def ifif(self):
"""
Test of If class
"""
true = myokit.Number(1)
false = myokit.Number(0)
two = myokit.Number(2)
three = myokit.Number(3)
x = myokit.If(true, two, three)
self.assertEqual(x.eval(), 2)
self.assertEqual(x.condition(), true)
x = myokit.If(true, three, two)
self.assertEqual(x.eval(), 3)
x = myokit.If(false, two, three)
self.assertEqual(x.eval(), 3)
self.assertEqual(x.condition(), false)
x = myokit.If(false, three, two)
self.assertEqual(x.eval(), 2)
# Conversion to piecewise
x = myokit.If(true, two, three).piecewise()
self.assertIsInstance(x, myokit.Piecewise)
self.assertEqual(x.eval(), 2)
x = myokit.If(true, three, two).piecewise()
self.assertIsInstance(x, myokit.Piecewise)
self.assertEqual(x.eval(), 3)
x = myokit.If(false, two, three).piecewise()
self.assertIsInstance(x, myokit.Piecewise)
self.assertEqual(x.eval(), 3)
x = myokit.If(false, three, two).piecewise()
self.assertIsInstance(x, myokit.Piecewise)
self.assertEqual(x.eval(), 2)
def _parse_expression(self, s, var=None):
"""
Attempts to read an expression from the given string ``s`` and parse it
using the context of variable ``var`` to resolve any references.
"""
s = str(s)
# Pre-process some basic html entities
entities = {
'&eq;': '==',
'≠': '!=',
'&neq;': '!=', # Not a html entity!
'<': '<',
'>': '>',
'≤': '<=',
'≥': '>=',
}
s = s.replace('&', '&')
for k, v in entities.items():
s = s.replace(k, v)
# Attempt to handle single a?b:c construct
if '?' in s:
c, v = s.split('?', 1)
if ':' in v:
v = v.split(':', 1)
else:
v = (v, '0')
return myokit.If(myokit.parse_expression(c, var),
myokit.parse_expression(v[0], var),
myokit.parse_expression(v[1], var))
return myokit.parse_expression(s, var)
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_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_logical(self):
# Tests printing logical operators and functions
a = myokit.Name(self.avar)
b = myokit.Number('12', 'pF')
c = myokit.Number(1)
ca = '<ci>a</ci>'
cb = ('<cn cellml:units="picofarad">12.0</cn>')
cc = ('<cn cellml:units="dimensionless">1.0</cn>')
# Not
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
c1 = ('<apply><gt/>'
'<cn cellml:units="dimensionless">5.0</cn>'
'<cn cellml:units="dimensionless">3.0</cn>'
'</apply>')
c2 = ('<apply><lt/>'
'<cn cellml:units="dimensionless">2.0</cn>'
'<cn cellml:units="dimensionless">1.0</cn>'
'</apply>')
x = myokit.Not(cond1)
self.assertWrite(x, '<apply><not/>' + c1 + '</apply>')
# And
x = myokit.And(cond1, cond2)
self.assertWrite(x, '<apply><and/>' + c1 + c2 + '</apply>')
# Or
x = myokit.Or(cond1, cond2)
self.assertWrite(x, '<apply><or/>' + c1 + c2 + '</apply>')
# 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_all(self):
w = myokit.formats.python.PythonExpressionWriter()
model = myokit.Model()
component = model.add_component('c')
avar = component.add_variable('a')
# Name
a = myokit.Name(avar)
self.assertEqual(w.ex(a), 'c.a')
# Number with unit
b = myokit.Number('12', 'pF')
self.assertEqual(w.ex(b), '12.0')
# Prefix plus
x = myokit.PrefixPlus(b)
self.assertEqual(w.ex(x), '12.0')
# Prefix minus
x = myokit.PrefixMinus(b)
self.assertEqual(w.ex(x), '(-12.0)')
# Plus
x = myokit.Plus(a, b)
self.assertEqual(w.ex(x), 'c.a + 12.0')
# Minus
x = myokit.Minus(a, b)
self.assertEqual(w.ex(x), 'c.a - 12.0')
# Multiply
x = myokit.Multiply(a, b)
self.assertEqual(w.ex(x), 'c.a * 12.0')
# Divide
x = myokit.Divide(a, b)
self.assertEqual(w.ex(x), 'c.a / 12.0')
# Quotient
x = myokit.Quotient(a, b)
self.assertEqual(w.ex(x), 'c.a // 12.0')
# Remainder
x = myokit.Remainder(a, b)
self.assertEqual(w.ex(x), 'c.a % 12.0')
# Power
x = myokit.Power(a, b)
self.assertEqual(w.ex(x), 'c.a ** 12.0')
# Sqrt
x = myokit.Sqrt(b)
self.assertEqual(w.ex(x), 'math.sqrt(12.0)')
# Exp
x = myokit.Exp(a)
self.assertEqual(w.ex(x), 'math.exp(c.a)')
# Log(a)
x = myokit.Log(b)
self.assertEqual(w.ex(x), 'math.log(12.0)')
# Log(a, b)
x = myokit.Log(a, b)
self.assertEqual(w.ex(x), 'math.log(c.a, 12.0)')
# Log10
x = myokit.Log10(b)
self.assertEqual(w.ex(x), 'math.log10(12.0)')
# Sin
x = myokit.Sin(b)
self.assertEqual(w.ex(x), 'math.sin(12.0)')
# Cos
x = myokit.Cos(b)
self.assertEqual(w.ex(x), 'math.cos(12.0)')
# Tan
x = myokit.Tan(b)
self.assertEqual(w.ex(x), 'math.tan(12.0)')
# ASin
x = myokit.ASin(b)
self.assertEqual(w.ex(x), 'math.asin(12.0)')
# ACos
x = myokit.ACos(b)
self.assertEqual(w.ex(x), 'math.acos(12.0)')
# ATan
x = myokit.ATan(b)
self.assertEqual(w.ex(x), 'math.atan(12.0)')
# Floor
x = myokit.Floor(b)
self.assertEqual(w.ex(x), 'math.floor(12.0)')
# Ceil
x = myokit.Ceil(b)
self.assertEqual(w.ex(x), 'math.ceil(12.0)')
# Abs
x = myokit.Abs(b)
self.assertEqual(w.ex(x), 'abs(12.0)')
# Equal
x = myokit.Equal(a, b)
self.assertEqual(w.ex(x), '(c.a == 12.0)')
# NotEqual
x = myokit.NotEqual(a, b)
self.assertEqual(w.ex(x), '(c.a != 12.0)')
# More
x = myokit.More(a, b)
self.assertEqual(w.ex(x), '(c.a > 12.0)')
# Less
x = myokit.Less(a, b)
self.assertEqual(w.ex(x), '(c.a < 12.0)')
# MoreEqual
x = myokit.MoreEqual(a, b)
self.assertEqual(w.ex(x), '(c.a >= 12.0)')
# LessEqual
x = myokit.LessEqual(a, b)
self.assertEqual(w.ex(x), '(c.a <= 12.0)')
# Not
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
