added transparency example + docs build

danjgale · Dec 20, 2022 · 804f162 · 804f162
1 parent b2dacf8
commit 804f162
Show file tree

Hide file tree

Showing 27 changed files with 99 additions and 25 deletions.
diff --git a/docs/auto_examples/examples/plot_example_01.rst b/docs/auto_examples/examples/plot_example_01.rst
@@ -79,7 +79,7 @@ stylizing for a clean-looking figure.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.218 seconds)
+   **Total running time of the script:** ( 0 minutes  0.225 seconds)
 
 
 .. _sphx_glr_download_auto_examples_examples_plot_example_01.py:

diff --git a/docs/auto_examples/examples/plot_example_01_codeobj.pickle b/docs/auto_examples/examples/plot_example_01_codeobj.pickle
diff --git a/docs/auto_examples/examples/plot_example_02.rst b/docs/auto_examples/examples/plot_example_02.rst
@@ -92,7 +92,7 @@ projected from MNI152 coordinates to fsLR surfaces using ``neuromaps``.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.306 seconds)
+   **Total running time of the script:** ( 0 minutes  0.318 seconds)
 
 
 .. _sphx_glr_download_auto_examples_examples_plot_example_02.py:

diff --git a/docs/auto_examples/examples/plot_example_02_codeobj.pickle b/docs/auto_examples/examples/plot_example_02_codeobj.pickle
diff --git a/docs/auto_examples/examples/sg_execution_times.rst b/docs/auto_examples/examples/sg_execution_times.rst
@@ -5,10 +5,10 @@
 
 Computation times
 =================
-**00:00.524** total execution time for **auto_examples_examples** files:
+**00:00.543** total execution time for **auto_examples_examples** files:
 
 +------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_examples_plot_example_02.py` (``plot_example_02.py``) | 00:00.306 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_examples_plot_example_02.py` (``plot_example_02.py``) | 00:00.318 | 0.0 MB |
 +------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_examples_plot_example_01.py` (``plot_example_01.py``) | 00:00.218 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_examples_plot_example_01.py` (``plot_example_01.py``) | 00:00.225 | 0.0 MB |
 +------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/auto_examples/images/sphx_glr_plot_tutorial_01_001.png b/docs/auto_examples/images/sphx_glr_plot_tutorial_01_001.png
diff --git a/docs/auto_examples/images/sphx_glr_plot_tutorial_02_002.png b/docs/auto_examples/images/sphx_glr_plot_tutorial_02_002.png
diff --git a/docs/auto_examples/images/sphx_glr_plot_tutorial_05_004.png b/docs/auto_examples/images/sphx_glr_plot_tutorial_05_004.png
diff --git a/docs/auto_examples/images/sphx_glr_plot_tutorial_06_003.png b/docs/auto_examples/images/sphx_glr_plot_tutorial_06_003.png
diff --git a/docs/auto_examples/images/thumb/sphx_glr_plot_tutorial_06_thumb.png b/docs/auto_examples/images/thumb/sphx_glr_plot_tutorial_06_thumb.png
diff --git a/docs/auto_examples/plot_tutorial_01.rst b/docs/auto_examples/plot_tutorial_01.rst
@@ -202,7 +202,7 @@ by the minimum and maximum values (this can be adjusted with the
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  1.262 seconds)
+   **Total running time of the script:** ( 0 minutes  0.987 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_tutorial_01.py:

diff --git a/docs/auto_examples/plot_tutorial_01_codeobj.pickle b/docs/auto_examples/plot_tutorial_01_codeobj.pickle
diff --git a/docs/auto_examples/plot_tutorial_02.rst b/docs/auto_examples/plot_tutorial_02.rst
@@ -121,7 +121,7 @@ parameter, if desired. Values range from 0 (black) to 1 (white). For example:
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.598 seconds)
+   **Total running time of the script:** ( 0 minutes  0.584 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_tutorial_02.py:

diff --git a/docs/auto_examples/plot_tutorial_02_codeobj.pickle b/docs/auto_examples/plot_tutorial_02_codeobj.pickle
diff --git a/docs/auto_examples/plot_tutorial_03.rst b/docs/auto_examples/plot_tutorial_03.rst
@@ -310,7 +310,7 @@ data match the number of vertices of the surface(s)!
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.920 seconds)
+   **Total running time of the script:** ( 0 minutes  0.941 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_tutorial_03.py:

diff --git a/docs/auto_examples/plot_tutorial_03_codeobj.pickle b/docs/auto_examples/plot_tutorial_03_codeobj.pickle
diff --git a/docs/auto_examples/plot_tutorial_04.rst b/docs/auto_examples/plot_tutorial_04.rst
@@ -266,7 +266,7 @@ For example:
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.971 seconds)
+   **Total running time of the script:** ( 0 minutes  0.961 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_tutorial_04.py:

