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 visualization electromagnetic spectrum

Datenvisualisierung-Elektromagnetischen-Spektrum Anhand des Moduls matplotlib sollen die Daten des elektromagnetischen Spektrums dargestellt werden. D

Pulsar 1 Sep 01, 2022
Create 3d loss surface visualizations, with optimizer path. Issues welcome!

MLVTK A loss surface visualization tool Simple feed-forward network trained on chess data, using elu activation and Adam optimizer Simple feed-forward

7 Dec 21, 2022
A command line tool for visualizing CSV/spreadsheet-like data

PerfPlotter Read data from CSV files using pandas and generate interactive plots using bokeh, which can then be embedded into HTML pages and served by

Gino Mempin 0 Jun 25, 2022
Sky attention heatmap of submissions to astrometry.net

astroheat Installation Requires Python 3.6+, Tested with Python 3.9.5 Install library dependencies pip install -r requirements.txt The program require

4 Jun 20, 2022
Some method of processing point cloud

Point-Cloud Some method of processing point cloud inversion the completion pointcloud to incomplete point cloud Some model of encoding point cloud to

Tan 1 Nov 19, 2021
RockNext is an Open Source extending ERPNext built on top of Frappe bringing enterprise ready utilization.

RockNext is an Open Source extending ERPNext built on top of Frappe bringing enterprise ready utilization.

Matheus Breguêz 13 Oct 12, 2022
Schema validation just got Pythonic

Schema validation just got Pythonic schema is a library for validating Python data structures, such as those obtained from config-files, forms, extern

Vladimir Keleshev 2.7k Jan 06, 2023
Seismic Waveform Inversion Toolbox-1.0

Seismic Waveform Inversion Toolbox (SWIT-1.0)

Haipeng Li 98 Dec 29, 2022
The plottify package is makes matplotlib plots more legible

plottify The plottify package is makes matplotlib plots more legible. It's a thin wrapper around matplotlib that automatically adjusts font sizes, sca

Andy Jones 97 Nov 04, 2022
termplotlib is a Python library for all your terminal plotting needs.

termplotlib termplotlib is a Python library for all your terminal plotting needs. It aims to work like matplotlib. Line plots For line plots, termplot

Nico Schlömer 553 Dec 30, 2022
Streamlit-template - A streamlit app template based on streamlit-option-menu

streamlit-template A streamlit app template for geospatial applications based on

Qiusheng Wu 41 Dec 10, 2022
This GitHub Repository contains Data Analysis projects that I have completed so far! While most of th project are focused on Data Analysis, some of them are also put here to show off other skills that I have learned.

Welcome to my Data Analysis projects page! This GitHub Repository contains Data Analysis projects that I have completed so far! While most of th proje

Kyle Dini 1 Jan 31, 2022
CompleX Group Interactions (XGI) provides an ecosystem for the analysis and representation of complex systems with group interactions.

XGI CompleX Group Interactions (XGI) is a Python package for the representation, manipulation, and study of the structure, dynamics, and functions of

Complex Group Interactions 67 Dec 28, 2022
🐞 📊 Ladybug extension to generate 2D charts

ladybug-charts Ladybug extension to generate 2D charts. Installation pip install ladybug-charts QuickStart import ladybug_charts API Documentation Loc

Ladybug Tools 3 Dec 30, 2022
Simple spectra visualization tool for astronomers

SpecViewer A simple visualization tool for astronomers. Dependencies Python = 3.7.4 PyQt5 = 5.15.4 pyqtgraph == 0.10.0 numpy = 1.19.4 How to use py

5 Oct 07, 2021
Visualize and compare datasets, target values and associations, with one line of code.

In-depth EDA (target analysis, comparison, feature analysis, correlation) in two lines of code! Sweetviz is an open-source Python library that generat

Francois Bertrand 2.3k Jan 05, 2023
Statistical data visualization using matplotlib

seaborn: statistical data visualization Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing

Michael Waskom 10.2k Dec 30, 2022
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
demir.ai Dataset Operations

demir.ai Dataset Operations With this application, you can have the empty values (nan/null) deleted or filled before giving your dataset to machine le

Ahmet Furkan DEMIR 8 Nov 01, 2022
Flow-based visual scripting for Python

A simple visual node editor for Python Ryven combines flow-based visual scripting with Python. It gives you absolute freedom for your nodes and a simp

Leon Thomm 3.1k Jan 06, 2023