Merge pull request #62 from the-virtual-brain/dev

HBP-206 Improve examples
the-virtual-brain · Nov 7, 2022 · a58fa90 · a58fa90
2 parents cbc46bd + 07d238e
commit a58fa90
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diff --git a/examples/notebooks/pyspike_examples.ipynb b/examples/notebooks/pyspike_examples.ipynb
@@ -30,9 +30,11 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "import pyspike as spk\n",
+    "import os\n",
+    "\n",
+    "data_path = os.path.expanduser(\"~/packages/PySpike/test/PySpike_testdata.txt\")\n",
+    "spike_trains = spk.load_spike_trains_from_txt(data_path, edges=(0, 4000))\n",
     "\n",
-    "spike_trains = spk.load_spike_trains_from_txt(\"/home/docker/packages/PySpike/test/PySpike_testdata.txt\",\n",
-    "                                              edges=(0, 4000))\n",
     "n_spike_trains = len(spike_trains)\n",
     "y_max = n_spike_trains\n",
     "plt.figure(figsize=(20, 10))\n",
@@ -89,7 +91,7 @@
     }
    ],
    "source": [
-    "spike_trains = spk.load_spike_trains_from_txt(\"/home/docker/packages/PySpike/test/PySpike_testdata.txt\", 4000)\n",
+    "spike_trains = spk.load_spike_trains_from_txt(data_path, 4000)\n",
     "\n",
     "plt.figure()\n",
     "isi_distance = spk.isi_distance_matrix(spike_trains)\n",

diff --git a/examples/tvb_annarchy/notebooks/ANNarchy basal ganglia exact maith resting simulation.ipynb b/examples/tvb_annarchy/notebooks/ANNarchy basal ganglia exact maith resting simulation.ipynb
diff --git a/examples/tvb_annarchy/notebooks/ANNarchy-spiking-cortex.ipynb b/examples/tvb_annarchy/notebooks/ANNarchy-spiking-cortex.ipynb
diff --git a/examples/tvb_annarchy/notebooks/TVB-corr-cortex-opt.ipynb b/examples/tvb_annarchy/notebooks/TVB-corr-cortex-opt.ipynb
@@ -45,9 +45,7 @@
     "from tvb_multiscale.tvb_annarchy.config import *\n",
     "\n",
     "work_path = os.getcwd()\n",
-    "data_path = os.path.join(work_path.split(\"tvb_annarchy\")[0], \"data/basal_ganglia\")\n",
-    "# data_path = os.path.join(work_path.split(\"packages\")[0], \n",
-    "#                          \"packages/tvb-multiscale/examples/data/basal_ganglia\")\n",
+    "data_path = os.path.expanduser(\"~/packages/tvb-multiscale/examples/data/basal_ganglia\")\n",
     "fit_data_path = os.path.join(data_path, \"ANNarchyFittedModels/dataFits_2020_02_05/databestfits\", )\n",
     "data_mode = \"patient\" # \"control\", \"patient\"\n",
     "control_data = os.path.join(fit_data_path, \"controlleft/OutputSim_Patient08.mat\")\n",

diff --git a/examples/tvb_nest/notebooks/basal_ganglia/__init__.py b/examples/tvb_nest/notebooks/basal_ganglia/__init__.py
diff --git a/examples/tvb_nest/notebooks/cerebellum/CerebWilsonCowanTVBonly.ipynb b/examples/tvb_nest/notebooks/cerebellum/CerebWilsonCowanTVBonly.ipynb
diff --git a/examples/tvb_nest/notebooks/cerebellum/CerebWilsonCowanTVBonly_Griffiths.ipynb b/examples/tvb_nest/notebooks/cerebellum/CerebWilsonCowanTVBonly_Griffiths.ipynb
diff --git a/examples/tvb_nest/notebooks/cerebellum/cereb.ipynb b/examples/tvb_nest/notebooks/cerebellum/cereb.ipynb
diff --git a/examples/tvb_nest/notebooks/cerebellum/cereb_no_nest_builders.ipynb b/examples/tvb_nest/notebooks/cerebellum/cereb_no_nest_builders.ipynb
diff --git a/examples/tvb_nest/notebooks/cerebellum/olivocerebellum_sim.ipynb b/examples/tvb_nest/notebooks/cerebellum/olivocerebellum_sim.ipynb