Skip to content
This repository was archived by the owner on Feb 26, 2025. It is now read-only.

update base notebooks to not use homedirs #163

Open
mgeplf wants to merge 3 commits into
base: master
Choose a base branch
from
Open

update base notebooks to not use homedirs #163

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
0a577e3
update base notebooks to use proj12/proj data
mgeplf Aug 16, 2022
c021f6f
Update notebooks due to libsonata additions
Aug 11, 2022
6fcd4f9
Update notebooks with the new figure size
Aug 26, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
40 changes: 20 additions & 20 deletions doc/source/notebooks/01_circuits.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -94,25 +94,25 @@
{
"data": {
"text/plain": [
"{'version': 2,\n",
" 'node_sets_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/nodes/node_sets.json',\n",
" 'networks': {'nodes': [{'nodes_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/nodes/thalamus_neurons/nodes.h5',\n",
" 'populations': {'thalamus_neurons': {'type': 'biophysical',\n",
" 'biophysical_neuron_models_dir': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/modelmanagement/20191105/memodels/hoc',\n",
" 'alternate_morphologies': {'neurolucida-asc': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/morphology_release/20191031/ascii',\n",
" 'h5v1': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/morphology_release/20191031/h5'}}}},\n",
" {'nodes_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/nodes/CorticoThalamic_projections/nodes.h5',\n",
" 'populations': {'CorticoThalamic_projections': {'type': 'virtual'}}},\n",
" {'nodes_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/nodes/MedialLemniscus_projections/nodes.h5',\n",
" 'populations': {'MedialLemniscus_projections': {'type': 'virtual'}}}],\n",
" 'edges': [{'edges_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/edges/thalamus_neurons__thalamus_neurons__chemical/edges.h5',\n",
"{'networks': {'edges': [{'edges_file': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/sonata/networks/edges/thalamus_neurons__thalamus_neurons__chemical/edges.h5',\n",
" 'populations': {'thalamus_neurons__thalamus_neurons__chemical': {'type': 'chemical'}}},\n",
" {'edges_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/edges/thalamus_neurons__thalamus_neurons__electrical_synapse/edges.h5',\n",
" {'edges_file': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/sonata/networks/edges/thalamus_neurons__thalamus_neurons__electrical_synapse/edges.h5',\n",
" 'populations': {'thalamus_neurons__thalamus_neurons__electrical_synapse': {'type': 'electrical'}}},\n",
" {'edges_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/edges/MedialLemniscus_projections__thalamus_neurons__chemical/edges.h5',\n",
" {'edges_file': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/sonata/networks/edges/MedialLemniscus_projections__thalamus_neurons__chemical/edges.h5',\n",
" 'populations': {'MedialLemniscus_projections__thalamus_neurons__chemical': {'type': 'chemical'}}},\n",
" {'edges_file': '/gpfs/bbp.cscs.ch/home/herttuai/snap/doc/source/notebooks/sonata/networks/edges/CorticoThalamic_projections__thalamus_neurons__chemical/edges.h5',\n",
" 'populations': {'CorticoThalamic_projections__thalamus_neurons__chemical': {'type': 'chemical'}}}]}}"
" {'edges_file': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/sonata/networks/edges/CorticoThalamic_projections__thalamus_neurons__chemical/edges.h5',\n",
" 'populations': {'CorticoThalamic_projections__thalamus_neurons__chemical': {'type': 'chemical'}}}],\n",
" 'nodes': [{'nodes_file': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/sonata/networks/nodes/thalamus_neurons/nodes.h5',\n",
" 'populations': {'thalamus_neurons': {'alternate_morphologies': {'h5v1': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/morphology_release/20191031/09_CloneMorphologies-h5v1',\n",
" 'neurolucida-asc': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/morphology_release/20191031/09_CloneMorphologies-ASC'},\n",
" 'biophysical_neuron_models_dir': '/gpfs/bbp.cscs.ch/project/proj82/home/iavarone/modelmanagement/20191105/output/emodels_hoc',\n",
" 'type': 'biophysical'}}},\n",
" {'nodes_file': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/sonata/networks/nodes/CorticoThalamic_projections/nodes.h5',\n",
" 'populations': {'CorticoThalamic_projections': {'type': 'virtual'}}},\n",
" {'nodes_file': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/sonata/networks/nodes/MedialLemniscus_projections/nodes.h5',\n",
" 'populations': {'MedialLemniscus_projections': {'type': 'virtual'}}}]},\n",
" 'node_sets_file': '/gpfs/bbp.cscs.ch/project/proj12/NSE/bluepysnap-functional-tests/sonata/networks/nodes/node_sets.json',\n",
" 'version': 2}"
]
},
"execution_count": 4,
Expand All @@ -132,7 +132,7 @@
{
"data": {
"text/plain": [
"<bluepysnap.nodes.Nodes at 0x2aaae172acd0>"
"<bluepysnap.nodes.Nodes at 0x2aaae3d8d100>"
]
},
"execution_count": 5,
Expand All @@ -152,7 +152,7 @@
{
"data": {
"text/plain": [
"<bluepysnap.edges.Edges at 0x2aaae172a510>"
"<bluepysnap.edges.Edges at 0x2aaae3d8d0a0>"
]
},
"execution_count": 6,
Expand All @@ -172,7 +172,7 @@
{
"data": {
"text/plain": [
"<bluepysnap.node_sets.NodeSets at 0x2aaae1737250>"
"<bluepysnap.node_sets.NodeSets at 0x2aaae3d8d460>"
]
},
"execution_count": 7,
Expand Down Expand Up @@ -210,7 +210,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.7"
}
},
"nbformat": 4,
Expand Down
60 changes: 25 additions & 35 deletions doc/source/notebooks/03_node_properties.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

