def test_load_partial(self):
# Test loading of partial files.
mpath = os.path.join(DIR_DATA, 'beeler-1977-model.mmt')
ppath = os.path.join(DIR_DATA, 'beeler-1977-protocol.mmt')
spath = os.path.join(DIR_DATA, 'beeler-1977-script.mmt')
m, p, x = myokit.load(mpath)
self.assertIsInstance(m, myokit.Model)
self.assertIsNone(p)
self.assertIsNone(x)
m, p, x = myokit.load(ppath)
self.assertIsNone(m)
self.assertIsInstance(p, myokit.Protocol)
self.assertIsNone(x)
m, p, x = myokit.load(spath)
self.assertIsNone(m)
self.assertIsNone(p)
self.assertTrue(isinstance(x, basestring))
self.assertRaises(myokit.SectionNotFoundError, myokit.load_model,
ppath)
self.assertRaises(myokit.SectionNotFoundError, myokit.load_model,
spath)
self.assertRaises(myokit.SectionNotFoundError, myokit.load_protocol,
mpath)
self.assertRaises(myokit.SectionNotFoundError, myokit.load_protocol,
spath)
self.assertRaises(myokit.SectionNotFoundError, myokit.load_script,
mpath)
self.assertRaises(myokit.SectionNotFoundError, myokit.load_script,
ppath)
def test_simulate(self):
"""Tests whether the simulate method works as expected. Tests
implicitly also whether the _set_parameters method works properly.
"""
# Test Case I: Linear Growth Model
# define parameters and times
parameters = [1, 2]
times = np.arange(25)
# expected
# init model in myokit
model, protocol, _ = myokit.load(self.file_linear_growth_model)
# set inital state of model
model.set_state([parameters[0]])
# set linear growth constant
model.set_value('central_compartment.lambda', parameters[1])
# instantiate and run simulation
simulation = myokit.Simulation(model, protocol)
myokit_result = simulation.run(duration=times[-1] + 1,
log=['central_compartment.drug'],
log_times=times)
expected_result = myokit_result.get('central_compartment.drug')
# assert that Model.simulate returns the same result.
model_result = self.linear_model.simulate(parameters, times)
assert np.array_equal(expected_result, model_result)
# Test case II: One Compartment Model (checks whether access of
# correct output works)
# define parameters and times
parameters = [0, 2, 4]
times = np.arange(25)
# expected
# init model in myokit
model, protocol, _ = myokit.load(self.file_one_comp_model)
# set inital state of model
model.set_state([parameters[0]])
# set clearance and volume
model.set_value('central_compartment.CL', parameters[1])
model.set_value('central_compartment.V', parameters[2])
# instantiate and run simulation
simulation = myokit.Simulation(model, protocol)
state_name = 'central_compartment.drug_concentration'
myokit_result = simulation.run(duration=times[-1] + 1,
log=[state_name],
log_times=times)
expected_result = myokit_result.get(state_name)
