TVB-3088 Merge notebooks display_surface_local_connectivity.ipynb int…

…o exploring_a_surface_mesh.ipynb (as the LC was not displayed)

tvb_documentation/demos/Demos.rst

@@ -113,7 +113,6 @@ examples.
 .. _Analyze Region Corrcoef: https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/analyze_region_corrcoef.ipynb
 .. _Compare Connectivity Normalization: https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/compare_connectivity_normalization.ipynb
 .. _Display Source Sensor Geometry: https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/display_source_sensor_geometry.ipynb
-.. _Display Surface Local Connectivity: https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/display_surface_local_connectivity.ipynb
 .. _Encrypt Files before upload in TVB Web GUI: https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/encrypt_data.ipynb
 .. _Exploring Epileptor 2D: https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/exploring_epileptor_2d.ipynb
 .. _Exploring Longer Time Series: https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/exploring_longer_time_series.ipynb
@@ -167,14 +166,6 @@ examples.
       `Display Source Sensor Geometry`_
 
 
-.. figure:: figures/display_surface_local_connectivity.png
-      :width: 200px
-      :figclass: demo-figure
-      :target: `Display Surface Local Connectivity`_
-
-      `Display Surface Local Connectivity`_
-
-
 .. figure:: figures/exploring_longer_time_series.png
       :width: 200px
       :figclass: demo-figure

tvb_library/tvb/simulator/plot/head_plotter_3d.py

@@ -37,12 +37,11 @@
     # To visualise the sensors and surface
     hp.display_source_sensor_geometry(surface, connectivity, meg_sensors, eeg_sensors)
 
-    # To visualise the sensors and surface
-    hp.display_surface_local_connectivity(cortex, local_connectivity)
+    # To visualise a Surface in 3D
+    hp.display_surface(surface)
 
 """
 
-import numpy as np
 import matplotlib.pyplot as plt
 from tvb.simulator.lab import *
 from deprecated import deprecated
@@ -53,7 +52,8 @@
 @deprecated(reason="Use tvb-widgets instead")
 class HeadPlotter3D(object):
 
-    def display_source_sensor_geometry(self, surface=None, conn=None, meg_sensors=None, eeg_sensors=None):
+    @staticmethod
+    def display_source_sensor_geometry(surface=None, conn=None, meg_sensors=None, eeg_sensors=None):
         # type: (surfaces.SkinAir, connectivity.Connectivity, sensors.SensorsMEG, sensors.SensorsEEG ) -> None
         """
         :param surface: Optional surfaces.SkinAir instance. When none, we will try loading a default
@@ -120,25 +120,14 @@ def plot(**plot_params):
         out = widgets.interactive_output(plot, params)
         display(control_box, out)
 
-    def display_surface_local_connectivity(self, ctx=None, loc_conn=None):
-        # type: (cortex.Cortex, local_connectivity.LocalConnectivity) -> None
+    @staticmethod
+    def display_surface(ctx):
+        # type: (surfaces.CorticalSurface) -> None
         """
-        :param cortex: Optional cortex.Cortex instance. When none, we will try loading a default
-        :param loc_conn: Optional. If None, and cortex local connectivity is None, we will try loading a default.
+        :param ctx: surface.CorticalSurfaceF
         """
-        # Start by configuring the cortical surface
-        if ctx is None:
-            ctx = cortex.Cortex.from_file()
-        if ctx.local_connectivity is None:
-            if loc_conn is None:
-                loc_conn = local_connectivity.LocalConnectivity(cutoff=20.0, surface=ctx.region_mapping_data.surface)
-            loc_conn.equation.parameters['sigma'] = 10.0
-            loc_conn.equation.parameters['amp'] = 1.0
-            ctx.local_connectivity = loc_conn
-        ctx.coupling_strength = np.array([0.0115])
         ctx.configure()
 
-        # plot 
         plt.figure()
         ax = plt.subplot(111, projection='3d')
         x, y, z = ctx.vertices.T