def unused_and_cycles(self):
"""
Test unused variable and cycle detection.
"""
m = Model('LotkaVolterra')
c0 = m.add_component('c0')
t = c0.add_variable('time')
t.set_rhs(Number(0))
t.set_binding('time')
c1 = m.add_component('c1')
m.add_component('c2')
c1_a = c1.add_variable('a')
c1_b = c1.add_variable('b')
c1_a.promote(1.0)
c1_a.set_rhs(Multiply(Name(c1_a), Number(0.5)))
c1_b.set_rhs(Multiply(Name(c1_a), Number(1.0)))
# b is unused, test if found
m.validate()
w = m.warnings()
self.assertEqual(len(w), 1)
self.assertEqual(type(w[0]), UnusedVariableError)
# b is used by c, c is unused, test if found
c1_c = c1.add_variable('c')
c1_c.set_rhs(Name(c1_b))
m.validate()
w = m.warnings()
self.assertEqual(len(w), 2)
self.assertEqual(type(w[0]), UnusedVariableError)
self.assertEqual(type(w[1]), UnusedVariableError)
# Test 1:1 cycle
c1_b.set_rhs(Name(c1_b))
self.assertRaises(CyclicalDependencyError, m.validate)
# Test longer cycles
c1_b.set_rhs(Multiply(Number(10), Name(c1_c)))
self.assertRaises(CyclicalDependencyError, m.validate)
# Reset
c1_b.set_rhs(Multiply(Name(c1_a), Number(1.0)))
m.validate()
# Test cycle involving state variable
c1_a.set_rhs(Name(c1_b))
m.validate()
c1_b.set_rhs(Multiply(Name(c1_a), Name(c1_b)))
self.assertRaises(CyclicalDependencyError, m.validate)
c1_b.set_rhs(Multiply(Name(c1_a), Name(c1_c)))
c1_c.set_rhs(Multiply(Name(c1_a), Number(3)))
m.validate()
w = m.warnings()
self.assertEqual(len(w), 0)
c1_c.set_rhs(Multiply(Name(c1_a), Name(c1_b)))
self.assertRaises(CyclicalDependencyError, m.validate)
def move_variable(self):
"""
Tests the method to move component variables to another component.
"""
# Create a model
m = Model('LotkaVolterra')
X = m.add_component('X')
a = X.add_variable('a')
a.set_rhs(3)
b = X.add_variable('b')
b1 = b.add_variable('b1')
b2 = b.add_variable('b2')
b1.set_rhs(1)
b2.set_rhs(Minus(Minus(Name(a), Name(b1)), Number(1)))
b.set_rhs(Plus(Name(b1), Name(b2)))
x = X.add_variable('x')
x.promote()
Y = m.add_component('Y')
c = Y.add_variable('c')
c.set_rhs(Minus(Name(a), Number(1)))
d = Y.add_variable('d')
d.set_rhs(2)
y = Y.add_variable('y')
y.promote()
x.set_rhs(
Minus(Multiply(Name(a), Name(x)),
Multiply(Multiply(Name(b), Name(x)), Name(y))))
x.set_state_value(10)
y.set_rhs(
Plus(Multiply(PrefixMinus(Name(c)), Name(y)),
Multiply(Multiply(Name(d), Name(x)), Name(y))))
y.set_state_value(5)
Z = m.add_component('Z')
t = Z.add_variable('total')
t.set_rhs(Plus(Name(x), Name(y)))
E = m.add_component('engine')
time = E.add_variable('time')
time.set_rhs(0)
time.set_binding('time')
# Move time variable into X
m.validate() # If not valid, this will raise an exception
E.move_variable(time, Z)
m.validate()
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 model_creation(self):
# Create a model
m = Model('LotkaVolterra')
# Add the first component
X = m.add_component('X')
self.assertEqual(X.qname(), 'X')
self.assertEqual(X.parent(), m)
self.assertIsInstance(X, Component)
self.assertIn(X.qname(), m)
self.assertEqual(len(m), 1)
# Add variable a
a = X.add_variable('a')
self.assertEqual(a, a)
self.assertIsInstance(a, Variable)
self.assertEqual(len(X), 1)
self.assertIn(a.name(), X)
a.set_rhs(3)
self.assertFalse(a.is_state())
self.assertFalse(a.is_intermediary())
self.assertTrue(a.is_constant())
self.assertEqual(a.lhs(), Name(a))
self.assertEqual(a.rhs(), Number(3))
self.assertEqual(a.rhs().eval(), 3)
self.assertEqual(a.code(), 'a = 3\n')