# assert that Model.simulate returns the same result.
model_result = self.one_comp_model.simulate(parameters, times)
assert np.array_equal(expected_result, model_result)
def set_state(self):
m, p, x = myokit.load(os.path.join(myotest.DIR_DATA, 'lr-1991.mmt'))
n = 4
s = myokit.Simulation1d(m, p, n)
sm = m.state()
ss = [s.state(x) for x in xrange(n)]
for si in ss:
self.assertEqual(sm, si)
# Test setting a single, global state
sx = [0] * 8
self.assertNotEqual(sm, sx)
s.set_state(sx)
for i in xrange(n):
self.assertEqual(sx, s.state(i))
self.assertEqual(sx * n, s.state())
s.set_state(sm)
self.assertEqual(sm * n, s.state())
# Test setting a single state
j = 1
s.set_state(sx, j)
for i in xrange(n):
if i == j:
self.assertEqual(s.state(i), sx)
else:
self.assertEqual(s.state(i), sm)
def run_simple(self):
# Load model
m = os.path.join(myotest.DIR_DATA, 'lr-1991.mmt')
m, p, x = myokit.load(m)
# Run a simple simulation
c = myokit.JacobianCalculator(m)
x, f, j, e = c.newton_root(damping=0.01, max_iter=50)
def test_set_state_1d(self):
# Test the set_state method in 1d
m, p, _ = myokit.load('example')
n = 10
s = myokit.SimulationOpenCL(m, p, n)
sm = m.state()
ss = [s.state(x) for x in range(n)]
for si in ss:
self.assertEqual(sm, si)
# Test setting a single, global state
sx = [0.0] * 8
self.assertNotEqual(sm, sx)
s.set_state(sx)
for i in range(n):
self.assertEqual(sx, s.state(i))
self.assertEqual(sx * n, s.state())
s.set_state(sm)
self.assertEqual(sm * n, s.state())
# Test setting a single state
j = 1
s.set_state(sx, j)
for i in range(n):
if i == j:
self.assertEqual(s.state(i), sx)
else:
self.assertEqual(s.state(i), sm)
def test_set_constant(self):
# Test :meth:`PSimulation.set_constant()` and
# :meth:`PSimulation.set_parameters()`
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
with WarningCollector() as c:
s = myokit.PSimulation(m,
p,
variables=['membrane.V'],
parameters=['ina.gNa'])
s.set_constant('ica.gCa', 1)
s.set_constant(m.get('ica.gCa'), 1)
# Variable is not a literal
self.assertRaisesRegex(ValueError, 'literal', s.set_constant,
'membrane.V', 1)
# Variable is in parameters list
self.assertRaisesRegex(ValueError, 'parameter', s.set_constant,
'ina.gNa', 1)
# Set parameter values
s.set_parameters([1])
self.assertRaisesRegex(ValueError, '1 values', s.set_parameters,
[1, 2])
s.set_parameters({'ina.gNa': 1})
s.set_parameters({m.get('ina.gNa'): 1})
self.assertRaisesRegex(ValueError, 'Unknown', s.set_parameters,
{'bert': 2})
self.assertRaisesRegex(ValueError, 'parameter', s.set_parameters,
{'ica.gCa': 2})
def test_progress_reporter(self):
# Test running with a progress reporter.
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
with WarningCollector() as c:
s = myokit.PSimulation(m,
p,
variables=['membrane.V'],
parameters=['ina.gNa'])
with myokit.tools.capture() as c:
s.run(2, progress=myokit.ProgressPrinter())
c = c.text().splitlines()
self.assertEqual(len(c), 2)
self.assertEqual(
c[0], '[0.0 minutes] 50.0 % done, estimated 0 seconds remaining')
self.assertEqual(
c[1], '[0.0 minutes] 100.0 % done, estimated 0 seconds remaining')
# Not a progress reporter
self.assertRaisesRegex(ValueError,
'ProgressReporter',
s.run,
1,
progress=12)
# Cancel from reporter
self.assertRaises(myokit.SimulationCancelledError,
s.run,
1,
progress=CancellingReporter(0))
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_current_arrows(self):
# Test the current arrows plot.
# Select matplotlib backend that doesn't require a screen
import matplotlib
matplotlib.use('template')
import matplotlib.pyplot as plt
# Run simulation, get currents
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
# Add dummy current, that never carries much charge and should be
# ignored
c = m.add_component('dummy')
x = c.add_variable('IDummy')
x.set_rhs('0 * membrane.V')
s = myokit.Simulation(m, p)
currents = ['ina.INa', 'ik1.IK1', 'ica.ICa', 'dummy.IDummy']
d = s.run(600, log=['engine.time', 'membrane.V'] + currents)
fig = plt.figure()
plots.current_arrows(d, 'membrane.V', currents)
plt.close(fig)
plt.show()
# Massive peak at final point
d = d.npview()
d['dummy.IDummy'][-1] = 100
fig = plt.figure()
plots.current_arrows(d, 'membrane.V', currents)
plt.close(fig)
plt.show()
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 __init__(self, mmtfile: str) -> None:
"""Initialises the model class.
Arguments:
mmtfile {str} -- Path to the mmtfile defining the model and the
protocol.
