def main():
modelname = os.path.join(modeldir, './chem_models/00001-sbml-l3v1.xml')
model = moose.mooseReadSBML(modelname, '/sbml')
c = moose.element('/clock')
moose.reinit()
moose.start(200)
check()
def main():
modelname = os.path.join(modeldir, './chem_models/00001-sbml-l3v1.xml' )
model = moose.mooseReadSBML( modelname, '/sbml' )
c = moose.element('/clock')
moose.reinit()
moose.start(200)
check( )
def main():
"""
This example illustrates loading, running of an SBML model defined in XML format.
Default this file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase.
Plots are setup.
Model is run for 20sec.
As a general rule we created model under '/path/model' and plots under '/path/graphs'.
If someone wants to load anyother file then
`python loadSbmlmodel filepath runtime`
"""
dfilepath = "../genesis/00001-sbml-l3v1.xml"
druntime = 20.0
msg = ""
try:
sys.argv[1]
except IndexError:
filepath = dfilepath
else:
filepath = sys.argv[1]
if not os.path.exists(filepath):
msg = "Filename or path does not exist", filepath, "loading default file", dfilepath
filepath = dfilepath
try:
sys.argv[2]
except:
runtime = druntime
else:
runtime = float(sys.argv[2])
sbmlId = moose.element('/')
# Loading the sbml file into MOOSE, models are loaded in path/model
sbmlId = moose.mooseReadSBML(filepath, '/sbml')
if isinstance(sbmlId, (list, tuple)):
print(sbmlId)
elif sbmlId.path != '/':
s1 = moose.element('/sbml/model/compartment/S1')
s2 = moose.element('/sbml/model/compartment/S2')
# Creating MOOSE Table, Table2 is for the chemical model
graphs = moose.Neutral('/sbml/graphs')
outputs1 = moose.Table2('/sbml/graphs/concS1')
outputs2 = moose.Table2('/sbml/graphs/concS2')
# connect up the tables
moose.connect(outputs1, 'requestOut', s1, 'getConc')
moose.connect(outputs2, 'requestOut', s2, 'getConc')
# gsl solver is added, default is ee
moose.mooseaddChemSolver(sbmlId.path, "ee")
# Reset and Run
moose.reinit()
moose.start(runtime)
return sbmlId, True, msg
return sbmlId, False, msg
def main():
"""
This example illustrates loading, running of an SBML model defined in XML format.
Default this file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase.
Plots are setup.
Model is run for 20sec.
As a general rule we created model under '/path/model' and plots under '/path/graphs'.
If someone wants to load anyother file then
`python loadSbmlmodel filepath runtime`
"""
dfilepath = "../genesis/00001-sbml-l3v1.xml"
druntime = 20.0
msg = ""
try:
sys.argv[1]
except IndexError:
filepath = dfilepath
else:
filepath = sys.argv[1]
if not os.path.exists(filepath):
msg = "Filename or path does not exist",filepath,"loading default file",dfilepath
filepath = dfilepath
try:
sys.argv[2]
except :
runtime = druntime
else:
runtime = float(sys.argv[2])
sbmlId = moose.element('/')
# Loading the sbml file into MOOSE, models are loaded in path/model
sbmlId = moose.mooseReadSBML(filepath,'/sbml')
if isinstance(sbmlId, (list, tuple)):
print(sbmlId)
elif sbmlId.path != '/':
s1 = moose.element('/sbml/model/compartment/S1')
s2= moose.element('/sbml/model/compartment/S2')
# Creating MOOSE Table, Table2 is for the chemical model
graphs = moose.Neutral( '/sbml/graphs' )
outputs1 = moose.Table2 ( '/sbml/graphs/concS1')
outputs2 = moose.Table2 ( '/sbml/graphs/concS2')
# connect up the tables
moose.connect( outputs1,'requestOut', s1, 'getConc' );
moose.connect( outputs2,'requestOut', s2, 'getConc' );
# gsl solver is added, default is ee
moose.mooseAddChemSolver(sbmlId.path,"ee")
# Reset and Run
moose.reinit()
moose.start(runtime)
return sbmlId,True,msg
return sbmlId,False,msg
def loadModels(filepath):
""" load models into moose if file, if moosepath itself it passes back the path and
delete solver if exist """
modelpath = '/'
loaded = False
if os.path.isfile(filepath) :
fpath, filename = os.path.split(filepath)
