def main():
utils.parser
nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml')
#mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41', 'vm')
table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0', 'vm')
moose.setClock(0, 5e-6)
moose.useClock(0, '/##', 'process')
moose.useClock(0, '/##', 'init')
moose.reinit()
utils.run(0.1)
graphviz.writeGraphviz(__file__+".dot", ignore='/library')
def main():
utils.parser
p = os.path.join(modeldir, "two_cells_nml_1.8/two_cells.nml")
nml.loadNeuroML_L123(p)
# mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget("/tableA", "/cells/purkinjeGroup_0/Dend_37_41", "vm")
table2 = utils.recordTarget("/tableB", "/cells/granuleGroup_0/Soma_0", "vm")
moose.setClock(0, 5e-6)
moose.useClock(0, "/##", "process")
moose.useClock(0, "/##", "init")
moose.reinit()
utils.run(0.1, verify=True)
graphviz.writeGraphviz("test_mumble.dot", ignore="/library")
utils.plotRecords({"Dend 37": table1, "Soma 0": table2}, outfile="%s.png" % sys.argv[0], subplot=True)
def main():
utils.parser
nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml')
#mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41',
'vm')
table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0',
'vm')
moose.setClock(0, 5e-6)
moose.useClock(0, '/##', 'process')
moose.useClock(0, '/##', 'init')
moose.reinit()
utils.run(0.1, verify=True)
graphviz.writeGraphviz(__file__ + ".dot", ignore='/library')
utils.plotTables([table1, table2])
def main():
utils.parser
nml.loadNeuroML_L123('./two_cells_nml_1.8/two_cells.nml')
#mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41', 'vm')
table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0', 'vm')
moose.setClock(0, 5e-6)
moose.useClock(0, '/##', 'process')
moose.useClock(0, '/##', 'init')
moose.reinit()
utils.run(0.1, verify=True)
graphviz.writeGraphviz(__file__+".dot", ignore='/library')
utils.plotRecords({ 'Dend 37' : table1, 'Soma 0' : table2 }
, outfile = '%s.png' % sys.argv[0]
, subplot = True
)
def main():
utils.parser
p = os.path.join(modeldir, 'two_cells_nml_1.8/two_cells.nml')
nml.loadNeuroML_L123(p)
#mumbl.loadMumbl("./two_cells_nml_1.8/mumbl.xml")
table1 = utils.recordTarget('/tableA', '/cells/purkinjeGroup_0/Dend_37_41',
'vm')
table2 = utils.recordTarget('/tableB', '/cells/granuleGroup_0/Soma_0',
'vm')
moose.setClock(0, 5e-6)
moose.useClock(0, '/##', 'process')
moose.useClock(0, '/##', 'init')
moose.reinit()
utils.run(0.1, verify=True)
graphviz.writeGraphviz('test_mumble.dot', ignore='/library')
utils.plotRecords({
'Dend 37': table1,
'Soma 0': table2
},
outfile='%s.png' % sys.argv[0],
subplot=True)
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, solver="gsl", 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
"""
num = 1
newTarget = target
while moose.exists(newTarget):
newTarget = target + "-" + str(num)
num = num + 1
target = newTarget
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, modelpath = loadGenCsp(target, filename, solver)
if moose.exists(moose.element(modelpath).path):
moose.Annotator(moose.element(modelpath).path +
'/info').modeltype = "kkit"
else:
print " path doesn't exists"
moose.le(modelpath)
else:
print 'Only kkit and prototype files can be loaded.'
