Merge pull request #152 from spinal-cord-7t/mb/jb

Convert notebook to jupyter books with outputs and host on GitHub pages
spinal-cord-7t · Nov 4, 2024 · 7c0dbea · 7c0dbea
2 parents a7e540f + 647befb
commit 7c0dbea
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Showing 6 changed files with 150 additions and 65 deletions.
diff --git a/.github/workflows/run_notebooks.yml b/.github/workflows/run_notebooks.yml
@@ -4,6 +4,11 @@ on:
   push:
     branches:
       - main  # Trigger the action on the main branch
+      - mb/jb
+
+permissions:
+  id-token: write
+  pages: write
 
 jobs:
   # Run the notebooks
@@ -46,51 +51,13 @@ jobs:
           # Make sure SCT can be called from within the environment
           sct_check_dependencies
 
-      - name: Run Jupyter Notebooks
+      - name: Run Jupyter Notebooks and build book
         continue-on-error: true  # Allow workflow to continue even if notebook execution fails
-        run: |
-          echo $PATH
-          mkdir -p executed_notebooks
-          for notebook in $(find . -name "*.ipynb"); do
-            echo "Executing $notebook"
-            jupyter nbconvert --to notebook --execute --allow-errors --inplace \
-              --output executed_notebooks/$(basename $notebook) $notebook \
-              2>&1 | tee -a notebook_execution.log || exit 1
-          done
-
-      - name: Check Execution Log
-        run: cat notebook_execution.log
-
-      - name: Upload Executed Notebooks
-        uses: actions/upload-artifact@v3
+        run: jupyter-book build .
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
         with:
-          name: executed-notebooks
-          path: executed_notebooks/
-
-  # Deploy to GitHub Pages (depends on run-notebooks)
-  deploy:
-    runs-on: ubuntu-latest
-    needs: run-notebooks  # Ensure this job runs after 'run-notebooks'
-
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v3
-
-      - name: Download Executed Notebooks
-        uses: actions/download-artifact@v3
-        with:
-          name: executed-notebooks
-          path: executed_notebooks/
-
-      - name: Copy Executed Notebooks to Pages Directory
-        run: |
-          COMMIT_SHA=$(git rev-parse --short HEAD)
-          mkdir -p gh-pages/$COMMIT_SHA
-          cp executed_notebooks/*.ipynb gh-pages/$COMMIT_SHA/
-
+          path: './_build/html'
       - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: gh-pages
-          publish_branch: gh-pages
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/_config.yml b/_config.yml
@@ -0,0 +1,26 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: "Multi-center benchmarking of cervical spinal cord RF coils at 7 T: A traveling spines study"
+author: NeuroPoly Lab
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+
+launch_buttons:
+  notebook_interface: jupyterlab
+  binderhub_url: https://mybinder.org
+
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/coil-qc-code/coil-qc-code  # Online location of your book
+  branch: mb/jb   # Which branch of the repository should be used when creating links (optional)
+
+only_build_toc_files: true
+
+execute:
+  timeout: 36000
+
diff --git a/_toc.yml b/_toc.yml
@@ -0,0 +1,8 @@
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: README.md
+chapters:
+- file: data_processing-human.ipynb
+- file: data_processing-phantom.ipynb
diff --git a/data_processing-human.ipynb b/data_processing-human.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "86a25f63",
+   "metadata": {},
+   "source": [
+    "# 7T coil comparison: processing of human data"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "0",
@@ -57,7 +65,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "3",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Download data from OpenNeuro ⏳\n",
@@ -97,7 +109,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "6",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Run segmentation on MP2RAGE scan ⏳\n",
@@ -121,7 +137,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "7",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Label vertebrae\n",
@@ -144,7 +164,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "8",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Crop MP2RAGE for faster processing and better registration results\n",
@@ -178,7 +202,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "10",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Segment spinal cord on TFL data (B1+ mapping) ⏳\n",
@@ -216,7 +244,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "11",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Register TFL data (B1+ mapping) to the MP2RAGE scan ⏳\n",
@@ -244,7 +276,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "12",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Register DREAM data (B1+ mapping) to the MP2RAGE scan ⏳\n",
@@ -266,7 +302,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "13",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Segment spinal cord on SNR data\n",
@@ -304,7 +344,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "14",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Register Rx coilQA data (SNR, g-factor) to the MP2RAGE scan ⏳\n",
@@ -326,7 +370,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "15",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Warping vertebral level to each flip angle and SNR map\n",
@@ -582,7 +630,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "21",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Extract B1+ and SNR along the spinal cord between levels C1 and T2 (included) and save data to CSV files\n",
@@ -952,7 +1004,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "34",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Co-register subjects across sites for better visualisation\n",

diff --git a/data_processing-phantom.ipynb b/data_processing-phantom.ipynb
@@ -51,7 +51,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "3",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Download data from OpenNeuro ⏳\n",
@@ -91,7 +95,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "6",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Convert the TFL flip angle maps to B1+ efficiency maps [nT/V] (inspired by code from Kyle Gilbert)\n",
@@ -142,7 +150,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "7",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# load DREAM FA maps acquired with different reference voltages\n",
@@ -244,7 +256,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "8",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Split SNR data across multiple volumes. The first volume corresponds to the SoS SNR reconstruction, which is\n",
@@ -270,7 +286,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "10",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "os.chdir(os.path.join(path_data, \"sub-CRMBM\", \"fmap\"))\n",
@@ -301,7 +321,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "12",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Create dictionary of labels across sites\n",
@@ -377,7 +401,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "15",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "scroll-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Extract B1+ and SNR along the spinal cord mask and save data to CSV files\n",

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-jupyter-book==0.13.0
+jupyter-book
 lxml_html_clean
 plotly
 seaborn