x = myokit.Not(cond1)
self.assertEqual(w.ex(x), 'not ((5.0 > 3.0))')
# And
x = myokit.And(cond1, cond2)
self.assertEqual(w.ex(x), '((5.0 > 3.0) and (2.0 < 1.0))')
# Or
x = myokit.Or(cond1, cond2)
self.assertEqual(w.ex(x), '((5.0 > 3.0) or (2.0 < 1.0))')
# If
x = myokit.If(cond1, a, b)
self.assertEqual(w.ex(x), '(c.a if (5.0 > 3.0) else 12.0)')
# Piecewise
c = myokit.Number(1)
x = myokit.Piecewise(cond1, a, cond2, b, c)
self.assertEqual(
w.ex(x),
'(c.a if (5.0 > 3.0) else (12.0 if (2.0 < 1.0) else 1.0))')
# Test fetching using ewriter method
w = myokit.formats.ewriter('python')
self.assertIsInstance(w, myokit.formats.python.PythonExpressionWriter)
# Test lhs method
w.set_lhs_function(lambda x: 'sheep')
self.assertEqual(w.ex(a), 'sheep')
# Test without a Myokit expression
self.assertRaisesRegex(ValueError, 'Unknown expression type', w.ex, 7)
def test_all(self):
w = myokit.formats.matlab.MatlabExpressionWriter()
model = myokit.Model()
component = model.add_component('c')
avar = component.add_variable('a')
# Name
a = myokit.Name(avar)
self.assertEqual(w.ex(a), 'c.a')
# Number with unit
b = myokit.Number('12', 'pF')
self.assertEqual(w.ex(b), '12.0')
# Prefix plus
x = myokit.PrefixPlus(b)
self.assertEqual(w.ex(x), '12.0')
# Prefix minus
x = myokit.PrefixMinus(b)
self.assertEqual(w.ex(x), '(-12.0)')
# Plus
x = myokit.Plus(a, b)
self.assertEqual(w.ex(x), 'c.a + 12.0')
# Minus
x = myokit.Minus(a, b)
self.assertEqual(w.ex(x), 'c.a - 12.0')
# Multiply
x = myokit.Multiply(a, b)
self.assertEqual(w.ex(x), 'c.a * 12.0')
# Divide
x = myokit.Divide(a, b)
self.assertEqual(w.ex(x), 'c.a / 12.0')
# Quotient
x = myokit.Quotient(a, b)
self.assertEqual(w.ex(x), 'floor(c.a / 12.0)')
# Remainder
x = myokit.Remainder(a, b)
self.assertEqual(w.ex(x), 'mod(c.a, 12.0)')
# Power
x = myokit.Power(a, b)
self.assertEqual(w.ex(x), 'c.a ^ 12.0')
# Sqrt
x = myokit.Sqrt(b)
self.assertEqual(w.ex(x), 'sqrt(12.0)')
# Exp
x = myokit.Exp(a)
self.assertEqual(w.ex(x), 'exp(c.a)')
# Log(a)
x = myokit.Log(b)
self.assertEqual(w.ex(x), 'log(12.0)')
# Log(a, b)
x = myokit.Log(a, b)
self.assertEqual(w.ex(x), '(log(c.a) / log(12.0))')
# Log10
x = myokit.Log10(b)
self.assertEqual(w.ex(x), 'log10(12.0)')
# Sin
x = myokit.Sin(b)
self.assertEqual(w.ex(x), 'sin(12.0)')
# Cos
x = myokit.Cos(b)
self.assertEqual(w.ex(x), 'cos(12.0)')
# Tan
x = myokit.Tan(b)
self.assertEqual(w.ex(x), 'tan(12.0)')
# ASin
x = myokit.ASin(b)
self.assertEqual(w.ex(x), 'asin(12.0)')
# ACos
x = myokit.ACos(b)
self.assertEqual(w.ex(x), 'acos(12.0)')
# ATan
x = myokit.ATan(b)
self.assertEqual(w.ex(x), 'atan(12.0)')
# Floor
x = myokit.Floor(b)
self.assertEqual(w.ex(x), 'floor(12.0)')
# Ceil
x = myokit.Ceil(b)
self.assertEqual(w.ex(x), 'ceil(12.0)')
# Abs
x = myokit.Abs(b)
self.assertEqual(w.ex(x), 'abs(12.0)')
# Equal
x = myokit.Equal(a, b)
self.assertEqual(w.ex(x), '(c.a == 12.0)')
# NotEqual
x = myokit.NotEqual(a, b)
self.assertEqual(w.ex(x), '(c.a != 12.0)')
# More
x = myokit.More(a, b)
self.assertEqual(w.ex(x), '(c.a > 12.0)')
# Less
x = myokit.Less(a, b)
self.assertEqual(w.ex(x), '(c.a < 12.0)')
# MoreEqual
x = myokit.MoreEqual(a, b)
self.assertEqual(w.ex(x), '(c.a >= 12.0)')
# LessEqual
x = myokit.LessEqual(a, b)
self.assertEqual(w.ex(x), '(c.a <= 12.0)')
# Not
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
x = myokit.Not(cond1)
self.assertEqual(w.ex(x), '!((5.0 > 3.0))')
# And
x = myokit.And(cond1, cond2)
self.assertEqual(w.ex(x), '((5.0 > 3.0) && (2.0 < 1.0))')
# Or
x = myokit.Or(cond1, cond2)
self.assertEqual(w.ex(x), '((5.0 > 3.0) || (2.0 < 1.0))')
# If (custom function)
x = myokit.If(cond1, a, b)
self.assertEqual(w.ex(x), 'ifthenelse((5.0 > 3.0), c.a, 12.0)')
# Piecewise
c = myokit.Number(1)
x = myokit.Piecewise(cond1, a, cond2, b, c)
self.assertEqual(
w.ex(x),
'ifthenelse((5.0 > 3.0), c.a, ifthenelse((2.0 < 1.0), 12.0, 1.0))')
# Test fetching using ewriter method
w = myokit.formats.ewriter('matlab')
self.assertIsInstance(w, myokit.formats.matlab.MatlabExpressionWriter)
# Test without a Myokit expression
self.assertRaisesRegex(ValueError, 'Unknown expression type', w.ex, 7)
def test_all(self):
w = myokit.formats.latex.LatexExpressionWriter()
model = myokit.Model()
component = model.add_component('c')
avar = component.add_variable('a')
# Model needs to be validated --> sets unames
avar.set_rhs(12)
avar.set_binding('time')
model.validate()
# Name
a = myokit.Name(avar)
self.assertEqual(w.ex(a), '\\text{a}')
# Number with unit
b = myokit.Number('12', 'pF')
self.assertEqual(w.ex(b), '12.0')
# Prefix plus
x = myokit.PrefixPlus(b)
self.assertEqual(w.ex(x), '12.0')
# Prefix minus
x = myokit.PrefixMinus(b)
self.assertEqual(w.ex(x), '\\left(-12.0\\right)')
# Prefix minus with bracket
x = myokit.PrefixMinus(myokit.Plus(a, b))
self.assertEqual(w.ex(x),
'\\left(-\\left(\\text{a}+12.0\\right)\\right)')
# Plus
x = myokit.Plus(a, b)
self.assertEqual(w.ex(x), '\\text{a}+12.0')
# Minus
x = myokit.Minus(a, b)
self.assertEqual(w.ex(x), '\\text{a}-12.0')
# Multiply
x = myokit.Multiply(a, b)
self.assertEqual(w.ex(x), '\\text{a}*12.0')
# Divide
x = myokit.Divide(a, b)
self.assertEqual(w.ex(x), '\\frac{\\text{a}}{12.0}')
