def setupRecordLFP():
from .. import sim
from netpyne.support.recxelectrode import RecXElectrode
nsites = len(sim.cfg.recordLFP)
saveSteps = int(np.ceil(sim.cfg.duration / sim.cfg.recordStep))
sim.simData['LFP'] = np.zeros((saveSteps, nsites))
if sim.cfg.saveLFPCells:
for c in sim.net.cells:
sim.simData['LFPCells'][c.gid] = np.zeros((saveSteps, nsites))
if not sim.net.params.defineCellShapes:
sim.net.defineCellShapes(
) # convert cell shapes (if not previously done already)
sim.net.calcSegCoords() # calculate segment coords for each cell
sim.net.recXElectrode = RecXElectrode(
sim) # create exctracellular recording electrode
if sim.cfg.createNEURONObj:
for cell in sim.net.compartCells:
nseg = cell._segCoords['p0'].shape[1]
sim.net.recXElectrode.calcTransferResistance(
cell.gid, cell._segCoords) # transfer resistance for each cell
cell.imembPtr = h.PtrVector(nseg) # pointer vector
cell.imembPtr.ptr_update_callback(
cell.setImembPtr
) # used for gathering an array of i_membrane values from the pointer vector
cell.imembVec = h.Vector(nseg)
sim.cvode.use_fast_imem(1) # make i_membrane_ a range variable
def loadSimData(filename, data=None):
"""
Function to load simulation data from a file
Parameters
----------
filename : str
The path and name of the file where the data is stored.
**Default:** *required*
data : dict
A dictionary containing a `simData` key.
**Default:** ``None``
"""
from .. import sim
if not data:
data = _loadFile(filename)
print('Loading simData...')
if 'simData' in data:
sim.allSimData = data['simData']
else:
print((' simData not found in file %s' % (filename)))
if 'net' in data:
if 'recXElectrode' in data['net']:
from netpyne.support.recxelectrode import RecXElectrode
xElectrode = data['net']['recXElectrode']
if False == isinstance(xElectrode, RecXElectrode):
xElectrode = RecXElectrode.fromJSON(xElectrode)
sim.net.recXElectrode = xElectrode
def setupRecordLFP():
"""
Function for/to <short description of `netpyne.sim.setup.setupRecordLFP`>
"""
from .. import sim
from netpyne.support.recxelectrode import RecXElectrode
nsites = len(sim.cfg.recordLFP)
saveSteps = int(np.ceil(sim.cfg.duration / sim.cfg.recordStep))
sim.simData['LFP'] = np.zeros((saveSteps, nsites))
if sim.cfg.saveLFPCells:
if sim.cfg.saveLFPCells == True:
cellsRecordLFP = utils.getCellsList(['all']) # record all cells
elif isinstance(sim.cfg.saveLFPCells, list):
cellsRecordLFP = utils.getCellsList(sim.cfg.saveLFPCells)
for c in cellsRecordLFP:
sim.simData['LFPCells'][c.gid] = np.zeros((saveSteps, nsites))
if sim.cfg.saveLFPPops:
if sim.cfg.saveLFPPops == True:
popsRecordLFP = list(sim.net.pops.keys()) # record all pops
elif isinstance(sim.cfg.saveLFPPops, list):
popsRecordLFP = [
p for p in sim.cfg.saveLFPPops
if p in list(sim.net.pops.keys())
] # only pops that exist
sim.net.popForEachGid = {}
for pop in popsRecordLFP:
sim.net.popForEachGid.update(
{gid: pop
for gid in sim.net.pops[pop].cellGids})
for pop in popsRecordLFP:
sim.simData['LFPPops'][pop] = np.zeros((saveSteps, nsites))
if not sim.net.params.defineCellShapes:
sim.net.defineCellShapes(
) # convert cell shapes (if not previously done already)
sim.net.calcSegCoords() # calculate segment coords for each cell
sim.net.recXElectrode = RecXElectrode.fromConfig(
sim.cfg) # create exctracellular recording electrode
if sim.cfg.createNEURONObj:
for cell in sim.net.compartCells:
nseg = cell._segCoords['p0'].shape[1]
sim.net.recXElectrode.calcTransferResistance(
cell.gid, cell._segCoords) # transfer resistance for each cell
cell.imembPtr = h.PtrVector(nseg) # pointer vector
cell.imembPtr.ptr_update_callback(
cell.setImembPtr
) # used for gathering an array of i_membrane values from the pointer vector
cell.imembVec = h.Vector(nseg)
sim.cvode.use_fast_imem(True) # make i_membrane_ a range variable
sim.cfg.use_fast_imem = True
def gatherDataFromFiles(gatherLFP=True,
saveFolder=None,
simLabel=None,
sim=None,
fileType='pkl',
saveMerged=False):
"""
Function to gather data from multiple files (from distributed or interval saving)
Parameters
----------
gatherLFP : bool
Whether or not to gather LFP data.
