<commit_before>"""
netparams.py

netParams is a dict containing a set of network parameters using a standardized structure

simConfig is a dict containing a set of simulation configurations using a standardized structure

Contributors: <EMAIL>
"""

netParams = {}  # dictionary to store sets of network parameters
simConfig = {}  # dictionary to store sets of simulation configurations


###############################################################################
#
# MPI HH TUTORIAL PARAMS
#
###############################################################################

###############################################################################
# NETWORK PARAMETERS
###############################################################################

netParams['scaleConnWeight'] = 0.001 # Connection weight scale factor

pnum = 5
cscale = 1
mscale = 1

# Population parameters
netParams['popParams'] = []  # create list of populations - each item will contain dict with pop params
netParams['popParams'].append({'popLabel': 'Psh','cellModel': 'Izhi2007b', 'cellType': 'RS', 'numCells': int(pnum)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'Pel','cellModel': 'Izhi2007b', 'cellType': 'RS', 'numCells': int(pnum)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'ES', 'cellModel': 'Izhi2007b', 'cellType': 'RS', 'numCells': int(80*cscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'ISL', 'cellModel': 'Izhi2007b', 'cellType': 'LTS', 'numCells': int(10*cscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'IS', 'cellModel': 'Izhi2007b', 'cellType': 'FS', 'numCells': int(10*cscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'EM', 'cellModel': 'Izhi2007b', 'cellType': 'RS', 'numCells': int(80*mscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'IML', 'cellModel': 'Izhi2007b', 'cellType': 'LTS', 'numCells': int(10*mscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'IM', 'cellModel': 'Izhi2007b', 'cellType': 'FS', 'numCells': int(10*mscale)}) # add dict with params for this pop 

netParams['popParams'].append({'popLabel': 'backgroundE', 'cellModel': 'NetStim', 'rate': 10, 'noise': 0.5})  # background inputs
netParams['popParams'].append({'popLabel': 'backgroundI', 'cellModel': 'NetStim', 'rate': 10, 'noise': 0.5})  # background inputs
netParams['popParams'].append({'popLabel': 'stimPsh', 'cellModel': 'NetStim', 'rate': 'variable', 'noise': 0}) # stim inputs for P_sh
netParams['popParams'].append({'popLabel': 'stimPel', 'cellModel': 'NetStim', 'rate': 'variable', 'noise': 0}) # stim inputs for P_el 
netParams['popParams'].append({'popLabel': 'stimEM','cellModel': 'NetStim', 'rate': 'variable', 'noise': 0}) # stim inputs for EM (explor movs) 


# Izhi cell params (used in cell properties)
izhiParams = {}
izhiParams['RS'] = {'mod':'Izhi2007b', 'C':1, 'k':0.7, 'vr':-60, 'vt':-40, 'vpeak':35, 'a':0.03, 'b':-2, 'c':-50, 'd':100, 'celltype':1}
izhiParams['LTS'] = {'mod':'Izhi2007b', 'C':1, 'k':1.0, 'vr':-56, 'vt':-42, 'vpeak':40, 'a':0.03, 'b':8, 'c':-53, 'd':20, 'celltype':4}
izhiParams['FS'] = {'mod':'Izhi2007b', 'C':0.2, 'k':1.0, 'vr':-55, 'vt':-40, 'vpeak':25, 'a':0.2, 'b':-2, 'c':-45, 'd':-55, 'celltype':5}

# Cell properties list
netParams['cellParams'] = []

## RS Izhi cell params
cellRule = {'label': 'RS_Izhi', 'conditions': {'cellType': 'RS', 'cellModel': 'Izhi2007b'}, 'sections': {}}
soma = {'geom': {}, 'pointps':{}}  #  soma
soma['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
soma['pointps']['Izhi'] = izhiParams['RS'] 
cellRule['sections'] = {'soma': soma}  # add sections to dict
netParams['cellParams'].append(cellRule)  # add dict to list of cell properties

## LTS Izhi cell params
cellRule = {'label': 'LTS_Izhi', 'conditions': {'cellType': 'LTS', 'cellModel': 'Izhi2007b'}, 'sections': {}}
soma = {'geom': {}, 'pointps':{}}  #  soma
soma['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
soma['pointps']['Izhi'] = izhiParams['LTS'] 
cellRule['sections'] = {'soma': soma}  # add sections to dict
netParams['cellParams'].append(cellRule)  # add dict to list of cell properties