# Quotient
# Not supported in latex!
x = myokit.Quotient(a, b)
self.assertEqual(
w.ex(x), '\\left\\lfloor\\frac{\\text{a}}{12.0}\\right\\rfloor')
# Remainder
x = myokit.Remainder(a, b)
self.assertEqual(w.ex(x), '\\bmod\\left(\\text{a},12.0\\right)')
# Power
x = myokit.Power(a, b)
self.assertEqual(w.ex(x), '\\text{a}^{12.0}')
# Power with brackets
x = myokit.Power(myokit.Plus(a, b), b)
self.assertEqual(w.ex(x), '\\left(\\text{a}+12.0\\right)^{12.0}')
# Sqrt
x = myokit.Sqrt(b)
self.assertEqual(w.ex(x), '\\sqrt{12.0}')
# Exp
x = myokit.Exp(a)
self.assertEqual(w.ex(x), '\\exp\\left(\\text{a}\\right)')
# Log(a)
x = myokit.Log(b)
self.assertEqual(w.ex(x), '\\log\\left(12.0\\right)')
# Log(a, b)
x = myokit.Log(a, b)
self.assertEqual(w.ex(x), '\\log_{12.0}\\left(\\text{a}\\right)')
# Log10
x = myokit.Log10(b)
self.assertEqual(w.ex(x), '\\log_{10.0}\\left(12.0\\right)')
# Sin
x = myokit.Sin(b)
self.assertEqual(w.ex(x), '\\sin\\left(12.0\\right)')
# Cos
x = myokit.Cos(b)
self.assertEqual(w.ex(x), '\\cos\\left(12.0\\right)')
# Tan
x = myokit.Tan(b)
self.assertEqual(w.ex(x), '\\tan\\left(12.0\\right)')
# ASin
x = myokit.ASin(b)
self.assertEqual(w.ex(x), '\\arcsin\\left(12.0\\right)')
# ACos
x = myokit.ACos(b)
self.assertEqual(w.ex(x), '\\arccos\\left(12.0\\right)')
# ATan
x = myokit.ATan(b)
self.assertEqual(w.ex(x), '\\arctan\\left(12.0\\right)')
# Floor
x = myokit.Floor(b)
self.assertEqual(w.ex(x), '\\left\\lfloor{12.0}\\right\\rfloor')
# Ceil
x = myokit.Ceil(b)
self.assertEqual(w.ex(x), '\\left\\lceil{12.0}\\right\\rceil')
# Abs
x = myokit.Abs(b)
self.assertEqual(w.ex(x), '\\lvert{12.0}\\rvert')
# Equal
x = myokit.Equal(a, b)
self.assertEqual(w.ex(x), '\\left(\\text{a}=12.0\\right)')
# NotEqual
x = myokit.NotEqual(a, b)
self.assertEqual(w.ex(x), '\\left(\\text{a}\\neq12.0\\right)')
# More
x = myokit.More(a, b)
self.assertEqual(w.ex(x), '\\left(\\text{a}>12.0\\right)')
# Less
x = myokit.Less(a, b)
self.assertEqual(w.ex(x), '\\left(\\text{a}<12.0\\right)')
# MoreEqual
x = myokit.MoreEqual(a, b)
self.assertEqual(w.ex(x), '\\left(\\text{a}\\geq12.0\\right)')
# LessEqual
x = myokit.LessEqual(a, b)
self.assertEqual(w.ex(x), '\\left(\\text{a}\\leq12.0\\right)')
# Not
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
x = myokit.Not(cond1)
self.assertEqual(w.ex(x), '\\not\\left(\\left(5.0>3.0\\right)\\right)')
# And
x = myokit.And(cond1, cond2)
self.assertEqual(
w.ex(x), '\\left(\\left(5.0>3.0\\right)\\and'
'\\left(2.0<1.0\\right)\\right)')
# Or
x = myokit.Or(cond1, cond2)
self.assertEqual(
w.ex(x), '\\left(\\left(5.0>3.0\\right)\\or'
'\\left(2.0<1.0\\right)\\right)')
# If
x = myokit.If(cond1, a, b)
self.assertEqual(
w.ex(x), 'if\\left(\\left(5.0>3.0\\right),\\text{a},12.0\\right)')
# Piecewise
c = myokit.Number(1)
x = myokit.Piecewise(cond1, a, cond2, b, c)
self.assertEqual(
w.ex(x), 'piecewise\\left(\\left(5.0>3.0\\right),\\text{a},'
'\\left(2.0<1.0\\right),12.0,1.0\\right)')
# Test fetching using ewriter method
w = myokit.formats.ewriter('latex')
self.assertIsInstance(w, myokit.formats.latex.LatexExpressionWriter)
# Test without a Myokit expression
self.assertRaisesRegex(ValueError, 'Unknown expression type', w.ex, 7)
def test_all(self):
# Single and double precision
ws = myokit.formats.cuda.CudaExpressionWriter()
wd = myokit.formats.cuda.CudaExpressionWriter(myokit.DOUBLE_PRECISION)
model = myokit.Model()
component = model.add_component('c')
avar = component.add_variable('a')
# Name
a = myokit.Name(avar)
self.assertEqual(ws.ex(a), 'c.a')
self.assertEqual(wd.ex(a), 'c.a')
# Number with unit
b = myokit.Number('12', 'pF')
self.assertEqual(ws.ex(b), '12.0f')
self.assertEqual(wd.ex(b), '12.0')
# Prefix plus
x = myokit.PrefixPlus(b)
self.assertEqual(ws.ex(x), '12.0f')
self.assertEqual(wd.ex(x), '12.0')
# Prefix minus
x = myokit.PrefixMinus(b)
self.assertEqual(ws.ex(x), '(-12.0f)')
self.assertEqual(wd.ex(x), '(-12.0)')
# Plus
x = myokit.Plus(a, b)
self.assertEqual(ws.ex(x), 'c.a + 12.0f')
