def createPopulations(self):
self.populationDict = {}
for population in self.network.findall(".//{"+nml_ns+"}population"):
cellname = population.attrib["cell_type"]
populationname = population.attrib["name"]
print "loading", populationname
## if cell does not exist in library load it from xml file
if not moose.exists('/library/'+cellname):
mmlR = MorphML(self.nml_params)
model_filenames = (cellname+'.xml', cellname+'.morph.xml')
success = False
for model_filename in model_filenames:
model_path = find_first_file(model_filename,self.model_dir)
if model_path is not None:
cellDict = mmlR.readMorphMLFromFile(model_path)
success = True
break
if not success:
raise IOError(
'For cell {0}: files {1} not found under {2}.'.format(
cellname, model_filenames, self.model_dir
)
)
self.cellSegmentDict.update(cellDict)
if cellname == 'LIF':
libcell = moose.LeakyIaF('/library/'+cellname)
else:
libcell = moose.Neuron('/library/'+cellname) #added cells as a Neuron class.
self.populationDict[populationname] = (cellname,{})
moose.Neutral('/cells')
for instance in population.findall(".//{"+nml_ns+"}instance"):
instanceid = instance.attrib['id']
location = instance.find('./{'+nml_ns+'}location')
rotationnote = instance.find('./{'+meta_ns+'}notes')
if rotationnote is not None:
## the text in rotationnote is zrotation=xxxxxxx
zrotation = float(string.split(rotationnote.text,'=')[1])
else:
zrotation = 0
## deep copies the library cell to an instance under '/cells' named as <arg3>
## /cells is useful for scheduling clocks as all sim elements are in /cells
cellid = moose.copy(libcell,moose.Neutral('/cells'),populationname+"_"+instanceid)
if cellname == 'LIF':
cell = moose.LeakyIaF(cellid)
self.populationDict[populationname][1][int(instanceid)]=cell
else:
cell = moose.Neuron(cellid) # No Cell class in MOOSE anymore! :( addded Neuron class - Chaitanya
self.populationDict[populationname][1][int(instanceid)]=cell
x = float(location.attrib['x'])*self.length_factor
y = float(location.attrib['y'])*self.length_factor
z = float(location.attrib['z'])*self.length_factor
self.translate_rotate(cell,x,y,z,zrotation)
def createPopulations(self):
self.populationDict = {}
for population in self.network.findall(".//{"+nml_ns+"}population"):
cellname = population.attrib["cell_type"]
populationname = population.attrib["name"]
print "loading", populationname
## if cell does not exist in library load it from xml file
if not self.library.has_key(cellname):
mmlR = MorphML(self.nml_params)
model_filenames = (cellname+'.xml', cellname+'.morph.xml')
success = False
for model_filename in model_filenames:
model_path = find_first_file(model_filename,self.model_dir)
if model_path is not None:
cellDict = mmlR.readMorphMLFromFile(model_path)
success = True
break
if not success:
raise IOError(
'For cell {0}: files {1} not found under {2}.'.format(
cellname, model_filenames, self.model_dir
)
)
self.cellSegmentDict.update(cellDict)
self.library[cellname] = cellDict
#self.populationDict[populationname] = (cellname,{})
for instance in population.findall(".//{"+nml_ns+"}instance"):
instanceid = instance.attrib['id']
location = instance.find('./{'+nml_ns+'}location')
rotationnote = instance.find('./{'+meta_ns+'}notes')
if rotationnote is not None:
zrotation = float(string.split(rotationnote.text,'=')[1])
else:
zrotation = 0
x = float(location.attrib['x'])*self.length_factor
y = float(location.attrib['y'])*self.length_factor
z = float(location.attrib['z'])*self.length_factor
self.populationDict.update(self.translate_rotate(populationname,instanceid,self.library[cellname],x,y,z,zrotation))
