def integrate_sensitivity(net, times, p=None, x0=None, rtol=None, varids=None):
"""
:param net:
:param times: list or tuple
:param atol:
:param rtol:
:param varids:
"""
if isinstance(times, tuple):
intermediate_output = True
else:
intermediate_output = False
t0 = times[0]
if t0 == 0:
_times = times
else:
_times = [0] + list(times)
if p is not None:
net.p = p
if x0 is None:
x0 = net.x0
if rtol is None:
rtol = RTOL
if not hasattr(net, 'res_function'):
net.compile()
out = Dynamics.integrate_sensitivity(net,
_times,
rtol=[rtol] * net.xdim,
fill_traj=intermediate_output)
if varids is not None:
if set(varids) < set(net.varids):
varids = itertools.product(varids, net.pids)
out = out.copy_subset(varids)
traj = out.values
times = out.timepoints
varids = out.key_column.keys()
if t0 != 0:
idx_t0 = list(times).index(t0)
times = times[idx_t0:]
traj = traj[idx_t0:]
traj = Trajectory(traj, index=pd.Index(times, name='time'), columns=varids)
return traj
def make_sens_traj(calcobject,params,times,senstrajfilename):
""" Make the sensitivity trajectory for the calculation
calcoject (same as in setup(...) above).
params: parameters as a KeyedList, sensitivity traj is
calculated at these parameters (should be same as in paramfile
in setup(...) above)
times: the timepoints in the sensitivity trajectory (1-d array)
senstrajfilename: the file to save the sensitivity trajectory to
Note that if times is very finely spaced, the
sensitivity trajectory will need a lot of storage space """
senstraj = Dynamics.integrate_sensitivity(calcobject, times, params, 1.0e-6)
save(senstraj,senstrajfilename)
def make_sens_traj(calcobject, params, times, senstrajfilename):
""" Make the sensitivity trajectory for the calculation
calcoject (same as in setup(...) above).
params: parameters as a KeyedList, sensitivity traj is
calculated at these parameters (should be same as in paramfile
in setup(...) above)
times: the timepoints in the sensitivity trajectory (1-d array)
senstrajfilename: the file to save the sensitivity trajectory to
Note that if times is very finely spaced, the
sensitivity trajectory will need a lot of storage space """
senstraj = Dynamics.integrate_sensitivity(calcobject, times, params,
1.0e-6)
save(senstraj, senstrajfilename)
