def test_csymbol(self):
# Test csymbol parsing
# A csymbol MathML's way to define extensions, e.g. functions or
# operators or symbols not defined in MathML. In Myokit we only
# support their use as a type of <ci>.
self.assertEqual(
self.p('<csymbol definitionURL="hello" />'),
myokit.Name('hello')
)
# Missing definition url
self.assertRaisesRegex(
mathml.MathMLError, 'must contain a definitionURL attribute',
self.p, '<csymbol>Hiya</csymbol>')
# Unknown variable
d = {'a': myokit.Name('a')}
p = mathml.MathMLParser(
lambda x, y: d[x],
lambda x, y: myokit.Number(x),
)
x = etree.fromstring('<csymbol definitionURL="a" />')
self.assertEqual(p.parse(x), myokit.Name('a'))
x = etree.fromstring('<csymbol definitionURL="b" />')
self.assertRaisesRegex(
mathml.MathMLError, 'Unable to create Name from csymbol',
p.parse, x)
def _add_dose_compartment(model, drug_amount, time_unit):
"""
Adds a dose compartment to the model with a linear absorption rate to
the connected compartment.
"""
# Add a dose compartment to the model
dose_comp = model.add_component_allow_renaming('dose')
# Create a state variable for the drug amount in the dose compartment
dose_drug_amount = dose_comp.add_variable('drug_amount')
dose_drug_amount.set_rhs(0)
dose_drug_amount.set_unit(drug_amount.unit())
dose_drug_amount.promote()
# Create an absorption rate variable
absorption_rate = dose_comp.add_variable('absorption_rate')
absorption_rate.set_rhs(1)
absorption_rate.set_unit(1 / time_unit)
# Add outflow expression to dose compartment
dose_drug_amount.set_rhs(
myokit.Multiply(myokit.PrefixMinus(myokit.Name(absorption_rate)),
myokit.Name(dose_drug_amount)))
# Add inflow expression to connected compartment
rhs = drug_amount.rhs()
drug_amount.set_rhs(
myokit.Plus(
rhs,
myokit.Multiply(myokit.Name(absorption_rate),
myokit.Name(dose_drug_amount))))
return dose_drug_amount
def equal(self):
"""
Test of __eq__ operators
"""
a1 = myokit.Number(4)
a2 = myokit.Number(5)
self.assertEqual(a1, a1)
self.assertEqual(a1, myokit.Number(4))
self.assertEqual(a1, myokit.Number(4.0))
self.assertNotEqual(a1, a2)
b1 = myokit.Name('test')
b2 = myokit.Name('tost')
self.assertEqual(b1, b1)
self.assertNotEqual(b1, b2)
c1 = myokit.PrefixPlus(a1)
c2 = myokit.PrefixPlus(a1)
self.assertEqual(c1, c1)
self.assertEqual(c1, c2)
c2 = myokit.PrefixPlus(a2)
self.assertNotEqual(c1, c2)
d1 = myokit.Plus(a1, a2)
d2 = myokit.Plus(a1, a2)
self.assertEqual(d1, d1)
self.assertEqual(d1, d2)
d2 = myokit.Plus(a2, a1)
self.assertNotEqual(d2, d1)
e1 = myokit.Sqrt(a1)
e2 = myokit.Sqrt(a1)
self.assertEqual(e1, e1)
self.assertEqual(e1, e2)
e2 = myokit.Sqrt(a2)
self.assertNotEqual(e1, e2)
def test_promote_demote(self):