self.assertEqual(wd.ex(x), 'c.a + 12.0')
# Minus
x = myokit.Minus(a, b)
self.assertEqual(ws.ex(x), 'c.a - 12.0f')
self.assertEqual(wd.ex(x), 'c.a - 12.0')
# Multiply
x = myokit.Multiply(a, b)
self.assertEqual(ws.ex(x), 'c.a * 12.0f')
self.assertEqual(wd.ex(x), 'c.a * 12.0')
# Divide
x = myokit.Divide(a, b)
self.assertEqual(ws.ex(x), 'c.a / 12.0f')
self.assertEqual(wd.ex(x), 'c.a / 12.0')
# Quotient
x = myokit.Quotient(a, b)
self.assertEqual(ws.ex(x), 'floorf(c.a / 12.0f)')
self.assertEqual(wd.ex(x), 'floor(c.a / 12.0)')
# Remainder
x = myokit.Remainder(a, b)
self.assertEqual(ws.ex(x), 'c.a - 12.0f * (floorf(c.a / 12.0f))')
self.assertEqual(wd.ex(x), 'c.a - 12.0 * (floor(c.a / 12.0))')
# Power
x = myokit.Power(a, b)
self.assertEqual(ws.ex(x), 'powf(c.a, 12.0f)')
self.assertEqual(wd.ex(x), 'pow(c.a, 12.0)')
# Square
x = myokit.Power(a, myokit.Number(2))
self.assertEqual(ws.ex(x), '(c.a * c.a)')
self.assertEqual(wd.ex(x), '(c.a * c.a)')
# Square with brackets
x = myokit.Power(myokit.Plus(a, b), myokit.Number(2))
self.assertEqual(ws.ex(x), '((c.a + 12.0f) * (c.a + 12.0f))')
self.assertEqual(wd.ex(x), '((c.a + 12.0) * (c.a + 12.0))')
# Sqrt
x = myokit.Sqrt(b)
self.assertEqual(ws.ex(x), 'sqrtf(12.0f)')
self.assertEqual(wd.ex(x), 'sqrt(12.0)')
# Exp
x = myokit.Exp(a)
self.assertEqual(ws.ex(x), 'expf(c.a)')
self.assertEqual(wd.ex(x), 'exp(c.a)')
# Log(a)
x = myokit.Log(b)
self.assertEqual(ws.ex(x), 'logf(12.0f)')
self.assertEqual(wd.ex(x), 'log(12.0)')
# Log(a, b)
x = myokit.Log(a, b)
self.assertEqual(ws.ex(x), '(logf(c.a) / logf(12.0f))')
self.assertEqual(wd.ex(x), '(log(c.a) / log(12.0))')
# Log10
x = myokit.Log10(b)
self.assertEqual(ws.ex(x), 'log10f(12.0f)')
self.assertEqual(wd.ex(x), 'log10(12.0)')
# Sin
x = myokit.Sin(b)
self.assertEqual(ws.ex(x), 'sinf(12.0f)')
self.assertEqual(wd.ex(x), 'sin(12.0)')
# Cos
x = myokit.Cos(b)
self.assertEqual(ws.ex(x), 'cosf(12.0f)')
self.assertEqual(wd.ex(x), 'cos(12.0)')
# Tan
x = myokit.Tan(b)
self.assertEqual(ws.ex(x), 'tanf(12.0f)')
self.assertEqual(wd.ex(x), 'tan(12.0)')
# ASin
x = myokit.ASin(b)
self.assertEqual(ws.ex(x), 'asinf(12.0f)')
self.assertEqual(wd.ex(x), 'asin(12.0)')
# ACos
x = myokit.ACos(b)
self.assertEqual(ws.ex(x), 'acosf(12.0f)')
self.assertEqual(wd.ex(x), 'acos(12.0)')
# ATan
x = myokit.ATan(b)
self.assertEqual(ws.ex(x), 'atanf(12.0f)')
self.assertEqual(wd.ex(x), 'atan(12.0)')
# Floor
x = myokit.Floor(b)
self.assertEqual(ws.ex(x), 'floorf(12.0f)')
self.assertEqual(wd.ex(x), 'floor(12.0)')
# Ceil
x = myokit.Ceil(b)
self.assertEqual(ws.ex(x), 'ceilf(12.0f)')
self.assertEqual(wd.ex(x), 'ceil(12.0)')
# Abs
x = myokit.Abs(b)
self.assertEqual(ws.ex(x), 'fabsf(12.0f)')
self.assertEqual(wd.ex(x), 'fabs(12.0)')
# Equal
x = myokit.Equal(a, b)
self.assertEqual(ws.ex(x), '(c.a == 12.0f)')
self.assertEqual(wd.ex(x), '(c.a == 12.0)')
# NotEqual
x = myokit.NotEqual(a, b)
self.assertEqual(ws.ex(x), '(c.a != 12.0f)')
self.assertEqual(wd.ex(x), '(c.a != 12.0)')
# More
x = myokit.More(a, b)
self.assertEqual(ws.ex(x), '(c.a > 12.0f)')
self.assertEqual(wd.ex(x), '(c.a > 12.0)')
# Less
x = myokit.Less(a, b)
self.assertEqual(ws.ex(x), '(c.a < 12.0f)')
self.assertEqual(wd.ex(x), '(c.a < 12.0)')
# MoreEqual
x = myokit.MoreEqual(a, b)
self.assertEqual(ws.ex(x), '(c.a >= 12.0f)')
self.assertEqual(wd.ex(x), '(c.a >= 12.0)')
# LessEqual
x = myokit.LessEqual(a, b)
self.assertEqual(ws.ex(x), '(c.a <= 12.0f)')
self.assertEqual(wd.ex(x), '(c.a <= 12.0)')
# Not
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
x = myokit.Not(cond1)
self.assertEqual(ws.ex(x), '!((5.0f > 3.0f))')
self.assertEqual(wd.ex(x), '!((5.0 > 3.0))')
# And
x = myokit.And(cond1, cond2)
self.assertEqual(ws.ex(x), '((5.0f > 3.0f) && (2.0f < 1.0f))')
self.assertEqual(wd.ex(x), '((5.0 > 3.0) && (2.0 < 1.0))')
# Or
x = myokit.Or(cond1, cond2)
self.assertEqual(ws.ex(x), '((5.0f > 3.0f) || (2.0f < 1.0f))')
self.assertEqual(wd.ex(x), '((5.0 > 3.0) || (2.0 < 1.0))')
