def test_pickling(self):
# Test pickling a simulation
# Test with myokit.Protocol
m, p, _ = myokit.load('example')
s1 = myokit.LegacySimulation(m, p)
s1.pre(123)
s_bytes = pickle.dumps(s1)
s2 = pickle.loads(s_bytes)
self.assertEqual(s1.time(), s2.time())
self.assertEqual(s1.state(), s2.state())
self.assertEqual(s1.default_state(), s2.default_state())
s1.run(123, log=myokit.LOG_NONE)
s2.run(123, log=myokit.LOG_NONE)
self.assertEqual(s1.time(), s2.time())
self.assertEqual(s1.state(), s2.state())
# Test simulation properties
s1.set_tolerance(1e-8, 1e-8)
s1.set_min_step_size(1e-2)
s1.set_max_step_size(0.1)
s2 = pickle.loads(pickle.dumps(s1))
s1.run(23, log=myokit.LOG_NONE)
s2.run(23, log=myokit.LOG_NONE)
self.assertEqual(s1.time(), s2.time())
self.assertEqual(s1.state(), s2.state())
# Test changed constants
s1.set_constant('membrane.C', 1.1)
s2 = pickle.loads(pickle.dumps(s1))
s1.run(17, log=myokit.LOG_NONE)
s2.run(17, log=myokit.LOG_NONE)
self.assertEqual(s1.time(), s2.time())
self.assertEqual(s1.state(), s2.state())
def setUpClass(cls):
# Test simulation creation.
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
cls.model = m
cls.protocol = p
cls.sim = myokit.LegacySimulation(cls.model, cls.protocol)
def test_pacing_values_at_event_transitions(self):
# Tests the value of the pacing signal at event transitions
# Create a simple model
m = myokit.Model()
c = m.add_component('c')
t = c.add_variable('t')
t.set_rhs(0)
t.set_binding('time')
v = c.add_variable('v')
v.set_rhs('0')
v.set_binding('pace')
x = c.add_variable('x')
x.set_rhs(0.1)
x.promote(0)
# Create step protocol
p = myokit.Protocol()
p.schedule(0, 0, 2)
p.schedule(1, 2, 2)
p.schedule(2, 4, 4)
p.schedule(3, 8, 2)
# Simulate with dynamic logging
s = myokit.LegacySimulation(m, p)
d = s.run(p.characteristic_time())
time = list(d.time())
value = list(d['c.v'])
if False:
for i, t in enumerate(d.time()):
t = str(np.round(t, 5))
print(t + ' ' * (10 - len(t)) + str(d['c.v'][i]))
# Values should be
# t 0 1 2 3 4 5 6 7 8 9 10
# p 0 0 1 1 2 2 2 2 3 3 0
self.assertEqual(value[time.index(0.0)], 0)
self.assertEqual(value[time.index(0.0) + 1], 0)
self.assertEqual(value[time.index(2.0) - 1], 0)
self.assertEqual(value[time.index(2.0)], 1)
self.assertEqual(value[time.index(2.0) + 1], 1)
self.assertEqual(value[time.index(4.0) - 1], 1)
self.assertEqual(value[time.index(4.0)], 2)
self.assertEqual(value[time.index(4.0) + 1], 2)
self.assertEqual(value[time.index(8.0) - 1], 2)
self.assertEqual(value[time.index(8.0)], 3)
self.assertEqual(value[time.index(8.0) + 1], 3)
self.assertEqual(value[time.index(10.0) - 1], 3)
self.assertEqual(value[time.index(10.0)], 0)
# Simulate with fixed logging
s.reset()
d = s.run(p.characteristic_time() + 1, log_times=d.time())
time2 = list(d.time())
value2 = list(d['c.v'])
self.assertEqual(time, time2)
self.assertEqual(value, value2)
def test_interpolation_and_pacing(self):