# Test variable promotion and demotion.
m = myokit.Model()
c = m.add_component('c')
v = c.add_variable('v')
v.set_rhs(3)
self.assertTrue(v.is_literal())
self.assertTrue(v.is_constant())
self.assertFalse(v.is_intermediary())
self.assertFalse(v.is_state())
self.assertEqual(v.lhs(), myokit.Name(v))
self.assertRaises(Exception, v.demote)
self.assertRaises(Exception, v.indice)
self.assertRaises(Exception, v.state_value)
v.promote(3)
self.assertFalse(v.is_literal())
self.assertFalse(v.is_constant())
self.assertFalse(v.is_intermediary())
self.assertTrue(v.is_state())
self.assertEqual(v.lhs(), myokit.Derivative(myokit.Name(v)))
self.assertEqual(v.indice(), 0)
self.assertEqual(v.state_value(), 3)
v.demote()
self.assertTrue(v.is_literal())
self.assertTrue(v.is_constant())
self.assertFalse(v.is_intermediary())
self.assertFalse(v.is_state())
self.assertEqual(v.lhs(), myokit.Name(v))
self.assertRaises(Exception, v.demote)
self.assertRaises(Exception, v.indice)
self.assertRaises(Exception, v.state_value)
# Test errors
v.promote(3)
self.assertRaisesRegex(Exception, 'already', v.promote, 4)
v.demote()
v.set_binding('time')
self.assertRaisesRegex(Exception, 'cannot be bound', v.promote, 4)
w = v.add_variable('w')
self.assertRaisesRegex(
Exception, 'only be added to Components', w.promote, 4)
# Test we can't demote a variable with references to its derivative
m = myokit.Model()
c = m.add_component('c')
x = c.add_variable('x')
x.set_rhs(3)
x.promote()
y = c.add_variable('y')
y.set_rhs('1 + dot(x)')
self.assertRaisesRegex(
Exception, 'references to its derivative', x.demote)
y.set_rhs('1 + x')
x.demote()
def create_dimless_tumour_growth_model():
r"""
Returns a tumour growth myokit model.
.. math::
\frac{\text{d}v}{\text{d}\tau} = \frac{a_1 v}
{v + a_0},
where the tumour volume :math:`v` and time :math:`\tau` are dimensionless
and measured in characteristic scales :math:`V^c_T` and :math:`t^c`.
The model parameters :math:`a_0` and :math:`a_1` are also dimensionless.
"""
# Instantiate model
model = Model()
# Add central compartment
central_comp = model.add_compartment('central')
# Add tumour growth variables to central compartment
volume_t = central_comp.add_variable('volume_t')
a_0 = central_comp.add_variable('a_0')
a_1 = central_comp.add_variable('a_1')
# Bind time
time = central_comp.add_variable('time')
time.set_binding('time')
# Set intial values (some default values) and units
time.set_rhs(0)
volume_t.set_rhs(0)
a_0.set_rhs(1) # Avoid ZeroDivisionError
a_1.set_rhs(0)
# Set units
time.set_unit('dimensionless')
volume_t.set_unit('dimensionless')
a_0.set_unit('dimensionless')
a_1.set_unit('dimensionless')
# Set rhs of tumor volume
# dot(volume_t) =
# (a_1 * volume_t) /
# (volume_t + a_0)
volume_t.promote()
volume_t.set_rhs(
myokit.Divide(myokit.Multiply(myokit.Name(a_1), myokit.Name(volume_t)),
myokit.Plus(myokit.Name(volume_t), myokit.Name(a_0))))
# Validate model
model.validate()
# Check units
model.check_units()
return model
def setUpClass(cls):
# Create a model with a variable
cls._model = myokit.Model()
component = cls._model.add_component('c')
bvar = component.add_variable('b')
bvar.set_rhs(1.23)
avar = component.add_variable('a')
avar.set_rhs('b')
cls._a = myokit.Name(avar)
cls._b = myokit.Name(bvar)
def _ex_name(self, e):
var = str(e)
# Check if this is a derivative
# See :meth:`SymPyExpressionWriter._ex_derivative()`.
if self._model:
if var[:4] == 'dot(' and var[-1:] == ')':
var = self._model.get(var[4:-1], myokit.Variable)
return myokit.Derivative(myokit.Name(var))
var = self._model.get(var, myokit.Variable)
return myokit.Name(var)
def fit(self, model, var, rng, report=None):
"""
Attempts to approximate suitable functions in the given model.
A variable ``var`` must be specified, as well as the range ``rng`` that
this variable is likely to take. A typical example would be the
variable ``membrane.V`` and the range ``(-100, 50)``.
The variable can be specified as a name (string), an object
representing a variable or an LhsExpression.
The range can be specified as any sequence type of length 2.
If the variable ``report`` is set, a small HTML based report will be
generated and stored in the directory indicated by ``report``.
"""
# Copy model
self.original_model = model
model = model.clone()
# Get left-hand side expression for variable
if isinstance(var, myokit.LhsExpression):
if isinstance(var, myokit.Derivative):
raise ValueError('Cannot fit with respect to a state.')