# If
x = myokit.If(cond1, a, b)
self.assertEqual(ws.ex(x), '((5.0f > 3.0f) ? c.a : 12.0f)')
self.assertEqual(wd.ex(x), '((5.0 > 3.0) ? c.a : 12.0)')
# Piecewise
c = myokit.Number(1)
x = myokit.Piecewise(cond1, a, cond2, b, c)
self.assertEqual(
ws.ex(x), '((5.0f > 3.0f) ? c.a : ((2.0f < 1.0f) ? 12.0f : 1.0f))')
self.assertEqual(wd.ex(x),
'((5.0 > 3.0) ? c.a : ((2.0 < 1.0) ? 12.0 : 1.0))')
# Test fetching using ewriter method
w = myokit.formats.ewriter('cuda')
self.assertIsInstance(w, myokit.formats.cuda.CudaExpressionWriter)
# Test without a Myokit expression
self.assertRaisesRegex(ValueError, 'Unknown expression type', w.ex, 7)
def test_logical(self):
# Single and double precision and native maths
ws = myokit.formats.opencl.OpenCLExpressionWriter()
wd = myokit.formats.opencl.OpenCLExpressionWriter(
myokit.DOUBLE_PRECISION)
wn = myokit.formats.opencl.OpenCLExpressionWriter(native_math=False)
a = myokit.Name(myokit.Model().add_component('c').add_variable('a'))
b = myokit.Number('12', 'pF')
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
condx = myokit.Number(1.2)
# Not
x = myokit.Not(cond1)
self.assertEqual(ws.ex(x), '!((5.0f > 3.0f))')
self.assertEqual(wd.ex(x), '!((5.0 > 3.0))')
self.assertEqual(wn.ex(x), '!((5.0f > 3.0f))')
x = myokit.Not(condx)
self.assertEqual(ws.ex(x), '!((1.2f != 0.0f))')
self.assertEqual(wd.ex(x), '!((1.2 != 0.0))')
self.assertEqual(wn.ex(x), '!((1.2f != 0.0f))')
# And
x = myokit.And(cond1, cond2)
self.assertEqual(ws.ex(x), '((5.0f > 3.0f) && (2.0f < 1.0f))')
self.assertEqual(wd.ex(x), '((5.0 > 3.0) && (2.0 < 1.0))')
self.assertEqual(wn.ex(x), '((5.0f > 3.0f) && (2.0f < 1.0f))')
x = myokit.And(condx, cond2)
self.assertEqual(ws.ex(x), '((1.2f != 0.0f) && (2.0f < 1.0f))')
self.assertEqual(wd.ex(x), '((1.2 != 0.0) && (2.0 < 1.0))')
self.assertEqual(wn.ex(x), '((1.2f != 0.0f) && (2.0f < 1.0f))')
x = myokit.And(cond1, condx)
self.assertEqual(ws.ex(x), '((5.0f > 3.0f) && (1.2f != 0.0f))')
self.assertEqual(wd.ex(x), '((5.0 > 3.0) && (1.2 != 0.0))')
self.assertEqual(wn.ex(x), '((5.0f > 3.0f) && (1.2f != 0.0f))')
# Or
x = myokit.Or(cond1, cond2)
self.assertEqual(ws.ex(x), '((5.0f > 3.0f) || (2.0f < 1.0f))')
self.assertEqual(wd.ex(x), '((5.0 > 3.0) || (2.0 < 1.0))')
self.assertEqual(wn.ex(x), '((5.0f > 3.0f) || (2.0f < 1.0f))')
x = myokit.Or(condx, cond2)
self.assertEqual(ws.ex(x), '((1.2f != 0.0f) || (2.0f < 1.0f))')
self.assertEqual(wd.ex(x), '((1.2 != 0.0) || (2.0 < 1.0))')
self.assertEqual(wn.ex(x), '((1.2f != 0.0f) || (2.0f < 1.0f))')
x = myokit.Or(cond1, condx)
self.assertEqual(ws.ex(x), '((5.0f > 3.0f) || (1.2f != 0.0f))')
self.assertEqual(wd.ex(x), '((5.0 > 3.0) || (1.2 != 0.0))')
self.assertEqual(wn.ex(x), '((5.0f > 3.0f) || (1.2f != 0.0f))')
# If
x = myokit.If(cond1, a, b)
self.assertEqual(ws.ex(x), '((5.0f > 3.0f) ? c.a : 12.0f)')
self.assertEqual(wd.ex(x), '((5.0 > 3.0) ? c.a : 12.0)')
self.assertEqual(wn.ex(x), '((5.0f > 3.0f) ? c.a : 12.0f)')
x = myokit.If(condx, a, b)
self.assertEqual(ws.ex(x), '((1.2f != 0.0f) ? c.a : 12.0f)')
self.assertEqual(wd.ex(x), '((1.2 != 0.0) ? c.a : 12.0)')
self.assertEqual(wn.ex(x), '((1.2f != 0.0f) ? c.a : 12.0f)')
# Piecewise
c = myokit.Number(1)
x = myokit.Piecewise(cond1, a, cond2, b, c)
self.assertEqual(
ws.ex(x), '((5.0f > 3.0f) ? c.a : ((2.0f < 1.0f) ? 12.0f : 1.0f))')
self.assertEqual(wd.ex(x),
'((5.0 > 3.0) ? c.a : ((2.0 < 1.0) ? 12.0 : 1.0))')
self.assertEqual(
wn.ex(x), '((5.0f > 3.0f) ? c.a : ((2.0f < 1.0f) ? 12.0f : 1.0f))')
x = myokit.Piecewise(condx, a, condx, b, c)
self.assertEqual(
ws.ex(x),
'((1.2f != 0.0f) ? c.a : ((1.2f != 0.0f) ? 12.0f : 1.0f))')
self.assertEqual(wd.ex(x),
'((1.2 != 0.0) ? c.a : ((1.2 != 0.0) ? 12.0 : 1.0))')
self.assertEqual(
wn.ex(x),
'((1.2f != 0.0f) ? c.a : ((1.2f != 0.0f) ? 12.0f : 1.0f))')
def test_reader_writer(self):
# Test using the proper reader/writer
try:
import sympy as sp
except ImportError:
print('Sympy not found, skipping test.')