## FS Izhi cell params
cellRule = {'label': 'FS_Izhi', 'conditions': {'cellType': 'FS', 'cellModel': 'Izhi2007b'}, 'sections': {}}
soma = {'geom': {}, 'pointps':{}}  #  soma
soma['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
soma['pointps']['Izhi'] = izhiParams['FS'] 
cellRule['sections'] = {'soma': soma}  # add sections to dict
netParams['cellParams'].append(cellRule)  # add dict to list of cell properties


# Synaptic mechanism parameters
netParams['synMechParams'] = []
netParams['synMechParams'].append({'label': 'AMPA', 'mod': 'Exp2Syn', 'tau1': 0.05, 'tau2': 5.3, 'e': 0}) # AMPA
netParams['synMechParams'].append({'label': 'NMDA', 'mod': 'Exp2Syn', 'tau1': 0.15, 'tau2': 1.50, 'e': 0}) # NMDA
netParams['synMechParams'].append({'label': 'GABA', 'mod': 'Exp2Syn', 'tau1': 0.07, 'tau2': 9.1, 'e': -80}) # GABAA


# Connectivity parameters
# STDPparams = {'hebbwt': 0.00001, 'antiwt':-0.000013, 'wmax': 50, 'RLon': 1 , 'RLhebbwt': 0.001, 'RLantiwt': -0.001, \
#     'tauhebb': 10, 'RLwindhebb': 50, 'useRLexp': 1, 'softthresh': 0, 'verbose':0}

STDPparams = {'hebbwt': 0.00001, 'antiwt':-0.00001, 'wmax': 50, 'RLon': 1 , 'RLhebbwt': 0.001, 'RLantiwt': -0.001, \
    'tauhebb': 10, 'RLwindhebb': 50, 'useRLexp': 0, 'softthresh': 0, 'verbose':0}

netParams['connParams'] = []  


# Background and stims

netParams['connParams'].append(
    {'preTags': {'popLabel': 'backgroundE'}, 'postTags': {'popLabel': ['ES', 'EM']}, # background -> Exc
    'connFunc': 'fullConn',
    'weight': 0.05, 
    'delay': 'uniform(1,5)',
    'synMech': 'NMDA'})  

netParams['connParams'].append(
    {'preTags': {'popLabel': 'backgroundI'}, 'postTags': {'popLabel': ['ISL', 'IML', 'IS', 'IM']}, # background -> Inh
    'connFunc': 'fullConn',
    'weight': 0.05, 
    'delay': 'uniform(1,5)',
    'synMech': 'NMDA'})   

netParams['connParams'].append(
    {'preTags': {'popLabel': 'stimPsh'}, 'postTags': {'popLabel': 'Psh'},  # Pstim_sh -> P_sh
    'weight': 0.1,                   
    'delay': 1,     
    'synMech': 'NMDA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'stimPel'}, 'postTags': {'popLabel': 'Pel'},  # Pstim_el -> P_el
    'weight': 0.1,                  
    'delay': 1,     
    'synMech': 'NMDA'})

netParams['connParams'].append(
    {'preTags': {'popLabel': 'stimEM'}, 'postTags': {'popLabel': 'EM'}, # EMstim-> Exc
    'connFunc': 'fullConn',
    'weight': 0.4, 
    'delay': 'uniform(1,5)',
    'synMech': 'NMDA'})  


# Sensory

netParams['connParams'].append(
    {'preTags': {'popLabel': ['Psh', 'Pel']}, 'postTags': {'popLabel': 'ES'},  # P_sh,P_el -> ES (plastic?)
    'weight': 4,      
    'probability': 0.1125*4,              
    'delay': 5,     
    'synMech': 'AMPA'})#,
#    'plasticity': {'mech': 'STDP', 'params': STDPparams}}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ES'}, 'postTags': {'popLabel': 'ES'},  # ES -> ES 
    'weight': 1.98,      
    'probability': 0.05625,              
    'delay': 5,     
    'synMech': 'AMPA'})


netParams['connParams'].append(
    {'preTags': {'popLabel': 'ES'}, 'postTags': {'popLabel': 'IS'},  # ES -> IS
    'weight': 0.48375,      
    'probability': 1.150,              
    'delay': 5,     
    'synMech': 'AMPA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ES'}, 'postTags': {'popLabel': 'ISL'},  # ES -> ISL
    'weight': 0.57375,      
    'probability': 0.575,              
    'delay': 5,     
    'synMech': 'AMPA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ES'}, 'postTags': {'popLabel': 'EM'},  # ES -> EM (plastic)
    'weight': 2.640,      
    'probability': 0.33750,              
    'delay': 5,     
    'synMech': 'AMPA',
    'plasticity': {'mech': 'STDP', 'params': STDPparams}})


