Merge pull request #62 from NeuroML/experimental

Updates to sonata import/export

examples/sonatatest/SimSonataExample.json

@@ -1,13 +1,13 @@
 {
     "SimSonataExample": {
-        "version": "NeuroMLlite v0.1.9", 
-        "network": "SonataExample.json", 
-        "duration": 1000.0, 
-        "dt": 0.01, 
-        "recordTraces": {
+        "version": "NeuroMLlite v0.5.8",
+        "network": "SonataExample.json",
+        "duration": 1000.0,
+        "dt": 0.01,
+        "record_traces": {
             "all": "*"
-        }, 
-        "recordSpikes": {
+        },
+        "record_spikes": {
             "pop0": "*"
         }
     }

examples/sonatatest/SonataExample.json

@@ -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
             }
-        ]
+        }
     }
 }

examples/sonatatest/SonataExample.py

@@ -106,8 +106,8 @@
     network=new_file,
     duration="1000",
     dt="0.01",
-    recordTraces={"all": "*"},
-    recordSpikes={"pop0": "*"},
+    record_traces={"all": "*"},
+    record_spikes={"pop0": "*"},
 )
 
 sim.to_json_file()

examples/sonatatest/circuit_config.json

@@ -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"
   }
 }

examples/sonatatest/components/point_neuron_models_dir/testcell.json

@@ -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
 }

examples/sonatatest/config.json

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

examples/sonatatest/network/SonataExample_node_types.csv

@@ -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 

examples/sonatatest/regenerateAndTest.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+set -ex
+
+python SonataExample.py -sonata
+
+python run_bmtk.py
+
+./run_pynml.jnml.sh

examples/sonatatest/run_bmtk.py

@@ -14,7 +14,6 @@ def run(config_file, simulator):
 
     elif simulator == "NEST":
         from bmtk.simulator import pointnet
-
         conf = pointnet.Config.from_json(config_file)
         conf.build_env()
         net = pointnet.PointNetwork.from_config(conf)
@@ -24,4 +23,4 @@ def run(config_file, simulator):
 
 
 if __name__ == "__main__":
-    run("config.json", "NEST")
+    run("config.json", "NEST")

examples/sonatatest/run_pynml.jnml.sh

@@ -1,5 +1,4 @@
 #!/bin/bash
-
-set -e
+set -ex
 
 pynml-sonata Back2NML config.json -jnml  

examples/sonatatest/simulation_config.json

@@ -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"
+    }
   }
 }

neuromllite/MDFHandler.py

@@ -409,7 +409,7 @@ def _comp_to_mdf_node(self, nmllite_comp, lems_comp_id, size=1, properties=None)
                 # node["parameters"][sv.name]["value"] = [0]*size
 
                 node["output_ports"][sv.name] = {"value": sv.name}
-                print_v("Adding %s as an output port"%sv.name)
+                print_v("Adding %s as an output port" % sv.name)
                 if sv.exposure:
                     node["output_ports"][sv.exposure] = {"value": sv.name}