Make install

_downloads/b0a32473b166cd7714a0a0f0aea9bf1c/example_spangy.ipynb

@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n\n===================================\nExample of Spectral Analysis of Gyrification (SPANGY) decomposition\nD. Germanaud*, J. Lefevre*,R. Toro, C. Fischer, J.Dubois, L. Hertz-Pannier,\nJ.F. Mangin, Larger is twistier:Spectral Analysis of Gyrification (SPANGY)\napplied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.\n===================================\n"
+        "\n\n# Example of Spectral Analysis of Gyrification (SPANGY) decomposition\n"
       ]
     },
     {
@@ -26,7 +26,7 @@
       },
       "outputs": [],
       "source": [
-        "import slam.io as sio\nimport numpy as np\nimport slam.differential_geometry as sdg\nimport slam.curvature as scurv\nfrom scipy.sparse.linalg import eigsh\nimport time\nimport slam.plot as splt\nimport matplotlib.pyplot as plt\nimport slam.spangy as spgy\n\n## LOAD MESH\nmesh = sio.load_mesh(\"../examples/data/example_mesh.gii\")\nN = 1500\n# Compute eigenpairs and mass matrix\neigVal, eigVects, lap_b = spgy.eigenpairs(mesh,N)\n\n## CURVATURE\nPrincipalCurvatures, PrincipalDir1, PrincipalDir2 = \\\n    scurv.curvatures_and_derivatives(mesh)\nmean_curv = 0.5 * (PrincipalCurvatures[0, :] + PrincipalCurvatures[1, :])\n\n# Plot of mean curvature on the mesh\nvisb_sc = splt.visbrain_plot(mesh=mesh, tex=mean_curv, caption='Mean Curvature', cmap='jet')\nvisb_sc.preview()\n\n## WHOLE BRAIN SPECTRUM\ngrouped_spectrum,group_indices,coefficients = spgy.spectrum(mean_curv, lap_b, eigVects, eigVal)\nlevels=len(group_indices)\n\n# a. Whole brain parameters\nmL_in_MM3=1000\nCM2_in_MM2=100\nvolume = mesh.volume\nsurface_area = mesh.area\nafp=np.sum(grouped_spectrum[1:])\nprint('** a. Whole brain parameters **')\nprint('Volume = %d mL, Area = %d cm^2, Analyze Folding Power = %f,' % (np.floor(volume/mL_in_MM3),np.floor(surface_area/CM2_in_MM2),afp))\n\n# b. Band number of parcels\nprint('** b. Band number of parcels **')\nprint('B4 = %f, B5 = %f, B6 = %f' % (0,0,0))\n\n# c. Band power\nprint('** c. Band power **')\nprint('B4 = %f, B5 = %f, B6 = %f' % (grouped_spectrum[4],grouped_spectrum[5],grouped_spectrum[6]))\n\n# d. Band relative power\nprint('** d. Band relative power **')\nprint('B4 = %0.5f, B5 = %0.5f , B6 = %0.5f' % (grouped_spectrum[4]/afp,grouped_spectrum[5]/afp,grouped_spectrum[6]/afp))\n\n# Create two subplots\nfig, (ax1, ax2) = plt.subplots(1, 2)\n# Plot the sqrt of the eigVals divided by 2*np.pi against the coefficients in the first subplot\nax1.plot(np.sqrt(eigVal[1:])/(2*np.pi),coefficients[1:])\nax1.set_xlabel('Frequency (m^{-1})')\nax1.set_ylabel('Coefficients')\n\n# Barplot for the nlevels and grouped spectrum in the second subplot\n# Barplot in ax2 between nlevels and grouped spectrum\nprint(grouped_spectrum)\nax2.bar(np.arange(0,levels),grouped_spectrum.squeeze())\nax2.set_xlabel('Spangy Frequency Bands')\nax2.set_ylabel('Power Spectrum')\n\nplt.show()\n\n## LOCAL SPECTRAL BANDS\nloc_dom_band, frecomposed = spgy.local_dominance_map(coefficients,mean_curv,levels,group_indices,eigVects)\n\n# Plot of spectral dominant bands on the mesh\nvisb_sc = splt.visbrain_plot(mesh=mesh, tex=loc_dom_band, caption='Local Dominant Band', cmap='jet')\nvisb_sc.preview()"
+        "import slam.io as sio\nimport numpy as np\nimport slam.differential_geometry as sdg\nimport slam.curvature as scurv\nfrom scipy.sparse.linalg import eigsh\nimport time\nimport slam.plot as splt\nimport matplotlib.pyplot as plt\nimport slam.spangy as spgy\n\n## D. Germanaud*, J. Lefevre*,R. Toro, C. Fischer, J.Dubois, L. Hertz-Pannier,\n## J.F. Mangin, Larger is twistier:Spectral Analysis of Gyrification (SPANGY)\n## applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.\n\n\n## LOAD MESH\nmesh = sio.load_mesh(\"../examples/data/example_mesh.gii\")\nN = 1500\n# Compute eigenpairs and mass matrix\neigVal, eigVects, lap_b = spgy.eigenpairs(mesh,N)\n\n## CURVATURE\nPrincipalCurvatures, PrincipalDir1, PrincipalDir2 = \\\n    scurv.curvatures_and_derivatives(mesh)\nmean_curv = 0.5 * (PrincipalCurvatures[0, :] + PrincipalCurvatures[1, :])\n\n# Plot of mean curvature on the mesh\nvisb_sc = splt.visbrain_plot(mesh=mesh, tex=mean_curv, caption='Mean Curvature', cmap='jet')\nvisb_sc.preview()\n\n## WHOLE BRAIN SPECTRUM\ngrouped_spectrum,group_indices,coefficients = spgy.spectrum(mean_curv, lap_b, eigVects, eigVal)\nlevels=len(group_indices)\n\n# a. Whole brain parameters\nmL_in_MM3=1000\nCM2_in_MM2=100\nvolume = mesh.volume\nsurface_area = mesh.area\nafp=np.sum(grouped_spectrum[1:])\nprint('** a. Whole brain parameters **')\nprint('Volume = %d mL, Area = %d cm^2, Analyze Folding Power = %f,' % (np.floor(volume/mL_in_MM3),np.floor(surface_area/CM2_in_MM2),afp))\n\n# b. Band number of parcels\nprint('** b. Band number of parcels **')\nprint('B4 = %f, B5 = %f, B6 = %f' % (0,0,0))\n\n# c. Band power\nprint('** c. Band power **')\nprint('B4 = %f, B5 = %f, B6 = %f' % (grouped_spectrum[4],grouped_spectrum[5],grouped_spectrum[6]))\n\n# d. Band relative power\nprint('** d. Band relative power **')\nprint('B4 = %0.5f, B5 = %0.5f , B6 = %0.5f' % (grouped_spectrum[4]/afp,grouped_spectrum[5]/afp,grouped_spectrum[6]/afp))\n\n# Create two subplots\nfig, (ax1, ax2) = plt.subplots(1, 2)\n# Plot the sqrt of the eigVals divided by 2*np.pi against the coefficients in the first subplot\nax1.plot(np.sqrt(eigVal[1:])/(2*np.pi),coefficients[1:])\nax1.set_xlabel('Frequency (m^{-1})')\nax1.set_ylabel('Coefficients')\n\n# Barplot for the nlevels and grouped spectrum in the second subplot\n# Barplot in ax2 between nlevels and grouped spectrum\nprint(grouped_spectrum)\nax2.bar(np.arange(0,levels),grouped_spectrum.squeeze())\nax2.set_xlabel('Spangy Frequency Bands')\nax2.set_ylabel('Power Spectrum')\n\nplt.show()\n\n## LOCAL SPECTRAL BANDS\nloc_dom_band, frecomposed = spgy.local_dominance_map(coefficients,mean_curv,levels,group_indices,eigVects)\n\n# Plot of spectral dominant bands on the mesh\nvisb_sc = splt.visbrain_plot(mesh=mesh, tex=loc_dom_band, caption='Local Dominant Band', cmap='jet')\nvisb_sc.preview()"
       ]
     }
   ],

