A toolkit to generate MR sequence diagrams

Overview

mrsd: a toolkit to generate MR sequence diagrams

mrsd is a Python toolkit to generate MR sequence diagrams, as shown below for the basic FLASH sequence.

FLASH sequence diagram generated with mrsd

mrsd is based on Matplotlib and additionally requires numpy. The code which generated the previous diagram is available in the examples direction, and an excerpt is shown below.

figure, plot = matplotlib.pyplot.subplots()
diagram = mrsd.Diagram(
    plot, ["RF", "$G_{slice}$", "$G_{phase}$", "$G_{readout}$", "Signal"])

# Slice-selective pulse of the first TR
diagram.sinc_pulse("RF", 0, RF_duration, 1)
diagram.gradient("$G_{slice}$", *RF[0], selection)
diagram.idle(["$G_{phase}$", "$G_{readout}$", "Signal"], *RF[0])

# Dead time until the start of encoding
diagram.idle_all(RF[0][1], encoding[0])

# Encoding: rewind slice-selection gradient, run phase gradient, prephase
# read-out gradient
diagram.gradient("$G_{slice}$", *encoding, rewind)
diagram.stepped_gradient("$G_{phase}$", *encoding, 1)
diagram.gradient("$G_{readout}$", *encoding, prephasing)
diagram.idle(["RF", "Signal"], *encoding)

# Readout, centered on TE
diagram.gradient("$G_{readout}$", *readout, dephasing)
diagram.readout("Signal", *readout, +1)
diagram.idle(["RF", "$G_{slice}$", "$G_{phase}$"], *readout)

# Idle until end of TR
diagram.idle_all(readout[1], RF[1][0])

# Start of next TR
diagram.sinc_pulse("RF", TR, RF_duration, 1)
diagram.gradient("$G_{slice}$", *RF[1], selection)
diagram.idle(["$G_{phase}$", "$G_{readout}$", "Signal"], *RF[1])
diagram.idle_all(TR+RF_duration/2, TR+RF_duration)

# Add annotations: flip angles and TE/TR intervals
diagram.annotate("RF", 0.2, r"$\alpha$", 1)
diagram.annotate("RF", TR+0.2, r"$\alpha$", 1)
diagram.interval(0, TE, -1.5, "TE", 10)
diagram.interval(0, TR, -2.5, "TR", 10)
Owner
Julien Lamy
Julien Lamy
Data Visualizer for Super Mario Kart (SNES)

Data Visualizer for Super Mario Kart (SNES)

MrL314 21 Nov 20, 2022
Draw datasets from within Jupyter.

drawdata This small python app allows you to draw a dataset in a jupyter notebook. This should be very useful when teaching machine learning algorithm

vincent d warmerdam 505 Nov 27, 2022
Python Data. Leaflet.js Maps.

folium Python Data, Leaflet.js Maps folium builds on the data wrangling strengths of the Python ecosystem and the mapping strengths of the Leaflet.js

6k Jan 02, 2023
Python toolkit for defining+simulating+visualizing+analyzing attractors, dynamical systems, iterated function systems, roulette curves, and more

Attractors A small module that provides functions and classes for very efficient simulation and rendering of iterated function systems; dynamical syst

1 Aug 04, 2021
A Simple Flask-Plotly Example for NTU 110-1 DSSI Class

A Simple Flask-Plotly Example for NTU 110-1 DSSI Class Live Demo Prerequisites We will use Flask and Ploty to build a Flask application. If you haven'

Ting Ni Wu 1 Dec 11, 2021
A python script editor for napari based on PyQode.

napari-script-editor A python script editor for napari based on PyQode. This napari plugin was generated with Cookiecutter using with @napari's cookie

Robert Haase 9 Sep 20, 2022
Pglive - Pglive package adds support for thread-safe live plotting to pyqtgraph

Live pyqtgraph plot Pglive package adds support for thread-safe live plotting to

Martin Domaracký 15 Dec 10, 2022
Arras.io Highest Scores Over Time Bar Chart Race

Arras.io Highest Scores Over Time Bar Chart Race This repo contains a python script (make_racing_bar_chart.py) that can generate a csv file which can

Road 2 Jan 16, 2022
A streamlit component for bi-directional communication with bokeh plots.

Streamlit Bokeh Events A streamlit component for bi-directional communication with bokeh plots. Its just a workaround till streamlit team releases sup

Ashish Shukla 123 Dec 25, 2022
Implementation of SOMs (Self-Organizing Maps) with neighborhood-based map topologies.

py-self-organizing-maps Simple implementation of self-organizing maps (SOMs) A SOM is an unsupervised method for learning a mapping from a discrete ne

Jonas Grebe 6 Nov 22, 2022
Simple Python interface for Graphviz

Simple Python interface for Graphviz

Sebastian Bank 1.3k Dec 26, 2022
Print matplotlib colors

mplcolors Tired of searching "matplotlib colors" every week/day/hour? This simple script displays them all conveniently right in your terminal emulato

Brandon Barker 32 Dec 13, 2022
Some problems of SSLC ( High School ) before outputs and after outputs

Some problems of SSLC ( High School ) before outputs and after outputs 1] A Python program and its output (output1) while running the program is given

Fayas Noushad 3 Dec 01, 2021
NorthPitch is a python soccer plotting library that sits on top of Matplotlib

NorthPitch is a python soccer plotting library that sits on top of Matplotlib.

Devin Pleuler 30 Feb 22, 2022
Create Badges with stats of Scratch User, Project and Studio. Use those badges in Github readmes, etc.

Scratch-Stats-Badge Create customized Badges with stats of Scratch User, Studio or Project. Use those badges in Github readmes, etc. Examples Document

Siddhesh Chavan 5 Aug 28, 2022
Moscow DEG 2021 elections plots

Построение графиков на основе публичных данных о ДЭГ в Москве в 2021г. Описание Скрипты в данном репозитории позволяют собственноручно построить графи

9 Jul 15, 2022
Smarthome Dashboard with Grafana & InfluxDB

Smarthome Dashboard with Grafana & InfluxDB This is a complete overhaul of my Raspberry Dashboard done with Flask. I switched from sqlite to InfluxDB

6 Oct 20, 2022
A python script to visualise explain plans as a graph using graphviz

README Needs to be improved Prerequisites Need to have graphiz installed on the machine. Refer to https://graphviz.readthedocs.io/en/stable/manual.htm

Edward Mallia 1 Sep 28, 2021
Simple function to plot multiple barplots in the same figure.

Simple function to plot multiple barplots in the same figure. Supports padding and custom color.

Matthias Jakobs 2 Feb 21, 2022