DOC improve flow with ngrok and cortex

Author: mvdoc

tutorials/movies_3T/00_setup_colab.py

@@ -8,7 +8,6 @@
 skip it if you run the tutorials on your machine.
 """
 # sphinx_gallery_thumbnail_path = "static/colab.png"
-#
 ###############################################################################
 # Change runtime to use a GPU
 # ---------------------------

tutorials/movies_3T/01_plot_explainable_variance.py

@@ -37,8 +37,6 @@
 references [1]_ [2]_ [3]_.
 """
 # sphinx_gallery_thumbnail_number = 1
-
-
 ###############################################################################
 # Path of the data directory
 # --------------------------
@@ -172,19 +170,11 @@
 #
 # The second mapper we provide maps the voxel data to a Freesurfer
 # average surface ("fsaverage"), that can be used in ``pycortex``.
-# First, let's download the "fsaverage" surface.
-
-import cortex
-
-surface = "fsaverage"
-
-if not hasattr(cortex.db, surface):
-    cortex.utils.download_subject(subject_id=surface)
-
-###############################################################################
+#
 # If you are running the notebook on Colab, you might need to update the
 # pycortex filestore as following:
 
+import cortex
 try:
     import google.colab  # noqa
     in_colab = True
@@ -201,11 +191,20 @@
     cortex.quickflat.utils.db = cortex.database.db
     cortex.quickflat.composite.db = cortex.database.db
 
+###############################################################################
+# Now, let's download the "fsaverage" surface.
+
+surface = "fsaverage"
+
+if not hasattr(cortex.db, surface):
+    cortex.utils.download_subject(subject_id=surface)
+
 ###############################################################################
 # Then, we load the "fsaverage" mapper. The mapper is a matrix of shape
 # (n_vertices, n_voxels), which maps each voxel to some vertices in the
 # fsaverage surface. It is stored as a sparse CSR matrix. The mapper is applied
 # with a dot product ``@`` (equivalent to ``np.dot``).
+
 from voxelwise_tutorials.io import load_hdf5_sparse_array
 voxel_to_fsaverage = load_hdf5_sparse_array(mapper_file,
                                             key='voxel_to_fsaverage')
@@ -220,14 +219,9 @@
 vertex = cortex.Vertex(ev_projected, surface, vmin=0, vmax=0.7, cmap='viridis')
 
 ###############################################################################
-# To start an interactive 3D viewer in the browser, use the ``webshow``
-# function.
-
-if False:
-    cortex.webshow(vertex, open_browser=False, port=8050)
-
-###############################################################################
-# If you are running the notebook on Colab, you need to tunnel the pycortex
+# To start an interactive 3D viewer in the browser, we can use the ``webshow``
+# function in pycortex.
+# If you are running the notebook on Colab, you first need to tunnel the pycortex
 # application out of Colab. To do so, use the following cell to start a tunnel
 # with ``ngrok`` and to get an address where the pycortex viewer will be made
 # accessible.
@@ -246,6 +240,17 @@
           f"{result}\n"
           "and not the one proposed by pycortex ('Open viewer: ...')\n")
 
+
+###############################################################################
+# Now you can start an interactive 3D viewer by changing ``run_webshow`` to
+# ``True`` and running the following cell.  If you are using Colab, remember to
+# use the address returned by ngrok in the cell above rather than the address
+# returned by this cell.
+
+run_webshow = False
+if run_webshow:
+    cortex.webshow(vertex, open_browser=False, port=8050)
+
 ###############################################################################
 # Alternatively, to plot a flatmap in a ``matplotlib`` figure, use the
 # `quickshow` function.
@@ -255,7 +260,6 @@
 
 from cortex.testing_utils import has_installed
 
-
 fig = cortex.quickshow(vertex, colorbar_location='right',
                        with_rois=has_installed("inkscape"))
 plt.show()