# Get equivalent variable from cloned model
var = model.get(var.var().qname())
lhs = myokit.Name(var)
else:
if type(var) in [str, unicode]:
lhs = myokit.Name(model.get(var))
elif isinstance(var, myokit.Variable):
# Get equivalent variable from cloned model
var = model.get(var.var().qname())
lhs = myokit.Name(var)
else:
raise ValueError(
'The argument "var" must be either an LhsExpression, a'
' Variable or a string referencing a model variable')
# Test suitability of variable
if lhs.is_constant():
raise ValueError('The given variable can not be constant.')
# Test suitability of range
if len(rng) < 2:
raise ValueError(
'The argument "rng" must contain the lower and'
' upper boundaries of the variable\'s name.')
if rng[0] == rng[1]:
raise ValueError(
'The given range must contain two distinct values.')
if rng[0] > rng[1]:
rng = rng.reverse()
# Reset list of changed variables
self._changed = []
# Go!
return self._fit(model, lhs, rng, report)
def _test_maths(self, version):
# Test maths is written (in selected ``version``)
# Create model
m1 = cellml.Model('m', version)
c1 = m1.add_component('c')
p1 = c1.add_variable('p', 'mole')
p1.set_initial_value(2)
q1 = c1.add_variable('q', 'dimensionless')
r1 = c1.add_variable('r', 'second')
r1.set_initial_value(0.1)
t1 = c1.add_variable('t', 'second')
m1.set_variable_of_integration(t1)
# Add component without maths
d1 = m1.add_component('d')
s1 = d1.add_variable('s', 'volt')
s1.set_initial_value(1.23)
# Add two equations
# Note: Numbers without units become dimensionless in CellML
eq1 = myokit.Equation(
myokit.Name(q1),
myokit.Plus(myokit.Number(3, myokit.units.mole), myokit.Name(p1)))
er1 = myokit.Equation(myokit.Derivative(myokit.Name(r1)),
myokit.Power(myokit.Name(q1), myokit.Number(2)))
q1.set_equation(eq1)
r1.set_equation(er1)
# Write and read
xml = cellml.write_string(m1)
m2 = cellml.parse_string(xml)
# Check results
p2, q2, r2, s2 = m2['c']['p'], m2['c']['q'], m2['c']['r'], m2['d']['s']
subst = {
myokit.Name(p1): myokit.Name(p2),
myokit.Name(q1): myokit.Name(q2),
myokit.Name(r1): myokit.Name(r2),
}
eq2 = eq1.clone(subst)
er2 = er1.clone(subst)
self.assertEqual(q2.equation(), eq2)
self.assertEqual(r2.equation(), er2)
self.assertEqual(s2.initial_value(),
myokit.Number(1.23, myokit.units.volt))
self.assertFalse(p2.is_state())
self.assertFalse(q2.is_state())
self.assertTrue(r2.is_state())
self.assertFalse(s2.is_state())
self.assertIs(m2.variable_of_integration(), m2['c']['t'])
def test_user_function(self):
# Test :class:`UserFunction` creation and methods.
# Create without arguments
f = myokit.UserFunction('bert', [], myokit.Number(12))
args = list(f.arguments())
self.assertEqual(len(args), 0)
self.assertEqual(f.convert([]), myokit.Number(12))
# Create with one argument
f = myokit.UserFunction('x', [myokit.Name('a')],
myokit.parse_expression('1 + a'))
self.assertEqual(len(list(f.arguments())), 1)
args = {myokit.Name('a'): myokit.Number(3)}
self.assertEqual(f.convert(args).eval(), 4)
# Create with two argument
f = myokit.UserFunction(
'x', [myokit.Name('a'), myokit.Name('b')],
myokit.parse_expression('a + b'))
self.assertEqual(len(list(f.arguments())), 2)
args = {
myokit.Name('a'): myokit.Number(3),
myokit.Name('b'): myokit.Number(4)
}
self.assertEqual(f.convert(args), myokit.parse_expression('3 + 4'))
# Call with wrong arguments
del (args[myokit.Name('a')])
self.assertRaisesRegex(ValueError, 'Wrong number', f.convert, args)
args[myokit.Name('c')] = myokit.Number(100)
self.assertRaisesRegex(ValueError, 'Missing input argument', f.convert,
args)
def test_remove_component(self):
