def loadFile(filename, target, merge=True):
"""Try to load a model from specified `filename` under the element
`target`.
if `merge` is True, the contents are just loaded at target. If
false, everything is deleted from the parent of target unless the
parent is root.
Returns
-------
a dict containing at least these three entries:
modeltype: type of the loaded model.
subtype: subtype of the loaded model, None if no specific subtype
modelroot: root element of the model, None if could not be located - as is the case with Python scripts
"""
istext = True
with open(filename, 'rb') as infile:
istext = mtypes.istextfile(infile)
if not istext:
print 'Cannot handle any binary formats yet'
return None
parent, child = posixpath.split(target)
p = moose.Neutral(parent)
if not merge and p.path != '/':
for ch in p.children:
moose.delete(ch)
try:
modeltype = mtypes.getType(filename)
subtype = mtypes.getSubtype(filename, modeltype)
except KeyError:
raise FileLoadError('Do not know how to handle this filetype: %s' % (filename))
pwe = moose.getCwe()
if modeltype == 'genesis':
if subtype == 'kkit' or subtype == 'prototype':
model = moose.loadModel(filename, target)
else:
print 'Only kkit and prototype files can be loaded.'
elif modeltype == 'cspace':
model = moose.loadModel(filename, target)
elif modeltype == 'xml' and subtype == 'neuroml':
model = neuroml.loadNeuroML_L123(filename)
else:
raise FileLoadError('Do not know how to handle this filetype: %s' % (filename))
moose.setCwe(pwe) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour
# TODO: check with Aditya how to specify the target for
# neuroml reader
return {'modeltype': modeltype,
'subtype': subtype,
'model': model}
def loadFile(filename, target, merge=True):
"""Try to load a model from specified `filename` under the element
`target`.
if `merge` is True, the contents are just loaded at target. If
false, everything is deleted from the parent of target unless the
parent is root.
Returns
-------
a dict containing at least these three entries:
modeltype: type of the loaded model.
subtype: subtype of the loaded model, None if no specific subtype
modelroot: root element of the model, None if could not be located - as is the case with Python scripts
"""
istext = True
with open(filename, 'rb') as infile:
istext = mtypes.istextfile(infile)
if not istext:
print 'Cannot handle any binary formats yet'
return None
parent, child = posixpath.split(target)
p = moose.Neutral(parent)
if not merge and p.path != '/':
for ch in p.children:
moose.delete(ch)
try:
modeltype = mtypes.getType(filename)
subtype = mtypes.getSubtype(filename, modeltype)
except KeyError:
raise FileLoadError('Do not know how to handle this filetype: %s' % (filename))
pwe = moose.getCwe()
#self.statusBar.showMessage('Loading model, please wait')
# app = QtGui.qApp
# app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) #shows a hourglass - or a busy/working arrow
if modeltype == 'genesis':
if subtype == 'kkit' or subtype == 'prototype':
model = moose.loadModel(filename, target,'gsl')
#Harsha: Moving the model under /modelname/model and graphs under /model/graphs
lmodel = moose.Neutral('%s/%s' %(model.path,"model"))
for compt in moose.wildcardFind(model.path+'/##[ISA=ChemCompt]'):
moose.move(compt.path,lmodel)
if not moose.exists(model.path+'/data'):
graphspath = moose.Neutral('%s/%s' %(model.path,"data"))
dataPath = moose.element(model.path+'/data')
i =0
nGraphs = moose.wildcardFind(model.path+'/graphs/##[TYPE=Table2]')
for graphs in nGraphs:
if not moose.exists(dataPath.path+'/graph_'+str(i)):
graphspath = moose.Neutral('%s/%s' %(dataPath.path,"graph_"+str(i)))
else:
graphspath = moose.element(dataPath.path+'/graph_'+str(i))
moose.move(graphs.path,graphspath)
if len(nGraphs) > 0:
i = i+1
#print " i ", i,moose.wildcardFind(model.path+'/moregraphs/##[TYPE=Table2]')
for moregraphs in moose.wildcardFind(model.path+'/moregraphs/##[TYPE=Table2]'):
if not moose.exists(dataPath.path+'/graph_'+str(i)):
graphspath = moose.Neutral('%s/%s' %(dataPath.path,"graph_"+str(i)))
else:
graphspath = moose.element(dataPath.path+'/graph_'+str(i))
moose.move(moregraphs.path,graphspath)
moose.delete(model.path+'/graphs')
moose.delete(model.path+'/moregraphs')
else:
print 'Only kkit and prototype files can be loaded.'
elif modeltype == 'cspace':
model = moose.loadModel(filename, target,'gsl')
#Harsha: Moving the model under /modelname/model and graphs under /model/graphs
lmodel = moose.Neutral('%s/%s' %(model.path,"model"))
for compt in moose.wildcardFind(model.path+'/##[ISA=ChemCompt]'):
moose.move(compt.path,lmodel)
if not moose.exists(model.path+'/data'):
graphspath = moose.Neutral('%s/%s' %(model.path,"data"))
dataPath = moose.element(model.path+'/data')
i =0
nGraphs = moose.wildcardFind(model.path+'/graphs/##[TYPE=Table2]')
for graphs in nGraphs:
if not moose.exists(dataPath.path+'/graph_'+str(i)):
graphspath = moose.Neutral('%s/%s' %(dataPath.path,"graph_"+str(i)))
else:
graphspath = moose.element(dataPath.path+'/graph_'+str(i))
moose.move(graphs.path,graphspath)
if len(nGraphs) > 0:
i = i+1
#print " i ", i,moose.wildcardFind(model.path+'/moregraphs/##[TYPE=Table2]')
for moregraphs in moose.wildcardFind(model.path+'/moregraphs/##[TYPE=Table2]'):
if not moose.exists(dataPath.path+'/graph_'+str(i)):
graphspath = moose.Neutral('%s/%s' %(dataPath.path,"graph_"+str(i)))
else:
graphspath = moose.element(dataPath.path+'/graph_'+str(i))
moose.move(moregraphs.path,graphspath)
moose.delete(model.path+'/graphs')
moose.delete(model.path+'/moregraphs')
addSolver(target,'gsl')
elif modeltype == 'xml':
if subtype == 'neuroml':
popdict, projdict = neuroml.loadNeuroML_L123(filename)
# Circus to get the container of populations from loaded neuroml
for popinfo in popdict.values():
for cell in popinfo[1].values():
solver = moose.HSolve(cell.path + "/hsolve")
solver.target = cell.path
# model = cell.parent
# break
# break
# Moving model to a new location under the model name
# model name is the filename without extension
model = moose.Neutral("/" + splitext(basename(filename))[0])
element = moose.Neutral(model.path + "/model")
if(moose.exists("/cells")) : moose.move("/cells" , element.path)
if(moose.exists("/elec")) : moose.move("/elec" , model.path)
if(moose.exists("/library")): moose.move("/library", model.path)
# moose.move("cells/", cell.path)
elif subtype == 'sbml':
model = moose.readSBML(filename,target,'gsl')
addSolver(target,'gsl')
else:
raise FileLoadError('Do not know how to handle this filetype: %s' % (filename))
moose.setCwe(pwe) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour
# TODO: check with Aditya how to specify the target for
# neuroml reader
# app.restoreOverrideCursor()
return {'modeltype': modeltype,
'subtype': subtype,
'model': model}