netParams['connParams'].append(
    {'preTags': {'popLabel': 'IS'}, 'postTags': {'popLabel': 'ES'},  # IS -> ES
    'weight': 4.5,      
    'probability': 0.495,              
    'delay': 5,     
    'synMech': 'GABA'}) 


netParams['connParams'].append(
    {'preTags': {'popLabel': 'IS'}, 'postTags': {'popLabel': 'IS'},  # IS -> IS
    'weight': 4.5,      
    'probability': 0.69750,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IS'}, 'postTags': {'popLabel': 'ISL'},  # IS -> ISL
    'weight': 4.5,      
    'probability': 0.38250,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ISL'}, 'postTags': {'popLabel': 'IS'},  # ISL -> ES
    'weight': 2.25,      
    'probability': 0.39375,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ISL'}, 'postTags': {'popLabel': 'IS'},  # ISL -> IS
    'weight': 2.25,      
    'probability': 0.59625,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ISL'}, 'postTags': {'popLabel': 'ISL'},  # ISL -> ISL
    'weight': 4.5,      
    'probability': 0.10125,              
    'delay': 5,     
    'synMech': 'GABA'}) 


netParams['connParams'].append(
    {'preTags': {'popLabel': 'EM'}, 'postTags': {'popLabel': 'ES'},  # EM -> ES 
    'weight': 0.72,      
    'probability': 0.01125,              
    'delay': 5,     
    'synMech': 'AMPA'})#,
#    'plasticity': {'mech': 'STDP', 'params': STDPparams}}) 


# Motor

netParams['connParams'].append(
    {'preTags': {'popLabel': 'EM'}, 'postTags': {'popLabel': 'EM'},  # EM -> EM 
    'weight': 1.782,      
    'probability': 0.05625,              
    'delay': 5,     
    'synMech': 'AMPA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'EM'}, 'postTags': {'popLabel': 'IM'},  # EM -> IM 
    'weight': 1.15,      
    'probability': 0.48375,          
    'delay': 5,     
    'synMech': 'AMPA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'EM'}, 'postTags': {'popLabel': 'IML'},  # EM -> IML
    'weight': 0.575,      
    'probability': 0.57375,              
    'delay': 5,     
    'synMech': 'AMPA'})  

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IM'}, 'postTags': {'popLabel': 'EM'},  # IM -> EM
    'weight': 9,      
    'probability': 0.495,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IM'}, 'postTags': {'popLabel': 'IM'},  # IM -> IM
    'weight': 4.5,      
    'probability': 0.69750,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IM'}, 'postTags': {'popLabel': 'IML'},  # IM -> IML 
    'weight': 4.5,      
    'probability': 0.38250,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IML'}, 'postTags': {'popLabel': 'EM'},  # IML -> EM 
    'weight': 2.49,      
    'probability': 0.39375,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IML'}, 'postTags': {'popLabel': 'IM'},  # IML -> IM 
    'weight': 2.25,      
    'probability': 0.59625,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IML'}, 'postTags': {'popLabel': 'IML'},  # IML -> IML
    'weight': 4.5,      
    'probability': 0.10125,              
    'delay': 5,     
    'synMech': 'GABA'}) 


###############################################################################
# SIMULATION PARAMETERS
###############################################################################

simConfig = {}  # dictionary to store simConfig

# Simulation parameters
simConfig['duration'] = 1*1e3 # Duration of the simulation, in ms
simConfig['dt'] = 0.1 # Internal integration timestep to use
simConfig['seeds'] = {'conn': 1, 'stim': 1, 'loc': 1} # Seeds for randomizers (connectivity, input stimulation and cell locations)
simConfig['createNEURONObj'] = True  # create HOC objects when instantiating network
simConfig['createPyStruct'] = True  # create Python structure (simulator-independent) when instantiating network
simConfig['timing'] = True  # show timing  and save to file
simConfig['verbose'] = True # show detailed messages 

