import sys
import os
import single_cell_parser as scp
installationDirectory = os.path.abspath(os.path.dirname(__file__))
evokedPrefix = os.path.join(installationDirectory, 'celltype_PSTH/')
L2EvokedName = evokedPrefix + 'L2_3x3_PSTH_UpState.param'
L34EvokedName = evokedPrefix + 'L34_3x3_PSTH_UpState.param'
L4pyEvokedName = evokedPrefix + 'L4py_3x3_PSTH_UpState.param'
L4spEvokedName = evokedPrefix + 'L4sp_3x3_PSTH_UpState.param'
L4ssEvokedName = evokedPrefix + 'L4ss_3x3_PSTH_UpState.param'
L5stEvokedName = evokedPrefix + 'L5st_3x3_PSTH_UpState.param'
L5ttEvokedName = evokedPrefix + 'L5tt_3x3_PSTH_UpState.param'
L6ccEvokedName = evokedPrefix + 'L6cc_3x3_PSTH_UpState.param'
L6ccinvEvokedName = evokedPrefix + 'L6ccinv_3x3_PSTH_UpState.param'
L6ctEvokedName = evokedPrefix + 'L6ct_3x3_PSTH_UpState.param'
VPMEvokedName = evokedPrefix + 'VPM_3x3_PSTH.param'
L1EvokedName = evokedPrefix + 'L1_3x3_PSTH_UpState.param'
L23TransEvokedName = evokedPrefix + 'L23Trans_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
L45PeakEvokedName = evokedPrefix + 'L45Peak_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
L45SymEvokedName = evokedPrefix + 'L45Sym_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
L56TransEvokedName = evokedPrefix + 'L56Trans_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
SymLocal1EvokedName = evokedPrefix + 'SymLocal1_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
SymLocal2EvokedName = evokedPrefix + 'SymLocal2_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
SymLocal3EvokedName = evokedPrefix + 'SymLocal3_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
SymLocal4EvokedName = evokedPrefix + 'SymLocal4_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
SymLocal5EvokedName = evokedPrefix + 'SymLocal5_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
SymLocal6EvokedName = evokedPrefix + 'SymLocal6_PSTH_active_timing_normalized_PW_1.0_SuW_0.5.param'
L2EvokedParam = scp.build_parameters(L2EvokedName)
L34EvokedParam = scp.build_parameters(L34EvokedName)
L4pyEvokedParam = scp.build_parameters(L4pyEvokedName)
L4spEvokedParam = scp.build_parameters(L4spEvokedName)
L4ssEvokedParam = scp.build_parameters(L4ssEvokedName)
L5stEvokedParam = scp.build_parameters(L5stEvokedName)
L5ttEvokedParam = scp.build_parameters(L5ttEvokedName)
L6ccEvokedParam = scp.build_parameters(L6ccEvokedName)
L6ccinvEvokedParam = scp.build_parameters(L6ccinvEvokedName)
L6ctEvokedParam = scp.build_parameters(L6ctEvokedName)
VPMEvokedParam = scp.build_parameters(VPMEvokedName)
L1EvokedParam = scp.build_parameters(L1EvokedName)
L23TransEvokedParam = scp.build_parameters(L23TransEvokedName)
L45PeakEvokedParam = scp.build_parameters(L45PeakEvokedName)
L45SymEvokedParam = scp.build_parameters(L45SymEvokedName)
L56TransEvokedParam = scp.build_parameters(L56TransEvokedName)
SymLocal1EvokedParam = scp.build_parameters(SymLocal1EvokedName)
SymLocal2EvokedParam = scp.build_parameters(SymLocal2EvokedName)