# Test if interpolation results in correct pacing values.
# When logging with discontinuous steps, in the adaptive time
# CVODE sim, the value of pace must be
# 1. The old value *before* the time of the event
# 2. The new value *at and after* the time of the event
# 3. Back to zero *at and after* the end of the event
# (Unless it ends sooner due to a new event arriving)
# Load model
m = myokit.load_model('example')
# Voltage-clamp V (but don't bind it directly)
v = m.label('membrane_potential')
v.demote()
v.set_rhs('-80 + 10 * engine.pace')
# Create protocol
p = myokit.Protocol()
p.schedule(level=1, start=0, duration=5, period=10)
# Create simulation
s = myokit.LegacySimulation(m, p)
# Test if this would result in multiple interpolation steps for logging
# i.e. test if the step before each transition was at least 2 log steps
# long
e = s.run(30).npview()
t = e.time()
for x in [5, 10, 15, 20, 25]:
i = e.find_after(x)
if not t[i] - t[i - 1] > 0.2:
raise Exception('Issue with test: use longer intervals!')
del(e, t, x, i)
# Now test if correct interpolated values are returned by periodic
# logging.
d = s.run(30, log_interval=0.1).npview()
# Test bound variable
p = d['engine.pace']
self.assertTrue(np.all(p[0:50] == 1))
self.assertTrue(np.all(p[50:100] == 0))
self.assertTrue(np.all(p[100:150] == 1))
self.assertTrue(np.all(p[150:200] == 0))
self.assertTrue(np.all(p[200:250] == 1))
self.assertTrue(np.all(p[250:300] == 0))
# Test variable dependent on bound variable
p = d['membrane.V']
self.assertTrue(np.all(p[0:50] == -70))
self.assertTrue(np.all(p[50:100] == -80))
self.assertTrue(np.all(p[100:150] == -70))
self.assertTrue(np.all(p[150:200] == -80))
self.assertTrue(np.all(p[200:250] == -70))
self.assertTrue(np.all(p[250:300] == -80))
def test_simulation_error_2(self):
# Test for simulation error detection: failure occurred too often.
# Cvode error (test failure occurred too many times)
m = self.model.clone()
v = m.get('membrane.V')
v.set_rhs(myokit.Multiply(v.rhs(), myokit.Number(1e18)))
s = myokit.LegacySimulation(m, self.protocol)
with WarningCollector():
self.assertRaisesRegex(
myokit.SimulationError, 'numerical error', s.run, 5000)
def test_last_evaluations_and_steps(self):
# Test :meth:`LegacySimulation.last_number_of_evaluations()` and
# :meth:`LegacySimulation.last_number_of_steps()`
s = myokit.LegacySimulation(self.model, self.protocol)
self.assertEqual(s.last_number_of_evaluations(), 0)
self.assertEqual(s.last_number_of_steps(), 0)
s.run(1)
self.assertTrue(s.last_number_of_evaluations() > 0)
self.assertTrue(s.last_number_of_steps() > 0)
self.assertNotEqual(
s.last_number_of_evaluations(), s.last_number_of_steps())
def test_apd(self):
# Test the apd rootfinding routine
s = myokit.LegacySimulation(
self.model, self.protocol, apd_var='membrane.V')
s.set_tolerance(1e-8, 1e-8)
d, apds = s.run(1800, log=myokit.LOG_NONE, apd_threshold=-70)
# Check with threshold equal to V
self.assertEqual(len(apds['start']), 2)
self.assertEqual(len(apds['duration']), 2)
self.assertAlmostEqual(apds['start'][0], 1.19, places=1)
self.assertAlmostEqual(apds['start'][1], 1001.19, places=1)
self.assertAlmostEqual(apds['duration'][0], 383.88262, places=0)
self.assertAlmostEqual(apds['duration'][1], 378.31448, places=0)
def test_last_state(self):
# Returns the last state before an error, or None.
m = self.model.clone()
istim = m.get('membrane.i_stim')
istim.set_rhs('engine.pace / stim_amplitude')
s = myokit.LegacySimulation(m, self.protocol)
self.assertIsNone(s.last_state())
s.run(1)
self.assertIsNone(s.last_state())
s.set_constant('membrane.i_stim.stim_amplitude', 0)
s.reset()
self.assertRaisesRegex(myokit.SimulationError, "at t = 0", s.run, 5)
self.assertEqual(len(s.last_state()), len(s.state()))
self.assertEqual(s.last_state(), s.state())
def test_point_list_2(self):
# Test how the point-list logging performs when some of the logging
# points overlap with protocol change points.
# Load model
m = myokit.load_model(os.path.join(DIR_DATA, 'lr-1991.mmt'))
# Voltage clamp
m.binding('pace').set_binding(None)
v = m.get('membrane.V')
v.demote()
v.set_rhs(0)
v.set_binding('pace')
#TODO: Implement chaining like this?