self.assertEqual(a.eq().code(), 'X.a = 3')
self.assertEqual(a.lhs().code(), 'X.a')
self.assertEqual(a.rhs().code(), '3')
self.assertEqual(a.eq(), Equation(Name(a), Number(3)))
# Check lhs
a_name1 = myokit.Name(a)
a_name2 = myokit.Name(a)
self.assertEqual(a_name1, a_name1)
self.assertEqual(a_name2, a_name2)
self.assertEqual(a_name1, a_name2)
self.assertEqual(a_name2, a_name1)
# Add variable b with two temporary variables
b = X.add_variable('b')
self.assertIsInstance(b, Variable)
self.assertEqual(len(X), 2)
self.assertIn(b.name(), X)
b1 = b.add_variable('b1')
self.assertEqual(len(b), 1)
self.assertIn(b1.name(), b)
self.assertIsInstance(b1, Variable)
b2 = b.add_variable('b2')
self.assertEqual(len(b), 2)
self.assertIn(b2.name(), b)
self.assertIsInstance(b2, Variable)
b1.set_rhs(1)
b2.set_rhs(Minus(Minus(Name(a), Name(b1)), Number(1)))
b.set_rhs(Plus(Name(b1), Name(b2)))
self.assertEqual(b.rhs().eval(), 2)
self.assertFalse(b.is_state())
self.assertFalse(b.is_intermediary())
self.assertTrue(b.is_constant())
self.assertEqual(b.lhs(), Name(b))
# Add state variable x
x = X.add_variable('x')
x.set_rhs(10)
x.promote()
self.assertNotEqual(x, X)
self.assertIsInstance(x, Variable)
self.assertEqual(len(X), 3)
self.assertIn(x.name(), X)
self.assertTrue(x.is_state())
self.assertFalse(x.is_intermediary())
self.assertFalse(x.is_constant())
self.assertEqual(x.lhs(), Derivative(Name(x)))
# Test demoting, promoting
x.demote()
self.assertFalse(x.is_state())
self.assertFalse(x.is_intermediary())
self.assertTrue(x.is_constant())
self.assertEqual(x.lhs(), Name(x))
x.promote()
self.assertTrue(x.is_state())
self.assertFalse(x.is_intermediary())
self.assertFalse(x.is_constant())
self.assertEqual(x.lhs(), Derivative(Name(x)))
x.demote()
x.promote()
x.demote()
x.promote()
self.assertTrue(x.is_state())
self.assertFalse(x.is_intermediary())
self.assertFalse(x.is_constant())
self.assertEqual(x.lhs(), Derivative(Name(x)))
# Add second component, variables
Y = m.add_component('Y')
self.assertNotEqual(X, Y)
self.assertEqual(len(m), 2)
c = Y.add_variable('c')
c.set_rhs(Minus(Name(a), Number(1)))
d = Y.add_variable('d')
d.set_rhs(2)
y = Y.add_variable('y')
y.promote()
# Set rhs for x and y
x.set_rhs(
Minus(Multiply(Name(a), Name(x)),
Multiply(Multiply(Name(b), Name(x)), Name(y))))
x.set_state_value(10)
self.assertEqual(x.rhs().code(), 'X.a * X.x - X.b * X.x * Y.y')
y.set_rhs(
Plus(Multiply(PrefixMinus(Name(c)), Name(y)),
Multiply(Multiply(Name(d), Name(x)), Name(y))))
y.set_state_value(5)
self.assertEqual(y.rhs().code(), '-Y.c * Y.y + Y.d * X.x * Y.y')
# Add another component, variables
Z = m.add_component('Z')
self.assertNotEqual(X, Z)
self.assertNotEqual(Y, Z)
self.assertEqual(len(m), 3)
t = Z.add_variable('total')
self.assertEqual(t.name(), 'total')
self.assertEqual(t.qname(), 'Z.total')
self.assertEqual(t.qname(X), 'Z.total')
self.assertEqual(t.qname(Z), 'total')
t.set_rhs(Plus(Name(x), Name(y)))
self.assertFalse(t.is_state())
self.assertFalse(t.is_constant())
self.assertTrue(t.is_intermediary())
self.assertEqual(t.rhs().code(), 'X.x + Y.y')
self.assertEqual(t.rhs().code(X), 'x + Y.y')
self.assertEqual(t.rhs().code(Y), 'X.x + y')
self.assertEqual(t.rhs().code(Z), 'X.x + Y.y')
# Add engine component
E = m.add_component('engine')
self.assertNotEqual(X, E)
self.assertNotEqual(Y, E)
self.assertNotEqual(Z, E)
self.assertEqual(len(m), 4)
time = E.add_variable('time')
time.set_rhs(0)
self.assertIsNone(time.binding())