return
# Create writer and reader
w = mypy.SymPyExpressionWriter()
r = mypy.SymPyExpressionReader(self._model)
# Name
a = self._a
ca = sp.Symbol('c.a')
self.assertEqual(w.ex(a), ca)
self.assertEqual(r.ex(ca), a)
# Number with unit
b = myokit.Number('12', 'pF')
cb = sp.Float(12)
self.assertEqual(w.ex(b), cb)
# Note: Units are lost in sympy im/ex-port!
#self.assertEqual(r.ex(cb), b)
# Number without unit
b = myokit.Number('12')
cb = sp.Float(12)
self.assertEqual(w.ex(b), cb)
self.assertEqual(r.ex(cb), b)
# Prefix plus
x = myokit.PrefixPlus(b)
self.assertEqual(w.ex(x), cb)
# Note: Sympy doesn't seem to have a prefix plus
self.assertEqual(r.ex(cb), b)
# Prefix minus
# Note: SymPy treats -x as Mul(NegativeOne, x)
# But for numbers just returns a number with a negative value
x = myokit.PrefixMinus(b)
self.assertEqual(w.ex(x), -cb)
self.assertEqual(float(r.ex(-cb)), float(x))
# Plus
x = myokit.Plus(a, b)
self.assertEqual(w.ex(x), ca + cb)
# Note: SymPy likes to re-order the operands...
self.assertEqual(float(r.ex(ca + cb)), float(x))
# Minus
x = myokit.Minus(a, b)
self.assertEqual(w.ex(x), ca - cb)
self.assertEqual(float(r.ex(ca - cb)), float(x))
# Multiply
x = myokit.Multiply(a, b)
self.assertEqual(w.ex(x), ca * cb)
self.assertEqual(float(r.ex(ca * cb)), float(x))
# Divide
x = myokit.Divide(a, b)
self.assertEqual(w.ex(x), ca / cb)
self.assertEqual(float(r.ex(ca / cb)), float(x))
# Quotient
x = myokit.Quotient(a, b)
self.assertEqual(w.ex(x), ca // cb)
self.assertEqual(float(r.ex(ca // cb)), float(x))
# Remainder
x = myokit.Remainder(a, b)
self.assertEqual(w.ex(x), ca % cb)
self.assertEqual(float(r.ex(ca % cb)), float(x))
# Power
x = myokit.Power(a, b)
self.assertEqual(w.ex(x), ca**cb)
self.assertEqual(float(r.ex(ca**cb)), float(x))
# Sqrt
x = myokit.Sqrt(a)
cx = sp.sqrt(ca)
self.assertEqual(w.ex(x), cx)
# Note: SymPy converts sqrt to power
self.assertEqual(float(r.ex(cx)), float(x))
# Exp
x = myokit.Exp(a)
cx = sp.exp(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Log(a)
x = myokit.Log(a)
cx = sp.log(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Log(a, b)
x = myokit.Log(a, b)
cx = sp.log(ca, cb)
self.assertEqual(w.ex(x), cx)
self.assertEqual(float(r.ex(cx)), float(x))
# Log10
x = myokit.Log10(b)
cx = sp.log(cb, 10)
self.assertEqual(w.ex(x), cx)
self.assertAlmostEqual(float(r.ex(cx)), float(x))
# Sin
x = myokit.Sin(a)
cx = sp.sin(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Cos
x = myokit.Cos(a)
cx = sp.cos(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Tan
x = myokit.Tan(a)
cx = sp.tan(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# ASin
x = myokit.ASin(a)
cx = sp.asin(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# ACos
x = myokit.ACos(a)
cx = sp.acos(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# ATan
x = myokit.ATan(a)
cx = sp.atan(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Floor
x = myokit.Floor(a)
cx = sp.floor(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Ceil
x = myokit.Ceil(a)
cx = sp.ceiling(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Abs
x = myokit.Abs(a)
cx = sp.Abs(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Equal
x = myokit.Equal(a, b)
cx = sp.Eq(ca, cb)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# NotEqual
x = myokit.NotEqual(a, b)
cx = sp.Ne(ca, cb)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# More
x = myokit.More(a, b)
cx = sp.Gt(ca, cb)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Less
x = myokit.Less(a, b)
cx = sp.Lt(ca, cb)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# MoreEqual
x = myokit.MoreEqual(a, b)
cx = sp.Ge(ca, cb)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# LessEqual
x = myokit.LessEqual(a, b)
cx = sp.Le(ca, cb)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Not
x = myokit.Not(a)
cx = sp.Not(ca)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# And
cond1 = myokit.More(a, b)
cond2 = myokit.Less(a, b)
c1 = sp.Gt(ca, cb)
c2 = sp.Lt(ca, cb)
x = myokit.And(cond1, cond2)
cx = sp.And(c1, c2)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Or
x = myokit.Or(cond1, cond2)
cx = sp.Or(c1, c2)
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# If
# Note: sympy only does piecewise, not if
x = myokit.If(cond1, a, b)
cx = sp.Piecewise((ca, c1), (cb, True))
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x.piecewise())
# Piecewise
c = myokit.Number(1)
cc = sp.Float(1)
x = myokit.Piecewise(cond1, a, cond2, b, c)
cx = sp.Piecewise((ca, c1), (cb, c2), (cc, True))
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Myokit piecewise's (like CellML's) always have a final True
# condition (i.e. an 'else'). SymPy doesn't require this, so test if
# we can import this --> It will add an "else 0"
x = myokit.Piecewise(cond1, a, myokit.Number(0))
cx = sp.Piecewise((ca, c1))
self.assertEqual(r.ex(cx), x)
# SymPy function without Myokit equivalent --> Should raise exception
cu = sp.principal_branch(cx, cc)
self.assertRaisesRegex(ValueError, 'Unsupported type', r.ex, cu)
# Derivative
m = self._model.clone()
avar = m.get('c.a')
r = mypy.SymPyExpressionReader(self._model)
avar.promote(4)
x = myokit.Derivative(self._a)
cx = sp.symbols('dot(c.a)')
self.assertEqual(w.ex(x), cx)
self.assertEqual(r.ex(cx), x)
# Equation
e = myokit.Equation(a, b)
ce = sp.Eq(ca, cb)
self.assertEqual(w.eq(e), ce)