# Test the removal of a component.
# Create model
m = myokit.Model('LotkaVolterra')
# Simplest case
X = m.add_component('X')
self.assertEqual(m.count_components(), 1)
m.remove_component(X)
self.assertEqual(m.count_components(), 0)
self.assertRaises(KeyError, m.remove_component, X)
# Test if orphaned
self.assertIsNone(X.parent())
# Re-adding
self.assertEqual(m.count_components(), 0)
X = m.add_component('X')
self.assertEqual(m.count_components(), 1)
# With internal variables and string name
a = X.add_variable('a')
a.set_rhs(myokit.Number(4))
b = X.add_variable('b')
b.set_rhs(myokit.Name(a))
m.remove_component('X')
self.assertEqual(m.count_components(), 0)
# With dependencies from another component
X = m.add_component('X')
a = X.add_variable('a')
a.set_rhs(myokit.Number(45))
b = X.add_variable('b')
b.set_rhs(myokit.Name(b))
Y = m.add_component('Y')
c = Y.add_variable('c')
c.set_rhs(myokit.Name(a))
d = Y.add_variable('d')
d.set_rhs(myokit.Name(c))
self.assertEqual(m.count_components(), 2)
self.assertRaises(myokit.IntegrityError, m.remove_component, X)
self.assertEqual(m.count_components(), 2)
# In the right order...
m.remove_component(Y)
self.assertEqual(m.count_components(), 1)
m.remove_component(X)
self.assertEqual(m.count_components(), 0)
def polynomial(self):
"""
Test of Polynomial class
"""
x = myokit.Name('x')
c = [
myokit.Number(5),
myokit.Number(4),
myokit.Number(3),
myokit.Number(2)
]
p = myokit.Polynomial(x, *c)
self.assertEqual(p.eval(subst={x: 0}), 5)
self.assertEqual(p.eval(subst={x: 1}), 14)
self.assertEqual(p.eval(subst={x: 2}), 41)
self.assertEqual(p.eval(subst={x: -1}), 2)
self.assertEqual(p.eval(subst={x: 0.5}), 8)
q = p.tree()
self.assertNotEqual(p, q)
for i in [-1, 0, 0.5, 1, 2]:
s = {x: i}
self.assertEqual(p.eval(subst=s), q.eval(subst=s))
q = p.tree(horner=False)
self.assertNotEqual(p, q)
for i in [-1, 0, 0.5, 1, 2]:
s = {x: i}
self.assertEqual(p.eval(subst=s), q.eval(subst=s))
def test_read_write(self):
# Test using the read() and write() methods
try:
import sympy as sp
except ImportError:
print('Sympy not found, skipping test.')
return
# Test writing and reading with a model
a = self._a
ca = sp.Symbol('c.a')
self.assertEqual(mypy.write(a), ca)
self.assertEqual(mypy.read(ca, self._model), a)
# Test doing it again, with a different model
m = myokit.Model()
a = m.add_component('cc').add_variable('aa')
a = myokit.Name(a)
ca = sp.Symbol('cc.aa')
self.assertEqual(mypy.write(a), ca)
self.assertEqual(mypy.read(ca, m), a)
# Test reading without a model
b = myokit.Number('12')
cb = sp.Float(12)
self.assertEqual(mypy.write(b), cb)
self.assertEqual(mypy.read(cb), b)
def test_conditionals(self):
# Tests if and piecewise writing
a = myokit.Name('a')
b = myokit.Number(1)
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
c1 = '<apply><gt/><cn>5.0</cn><cn>3.0</cn></apply>'
c2 = '<apply><lt/><cn>2.0</cn><cn>1.0</cn></apply>'
# If
e = myokit.If(cond1, a, b)
x = (
'<piecewise>'
'<piece><ci>a</ci>' + c1 + '</piece>'
'<otherwise><cn>1.0</cn></otherwise>'
'</piecewise>'
)
self.assertWrite(e, x)
# Piecewise
e = myokit.Piecewise(cond1, a, cond2, b, myokit.Number(100))
x = (
'<piecewise>'
'<piece><ci>a</ci>' + c1 + '</piece>'
'<piece><cn>1.0</cn>' + c2 + '</piece>'
'<otherwise><cn>100.0</cn></otherwise>'
'</piecewise>'
)
self.assertWrite(e, x)
def test_inequalities(self):
# Test parsing (in)equalities
# Equal
a = myokit.Name('a')
b = myokit.Number(1.0)
e = myokit.Equal(a, b)
x = '<apply><eq/><ci>a</ci><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# NotEqual
e = myokit.NotEqual(a, b)
x = '<apply><neq/><ci>a</ci><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# More
e = myokit.More(a, b)
x = '<apply><gt/><ci>a</ci><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# Less
e = myokit.Less(a, b)
x = '<apply><lt/><ci>a</ci><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# MoreEqual
e = myokit.MoreEqual(a, b)
x = '<apply><geq/><ci>a</ci><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# LessEqual
e = myokit.LessEqual(a, b)
x = '<apply><leq/><ci>a</ci><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
def test_constants(self):
