- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-08-02 15:14:59+12:00
- Desc:
- Add the BG of a chemical reaction
- Permanent Source URI:
- https://models.cellml.org/workspace/6bc/rawfile/c856b59f39db721d14e9e3e77a231ff986471f95/Scripts/simExpNrst.py
# Simulate experiments
import opencor as oc
import numpy as np
def simExp(simfile, savefiles,start, ending, pointInterval,varSet,varLoop,varSave):
# Load the simulation file
simulation = oc.open_simulation(simfile)
# The data object houses all the relevant information
# and pointers to the OpenCOR internal data representations
data = simulation.data()
data.set_point_interval(pointInterval)
# Variable to loop
loopPair = list(varLoop.values())[0]
loopValues=list(loopPair.values())[0]
nLoop=len(loopValues)
dtime=(ending-start)/nLoop
# Data to save
varName = np.array(list(varSave))
vars = np.reshape(varName, (1, len(varName)))
# Create a matrix r to save the data
indexStart = 0
indexEnd = int(dtime/pointInterval)
rows=indexEnd-indexStart
r = np.zeros((rows,len(varName)))
r_temp=np.copy(r) # must be a copy, otherwise pass address!
# Run the simulation
# Do NOT reset states and parameters
simulation.reset(False)
for k in range(nLoop):
data.set_starting_point(dtime*k)
data.set_ending_point(dtime*(k+1))
# Set parameter values
for j, ivar in enumerate(list(varLoop)):
loopPair = list(varLoop.values())[j]
loopType=list(loopPair)[0]
loopValues=list(loopPair.values())[0]
if loopType=='constants':
data.constants()[ivar] = loopValues[k]
elif loopType=='algebraic':
data.algebraic()[ivar] = loopValues[k]
elif loopType=='states':
data.states()[ivar] = loopValues[k]
else:
sys.exit("Wrong type of the variable")
for setVar, setPair in varSet.items():
setType = list(setPair)[0]
setValue= list(setPair.values())[0]
if setType=='constants':
data.constants()[setVar] = setValue
elif setType=='algebraic':
data.algebraic()[setVar] = setValue
elif setType=='states':
data.states()[setVar] = setValue
else:
sys.exit("Wrong type of the variable")
simulation.run()
# Access simulation results
results = simulation.results()
if k%1000==0:
print(savefiles,'k=',k)
# Grab specific variable results
m=0
for saveVar, savePair in varSave.items():
saveType = list(savePair)[0]
if saveType =='constants':
tempr = results.constants()[saveVar].values()[:-1]
elif saveType =='algebraic':
tempr = results.algebraic()[saveVar].values()[:-1]
elif saveType =='states':
tempr = results.states()[saveVar].values()[:-1]
elif saveType =='voi':
tempr = results.voi().values()[:-1]
else:
sys.exit("Wrong type of the variable")
if k==0:
r[:,m] = tempr
else:
r_temp[:,m]=tempr
m=m+1
if k>0:
r=np.vstack((r,r_temp))
# clear the results
simulation.clear_results()
# Save the simulation result for all
filename='%s.csv' % (savefiles[0])
np.savetxt(filename, vars, fmt='%s',delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
print(filename)