#m.get('membrane.V').demote().set_rhs(0).set_binding('pace')
# Create step protocol
dt = 0.1
steps = [
[-80, 250.1],
[-120, 50],
[-80, 200],
[40, 1000],
[-120, 500],
[-80, 1000],
[-30, 3500],
[-120, 500],
[-80, 1000],
]
p = myokit.Protocol()
for f, t in steps:
p.add_step(f, t)
# Create set of times that overlap with change points
times = np.arange(80000) * dt
# Create simulation
s = myokit.LegacySimulation(m, p)
# Run
d = s.run(8000, log_times=times).npview()
# Check if logging points show correct pacing value
# In an earlier implementation, rounding errors and a difference in the
# implementation of passing logpoints and passing protocol points could
# cause the log point to be just before the protocol change.
# In this case, a change at t=120.0 would only be picked up at t=120.1
# (but not consistently!)
# The below code checks for this
offset = 0
for v, t in steps[:-1]:
offset += t
e = d.trim(offset - dt, offset + 2 * dt)
self.assertNotEqual(e['membrane.V'][0], e['membrane.V'][1])
def test_apd_tracking(self):
# Test the APD calculation method.
# More testing is done in test_datalog.py!
# Apd var is not a state
v = self.model.get('ina.INa')
self.assertRaisesRegex(
ValueError, 'must be a state', myokit.LegacySimulation, self.model,
self.protocol, apd_var=v)
# Set a valid apd variable
v = self.model.get('ik.x')
sim = myokit.LegacySimulation(
self.model, self.protocol, apd_var=v)
sim.run(1, apd_threshold=12)
# No apd var given, but threshold provided
self.assertRaisesRegex(
ValueError, 'without apd_var', self.sim.run, 1, apd_threshold=12)
def test_sim_stats(self):
# Test extraction of simulation statistics
m, p, _ = myokit.load('example')
rt = m['engine'].add_variable('realtime')
rt.set_rhs(0)
rt.set_binding('realtime')
ev = m['engine'].add_variable('evaluations')
ev.set_rhs(0)
ev.set_binding('evaluations')
s = myokit.LegacySimulation(m, p)
d = s.run(100, log=myokit.LOG_BOUND).npview()
self.assertIn('engine.realtime', d)
self.assertIn('engine.evaluations', d)
rt, ev = d['engine.realtime'], d['engine.evaluations']
self.assertEqual(len(d.time()), len(rt))
self.assertEqual(len(d.time()), len(ev))
self.assertTrue(np.all(rt >= 0))
self.assertTrue(np.all(ev >= 0))
self.assertTrue(np.all(rt[1:] >= rt[:-1]))
self.assertTrue(np.all(ev[1:] >= ev[:-1]))
def test_progress_reporter(self):