"""
# load model and protocol
model, protocol, _ = myokit.load(mmtfile)
# get dose events from protocol
self.mmt_dose_events = self._get_mmt_dose_events(protocol)
# get state, parameter and output names
self.state_names = [state.qname() for state in model.states()]
self.state_dimension = model.count_states()
self.output_names = []
self.output_dimension = None
self.parameter_names = self._get_parameter_names(model)
self.number_parameters_to_fit = model.count_variables(inter=False,
bound=False
)
# instantiate the simulation
self.simulation = myokit.Simulation(model, protocol)
self.model = model
def test_simulate(self):
"""Tests whether the simulate method works as expected. Tests implicitly also whether the _set_parameters method
works properly.
"""
# Test case I: 1-compartment model
parameters = [0, 2, 4] # different from initialised parameters
times = np.arange(25)
# expected
model, protocol, _ = myokit.load(self.file_name)
model.set_state([parameters[0]])
model.set_value('central_compartment.CL', parameters[1])
model.set_value('central_compartment.V', parameters[2])
simulation = myokit.Simulation(model, protocol)
myokit_result = simulation.run(
duration=times[-1] + 1,
log=['central_compartment.drug_concentration'],
log_times=times)
expected_result = myokit_result.get(
'central_compartment.drug_concentration')
# assert that Model.simulate returns the same result.
model_result = self.one_comp_model.simulate(parameters, times)
assert np.array_equal(expected_result, model_result)
def setUpClass(self):
"""
Test simulation creation.
"""
m, p, x = myokit.load(os.path.join(myotest.DIR_DATA, 'lr-1991.mmt'))
self.model = m
self.protocol = p
self.sim = myokit.Simulation(self.model, self.protocol)
def test_myokit_import():
"""Test that Myokit can be loaded.
Uses the Myokit builtin example.
"""
m, p, x = myokit.load('example')
s = myokit.Simulation(m, p)
assert isinstance(s, myokit.Simulation)
assert True
def test_periodic(self):
# Test periodic logging.
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
with WarningCollector():
s = myokit.PSimulation(
m, p, variables=['membrane.V'], parameters=['ina.gNa'])
# 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)
# Negative or 0 log interval --> Log every step
s.set_step_size(0.01)
d, dp = s.run(1, log_interval=0)
self.assertEqual(len(d.time()), 101)
d, dp = s.run(1, log_interval=-1)
self.assertEqual(len(d.time()), 101)
def test_timeout_progress_reporter(self):
m, p, x = myokit.load('example')
s = myokit.Simulation(m, p)
t = myokit.Timeout(0.1)
with self.assertRaises(myokit.SimulationCancelledError):
s.run(100000, progress=t)
t = myokit.Timeout(3600)
s.run(100, progress=t)
def run_simple(self):
# Load model
m = os.path.join(myotest.DIR_DATA, 'lr-1991.mmt')
m, p, x = myokit.load(m)
# Run a tiny simulation
s = myokit.PSimulation(m,
p,
variables=['membrane.V'],
parameters=['ina.gNa', 'ica.gCa'])
s.set_step_size(0.002)
d, dp = s.run(10, log_interval=2)
def simulation(name='plain'):
# Load model and protocol
m, p, _ = myokit.load('example')
sens = (
('ina.m', 'dot(ina.m)', 'ina.INa'),
('ina.gNa', 'init(ina.m)')
)
if name == 'plain':
s = myokit.Simulation(m, p)
def c():
s.run(100)
elif name == 'sens':
s = myokit.Simulation(m, p, sens)
def c():
s.run(100)
elif name == 'realtime':
# Realtime tracking
# Note: This doesn't show much: Python re-uses strings etc. so can
# delete some decrefs without seeing it here!
v = m.get('engine').add_variable('realtime')
v.set_rhs(0)
v.set_binding('realtime')
s = myokit.Simulation(m, p)
def c():
s.run(100)
elif name == 'apd':
# APD measuring
# Note: Can remove some decrefs without seeing results here...
s = myokit.Simulation(m, p)
def c():
s.run(1000, apd_variable='membrane.V', apd_threshold=-1)
elif name == 'log_times':
# Point-list logging
s = myokit.Simulation(m, p, sens)
def c():
s.reset()
s.run(1000, log_times=[0, 100, 500])
else:
raise ValueError(f'Unknown test: simulation {name}')
print(f'Testing simulation: {name}')
test(c)
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(self):
"""
Test the export functions for this exporter type.