time.set_binding('time')
self.assertIsNotNone(time.binding())
# Check state
state = [i for i in m.states()]
self.assertEqual(len(state), 2)
self.assertIn(x, state)
self.assertIn(y, state)
# Test variable iterators
def has(*v):
for var in v:
self.assertIn(var, vrs)
self.assertEqual(len(vrs), len(v))
vrs = [i for i in m.variables()]
has(a, b, c, d, x, y, t, time)
vrs = [i for i in m.variables(deep=True)]
has(a, b, c, d, x, y, t, b1, b2, time)
vrs = [i for i in m.variables(const=True)]
has(a, b, c, d)
vrs = [i for i in m.variables(const=True, deep=True)]
has(a, b, c, d, b1, b2)
vrs = [i for i in m.variables(const=False)]
has(x, y, t, time)
vrs = [i for i in m.variables(const=False, deep=True)]
has(x, y, t, time)
vrs = [i for i in m.variables(state=True)]
has(x, y)
vrs = [i for i in m.variables(state=True, deep=True)]
has(x, y)
vrs = [i for i in m.variables(state=False)]
has(a, b, c, d, t, time)
vrs = [i for i in m.variables(state=False, deep=True)]
has(a, b, c, d, t, b1, b2, time)
vrs = [i for i in m.variables(inter=True)]
has(t)
vrs = [i for i in m.variables(inter=True, deep=True)]
has(t)
vrs = [i for i in m.variables(inter=False)]
has(a, b, c, d, x, y, time)
vrs = [i for i in m.variables(inter=False, deep=True)]
has(a, b, c, d, x, y, b1, b2, time)
vrs = [i for i in m.variables(const=True, state=True)]
has()
vrs = [i for i in m.variables(const=True, state=False)]
has(a, b, c, d)
# Test equation iteration
eq = [eq for eq in X.equations(deep=False)]
self.assertEqual(len(eq), 3)
eq = [eq for eq in X.equations(deep=True)]
self.assertEqual(len(eq), 5)
eq = [eq for eq in Y.equations(deep=False)]
self.assertEqual(len(eq), 3)
eq = [eq for eq in Y.equations(deep=True)]
self.assertEqual(len(eq), 3)
eq = [eq for eq in Z.equations(deep=False)]
self.assertEqual(len(eq), 1)
eq = [eq for eq in Z.equations(deep=True)]
self.assertEqual(len(eq), 1)
eq = [eq for eq in E.equations(deep=False)]
self.assertEqual(len(eq), 1)
eq = [eq for eq in E.equations(deep=True)]
self.assertEqual(len(eq), 1)
eq = [eq for eq in m.equations(deep=False)]
self.assertEqual(len(eq), 8)
eq = [eq for eq in m.equations(deep=True)]
self.assertEqual(len(eq), 10)
# Test dependency mapping
def has(var, *dps):
lst = vrs[m.get(var).lhs() if type(var) == str else var]
self.assertEqual(len(lst), len(dps))
for d in dps:
d = m.get(d).lhs() if type(d) == str else d
self.assertIn(d, lst)
vrs = m.map_shallow_dependencies(omit_states=False)
self.assertEqual(len(vrs), 12)
has('X.a')
has('X.b', 'X.b.b1', 'X.b.b2')
has('X.b.b1')
has('X.b.b2', 'X.a', 'X.b.b1')
has('X.x', 'X.a', 'X.b', Name(x), Name(y))
has(Name(x))
has('Y.c', 'X.a')
has('Y.d')
has('Y.y', 'Y.c', 'Y.d', Name(x), Name(y))
has(Name(y))
has('Z.total', Name(x), Name(y))
vrs = m.map_shallow_dependencies()
self.assertEqual(len(vrs), 10)
has('X.a')
has('X.b', 'X.b.b1', 'X.b.b2')
has('X.b.b1')
has('X.b.b2', 'X.a', 'X.b.b1')
has('X.x', 'X.a', 'X.b')
has('Y.c', 'X.a')
has('Y.d')
has('Y.y', 'Y.c', 'Y.d')
has('Z.total')
vrs = m.map_shallow_dependencies(collapse=True)
self.assertEqual(len(vrs), 8)
has('X.a')
has('X.b', 'X.a')
has('X.x', 'X.a', 'X.b')
has('Y.c', 'X.a')
has('Y.d')
has('Y.y', 'Y.c', 'Y.d')
has('Z.total')
# Validate
m.validate()
# Get solvable order
order = m.solvable_order()
self.assertEqual(len(order), 5)
self.assertIn('*remaining*', order)
self.assertIn('X', order)
self.assertIn('Y', order)
self.assertIn('Z', order)
# Check that X comes before Y
pos = dict([(name, k) for k, name in enumerate(order)])
