Reorder notebooks and improve naming

Author: mvdoc

tutorials/Makefile

@@ -22,22 +22,22 @@ NBDIR = notebooks/shortclips
 
 merge-notebooks:
 	python merge_notebooks.py \
-		$(NBDIR)/00_setup_colab.ipynb \
-		$(NBDIR)/01_plot_explainable_variance.ipynb \
-		$(NBDIR)/02_plot_ridge_regression.ipynb \
-		$(NBDIR)/03_plot_wordnet_model.ipynb \
-		$(NBDIR)/04_plot_hemodynamic_response.ipynb \
-		$(NBDIR)/05_plot_motion_energy_model.ipynb \
-		$(NBDIR)/06_plot_banded_ridge_model.ipynb \
+		$(NBDIR)/01_setup_colab.ipynb \
+		$(NBDIR)/03_compute_explainable_variance.ipynb \
+		$(NBDIR)/04_understand_ridge_regression.ipynb \
+		$(NBDIR)/05_fit_wordnet_model.ipynb \
+		$(NBDIR)/06_visualize_hemodynamic_response.ipynb \
+		$(NBDIR)/08_fit_motion_energy_model.ipynb \
+		$(NBDIR)/09_fit_banded_ridge_model.ipynb \
 		> $(NBDIR)/merged_for_colab.ipynb
 	echo "Saved in $(NBDIR)/merged_for_colab.ipynb"
 
 	python merge_notebooks.py \
-		$(NBDIR)/00_setup_colab.ipynb \
-		$(NBDIR)/01_plot_explainable_variance.ipynb \
-		$(NBDIR)/03_plot_wordnet_model.ipynb \
-		$(NBDIR)/05_plot_motion_energy_model.ipynb \
-		$(NBDIR)/06_plot_banded_ridge_model.ipynb \
+		$(NBDIR)/01_setup_colab.ipynb \
+		$(NBDIR)/03_compute_explainable_variance.ipynb \
+		$(NBDIR)/05_fit_wordnet_model.ipynb \
+		$(NBDIR)/08_fit_motion_energy_model.ipynb \
+		$(NBDIR)/09_fit_banded_ridge_model.ipynb \
 		> $(NBDIR)/merged_for_colab_model_fitting.ipynb
 	echo "Saved in $(NBDIR)/merged_for_colab_model_fitting.ipynb"
 

tutorials/_toc.yml

@@ -9,14 +9,14 @@ sections:
 - file: notebooks/shortclips/README
   title: Shortclips tutorial
   sections:
-  - file: notebooks/shortclips/00_download_shortclips
-  - file: notebooks/shortclips/01_plot_explainable_variance
-  - file: notebooks/shortclips/02_plot_ridge_regression
-  - file: notebooks/shortclips/03_plot_wordnet_model
-  - file: notebooks/shortclips/04_plot_hemodynamic_response
-  - file: notebooks/shortclips/05_plot_motion_energy_model
-  - file: notebooks/shortclips/06_plot_banded_ridge_model
+  - file: notebooks/shortclips/02_download_shortclips
+  - file: notebooks/shortclips/03_compute_explainable_variance
+  - file: notebooks/shortclips/04_understand_ridge_regression
+  - file: notebooks/shortclips/05_fit_wordnet_model
+  - file: notebooks/shortclips/06_visualize_hemodynamic_response
   - file: notebooks/shortclips/07_extract_motion_energy
+  - file: notebooks/shortclips/08_fit_motion_energy_model
+  - file: notebooks/shortclips/09_fit_banded_ridge_model
 - file: notebooks/vim2/README
   title: Vim-2 tutorial (optional)
   sections:

…otebooks/shortclips/00_setup_colab.ipynb …otebooks/shortclips/01_setup_colab.ipynbtutorials/notebooks/shortclips/00_setup_colab.ipynb renamed to tutorials/notebooks/shortclips/01_setup_colab.ipynb tutorials/notebooks/shortclips/00_setup_colab.ipynb renamed to tutorials/notebooks/shortclips/01_setup_colab.ipynb

@@ -8,8 +8,12 @@
         "# Setup Google Colab\n",
         "\n",
         "In this script, we setup a Google Colab environment. This script will only work\n",
-        "when run from [Google Colab](https://colab.research.google.com/)). You can\n",
-        "skip it if you run the tutorials on your machine.\n"
+        "when run from [Google Colab](https://colab.research.google.com/). You can\n",
+        "skip it if you run the tutorials on your machine.\n",
+        "\n",
+        "> **Note:** This script will install all the required dependencies and download the data.\n",
+        "> It will take around 10 minutes to run, but you need to run it only once in your Colab session.\n",
+        "> If your Colab session is disconnected, you will need to run this script again."
       ]
     },
     {
@@ -22,15 +26,15 @@
         "In Google Colab you can request access to a GPU by changing the runtime type.\n",
         "To do so, click the following menu options in Google Colab:\n",
         "\n",
-        "(Menu) \"Runtime\" -> \"Change runtime type\" -> \"Hardware accelerator\" -> \"GPU\".\n",
+        "> (Menu) \"Runtime\" -> \"Change runtime type\" -> \"Hardware accelerator\" -> \"GPU\".\n",
         "\n"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Download the data and install all required dependencies\n",
+        "## Install all required dependencies and download the data\n",
         "\n",
         "Uncomment and run the following cell to download the required packages.\n",
         "\n"

…/shortclips/00_download_shortclips.ipynb …/shortclips/02_download_shortclips.ipynbtutorials/notebooks/shortclips/00_download_shortclips.ipynb renamed to tutorials/notebooks/shortclips/02_download_shortclips.ipynb tutorials/notebooks/shortclips/00_download_shortclips.ipynb renamed to tutorials/notebooks/shortclips/02_download_shortclips.ipynb

@@ -15,7 +15,7 @@
         "Linear regression is a method to model the relation between some input\n",
         "variables $X \\in \\mathbb{R}^{(n \\times p)}$ (the features) and an output\n",
         "variable $y \\in \\mathbb{R}^{n}$ (the target). Specifically, linear\n",
-        "regression uses a vector of coefficient $w \\in \\mathbb{R}^{p}$` to\n",
+        "regression uses a vector of coefficient $w \\in \\mathbb{R}^{p}$ to\n",
         "predict the output\n",
         "\n",
         "\\begin{align}\\hat{y} = Xw\\end{align}\n",
@@ -30,15 +30,6 @@
         "least squares* (OLS).\n"
       ]
     },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "collapsed": false
-      },
-      "outputs": [],
-      "source": []
-    },
     {
       "cell_type": "markdown",
       "metadata": {},