# Recording 
simConfig['recordCells'] = ['all']  # list of cells to record from 
simConfig['recordTraces'] = {}
# 'V':{'sec':'soma','loc':0.5,'var':'v'}, 
#     'u':{'sec':'soma', 'pointp':'Izhi', 'var':'u'}, 
#     'I':{'sec':'soma', 'pointp':'Izhi', 'var':'i'}, 
#     'NMDA_g': {'sec':'soma', 'loc':0.5, 'synMech':'NMDA', 'var':'g'},
#     'NMDA_i': {'sec':'soma', 'loc':0.5, 'synMech':'NMDA', 'var':'i'},
#     'GABA_g': {'sec':'soma', 'loc':0.5, 'synMech':'GABA', 'var':'g'},
#     'GABA_i': {'sec':'soma', 'loc':0.5, 'synMech':'GABA', 'var':'i'}}
simConfig['recordStim'] = True  # record spikes of cell stims
simConfig['recordStep'] = 1.0 # Step size in ms to save data (eg. V traces, LFP, etc)

# Saving
simConfig['filename'] = 'simdata'  # Set file output name
simConfig['saveFileStep'] = 1000 # step size in ms to save data to disk
simConfig['savePickle'] = False # Whether or not to write spikes etc. to a .mat file
simConfig['saveJson'] = False # Whether or not to write spikes etc. to a .mat file
simConfig['saveMat'] = False # Whether or not to write spikes etc. to a .mat file
simConfig['saveTxt'] = False # save spikes and conn to txt file
simConfig['saveDpk'] = False # save to a .dpk pickled file


# Analysis and plotting 
simConfig['plotRaster'] = True # Whether or not to plot a raster
simConfig['plotCells'] = [] #'Pel', 'Psh', 'ES', 'EM', 'IM', 'IS'] # plot recorded traces for this list of cells
simConfig['plotLFPSpectrum'] = False # plot power spectral density
simConfig['maxspikestoplot'] = 3e8 # Maximum number of spikes to plot
simConfig['plotConn'] = False # whether to plot conn matrix
simConfig['plotWeightChanges'] = False # whether to plot weight changes (shown in conn matrix)
simConfig['plot3dArch'] = False # plot 3d architecture


<commit_msg>Minor Change<commit_after>"""
netparams.py

netParams is a dict containing a set of network parameters using a standardized structure

simConfig is a dict containing a set of simulation configurations using a standardized structure

Contributors: <EMAIL>
"""

netParams = {}  # dictionary to store sets of network parameters
simConfig = {}  # dictionary to store sets of simulation configurations


###############################################################################
#
# MPI HH TUTORIAL PARAMS
#
###############################################################################

###############################################################################
# NETWORK PARAMETERS
###############################################################################

netParams['scaleConnWeight'] = 0.001 # Connection weight scale factor

pnum = 5
cscale = 1
mscale = 1

# Population parameters
netParams['popParams'] = []  # create list of populations - each item will contain dict with pop params
netParams['popParams'].append({'popLabel': 'Psh','cellModel': 'Izhi2007b', 'cellType': 'RS', 'numCells': int(pnum)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'Pel','cellModel': 'Izhi2007b', 'cellType': 'RS', 'numCells': int(pnum)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'ES', 'cellModel': 'Izhi2007b', 'cellType': 'RS', 'numCells': int(80*cscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'ISL', 'cellModel': 'Izhi2007b', 'cellType': 'LTS', 'numCells': int(10*cscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'IS', 'cellModel': 'Izhi2007b', 'cellType': 'FS', 'numCells': int(10*cscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'EM', 'cellModel': 'Izhi2007b', 'cellType': 'RS', 'numCells': int(80*mscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'IML', 'cellModel': 'Izhi2007b', 'cellType': 'LTS', 'numCells': int(10*mscale)}) # add dict with params for this pop 
netParams['popParams'].append({'popLabel': 'IM', 'cellModel': 'Izhi2007b', 'cellType': 'FS', 'numCells': int(10*mscale)}) # add dict with params for this pop 

netParams['popParams'].append({'popLabel': 'backgroundE', 'cellModel': 'NetStim', 'rate': 10, 'noise': 0.5})  # background inputs
netParams['popParams'].append({'popLabel': 'backgroundI', 'cellModel': 'NetStim', 'rate': 10, 'noise': 0.5})  # background inputs
netParams['popParams'].append({'popLabel': 'stimPsh', 'cellModel': 'NetStim', 'rate': 'variable', 'noise': 0}) # stim inputs for P_sh
netParams['popParams'].append({'popLabel': 'stimPel', 'cellModel': 'NetStim', 'rate': 'variable', 'noise': 0}) # stim inputs for P_el 
netParams['popParams'].append({'popLabel': 'stimEM','cellModel': 'NetStim', 'rate': 'variable', 'noise': 0}) # stim inputs for EM (explor movs) 


