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 <ingmatteomancini@gmail.com>
Co-authored-by: Alexandre D'Astous <po09i@hotmail.com>

.github/workflows/main.yml

@@ -0,0 +1,43 @@
+name: deploy-book
+
+# Only run this when the v2 branch changes
+on:
+  push:
+    branches:
+    - main
+    # If your git repository has the Jupyter Book within some-subfolder next to
+    # unrelated files, you can make this run only if a file within that specific
+    # folder has been modified.
+    # paths:
+    # - source/**
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    # Install dependencies
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        pip install -r binder/requirements.txt
+    - name: Postbuild
+      run: |
+        chmod +xxx binder/postBuild
+        binder/postBuild
+    # Build the book
+    - name: Build the book
+      run: |
+        jupyter-book build content/index.ipynb --builder singlehtml
+    # Push the book's HTML to github-pages
+    - name: GitHub Pages action
+      uses: peaceiris/actions-gh-pages@v3.6.1
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./content/_build/_page/index/singlehtml

.gitignore

@@ -1,2 +1,3 @@
 .DS_Store
-.ipynb_checkpoints
+.ipynb_checkpoints
+content/_build/

binder/requirements.txt

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+jupyter-book==0.13.0
+lxml_html_clean
+nibabel
+pandas
+plotly
+scipy

binder/runtime.txt

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+python-3.8

content/_config.yml

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

content/_static/custom.css

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

content/_toc.yml

@@ -0,0 +1,5 @@
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-article
+root: paper

content/index.ipynb

@@ -0,0 +1,187 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# MRathon 2024 - NeuroLibre preprint project\n",
+    "\n",
+    "Hello world!\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Figure 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide_input",
+     "remove_output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "from scipy.fft import fftn, ifftn, fftshift\n",
+    "import plotly.express as px\n",
+    "import plotly.graph_objects as go\n",
+    "from plotly.subplots import make_subplots\n",
+    "from IPython.display import display, HTML\n",
+    "from plotly.offline import init_notebook_mode, iplot, plot\n",
+    "\n",
+    "init_notebook_mode(connected=True)\n",
+    "vol_size = (128, 128, 128)\n",
+    "vol_centre = (vol_size[1] // 2, vol_size[2] // 2)\n",
+    "offset = (10, 20)\n",
+    "radius_inner = 10\n",
+    "radius_outer = 40\n",
+    "cylinder_base = np.zeros(vol_size)\n",
+    "cylinder_internal = np.zeros(vol_size)\n",
+    "\n",
+    "x = np.arange(-vol_size[1]//2,vol_size[1]//2,dtype=float)\n",
+    "y = x\n",
+    "z = x\n",
+    "X,Y,Z = np.meshgrid(x,y,z)\n",
+    "\n",
+    "cylinder_base[X**2+Y**2<=radius_outer**2] = 1\n",
+    "\n",
+    "cylinder_internal[(X-offset[0])**2+(Y-offset[1])**2<=radius_inner**2] += 0.1\n",
+    "\n",
+    "kx = X\n",
+    "ky = Y\n",
+    "kz = Z\n",
+    "KK = (kx**2 + ky**2 + kz**2)\n",
+    "KK[KK==0] = np.nan\n",
+    "dipole_kernel = 2./3 - (kx**2)/(KK)\n",
+    "dipole_kernel[(kx**2 + ky**2 + kz**2) == 0] = 0\n",
+    "\n",
+    "fieldmap = np.real(ifftn(fftshift(dipole_kernel) * (fftn(cylinder_internal))))\n",
+    "\n",
+    "idx = 64\n",
+    "\n",
+    "fig = make_subplots(rows=1, cols=3, shared_xaxes=False, horizontal_spacing=0.1,\n",
+    "                    subplot_titles=(\"Geometry\",\n",
+    "                                    \"Dipole kernel\",\n",
+    "                                    \"Fieldmap\"),\n",
+    "                    specs=[[{\"type\": \"Heatmap\"}, {\"type\": \"Heatmap\"}, {\"type\": \"Heatmap\"}]])\n",
+    "fig.add_trace(go.Heatmap(z=cylinder_base[:,:,idx]+cylinder_internal[:,:,64], colorscale='gray'), 1, 1)\n",
+    "fig.add_trace(go.Heatmap(z=dipole_kernel[:,:,idx], colorscale='gray'), 1, 2)\n",
+    "fig.add_trace(go.Heatmap(z=fieldmap[:,:,idx], colorscale='gray'), 1, 3)\n",
+    "\n",
+    "plot(fig, filename = 'geometry.html')\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove_input",
+     "report_output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "display(HTML('geometry.html'))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Figure 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide_input",
+     "remove_output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "fig = go.Figure()\n",
+    "\n",
+    "echo_times = [10, 30, 50]\n",
+    "for step in echo_times:\n",
+    "    fig.add_trace(\n",
+    "        go.Heatmap(\n",
+    "            visible=False,\n",
+    "            z=(fieldmap[:,:,idx]*step) % np.pi,\n",
+    "            colorscale='gray'))\n",
+    "\n",
+    "fig.data[0].visible = True\n",
+    "\n",
+    "# Create and add slider\n",
+    "steps = []\n",
+    "for i in range(len(fig.data)):\n",
+    "    step = dict(\n",
+    "        method=\"update\",\n",
+    "        args=[{\"visible\": [False] * len(fig.data)},\n",
+    "              {\"title\": \"TE=\" + str(echo_times[i]) + \" ms\"}],  # layout attribute\n",
+    "    )\n",
+    "    step[\"args\"][0][\"visible\"][i] = True  # Toggle i'th trace to \"visible\"\n",
+    "    steps.append(step)\n",
+    "\n",
+    "sliders = [dict(\n",
+    "    active=10,\n",
+    "    currentvalue={\"prefix\": \"Frequency: \"},\n",
+    "    pad={\"t\": 50},\n",
+    "    steps=steps\n",
+    ")]\n",
+    "\n",
+    "fig.update_layout(\n",
+    "    sliders=sliders\n",
+    ")\n",
+    "\n",
+    "plot(fig, filename = 'cylinder.html')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove_input",
+     "report_output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "display(HTML('cylinder.html'))"
+   ]
+  }
+ ],
+ "metadata": {
+  "celltoolbar": "Tags",
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

paper.bib

@@ -0,0 +1 @@
+

paper.md

@@ -0,0 +1,29 @@
+---
+title: B0 mapping
+
+tags:
+  - NeuroLibre
+authors:
+   - name: MRathon Group
+    orcid: 
+    affiliation: 1
+
+affiliations:
+ - name: Singapore
+   index: 1
+
+
+date: 3 May 2024
+bibliography: paper.bib
+
+---
+
+# Summary
+
+# Statement of need
+
+# Figures
+
+# Acknowledgements
+
+## References