# Tests parsing of MathML special constants.
# Pi
import math
x = self.p('<pi/>')
self.assertAlmostEqual(math.pi, float(x))
# Test e
import math
x = self.p('<exponentiale/>')
self.assertAlmostEqual(math.e, float(x))
# Test booleans
import math
x = self.p('<true/>')
self.assertEqual(float(x), 1)
x = self.p('<false/>')
self.assertEqual(float(x), 0)
# Nan and inf
x = self.p('<notanumber/>')
self.assertTrue(math.isnan(float(x)))
x = self.p('<infinity/>')
self.assertEqual(float(x), float('inf'))
# Test constants are handled via the number factory
xml = '<pi/>'
x = mathml.parse_mathml_etree(
etree.fromstring(xml),
lambda x, y: myokit.Name(x),
lambda x, y: myokit.Number(x, myokit.units.volt),
)
self.assertEqual(x.unit(), myokit.units.volt)
def test_name_and_numbers(self):
# Test name and number writing
self.assertWrite(myokit.Name('a'), '<ci>a</ci>')
# Number without unit
self.assertWrite(myokit.Number(0), '<cn>0.0</cn>')
self.assertWrite(myokit.Number(1), '<cn>1.0</cn>')
# Number with unit
# Unit isn't exported by default!
self.assertWrite(myokit.Number('-12', 'pF'), '<cn>-12.0</cn>')
# Number with e notation (note that Python will turn e.g. 1e3 into
# 1000, so must pick tests carefully)
self.assertWrite(myokit.Number(1e3), '<cn>1000.0</cn>')
self.assertWrite(myokit.Number(1e-3), '<cn>0.001</cn>')
self.assertWrite(
myokit.Number(1e-6),
'<cn type="e-notation">1<sep/>-6</cn>')
self.assertWrite(
myokit.Number(2.3e24),
'<cn type="e-notation">2.3<sep/>24</cn>')
# myokit.float.str(1.23456789) = 1.23456788999999989e+00
self.assertWrite(
myokit.Number(1.23456789), '<cn>1.23456788999999989</cn>')
def test_conditionals(self):
# Tests if and piecewise writing
a = myokit.Name('a')
b = myokit.Number(1)
c = myokit.Number(1)
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
ca = '<mi>a</mi>'
cb = '<mn>1.0</mn>'
cc = '<mn>1.0</mn>'
c1 = '<mrow><mn>5.0</mn><mo>></mo><mn>3.0</mn></mrow>'
c2 = '<mrow><mn>2.0</mn><mo><</mo><mn>1.0</mn></mrow>'
# If
x = myokit.If(cond1, a, b)
self.assertWrite(
x, '<piecewise>'
'<piece>' + ca + c1 + '</piece>'
'<otherwise>' + cb + '</otherwise>'
'</piecewise>')
# Piecewise
x = myokit.Piecewise(cond1, a, cond2, b, c)
self.assertWrite(
x, '<piecewise>'
'<piece>' + ca + c1 + '</piece>'
'<piece>' + cb + c2 + '</piece>'
'<otherwise>' + cc + '</otherwise>'
'</piecewise>')
def test_functions(self):
# Test printing functions
a = myokit.Name(self.avar)
b = myokit.Number('12', 'pF')
ca = '<ci>a</ci>'
cb = ('<cn cellml:units="picofarad">12.0</cn>')
# Power
x = myokit.Power(a, b)
self.assertWrite(x, '<apply><power/>' + ca + cb + '</apply>')
# Sqrt
x = myokit.Sqrt(b)
self.assertWrite(x, '<apply><root/>' + cb + '</apply>')
# Exp
x = myokit.Exp(a)
self.assertWrite(x, '<apply><exp/>' + ca + '</apply>')
# Floor
x = myokit.Floor(b)
self.assertWrite(x, '<apply><floor/>' + cb + '</apply>')
# Ceil
x = myokit.Ceil(b)
self.assertWrite(x, '<apply><ceiling/>' + cb + '</apply>')
# Abs
x = myokit.Abs(b)
self.assertWrite(x, '<apply><abs/>' + cb + '</apply>')
def test_inequalities(self):