elif modeltype == 'cspace':
model, modelpath = loadGenCsp(target, filename)
if moose.exists(modelpath):
moose.Annotator(
(moose.element(modelpath).path + '/info')).modeltype = "cspace"
addSolver(modelpath, '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':
if target != '/':
if moose.exists(target):
moose.delete(target)
model = mooseReadSBML(filename, target)
if moose.exists(moose.element(model).path):
moose.Annotator(moose.element(model).path +
'/info').modeltype = "sbml"
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}
def loadFile(filename, target, solver="gsl", 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
"""
num = 1
newTarget = target
while moose.exists(newTarget):
newTarget = target + "-" + str(num)
num = num + 1
target = newTarget
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, modelpath = loadGenCsp(target, filename, solver)
if moose.exists(moose.element(modelpath).path):
moose.Annotator(moose.element(modelpath).path + "/info").modeltype = "kkit"
else:
print(" path doesn't exists")
moose.le(modelpath)
else:
print("Only kkit and prototype files can be loaded.")
elif modeltype == "cspace":
model, modelpath = loadGenCsp(target, filename)
if moose.exists(modelpath):
moose.Annotator((moose.element(modelpath).path + "/info")).modeltype = "cspace"
addSolver(modelpath, "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 list(popdict.values()):
for cell in list(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":
if target != "/":
if moose.exists(target):
moose.delete(target)
model = mooseReadSBML(filename, target)
if moose.exists(moose.element(model).path):
moose.Annotator(moose.element(model).path + "/info").modeltype = "sbml"
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}
def loadFile(filename, target, solver="gsl", 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
"""
loaderror = ""
num = 1
libsfound = True
model = '/'
newTarget = target
while moose.exists(newTarget):
newTarget = target + "-" + str(num)
num = num + 1
target = newTarget
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, modelpath = loadGenCsp(target, filename, solver)
xcord, ycord = [], []
if moose.exists(moose.element(modelpath).path):
process = True
compt = len(moose.wildcardFind(modelpath +
'/##[ISA=CubeMesh]'))
if not compt:
loaderror = "Model has no compartment, atleast one compartment should exist to display the widget"
process = False
else:
p = len(moose.wildcardFind(modelpath +
'/##[ISA=PoolBase]'))
if p < 2:
loaderror = "Model has no pool, atleast two pool should exist to display the widget"
process = False
if process:
if moose.exists(moose.element(modelpath).path):
mObj = moose.wildcardFind(
moose.element(modelpath).path + '/##[ISA=PoolBase]' +
',' + moose.element(modelpath).path +
'/##[ISA=ReacBase]' + ',' +
moose.element(modelpath).path + '/##[ISA=EnzBase]' +
',' + moose.element(modelpath).path +
'/##[ISA=StimulusTable]')
for p in mObj:
if not isinstance(moose.element(p.parent),
moose.CplxEnzBase):
xcord.append(moose.element(p.path + '/info').x)
ycord.append(moose.element(p.path + '/info').y)
recalculatecoordinatesforKkit(mObj, xcord, ycord)
for ememb in moose.wildcardFind(
moose.element(modelpath).path +
'/##[ISA=EnzBase]'):
objInfo = ememb.path + '/info'
#Enzyme's textcolor (from kkit) will be bgcolor (in moose)
if moose.exists(objInfo):
bgcolor = moose.element(objInfo).color
moose.element(objInfo).color = moose.element(
objInfo).textColor
moose.element(objInfo).textColor = bgcolor
moose.Annotator(moose.element(modelpath).path +
'/info').modeltype = "kkit"
else:
print(" path doesn't exists")
moose.le(modelpath)
else:
print('Only kkit and prototype files can be loaded.')
elif modeltype == 'cspace':
model, modelpath = loadGenCsp(target, filename)
if moose.exists(modelpath):
moose.Annotator(
(moose.element(modelpath).path + '/info')).modeltype = "cspace"
addSolver(modelpath, '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':
foundLibSBML_ = False
try:
import libsbml
foundLibSBML_ = True
except ImportError:
pass
if foundLibSBML_:
if target != '/':
if moose.exists(target):
moose.delete(target)
model, loaderror = mooseReadSBML(filename, target)
if moose.exists(moose.element(model).path):
moose.Annotator(moose.element(model).path +
'/info').modeltype = "sbml"
addSolver(target, 'gsl')
libsfound = foundLibSBML_
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,
'foundlib': libsfound,
'loaderror': loaderror
}
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}
