def evaluate(expression):
"""
Evaluates an expression in mmt syntax.
"""
import myokit
try:
e = myokit.parse_expression(expression)
e = e.eval() if e.is_literal() else e
print(expression + ' = ' + str(e))
except myokit.ParseError as ex:
print(myokit.format_parse_error(ex, iter([expression])))
def test_model_creation(self):
m = myokit.load_model(os.path.join(DIR_DATA, 'lr-1991.mmt'))
# Test components
self.assertEqual(len(m), 9)
self.assertIn('engine', m)
self.assertIn('membrane', m)
self.assertIn('cell', m)
self.assertIn('ina', m)
self.assertIn('ik1', m)
self.assertIn('ica', m)
self.assertIn('ib', m)
self.assertIn('ik', m)
self.assertIn('ikp', m)
# Test state
states = [
'membrane.V', 'ina.m', 'ina.h', 'ina.j', 'ica.d', 'ica.f', 'ik.x',
'ica.Ca_i'
]
values = [
-84.5286, 0.0017, 0.9832, 0.995484, 0.000003, 1, 0.0057, 0.0002
]
out = ', '.join([str(x) for x in m.states()])
ref = ', '.join(states)
self.assertEqual(ref, out)
for k, eq in enumerate(m.inits()):
self.assertEqual(eq.rhs.eval(), values[k])
# Test state parsing / setting
m.set_state(values)
for k, eq in enumerate(m.inits()):
self.assertEqual(eq.rhs.eval(), values[k])
s = dict(zip(states, values))
m.set_state(s)
for k, eq in enumerate(m.inits()):
self.assertEqual(eq.rhs.eval(), values[k])
s = '\n'.join([str(a) + '=' + str(b) for a, b in s.items()])
m.set_state(s)
for k, eq in enumerate(m.inits()):
self.assertEqual(eq.rhs.eval(), values[k])
# Test cloning
try:
m2 = m.clone()
except Exception as e:
s = m.code(line_numbers=True)
print('\n')
print(s)
print('-' * 80)
print(myokit.format_parse_error(e, s.splitlines()))
raise e
self.assertEqual(m.code(), m2.code())
def step(source, ref, ini, raw):
"""
Loads a model and evaluates the state vector derivatives.
"""
import sys
import myokit
# Parse reference file, if given
if ref and not raw:
print('Reading reference file...')
try:
ref = myokit.load_model(ref[0])
print('Reference model loaded successfully.')
except Exception:
ref = myokit.load_state(ref[0])
print('Reference file read successfully.')
# Parse initial value file, if given
if ini:
if not raw:
print('Reading initial value file...')
ini = myokit.load_state(ini[0])
if not raw:
print('Initial value file read successfully.')
# Load myokit model
try:
if not raw:
print('Reading model from ' + source + '...')
model = myokit.load_model(source)
if not raw:
print('Model ' + model.name() + ' read successfully.')
except myokit.ParseError as ex:
print(myokit.format_parse_error(ex, source))
sys.exit(1)
# Ensure proper ordering of reference and initial value files
if ref and not isinstance(ref, myokit.Model):
ref = model.map_to_state(ref)
# Evaluate all derivatives, show the results
try:
if raw:
derivs = model.eval_state_derivatives(state=ini)
print('\n'.join([myokit.strfloat(x) for x in derivs]))
else:
print(myokit.step(model, initial=ini, reference=ref))
except myokit.NumericalError as ee:
e = 'Numerical error'
n = line_width - len(e) - 2
print('-' * int(n / 2) + ' ' + e + ' ' + '-' * (n - int(n / 2)))
print('A numerical error occurred:')
print(str(ee))
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())
def _parse(self, path, model):
"""
Parses a ChannelML channel and adds it to the given model.
Returns the new :class:`myokit.Component`.
"""
# Check model: get membrane potential varialbe
vvar = model.label('membrane_potential')
if vvar is None:
raise ChannelMLError(
'No variable labelled "membrane_potential" was found. This is'
' required when adding ChannelML channels to existing models.')
# Parse XML
path = os.path.abspath(os.path.expanduser(path))
dom = xml.dom.minidom.parse(path)
# Get channelml tag
root = dom.getElementsByTagName('channelml')
try:
root = root[0]
except IndexError:
raise ChannelMLError(
'Unknown root element in xml document. Expecting a tag of type'
' <channelml>.')
# Extract meta data
meta = self._rip_meta(root)
# Get channeltype tag
root = root.getElementsByTagName('channel_type')
try:
root = root[0]
except IndexError:
raise ChannelMLError(
'No <channel_type> element found inside <channelml> element.'