# Test writing (in)equalities
a = myokit.Name(self.avar)
b = myokit.Number('12', 'pF')
ca = '<mi>c.a</mi>'
cb = '<mn>12.0</mn>'
# Equal
x = myokit.Equal(a, b)
self.assertWrite(x, '<mrow>' + ca + '<mo>==</mo>' + cb + '</mrow>')
# NotEqual
x = myokit.NotEqual(a, b)
self.assertWrite(x, '<mrow>' + ca + '<mo>!=</mo>' + cb + '</mrow>')
# More
x = myokit.More(a, b)
self.assertWrite(x, '<mrow>' + ca + '<mo>></mo>' + cb + '</mrow>')
# Less
x = myokit.Less(a, b)
self.assertWrite(x, '<mrow>' + ca + '<mo><</mo>' + cb + '</mrow>')
# MoreEqual
# Named version ≥ is not output, shows decimal code instead
x = myokit.MoreEqual(a, b)
self.assertWrite(x,
'<mrow>' + ca + '<mo>≥</mo>' + cb + '</mrow>')
# LessEqual
# Named version ≤ is not output, shows decimal code instead
x = myokit.LessEqual(a, b)
self.assertWrite(x,
'<mrow>' + ca + '<mo>≤</mo>' + cb + '</mrow>')
def test_inequalities(self):
# Tests printing inequalities
a = myokit.Name(self.avar)
b = myokit.Number('12', 'pF')
ca = '<ci>a</ci>'
cb = ('<cn cellml:units="picofarad">12.0</cn>')
# Equal
x = myokit.Equal(a, b)
self.assertWrite(x, '<apply><eq/>' + ca + cb + '</apply>')
# NotEqual
x = myokit.NotEqual(a, b)
self.assertWrite(x, '<apply><neq/>' + ca + cb + '</apply>')
# More
x = myokit.More(a, b)
self.assertWrite(x, '<apply><gt/>' + ca + cb + '</apply>')
# Less
x = myokit.Less(a, b)
self.assertWrite(x, '<apply><lt/>' + ca + cb + '</apply>')
# MoreEqual
x = myokit.MoreEqual(a, b)
self.assertWrite(x, '<apply><geq/>' + ca + cb + '</apply>')
# LessEqual
x = myokit.LessEqual(a, b)
self.assertWrite(x, '<apply><leq/>' + ca + cb + '</apply>')
def test_arithmetic(self):
# Test basic arithmetic
a = myokit.Name(self.avar)
b = myokit.Number('12', 'pF')
ca = '<ci>a</ci>'
cb = ('<cn cellml:units="picofarad">12.0</cn>')
# Prefix plus
x = myokit.PrefixPlus(b)
self.assertWrite(x, '<apply><plus/>' + cb + '</apply>')
# Prefix minus
x = myokit.PrefixMinus(b)
self.assertWrite(x, '<apply><minus/>' + cb + '</apply>')
# Plus
x = myokit.Plus(a, b)
self.assertWrite(x, '<apply><plus/>' + ca + cb + '</apply>')
# Minus
x = myokit.Minus(a, b)
self.assertWrite(x, '<apply><minus/>' + ca + cb + '</apply>')
# Multiply
x = myokit.Multiply(a, b)
self.assertWrite(x, '<apply><times/>' + ca + cb + '</apply>')
# Divide
x = myokit.Divide(a, b)
self.assertWrite(x, '<apply><divide/>' + ca + cb + '</apply>')
def test_units(self):
# Test writing of units
u1 = myokit.parse_unit('kg*m^2/mole^3 (0.123)')
m1 = cellml.Model('mmm')
m1.add_units('flibbit', u1)
m1.add_units('special_volt', myokit.units.Volt)
d = m1.add_component('ddd')
q = d.add_variable('q', 'flibbit')
q.set_equation(myokit.Equation(myokit.Name(q), myokit.Number(2, u1)))
xml = cellml.write_string(m1)
m2 = cellml.parse_string(xml)
q = m2['ddd']['q']
self.assertEqual(q.units().name(), 'flibbit')
self.assertEqual(q.units().myokit_unit(), u1)
self.assertEqual(
m2.find_units('special_volt').myokit_unit(), myokit.units.volt)
# Dimensionless units with a multiplier
u1 = myokit.parse_unit('1 (0.123)')
m1 = cellml.Model('mmm')
m1.add_units('flibbit', u1)
xml = cellml.write_string(m1)
