def test_benchmarker(self):
# Test the benchmarker.
b = myokit.Benchmarker()
x = [0] * 1000
t0 = b.time()
self.assertTrue(t0 >= 0)
x = [0] * 1000
t1 = b.time()
self.assertTrue(t1 >= t0)
x = [0] * 1000
t2 = b.time()
self.assertTrue(t2 >= t1)
for i in range(1000):
x = [0] * 1000
t3 = b.time()
self.assertTrue(t3 >= t2)
b.reset()
t4 = b.time()
self.assertTrue(t4 < t3)
self.assertEqual(b.format(1), '1 second')
self.assertEqual(b.format(61), '1 minute, 1 second')
self.assertEqual(b.format(60), '1 minute, 0 seconds')
self.assertEqual(b.format(180), '3 minutes, 0 seconds')
self.assertEqual(b.format(3600), '1 hour, 0 minutes, 0 seconds')
self.assertEqual(b.format(3661), '1 hour, 1 minute, 1 second')
self.assertEqual(b.format(3600 * 24),
'1 day, 0 hours, 0 minutes, 0 seconds')
self.assertEqual(b.format(3600 * 24 * 7),
'1 week, 0 days, 0 hours, 0 minutes, 0 seconds')
def enter(self, msg=None):
self.b = myokit.Benchmarker()
def test_benchmarker(self):
# Deprecated alias of myokit.tools.Benchmarker
with WarningCollector() as c:
b = myokit.Benchmarker()
self.assertIn('`myokit.Benchmarker` is deprecated', c.text())
self.assertIsInstance(b, myokit.tools.Benchmarker)
def __init__(self, digits=1):
super(ProgressPrinter, self).__init__()
self._b = myokit.Benchmarker()
self._f = None
self._d = int(digits)
def fixed_form_pacing_ansic(self):
"""
Tests the Ansi-C fixed-form pacing system.
"""
if False:
# Graphical test, just for playing with the pacing system
m, p, x = myokit.load('example')
s = myokit.Simulation(m, p)
d = s.run(500).npview()
# Get time and voltage
t = d.time()
v = d['membrane.V']
# Plot trace
import matplotlib.pyplot as pl
pl.figure()
pl.plot(t, v, 'x')
# Get some points halfway, 1/4 of the way, and 3/4 of the way
# between the known points
t2 = t[:-1] + 0.25 * (t[1:] - t[:-1])
t3 = t[:-1] + 0.5 * (t[1:] - t[:-1])
t4 = t[:-1] + 0.75 * (t[1:] - t[:-1])
t2 = np.concatenate((t2, t3, t4))
del (t3, t4)
# Get the pacing value at the points, measure how long it takes
pacing = myotest.AnsicFixedFormPacing(list(t), list(v))
b = myokit.Benchmarker()
v2 = [pacing.pace(x) for x in t2]
print(b.time())
# Plot the new points
pl.plot(t2, v2, '.', color='green')
pl.show()
# Quite
import sys
sys.exit(1)
# Test input checking
times = 1
values = [1, 2]
self.assertRaises(Exception, myotest.AnsicFixedFormPacing)
self.assertRaises(Exception, myotest.AnsicFixedFormPacing, 1)
self.assertRaises(Exception, myotest.AnsicFixedFormPacing, 1, 2)
self.assertRaises(Exception, myotest.AnsicFixedFormPacing, [1], [2])
self.assertRaises(Exception, myotest.AnsicFixedFormPacing, [1, 2], [2])
self.assertRaises(Exception, myotest.AnsicFixedFormPacing, [2, 1],
[2, 2])
myotest.AnsicFixedFormPacing([1, 2], [1, 2])
# Test with small lists
values = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]
times = [0, 0, 1, 1, 1, 2, 2, 2, 3, 4, 5, 7]
values = range(len(times))
pacing = myotest.AnsicFixedFormPacing(times, values)
def test(value, index):
self.assertEquals(pacing.pace(value), index)
test(-1, 0)
test(0, 1)
test(1, 2)
test(2, 5)
test(3, 8)
test(4, 9)
test(5, 10)
test(7, 11)
test(8, 11)
test(1.5, 4.5)
test(1.75, 4.75)
test(6, 10.5)
test(5.5, 10.25)
def run(source, debug, debugfile):
"""
Runs an mmt file script.
"""
import sys
import myokit
# Debug?
myokit.DEBUG = myokit.DEBUG or debug or debugfile
# Read mmt file
try:
print('Reading model from ' + source)
b = myokit.Benchmarker()
(model, protocol, script) = myokit.load(source)
print('File loaded in ' + str(b.time()) + ' seconds')
if model is None:
print('No model definition found')
else:
print('Model read successfully')
print(model.format_warnings())
model.solvable_order()
except myokit.ParseError as ex:
print(myokit.format_parse_error(ex, source))
sys.exit(1)
# Set up pacing protocol
if protocol is None:
print('No protocol definition found')
print('Preparing default pacing protocol (1ms stimulus, 1bpm)')
protocol = myokit.pacing.blocktrain(1000, 1)
# Set up script
if script is None:
if model is None:
print('No script or model found, terminating')
sys.exit(1)
else:
print('No embedded script found, using default.')
script = myokit.default_script()
else:
print('Using embedded script')
# Run, capture output and write to file
if debugfile:
debugfile = debugfile[0]
with open(debugfile, 'w') as f:
stdout = sys.stdout
try:
sys.stdout = f
line_numbers = myokit.DEBUG_LINE_NUMBERS
myokit.DEBUG_LINE_NUMBERS = False
myokit.run(model, protocol, script)
except SystemExit:
pass
finally:
sys.stdout = stdout
myokit.DEBUG_LINE_NUMBERS = line_numbers
print('Output written to ' + str(debugfile))
else:
# Show script
printline()
lines = script.splitlines()
template = '{:>3d} {:s}'
i = 0
for line in lines:
i += 1
print(template.format(i, line))
printline()
# Run!
myokit.run(model, protocol, script)