**Default:** ``True`` gathers LFP data if available.
**Options:** ``False`` does not gather LFP data.
saveFolder : str
Name of the directory where data files are located.
**Default:** ``None`` attempts to auto-locate the data directory.
"""
import os
if not sim:
from netpyne import sim
if getattr(sim, 'rank', None) is None:
sim.initialize()
sim.timing('start', 'gatherTime')
if sim.rank == 0:
fileType = fileType.lower()
if fileType not in ['pkl', 'json']:
print(
f"Could not gather data from '.{fileType}' files. Only .pkl and .json are supported so far."
)
return False
if not simLabel:
simLabel = sim.cfg.simLabel
if not saveFolder:
saveFolder = sim.cfg.saveFolder
nodeDataDir = os.path.join(saveFolder, simLabel + '_node_data')
print(f"\nSearching for .{fileType} node files in {nodeDataDir} ...")
simLabels = [
f.replace(f'_node_0.{fileType}', '')
for f in os.listdir(nodeDataDir)
if f.endswith(f'_node_0.{fileType}')
]
if len(simLabels) == 0:
print(f"Could not gather data from files. No node files found.")
return False
mergedFiles = []
for simLabel in simLabels:
allSimData = Dict()
allCells = []
allPops = ODict()
print('\nGathering data from files for simulation: %s ...' %
(simLabel))
simDataVecs = ['spkt', 'spkid', 'stims'] + list(
sim.cfg.recordTraces.keys())
singleNodeVecs = ['t']
if sim.cfg.recordDipolesHNN:
_aggregateDipoles()
simDataVecs.append('dipole')
fileData = {'simData': sim.simData}
fileList = sorted([
f for f in os.listdir(nodeDataDir)
if (f.startswith(simLabel +
'_node') and f.endswith(f'.{fileType}'))
])
for ifile, file in enumerate(fileList):
print(' Merging data file: %s' % (file))
with open(os.path.join(nodeDataDir, file), 'rb') as openFile:
if fileType == 'pkl':
data = pickle.load(openFile)
elif fileType == 'json':
import json
data = json.load(openFile)
if 'cells' in data.keys():
if fileType == 'pkl':
allCells.extend([
cell.__getstate__() for cell in data['cells']
])
else:
allCells.extend(data['cells'])
if 'pops' in data.keys():
loadedPops = data['pops']
if fileType == 'pkl':
for popLabel, pop in loadedPops.items():
allPops[popLabel] = pop['tags']
elif fileType == 'json':
# if populations order is not preserved (which is inherently the case for JSON), need to sort them again
loadedPops = list(loadedPops.items())
def sort(popKeyAndValue):
# the assumption while sorting is that populations order corresponds to cell gids in this population
cellGids = popKeyAndValue[1]['cellGids']
if len(cellGids) > 0:
return cellGids[0]
else:
return -1
loadedPops.sort(key=sort)
for popLabel, pop in loadedPops:
allPops[popLabel] = pop['tags']
if 'simConfig' in data.keys():
setup.setSimCfg(data['simConfig'])
if 'net' in data and gatherLFP:
if 'recXElectrode' in data['net']:
xElectrode = data['net']['recXElectrode']
if False == isinstance(xElectrode, RecXElectrode):
xElectrode = RecXElectrode.fromJSON(xElectrode)
sim.net.recXElectrode = xElectrode
nodePopsCellGids = {
popLabel: list(pop['cellGids'])
for popLabel, pop in data['pops'].items()
}
if ifile == 0 and gatherLFP and 'LFP' in data['simData']:
lfpData = data['simData']['LFP']
if False == isinstance(lfpData, np.ndarray):
lfpData = np.array(lfpData)
data['simData']['LFP'] = lfpData
allSimData['LFP'] = np.zeros(lfpData.shape)
if 'LFPPops' in data['simData']:
allSimData['LFPPops'] = {
p: np.zeros(lfpData.shape)
for p in data['simData']['LFPPops'].keys()
}
for key, value in data['simData'].items():
if key in simDataVecs:
if isinstance(value, dict):
for key2, value2 in value.items():
if isinstance(value2, dict):
allSimData[key].update(
Dict({key2: Dict()}))
for stim, value3 in value2.items():