# There's no backwards equivalent for this!
# The ereader can handle it, but it becomes and Equals expression.
# Test sympy division
del (m, avar, x, cx, e, ce)
a = self._model.get('c.a')
b = self._model.get('c').add_variable('bbb')
b.set_rhs('1 / a')
e = b.rhs()
ce = w.ex(b.rhs())
e = r.ex(ce)
self.assertEqual(
e,
myokit.Multiply(myokit.Number(1),
myokit.Power(myokit.Name(a), myokit.Number(-1))))
# Test sympy negative numbers
a = self._model.get('c.a')
e1 = myokit.PrefixMinus(myokit.Name(a))
ce = w.ex(e1)
e2 = r.ex(ce)
self.assertEqual(e1, e2)
def add_embedded_protocol(model, protocol, add_oxmeta_annotations=True):
"""
Attempts to convert a :class:`myokit.Protocol` to a (discontinuous)
expression and embed it in the given :class`myokit.Model`.
Returns ``True`` if the model was succesfully updated.
This method is designed for protocols that contain a single, indefinitely
recurring event (e.g. cell pacing protocols), and doesn't handle other
forms of protocol.
If ``add_oxmeta_annotations`` is set to ``True``, the method will add
the relevant ``oxmeta`` annotations to any newly created variables
"""
# Get time variable
time = model.time()
if time is None:
return False
# Get pacing variable
v_pace = model.binding('pace')
if v_pace is None:
# Nothing bound to pace: Might be able to add protocol, but there'd be
# no point to it!
return False
# Check protocol has only a single event
if len(protocol) != 1:
return False
# Check it's an indefinitely recurring periodic event
event = protocol.head()
if event.period() == 0 or event.multiplier() != 0:
return False
# Check for existing stimulus variables
stim_info = stimulus_current_info(model)
v_current = stim_info['current']
v_amplitude = stim_info['amplitude']
e_amplitude = stim_info['amplitude_expression']
v_offset = stim_info['offset']
v_period = stim_info['period']
v_duration = stim_info['duration']
# Don't add a stimulus if there's already periodic stimulus variables about
if v_offset is not None or v_period is not None or v_duration is not None:
return False
del (v_offset, v_period, v_duration)
# Determine variable to update: pace or i_stim
if v_current is None or (v_amplitude is None and e_amplitude is None):
# Unable to set current as (...) * amplitude? Then update v_pace
updating_current = False
# VarOwner to add variables to
parent = v_pace
else:
# Able to set current as (...) * amplitude? Then update v_current
updating_current = True
# VarOwner to add variables to
parent = v_current
# Start modifying model
# Add new child variables with stimulus properties
v_offset = parent.add_variable_allow_renaming('offset')
v_offset.set_unit(time.unit())
v_offset.set_rhs(myokit.Number(event.start(), time.unit()))
v_period = parent.add_variable_allow_renaming('period')
v_period.set_unit(time.unit())
v_period.set_rhs(myokit.Number(event.period(), time.unit()))
v_duration = parent.add_variable_allow_renaming('duration')
v_duration.set_unit(time.unit())
v_duration.set_rhs(myokit.Number(event.duration(), time.unit()))
# Add oxmeta annotations for web lab
if updating_current and add_oxmeta_annotations:
v_offset.meta['oxmeta'] = 'membrane_stimulus_current_offset'
v_period.meta['oxmeta'] = 'membrane_stimulus_current_period'
v_duration.meta['oxmeta'] = 'membrane_stimulus_current_duration'
if v_amplitude is not None and 'oxmeta' not in v_amplitude.meta:
v_amplitude.meta['oxmeta'] = 'membrane_stimulus_current_amplitude'
# Create expression for pacing signal
pace_term = myokit.If(
myokit.Less(
myokit.Remainder(
myokit.Minus(myokit.Name(time), myokit.Name(v_offset)),
myokit.Name(v_period)), myokit.Name(v_duration)),
myokit.Number(event.level(), v_pace.unit()),
myokit.Number(0, v_pace.unit()))
if updating_current:
# Update current variable
if e_amplitude is None:
e_amplitude = myokit.Name(v_amplitude)
v_current.set_rhs(myokit.Multiply(pace_term, e_amplitude))
# Unbind pacing variable and remove if unused
v_pace.set_binding(None)
v_pace.set_rhs(myokit.Number(0, v_pace.unit()))
_remove_nested(v_pace)
if len(list(v_pace.refs_by())) == 0:
v_pace.parent().remove_variable(v_pace)
else:
# Update pacing variable
v_pace.set_rhs(pace_term)
# Unbind pacing variable
v_pace.set_binding(None)
