Test suite & minor updates to examples & updates to 300_pointneuron example

.gitignore

@@ -12,3 +12,27 @@ examples/**/output/config.json
 .cache
 **/mechanisms/x86_64
 .ipynb_checkpoints/
+/examples/sim_tests/intfire/*/test/x86_64
+/examples/sim_tests/intfire/*/test/LEMS*.xml
+/examples/sim_tests/intfire/*/test/*.dat
+/examples/sim_tests/intfire/*/test/report*txt
+/examples/sim_tests/intfire/*/test/*spikes
+/examples/sim_tests/intfire/*/test/*.net.nml
+/examples/sim_tests/intfire/*/test/*_nrn.py
+/examples/sim_tests/intfire/*/test/*.mod
+/examples/sim_tests/intfire/*/test/output/*h5
+/examples/sim_tests/intfire/*/test/output/log.txt
+/examples/sim_tests/intfire/*/test/output/*dat
+/examples/checkouth5.sh
+/examples/300_pointneurons/*.mod
+/examples/300_pointneurons/LEMS_Sim_sim.xml
+/examples/300_pointneurons/*_nrn.py
+/examples/300_pointneurons/*spikes
+/examples/300_pointneurons/output/*.dat
+/examples/300_pointneurons/report.txt
+/examples/300_pointneurons/*.dat
+/examples/300_pointneurons/x86_64
+/examples/300_pointneurons/comparison_V_m.png
+/examples/300_pointneurons/sim.net.nml
+/examples/300_pointneurons/output/membrane_potential.h5
+/examples/300_pointneurons/output/spikes.h5

examples/300_cells/analyze_output.py

@@ -0,0 +1,12 @@
+import sys
+from bmtk.analyzer.visualization.spikes import plot_spikes
+
+
+sys.path.append("../sim_tests/shared_components/scripts")
+
+from analyze_output_utils import plot_data
+
+if __name__ == '__main__':
+
+    plot_data('output/membrane_potential.h5', 'mV', 'Membrane Potential', show_already=True, max_num_traces=12)
+    plot_spikes('network/internal_nodes.h5', 'network/internal_node_types.csv', 'output/spikes.h5', group_key='model_name')

examples/300_cells/plot_spikes.py

@@ -0,0 +1,15 @@
+from bmtk.analyzer.visualization.spikes import plot_spikes
+import sys
+
+title = None
+if len(sys.argv)>1:
+    title = 'Simulator: %s'%sys.argv[1]
+
+# Note: depends on https://github.com/AllenInstitute/bmtk/pull/73
+plot_spikes('network/internal_nodes.h5', 
+            'network/internal_node_types.csv', 
+            'output/spikes.h5', 
+            group_key='model_name', 
+            legend=False,
+            title=title,
+            font_size=13)

examples/300_cells/simulation_config.json

@@ -22,7 +22,7 @@
     "v_init": -80
   },
 
-  "node_sets_file": "node_sets.json",
+  "node_sets_file": "$BASE_DIR/node_sets.json",
 
   "inputs": {
     "external_spike_trains": {

examples/300_intfire/network/tw_node_types.csv

@@ -1,2 +1,2 @@
-node_type_id model_type ei location model_name
+node_type_id model_type ei model_name location
 100 virtual e TW TW

examples/300_intfire/network/v1_node_types.csv

@@ -1,3 +1,3 @@
-node_type_id ei model_name location model_template model_type dynamics_params
-100 e LIF_exc VisL4 nrn:IntFire1 point_process IntFire1_exc_1.json
-101 i LIF_inh VisL4 nrn:IntFire1 point_process IntFire1_inh_1.json
+node_type_id ei location model_template model_type dynamics_params model_name
+100 e VisL4 nrn:IntFire1 point_process IntFire1_exc_1.json LIF_exc
+101 i VisL4 nrn:IntFire1 point_process IntFire1_inh_1.json LIF_inh

examples/300_intfire/simulation_config.json

@@ -1,7 +1,8 @@
 {
   "manifest": {
-    "$OUTPUT_DIR": "./output",
-    "$INPUT_DIR": "./inputs",
+    "$BASE_DIR": ".",
+    "$OUTPUT_DIR": "$BASE_DIR/output",
+    "$INPUT_DIR": "$BASE_DIR/inputs",
     "$COMPONENT_DIR": "../shared_components"
   },
 
@@ -16,7 +17,7 @@
 
   "target_simulator":"NEURON",
 
-  "node_sets_file": "node_sets.json",
+  "node_sets_file": "$BASE_DIR/node_sets.json",
 