diff --git a/docs/auto_examples/plot_tutorial_04_codeobj.pickle b/docs/auto_examples/plot_tutorial_04_codeobj.pickle
diff --git a/docs/auto_examples/plot_tutorial_05.ipynb b/docs/auto_examples/plot_tutorial_05.ipynb
@@ -87,14 +87,25 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Be sure to check out `sphx_glr_auto_examples_examples_plot_example_01.py`\nfor another example of colorbar styling.\n\n"
+        "Be sure to check out `sphx_glr_auto_examples_examples_plot_example_01.py`\nfor another example of colorbar styling.\n\n## Transparency\n\nThe transparency of the plotting layers can be adjusted by the ``alpha`` \nparameter. This may be preferred in cases with overlapping plotting layers.\nWe can recreate the example above with transparent maps like so:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "p = Plot(lh, rh)\np.add_layer({'left': sulc_lh, 'right': sulc_rh}, cmap='binary_r', cbar=False)\np.add_layer(default, cmap='GnBu_r', cbar_label='Default mode', alpha=.5)\np.add_layer(fronto, cmap='YlOrBr_r', cbar_label='Frontoparietal', alpha=.5)\nfig = p.build(cbar_kws=kws)\nfig.show()"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        ""
+        "Although these particular maps are largely non-overlapping, you can see some\nsmall overlap at the edges of the  default mode and frontoparietal clusters \nthanks to the transparency.\n\n"
       ]
     }
   ],

diff --git a/docs/auto_examples/plot_tutorial_05.py b/docs/auto_examples/plot_tutorial_05.py
@@ -92,8 +92,23 @@
 ###############################################################################
 # Be sure to check out :ref:`sphx_glr_auto_examples_examples_plot_example_01.py`
 # for another example of colorbar styling.
-
+#
+# Transparency
+# ------------
+#
+# The transparency of the plotting layers can be adjusted by the ``alpha`` 
+# parameter. This may be preferred in cases with overlapping plotting layers.
+# We can recreate the example above with transparent maps like so:
+p = Plot(lh, rh)
+p.add_layer({'left': sulc_lh, 'right': sulc_rh}, cmap='binary_r', cbar=False)
+p.add_layer(default, cmap='GnBu_r', cbar_label='Default mode', alpha=.5)
+p.add_layer(fronto, cmap='YlOrBr_r', cbar_label='Frontoparietal', alpha=.5)
+fig = p.build(cbar_kws=kws)
+fig.show()
 ###############################################################################
+# Although these particular maps are largely non-overlapping, you can see some
+# small overlap at the edges of the  default mode and frontoparietal clusters 
+# thanks to the transparency.
 #
 # .. _matplotlib colormap: https://matplotlib.org/stable/tutorials/colors/colormaps.html#sphx-glr-tutorials-colors-colormaps-py
 # .. _custom colormap: https://matplotlib.org/stable/tutorials/colors/colormap-manipulation.html

diff --git a/docs/auto_examples/plot_tutorial_05.py.md5 b/docs/auto_examples/plot_tutorial_05.py.md5
@@ -1 +1 @@
-98eba5e7baf682b0d41b5693f10b0930
+88c5f5b7de8ab61eb93c958b6aba4d79
diff --git a/docs/auto_examples/plot_tutorial_05.rst b/docs/auto_examples/plot_tutorial_05.rst
@@ -172,12 +172,45 @@ cleaner look:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 93-95
+.. GENERATED FROM PYTHON SOURCE LINES 93-102
 
 Be sure to check out :ref:`sphx_glr_auto_examples_examples_plot_example_01.py`
 for another example of colorbar styling.
 
-.. GENERATED FROM PYTHON SOURCE LINES 97-101
+Transparency
+------------
+
+The transparency of the plotting layers can be adjusted by the ``alpha`` 
+parameter. This may be preferred in cases with overlapping plotting layers.
+We can recreate the example above with transparent maps like so:
+
+.. GENERATED FROM PYTHON SOURCE LINES 102-108
+
+.. code-block:: default
+
+    p = Plot(lh, rh)
+    p.add_layer({'left': sulc_lh, 'right': sulc_rh}, cmap='binary_r', cbar=False)
+    p.add_layer(default, cmap='GnBu_r', cbar_label='Default mode', alpha=.5)
+    p.add_layer(fronto, cmap='YlOrBr_r', cbar_label='Frontoparietal', alpha=.5)
+    fig = p.build(cbar_kws=kws)
+    fig.show()
+
+
+
+.. image-sg:: /auto_examples/images/sphx_glr_plot_tutorial_05_004.png
+   :alt: Frontoparietal, Default mode
+   :srcset: /auto_examples/images/sphx_glr_plot_tutorial_05_004.png
+   :class: sphx-glr-single-img
+
+
+
+
+
+.. GENERATED FROM PYTHON SOURCE LINES 109-117
+
+Although these particular maps are largely non-overlapping, you can see some
+small overlap at the edges of the  default mode and frontoparietal clusters 
+thanks to the transparency.
 
