TVB-3079 Change the used connectivity in the example simulate_surface…

…_seeg_eeg_meg.ipynb, to not have subcortical regions, until bug TVB-3018 gets fixed

tvb_documentation/demos/simulate_surface_seeg_eeg_meg.ipynb

@@ -33,48 +33,84 @@
     "\n",
     "oscillator = models.Generic2dOscillator(a=numpy.array([0.1]), tau=numpy.array([2.0]))\n",
     "\n",
-    "white_matter = connectivity.Connectivity.from_file('connectivity_192.zip')\n",
+    "white_matter = connectivity.Connectivity.from_file(\"connectivity_76.zip\") # TVB-3018: \"connectivity_192.zip\"\n",
     "white_matter.speed = numpy.array([4.0])\n",
     "white_matter_coupling = coupling.Difference(a=numpy.array([0.014]))\n",
     "\n",
-    "rm_f_name = 'regionMapping_16k_192.txt'\n",
+    "rm_f_name = 'regionMapping_16k_76.txt' # TVB-3018: 'regionMapping_16k_192.txt'\n",
     "rm = RegionMapping.from_file(rm_f_name)\n",
     "sensorsEEG = SensorsEEG.from_file('eeg_unitvector_62.txt.bz2')\n",
     "prEEG = ProjectionSurfaceEEG.from_file('projection_eeg_62_surface_16k.mat', matlab_data_name=\"ProjectionMatrix\")\n",
     "\n",
     "heunint = integrators.HeunStochastic(\n",
     "    dt=2**-4,\n",
     "    noise=noise.Additive(nsig=numpy.array([2 ** -5, ]))\n",
-    ")\n",
-    "\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Monitors\n",
+    "See shown here 3 different ways of configuring monitors.\n",
+    "These methods are available for all projection monitors"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "fsamp = 1e3/1024.0 # 1024 Hz\n",
-    "# See shown here 3 different ways of configuring monitors.\n",
-    "# These methods are available for all projection monitors\n",
+    "\n",
     "monitor_MEG=monitors.MEG.from_file(rm_f_name=rm_f_name)\n",
     "monitor_MEG.period=fsamp\n",
     "mons = (\n",
     "    monitors.EEG(sensors=sensorsEEG, projection=prEEG, region_mapping=rm, period=fsamp),\n",
     "    monitor_MEG,\n",
     "    monitors.iEEG.from_file('seeg_588.txt', 'projection_seeg_588_surface_16k.npy', rm_f_name=rm_f_name, period=fsamp),\n",
-    "    monitors.ProgressLogger(period=100.0),\n",
+    "    monitors.ProgressLogger(period=10.0),\n",
     ")\n",
     "\n",
     "local_coupling_strength = numpy.array([2 ** -10])\n",
-    "default_cortex = Cortex.from_file(region_mapping_file='regionMapping_16k_192.txt')\n",
+    "default_cortex = Cortex.from_file(region_mapping_file=rm_f_name)\n",
     "default_cortex.region_mapping_data.connectivity = white_matter\n",
-    "default_cortex.coupling_strength = local_coupling_strength\n",
-    "\n",
+    "default_cortex.coupling_strength = local_coupling_strength"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Bellow, adjust the simulation length to match your machine and needs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "sim = simulator.Simulator(\n",
     "    model=oscillator,\n",
     "    connectivity=white_matter,\n",
     "    coupling=white_matter_coupling,\n",
     "    integrator=heunint,\n",
     "    monitors=mons,\n",
     "    surface=default_cortex,\n",
-    "    simulation_length=10.0\n",
+    "    simulation_length=200.0\n",
     ")\n",
-    "sim.configure()\n",
-    "\n",
+    "sim.configure()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "eeg, meg, seeg, _ = sim.run()"
    ]
   },
@@ -105,7 +141,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -119,7 +155,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,