   "conditions": {
     "celsius": 34.0,

examples/300_intfire/test_pynn.py

@@ -0,0 +1,7 @@
+from pyNN.serialization import import_from_sonata, load_sonata_simulation_plan
+import pyNN.neuron as sim
+
+simulation_plan = load_sonata_simulation_plan("simulation_config.json")
+simulation_plan.setup(sim)
+net = import_from_sonata("circuit_config.json", sim)
+simulation_plan.execute(net)

examples/300_pointneurons/build_network.py

@@ -134,18 +134,14 @@ def n_connections(src, trg, prob=0.5, min_syns=2, max_syns=7):
 cm = external.add_edges(target=internal.nodes(ei='e'), source=external.nodes(),
                         connection_rule=lambda *_: np.random.binomial(1, .7),
                         dynamics_params='ExcToExc.json',
-                        model_template='static_synapse',
-                        # syn_weight=50.0,
-                        delay=2.0)
+                        model_template='static_synapse')
 cm.add_properties('syn_weight', rule=50.0, dtypes=np.float)
 
 
 cm = external.add_edges(target=internal.nodes(ei='i'), source=external.nodes(),
                         connection_rule=lambda *_: np.random.binomial(1, .7),
                         dynamics_params='ExcToInh.json',
-                        model_template='static_synapse',
-                        # syn_weight=75.0,
-                        delay=2.0)
+                        model_template='static_synapse')
 cm.add_properties('syn_weight', rule=65.0, dtypes=np.float)
 
 

examples/300_pointneurons/network/external_internal_edge_types.csv

@@ -1,3 +1,3 @@
-edge_type_id target_query source_query delay dynamics_params model_template
-100 ei=='e' * 2.0 ExcToExc.json nest:static_synapse
-101 ei=='i' * 2.0 ExcToInh.json nest:static_synapse
+edge_type_id target_query source_query dynamics_params model_template
+100 ei=='e' * ExcToExc.json static_synapse
+101 ei=='i' * ExcToInh.json static_synapse

examples/300_pointneurons/network/internal_internal_edge_types.csv

@@ -1,5 +1,5 @@
 edge_type_id target_query source_query delay dynamics_params model_template
-100 ei=='e' ei=='e' 2.0 ExcToExc.json nest:static_synapse
-101 ei=='i' ei=='e' 2.0 ExcToInh.json nest:static_synapse
-102 ei=='e' ei=='i' 2.0 InhToExc.json nest:static_synapse
-103 ei=='i' ei=='i' 2.0 InhToInh.json nest:static_synapse
+100 ei=='e' ei=='e' 2.0 ExcToExc.json static_synapse
+101 ei=='i' ei=='e' 2.0 ExcToInh.json static_synapse
+102 ei=='e' ei=='i' 2.0 InhToExc.json static_synapse
+103 ei=='i' ei=='i' 2.0 InhToInh.json static_synapse

examples/300_pointneurons/plot_potential.py

@@ -33,7 +33,8 @@ def plot_vars(file_names, cell_var='v', gid_list=[], t_min=None, t_max=None):
     for fn in file_names:
         try:
             cell_var_files.append(CellVarsFile(fn, h5_root="/report/internal"))
-        except KeyError:
+        except KeyError as e:
+            print('Exception: %s'%e)
             cell_var_files.append(CellVarsFile(fn))
 
     # get first spike file and properties
@@ -47,6 +48,14 @@ def plot_vars(file_names, cell_var='v', gid_list=[], t_min=None, t_max=None):
         for i, cvf in enumerate(cell_var_files):
             # plot all traces
             ax[subplot].plot(cvf.time_trace, cvf.data(gid, cell_var), label=file_names[i])
+            time_steps = cvf.time_trace
+            data = cvf.data(gid, cell_var)
+            fn = 'output/gid_%s.dat'%gid
+            f = open(fn,'w')
+            print('Writing %i points to %s'%(len(time_steps), fn))
+            for ti in range(len(time_steps)):
+                f.write('%s\t%s\n'%(time_steps[ti]/1000,data[ti]/1000))
+            f.close()
 
         ax[subplot].yaxis.set_label_position("right")
         ax[subplot].set_ylabel('gid {}'.format(gid), fontsize='xx-small')
@@ -58,6 +67,10 @@ def plot_vars(file_names, cell_var='v', gid_list=[], t_min=None, t_max=None):
             # Use the last plot to get the legend
             handles, labels = ax[subplot].get_legend_handles_labels()
             fig.legend(handles, labels, loc='upper right')
+
+    for cvf in cell_var_files:
+        # Note: depends on: https://github.com/AllenInstitute/bmtk/pull/73
+        cvf.close()
 
     plt.show()
 

examples/300_pointneurons/plot_spikes.py

@@ -1,3 +1,15 @@
 from bmtk.analyzer.visualization.spikes import plot_spikes
+import sys
 