 .. _matplotlib colormap: https://matplotlib.org/stable/tutorials/colors/colormaps.html#sphx-glr-tutorials-colors-colormaps-py
 .. _custom colormap: https://matplotlib.org/stable/tutorials/colors/colormap-manipulation.html
@@ -188,7 +221,7 @@ for another example of colorbar styling.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.573 seconds)
+   **Total running time of the script:** ( 0 minutes  0.783 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_tutorial_05.py:

diff --git a/docs/auto_examples/plot_tutorial_05_codeobj.pickle b/docs/auto_examples/plot_tutorial_05_codeobj.pickle
diff --git a/docs/auto_examples/plot_tutorial_06.rst b/docs/auto_examples/plot_tutorial_06.rst
@@ -183,7 +183,7 @@ only need to show the left lateral view
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.524 seconds)
+   **Total running time of the script:** ( 0 minutes  0.506 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_tutorial_06.py:

diff --git a/docs/auto_examples/plot_tutorial_06_codeobj.pickle b/docs/auto_examples/plot_tutorial_06_codeobj.pickle
diff --git a/docs/auto_examples/sg_execution_times.rst b/docs/auto_examples/sg_execution_times.rst
@@ -5,18 +5,18 @@
 
 Computation times
 =================
-**00:04.848** total execution time for **auto_examples** files:
+**00:04.761** total execution time for **auto_examples** files:
 
 +-----------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_tutorial_01.py` (``plot_tutorial_01.py``) | 00:01.262 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_tutorial_01.py` (``plot_tutorial_01.py``) | 00:00.987 | 0.0 MB |
 +-----------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_tutorial_04.py` (``plot_tutorial_04.py``) | 00:00.971 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_tutorial_04.py` (``plot_tutorial_04.py``) | 00:00.961 | 0.0 MB |
 +-----------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_tutorial_03.py` (``plot_tutorial_03.py``) | 00:00.920 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_tutorial_03.py` (``plot_tutorial_03.py``) | 00:00.941 | 0.0 MB |
 +-----------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_tutorial_02.py` (``plot_tutorial_02.py``) | 00:00.598 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_tutorial_05.py` (``plot_tutorial_05.py``) | 00:00.783 | 0.0 MB |
 +-----------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_tutorial_05.py` (``plot_tutorial_05.py``) | 00:00.573 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_tutorial_02.py` (``plot_tutorial_02.py``) | 00:00.584 | 0.0 MB |
 +-----------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_tutorial_06.py` (``plot_tutorial_06.py``) | 00:00.524 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_tutorial_06.py` (``plot_tutorial_06.py``) | 00:00.506 | 0.0 MB |
 +-----------------------------------------------------------------------------+-----------+--------+
diff --git a/tutorials/plot_tutorial_05.py b/tutorials/plot_tutorial_05.py
@@ -92,8 +92,23 @@
 ###############################################################################
 # Be sure to check out :ref:`sphx_glr_auto_examples_examples_plot_example_01.py`
 # for another example of colorbar styling.
-
+#
+# Transparency
+# ------------
+#
+# The transparency of the plotting layers can be adjusted by the ``alpha`` 
+# parameter. This may be preferred in cases with overlapping plotting layers.
+# We can recreate the example above with transparent maps like so:
+p = Plot(lh, rh)
+p.add_layer({'left': sulc_lh, 'right': sulc_rh}, cmap='binary_r', cbar=False)
+p.add_layer(default, cmap='GnBu_r', cbar_label='Default mode', alpha=.5)
+p.add_layer(fronto, cmap='YlOrBr_r', cbar_label='Frontoparietal', alpha=.5)
+fig = p.build(cbar_kws=kws)
+fig.show()
 ###############################################################################
+# Although these particular maps are largely non-overlapping, you can see some
+# small overlap at the edges of the  default mode and frontoparietal clusters 
+# thanks to the transparency.
 #
 # .. _matplotlib colormap: https://matplotlib.org/stable/tutorials/colors/colormaps.html#sphx-glr-tutorials-colors-colormaps-py
 # .. _custom colormap: https://matplotlib.org/stable/tutorials/colors/colormap-manipulation.html