# Izhi cell params (used in cell properties)
izhiParams = {}
izhiParams['RS'] = {'mod':'Izhi2007b', 'C':1, 'k':0.7, 'vr':-60, 'vt':-40, 'vpeak':35, 'a':0.03, 'b':-2, 'c':-50, 'd':100, 'celltype':1}
izhiParams['LTS'] = {'mod':'Izhi2007b', 'C':1, 'k':1.0, 'vr':-56, 'vt':-42, 'vpeak':40, 'a':0.03, 'b':8, 'c':-53, 'd':20, 'celltype':4}
izhiParams['FS'] = {'mod':'Izhi2007b', 'C':0.2, 'k':1.0, 'vr':-55, 'vt':-40, 'vpeak':25, 'a':0.2, 'b':-2, 'c':-45, 'd':-55, 'celltype':5}

# Cell properties list
netParams['cellParams'] = []

## RS Izhi cell params
cellRule = {'label': 'RS_Izhi', 'conditions': {'cellType': 'RS', 'cellModel': 'Izhi2007b'}, 'sections': {}}
soma = {'geom': {}, 'pointps':{}}  #  soma
soma['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
soma['pointps']['Izhi'] = izhiParams['RS'] 
cellRule['sections'] = {'soma': soma}  # add sections to dict
netParams['cellParams'].append(cellRule)  # add dict to list of cell properties

## LTS Izhi cell params
cellRule = {'label': 'LTS_Izhi', 'conditions': {'cellType': 'LTS', 'cellModel': 'Izhi2007b'}, 'sections': {}}
soma = {'geom': {}, 'pointps':{}}  #  soma
soma['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
soma['pointps']['Izhi'] = izhiParams['LTS'] 
cellRule['sections'] = {'soma': soma}  # add sections to dict
netParams['cellParams'].append(cellRule)  # add dict to list of cell properties

## FS Izhi cell params
cellRule = {'label': 'FS_Izhi', 'conditions': {'cellType': 'FS', 'cellModel': 'Izhi2007b'}, 'sections': {}}
soma = {'geom': {}, 'pointps':{}}  #  soma
soma['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
soma['pointps']['Izhi'] = izhiParams['FS'] 
cellRule['sections'] = {'soma': soma}  # add sections to dict
netParams['cellParams'].append(cellRule)  # add dict to list of cell properties


# Synaptic mechanism parameters
netParams['synMechParams'] = []
netParams['synMechParams'].append({'label': 'AMPA', 'mod': 'Exp2Syn', 'tau1': 0.05, 'tau2': 5.3, 'e': 0}) # AMPA
netParams['synMechParams'].append({'label': 'NMDA', 'mod': 'Exp2Syn', 'tau1': 0.15, 'tau2': 1.50, 'e': 0}) # NMDA
netParams['synMechParams'].append({'label': 'GABA', 'mod': 'Exp2Syn', 'tau1': 0.07, 'tau2': 9.1, 'e': -80}) # GABAA


# Connectivity parameters
# STDPparams = {'hebbwt': 0.00001, 'antiwt':-0.000013, 'wmax': 50, 'RLon': 1 , 'RLhebbwt': 0.001, 'RLantiwt': -0.001, \
#     'tauhebb': 10, 'RLwindhebb': 50, 'useRLexp': 1, 'softthresh': 0, 'verbose':0}

STDPparams = {'hebbwt': 0.00001, 'antiwt':-0.00001, 'wmax': 50, 'RLon': 1 , 'RLhebbwt': 0.001, 'RLantiwt': -0.001, \
    'tauhebb': 10, 'RLwindhebb': 50, 'useRLexp': 0, 'softthresh': 0, 'verbose':0}

netParams['connParams'] = []  


