Add notebook entry on how to plot PSTH frequencies against a certain …

…group (#266) Also, updated the simulation config path to a working config.
BlueBrain · Jul 22, 2024 · 8b827ca · 8b827ca
1 parent 5ac6de7
commit 8b827ca
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Showing 3 changed files with 109 additions and 69 deletions.
diff --git a/doc/source/notebooks/05_simulations.ipynb b/doc/source/notebooks/05_simulations.ipynb
@@ -39,7 +39,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation_path = \"/gpfs/bbp.cscs.ch/project/proj42/circuits/CA1.O1/mooc-circuit/simulation_config_bluepy_examples.json\"\n",
+    "simulation_path = \"/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/simulation_config_bluepy_examples.json\"\n",
     "simulation = bluepysnap.Simulation(simulation_path)"
    ]
   },
@@ -69,21 +69,24 @@
     {
      "data": {
       "text/plain": [
-       "{'run': {'tstop': 1000.0, 'dt': 0.025, 'seed': 264118},\n",
-       " 'target_simulator': 'CORENEURON',\n",
-       " 'network': '/gpfs/bbp.cscs.ch/project/proj42/circuits/CA1.O1/mooc-circuit/circuit_config.json',\n",
+       "{'inputs': None,\n",
+       " 'network': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/mooc_circuit.json',\n",
        " 'node_sets_file': '/gpfs/bbp.cscs.ch/project/proj42/circuits/CA1.O1/mooc-circuit/node_sets.json',\n",
-       " 'inputs': {},\n",
-       " 'output': {'output_dir': '/gpfs/bbp.cscs.ch/project/proj42/circuits/CA1.O1/mooc-circuit/simulations/sonata_report',\n",
-       "  'log_file': 'simout-914515.log',\n",
+       " 'output': {'log_file': 'simout-914515.log',\n",
+       "  'output_dir': '/gpfs/bbp.cscs.ch/project/proj42/circuits/CA1.O1/mooc-circuit/simulations/sonata_report',\n",
        "  'spikes_file': 'out.h5',\n",
-       "  'spikes_sort_order': 'time'},\n",
+       "  'spikes_sort_order': 'by_time'},\n",
        " 'reports': {'soma_report': {'cells': 'CA1',\n",
-       "   'variable_name': 'v',\n",
-       "   'sections': 'soma',\n",
-       "   'enabled': True,\n",
        "   'dt': 0.1,\n",
-       "   'file_name': 'soma'}}}"
+       "   'enabled': True,\n",
+       "   'end_time': 1000,\n",
+       "   'file_name': 'soma',\n",
+       "   'sections': 'soma',\n",
+       "   'start_time': 0,\n",
+       "   'type': 'compartment',\n",
+       "   'variable_name': 'v'}},\n",
+       " 'run': {'dt': 0.025, 'random_seed': 264118, 'tstop': 1000.0},\n",
+       " 'target_simulator': 'CORENEURON'}"
       ]
      },
      "execution_count": 3,
@@ -103,7 +106,7 @@
     {
      "data": {
       "text/plain": [
-       "{'tstop': 1000.0, 'dt': 0.025, 'seed': 264118}"
+       "<libsonata._libsonata.Run at 0x2aaae3d3d1b0>"
       ]
      },
      "execution_count": 4,
@@ -163,7 +166,7 @@
     {
      "data": {
       "text/plain": [
-       "{}"
+       "<libsonata._libsonata.Conditions at 0x2aaae3d3dc30>"
       ]
      },
      "execution_count": 7,
@@ -203,7 +206,7 @@
     {
      "data": {
       "text/plain": [
-       "<bluepysnap.circuit.Circuit at 0x7f4e0eb07250>"
+       "<bluepysnap.circuit.Circuit at 0x2aaae3d3f5e0>"
       ]
      },
      "execution_count": 9,
@@ -223,7 +226,7 @@
     {
      "data": {
       "text/plain": [
-       "<bluepysnap.node_sets.NodeSets at 0x7f4e0eb07050>"
+       "<bluepysnap.node_sets.NodeSets at 0x2aaae3d3f7f0>"
       ]
      },
      "execution_count": 10,
@@ -243,7 +246,7 @@
     {
      "data": {
       "text/plain": [
-       "<bluepysnap.spike_report.SpikeReport at 0x7f4e0eb1b190>"
+       "<bluepysnap.spike_report.SpikeReport at 0x2aaae3d3f610>"
       ]
      },
      "execution_count": 11,
@@ -263,7 +266,7 @@
     {
      "data": {
       "text/plain": [
-       "{'soma_report': <bluepysnap.frame_report.SomaReport at 0x7f4e0fb32e90>}"
+       "{'soma_report': <bluepysnap.frame_report.SomaReport at 0x2aaae3d3fe50>}"
       ]
      },
      "execution_count": 12,
@@ -286,7 +289,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python3",
    "language": "python",
    "name": "python3"
   },
@@ -300,7 +303,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.12"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,