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converted to new indexed structure #4

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4 changes: 4 additions & 0 deletions gui_tut1/index.npjson
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@@ -0,0 +1,4 @@
{
"simConfig_python": "src/cfg.py",
"netParams_python": "src/netParams.py"
}
16 changes: 16 additions & 0 deletions gui_tut1/src/cfg.py
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from netpyne import specs

# Simulation options
cfg = specs.SimConfig() # object of class SimConfig to store simulation configuration

cfg.duration = 0.2*1e3 # Duration of the simulation, in ms
cfg.dt = 0.1 # Internal integration timestep to use
cfg.verbose = False # Show detailed messages
cfg.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'},
'V_dend': {'sec': 'dend', 'loc': 1.0, 'var':'v'}} # Dict with traces to record
cfg.recordCells = [0]
cfg.recordStep = 0.1 # Step size in ms to save data (eg. V traces, LFP, etc)
cfg.filename = 'gui_tut1' # Set file output name
cfg.saveJson = False # Save params, network and sim output to pickle file
cfg.analysis['iplotTraces'] = {'include': [0], 'overlay': True}
cfg.analysis['iplotRaster'] = {'markerSize': 5, 'showFig': True}
23 changes: 0 additions & 23 deletions gui_tut1.py → gui_tut1/src/netParams.py
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Expand Up @@ -37,26 +37,3 @@
'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)
0 cells/PTcell.hoc → gui_tut2/cells/PTcell.hoc
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0 cells/SRI.hoc → gui_tut2/cells/SRI.hoc
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5 changes: 5 additions & 0 deletions gui_tut2/index.npjson
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{
"mod_folder": "../mod",
"simConfig_python": "src/cfg.py",
"netParams_python": "src/netParams.py"
}
16 changes: 16 additions & 0 deletions gui_tut2/src/cfg.py
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from netpyne import specs

# Simulation options
cfg = specs.SimConfig() # object of class SimConfig to store simulation configuration

cfg.duration = 0.5*1e3 # Duration of the simulation, in ms
cfg.dt = 0.1 # Internal integration timestep to use
cfg.hParams['celsius'] = 34
cfg.verbose = False # Show detailed messages
cfg.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'}} # Dict with traces to record
cfg.recordStep = 0.1 # Step size in ms to save data (eg. V traces, LFP, etc)
cfg.filename = 'model_output' # Set file output name
cfg.savePickle = False # Save params, network and sim output to pickle file

cfg.analysis['iplotRaster'] = {'markerSize': 5, 'showFig': True}
cfg.analysis['iplotTraces'] = {'include': [0,2], 'oneFigPer': 'trace'}
24 changes: 0 additions & 24 deletions gui_tut2.py → gui_tut2/src/netParams.py
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Expand Up @@ -43,27 +43,3 @@
'delay': 5,
'synMech': 'GABA',
'sec': 'soma'}


# Simulation options
simConfig = specs.SimConfig() # object of class SimConfig to store simulation configuration

simConfig.duration = 0.5*1e3 # Duration of the simulation, in ms
simConfig.dt = 0.1 # Internal integration timestep to use
simConfig.hParams['celsius'] = 34
simConfig.verbose = False # Show detailed messages
simConfig.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'}} # Dict with traces to record
simConfig.recordStep = 0.1 # Step size in ms to save data (eg. V traces, LFP, etc)
simConfig.filename = 'model_output' # Set file output name
simConfig.savePickle = False # Save params, network and sim output to pickle file

simConfig.analysis['iplotRaster'] = {'markerSize': 5, 'showFig': True}
simConfig.analysis['iplotTraces'] = {'include': [0,2], 'oneFigPer': 'trace'}

if __name__ == '__main__':
netpyne_geppetto.netParams=netParams
netpyne_geppetto.simConfig=simConfig


#from netpyne import sim
#sim.createSimulateAnalyze(netParams, simConfig)
0 cells/CSTR6.py → gui_tut3/cells/CSTR6.py
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0 cells/CSTR_cellParams.json → gui_tut3/cells/CSTR_cellParams.json
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0 cells/FScell.hoc → gui_tut3/cells/FScell.hoc
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5 changes: 5 additions & 0 deletions gui_tut3/index.npjson
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{
"mod_folder": "../mod",
"simConfig_python": "src/cfg.py",
"netParams_python": "src/netParams.py"
}
31 changes: 31 additions & 0 deletions gui_tut3/src/cfg.py
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from netpyne import specs
from src.netParams import netParams