' Import of <synapse_type> and <ion_concentration> is not'
' supported.')
# Add channel component
name = self._sanitise_name(root.getAttribute('name'))
if name in model:
name_root = name
i = 2
while name in model:
name = name_root + '_' + str(i)
i += 1
component = model.add_component(name)
# Add alias to membrane potential
component.add_alias('v', vvar)
# Add meta-data
component.meta['desc'] = meta
# Find current-voltage relation
cvr = root.getElementsByTagName('current_voltage_relation')
if len(cvr) < 1:
raise ChannelMLError(
'Channel model must contain a current voltage relation.')
elif len(cvr) > 1:
warnings.warn(
'Multiple current voltage relations found, ignoring all but'
' first.')
cvr = cvr[0]
# Check for q10
try:
q10 = cvr.getElementsByTagName('q10_settings')[0]
component.meta['experimental_temperature'] = str(
q10.getAttribute('experimental_temp'))
except IndexError:
pass
# Add reversal potential
E = 0
if cvr.hasAttribute('default_erev'):
E = float(cvr.getAttribute('default_erev'))
evar = component.add_variable('E')
evar.meta['desc'] = 'Reversal potential'
evar.set_rhs(E)
# Get maximum conductance
gmax = 1.0
if cvr.hasAttribute('default_gmax'):
gmax = float(cvr.getAttribute('default_gmax'))
gmaxvar = component.add_variable('gmax')
gmaxvar.set_rhs(gmax)
gmaxvar.meta['desc'] = 'Maximum conductance'
# Add gates
gvars = []
for gate in cvr.getElementsByTagName('gate'):
gname = self._sanitise_name(gate.getAttribute('name'))
gvar = component.add_variable(gname)
gvar.promote(0)
cstate = gate.getElementsByTagName('closed_state')
cstate = cstate[0].getAttribute('id')
ostate = gate.getElementsByTagName('open_state')
ostate = ostate[0].getAttribute('id')
# Transitions
trans = gate.getElementsByTagName('transition')
if len(trans) > 0:
# Use "transitions" definition
if len(trans) != 2:
raise ChannelMLError(
'Expecting exactly 2 transitions for gate <' + gname +
'>.')
# Get closed-to-open state
tco = None
for t in trans:
if t.getAttribute('to') == ostate and \
t.getAttribute('from') == cstate:
tco = t
break
if tco is None:
raise ChannelMLError(
'Unable to find closed-to-open transition for gate <' +
gname + '>')
# Get open-to-closed state
toc = None
for t in trans:
if t.getAttribute('to') == cstate and \
t.getAttribute('from') == ostate:
toc = t
break
if toc is None:
raise ChannelMLError(
'Unable to find open-to-closed transition for gate <' +
gname + '>')
# Add closed-to-open transition
tname = self._sanitise_name(tco.getAttribute('name'))
tcovar = gvar.add_variable(tname)
expr = str(tco.getAttribute('expr'))
try:
tcovar.set_rhs(self._parse_expression(expr, tcovar))
except myokit.ParseError as e:
warnings.warn('Error parsing expression for closed-to-open'
' transition in gate <' + gname + '>: ' +
myokit.format_parse_error(e))
tcovar.meta['expression'] = str(expr)
# Add open-to-closed transition
tname = self._sanitise_name(toc.getAttribute('name'))
tocvar = gvar.add_variable(tname)
expr = str(toc.getAttribute('expr'))
try:
tocvar.set_rhs(self._parse_expression(expr, tocvar))
except myokit.ParseError as e:
warnings.warn('Error parsing expression for open-to-closed'
' transition in gate <' + gname + '>: ' +
myokit.format_parse_error(e))
tocvar.meta['expression'] = str(expr)
# Write equation for gate
gvar.set_rhs(
Minus(Multiply(Name(tcovar), Minus(Number(1), Name(gvar))),
Multiply(Name(tocvar), Name(gvar))))
else:
# Use "steady-state & time_course" definition
ss = gate.getElementsByTagName('steady_state')
tc = gate.getElementsByTagName('time_course')
if len(ss) < 1 or len(tc) < 1:
raise ChannelMLError(
'Unable to find transitions or steady state and'
' time course for gate <' + gname + '>.')