self.assertLess(pos['X'], pos['Y'])
self.assertEqual(pos['*remaining*'], 4)
# Check component equation lists
eqs = order['*remaining*']
self.assertEqual(len(eqs), 0)
eqs = order['Z']
self.assertEqual(len(eqs), 1)
self.assertEqual(eqs[0].code(), 'Z.total = X.x + Y.y')
eqs = order['Y']
self.assertEqual(len(eqs), 3)
self.assertEqual(eqs[2].code(),
'dot(Y.y) = -Y.c * Y.y + Y.d * X.x * Y.y')
eqs = order['X']
self.assertEqual(len(eqs), 5)
self.assertEqual(eqs[0].code(), 'X.a = 3')
self.assertEqual(eqs[1].code(), 'b1 = 1')
self.assertEqual(eqs[2].code(), 'b2 = X.a - b1 - 1')
self.assertEqual(eqs[3].code(), 'X.b = b1 + b2')
# Test model export and cloning
code1 = m.code()
code2 = m.clone().code()
self.assertEqual(code1, code2)
def remove_variable(self):
"""
Tests the removal of a variable.
"""
# Create a model
m = Model('LotkaVolterra')
# Add a variable 'a'
X = m.add_component('X')
# Simplest case
a = X.add_variable('a')
self.assertEqual(X.count_variables(), 1)
X.remove_variable(a)
self.assertEqual(X.count_variables(), 0)
self.assertRaises(Exception, X.remove_variable, a)
# Test re-adding
a = X.add_variable('a')
a.set_rhs(Number(5))
self.assertEqual(X.count_variables(), 1)
# Test deleting dependent variables
b = X.add_variable('b')
self.assertEqual(X.count_variables(), 2)
b.set_rhs(Plus(Number(3), Name(a)))
# Test blocking of removal
self.assertRaises(IntegrityError, X.remove_variable, a)
self.assertEqual(X.count_variables(), 2)
# Test removal in the right order
X.remove_variable(b)
self.assertEqual(X.count_variables(), 1)
X.remove_variable(a)
self.assertEqual(X.count_variables(), 0)
# Test reference to current state variable values
a = X.add_variable('a')
a.set_rhs(Number(5))
a.promote()
b = X.add_variable('b')
b.set_rhs(Plus(Number(3), Name(a)))
self.assertRaises(IntegrityError, X.remove_variable, a)
X.remove_variable(b)
X.remove_variable(a)
self.assertEqual(X.count_variables(), 0)
# Test reference to current state variable values with "self"-ref
a = X.add_variable('a')
a.promote()
a.set_rhs(Name(a))
X.remove_variable(a)
# Test it doesn't interfere with normal workings
a = X.add_variable('a')
a.promote()
a.set_rhs(Name(a))
b = X.add_variable('b')
b.set_rhs(Name(a))
self.assertRaises(IntegrityError, X.remove_variable, a)
X.remove_variable(b)
X.remove_variable(a)
# Test reference to dot
a = X.add_variable('a')
a.set_rhs(Number(5))
a.promote()
b = X.add_variable('b')
b.set_rhs(Derivative(Name(a)))
self.assertRaises(IntegrityError, X.remove_variable, a)
X.remove_variable(b)
X.remove_variable(a)
# Test if orphaned
self.assertIsNone(b.parent())
# Test deleting variable with nested variables
a = X.add_variable('a')
b = a.add_variable('b')
b.set_rhs(Plus(Number(2), Number(2)))
a.set_rhs(Multiply(Number(3), Name(b)))
self.assertRaises(IntegrityError, X.remove_variable, a)
self.assertEqual(a.count_variables(), 1)
self.assertEqual(X.count_variables(), 1)
# Test recursive deleting
X.remove_variable(a, recursive=True)
self.assertEqual(a.count_variables(), 0)
self.assertEqual(X.count_variables(), 0)
# Same with dot(a) = a, b = 3 * a
a = X.add_variable('a')
a.promote(0.123)
b = a.add_variable('b')
b.set_rhs(Multiply(Number(3), Name(a)))
a.set_rhs(Name(b))
self.assertRaises(IntegrityError, X.remove_variable, a)
self.assertRaises(IntegrityError, a.remove_variable, b)
self.assertRaises(IntegrityError, a.remove_variable, b, True)
X.remove_variable(a, recursive=True)