MNT simplify the pycortex database reload in colab

Author: TomDLT

tutorials/movies_3T/00_setup_colab.py

@@ -52,13 +52,8 @@
 os.environ['VOXELWISE_TUTORIALS_DATA'] = "/content"
 
 import cortex
-filestore = "/content/pycortex/filestore/"
-cortex.options.config['basic']['filestore'] = filestore
+cortex.db.__init__("/content/pycortex/filestore/")  # change filestore inplace
 cortex.options.config['webgl']['colormaps'] = "/content/pycortex/filestore/colormaps"
-cortex.database.db = cortex.database.Database(filestore)
-cortex.db = cortex.database.db
-cortex.utils.db = cortex.database.db
-cortex.dataset.braindata.db = cortex.database.db
 
 import sklearn
 sklearn.set_config(assume_finite=True)

tutorials/movies_3T/01_plot_explainable_variance.py

@@ -112,7 +112,7 @@
 plt.show()
 
 ###############################################################################
-# We see that many voxels have low explainable variance. This is 
+# We see that many voxels have low explainable variance. This is
 # expected, since many voxels are not driven by a visual stimulus, and their
 # response changes over repeats of the same stimulus.
 # We also see that some voxels have high explainable variance (around 0.7). The
@@ -171,41 +171,17 @@
 # The second mapper we provide maps the voxel data to a Freesurfer
 # average surface ("fsaverage"), that can be used in ``pycortex``.
 #
-# If you are running the notebook on Colab, you might need to update the
-# pycortex filestore as following:
+# First, let's download the "fsaverage" surface.
 
 import cortex
-try:
-    import google.colab  # noqa
-    in_colab = True
-except ImportError:
-    in_colab = False
-print(in_colab)
-
-if in_colab:
-    filestore = cortex.options.config['basic']['filestore']
-    cortex.database.db = cortex.database.Database(filestore)
-    cortex.db = cortex.database.db
-    cortex.utils.db = cortex.database.db
-    cortex.dataset.braindata.db = cortex.database.db
-    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)
-    # reinitialize pycortex's database to update available subjects
-    filestore = cortex.options.config['basic']['filestore']
-    cortex.database.db = cortex.database.Database(filestore)
-    cortex.db = cortex.database.db
-    cortex.utils.db = cortex.database.db
-    cortex.dataset.braindata.db = cortex.database.db
-    cortex.quickflat.utils.db = cortex.database.db
-    cortex.quickflat.composite.db = cortex.database.db
+    cortex.utils.download_subject(subject_id=surface,
+                                  pycortex_store=cortex.db.filestore)
+    cortex.db._subjects = None  # force filestore reload
+    assert hasattr(cortex.db, surface)
 
 ###############################################################################
 # Then, we load the "fsaverage" mapper. The mapper is a matrix of shape
@@ -228,11 +204,17 @@
 
 ###############################################################################
 # 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.
+# 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.
+
+try:
+    import google.colab  # noqa
+    in_colab = True
+except ImportError:
+    in_colab = False
+print(in_colab)
 
 if in_colab:
     from IPython import get_ipython
@@ -248,7 +230,6 @@
           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
@@ -272,7 +253,6 @@
                        with_rois=has_installed("inkscape"))
 plt.show()
 
-
 ###############################################################################
 # References
 # ----------

tutorials/notebooks/movies_3T/00_download_vim5.ipynb

@@ -100,7 +100,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.3"
+      "version": "3.7.3"
     }
   },
   "nbformat": 4,

tutorials/notebooks/movies_3T/00_load_colab.ipynb

@@ -76,7 +76,7 @@
       },
       "outputs": [],
       "source": [
-        "import os\nos.environ['VOXELWISE_TUTORIALS_DATA'] = \"/content\"\n\nimport cortex\nfilestore = \"/content/pycortex/filestore/\"\ncortex.options.config['basic']['filestore'] = filestore\ncortex.options.config['webgl']['colormaps'] = \"/content/pycortex/filestore/colormaps\"\ncortex.database.db = cortex.database.Database(filestore)\ncortex.db = cortex.database.db\ncortex.utils.db = cortex.database.db\ncortex.dataset.braindata.db = cortex.database.db\n\nimport sklearn\nsklearn.set_config(assume_finite=True)"
+        "import os\nos.environ['VOXELWISE_TUTORIALS_DATA'] = \"/content\"\n\nimport cortex\ncortex.db.__init__(\"/content/pycortex/filestore/\")  # change filestore inplace\ncortex.options.config['webgl']['colormaps'] = \"/content/pycortex/filestore/colormaps\"\n\nimport sklearn\nsklearn.set_config(assume_finite=True)"
       ]
     },
     {
@@ -103,7 +103,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.3"
+      "version": "3.7.3"
     }
   },
   "nbformat": 4,