"""
# Load model, protocol
m, p, x = myokit.load('example')
# Get exporter
e = formats.exporter(self._exporter)
# Ok? Then update class name for nice error message (!)
self.__class__.__name__ = 'ExportTest' + e.__class__.__name__
# Create empty output directory as subdirectory of DIR_OUT
path = os.path.join(myotest.DIR_OUT, self._exporter)
if os.path.exists(path):
shutil.rmtree(path)
os.makedirs(path)
try:
# Try exports
exports = 0
# Try model export
if e.supports_model():
exports += 1
fpath = os.path.join(path, 'model.txt')
ret = e.model(fpath, m)
self.assertIsNone(ret)
self.assertTrue(os.path.isfile(fpath))
else:
self.assertRaises(NotImplementedError, e.model, path, m)
# Try runnable export
if e.supports_runnable():
exports += 1
# Check without protocol
dpath = os.path.join(path, 'runnable1')
ret = e.runnable(dpath, m)
self.assertIsNone(ret)
self.assertTrue(os.path.isdir(dpath))
self.assertTrue(len(os.listdir(dpath)) > 0)
# Check with protocol
dpath = os.path.join(path, 'runnable2')
ret = e.runnable(dpath, m, p)
self.assertIsNone(ret)
self.assertTrue(os.path.isdir(dpath))
self.assertTrue(len(os.listdir(dpath)) > 0)
else:
self.assertRaises(NotImplementedError, e.runnable, path, m, p)
# Test if any exports were available
if exports == 0:
raise Exception(
'No types of export supported by: ' + self._exporter)
finally:
if os.path.exists(path) and os.path.isdir(path):
if not myotest.DEBUG:
shutil.rmtree(path)
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 get_parameter_vals(self, parameters: List[str]) -> Dict[str, float]:
"""Get the value of current model parameters.
Args:
parameters (List[str]): Names of parameter values to retrieve.
"""
m, _, _ = myokit.load(self.modelfile)
parameter_values = {}
for p in parameters:
if m.has_variable(p):
parameter_values[p] = m.get(p).value()
else:
parameter_values[p] = np.nan
return parameter_values
def run(path, filename=None):
"""
Run all the mmt files in a given directory `path`.
If `filename` is given, only the file with that name from `path` is run.
"""
# Get absolute path
path = os.path.abspath(path)
# Change to dir
os.chdir(path)
# Run all
glob = '*.mmt'
found = False
for fn in fnmatch.filter(os.listdir(path), glob):
# Real file?
if filename is not None:
if fn != filename:
continue
else:
found = True
# Load and run
try:
print('Loading ' + fn)
m, p, x = myokit.load(os.path.join(path, fn))
try:
print('Running...')
myokit.run(m, p, x)
except Exception:
print(traceback.format_exc())
except Exception:
print('Unable to load.')
print(traceback.format_exc())
try:
pl.close('all')
except Exception:
pass
# Tidy up
del (m, p, x)
gc.collect()
print('-' * 70)
if filename is not None and not found:
print('Unable to find file: ' + str(filename))
else:
print('Done!')
def test_load_save_state_bin(self):
# Test loading/saving state in binary format.
m, p, x = myokit.load('example')
with TemporaryDirectory() as d:
# Test save and load with double precision
f = d.path('state.bin')
myokit.save_state_bin(f, m.state())
self.assertEqual(myokit.load_state_bin(f), m.state())
# Test save and load with single precision
f = d.path('state.bin')
myokit.save_state_bin(f, m.state(), myokit.SINGLE_PRECISION)
d = np.array(myokit.load_state_bin(f)) - np.array(m.state())
self.assertTrue(np.all(np.abs(d) < 1e-5)) # Not very precise!