m2 = cellml.parse_string(xml)
u2 = m2.find_units('flibbit')
u2 = u2.myokit_unit()
self.assertEqual(u1, u2)
def test_functions(self):
# Tests writing basic functions
a = myokit.Name(self.avar)
b = myokit.Number('12', 'pF')
ca = '<mi>c.a</mi>'
cb = '<mn>12.0</mn>'
# Power
x = myokit.Power(a, b)
self.assertWrite(x, '<msup>' + ca + cb + '</msup>')
# Sqrt
x = myokit.Sqrt(b)
self.assertWrite(
x, '<mrow><mi>root</mi><mfenced>' + cb + '</mfenced></mrow>')
# Exp
x = myokit.Exp(a)
self.assertWrite(x, '<msup><mi>e</mi>' + ca + '</msup>')
# Log(a)
x = myokit.Log(b)
self.assertWrite(
x, '<mrow><mi>ln</mi><mfenced>' + cb + '</mfenced></mrow>')
# Log(a, b)
x = myokit.Log(a, b)
self.assertWrite(
x, '<mrow><msub><mi>log</mi>' + cb + '</msub>'
'<mfenced>' + ca + '</mfenced></mrow>')
# Log10
x = myokit.Log10(b)
self.assertWrite(
x, '<mrow><mi>log</mi><mfenced>' + cb + '</mfenced></mrow>')
# Floor
x = myokit.Floor(b)
self.assertWrite(
x, '<mrow><mi>floor</mi><mfenced>' + cb + '</mfenced></mrow>')
# Ceil
x = myokit.Ceil(b)
self.assertWrite(
x, '<mrow><mi>ceiling</mi><mfenced>' + cb + '</mfenced></mrow>')
# Abs
x = myokit.Abs(b)
self.assertWrite(
x, '<mrow><mi>abs</mi><mfenced>' + cb + '</mfenced></mrow>')
# Quotient
x = myokit.Quotient(a, b)
self.assertWrite(x, '<mrow>' + ca + '<mo>//</mo>' + cb + '</mrow>')
# Remainder
x = myokit.Remainder(a, b)
self.assertWrite(x, '<mrow>' + ca + '<mo>%</mo>' + cb + '</mrow>')
def test_functions(self):
# Tests writing basic functions
# Power
a = myokit.Name('a')
b = myokit.Number(1)
e = myokit.Power(a, b)
x = '<apply><power/><ci>a</ci><cn>1.0</cn></apply>'
self.assertWrite(e, x)
# Sqrt
e = myokit.Sqrt(b)
x = '<apply><root/><cn>1.0</cn></apply>'
self.assertWrite(e, x)
# Exp
e = myokit.Exp(a)
x = '<apply><exp/><ci>a</ci></apply>'
self.assertWrite(e, x)
# Log(a)
e = myokit.Log(b)
x = '<apply><ln/><cn>1.0</cn></apply>'
self.assertWrite(e, x)
# Log(a, b)
e = myokit.Log(a, b)
x = '<apply><log/><logbase><cn>1.0</cn></logbase><ci>a</ci></apply>'
self.assertWrite(e, x)
# Log10
e = myokit.Log10(b)
x = '<apply><log/><cn>1.0</cn></apply>'
self.assertWrite(e, x)
# Floor
e = myokit.Floor(b)
x = '<apply><floor/><cn>1.0</cn></apply>'
self.assertWrite(e, x)
# Ceil
e = myokit.Ceil(b)
x = '<apply><ceiling/><cn>1.0</cn></apply>'
self.assertWrite(e, x)
# Abs
e = myokit.Abs(b)
x = '<apply><abs/><cn>1.0</cn></apply>'
self.assertWrite(e, x)
# Quotient
e = myokit.Quotient(a, b)
x = '<apply><quotient/><ci>a</ci><cn>1.0</cn></apply>'
self.assertWrite(e, x)
# Remainder
e = myokit.Remainder(a, b)
x = '<apply><rem/><ci>a</ci><cn>1.0</cn></apply>'
self.assertWrite(e, x)
def create_myokit_model(self):
if self.pk_model is None:
pk_model = myokit.Model()
else:
pk_model = self.create_myokit_dosed_pk_model()
if self.pd_model is None:
pd_model = myokit.Model()
else:
pd_model = self.pd_model.create_myokit_model()
have_both_models = (self.pk_model is not None
and self.pd_model is not None)
have_no_models = (self.pk_model is None and self.pd_model is None)
# use pk model as the base and import the pd model
pkpd_model = pk_model
