def run_simple(self):
# Load model
m = os.path.join(myotest.DIR_DATA, 'lr-1991.mmt')
m, p, x = myokit.load(m)
# Run a simulation
s = myokit.ICSimulation(m, p)
d, e = s.run(20, log_interval=5)
# Create a datablock from the simulation log
b = s.block(d, e)
del (d, e)
# Calculate eigenvalues
b.eigenvalues('derivatives')
def test_basic(self):
# Test basic usage.
# Load model
m, p, _ = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
n = m.count_states()
# Run a simulation
with WarningCollector() as c:
s = myokit.ICSimulation(m, p)
self.assertIn('`ICSimulation` is deprecated', c.text())
self.assertEqual(s.time(), 0)
self.assertEqual(s.state(), m.state())
self.assertEqual(s.default_state(), m.state())
self.assertTrue(np.all(s.derivatives() == np.eye(n)))
d, e = s.run(20, log_interval=5)
self.assertEqual(s.time(), 20)
self.assertNotEqual(s.state(), m.state())
self.assertEqual(s.default_state(), m.state())
self.assertFalse(np.all(s.derivatives() == np.eye(n)))
# Create a datablock from the simulation log
b = s.block(d, e)
# Calculate eigenvalues
b.eigenvalues('derivatives')
# Log with missing time value
d2 = d.clone()
del(d2['engine.time'])
self.assertRaisesRegex(ValueError, 'time', s.block, d2, e)
# Wrong size derivatives array
self.assertRaisesRegex(ValueError, 'shape', s.block, d, e[:-1])
# Time can't be negative
self.assertRaises(ValueError, s.run, -1)
# Test running without a protocol
s.set_protocol(None)
s.run(1)
# Test step size is > 0
self.assertRaises(ValueError, s.set_step_size, 0)
# Test negative log interval is ignored
s.run(1, log_interval=-1)
def periodic(self):
"""
Test periodic logging.
"""
m, p, x = myokit.load(os.path.join(myotest.DIR_DATA, 'lr-1991.mmt'))
s = myokit.ICSimulation(m, p)
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, log=['engine.time'], 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, log=['engine.time'], 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, log=['engine.time'], log_interval=0.5)
d, e = s.run(2, log=d, log_interval=0.5)
d, e = s.run(2, log=d, 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 test_periodic(self):
# Test periodic logging.
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
with WarningCollector():
s = myokit.ICSimulation(m, p)
# 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, log=['engine.time'], 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, log=['engine.time'], 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, log=['engine.time'], log_interval=0.5)
d, e = s.run(2, log=d, log_interval=0.5)
d, e = s.run(2, log=d, 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 test_progress_reporter(self):
# Test running with a progress reporter.
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
# Test using a progress reporter
with WarningCollector() as c:
s = myokit.ICSimulation(m, p)
with myokit.tools.capture() as c:
s.run(110, progress=myokit.ProgressPrinter())
c = c.text().splitlines()
self.assertTrue(len(c) > 0)
# Not a progress reporter
self.assertRaisesRegex(
ValueError, 'ProgressReporter', s.run, 5, progress=12)
# Cancel from reporter
self.assertRaises(
myokit.SimulationCancelledError, s.run, 1,
progress=CancellingReporter(0))