Merge pull request #379 from MetaCell/issue/375-dev

Fixed importModel to transform dict to specs object. Added test cases.

Author: Lucas Rebscher

netpyne_ui/netpyne_geppetto.py

@@ -231,6 +231,12 @@ def importModel(self, modelParameters):
                 # Import Model attributes
                 self.netParams = getattr(net_params_module_name, str(modelParameters["netParamsVariable"]))
 
+                if isinstance(self.netParams, dict):
+                  self.netParams = specs.NetParams(self.netParams)
+
+                if isinstance(self.simConfig, dict):
+                  self.simConfig = specs.SimConfig(self.simConfig)
+
                 for key, value in self.netParams.cellParams.items():
                     if hasattr(value, 'todict'):
                         self.netParams.cellParams[key] = value.todict()

tests/backend/models/gui_import_dict.py

@@ -0,0 +1,69 @@
+from netpyne import specs
+
+# Network parameters
+netParams = {} # object of class NetParams to store the network parameters
+
+netParams['cellParams'] = {}
+netParams['popParams'] = {}
+netParams['stimSourceParams'] = {}
+netParams['stimTargetParams'] = {}
+netParams['synMechParams'] = {}
+netParams['connParams'] = {}
+
+## Cell parameters
+secs = {}	# dict with section info
+secs['soma'] = {'geom': {}, 'mechs': {}}
+secs['soma']['geom'] = {'diam': 12, 'L': 12, 'Ra': 100.0, 'cm': 1}  	 						# soma geometry
+secs['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.0003, 'el': -54.3} 		# soma hh mechanism
+
+secs['dend'] = {'geom': {}, 'mechs': {}}
+secs['dend']['geom'] = {'diam': 1.0, 'L': 200.0, 'Ra': 100.0, 'cm': 1}
+secs['dend']['topol'] = {'parentSec': 'soma', 'parentX': 1.0, 'childX': 0}						# dend geometry
+secs['dend']['mechs']['pas'] = {'g': 0.001, 'e': -70} 		 		                            # dend pas mechanism
+
+netParams['cellParams']['pyr'] = {'secs': secs}  												    # add dict to list of cell parameters
+	
+## Population parameters
+netParams['popParams']['E'] = {'cellType': 'pyr', 'numCells': 40}
+
+ # Stimulation parameters
+netParams['stimSourceParams']['IClamp1'] = {'type': 'IClamp', 'dur': 5, 'del': 20, 'amp': 0.1}
+netParams['stimTargetParams']['IClamp1->cell0'] = {'source': 'IClamp1', 'conds': {'cellList':[0]}, 'sec':'dend', 'loc':1.0}
+
+
+# Synaptic mechanism parameters
+netParams['synMechParams']['exc'] = {'mod': 'Exp2Syn', 'tau1': 0.1, 'tau2': 1.0, 'e': 0}
+
+
+# Connectivity parameters
+netParams['connParams']['E->E'] = {
+    'preConds': {'pop': 'E'},
+    'postConds': {'pop': 'E'},
+    'weight': 0.005,                    # weight of each connection
+    'probability': 0.1,
+    'delay': 5,     # delay min=0.2, mean=13.0, var = 1.4
+    'synMech': 'exc',
+    'sec': 'dend'}
+
+# Simulation options
+simConfig = specs.SimConfig()		# object of class SimConfig to store simulation configuration
+
+simConfig.duration = 0.2*1e3 			# Duration of the simulation, in ms
+simConfig.dt = 0.1 				# Internal integration timestep to use
+simConfig.verbose = False  			# Show detailed messages 
+simConfig.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'},
+						 'V_dend': {'sec': 'dend', 'loc': 1.0, 'var':'v'}}  # Dict with traces to record
+simConfig.recordCells = [0]
+simConfig.recordStep = 0.1 			# Step size in ms to save data (eg. V traces, LFP, etc)
+simConfig.filename = 'gui_tut1'  # Set file output name
+simConfig.saveJson = False		# Save params, network and sim output to pickle file
+simConfig.analysis['iplotTraces'] = {'include': [0], 'overlay': True}
+simConfig.analysis['iplotRaster'] = {'markerSize': 5, 'showFig': True}
+ 
+
+if __name__ == '__main__':
+    netpyne_geppetto.netParams=netParams
+    netpyne_geppetto.simConfig=simConfig
+
+#from netpyne import sim
+#sim.createSimulateAnalyze(netParams, simConfig)

tests/backend/netypne_model_importer_test.py

@@ -0,0 +1,68 @@
+import unittest
+import os
+import sys
+import logging
+import json, urllib.request
+
+import netpyne
+
+from netpyne import specs, sim
+from netpyne_ui.netpyne_model_interpreter import NetPyNEModelInterpreter
+import neuron
+import subprocess
+
+from netpyne_ui.netpyne_geppetto import NETPYNE_WORKDIR_PATH
+from netpyne_ui.netpyne_geppetto import NetPyNEGeppetto
+
+netpyne.__gui__ = False
+sys.path.insert(0, NETPYNE_WORKDIR_PATH)
+
+class TestNetPyNEModelInterpreter(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        HERE = os.path.dirname(os.path.realpath(__file__))
+        ROOT = os.path.dirname(HERE)
+        cls.path = NETPYNE_WORKDIR_PATH
+        modelpath = os.path.join(NETPYNE_WORKDIR_PATH, 'mod')
+        subprocess.call(["rm", "-r", os.path.join(modelpath, "x86_64")])
+        owd = os.getcwd()
+        os.chdir(modelpath)
+        p = subprocess.check_output(["nrnivmodl"])
+        os.chdir(owd)
+        try:
+            neuron.load_mechanisms(modelpath)
+        except:
+            logging.error("Error loading mechanisms", exc_info=True)
+
+    def test_dict_import_1(self):
+        print("------------------------------------")
+        print("Dictionary transform importModel:")
+        print("------------------------------------")
+        
+        # response = urllib.request.urlopen("https://www.opensourcebrain.org/projects/netpyneshowcase/repository/revisions/test_py36/raw/NetPyNE/UI/HHCellNetwork.txt.json")        
+        netpyne_info = {} #json.loads(response.read())
+
+        # print(type(netpyne_info['net']['params']))
+
+        path = next(filter(lambda p: os.path.join('tests', 'backend') in p, sys.path), None)
+
+        netpyne_info['compileMod'] = False
+        netpyne_info['loadMod'] = False
+        netpyne_info['modFolder'] = "mod"
+        netpyne_info['netParamsPath'] = os.path.join(path, 'models')
+        netpyne_info['netParamsModuleName'] = "gui_import_dict"
+        netpyne_info['netParamsVariable'] = "netParams"
+        netpyne_info['simConfigPath'] = os.path.join(path, 'models')
+        netpyne_info['simConfigModuleName'] = "gui_import_dict"
+        netpyne_info['simConfigVariable'] = "simConfig"
+
+        netpyne = NetPyNEGeppetto()
+        netpyne.importModel(netpyne_info)
+
+if __name__ == '__main__':
+    try:
+        unittest.main()
+    except SystemExit as inst:
+        if inst.args[0]:  # raised by sys.exit(True) when tests failed
+            raise