def periodic(self):
"""
Test periodic logging.
"""
m, p, x = myokit.load(os.path.join(myotest.DIR_DATA, 'lr-1991.mmt'))
s = myokit.FiberTissueSimulation(
m, m, p, ncells_fiber=(1, 1), ncells_tissue=(1, 1))
if DEBUG:
print('= ' + s.__class__.__name__ + ' :: Periodic logging =')
# Set tolerance for equality testing
emax = 1e-2 # Time steps for logging are approximate
# Test 1: Simple 5 ms simulation, log_interval 0.5 ms
d, e = s.run(
5, logf=['engine.time'], logt=myokit.LOG_NONE, log_interval=0.5)
d = d.npview()
t = d['engine.time']
q = np.arange(0, 5, 0.5)
if DEBUG:
print(t)
print(q)
print('- ' * 10)
self.assertEqual(len(t), len(q))
self.assertTrue(np.max(np.abs(t - q)) < emax)
# Test 2: Very short simulation
s.reset()
d, e = s.run(
1, logf=['engine.time'], logt=myokit.LOG_NONE, log_interval=0.5)
d = d.npview()
t = d['engine.time']
q = np.arange(0, 1, 0.5)
if DEBUG:
print(t)
print(q)
print('- ' * 10)
self.assertEqual(len(t), len(q))
self.assertTrue(np.max(np.abs(t - q)) < emax)
# Test 3: Stop and start a simulation
s.reset()
d, e = s.run(
1, logf=['engine.time'], logt=myokit.LOG_NONE, log_interval=0.5)
d, e = s.run(2, logf=d, logt=myokit.LOG_NONE, log_interval=0.5)
d, e = s.run(2, logf=d, logt=myokit.LOG_NONE, log_interval=0.5)
d = d.npview()
t = d['engine.time']
q = np.arange(0, 5, 0.5)
if DEBUG:
print(t)
print(q)
print('- ' * 10)
self.assertEqual(len(t), len(q))
self.assertTrue(np.max(np.abs(t - q)) < emax)
def s1(self):
if self._s1 is None:
self._s1 = myokit.FiberTissueSimulation(
self.mf,
self.mt,
self.p1,
ncells_fiber=(self.nfx, self.nfy),
ncells_tissue=(self.ntx, self.nty),
nx_paced=10,
g_fiber=(235, 100),
g_tissue=(9, 5),
g_fiber_tissue=9,
dt=0.0012,
)
return self._s1
def s0(self):
# Shared 2x1 simulation
if self._s0 is None:
self._s0 = myokit.FiberTissueSimulation(
self.mt,
self.mt,
self.p,
ncells_fiber=(1, 1),
ncells_tissue=(1, 1),
nx_paced=1,
g_fiber=(0, 0),
g_tissue=(0, 0),
g_fiber_tissue=0,
precision=myokit.DOUBLE_PRECISION,
dt=0.01,
)
return self._s0
def run_simple(self):
# Load models
mf = os.path.join(myotest.DIR_DATA, 'dn-1985-normalised.mmt')
mt = os.path.join(myotest.DIR_DATA, 'lr-1991.mmt')
mf = myokit.load_model(mf)
mt = myokit.load_model(mt)
# Run times
run = .1
# Create pacing protocol
p = myokit.pacing.blocktrain(1000, 2.0, offset=.01)
# Fiber/Tissue sizes
nfx = 8
nfy = 4
ntx = 8
nty = 8
# Create simulation
s = myokit.FiberTissueSimulation(mf,
mt,
p,
ncells_fiber=(nfx, nfy),
ncells_tissue=(ntx, nty),
nx_paced=10,
g_fiber=(235, 100),
g_tissue=(9, 5),
g_fiber_tissue=9)
s.set_step_size(0.0012)
# Set up logging
logf = [
'engine.time',
'membrane.V',
'isi.isiCa',
]
logt = [
'membrane.V',
'ica.Ca_i',
'ica.ICa',
]
# Run simulation
with myokit.PyCapture():
logf, logt = s.run(run, logf=logf, logt=logt, log_interval=0.01)
def test_against_cvode(self):
# Compare the fiber-tissue simulation output with CVODE output
# Load model
m = myokit.load_model(os.path.join(DIR_DATA, 'lr-1991.mmt'))
# Create pacing protocol
p = myokit.pacing.blocktrain(1000, 2.0, offset=0)
# Create simulation
s1 = myokit.FiberTissueSimulation(
m,
m,
p,
ncells_fiber=(1, 1),
ncells_tissue=(1, 1),
nx_paced=1,
g_fiber=(0, 0),
g_tissue=(0, 0),
g_fiber_tissue=0,
precision=myokit.DOUBLE_PRECISION,
)
s1.set_step_size(0.01)
# Set up logging
logvars = ['engine.time', 'engine.pace', 'membrane.V', 'ica.ICa']
logt = myokit.LOG_NONE
# Run simulation
tmax = 100
dlog = 0.1
with myokit.PyCapture():
d1, logt = s1.run(tmax, logf=logvars, logt=logt, log_interval=dlog)
del(logt)
d1 = d1.npview()
# Run CVODE simulation
s2 = myokit.Simulation(m, p)
s2.set_tolerance(1e-8, 1e-8)
d2 = s2.run(tmax, logvars, log_interval=dlog).npview()
# Check implementation of logging point selection
e0 = np.max(np.abs(d1.time() - d2.time()))
# Check implementation of pacing
r1 = d1['engine.pace'] - d2['engine.pace']
e1 = np.sum(r1**2)
# Check membrane potential (will have some error!)
# Using MRMS from Marsh, Ziaratgahi, Spiteri 2012
r2 = d1['membrane.V', 0, 0] - d2['membrane.V']
r2 /= (1 + np.abs(d2['membrane.V']))
e2 = np.sqrt(np.sum(r2**2) / len(r2))
# Check logging of intermediary variables
r3 = d1['ica.ICa', 0, 0] - d2['ica.ICa']
r3 /= (1 + np.abs(d2['ica.ICa']))
e3 = np.sqrt(np.sum(r3**2) / len(r3))
if debug:
import matplotlib.pyplot as plt
print('Event at t=0')
print(d1.time()[:7])
print(d2.time()[:7])
print(d1.time()[-7:])
print(d2.time()[-7:])
print(e0)
plt.figure()
plt.suptitle('Pacing signals')
plt.subplot(2, 1, 1)
plt.plot(d1.time(), d1['engine.pace'], label='FiberTissue')
plt.plot(d2.time(), d2['engine.pace'], label='CVODE')
plt.legend()
plt.subplot(2, 1, 2)
plt.plot(d1.time(), r1)
print(e1)
plt.figure()
plt.suptitle('Membrane potential')
plt.subplot(2, 1, 1)
plt.plot(d1.time(), d1['membrane.V', 0, 0], label='FiberTissue')
plt.plot(d2.time(), d2['membrane.V'], label='CVODE')
plt.legend()
plt.subplot(2, 1, 2)
plt.plot(d1.time(), r2)
print(e2)
plt.figure()
plt.suptitle('Calcium current')
plt.subplot(2, 1, 1)
plt.plot(d1.time(), d1['ica.ICa', 0, 0], label='FiberTissue')
plt.plot(d2.time(), d2['ica.ICa'], label='CVODE')
plt.legend()
plt.subplot(2, 1, 2)
plt.plot(d1.time(), r2)
print(e3)
plt.show()
self.assertLess(e0, 1e-10)
self.assertLess(e1, 1e-14)
self.assertLess(e2, 0.05)
self.assertLess(e3, 0.01)