# default model is one with just time
if have_no_models:
pkpd_model = myokit.parse_model('''
[[model]]
[myokit]
time = 0 [s] bind time
in [s]
''')
# remove time binding if
if have_both_models:
time_var = pd_model.get('myokit.time')
time_var.set_binding(None)
pd_components = list(pd_model.components())
pd_names = [c.name().replace('myokit', 'PD') for c in pd_components]
if pd_components:
pkpd_model.import_component(
pd_components,
new_name=pd_names,
)
# remove imported time var
if have_both_models:
imported_pd_component = pkpd_model.get('PD')
imported_time = imported_pd_component.get('time')
imported_pd_component.remove_variable(imported_time)
# do mappings
for mapping in self.mappings.all():
pd_var = pkpd_model.get(
mapping.pd_variable.qname.replace('myokit', 'PD'))
pk_var = pkpd_model.get(mapping.pk_variable.qname)
unit_conversion_multiplier = myokit.Unit.conversion_factor(
pk_var.unit(), pd_var.unit())
pd_var.set_rhs(
myokit.Multiply(myokit.Number(unit_conversion_multiplier),
myokit.Name(pk_var)))
pkpd_model.validate()
return pkpd_model
def p(self, xml):
""" Parses a MathML string and returns a myokit.Expression. """
return mathml.parse_mathml_etree(
etree.fromstring(xml),
lambda x, y: myokit.Name(x),
lambda x, y: myokit.Number(x),
)
def variable_factory(name, element):
try:
var = component.variable(name)
except KeyError:
raise CellMLParsingError(
'Variable references in equation must name a variable from'
' the local component (4.4.2.1).', element)
return myokit.Name(var)
def test_piecewise_polynomial(self):
"""
Test piecewise polynomial
"""
# Set up test space
x = np.linspace(-10, 10, 10000)
# Test number one
knots = [1, 2]
coeff = [
[0.123, 0.456, 2.789, -0.123, -0.456],
[5.4123, -0.1456, 7.789, -0.123, -0.456],
[-40.6123, 0.2456, -0.86453, 0.23, -0.753],
]
f = approx.PiecewisePolynomial(coeff, knots)
g = f.myokit_form(myokit.Name('x')).pyfunc()
if myotest.DEBUG:
import matplotlib.pyplot as pl
pl.figure()
p0 = approx.Polynomial(coeff[0])
p1 = approx.Polynomial(coeff[1])
p2 = approx.Polynomial(coeff[2])
pl.plot(x, p0(x), label='p0')
pl.plot(x, p1(x), label='p1')
pl.plot(x, p2(x), label='p2')
pl.plot(x, f(x), label='f')
pl.plot(x, g(x), label='g')
pl.legend(loc='lower left')
pl.show()
self.assertTrue(np.all(np.abs(f(x) - g(x)) < 1e-15))
# Test number two
knots = [-5.0, 1.0, 3.123]
coeff = [
[0.123, 0.456, 2.789, -0.123, -0.456, 0.0035],
[5.4123, -0.1456, 7.789, -0.123, -0.456, 0.023],
[-40.6123, 0.2456, -0.86453, 0.23, -0.753, 0.4262],
[-20.4123, -2.0156, 1.79, -0.00642, -0.2632, -1.098],
]
f = approx.PiecewisePolynomial(coeff, knots)
g = f.myokit_form(myokit.Name('x')).pyfunc()
self.assertTrue(np.all(np.abs(f(x) - g(x)) < 1e-15))
# Test cloning
h = approx.PiecewisePolynomial(f)
self.assertTrue(np.all(np.abs(f(x) - h(x)) < 1e-15))
def parse_mathml_string(s):
"""
Parses a MathML string that should contain a single expression.
"""
import xml.etree.ElementTree as etree
p = MathMLParser(
lambda x, y: myokit.Name(x),
lambda x, y: myokit.Number(x),
)
return p.parse(etree.fromstring(s))