# Background and stims

netParams['connParams'].append(
    {'preTags': {'popLabel': 'backgroundE'}, 'postTags': {'popLabel': ['ES', 'EM']}, # background -> Exc
    'connFunc': 'fullConn',
    'weight': 0.05, 
    'delay': 'uniform(1,5)',
    'synMech': 'NMDA'})  

netParams['connParams'].append(
    {'preTags': {'popLabel': 'backgroundI'}, 'postTags': {'popLabel': ['ISL', 'IML', 'IS', 'IM']}, # background -> Inh
    'connFunc': 'fullConn',
    'weight': 0.05, 
    'delay': 'uniform(1,5)',
    'synMech': 'NMDA'})   

netParams['connParams'].append(
    {'preTags': {'popLabel': 'stimPsh'}, 'postTags': {'popLabel': 'Psh'},  # Pstim_sh -> P_sh
    'weight': 0.1,                   
    'delay': 1,     
    'synMech': 'NMDA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'stimPel'}, 'postTags': {'popLabel': 'Pel'},  # Pstim_el -> P_el
    'weight': 0.1,                  
    'delay': 1,     
    'synMech': 'NMDA'})

netParams['connParams'].append(
    {'preTags': {'popLabel': 'stimEM'}, 'postTags': {'popLabel': 'EM'}, # EMstim-> Exc
    'connFunc': 'fullConn',
    'weight': 0.4, 
    'delay': 'uniform(1,5)',
    'synMech': 'NMDA'})  


# Sensory

netParams['connParams'].append(
    {'preTags': {'popLabel': ['Psh', 'Pel']}, 'postTags': {'popLabel': 'ES'},  # P_sh,P_el -> ES (plastic?)
    'weight': 4,      
    'probability': 0.1125,              
    'delay': 5,     
    'synMech': 'AMPA'})#,
#    'plasticity': {'mech': 'STDP', 'params': STDPparams}}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ES'}, 'postTags': {'popLabel': 'ES'},  # ES -> ES 
    'weight': 1.98,      
    'probability': 0.05625,              
    'delay': 5,     
    'synMech': 'AMPA'})


netParams['connParams'].append(
    {'preTags': {'popLabel': 'ES'}, 'postTags': {'popLabel': 'IS'},  # ES -> IS
    'weight': 0.48375,      
    'probability': 1.150,              
    'delay': 5,     
    'synMech': 'AMPA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ES'}, 'postTags': {'popLabel': 'ISL'},  # ES -> ISL
    'weight': 0.57375,      
    'probability': 0.575,              
    'delay': 5,     
    'synMech': 'AMPA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ES'}, 'postTags': {'popLabel': 'EM'},  # ES -> EM (plastic)
    'weight': 2.640,      
    'probability': 0.33750,              
    'delay': 5,     
    'synMech': 'AMPA',
    'plasticity': {'mech': 'STDP', 'params': STDPparams}})


netParams['connParams'].append(
    {'preTags': {'popLabel': 'IS'}, 'postTags': {'popLabel': 'ES'},  # IS -> ES
    'weight': 4.5,      
    'probability': 0.495,              
    'delay': 5,     
    'synMech': 'GABA'}) 


netParams['connParams'].append(
    {'preTags': {'popLabel': 'IS'}, 'postTags': {'popLabel': 'IS'},  # IS -> IS
    'weight': 4.5,      
    'probability': 0.69750,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IS'}, 'postTags': {'popLabel': 'ISL'},  # IS -> ISL
    'weight': 4.5,      
    'probability': 0.38250,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ISL'}, 'postTags': {'popLabel': 'IS'},  # ISL -> ES
    'weight': 2.25,      
    'probability': 0.39375,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ISL'}, 'postTags': {'popLabel': 'IS'},  # ISL -> IS
    'weight': 2.25,      
    'probability': 0.59625,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'ISL'}, 'postTags': {'popLabel': 'ISL'},  # ISL -> ISL
    'weight': 4.5,      
    'probability': 0.10125,              
    'delay': 5,     
    'synMech': 'GABA'}) 


netParams['connParams'].append(
    {'preTags': {'popLabel': 'EM'}, 'postTags': {'popLabel': 'ES'},  # EM -> ES 
    'weight': 0.72,      
    'probability': 0.01125,              
    'delay': 5,     
    'synMech': 'AMPA'})#,
#    'plasticity': {'mech': 'STDP', 'params': STDPparams}}) 