SymLocal3EvokedParam = scp.build_parameters(SymLocal3EvokedName)
SymLocal4EvokedParam = scp.build_parameters(SymLocal4EvokedName)
SymLocal5EvokedParam = scp.build_parameters(SymLocal5EvokedName)
SymLocal6EvokedParam = scp.build_parameters(SymLocal6EvokedName)
evokedTemplates = {'L2': L2EvokedParam,\
'L34': L34EvokedParam,\
'L4py': L4pyEvokedParam,\
'L4sp': L4spEvokedParam,\
'L4ss': L4ssEvokedParam,\
'L5st': L5stEvokedParam,\
'L5tt': L5ttEvokedParam,\
'L6cc': L6ccEvokedParam,\
'L6ccinv': L6ccinvEvokedParam,\
'L6ct': L6ctEvokedParam,\
'VPM': VPMEvokedParam,\
'L1': L1EvokedParam,\
'L23Trans': L23TransEvokedParam,\
'L45Peak': L45PeakEvokedParam,\
'L45Sym': L45SymEvokedParam,\
'L56Trans': L56TransEvokedParam,\
'SymLocal1': SymLocal1EvokedParam,\
'SymLocal2': SymLocal2EvokedParam,\
'SymLocal3': SymLocal3EvokedParam,\
'SymLocal4': SymLocal4EvokedParam,\
'SymLocal5': SymLocal5EvokedParam,\
'SymLocal6': SymLocal6EvokedParam,\
}
# anatomical PC + surround columns (3x3)
# ranging from (potentially) 1-9, starting at row-1, arc-1,
# then increasing by arc and then by row up to row+1, arc+1
# e.g. for C2: B1=1, B2=2, B3=3, C1=4, C2=5, C3=6, D1=7, D2=8, D3=9
surroundColumns = {'A1': {'Alpha': 4, 'A1': 5, 'A2': 6, 'B1': 8, 'B2': 9},\
'A2': {'A1': 4, 'A2': 5, 'A3': 6, 'B1': 7, 'B2': 8, 'B3': 9},\
'A3': {'A2': 4, 'A3': 5, 'A4': 6, 'B2': 7, 'B3': 8, 'B4': 9},\
'A4': {'A3': 4, 'A4': 5, 'B3': 7, 'B4': 8},\
'Alpha': {'Alpha': 5, 'A1': 6, 'Beta': 8, 'B1': 9},\
'B1': {'Alpha': 1, 'A1': 2, 'A2': 3, 'Beta': 4, 'B1': 5, 'B2': 6, 'C1': 8, 'C2': 9},\
'B2': {'A1': 1, 'A2': 2, 'A3': 3, 'B1': 4, 'B2': 5, 'B3': 6, 'C1': 7, 'C2': 8, 'C3': 9},\
'B3': {'A2': 1, 'A3': 2, 'A4': 3, 'B2': 4, 'B3': 5, 'B4': 6, 'C2': 7, 'C3': 8, 'C4': 9},\
'B4': {'A3': 1, 'A4': 2, 'B3': 4, 'B4': 5, 'C3': 7, 'C4': 8},\
'Beta': {'Alpha': 2, 'Beta': 5, 'B1': 6, 'Gamma': 8, 'C1': 9},\
'C1': {'Beta': 1, 'B1': 2, 'B2': 3, 'Gamma': 4, 'C1': 5, 'C2': 6, 'D1': 8, 'D2': 9},\
'C2': {'B1': 1, 'B2': 2, 'B3': 3, 'C1': 4, 'C2': 5, 'C3': 6, 'D1': 7, 'D2': 8, 'D3': 9},\
'C3': {'B2': 1, 'B3': 2, 'B4': 3, 'C2': 4, 'C3': 5, 'C4': 6, 'D2': 7, 'D3': 8, 'D4': 9},\
'C4': {'B3': 1, 'B4': 2, 'C3': 4, 'C4': 5, 'D3': 7, 'D4': 8},\
'Gamma': {'Beta': 2, 'Gamma': 5, 'C1': 6, 'Delta': 8, 'D1': 9},\
'D1': {'Gamma': 1, 'C1': 2, 'C2': 3, 'Delta': 4, 'D1': 5, 'D2': 6, 'E1': 8, 'E2': 9},\
'D2': {'C1': 1, 'C2': 2, 'C3': 3, 'D1': 4, 'D2': 5, 'D3': 6, 'E1': 7, 'E2': 8, 'E3': 9},\
'D3': {'C2': 1, 'C3': 2, 'C4': 3, 'D2': 4, 'D3': 5, 'D4': 6, 'E2': 7, 'E3': 8, 'E4': 9},\
'D4': {'C3': 1, 'C4': 2, 'D3': 4, 'D4': 5, 'E3': 7, 'E4': 8},\
'Delta': {'Gamma': 2, 'Delta': 5, 'D1': 6, 'E1': 9},\
'E1': {'Delta': 1, 'D1': 2, 'D2': 3, 'E1': 5, 'E2': 6},\
'E2': {'D1': 1, 'D2': 2, 'D3': 3, 'E1': 4, 'E2': 5, 'E3': 6},\
'E3': {'D2': 1, 'D3': 2, 'D4': 3, 'E2': 4, 'E3': 5, 'E4': 6},\
'E4': {'D3': 1, 'D4': 2, 'E3': 4, 'E4': 5}}
# correspondence between anatomical column
# and whisker PSTH relative to PW whisker
# (e.g, C2 whisker deflection in B1
# looks like D3 whisker deflection in C2)
surroundPSTHLookup = {1: 'D3', 2: 'D2', 3: 'D1', 4: 'C3', 5: 'C2',\
