def test_progress_printer(self):
# Test basic functionality.
# Zero call
with myokit.tools.capture() as c:
p = myokit.ProgressPrinter()
self.assertTrue(p.update(0))
pattern1 = re.compile(
r'\[[0-9]{1}\.[0-9]{1} minutes\] [0-9]+(.[0-9])? % done')
lines = c.text().splitlines()
self.assertTrue(len(lines) > 0)
for line in lines:
self.assertTrue(pattern1.match(line))
# Normal call
with myokit.tools.capture() as c:
p = myokit.ProgressPrinter()
self.assertTrue(p.update(0.49))
pattern2 = re.compile(
r'\[[0-9]{1}\.[0-9]{1} minutes] [0-9]+(.[0-9])? % done,'
r' estimated [0-9]{1} seconds remaining')
lines = c.text().splitlines()
self.assertTrue(len(lines) > 0)
for line in lines:
self.assertTrue(pattern2.match(line))
# Call that will take minutes
with myokit.tools.capture() as c:
p = myokit.ProgressPrinter()
time.sleep(0.1)
self.assertTrue(p.update(1e-3))
self.assertIn('minutes remaining', c.text())
# Note: Printer must be created withing capture, otherwise it
# will print to stdout (which won't have been redirected yet).
# Status every ten percent
with myokit.tools.capture() as c:
p = myokit.ProgressPrinter(digits=-1)
self.assertTrue(p.update(0))
self.assertTrue(p.update(0.08))
self.assertTrue(p.update(0.18))
self.assertTrue(p.update(0.19))
self.assertTrue(p.update(0.199))
self.assertTrue(p.update(1))
lines = c.text().splitlines()
self.assertTrue(len(lines), 3)
self.assertTrue(pattern1.match(lines[0]))
self.assertTrue(pattern2.match(lines[1]))
self.assertTrue(pattern2.match(lines[2]))
def test_progress_reporter(self):
# Test running with a progress reporter.
# Test if it works
sim = myokit.Simulation(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_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 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))
def test_with_progress_reporter(self):
# Test running with a progress reporter.
m, p, _ = myokit.load(os.path.join(DIR_DATA, 'lr-1991.mmt'))
# Test using a progress reporter
s = myokit.Simulation1d(m, p, ncells=5)
s.set_step_size(0.05)
with myokit.PyCapture() 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))
def test_run_progress(self):
# Tests running with a progress reporter.
pass
# Run with a progress reporter
with myokit.tools.capture() as c:
self.s1.run(3, progress=myokit.ProgressPrinter())
self.assertTrue(c.text() != '')
# Cancel using a progress reporter
self.assertRaises(
myokit.SimulationCancelledError,
self.s1.run, 20, progress=CancellingReporter(0))
# Run with invalid progress reporter
try:
self.assertRaisesRegex(ValueError, 'subclass of myokit.ProgressR',
self.s1.run, 1, progress=12)
finally:
self.s1.reset()
def simulate_ohara_ap(drug=None, concentration=0, beats=2, cl=1):
"""
Generates APs with the O'Hara model.
"""
# Convert CL to milliseconds
cl *= 1000
# Load model
model = myokit.load_model('ohara-2011.mmt')
# Load protocol
protocol = myokit.pacing.blocktrain(period=cl, duration=0.5, offset=50)
# Add drug block scalings
scales = {}
def hill(x, ic50, h=1):
return 1 / (1 + (x / ic50)**h)
def add(current, x, ic50):
f = hill(x, ic50)
if current in scales:
scales[current] *= f
else:
scales[current] = f
# Add drug scales
if drug is None or drug == 'paracetamol':
pass
elif drug == 'dofetilide':
add('ikr.IKr', concentration, 5.2e-3)
add('ina.INa', concentration, 147.9)
add('ical.ICaL', concentration, 26.7)
add('iks.IKs', concentration, 415.8)
elif drug == 'quinidine':
add('ikr.IKr', concentration, 0.3)
add('ina.INa', concentration, 16.6)
add('ical.ICaL', concentration, 15.6)
elif drug == 'sotalol':
add('ikr.IKr', concentration, 111.4)
add('ina.INa', concentration, 7013.9)
add('ical.ICaL', concentration, 193.3)
elif drug == 'sotalol-okada':
add('ikr.IKr', concentration, 356.4)
#add('ina.INa', concentration, 7013.9)
#add('ical.ICaL', concentration, 193.3)
elif drug == 'verapamil':
add('ikr.IKr', concentration, 0.25)
add('ina.INa', concentration, 32.5)
add('ical.ICaL', concentration, 0.2)
else:
raise ValueError('Unknown drug: ' + str(drug))
# Apply scalings
for var, scale in scales.iteritems():
v = model.get(var)
v.set_rhs(myokit.Multiply(myokit.Number(scale), v.rhs()))
# Simulate with modified model
sim = myokit.Simulation(model, protocol)
# Pre-pace for some beats
p = myokit.ProgressPrinter()
sim.pre(100 * cl, progress=p)
# Log some beats
p = myokit.ProgressPrinter()
log = sim.run(beats * cl,
log=['engine.time', 'membrane.V'],
log_interval=DT * 1e3,
progress=p).npview()
# Convert to seconds and volts
log['engine.time'] *= 1e-3
log['membrane.V'] *= 1e-3
# Return
return log