# Motor

netParams['connParams'].append(
    {'preTags': {'popLabel': 'EM'}, 'postTags': {'popLabel': 'EM'},  # EM -> EM 
    'weight': 1.782,      
    'probability': 0.05625,              
    'delay': 5,     
    'synMech': 'AMPA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'EM'}, 'postTags': {'popLabel': 'IM'},  # EM -> IM 
    'weight': 1.15,      
    'probability': 0.48375,          
    'delay': 5,     
    'synMech': 'AMPA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'EM'}, 'postTags': {'popLabel': 'IML'},  # EM -> IML
    'weight': 0.575,      
    'probability': 0.57375,              
    'delay': 5,     
    'synMech': 'AMPA'})  

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IM'}, 'postTags': {'popLabel': 'EM'},  # IM -> EM
    'weight': 9,      
    'probability': 0.495,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IM'}, 'postTags': {'popLabel': 'IM'},  # IM -> IM
    'weight': 4.5,      
    'probability': 0.69750,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IM'}, 'postTags': {'popLabel': 'IML'},  # IM -> IML 
    'weight': 4.5,      
    'probability': 0.38250,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IML'}, 'postTags': {'popLabel': 'EM'},  # IML -> EM 
    'weight': 2.49,      
    'probability': 0.39375,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IML'}, 'postTags': {'popLabel': 'IM'},  # IML -> IM 
    'weight': 2.25,      
    'probability': 0.59625,              
    'delay': 5,     
    'synMech': 'GABA'}) 

netParams['connParams'].append(
    {'preTags': {'popLabel': 'IML'}, 'postTags': {'popLabel': 'IML'},  # IML -> IML
    'weight': 4.5,      
    'probability': 0.10125,              
    'delay': 5,     
    'synMech': 'GABA'}) 


###############################################################################
# SIMULATION PARAMETERS
###############################################################################

simConfig = {}  # dictionary to store simConfig

# Simulation parameters
simConfig['duration'] = 1*1e3 # Duration of the simulation, in ms
simConfig['dt'] = 0.1 # Internal integration timestep to use
simConfig['seeds'] = {'conn': 1, 'stim': 1, 'loc': 1} # Seeds for randomizers (connectivity, input stimulation and cell locations)
simConfig['createNEURONObj'] = True  # create HOC objects when instantiating network
simConfig['createPyStruct'] = True  # create Python structure (simulator-independent) when instantiating network
simConfig['timing'] = True  # show timing  and save to file
simConfig['verbose'] = True # show detailed messages 

# Recording 
simConfig['recordCells'] = ['all']  # list of cells to record from 
simConfig['recordTraces'] = {}
# 'V':{'sec':'soma','loc':0.5,'var':'v'}, 
#     'u':{'sec':'soma', 'pointp':'Izhi', 'var':'u'}, 
#     'I':{'sec':'soma', 'pointp':'Izhi', 'var':'i'}, 
#     'NMDA_g': {'sec':'soma', 'loc':0.5, 'synMech':'NMDA', 'var':'g'},
#     'NMDA_i': {'sec':'soma', 'loc':0.5, 'synMech':'NMDA', 'var':'i'},
#     'GABA_g': {'sec':'soma', 'loc':0.5, 'synMech':'GABA', 'var':'g'},
#     'GABA_i': {'sec':'soma', 'loc':0.5, 'synMech':'GABA', 'var':'i'}}
simConfig['recordStim'] = True  # record spikes of cell stims
simConfig['recordStep'] = 1.0 # Step size in ms to save data (eg. V traces, LFP, etc)

# Saving
simConfig['filename'] = 'simdata'  # Set file output name
simConfig['saveFileStep'] = 1000 # step size in ms to save data to disk
simConfig['savePickle'] = False # Whether or not to write spikes etc. to a .mat file
simConfig['saveJson'] = False # Whether or not to write spikes etc. to a .mat file
simConfig['saveMat'] = False # Whether or not to write spikes etc. to a .mat file
simConfig['saveTxt'] = False # save spikes and conn to txt file
simConfig['saveDpk'] = False # save to a .dpk pickled file


# Analysis and plotting 
simConfig['plotRaster'] = True # Whether or not to plot a raster
simConfig['plotCells'] = [] #'Pel', 'Psh', 'ES', 'EM', 'IM', 'IS'] # plot recorded traces for this list of cells
simConfig['plotLFPSpectrum'] = False # plot power spectral density
simConfig['maxspikestoplot'] = 3e8 # Maximum number of spikes to plot
simConfig['plotConn'] = False # whether to plot conn matrix
simConfig['plotWeightChanges'] = False # whether to plot weight changes (shown in conn matrix)
simConfig['plot3dArch'] = False # plot 3d architecture



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