allSimData[key][key2].update(
{stim: list(value3)})
elif key == 'dipole':
allSimData[key][key2] = np.add(
allSimData[key][key2],
value2.as_numpy())
else:
allSimData[key].update(
{key2: list(value2)})
else:
allSimData[key] = list(
allSimData[key]) + list(value)
elif gatherLFP and key == 'LFP':
allSimData['LFP'] += np.array(value)
elif gatherLFP and key == 'LFPPops':
for p in value:
allSimData['LFPPops'][p] += np.array(value[p])
elif key == 'dipoleSum':
if key not in allSimData.keys():
allSimData[key] = value
else:
allSimData[key] += value
elif key not in singleNodeVecs:
allSimData[key].update(value)
if file == fileList[0]:
for key in singleNodeVecs:
allSimData[key] = list(fileData['simData'][key])
allPopsCellGids = {
popLabel: []
for popLabel in nodePopsCellGids
}
else:
for popLabel, popCellGids in nodePopsCellGids.items():
allPopsCellGids[popLabel].extend(popCellGids)
mergedFiles.append(file)
if len(allSimData['spkt']) > 0:
allSimData['spkt'], allSimData['spkid'] = zip(
*sorted(zip(allSimData['spkt'], allSimData['spkid'])))
allSimData['spkt'], allSimData['spkid'] = list(
allSimData['spkt']), list(allSimData['spkid'])
sim.allSimData = allSimData
sim.net.allCells = sorted(allCells, key=lambda k: k['gid'])
for popLabel, pop in allPops.items():
pop['cellGids'] = sorted(allPopsCellGids[popLabel])
sim.net.allPops = allPops
## Print statistics
sim.pc.barrier()
if sim.rank != 0:
sim.pc.barrier()
else:
sim.timing('stop', 'gatherTime')
if sim.cfg.timing:
print((' Done; gather time = %0.2f s.' %
sim.timingData['gatherTime']))
if saveMerged:
print('\nSaving merged data into single file ...')
saved = sim.saveData()
if len(saved) > 0:
# if single file saved successfully, clean up node data
for file in mergedFiles:
path = os.path.join(nodeDataDir, file)
os.remove(path)
print('\nAnalyzing...')
sim.totalSpikes = len(sim.allSimData['spkt'])
sim.totalSynapses = sum(
[len(cell['conns']) for cell in sim.net.allCells])
if sim.cfg.createPyStruct:
if sim.cfg.compactConnFormat:
preGidIndex = sim.cfg.compactConnFormat.index(
'preGid') if 'preGid' in sim.cfg.compactConnFormat else 0
sim.totalConnections = sum([
len(set([conn[preGidIndex] for conn in cell['conns']]))
for cell in sim.net.allCells
])
else:
sim.totalConnections = sum([
len(set([conn['preGid'] for conn in cell['conns']]))
for cell in sim.net.allCells
])
else:
sim.totalConnections = sim.totalSynapses
sim.numCells = len(sim.net.allCells)
if sim.totalSpikes > 0:
sim.firingRate = float(
sim.totalSpikes) / sim.numCells / sim.cfg.duration * 1e3
else:
sim.firingRate = 0
if sim.numCells > 0:
sim.connsPerCell = sim.totalConnections / float(sim.numCells)
sim.synsPerCell = sim.totalSynapses / float(sim.numCells)
else:
sim.connsPerCell = 0
sim.synsPerCell = 0
print((' Cells: %i' % (sim.numCells)))
print((' Connections: %i (%0.2f per cell)' %
(sim.totalConnections, sim.connsPerCell)))
if sim.totalSynapses != sim.totalConnections:
print((' Synaptic contacts: %i (%0.2f per cell)' %
(sim.totalSynapses, sim.synsPerCell)))
print((' Spikes: %i (%0.2f Hz)' % (sim.totalSpikes, sim.firingRate)))
if 'runTime' in sim.timingData:
print((' Simulated time: %0.1f s; %i workers' %
(sim.cfg.duration / 1e3, sim.nhosts)))
print((' Run time: %0.2f s' % (sim.timingData['runTime'])))
if sim.cfg.printPopAvgRates and not sim.cfg.gatherOnlySimData:
trange = sim.cfg.printPopAvgRates if isinstance(
sim.cfg.printPopAvgRates, list) else None
sim.allSimData['popRates'] = sim.analysis.popAvgRates(
tranges=trange)
if 'plotfI' in sim.cfg.analysis:
sim.analysis.calculatefI()
sim.allSimData['avgRate'] = sim.firingRate