ss = ss[0]
tc = tc[0]
# Add steady-state variable
ssname = self._sanitise_name(ss.getAttribute('name'))
ssvar = gvar.add_variable(ssname)
expr = str(ss.getAttribute('expr'))
try:
ssvar.set_rhs(self._parse_expression(expr, ssvar))
except myokit.ParseError as e:
warnings.warn(
'Error parsing expression for steady state in gate <' +
gname + '>: ' + myokit.format_parse_error(e))
ssvar.meta['expression'] = str(expr)
# Add time course variable
tcname = self._sanitise_name(tc.getAttribute('name'))
tcvar = gvar.add_variable(tcname)
expr = str(tc.getAttribute('expr'))
try:
tcvar.set_rhs(self._parse_expression(expr, tcvar))
except myokit.ParseError as e:
warnings.warn(
'Error parsing expression for time course in gate <' +
gname + '>: ' + myokit.format_parse_error(e))
tcvar.meta['expression'] = str(expr)
# Write expression for gate
gvar.set_rhs(
Divide(Minus(Name(ssvar), Name(gvar)), Name(tcvar)))
power = int(gate.getAttribute('instances'))
if power > 1:
gvars.append(Power(Name(gvar), Number(power)))
else:
gvars.append(Name(gvar))
if len(gvars) < 1:
raise ChannelMLError(
'Current voltage relation requires at least one gate.')
# Add current variable
ivar = component.add_variable('I')
ivar.meta['desc'] = 'Current'
expr = Name(gmaxvar)
while gvars:
expr = Multiply(expr, gvars.pop())
expr = Multiply(expr, Minus(Name(vvar), Name(evar)))
ivar.set_rhs(expr)
# Done, return component
return component
def test_format_parse_error(self):
"""
Test format_parse_error.
"""
# Test basic formatting, with and without source
bad = ' 5 + / 2'
try:
myokit.parse_expression(bad)
except myokit.ParseError as e:
# No source
self.assertEqual(
myokit.format_parse_error(e), '\n'.join([
'Syntax error',
' Unexpected token SLASH "/" expecting expression',
'On line 1 character 8',
]))
# List-of-strings source
self.assertEqual(
myokit.format_parse_error(e, source=[bad]), '\n'.join([
'Syntax error',
' Unexpected token SLASH "/" expecting expression',
'On line 1 character 8', ' 5 + / 2', ' ^'
]))
# File source
with TemporaryDirectory() as d:
path = d.path('mmt')
with open(path, 'w') as f:
f.write(bad + '\n')
myokit.format_parse_error(e, source=path),
'\n'.join([
'Syntax error',
' Unexpected token SLASH "/" expecting expression',
'On line 1 character 8', ' 5 + / 2', ' ^'
])
# Line doesn't exist in source
self.assertEqual(
myokit.format_parse_error(e, source=[]), '\n'.join([
'Syntax error',
' Unexpected token SLASH "/" expecting expression',
'On line 1 character 8',
]))
# Char doesn't exist in source
self.assertEqual(
myokit.format_parse_error(e, source=['x']), '\n'.join([
'Syntax error',
' Unexpected token SLASH "/" expecting expression',
'On line 1 character 8',
]))
# Very long lines
bad = ' 1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 100 + 1000 + 11'
bad += ' + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22'
bad += ' + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31'
# Error near start
error = '\n'.join([
'Syntax error',
' Unexpected token SLASH "/" expecting expression',
'On line 1 character 12',
' 1 + 2 + / 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 100 + 1000 + ..',
' ^',
])
b = bad[:12] + '/ ' + bad[12:]
try:
myokit.parse_expression(b)
except myokit.ParseError as e:
self.assertEqual(myokit.format_parse_error(e, source=[b]), error)
error = '\n'.join([
'Syntax error',
' Unexpected token SLASH "/" expecting expression',
'On line 1 character 83',
' ..+ 12 + 13 + 14 + 15 + / 16 + 17 + 18 + 19 + 20 + 21 + 22..',
' ^',
])
b = bad[:83] + '/ ' + bad[83:]
try:
myokit.parse_expression(b)
except myokit.ParseError as e:
self.assertEqual(myokit.format_parse_error(e, source=[b]), error)
error = '\n'.join([
'Syntax error',
' Unexpected token SLASH "/" expecting expression',
'On line 1 character 133',
' ..+ 21 + 22 + 23 + 24 + 25 + / 26 + 27 + 28 + 29 + 30 + 31',
' ^',
])
b = bad[:133] + '/ ' + bad[133:]
try:
myokit.parse_expression(b)
except myokit.ParseError as e:
self.assertEqual(myokit.format_parse_error(e, source=[b]), error)
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)