# Test running with a progress reporter.
# Test if it works
sim = myokit.LegacySimulation(self.model, self.protocol)
with myokit.tools.capture() as c:
sim.run(110, progress=myokit.ProgressPrinter())
c = c.text().splitlines()
self.assertEqual(len(c), 2)
p = re.compile(re.escape('[0.0 minutes] 1.9 % done, estimated ') +
'[0-9]+' + re.escape(' seconds remaining'))
self.assertIsNotNone(p.match(c[0]))
p = re.compile(re.escape('[0.0 minutes] 100.0 % done, estimated ') +
'[0-9]+' + re.escape(' seconds remaining'))
self.assertIsNotNone(p.match(c[1]))
# Not a progress reporter
self.assertRaisesRegex(
ValueError, 'ProgressReporter', self.sim.run, 5, progress=12)
# Cancel from reporter
self.assertRaises(
myokit.SimulationCancelledError, self.sim.run, 1,
progress=CancellingReporter(0))
def test_cvode_simulation_with_zero_states(self):
# Tests running cvode simulations on models with no ODEs
# Create a model without states
m1 = myokit.Model()
c = m1.add_component('c')
t = c.add_variable('t')
t.set_rhs(0)
t.set_binding('time')
v = c.add_variable('v')
v.set_rhs('0')
v.set_binding('pace')
w = c.add_variable('w')
w.set_rhs('2 * v')
# Create a model with a state
m2 = m1.clone()
z = m2.get('c').add_variable('z')
z.set_rhs(0.1)
z.promote(0)
# Test without protocol and dynamic logging
s1 = myokit.LegacySimulation(m1)
d1 = s1.run(5)
self.assertEqual(len(d1.time()), 2)
self.assertEqual(list(d1.time()), [0, 5])
self.assertEqual(list(d1['c.w']), [0, 0])
s2 = myokit.LegacySimulation(m2)
d2 = s2.run(6, log_times=d1.time())
self.assertEqual(d1.time(), d2.time())
self.assertEqual(d1['c.w'], d2['c.w'])
# Test with a protocol and dynamic logging
p = myokit.Protocol()
p.schedule(0, 0, 2)
p.schedule(1, 2, 2)
p.schedule(2, 4, 4)
p.schedule(3, 8, 2)
s1.reset()
s1.set_protocol(p)
d1 = s1.run(p.characteristic_time())
self.assertEqual(len(d1.time()), 5)
self.assertEqual(list(d1.time()), [0, 2, 4, 8, 10])
self.assertEqual(list(d1['c.w']), [0, 2, 4, 6, 0])
s2.reset()
s2.set_protocol(p)
d2 = s2.run(p.characteristic_time() + 1, log_times=d1.time())
self.assertEqual(d1.time(), d2.time())
self.assertEqual(d1['c.w'], d2['c.w'])
# Test with fixed logging times
s1.reset()
d1 = s1.run(p.characteristic_time() + 1, log_times=d1['c.t'])
self.assertEqual(list(d1.time()), [0, 2, 4, 8, 10])
self.assertEqual(list(d1['c.w']), [0, 2, 4, 6, 0])
s2.reset()
d2 = s2.run(p.characteristic_time() + 1, log_times=d1.time())
self.assertEqual(d1.time(), d2.time())
self.assertEqual(d1['c.w'], d2['c.w'])
# Test appending to log
s1.reset()
d1 = s1.run(5)
d1 = s1.run(5, log=d1)
self.assertEqual(list(d1.time()), [0, 2, 4, 5, 8, 10])
self.assertEqual(list(d1['c.w']), [0, 2, 4, 4, 6, 0])
# Test with a log interval
s1.reset()
d1 = s1.run(11, log_interval=1)
self.assertEqual(list(d1.time()), [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
self.assertEqual(list(d1['c.w']), [0, 0, 2, 2, 4, 4, 4, 4, 6, 6, 0])
def test_point_list(self):
# Test logging with a preset list of points.
# Load model
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
# Create simulation
s = myokit.LegacySimulation(m, p)
# Don't allow decreasing values
times = [1, 2, 1]
self.assertRaisesRegex(
ValueError, 'non-decreasing', s.run, 5, log_times=times)
# Can't use together with a log interval
self.assertRaisesRegex(
ValueError, 'simultaneously', s.run, 5, log_interval=1,
log_times=[1, 2, 3])
# Get some odd times
times = np.linspace(0, 90, 999)
# Test!
s.reset()
d = s.run(100, log_times=times).npview()
self.assertTrue(np.all(d.time() == times))
# Reset and run again
s.reset()
d = s.run(100, log_times=times).npview()
self.assertTrue(np.all(d.time() == times))
# Run in parts
s.reset()
d = s.run(50, log_times=times)
self.assertEqual(len(d.time()), np.where(times >= 50)[0][0])
d = s.run(50, log=d, log_times=times).npview()
self.assertTrue(np.all(d.time() == times))
# Pre-pacing
s.reset()
s.pre(50)
s.run(100, log_times=times)
self.assertTrue(np.all(d.time() == times))
# Partial logging
s.reset()
s.run(10)
d = s.run(10, log_times=times)
imin = np.where(times >= 10)[0][0]
imax = np.where(times >= 20)[0][0]
self.assertEqual(len(d.time()), imax - imin)
self.assertTrue(np.all(d.time() == times[imin:imax]))
s.run(20)
d = s.run(15, log_times=times)
imin = np.where(times >= 40)[0][0]
imax = np.where(times >= 55)[0][0]
self.assertEqual(len(d.time()), imax - imin)
self.assertTrue(np.all(d.time() == times[imin:imax]))
# Get some regular times
times = [0, 1, 2, 3, 4, 5]
s.reset()
d = s.run(6, log_times=times).npview()
self.assertEqual(len(d.time()), len(times))
self.assertTrue(np.all(d.time() == times))
# Repeated points
times = [0, 0, 0, 5, 5, 5]
s.reset()
d = s.run(6, log_times=times).npview()
self.assertEqual(len(d.time()), len(times))
self.assertTrue(np.all(d.time() == times))