tutorials/notebooks/movies_3T/00_setup_colab.ipynb

@@ -170,7 +170,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "We see that many voxels have low explainable variance. This is \nexpected, since many voxels are not driven by a visual stimulus, and their\nresponse changes over repeats of the same stimulus.\nWe also see that some voxels have high explainable variance (around 0.7). The\nresponses in these voxels are highly consistent across repetitions of the\nsame stimulus. Thus, they are good targets for encoding models.\n\n"
+        "We see that many voxels have low explainable variance. This is\nexpected, since many voxels are not driven by a visual stimulus, and their\nresponse changes over repeats of the same stimulus.\nWe also see that some voxels have high explainable variance (around 0.7). The\nresponses in these voxels are highly consistent across repetitions of the\nsame stimulus. Thus, they are good targets for encoding models.\n\n"
       ]
     },
     {
@@ -209,7 +209,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Map to \"fsaverage\"\n\nThe second mapper we provide maps the voxel data to a Freesurfer\naverage surface (\"fsaverage\"), that can be used in ``pycortex``.\n\nIf you are running the notebook on Colab, you might need to update the\npycortex filestore as following:\n\n"
+        "## Map to \"fsaverage\"\n\nThe second mapper we provide maps the voxel data to a Freesurfer\naverage surface (\"fsaverage\"), that can be used in ``pycortex``.\n\nFirst, let's download the \"fsaverage\" surface.\n\n"
       ]
     },
     {
@@ -220,25 +220,7 @@
       },
       "outputs": [],
       "source": [
-        "import cortex\ntry:\n    import google.colab  # noqa\n    in_colab = True\nexcept ImportError:\n    in_colab = False\nprint(in_colab)\n\nif in_colab:\n    filestore = cortex.options.config['basic']['filestore']\n    cortex.database.db = cortex.database.Database(filestore)\n    cortex.db = cortex.database.db\n    cortex.utils.db = cortex.database.db\n    cortex.dataset.braindata.db = cortex.database.db\n    cortex.quickflat.utils.db = cortex.database.db\n    cortex.quickflat.composite.db = cortex.database.db"
-      ]
-    },
-    {
-      "cell_type": "markdown",
-      "metadata": {},
-      "source": [
-        "Now, let's download the \"fsaverage\" surface.\n\n"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "collapsed": false
-      },
-      "outputs": [],
-      "source": [
-        "surface = \"fsaverage\"\n\nif not hasattr(cortex.db, surface):\n    cortex.utils.download_subject(subject_id=surface)\n    # reinitialize pycortex's database to update available subjects\n    filestore = cortex.options.config['basic']['filestore']\n    cortex.database.db = cortex.database.Database(filestore)\n    cortex.db = cortex.database.db\n    cortex.utils.db = cortex.database.db\n    cortex.dataset.braindata.db = cortex.database.db\n    cortex.quickflat.utils.db = cortex.database.db\n    cortex.quickflat.composite.db = cortex.database.db"
+        "import cortex\n\nsurface = \"fsaverage\"\n\nif not hasattr(cortex.db, surface):\n    cortex.utils.download_subject(subject_id=surface,\n                                  pycortex_store=cortex.db.filestore)\n    cortex.db._subjects = None  # force filestore reload\n    assert hasattr(cortex.db, surface)"
       ]
     },
     {
@@ -281,7 +263,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "To start an interactive 3D viewer in the browser, we can use the ``webshow``\nfunction in pycortex.\nIf you are running the notebook on Colab, you first need to tunnel the pycortex\napplication out of Colab. To do so, use the following cell to start a tunnel\nwith ``ngrok`` and to get an address where the pycortex viewer will be made\naccessible.\n\n"
+        "To start an interactive 3D viewer in the browser, we can use the ``webshow``\nfunction in pycortex. If you are running the notebook on Colab, you first\nneed to tunnel the pycortex application out of Colab. To do so, use the\nfollowing cell to start a tunnel with ``ngrok`` and to get an address where\nthe pycortex viewer will be made accessible.\n\n"
       ]
     },
     {
@@ -292,7 +274,7 @@
       },
       "outputs": [],
       "source": [
-        "if in_colab:\n    from IPython import get_ipython\n    get_ipython().system_raw('./ngrok http 8050 &')\n    plt.pause(1)\n\n    command = \"\"\"\n        curl -s http://localhost:4040/api/tunnels | python3 -c \\\n        \"import sys, json; print(json.load(sys.stdin)['tunnels'][0]['public_url'])\"\n        \"\"\"\n    result = get_ipython().getoutput(command, split=True)\n    print(\"Use the following address to connect to the brain viewer:\\n\"\n          f\"{result}\\n\"\n          \"and not the one proposed by pycortex ('Open viewer: ...')\\n\")"
+        "try:\n    import google.colab  # noqa\n    in_colab = True\nexcept ImportError:\n    in_colab = False\nprint(in_colab)\n\nif in_colab:\n    from IPython import get_ipython\n    get_ipython().system_raw('./ngrok http 8050 &')\n    plt.pause(1)\n\n    command = \"\"\"\n        curl -s http://localhost:4040/api/tunnels | python3 -c \\\n        \"import sys, json; print(json.load(sys.stdin)['tunnels'][0]['public_url'])\"\n        \"\"\"\n    result = get_ipython().getoutput(command, split=True)\n    print(\"Use the following address to connect to the brain viewer:\\n\"\n          f\"{result}\\n\"\n          \"and not the one proposed by pycortex ('Open viewer: ...')\\n\")"
       ]
     },
     {
@@ -355,7 +337,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.3"
+      "version": "3.7.3"
     }
   },
   "nbformat": 4,

tutorials/notebooks/movies_3T/01_plot_explainable_variance.ipynb

@@ -653,7 +653,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.3"
+      "version": "3.7.3"
     }
   },
   "nbformat": 4,

tutorials/notebooks/movies_3T/02_plot_wordnet_model.ipynb

@@ -352,7 +352,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.3"
+      "version": "3.7.3"
     }
   },
   "nbformat": 4,

tutorials/notebooks/movies_3T/03_plot_hemodynamic_response.ipynb

@@ -341,7 +341,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.3"
+      "version": "3.7.3"
     }
   },
   "nbformat": 4,

tutorials/notebooks/movies_3T/04_plot_motion_energy_model.ipynb

@@ -510,7 +510,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.3"
+      "version": "3.7.3"
     }
   },
   "nbformat": 4,