-plot_spikes('network/internal_nodes.h5', 'network/internal_node_types.csv', 'output/spikes.h5', group_key='model_name')
+title = None
+if len(sys.argv)>1:
+    title = 'Simulator: %s'%sys.argv[1]
+
+# Note: depends on https://github.com/AllenInstitute/bmtk/pull/73
+plot_spikes('network/internal_nodes.h5', 
+            'network/internal_node_types.csv', 
+            'output/spikes.h5', 
+            group_key='model_name', 
+            legend=False,
+            title=title,
+            font_size=13)

examples/300_pointneurons/run_PyNN.py

@@ -4,4 +4,4 @@
 simulation_plan = load_sonata_simulation_plan("simulation_config.json")
 simulation_plan.setup(sim)
 net = import_from_sonata("circuit_config.json", sim)
-simulation_plan.execute(net)
+simulation_plan.execute(net)

examples/300_pointneurons/run_pynml.jnmlnrn.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+set -e
+
+pynml-sonata sim config.json -neuron  

examples/300_pointneurons/simulation_config.json

@@ -7,7 +7,7 @@
 
   "run": {
     "tstop": 1500.0,
-    "dt": 0.001,
+    "dt": 0.01,
     "nsteps_block": 5000
   },
 
@@ -20,7 +20,7 @@
     "v_init": -80
   },
 
-  "node_sets_file": "node_sets.json",
+  "node_sets_file": "$BASE_DIR/node_sets.json",
 
   "inputs": {
     "external_spike_trains": {

examples/5_cells_iclamp/network/biophysical_node_types.csv

@@ -1,6 +1,6 @@
-node_type_id model_processing model_type model_template morphology ei model_name
-104 aibs_perisomatic biophysical nml:Cell_473862421.cell.nml Pvalb_469628681_m i PV2
-100 aibs_perisomatic biophysical nml:Cell_472363762.cell.nml Scnn1a_473845048_m e Scnn1a
-101 aibs_perisomatic biophysical nml:Cell_473863510.cell.nml Rorb_325404214_m e Rorb
-102 aibs_perisomatic biophysical nml:Cell_473863035.cell.nml Nr5a1_471087815_m e Nr5a1
-103 aibs_perisomatic biophysical nml:Cell_472912177.cell.nml Pvalb_470522102_m i PV1
+node_type_id ei model_processing morphology model_template model_type model_name
+104 i aibs_perisomatic Pvalb_469628681_m nml:Cell_473862421.cell.nml biophysical PV2
+100 e aibs_perisomatic Scnn1a_473845048_m nml:Cell_472363762.cell.nml biophysical Scnn1a
+101 e aibs_perisomatic Rorb_325404214_m nml:Cell_473863510.cell.nml biophysical Rorb
+102 e aibs_perisomatic Nr5a1_471087815_m nml:Cell_473863035.cell.nml biophysical Nr5a1
+103 i aibs_perisomatic Pvalb_470522102_m nml:Cell_472912177.cell.nml biophysical PV1

examples/5_cells_iclamp/simulation_config.json

@@ -23,7 +23,7 @@
     "v_init": -80
   },
 
-  "node_sets_file": "node_sets.json",
+  "node_sets_file": "$BASE_DIR/node_sets.json",
 
   "inputs": {
  	"current_clamp_1": {

examples/9_cells/network/cortex_node_types.csv

@@ -1,4 +1,4 @@
-node_type_id ei model_processing model_type model_template morphology dynamics_params model_name
-100 e aibs_perisomatic biophysical nml:nml/Cell_472363762.cell.nml Scnn1a_473845048_m NONE Scnn1a
-101 e aibs_perisomatic biophysical nml:nml/Cell_473863510.cell.nml Rorb_325404214_m NONE Rorb
-102 e aibs_perisomatic biophysical nml:nml/Cell_473863035.cell.nml Nr5a1_471087815_m NONE Nr5a1
+node_type_id ei model_processing model_type model_template morphology dynamics_params model_name
+100 e aibs_perisomatic biophysical nml:nml/Cell_472363762.cell.nml Scnn1a_473845048_m NONE Scnn1a
+101 e aibs_perisomatic biophysical nml:nml/Cell_473863510.cell.nml Rorb_325404214_m NONE Rorb
+102 e aibs_perisomatic biophysical nml:nml/Cell_473863035.cell.nml Nr5a1_471087815_m NONE Nr5a1

