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MRathon deliverable - NeuroLibre-ready setup (#12)
* Moved notebooks to content folder * Added requirements.txt . * First draft of cylinder-based simulations. * Fixed requirements.txt . * Make template jupyter book files * Add empty binder files * Add github pages action * Add github pages action * Add jupyterbook requirement * Add missing xml req * Added first plots to cylinder simulations. * Add template plotly figure * Add neurolibre paper.md * Update requirements * Added slider-based figure. * Add interactive figures * Update main.yml * Delete cylinder_sim.ipynb * Update _config.yml * Remove html files --------- Co-authored-by: Matteo Mancini <[email protected]> Co-authored-by: Alexandre D'Astous <[email protected]>
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‎.github/workflows/main.yml

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name: deploy-book
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# Only run this when the v2 branch changes
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on:
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push:
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branches:
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- main
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# If your git repository has the Jupyter Book within some-subfolder next to
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# unrelated files, you can make this run only if a file within that specific
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# folder has been modified.
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# paths:
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# - source/**
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# This job installs dependencies, build the book, and pushes it to `gh-pages`
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jobs:
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deploy-book:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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# Install dependencies
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- name: Set up Python 3.8
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uses: actions/setup-python@v1
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with:
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python-version: 3.8
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- name: Install dependencies
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run: |
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pip install -r binder/requirements.txt
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- name: Postbuild
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run: |
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chmod +xxx binder/postBuild
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binder/postBuild
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# Build the book
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- name: Build the book
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run: |
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jupyter-book build content/index.ipynb --builder singlehtml
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# Push the book's HTML to github-pages
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- name: GitHub Pages action
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uses: peaceiris/[email protected]
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./content/_build/_page/index/singlehtml

‎.gitignore

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.DS_Store
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.ipynb_checkpoints
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.ipynb_checkpoints
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content/_build/

‎binder/postBuild

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‎binder/requirements.txt

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jupyter-book==0.13.0
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lxml_html_clean
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nibabel
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pandas
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plotly
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scipy

‎binder/runtime.txt

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python-3.8

‎content/_config.yml

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# Book settings
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# Learn more at https://jupyterbook.org/customize/config.html
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title: B0 mapping
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logo: logo.png
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# Force re-execution of notebooks on each build.
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# See https://jupyterbook.org/content/execute.html
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execute:
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execute_notebooks: force
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launch_buttons:
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notebook_interface: "jupyterlab"
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# Information about where the book exists on the web
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repository:
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url: https://github.com/qMRLab/qMRI-MOOC_B0-module # Online location of your book
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path_to_book: content # Optional path to your book, relative to the repository root
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branch: main # Which branch of the repository should be used when creating links (optional)
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only_build_toc_files: true
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execute:
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timeout: 600
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sphinx:
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local_extensions : # A list of local extensions to load by sphinx specified by "name: path" items
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recursive_update : false # A boolean indicating whether to overwrite the Sphinx config (true) or recursively update
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config : # key-value pairs to directly over-ride the Sphinx configuration
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bibtex_reference_style: author_year
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bibtex_default_style: plain
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bibtex_tooltips: true
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html_static_path: ['_static']
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html_css_files: ['custom.css']
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bibtex_bibfiles:
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- ../paper.bib

‎content/_static/custom.css

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p {
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text-align: justify;
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}
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a {
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color: #870000!important;
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}
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a:hover {
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color: brick!important;
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}
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a:visited {
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color: #6f42c1!important;
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}
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body, h1, h2, h3, h4, h5 {
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font-family: 'STIX Two Text';
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}
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h1 {
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color: #342727!important;
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}
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.caption {
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text-align:justify;
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line-height:1.25;
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font-size:80%
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}
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#site-navigation {
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display: none;
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}
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#main-content{
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margin: 0 auto;
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}
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.fa, .far, .fas {
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color: red;
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}
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.header-article::after{
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content: url('https://neurolibre.org/assets/joss2-b7ea8dd1f24ce2b0825db17e3495576253ba4c64df3384a66354713d76c40a75.svg');
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width: 150px;
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height: 80px;
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position: relative;
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right: 10px;
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}
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.header-article::before{
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content: url('https://raw.githubusercontent.com/neurolibre/brand/b5e10e051a0059824ca2f4204e1288927e551d49/svg/neurolibre_logo.svg');
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width: 33px;
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height: 33px;
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position: absolute;
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left: 10px;
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}

‎content/_toc.yml

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# Table of contents
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# Learn more at https://jupyterbook.org/customize/toc.html
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format: jb-article
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root: paper

‎chapter4_1.ipynb ‎content/chapter4_1.ipynb

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‎chapter4_2.ipynb ‎content/chapter4_2.ipynb

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‎chapter4_3.ipynb ‎content/chapter4_3.ipynb