_downloads/c7a379ff1b73b7b2972fd8542e5e55ef/example_spangy.py

@@ -3,9 +3,6 @@
 
 ===================================
 Example of Spectral Analysis of Gyrification (SPANGY) decomposition
-D. Germanaud*, J. Lefevre*,R. Toro, C. Fischer, J.Dubois, L. Hertz-Pannier,
-J.F. Mangin, Larger is twistier:Spectral Analysis of Gyrification (SPANGY)
-applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.
 ===================================
 """
 import slam.io as sio
@@ -18,6 +15,11 @@
 import matplotlib.pyplot as plt
 import slam.spangy as spgy
 
+## D. Germanaud*, J. Lefevre*,R. Toro, C. Fischer, J.Dubois, L. Hertz-Pannier,
+## J.F. Mangin, Larger is twistier:Spectral Analysis of Gyrification (SPANGY)
+## applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.
+
+
 ## LOAD MESH
 mesh = sio.load_mesh("../examples/data/example_mesh.gii")
 N = 1500

_sources/auto_examples/example_spangy.rst.txt

@@ -22,12 +22,9 @@
 
 ===================================
 Example of Spectral Analysis of Gyrification (SPANGY) decomposition
-D. Germanaud*, J. Lefevre*,R. Toro, C. Fischer, J.Dubois, L. Hertz-Pannier,
-J.F. Mangin, Larger is twistier:Spectral Analysis of Gyrification (SPANGY)
-applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.
 ===================================
 
