From 1a00042f738aa1d2a0141bfd3e8c7e0a2877848b Mon Sep 17 00:00:00 2001
From: Mathieu Boudreau <emb6150@gmail.com>
Date: Tue, 6 Feb 2024 14:59:01 -0400
Subject: [PATCH] Try a Colab-compatibility version

---
 content/index.ipynb | 111 +++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 109 insertions(+), 2 deletions(-)

diff --git a/content/index.ipynb b/content/index.ipynb
index ca96247..5255e17 100644
--- a/content/index.ipynb
+++ b/content/index.ipynb
@@ -12,7 +12,15 @@
    "outputs": [],
    "source": [
     "build = 'archive' # 'archive' uses the neurolibre archive of the data., 'latest' would download the latest versions of the data.\n",
-    "notebook = 'figures'"
+    "notebook = 'figures' # figures: no processing, use downloaded processed data and do figures & stats,\n",
+    "                     # jupyter: if some processed data exists, cleanup; Reprocess data\n",
+    "                     # colab: download and process data from scratch in Google Colab\n",
+    "\n",
+    "try:\n",
+    "  import google.colab\n",
+    "  notebook = 'colab'\n",
+    "except:\n",
+    "  pass"
    ]
   },
   {
@@ -268,6 +276,76 @@
     "import statsmodels.api as sm"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove_input",
+     "remove_output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# Start timer\n",
+    "start_time = datetime.now()\n",
+    "\n",
+    "# Check where we are\n",
+    "!pwd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove_input",
+     "remove_output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# Google Colab-Only\n",
+    "# ⚠️ No need to run this cell if you run this notebook locally and already have these dependencies installed.\n",
+    "\n",
+    "if notebook == 'colab':\n",
+    "    # Install packages on system\n",
+    "    !sudo apt-get update\n",
+    "    !sudo apt-get install git-annex\n",
+    "\n",
+    "    # Install Python libaries\n",
+    "    !wget -O requirements.txt https://raw.githubusercontent.com/shimming-toolbox/rf-shimming-7t/main/requirements.txt\n",
+    "    !pip install -r requirements.txt\n",
+    "\n",
+    "    # Install SCT ⏳\n",
+    "    !git clone --depth 1 https://github.com/spinalcordtoolbox/spinalcordtoolbox.git\n",
+    "    !yes | spinalcordtoolbox/install_sct\n",
+    "    os.environ['PATH'] += f\":/content/spinalcordtoolbox/bin\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove_input",
+     "remove_output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# Download data and define path variables\n",
+    "\n",
+    "# Google Colab-Only\n",
+    "if notebook=='colab':\n",
+    "    !datalad install https://github.com/OpenNeuroDatasets/ds004906.git\n",
+    "    os.chdir(\"ds004906\")\n",
+    "    !datalad get . # uncomment for production\n",
+    "    # !datalad get sub-01/  # debugging\n",
+    "    # Get derivatives containing manual labels\n",
+    "    !datalad get derivatives"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -296,7 +374,8 @@
     }
    ],
    "source": [
-    "os.chdir(\"../data/rf-shimming-7t/ds004906\")\n",
+    "if notebook!='colab':\n",
+    "    os.chdir(\"../data/rf-shimming-7t/ds004906\")\n",
     "\n",
     "path_data = os.getcwd()\n",
     "print(f\"path_data: {path_data}\")\n",
@@ -1717,6 +1796,34 @@
     ":filter: docname in docnames\n",
     "```"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove_input",
+     "remove_output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# Indicate duration of data processing\n",
+    "\n",
+    "end_time = datetime.now()\n",
+    "total_time = (end_time - start_time).total_seconds()\n",
+    "\n",
+    "# Convert seconds to a timedelta object\n",
+    "total_time_delta = timedelta(seconds=total_time)\n",
+    "\n",
+    "# Format the timedelta object to a string\n",
+    "formatted_time = str(total_time_delta)\n",
+    "\n",
+    "# Pad the string representation if less than an hour\n",
+    "formatted_time = formatted_time.rjust(8, '0')\n",
+    "\n",
+    "print(f\"Total Runtime [hour:min:sec]: {formatted_time}\")"
+   ]
   }
  ],
  "metadata": {