# It worked!
return True
def test_all(self):
w = myokit.formats.ewriter('easyml')
model = myokit.Model()
component = model.add_component('c')
avar = component.add_variable('a')
# Name
a = myokit.Name(avar)
self.assertEqual(w.ex(a), 'c.a')
# Number with unit
b = myokit.Number('12', 'pF')
self.assertEqual(w.ex(b), '12.0')
# Integer
c = myokit.Number(1)
self.assertEqual(w.ex(c), '1.0')
# Integer
# Prefix plus
x = myokit.PrefixPlus(b)
self.assertEqual(w.ex(x), '12.0')
# Prefix minus
x = myokit.PrefixMinus(b)
self.assertEqual(w.ex(x), '(-12.0)')
# Plus
x = myokit.Plus(a, b)
self.assertEqual(w.ex(x), 'c.a + 12.0')
# Minus
x = myokit.Minus(a, b)
self.assertEqual(w.ex(x), 'c.a - 12.0')
# Multiply
x = myokit.Multiply(a, b)
self.assertEqual(w.ex(x), 'c.a * 12.0')
# Divide
x = myokit.Divide(a, b)
self.assertEqual(w.ex(x), 'c.a / 12.0')
# Quotient
x = myokit.Quotient(a, b)
with WarningCollector() as c:
self.assertEqual(w.ex(x), 'floor(c.a / 12.0)')
# Remainder
x = myokit.Remainder(a, b)
with WarningCollector() as c:
self.assertEqual(w.ex(x), 'c.a - 12.0 * (floor(c.a / 12.0))')
# Power
x = myokit.Power(a, b)
self.assertEqual(w.ex(x), 'pow(c.a, 12.0)')
# Sqrt
x = myokit.Sqrt(b)
self.assertEqual(w.ex(x), 'sqrt(12.0)')
# Exp
x = myokit.Exp(a)
self.assertEqual(w.ex(x), 'exp(c.a)')
# Log(a)
x = myokit.Log(b)
self.assertEqual(w.ex(x), 'log(12.0)')
# Log(a, b)
x = myokit.Log(a, b)
self.assertEqual(w.ex(x), '(log(c.a) / log(12.0))')
# Log10
x = myokit.Log10(b)
self.assertEqual(w.ex(x), 'log10(12.0)')
# Sin
with WarningCollector() as c:
x = myokit.Sin(b)
self.assertEqual(w.ex(x), 'sin(12.0)')
# Cos
x = myokit.Cos(b)
self.assertEqual(w.ex(x), 'cos(12.0)')
# Tan
x = myokit.Tan(b)
self.assertEqual(w.ex(x), 'tan(12.0)')
# ASin
x = myokit.ASin(b)
self.assertEqual(w.ex(x), 'asin(12.0)')
# ACos
x = myokit.ACos(b)
self.assertEqual(w.ex(x), 'acos(12.0)')
# ATan
x = myokit.ATan(b)
self.assertEqual(w.ex(x), 'atan(12.0)')
with WarningCollector() as c:
# Floor
x = myokit.Floor(b)
self.assertEqual(w.ex(x), 'floor(12.0)')
# Ceil
x = myokit.Ceil(b)
self.assertEqual(w.ex(x), 'ceil(12.0)')
# Abs
x = myokit.Abs(b)
self.assertEqual(w.ex(x), 'fabs(12.0)')
# Equal
x = myokit.Equal(a, b)
self.assertEqual(w.ex(x), '(c.a == 12.0)')
# NotEqual
x = myokit.NotEqual(a, b)
self.assertEqual(w.ex(x), '(c.a != 12.0)')
# More
x = myokit.More(a, b)
self.assertEqual(w.ex(x), '(c.a > 12.0)')
# Less
x = myokit.Less(a, b)
self.assertEqual(w.ex(x), '(c.a < 12.0)')
# MoreEqual
x = myokit.MoreEqual(a, b)
self.assertEqual(w.ex(x), '(c.a >= 12.0)')
# LessEqual
x = myokit.LessEqual(a, b)
self.assertEqual(w.ex(x), '(c.a <= 12.0)')
# Not
cond1 = myokit.parse_expression('5 > 3')
cond2 = myokit.parse_expression('2 < 1')
x = myokit.Not(cond1)
self.assertEqual(w.ex(x), '!((5.0 > 3.0))')
# And
x = myokit.And(cond1, cond2)
self.assertEqual(w.ex(x), '((5.0 > 3.0) and (2.0 < 1.0))')
# Or
x = myokit.Or(cond1, cond2)
self.assertEqual(w.ex(x), '((5.0 > 3.0) or (2.0 < 1.0))')
# If
x = myokit.If(cond1, a, b)
self.assertEqual(w.ex(x), '((5.0 > 3.0) ? c.a : 12.0)')
# Piecewise
c = myokit.Number(1)
x = myokit.Piecewise(cond1, a, cond2, b, c)
self.assertEqual(w.ex(x),
'((5.0 > 3.0) ? c.a : ((2.0 < 1.0) ? 12.0 : 1.0))')
# Test without a Myokit expression
self.assertRaisesRegex(ValueError, 'Unknown expression type', w.ex, 7)
def test_conditionals(self):
# Tests if and piecewise parsing
# If
a = myokit.Name('c.a')
b = myokit.Number(1.0)
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>'
e = myokit.If(cond1, a, b)
x = (
'<piecewise>'
'<piece><ci>c.a</ci>' + c1 + '</piece>'
'<otherwise><cn>1.0</cn></otherwise>'
'</piecewise>'
)
self.assertEqual(self.p(x), e.piecewise())
# Piecewise
e = myokit.Piecewise(cond1, a, cond2, b, myokit.Number(100))
x = (
'<piecewise>'
'<piece><ci>c.a</ci>' + c1 + '</piece>'
'<piece><cn>1.0</cn>' + c2 + '</piece>'
'<otherwise><cn>100.0</cn></otherwise>'
'</piecewise>'
)
self.assertEqual(self.p(x), e)
# Piecewise with extra otherwise
x = (
'<piecewise>'
' <piece>'
' <cn>1.0</cn><apply><eq/><cn>1.0</cn><cn>1.0</cn></apply>'
' </piece>'
' <otherwise>'
' <cn>2</cn>'
' </otherwise>'
' <otherwise>'
' <cn>3</cn>'
' </otherwise>'
'</piecewise>'
)
self.assertRaisesRegex(
mathml.MathMLError, 'Found more than one <otherwise>', self.p, x)
# Check otherwise is automatically added if not given
x = (
'<piecewise>'
' <piece>'
' <cn>2</cn><apply><eq/><cn>1.0</cn><cn>1.0</cn></apply>'
' </piece>'
' <piece>'
' <cn>1.0</cn><apply><eq/><cn>1.0</cn><cn>1.0</cn></apply>'
' </piece>'
'</piecewise>'
)
e = self.p(x)
pieces = list(e.pieces())
self.assertEqual(len(pieces), 3)
self.assertEqual(pieces[0], myokit.Number(2))
self.assertEqual(pieces[1], myokit.Number(1))
self.assertEqual(pieces[2], myokit.Number(0))
# Too much stuff in a piece
x = (
'<piecewise>'
' <piece>'
' <cn>1</cn><apply><eq/><cn>1</cn><cn>1</cn></apply>'
' <cn>2</cn>'
' </piece>'
' <otherwise>'
' <cn>3</cn>'
' </otherwise>'
'</piecewise>'
)
self.assertRaisesRegex(
mathml.MathMLError, '<piece> element must have exactly 2 children',
self.p, x)
# Too much stuff in an otherwise
x = (
'<piecewise>'
' <piece>'
' <cn>1</cn><apply><eq/><cn>1</cn><cn>1</cn></apply>'
' </piece>'
' <otherwise>'
' <cn>3</cn><ci>x</ci>'
' </otherwise>'
'</piecewise>'
)
self.assertRaisesRegex(
mathml.MathMLError, '<otherwise> element must have exactly 1',
self.p, x)
# Unexpected tag in piecwise
x = (
'<piecewise>'
' <piece>'
' <cn>1.0</cn><apply><eq/><cn>1.0</cn><cn>1.0</cn></apply>'
' </piece>'
' <otherwise>'
' <cn>3</cn>'
' </otherwise>'
' <apply><eq/><cn>1.0</cn><cn>1.0</cn></apply>'
'</piecewise>'
)
self.assertRaisesRegex(
mathml.MathMLError, 'Unexpected content in <piecewise>', self.p, x)