-.. GENERATED FROM PYTHON SOURCE LINES 11-84
+.. GENERATED FROM PYTHON SOURCE LINES 8-86
 
 
 
@@ -107,6 +104,11 @@ applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.
     import matplotlib.pyplot as plt
     import slam.spangy as spgy
 
+    ## D. Germanaud*, J. Lefevre*,R. Toro, C. Fischer, J.Dubois, L. Hertz-Pannier,
+    ## J.F. Mangin, Larger is twistier:Spectral Analysis of Gyrification (SPANGY)
+    ## applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.
+
+
     ## LOAD MESH
     mesh = sio.load_mesh("../examples/data/example_mesh.gii")
     N = 1500
@@ -174,7 +176,7 @@ applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  31.582 seconds)
+   **Total running time of the script:** ( 0 minutes  32.380 seconds)
 
 
 .. _sphx_glr_download_auto_examples_example_spangy.py:

_sources/auto_examples/sg_execution_times.rst.txt

@@ -5,10 +5,10 @@
 
 Computation times
 =================
-**00:00.171** total execution time for **auto_examples** files:
+**00:32.380** total execution time for **auto_examples** files:
 
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_example_surface_profiling.py` (``example_surface_profiling.py``)                       | 00:00.171 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_example_spangy.py` (``example_spangy.py``)                                             | 00:32.380 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
 | :ref:`sphx_glr_auto_examples_example_basics.py` (``example_basics.py``)                                             | 00:00.000 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
@@ -38,7 +38,7 @@ Computation times
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
 | :ref:`sphx_glr_auto_examples_example_remeshing.py` (``example_remeshing.py``)                                       | 00:00.000 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_example_spangy.py` (``example_spangy.py``)                                             | 00:00.000 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_example_surface_profiling.py` (``example_surface_profiling.py``)                       | 00:00.000 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+
 | :ref:`sphx_glr_auto_examples_example_texture.py` (``example_texture.py``)                                           | 00:00.000 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------------------+-----------+--------+

auto_examples/example_spangy.html

@@ -4,7 +4,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>&lt;no title&gt; &#8212; slam 0.0.1 documentation</title>
+    <title>Example of Spectral Analysis of Gyrification (SPANGY) decomposition &#8212; slam 0.0.1 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../_static/gallery.css" />
@@ -70,7 +70,8 @@
      href="#">Page <b class="caret"></b></a>
   <ul class="dropdown-menu localtoc"
       role="menu"
-      aria-labelledby="dLabelLocalToc"><ul class="simple">
+      aria-labelledby="dLabelLocalToc"><ul>
+<li><a class="reference internal" href="#">Example of Spectral Analysis of Gyrification (SPANGY) decomposition</a></li>
 </ul>
 </ul>
 </li>
@@ -111,9 +112,8 @@
 <p>Click <a class="reference internal" href="#sphx-glr-download-auto-examples-example-spangy-py"><span class="std std-ref">here</span></a>
 to download the full example code</p>
 </div>
-<p class="sphx-glr-example-title">J.F. Mangin, Larger is twistier:Spectral Analysis of Gyrification (SPANGY)
-applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.
-===================================</p>
+<div class="sphx-glr-example-title section" id="example-of-spectral-analysis-of-gyrification-spangy-decomposition">
+<span id="example-spangy"></span><span id="sphx-glr-auto-examples-example-spangy-py"></span><h1>Example of Spectral Analysis of Gyrification (SPANGY) decomposition<a class="headerlink" href="#example-of-spectral-analysis-of-gyrification-spangy-decomposition" title="Permalink to this headline">¶</a></h1>
 <ul class="sphx-glr-horizontal">
 <li><img alt="example spangy" class="sphx-glr-multi-img" src="../_images/sphx_glr_example_spangy_001.png" />
 </li>
@@ -166,6 +166,11 @@
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">import</span> <span class="nn">slam.spangy</span> <span class="k">as</span> <span class="nn">spgy</span>
 
