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Hotfix NML2. If self.network not found, sett the temperate to 25 deg C. #319

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Merged
merged 3 commits into from
Oct 18, 2018
Merged

Hotfix NML2. If self.network not found, sett the temperate to 25 deg C. #319

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556ebef
Hotfix. If self.network not found, sett the temperate to 25 deg C.
Oct 17, 2018
0b208c8
Now user can pass verbose option to mooseReadNML2
Oct 18, 2018
6375834
Works after disabling alpha and beta properties.
Oct 18, 2018
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4 changes: 2 additions & 2 deletions python/moose/moose.py
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Original file line number Diff line number Diff line change
Expand Up @@ -222,15 +222,15 @@ def mergeChemModel(src, des):
return False

# NML2 reader and writer function.
def mooseReadNML2( modelpath ):
def mooseReadNML2( modelpath, verbose = False ):
"""Read NeuroML model (version 2) and return reader object.
"""
global nml2Import_
if not nml2Import_:
mu.warn( nml2ImportError_ )
raise RuntimeError( "Could not load NML2 support." )

reader = _neuroml2.NML2Reader( )
reader = _neuroml2.NML2Reader( verbose = verbose )
reader.read( modelpath )
return reader

Expand Down
39 changes: 22 additions & 17 deletions python/moose/neuroml2/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,7 @@ def __init__(self, verbose=False):
self.pop_to_cell_type = {}
self.seg_id_to_comp_name = {}
self.paths_to_chan_elements = {}
self.network = None

def read(self, filename, symmetric=True):
filename = os.path.realpath( filename )
Expand All @@ -139,9 +140,9 @@ def read(self, filename, symmetric=True):

if len(self.doc.networks)>=1:
self.network = self.doc.networks[0]

moose.celsius = self._getTemperature()


self.importConcentrationModels(self.doc)
self.importIonChannels(self.doc)
self.importInputs(self.doc)
Expand All @@ -156,10 +157,13 @@ def read(self, filename, symmetric=True):
mu.info("Read all from %s"%filename)

def _getTemperature(self):
if self.network.type=="networkWithTemperature":
return SI(self.network.temperature)
else:
return 0 # Why not, if there's no temp dependence in nml..?
if self.network is not None:
if self.network.type=="networkWithTemperature":
return SI(self.network.temperature)
else:
# Why not, if there's no temp dependence in nml..?
return 0
return SI('25')

def getCellInPopulation(self, pop_id, index):
return self.cells_in_populations[pop_id][index]
Expand Down Expand Up @@ -400,11 +404,8 @@ def calculateRateFn(self, ratefn, vmin, vmax, tablen=3000, vShift='0mV'):
mu.info("Using %s to evaluate rate"%ct.name)
rate = []
for v in tab:
vals = pynml.evaluate_component(ct
, req_variables =
{'v':'%sV'%v,'vShift':vShift,'temperature':self._getTemperature()}
)
# mu.info vals
req_vars = {'v':'%sV'%v,'vShift':vShift,'temperature':self._getTemperature()}
vals = pynml.evaluate_component(ct, req_variables = req_vars)
if 'x' in vals:
rate.append(vals['x'])
if 't' in vals:
Expand All @@ -413,6 +414,9 @@ def calculateRateFn(self, ratefn, vmin, vmax, tablen=3000, vShift='0mV'):
rate.append(vals['r'])
return np.array(rate)

print( "[WARN ] Could not determine rate: %s %s %s" %(ratefn.type,vmin,vmax))
return np.array([])

def importChannelsToCell(self, nmlcell, moosecell, membrane_properties):
sg_to_segments = self._cell_to_sg[nmlcell]
for chdens in membrane_properties.channel_densities + membrane_properties.channel_density_v_shifts:
Expand Down Expand Up @@ -480,10 +484,11 @@ def _is_standard_nml_rate(self, rate):
def createHHChannel(self, chan, vmin=-150e-3, vmax=100e-3, vdivs=5000):
mchan = moose.HHChannel('%s/%s' % (self.lib.path, chan.id))
mgates = [moose.element(x) for x in [mchan.gateX, mchan.gateY, mchan.gateZ]]
assert(len(chan.gate_hh_rates) <= 3) # We handle only up to 3 gates in HHCHannel
assert len(chan.gate_hh_rates)<=3, "We handle only up to 3 gates in HHCHannel"

if self.verbose:
mu.info('== Creating channel: %s (%s) -> %s (%s)'%(chan.id, chan.gate_hh_rates, mchan, mgates))

all_gates = chan.gates + chan.gate_hh_rates
for ngate, mgate in zip(all_gates,mgates):
if mgate.name.endswith('X'):
Expand All @@ -505,9 +510,7 @@ def createHHChannel(self, chan, vmin=-150e-3, vmax=100e-3, vdivs=5000):
# refering to tau_inf and m_inf??
fwd = ngate.forward_rate
rev = ngate.reverse_rate

self.paths_to_chan_elements['%s/%s'%(chan.id,ngate.id)] = '%s/%s'%(chan.id,mgate.name)

q10_scale = 1
if ngate.q10_settings:
if ngate.q10_settings.type == 'q10Fixed':
Expand All @@ -529,6 +532,7 @@ def createHHChannel(self, chan, vmin=-150e-3, vmax=100e-3, vdivs=5000):
if (fwd is not None) and (rev is not None):
alpha = self.calculateRateFn(fwd, vmin, vmax, vdivs)
beta = self.calculateRateFn(rev, vmin, vmax, vdivs)

mgate.tableA = q10_scale * (alpha)
mgate.tableB = q10_scale * (alpha + beta)

Expand All @@ -547,8 +551,9 @@ def createHHChannel(self, chan, vmin=-150e-3, vmax=100e-3, vdivs=5000):
tau = 1 / (alpha + beta)
if inf is not None:
inf = self.calculateRateFn(inf, vmin, vmax, vdivs)
mgate.tableA = q10_scale * (inf / tau)
mgate.tableB = q10_scale * (1 / tau)
if len(inf) > 0:
mgate.tableA = q10_scale * (inf / tau)
mgate.tableB = q10_scale * (1 / tau)

if self.verbose:
mu.info('%s: Created %s for %s'%(self.filename,mchan.path,chan.id))
Expand Down Expand Up @@ -582,7 +587,7 @@ def importInputs(self, doc):

def importIonChannels(self, doc, vmin=-150e-3, vmax=100e-3, vdivs=5000):
if self.verbose:
mu.info('%s : Importing the ion channels' % self.filename )
mu.info('%s: Importing the ion channels' % self.filename )

for chan in doc.ion_channel+doc.ion_channel_hhs:
if chan.type == 'ionChannelHH':
Expand All @@ -596,7 +601,7 @@ def importIonChannels(self, doc, vmin=-150e-3, vmax=100e-3, vdivs=5000):
self.nml_to_moose[chan] = mchan
self.proto_chans[chan.id] = mchan
if self.verbose:
mu.info( self.filename + ' : Created ion channel %s for %s %s'%(
mu.info( self.filename + ': Created ion channel %s for %s %s'%(
mchan.path, chan.type, chan.id))

def importConcentrationModels(self, doc):
Expand Down