18 changes: 7 additions & 11 deletions doc/source/notebooks/04_edge_properties.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

41 changes: 22 additions & 19 deletions doc/source/notebooks/05_simulations.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)"
]
},
Expand Down Expand Up @@ -69,21 +69,24 @@
{
"data": {
"text/plain": [
"{'run': {'tstop': 1000.0, 'dt': 0.025, 'seed': 264118},\n",
" 'target_simulator': 'CORENEURON',\n",
"{'inputs': None,\n",
" 'network': '/gpfs/bbp.cscs.ch/project/proj42/circuits/CA1.O1/mooc-circuit/circuit_config.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,
Expand All @@ -103,7 +106,7 @@
{
"data": {
"text/plain": [
"{'tstop': 1000.0, 'dt': 0.025, 'seed': 264118}"
"{'dt': 0.025, 'random_seed': 264118, 'tstop': 1000.0}"
]
},
"execution_count": 4,
Expand Down Expand Up @@ -203,7 +206,7 @@
{
"data": {
"text/plain": [
"<bluepysnap.circuit.Circuit at 0x7f4e0eb07250>"
"<bluepysnap.circuit.Circuit at 0x2aaae3d924f0>"
]
},
"execution_count": 9,
Expand All @@ -223,7 +226,7 @@
{
"data": {
"text/plain": [
"<bluepysnap.node_sets.NodeSets at 0x7f4e0eb07050>"
"<bluepysnap.node_sets.NodeSets at 0x2aaae3d92400>"
]
},
"execution_count": 10,
Expand All @@ -243,7 +246,7 @@
{
"data": {
"text/plain": [
"<bluepysnap.spike_report.SpikeReport at 0x7f4e0eb1b190>"
"<bluepysnap.spike_report.SpikeReport at 0x2aaab7f1a2e0>"
]
},
"execution_count": 11,
Expand All @@ -263,7 +266,7 @@
{
"data": {
"text/plain": [
"{'soma_report': <bluepysnap.frame_report.SomaReport at 0x7f4e0fb32e90>}"
"{'soma_report': <bluepysnap.frame_report.SomaReport at 0x2aaae3d9e520>}"
]
},
"execution_count": 12,
Expand All @@ -286,7 +289,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -300,9 +303,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.12"
"version": "3.9.7"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
48 changes: 19 additions & 29 deletions doc/source/notebooks/06_spike_reports.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

Loading