aspects of the device including B_DEV, M, T1, T2, and can send RF pulses with a specific applied magnetic field. The NMR simulator relies on the Vispy open source graphics library.

Usage

Python Enviroment Configuration

To setup the python enviroment, first create your venv by running python3 -m venv venv then activate your venv by running source venv/bin/activate. Install all of the required packages by running pip3 install -r requirements.txt.

Start the program

To run the simulator run python3 NMR_SIM.py. You may want to use a screen split function so that you can see all 4 windows at one time.

Configure simulation

To configure enromental variables of the simulator, use the config command in the command console. You can configure the magnetic field of the device (B_DEV), T1 and T2 (T1 and T2), and net starting magnetization (M) with the following commands

1. config B_DEV <Bx> <By> <Bz>
2. config M <Bx> <By> <Bz>
3. config T1 <value>
4. config T2 <value>

Start the simulation

You can start the simulation by running start. You can pause the simulation by running pause.

Initiating radio pulse

You can initiate a radio pule with the following commands: pulse <duration> or pulse <duration> <Bx> <By> <Bz>

Capture a photo of the simulation

You can capture a photo of the current frame by running capture <filename>.png

Fourier Transform to see the final NMR spectrum

Viewing the FID graph run fft <t1> <t2> to initiate an fourier transform with the data between t=t1 and t=t2.

Model Noise

To model a noisy enviroment run sh noisy.sh <pulse_timing> to snd in short radio bursts every <pulse_timing> seconds.