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‎content/figure.html

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‎content/index.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# MRathon 2024 - NeuroLibre preprint project\n",
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"\n",
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"Hello world!\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Figure 1"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide_input",
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"remove_output"
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]
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},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"from scipy.fft import fftn, ifftn, fftshift\n",
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"import plotly.express as px\n",
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"import plotly.graph_objects as go\n",
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"from plotly.subplots import make_subplots\n",
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"from IPython.display import display, HTML\n",
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"from plotly.offline import init_notebook_mode, iplot, plot\n",
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"\n",
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"init_notebook_mode(connected=True)\n",
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"vol_size = (128, 128, 128)\n",
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"vol_centre = (vol_size[1] // 2, vol_size[2] // 2)\n",
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"offset = (10, 20)\n",
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"radius_inner = 10\n",
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"radius_outer = 40\n",
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"cylinder_base = np.zeros(vol_size)\n",
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"cylinder_internal = np.zeros(vol_size)\n",
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"\n",
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"x = np.arange(-vol_size[1]//2,vol_size[1]//2,dtype=float)\n",
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"y = x\n",
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"z = x\n",
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"X,Y,Z = np.meshgrid(x,y,z)\n",
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"\n",
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"cylinder_base[X**2+Y**2<=radius_outer**2] = 1\n",
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"\n",
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"cylinder_internal[(X-offset[0])**2+(Y-offset[1])**2<=radius_inner**2] += 0.1\n",
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"\n",
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"kx = X\n",
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"ky = Y\n",
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"kz = Z\n",
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"KK = (kx**2 + ky**2 + kz**2)\n",
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"KK[KK==0] = np.nan\n",
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"dipole_kernel = 2./3 - (kx**2)/(KK)\n",
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"dipole_kernel[(kx**2 + ky**2 + kz**2) == 0] = 0\n",
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"\n",
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"fieldmap = np.real(ifftn(fftshift(dipole_kernel) * (fftn(cylinder_internal))))\n",
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"\n",
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"idx = 64\n",
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"\n",
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"fig = make_subplots(rows=1, cols=3, shared_xaxes=False, horizontal_spacing=0.1,\n",
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" subplot_titles=(\"Geometry\",\n",
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" \"Dipole kernel\",\n",
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" \"Fieldmap\"),\n",
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" specs=[[{\"type\": \"Heatmap\"}, {\"type\": \"Heatmap\"}, {\"type\": \"Heatmap\"}]])\n",
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"fig.add_trace(go.Heatmap(z=cylinder_base[:,:,idx]+cylinder_internal[:,:,64], colorscale='gray'), 1, 1)\n",
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"fig.add_trace(go.Heatmap(z=dipole_kernel[:,:,idx], colorscale='gray'), 1, 2)\n",
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"fig.add_trace(go.Heatmap(z=fieldmap[:,:,idx], colorscale='gray'), 1, 3)\n",
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"\n",
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"plot(fig, filename = 'geometry.html')\n",
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"\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"remove_input",
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"report_output"
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]
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},
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"outputs": [],
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"source": [
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"display(HTML('geometry.html'))"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Figure 2"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide_input",
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"remove_output"
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]
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},
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"outputs": [],
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"source": [
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"fig = go.Figure()\n",
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"\n",
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"echo_times = [10, 30, 50]\n",
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"for step in echo_times:\n",
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" fig.add_trace(\n",
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" go.Heatmap(\n",
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" visible=False,\n",
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" z=(fieldmap[:,:,idx]*step) % np.pi,\n",
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" colorscale='gray'))\n",
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"\n",
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"fig.data[0].visible = True\n",
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"\n",
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"# Create and add slider\n",
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"steps = []\n",
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"for i in range(len(fig.data)):\n",
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" step = dict(\n",
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" method=\"update\",\n",
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" args=[{\"visible\": [False] * len(fig.data)},\n",
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" {\"title\": \"TE=\" + str(echo_times[i]) + \" ms\"}], # layout attribute\n",
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" )\n",
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" step[\"args\"][0][\"visible\"][i] = True # Toggle i'th trace to \"visible\"\n",
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" steps.append(step)\n",
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"\n",
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"sliders = [dict(\n",
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" active=10,\n",
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" currentvalue={\"prefix\": \"Frequency: \"},\n",
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" pad={\"t\": 50},\n",
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" steps=steps\n",
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")]\n",
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"\n",
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"fig.update_layout(\n",
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" sliders=sliders\n",
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")\n",
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"\n",
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"plot(fig, filename = 'cylinder.html')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"remove_input",
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"report_output"
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]
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},
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"outputs": [],
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"source": [
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"display(HTML('cylinder.html'))"
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]
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}
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],
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"metadata": {
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"celltoolbar": "Tags",
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.13"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎content/logo.png

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‎paper.bib

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‎paper.md

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---
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title: B0 mapping
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tags:
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- NeuroLibre
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authors:
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- name: MRathon Group
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orcid:
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affiliation: 1
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affiliations:
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- name: Singapore
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index: 1
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date: 3 May 2024
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bibliography: paper.bib
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---
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# Summary
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# Statement of need
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# Figures
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# Acknowledgements
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## References

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