examples/sim_tests/intfire/one_cell_iclamp_nest/bmtk_build/build_network.py

@@ -0,0 +1,26 @@
+#!/bin/env python
+
+# Sonata Simulator Test Suite
+# 1-cell circuit, integrate and fire cell, current clamp input
+
+# Authors: Padraig Gleeson @ UCL
+
+from bmtk.builder import NetworkBuilder
+
+net = NetworkBuilder("one_cell_iclamp")
+
+pos_x, pos_y = [0,0]
+
+template = 'nest:iaf_psc_alpha'
+
+net.add_nodes(N=1, pop_name='LIF_exc', location='VisL4', ei='e',
+              model_type='point_process',  # use point_process to indicate we are using point model cells
+              model_template=template,
+              x=pos_x, y=pos_y,
+              dynamics_params='473863035_point.json')
+
+
+net.build()
+net.save(output_dir='../input/network')
+
+print 'Built: %s'%net.name

examples/sim_tests/intfire/one_cell_iclamp_nest/input/circuit_config.json

@@ -0,0 +1,24 @@
+{
+  "manifest": {
+    "$NETWORK_DIR": "../input/network",
+    "$COMPONENT_DIR": "../../../shared_components"
+  },
+
+  "components": {
+    "synaptic_models_dir": "$COMPONENT_DIR/synaptic_models",
+    "mechanisms_dir":"$COMPONENT_DIR/mechanisms",
+    "point_neuron_models_dir": "$COMPONENT_DIR/point_neuron_models_dir"
+  },
+
+  "networks": {
+    "nodes": [
+      {
+        "nodes_file": "$NETWORK_DIR/one_cell_iclamp_nodes.h5",
+        "node_types_file": "$NETWORK_DIR/one_cell_iclamp_node_types.csv"
+      }
+    ]
+  },
+
+
+  "target_simulator": "NEST"
+}

examples/sim_tests/intfire/one_cell_iclamp_nest/input/config.json

@@ -0,0 +1,4 @@
+{
+  "network": "./circuit_config.json",
+  "simulation": "./simulation_config.json"
+}

examples/sim_tests/intfire/one_cell_iclamp_nest/input/network/one_cell_iclamp_node_types.csv

@@ -0,0 +1,2 @@
+node_type_id ei model_type pop_name location model_template x y dynamics_params
+100 e point_process LIF_exc VisL4 nest:iaf_psc_alpha 0 0 473863035_point.json

examples/sim_tests/intfire/one_cell_iclamp_nest/input/node_sets.json

@@ -0,0 +1,5 @@
+{
+    "point_nodes": {
+        "model_type": "point_process"
+    }
+}

examples/sim_tests/intfire/one_cell_iclamp_nest/input/simulation_config.json

@@ -0,0 +1,57 @@
+{
+  "manifest": {
+    "$OUTPUT_DIR": "../test/output",
+    "$INPUT_DIR": "../input"
+  },
+
+  "run": {
+    "tstop": 1000.0,
+    "dt": 0.01,
+    "spike_threshold": -15,
+    "nsteps_block": 10000
+  },
+
+  "target_simulator":"NEST",
+
+  "network": "$INPUT_DIR/circuit_config.json",
+
+  "conditions": {
+    "celsius": 34.0,
+    "v_init": -80
+  },
+
+  "node_sets_file": "$INPUT_DIR/node_sets.json", 
+
+  "mechanisms_dir": "../shared_components_mechanisms",
+
+
+  "inputs": {
+ 	"current_clamp_1": {
+      "input_type": "current_clamp",
+      "module": "IClamp",
+      "node_set": "point_nodes",
+      "amp": 190.0,
+      "delay": 100.0,
+      "duration": 800.0
+    }
+  },
+
+  "output":{ 
+    "output_dir": "$OUTPUT_DIR",
+    "log_file": "log.txt",
+    "spikes_file": "spikes.h5",
+    "spikes_sort_order": "time"
+  },
+
+  "reports": {
+
+    "membrane_potential": {
+      "cells": "point_nodes",
+      "variable_name": "V_m",
+      "module": "multimeter_report",
+      "sections": "soma",
+      "enabled": true
+    }
+
+  }
+}

examples/sim_tests/intfire/one_cell_iclamp_nest/test/analyze_output.py

@@ -0,0 +1,9 @@
+import sys
+
+sys.path.append("../../../shared_components/scripts")
+
+from analyze_output_utils import plot_data
+
+if __name__ == '__main__':
+
+    plot_data('output/membrane_potential.h5', 'mV', 'Membrane Potential')