6: 'C1', 7: 'B3', 8: 'B2', 9: 'B1'}
deflectionOffset = 245.0 #ms; to allow same analysis as CDK JPhys 2007
def create_network_parameter(templateParamName, cellNumberFileName, synFileName, conFileName, whisker, outFileName):
print '*************'
print 'creating network parameter file from template %s' % templateParamName
print '*************'
templateParam = scp.build_parameters(templateParamName)
cellTypeColumnNumbers = load_cell_number_file(cellNumberFileName)
nwParam = scp.NTParameterSet({'info': templateParam.info, 'NMODL_mechanisms': templateParam.NMODL_mechanisms})
nwParam.network = {}
for cellType in templateParam.network.keys():
cellTypeParameters = templateParam.network[cellType]
for column in cellTypeColumnNumbers[cellType].keys():
numberOfCells = cellTypeColumnNumbers[cellType][column]
if numberOfCells == 0:
continue
cellTypeName = cellType + '_' + column
nwParam.network[cellTypeName] = cellTypeParameters.tree_copy()
PSTH = whisker_evoked_PSTH(column, whisker, cellType)
if PSTH is not None:
interval = nwParam.network[cellTypeName].pop('interval')
nwParam.network[cellTypeName].celltype = {'spiketrain': {'interval': interval}}
nwParam.network[cellTypeName].celltype['pointcell'] = PSTH
nwParam.network[cellTypeName].celltype['pointcell']['offset'] = deflectionOffset
nwParam.network[cellTypeName].cellNr = numberOfCells
nwParam.network[cellTypeName].synapses.distributionFile = synFileName
nwParam.network[cellTypeName].synapses.connectionFile = conFileName
nwParam.save(outFileName)
def whisker_evoked_PSTH(column, deflectedWhisker, cellType):
columns = surroundColumns[deflectedWhisker].keys()
evokedTypes = evokedTemplates.keys()
if column not in columns or cellType not in evokedTypes:
return None
evokedTemplate = evokedTemplates[cellType]
PSTHwhisker = surroundPSTHLookup[surroundColumns[deflectedWhisker][column]]
PSTHstr = cellType + '_' + PSTHwhisker
PSTH = evokedTemplate[PSTHstr]
return PSTH
def load_cell_number_file(cellNumberFileName):
cellTypeColumnNumbers = {}
with open(cellNumberFileName, 'r') as cellNumberFile:
lineCnt = 0
for line in cellNumberFile:
if line:
lineCnt += 1
if lineCnt <= 1:
continue
splitLine = line.strip().split('\t')
column = splitLine[0]
cellType = splitLine[1]
numberOfCells = int(splitLine[2])
if not cellTypeColumnNumbers.has_key(cellType):
cellTypeColumnNumbers[cellType] = {}
cellTypeColumnNumbers[cellType][column] = numberOfCells
return cellTypeColumnNumbers
if __name__ == '__main__':
if len(sys.argv) == 6:
templateParamName = sys.argv[1]
cellNumberFileName = sys.argv[2]
synFileName = sys.argv[3]
conFileName = synFileName[:-4] + '.con'
whisker = sys.argv[4]
outFileName = sys.argv[5]
create_network_parameter(templateParamName, cellNumberFileName, synFileName, conFileName, whisker, outFileName)
else:
print 'parameters: [ongoingTemplateParamName] [cellNumberFileName] [synFileName (absolute path)] [deflected whisker] [outFileName]'