#------------------------------------------------------------------------------
#
# SIMULATION CONFIGURATION
#
#------------------------------------------------------------------------------

# Run parameters
cfg = specs.SimConfig() # object of class simConfig to store simulation configuration
cfg.duration = 1.0*1e3 # Duration of the simulation, in ms
cfg.hParams['v_init'] = -65 # set v_init to -65 mV
cfg.dt = 0.1 # Internal integration timestep to use
cfg.verbose = False # Show detailed messages
cfg.recordStep = 1 # Step size in ms to save data (eg. V traces, LFP, etc)
cfg.filename = 'rxd_net' # Set file output name


# Recording/plotting parameters
cfg.recordTraces = {'V_soma':{'sec': 'soma','loc': 0.5,'var': 'v'},
'ik_soma': {'sec': 'soma', 'loc': 0.5, 'var': 'ik'},
'cai_soma': {'sec': 'soma', 'loc':0.5, 'var': 'cai'},
'cao_soma': {'sec': 'soma', 'loc': 0.5, 'var': 'cao'}}

cfg.recordLFP = [[-15, y, 1.0*netParams.sizeZ] for y in range(int(netParams.sizeY/3), int(netParams.sizeY), int(netParams.sizeY/3))]

cfg.analysis['iplotTraces'] ={'include': [0]}
cfg.analysis['iplotRaster'] = {'orderBy': 'y', 'orderInverse': True, 'saveFig': True, 'figSize': (9,3)} # Plot a raster
cfg.analysis['iplotLFP'] = {'includeAxon': False, 'figSize': (6,10), 'saveFig': True}
cfg.analysis['iplotRxDConcentration'] = {'speciesLabel': 'ca', 'regionLabel': 'ecs'}
44 changes: 0 additions & 44 deletions gui_tut3.py → gui_tut3/src/netParams.py
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Expand Up @@ -121,47 +121,3 @@

### rates
netParams.rxdParams['rates'] = {'ip3rg': {'species': h_gate, 'rate': '(1. / (1 + 1000. * ca[cyt] / (0.3)) - %s) / ip3rtau'%(h_gate)}}




#------------------------------------------------------------------------------
#
# SIMULATION CONFIGURATION
#
#------------------------------------------------------------------------------

# Run parameters
simConfig = specs.SimConfig() # object of class simConfig to store simulation configuration
simConfig.duration = 1.0*1e3 # Duration of the simulation, in ms
simConfig.hParams['v_init'] = -65 # set v_init to -65 mV
simConfig.dt = 0.1 # Internal integration timestep to use
simConfig.verbose = False # Show detailed messages
simConfig.recordStep = 1 # Step size in ms to save data (eg. V traces, LFP, etc)
simConfig.filename = 'rxd_net' # Set file output name


# Recording/plotting parameters
simConfig.recordTraces = {'V_soma':{'sec': 'soma','loc': 0.5,'var': 'v'},
'ik_soma': {'sec': 'soma', 'loc': 0.5, 'var': 'ik'},
'cai_soma': {'sec': 'soma', 'loc':0.5, 'var': 'cai'},
'cao_soma': {'sec': 'soma', 'loc': 0.5, 'var': 'cao'}}

simConfig.recordLFP = [[-15, y, 1.0*netParams.sizeZ] for y in range(int(netParams.sizeY/3), int(netParams.sizeY), int(netParams.sizeY/3))]

simConfig.analysis['iplotTraces'] ={'include': [0]}
simConfig.analysis['iplotRaster'] = {'orderBy': 'y', 'orderInverse': True, 'saveFig': True, 'figSize': (9,3)} # Plot a raster
simConfig.analysis['iplotLFP'] = {'includeAxon': False, 'figSize': (6,10), 'saveFig': True}
simConfig.analysis['iplotRxDConcentration'] = {'speciesLabel': 'ca', 'regionLabel': 'ecs'}



# ------------------------------------------------------------
# Run sim
# ------------------------------------------------------------
if __name__ == '__main__':
netpyne_geppetto.netParams=netParams
netpyne_geppetto.simConfig=simConfig

#from netpyne import sim
#sim.createSimulateAnalyze(netParams, simConfig)
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