+<span class="c1">## D. Germanaud*, J. Lefevre*,R. Toro, C. Fischer, J.Dubois, L. Hertz-Pannier,</span>
+<span class="c1">## J.F. Mangin, Larger is twistier:Spectral Analysis of Gyrification (SPANGY)</span>
+<span class="c1">## applied to adult brain size polymorphism,Neuroimage, 63 (3), 1257-1272, 2012.</span>
+
+
 <span class="c1">## LOAD MESH</span>
 <span class="n">mesh</span> <span class="o">=</span> <span class="n">sio</span><span class="o">.</span><span class="n">load_mesh</span><span class="p">(</span><span class="s2">&quot;../examples/data/example_mesh.gii&quot;</span><span class="p">)</span>
 <a href="https://docs.python.org/3/library/functions.html#int" title="builtins.int" class="sphx-glr-backref-module-builtins sphx-glr-backref-type-py-class sphx-glr-backref-instance"><span class="n">N</span></a> <span class="o">=</span> <span class="mi">1500</span>
@@ -230,7 +235,7 @@
 <span class="n">visb_sc</span><span class="o">.</span><span class="n">preview</span><span class="p">()</span>
 </pre></div>
 </div>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> ( 0 minutes  31.582 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> ( 0 minutes  32.380 seconds)</p>
 <div class="sphx-glr-footer class sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-example-spangy-py">
 <div class="sphx-glr-download sphx-glr-download-python docutils container">
 <p><a class="reference download internal" download="" href="../_downloads/c7a379ff1b73b7b2972fd8542e5e55ef/example_spangy.py"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Python</span> <span class="pre">source</span> <span class="pre">code:</span> <span class="pre">example_spangy.py</span></code></a></p>
@@ -240,6 +245,7 @@
 </div>
 </div>
 <p class="sphx-glr-signature"><a class="reference external" href="https://sphinx-gallery.github.io">Gallery generated by Sphinx-Gallery</a></p>
+</div>
 
 
     </div>

auto_examples/index.html

@@ -197,7 +197,7 @@
 </div>
 <div class="sphx-glr-thumbcontainer" tooltip="Example of Spectral Analysis of Gyrification (SPANGY) decomposition"><div class="figure align-default" id="id15">
 <img alt="Example of Spectral Analysis of Gyrification (SPANGY) decomposition" src="../_images/sphx_glr_example_spangy_thumb.png" />
-<p class="caption"><span class="caption-text"><span class="xref std std-ref">sphx_glr_auto_examples_example_spangy.py</span></span><a class="headerlink" href="#id15" title="Permalink to this image">¶</a></p>
+<p class="caption"><span class="caption-text"><a class="reference internal" href="example_spangy.html#sphx-glr-auto-examples-example-spangy-py"><span class="std std-ref">Example of Spectral Analysis of Gyrification (SPANGY) decomposition</span></a></span><a class="headerlink" href="#id15" title="Permalink to this image">¶</a></p>
 </div>
 </div><div class="toctree-wrapper compound">
 </div>

auto_examples/sg_execution_times.html

@@ -109,16 +109,16 @@
 
   <div class="section" id="computation-times">
 <span id="sphx-glr-auto-examples-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Permalink to this headline">¶</a></h1>
-<p><strong>00:00.171</strong> total execution time for <strong>auto_examples</strong> files:</p>
+<p><strong>00:32.380</strong> total execution time for <strong>auto_examples</strong> files:</p>
 <table class="docutils align-default">
 <colgroup>
 <col style="width: 86%" />
 <col style="width: 8%" />
 <col style="width: 6%" />
 </colgroup>
 <tbody>
-<tr class="row-odd"><td><p><a class="reference internal" href="example_surface_profiling.html#sphx-glr-auto-examples-example-surface-profiling-py"><span class="std std-ref">example of surface profiling in slam</span></a> (<code class="docutils literal notranslate"><span class="pre">example_surface_profiling.py</span></code>)</p></td>
-<td><p>00:00.171</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="example_spangy.html#sphx-glr-auto-examples-example-spangy-py"><span class="std std-ref">Example of Spectral Analysis of Gyrification (SPANGY) decomposition</span></a> (<code class="docutils literal notranslate"><span class="pre">example_spangy.py</span></code>)</p></td>
+<td><p>00:32.380</p></td>
 <td><p>0.0 MB</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="example_basics.html#sphx-glr-auto-examples-example-basics-py"><span class="std std-ref">Show basic use of slam</span></a> (<code class="docutils literal notranslate"><span class="pre">example_basics.py</span></code>)</p></td>
@@ -177,7 +177,7 @@
 <td><p>00:00.000</p></td>
 <td><p>0.0 MB</p></td>
 </tr>
-<tr class="row-even"><td><p><span class="xref std std-ref">sphx_glr_auto_examples_example_spangy.py</span> (<code class="docutils literal notranslate"><span class="pre">example_spangy.py</span></code>)</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="example_surface_profiling.html#sphx-glr-auto-examples-example-surface-profiling-py"><span class="std std-ref">example of surface profiling in slam</span></a> (<code class="docutils literal notranslate"><span class="pre">example_surface_profiling.py</span></code>)</p></td>
 <td><p>00:00.000</p></td>
 <td><p>0.0 MB</p></td>
 </tr>