- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-06-28 15:54:52+12:00
- Desc:
- Add Markov states
- Permanent Source URI:
- https://models.cellml.org/workspace/6bc/rawfile/6dc0ec3b88004d6d2aff5ddf20061aa3cb35d7da/Scripts/simExp.py
# Simulate experiments
import opencor as oc
import numpy as np
def simExp(simfile, savefiles,start, ending, pointInterval,indexStart,indexEnd,varSet,varLoop,varSave):
# Allow one variable to loop
if len(varLoop)>1:
sys.exit("The number of the variables to loop is greater than 1")
# 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_starting_point(start)
data.set_ending_point(ending)
data.set_point_interval(pointInterval)
# If need to save peak value
peak=False
getallSave = list(varSave.values())
for i,geti in enumerate(getallSave):
if True in geti.values():
peak=True
# Variable to loop
loopVar=list(varLoop)[0]
loopPair = list(varLoop.values())[0]
loopType=list(loopPair)[0]
loopValues=list(loopPair.values())[0]
print(loopVar,loopValues)
# Data to save
varName = np.array(list(varSave))
vars = np.reshape(varName, (1, len(varName)))
# Create a matrix r to save the data
rows=indexEnd-indexStart
if len(savefiles)==1 and (rows==1 or peak==True):
r = np.zeros((len(loopValues),len(varName)))
finalSave=True
else:
r = np.zeros((rows,len(varName)))
finalSave=False
# Run the simulation
for k, ivalue in enumerate(loopValues):
# Reset states and parameters
simulation.reset(True)
# Set parameter values
if loopType=='constants':
data.constants()[loopVar] = ivalue
elif loopType=='algebraic':
data.algebraic()[loopVar] = ivalue
elif loopType=='states':
data.states()[loopVar] = ivalue
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()
# Grab specific variable results
m=0
for saveVar, savePair in varSave.items():
saveType = list(savePair)[0]
fpeak = list(savePair.values())[0]
if saveType =='constants':
tempr = results.constants()[saveVar].values()[indexStart:indexEnd]
elif saveType =='algebraic':
tempr = results.algebraic()[saveVar].values()[indexStart:indexEnd]
elif saveType =='states':
tempr = results.states()[saveVar].values()[indexStart:indexEnd]
elif saveType =='voi':
tempr = results.voi().values()[indexStart:indexEnd]
else:
sys.exit("Wrong type of the variable")
if finalSave==False:
r[:,m] = tempr
else:
if fpeak == True:
index_max = np.argmax(abs(tempr))
r[k,m] = tempr[index_max]
else:
r[k,m] = tempr[-1]
m=m+1
if finalSave==False:
# Save the simulation result of the last run
filename='%s.csv' % (savefiles[k])
np.savetxt(filename, vars, fmt='%s',delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
# clear the results
simulation.clear_results()
if finalSave==True:
# 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)
