-
Notifications
You must be signed in to change notification settings - Fork 10
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #62 from NeuroML/experimental
Updates to sonata import/export
- Loading branch information
Showing
15 changed files
with
149 additions
and
152 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,64 @@ | ||
| { | ||
| "SonataExample": { | ||
| "version": "NeuroMLlite v0.1.9", | ||
| "version": "NeuroMLlite v0.5.8", | ||
| "notes": "Example for testing Sonata", | ||
| "parameters": { | ||
| "input_del": 100, | ||
| "input_dur": 800, | ||
| "input_amp": 0.19 | ||
| }, | ||
| "notes": "Example for testing Sonata", | ||
| "cells": [ | ||
| { | ||
| "testcell": { | ||
| "pynn_cell": "IF_cond_alpha", | ||
| "parameters": { | ||
| "tau_refrac": 3, | ||
| "tau_m": 22.1, | ||
| "i_offset": 0, | ||
| "cm": 0.117, | ||
| "v_thresh": -47, | ||
| "v_rest": -78, | ||
| "v_reset": -50 | ||
| } | ||
| } | ||
| "input_amp": 0.19, | ||
| "input_del": 100, | ||
| "input_dur": 800 | ||
| }, | ||
| "cells": { | ||
| "testcell": { | ||
| "parameters": { | ||
| "i_offset": 0, | ||
| "cm": 0.117, | ||
| "tau_m": 22.1, | ||
| "tau_refrac": 3, | ||
| "v_reset": -50, | ||
| "v_rest": -78, | ||
| "v_thresh": -47 | ||
| }, | ||
| "pynn_cell": "IF_cond_alpha" | ||
| } | ||
| ], | ||
| "input_sources": [ | ||
| { | ||
| "i_clamp": { | ||
| "pynn_input": "DCSource", | ||
| "parameters": { | ||
| "start": "input_del", | ||
| "stop": "input_del+input_dur", | ||
| "amplitude": "input_amp" | ||
| } | ||
| } | ||
| }, | ||
| "input_sources": { | ||
| "i_clamp": { | ||
| "parameters": { | ||
| "amplitude": "input_amp", | ||
| "start": "input_del", | ||
| "stop": "input_del+input_dur" | ||
| }, | ||
| "pynn_input": "DCSource" | ||
| } | ||
| ], | ||
| "regions": [ | ||
| { | ||
| "region1": { | ||
| "x": 0.0, | ||
| "y": 0.0, | ||
| "z": 0.0, | ||
| "width": 1000.0, | ||
| "height": 100.0, | ||
| "depth": 1000.0 | ||
| } | ||
| }, | ||
| "regions": { | ||
| "region1": { | ||
| "x": 0.0, | ||
| "y": 0.0, | ||
| "z": 0.0, | ||
| "width": 1000.0, | ||
| "height": 100.0, | ||
| "depth": 1000.0 | ||
| } | ||
| ], | ||
| "populations": [ | ||
| { | ||
| "pop0": { | ||
| "size": 2, | ||
| "component": "testcell", | ||
| "properties": { | ||
| "color": "1 0 0" | ||
| }, | ||
| "random_layout": { | ||
| "region": "region1" | ||
| } | ||
| }, | ||
| "populations": { | ||
| "pop0": { | ||
| "size": 2, | ||
| "component": "testcell", | ||
| "properties": { | ||
| "color": "1 0 0" | ||
| }, | ||
| "random_layout": { | ||
| "region": "region1" | ||
| } | ||
| } | ||
| ], | ||
| "inputs": [ | ||
| { | ||
| "stim": { | ||
| "input_source": "i_clamp", | ||
| "population": "pop0", | ||
| "percentage": 50.0 | ||
| } | ||
| }, | ||
| "inputs": { | ||
| "stim": { | ||
| "input_source": "i_clamp", | ||
| "population": "pop0", | ||
| "percentage": 50 | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,18 @@ | ||
| { | ||
| "manifest": { | ||
| "$NETWORK_DIR": "./network", | ||
| "$COMPONENT_DIR": "./components" | ||
| }, | ||
| "components": { | ||
| "synaptic_models_dir": "$COMPONENT_DIR/synaptic_models", | ||
| "point_neuron_models_dir": "$COMPONENT_DIR/point_neuron_models_dir" | ||
| }, | ||
| "networks": { | ||
| "nodes": [ | ||
| { | ||
| "node_types_file": "$NETWORK_DIR/SonataExample_node_types.csv", | ||
| "nodes_file": "$NETWORK_DIR/SonataExample_nodes.sonata.h5" | ||
| "nodes_file": "$NETWORK_DIR/SonataExample_nodes.sonata.h5", | ||
| "node_types_file": "$NETWORK_DIR/SonataExample_node_types.csv" | ||
| } | ||
| ] | ||
| }, | ||
| "components": { | ||