# End points not included, unless also visited!
s.reset()
s.run(5)
d = s.run(5, log_times=times).npview()
self.assertEqual(len(d.time()), 3)
self.assertTrue(np.all(d.time() == times[3:]))
d = s.run(5, log_times=times).npview()
self.assertEqual(len(d.time()), 0)
# Empty list is same as none
s.reset()
d = s.run(1, log_times=[])
self.assertNotEqual(len(d.time()), 0)
def test_periodic(self):
# Test periodic logging
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
s = myokit.LegacySimulation(m, p)
self.periodic(s)
def test_dynamic(self):
# Test dynamic logging.
emax = 1e-6 # Used for equality testing
if debug:
print('= Simulation :: Dynamic logging =')
# Load model & protocol
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
# Create simulation
s = myokit.LegacySimulation(m, p)
#
# Test 1: Simple 5 ms simulation, log_interval 0.5 ms
#
d = s.run(50, log=['engine.time'])
t = d['engine.time']
if debug:
print(t[:2])
print(t[-2:])
print('- ' * 10)
# Test first point not double
self.assertGreater(t[1], t[0])
# Test last point not double
self.assertGreater(t[-1], t[-2])
# Test first point is 0
self.assertTrue(np.abs(t[0] - 0) < emax)
# Test last point is 50
self.assertTrue(np.abs(t[-1] - 50) < emax)
#
# Test 2: Very short simulation
#
s.reset()
d = s.run(1, log=['engine.time'])
t = d['engine.time']
if debug:
print(t[:2])
print(t[-2:])
print('- ' * 10)
# Test first point not double
self.assertGreater(t[1], t[0])
# Test last point not double
self.assertGreater(t[-1], t[-2])
# Test first point is 0
self.assertTrue(np.abs(t[0] - 0) < emax)
# Test last point is 50
self.assertTrue(np.abs(t[-1] - 1) < emax)
#
# Test 3: Stop and start a simulation
#
s.reset()
d = s.run(2, log=['engine.time'])
t = d['engine.time']
n = len(d['engine.time'])
if debug:
print(d['engine.time'][:2])
# Test first point not double
self.assertGreater(t[1], t[0])
# Test last point not double
self.assertGreater(t[-1], t[-2])
# Test first point is 0
self.assertTrue(np.abs(t[0] - 0) < emax)
# Test last point is 2
self.assertTrue(np.abs(t[-1] - 2) < emax)
d = s.run(13, log=d)
t = d['engine.time']
if debug:
print(t[n - 2:n + 2])
# Test last point not double
self.assertGreater(t[-1], t[-2])
# Test last point is 2+13
self.assertTrue(np.abs(t[-1] - 15) < emax)
# Test intermediary points are different
self.assertGreater(t[n], t[n - 1])
n = len(d['engine.time'])
d = s.run(15, log=d)
t = d['engine.time']
if debug:
print(t[n - 2:n + 2])
# Test last point not double
self.assertGreater(t[-1], t[-2])
# Test last point is 2 + 13 + 15
self.assertTrue(np.abs(t[-1] - 30) < emax)
# Test intermediary points are different
self.assertGreater(t[n], t[n - 1])
n = len(d['engine.time'])
d = s.run(20, log=d)
t = d['engine.time']
if debug:
print(t[n - 2:n + 2])
print(t[-2:])
print('- ' * 10)
# Test last point not double
self.assertGreater(t[-1], t[-2])
# Test last point is 2 + 13 + 15 + 20
self.assertTrue(np.abs(t[-1] - 50) < emax)
# Test intermediary points are different
self.assertGreater(t[n], t[n - 1])