def test_set_constant(self):
# Test :meth:`Simulation.set_constant()`.
# Literal
self.sim.set_constant('cell.Na_i', 11)
self.assertRaises(KeyError, self.sim.set_constant, 'cell.Bert', 11)
# Parameter (needs sensitivies set)
m, p, x = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
sim = myokit.Simulation(m, p, (['ib.Ib'], ['ib.gb']))
sim.set_constant('ib.gb', 20)
# Calculated constant
self.assertRaisesRegex(ValueError, 'not a literal',
self.sim.set_constant, 'ina.ENa', 11)
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 iterdir(path, guarantee_model_names=True):
"""
Iterates over a directory yielding tuples ``(model, protocol)`` where
``model`` is a :class:`myokit.Model` and ``protocol`` is a
:class:`myokit.Protocol`.
Depending on the contents of the found files, some entries might not have a
protocol. Files without a model are skipped.
The results will be yielded ordered by filename.
The method does not descend into child directories.
If ``guarantee_model_names`` is ``True`` (default), models that do not
specify a ``name`` meta-attribute will be given their filename as name.
This ensures every model read by this method has a name meta-property.
"""
# Fix path
path = os.path.expanduser(os.path.abspath(path))
if not os.path.isdir(path):
raise ValueError('Given path is not a directory.')
# Scan files
for fname in sorted(os.listdir(path)):
fpath = os.path.join(path, fname)
# Check if it's a model file
if not os.path.isfile(fpath):
continue
base, ext = os.path.splitext(fname)
if ext != '.mmt':
continue
# Read model & protocol
model, protocol, x = myokit.load(fpath)
# Skip files without model
if model is None:
continue
# Set name attribute
if guarantee_model_names:
if not model.name():
model.meta['name'] = base
# Yield
yield model, protocol
def run_simple(self):
# Load model
m = os.path.join(myotest.DIR_DATA, 'lr-1991.mmt')
m, p, x = myokit.load(m)
v = m.binding('diffusion_current')
if v is not None:
v.set_binding(None)
# Run a simulation, save all states & bound values
s = myokit.Simulation(m, p)
s.pre(10)
s.reset()
d = s.run(20, log=myokit.LOG_STATE + myokit.LOG_BOUND)
# Calculate the dominant eigenvalues for each log position
g = myokit.JacobianTracer(m)
b = g.jacobians(d)
b.dominant_eigenvalues('jacobians')
b.largest_eigenvalues('jacobians')
def _build_simulation(self):
"""Creates a class instance of myokit.Model and myokit.Simulation.
Raises:
ValueError: Cannot find voltage parameter in model.
"""
m, _, _ = myokit.load(self.modelfile)
try:
v = m.get(self.vvar)
except:
raise ValueError('Model does not have vvar: {}'
.format(self.vvar))
if v.is_state():
v.demote()
v.set_rhs(0)
v.set_binding(None)
self._sim = myokit.Simulation(m)
def mmt_export(exporter, source, target):
"""
Exports a myokit model.
"""
import sys
import myokit
import myokit.formats
# Get exporter
exporter = myokit.formats.exporter(exporter)
# Set to auto-print
logger = exporter.logger()
logger.set_live(True)
logger.log_flair(str(exporter.__class__.__name__))
# Parse input file
try:
logger.log('Reading model from ' + myokit.format_path(source))
model, protocol, script = myokit.load(source)
except myokit.ParseError as ex:
logger.log(myokit.format_parse_error(ex, source))
sys.exit(1)
# Must have model
if model is None:
logger.log('Error: Imported file must contain model definition.')
sys.exit(1)
else:
logger.log('Model read successfully')
# Export model or runnable
if exporter.supports_model():
# Export model
logger.log('Exporting model')
exporter.model(target, model)
else:
# Export runnable
logger.log('Exporting runnable')
if protocol is None:
logger.log('No protocol found.')
else:
logger.log('Using embedded protocol.')
exporter.runnable(target, model, protocol)
logger.log_flair('Export successful')
logger.log(exporter.info())