| "point_neuron_models_dir": "$COMPONENT_DIR/point_neuron_models_dir", | ||
| "synaptic_models_dir": "$COMPONENT_DIR/synaptic_models" | ||
| }, | ||
| "manifest": { | ||
| "$NETWORK_DIR": "./network", | ||
| "$COMPONENT_DIR": "./components" | ||
| } | ||
| } |
14 changes: 7 additions & 7 deletions
14
examples/sonatatest/components/point_neuron_models_dir/testcell.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,9 +1,9 @@ | ||
| { | ||
| "tau_m": 22.1, | ||
| "V_th": -47.0, | ||
| "I_e": 0.0, | ||
| "C_m": 117.0, | ||
| "V_reset": -50.0, | ||
| "t_ref": 3.0, | ||
| "E_L": -78.0 | ||
| "E_L": -78.0, | ||
| "C_m": 117.0, | ||
| "tau_m": 22.1, | ||
| "t_ref": 3.0, | ||
| "V_th": -47.0, | ||
| "V_reset": -50.0, | ||
| "I_e": 0.0 | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| { | ||
| "network": "./circuit_config.json", | ||
| "network": "./circuit_config.json", | ||
| "simulation": "./simulation_config.json" | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,2 @@ | ||
| node_type_id dynamics_params pop_name model_template model_type model_name | ||
| 100 testcell.json pop0 nest:iaf_psc_alpha point_process testcell | ||
| node_type_id pop_name model_name model_template model_type dynamics_params | ||
| 100 pop0 testcell nest:iaf_psc_alpha point_process testcell.json |
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| #!/bin/bash | ||
| set -ex | ||
|
|
||
| python SonataExample.py -sonata | ||
|
|
||
| python run_bmtk.py | ||
|
|
||
| ./run_pynml.jnml.sh |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,4 @@ | ||
| #!/bin/bash | ||
|
|
||
| set -e | ||
| set -ex | ||
|
|
||
| pynml-sonata Back2NML config.json -jnml |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,45 @@ | ||
| { | ||
| "inputs": { | ||
| "stim": { | ||
| "input_type": "current_clamp", | ||
| "node_set": "inputset_stim_i_clamp", | ||
| "module": "IClamp", | ||
| "delay": 100.0, | ||
| "duration": 800.0, | ||
| "amp": 190.00000000000003 | ||
| } | ||
| }, | ||
| "target_simulator": "NEST", | ||
| "reports": { | ||
| "membrane_potential": { | ||
| "enabled": true, | ||
| "cells": "point_nodes", | ||
| "sections": "soma", | ||
| "module": "multimeter_report", | ||
| "variable_name": "V_m" | ||
| } | ||
| }, | ||
| "manifest": { | ||
| "$OUTPUT_DIR": "./output", | ||
| "$INPUT_DIR": "./" | ||
| }, | ||
| "run": { | ||
| "tstop": 1000.0, | ||
| "tstop": 1000.0, | ||
| "dt": 0.01 | ||
| }, | ||
| }, | ||
| "target_simulator": "NEST", | ||
| "manifest": { | ||
| "$OUTPUT_DIR": "./output", | ||
| "$INPUT_DIR": "./" | ||
| }, | ||
| "output": { | ||
| "output_dir": "$OUTPUT_DIR", | ||
| "log_file": "log.txt", | ||
| "spikes_file": "spikes.h5", | ||
| "spikes_sort_order": "time" | ||
| }, | ||
| "node_sets": { | ||
| "point_nodes": { | ||
| "model_type": "point_process" | ||
| }, | ||
| }, | ||
| "inputset_stim_i_clamp": { | ||
| "model_type": "point_process", | ||
| "model_type": "point_process", | ||
| "population": "pop0" | ||
| } | ||
| }, | ||
| "output": { | ||
| "spikes_sort_order": "time", | ||
| "spikes_file": "spikes.h5", | ||
| "log_file": "log.txt", | ||
| "output_dir": "$OUTPUT_DIR" | ||
| }, | ||
| "reports": { | ||
| "membrane_potential": { | ||
| "cells": "point_nodes", | ||
| "variable_name": "V_m", | ||
| "module": "multimeter_report", | ||
| "sections": "soma", | ||
| "enabled": true | ||
| } | ||
| }, | ||
| "inputs": { | ||
| "stim": { | ||
| "input_type": "current_clamp", | ||
| "module": "IClamp", | ||
| "amp": 190.00000000000003, | ||
| "delay": 100.0, | ||
| "duration": 800.0, | ||
| "node_set": "inputset_stim_i_clamp" | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.