# print " head and tail ",head, " ",tail
# modelpath = filename[filename.rfind('/'): filename.rfind('.')]
# print "modelpath ",modelpath
# ext = os.path.splitext(filename)[1]
# filename = filename.strip()
modelpath = '/'+filename[:filename.rfind('.')]
modeltype = mtypes.getType(filepath)
subtype = mtypes.getSubtype(filepath, modeltype)
if subtype == 'kkit' or modeltype == "cspace":
if moose.exists(modelpath):
moose.delete(modelpath)
moose.loadModel(filepath,modelpath)
loaded = True
elif subtype == 'sbml':
if moose.exists(modelpath):
moose.delete(modelpath)
moose.mooseReadSBML(filepath,modelpath)
loaded = True
else:
print("This file is not supported for mergering")
modelpath = moose.Shell('/')
elif moose.exists(filepath):
modelpath = filepath
loaded = True
return modelpath,loaded
def loadModels(filepath):
""" load models into moose if file, if moosepath itself it passes back the path and
delete solver if exist """
modelpath = '/'
loaded = False
if os.path.isfile(filepath):
fpath, filename = os.path.split(filepath)
# print " head and tail ",head, " ",tail
# modelpath = filename[filename.rfind('/'): filename.rfind('.')]
# print "modelpath ",modelpath
# ext = os.path.splitext(filename)[1]
# filename = filename.strip()
modelpath = '/' + filename[:filename.rfind('.')]
modeltype = mtypes.getType(filepath)
subtype = mtypes.getSubtype(filepath, modeltype)
if subtype == 'kkit' or modeltype == "cspace":
if moose.exists(modelpath):
moose.delete(modelpath)
moose.loadModel(filepath, modelpath)
loaded = True
elif subtype == 'sbml':
if moose.exists(modelpath):
moose.delete(modelpath)
moose.mooseReadSBML(filepath, modelpath)
loaded = True
else:
print("This file is not supported for mergering")
modelpath = moose.Shell('/')
elif moose.exists(filepath):
modelpath = filepath
loaded = True
return modelpath, loaded
def test_sbml():
modelname = os.path.join(sdir_, '..', 'data', '00001-sbml-l3v1.xml')
model = moose.mooseReadSBML( modelname, '/sbml' )
if not model:
print("Most likely python-libsbml is not installed.")
return 0
moose.reinit()
moose.start(200)
# TODO: Add more tests here.
p = moose.wildcardFind( '/sbml/##' )
assert len(p) == 8
names = ['compartment', 'mesh', 'S1', 'info', 'S2', 'info', 'reaction1']
for x in p:
assert x.name in names
def dumpTweakedModelFile(args, params, results):
filename, file_extension = os.path.splitext(args.model)
resfname, res_ext = os.path.splitext(args.file)
if file_extension == ".xml":
modelId, errormsg = moose.mooseReadSBML(args.model, 'model', 'ee')
tweakParams(params, results.x)
moose.mooseWriteSBML(modelId.path, resfname + "_tweaked.xml")
moose.delete(modelId)
elif file_extension == ".g":
modelId = moose.loadModel(args.model, 'model', 'ee')
tweakParams(params, results.x)
moose.mooseWriteKkit(modelId.path, resfname + "_tweaked.g")
moose.delete(modelId)
else:
print("Warning: dumpTweakedModelFile: Don't know file type for {}".
format(args.model))