forked from ABRG-Models/IzhikevichABC
/
update_abc_model_xml.py
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update_abc_model_xml.py
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# Update the model in modeldir (experiment expt) using the given model
# parameters. Write out new model.xml file and updated experiment.xml
# file.
def update_abc_model_xml (modeldir,expt,a,b,c,d,A,B,C,T,SI,vpeak,vinit,uinit):
modelxml = modeldir+'/model.xml';
exptxml = modeldir+'/experiment'+`expt`+'.xml';
# We have to deal with the namespace used in the model.xml file.
ns = {'UL': 'http://www.shef.ac.uk/SpineMLNetworkLayer',
'LL': 'http://www.shef.ac.uk/SpineMLLowLevelNetworkLayer'}
# Parse the model to find the parameters.
import xml.etree.ElementTree as et
et.register_namespace('', "http://www.shef.ac.uk/SpineMLNetworkLayer")
et.register_namespace('LL', "http://www.shef.ac.uk/SpineMLLowLevelNetworkLayer")
tree = et.parse(modelxml)
root = tree.getroot()
updated = 0
for child in root.findall('./*/LL:Neuron/', ns):
nm = child.get('name')
#print 'Model file ', nm;
if nm == 'a':
_a = float(child.find('*').get('value'))
if a != _a:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `a`)
updated = 1
elif nm == 'b':
_b = float(child.find('*').get('value'))
if b != _b:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `b`)
updated = 1
elif nm == 'c':
_c = float(child.find('*').get('value'))
if c != _c:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `c`)
updated = 1
elif nm == 'd':
_d = float(child.find('*').get('value'))
if d != _d:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `d`)
updated = 1
elif nm == 'A':
_A = float(child.find('*').get('value'))
if A != _A:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `A`)
updated = 1
elif nm == 'B':
_B = float(child.find('*').get('value'))
if B != _B:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `B`)
updated = 1
elif nm == 'C':
_C = float(child.find('*').get('value'))
if C != _C:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `C`)
updated = 1
elif nm == 'T':
_T = float(child.find('*').get('value'))
if T != _T:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `T`)
updated = 1
elif nm == 'SI':
_SI = float(child.find('*').get('value'))
if SI != _SI:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `SI`)
updated = 1
elif nm == 'v':
_vinit = float(child.find('*').get('value'))
if vinit != _vinit:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `vinit`)
updated = 1
elif nm == 'u':
_uinit = float(child.find('*').get('value'))
if uinit != _uinit:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `uinit`)
updated = 1
elif nm == 'Vpeak':
_vpeak = float(child.find('*').get('value'))
if vpeak != _vpeak:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `vpeak`)
updated = 1
if (updated > 0):
tree.write(modelxml)
# Parse the expt data to find the currents and any parameter overrides
updated = 0
tree = et.parse(exptxml)
root = tree.getroot()
for child in root.findall('.//UL:Property', ns): # or './*'
nm = child.get('name')
#print 'Expt file ', nm
if nm == 'a':
_a = float(child.find('UL:FixedValue').get('value'))
print '_a: ', _a
if a != _a:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `a`)
updated = 1
elif nm == 'b':
_b = float(child.find('*').get('value'))
if b != _b:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `b`)
updated = 1
elif nm == 'c':
_c = float(child.find('*').get('value'))
if c != _c:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `c`)
updated = 1
elif nm == 'd':
_d = float(child.find('*').get('value'))
if d != _d:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `d`)
updated = 1
elif nm == 'A':
_A = float(child.find('*').get('value'))
if A != _A:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `A`)
updated = 1
elif nm == 'B':
_B = float(child.find('*').get('value'))
if B != _B:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `B`)
updated = 1
elif nm == 'C':
_C = float(child.find('*').get('value'))
if C != _C:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `C`)
updated = 1
elif nm == 'T':
_T = float(child.find('*').get('value'))
if T != _T:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `T`)
updated = 1
elif nm == 'SI':
_SI = float(child.find('*').get('value'))
if SI != _SI:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `SI`)
updated = 1
elif nm == 'v':
_vinit = float(child.find('*').get('value'))
if vinit != _vinit:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `vinit`)
updated = 1
elif nm == 'u':
_uinit = float(child.find('*').get('value'))
if uinit != _uinit:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `uinit`)
updated = 1
elif nm == 'Vpeak':
_vpeak = float(child.find('*').get('value'))
if vpeak != _vpeak:
fixedvalue = child.find('UL:FixedValue', ns)
fixedvalue.set('value', `vpeak`)
updated = 1
if (updated > 0):
tree.write(exptxml)