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_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 test_functions(self):
# Tests parsing 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.assertEqual(self.p(x), e)
#TODO: Degree etc.
# Exp
e = myokit.Exp(a)
x = '<apply><exp/><ci>a</ci></apply>'
self.assertEqual(self.p(x), e)
# No operands
x = '<apply><exp/></apply>'
self.assertRaisesRegex(
mathml.MathMLError, 'Expecting 1 operand\(s\)', self.p, x)
# Too many operands
x = '<apply><exp/><cn>1</cn><cn>2</cn></apply>'
self.assertRaisesRegex(
mathml.MathMLError, 'Expecting 1 operand\(s\)', self.p, x)
# Floor
e = myokit.Floor(b)
x = '<apply><floor/><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# Ceil
e = myokit.Ceil(b)
x = '<apply><ceiling/><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# Abs
e = myokit.Abs(b)
x = '<apply><abs/><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# Quotient
e = myokit.Quotient(a, b)
x = '<apply><quotient/><ci>a</ci><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
# Remainder
e = myokit.Remainder(a, b)
x = '<apply><rem/><ci>a</ci><cn>1.0</cn></apply>'
self.assertEqual(self.p(x), e)
def _ex_quotient(self, e):
return self.ex(myokit.Floor(myokit.Divide(e[0], e[1])))
def _ex_quotient(self, e):
# Note that this _must_ round towards minus infinity.
# See myokit.Quotient.
# Assuming it follows C and so we need a custom implementation.
return self.ex(myokit.Floor(myokit.Divide(e[0], e[1])))
def _ex_quotient(self, e, t):
# CellML 1.0 subset doesn't contain quotient
# Note that this _must_ round towards minus infinity!
# See myokit.Quotient !
return self.ex(myokit.Floor(myokit.Divide(e[0], e[1])), t)
def _ex_quotient(self, e, t):
# Note that this _must_ round towards minus infinity!
# See myokit.Quotient !
return self.ex(myokit.Floor(myokit.Divide(e[0], e[1])), t)
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_functions(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')
# Power
x = myokit.Power(a, b)
self.assertEqual(ws.ex(x), 'pow(c.a, 12.0f)')
self.assertEqual(wd.ex(x), 'pow(c.a, 12.0)')
self.assertEqual(wn.ex(x), 'pow(c.a, 12.0f)')
# 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)')
self.assertEqual(wn.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))')
self.assertEqual(wn.ex(x), '((c.a + 12.0f) * (c.a + 12.0f))')
# Sqrt
x = myokit.Sqrt(b)
self.assertEqual(ws.ex(x), 'native_sqrt(12.0f)')
self.assertEqual(wd.ex(x), 'native_sqrt(12.0)')
self.assertEqual(wn.ex(x), 'sqrt(12.0f)')
# Exp
x = myokit.Exp(a)
self.assertEqual(ws.ex(x), 'native_exp(c.a)')
self.assertEqual(wd.ex(x), 'native_exp(c.a)')
self.assertEqual(wn.ex(x), 'exp(c.a)')
# Log(a)
x = myokit.Log(b)
self.assertEqual(ws.ex(x), 'native_log(12.0f)')
self.assertEqual(wd.ex(x), 'native_log(12.0)')
self.assertEqual(wn.ex(x), 'log(12.0f)')
# Log(a, b)
x = myokit.Log(a, b)
self.assertEqual(ws.ex(x), '(native_log(c.a) / native_log(12.0f))')
self.assertEqual(wd.ex(x), '(native_log(c.a) / native_log(12.0))')
self.assertEqual(wn.ex(x), '(log(c.a) / log(12.0f))')
# Log10
x = myokit.Log10(b)
self.assertEqual(ws.ex(x), 'native_log10(12.0f)')
self.assertEqual(wd.ex(x), 'native_log10(12.0)')
self.assertEqual(wn.ex(x), 'log10(12.0f)')
# Sin
x = myokit.Sin(b)
self.assertEqual(ws.ex(x), 'native_sin(12.0f)')
self.assertEqual(wd.ex(x), 'native_sin(12.0)')
self.assertEqual(wn.ex(x), 'sin(12.0f)')
# Cos
x = myokit.Cos(b)
self.assertEqual(ws.ex(x), 'native_cos(12.0f)')
self.assertEqual(wd.ex(x), 'native_cos(12.0)')
self.assertEqual(wn.ex(x), 'cos(12.0f)')
# Tan
x = myokit.Tan(b)
self.assertEqual(ws.ex(x), 'native_tan(12.0f)')
self.assertEqual(wd.ex(x), 'native_tan(12.0)')
self.assertEqual(wn.ex(x), 'tan(12.0f)')
# ASin
x = myokit.ASin(b)
self.assertEqual(ws.ex(x), 'asin(12.0f)')
self.assertEqual(wd.ex(x), 'asin(12.0)')
self.assertEqual(wn.ex(x), 'asin(12.0f)')
# ACos
x = myokit.ACos(b)
self.assertEqual(ws.ex(x), 'acos(12.0f)')
self.assertEqual(wd.ex(x), 'acos(12.0)')
self.assertEqual(wn.ex(x), 'acos(12.0f)')
# ATan
x = myokit.ATan(b)
self.assertEqual(ws.ex(x), 'atan(12.0f)')
self.assertEqual(wd.ex(x), 'atan(12.0)')
self.assertEqual(wn.ex(x), 'atan(12.0f)')
# Floor
x = myokit.Floor(b)
self.assertEqual(ws.ex(x), 'floor(12.0f)')
self.assertEqual(wd.ex(x), 'floor(12.0)')
self.assertEqual(wn.ex(x), 'floor(12.0f)')
# Ceil
x = myokit.Ceil(b)
self.assertEqual(ws.ex(x), 'ceil(12.0f)')
self.assertEqual(wd.ex(x), 'ceil(12.0)')
self.assertEqual(wn.ex(x), 'ceil(12.0f)')
# Abs
x = myokit.Abs(b)
self.assertEqual(ws.ex(x), 'fabs(12.0f)')
self.assertEqual(wd.ex(x), 'fabs(12.0)')
self.assertEqual(wn.ex(x), 'fabs(12.0f)')
def _ex_quotient(self, e):
# Use floor to round towards minus infinity
return self.ex(myokit.Floor(myokit.Divide(e[0], e[1])))
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 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 _ex_floor(self, e):
return myokit.Floor(self.ex(e.args[0]))
def _parse_apply(self, apply_element):
"""
Parses an ``<apply>`` element.
"""
# Apply must have kids
if len(apply_element) == 0:
raise MathMLError('Apply must contain at least one child element.',
apply_element)
# Get first child
iterator = iter(apply_element)
element = self._next(iterator)
# Decide what to do based on first child
_, name = split(element.tag)
# Handle derivative
if name == 'diff':
return self._parse_derivative(element, iterator)
# Algebra (unary/binary/n-ary operators)
elif name == 'plus':
return self._parse_nary(element, iterator, myokit.Plus,
myokit.PrefixPlus)
elif name == 'minus':
return self._parse_nary(element, iterator, myokit.Minus,
myokit.PrefixMinus)
elif name == 'times':
return self._parse_nary(element, iterator, myokit.Multiply)
elif name == 'divide':
return self._parse_nary(element, iterator, myokit.Divide)
# Basic functions
elif name == 'exp':
return myokit.Exp(*self._eat(element, iterator))
elif name == 'ln':
return myokit.Log(*self._eat(element, iterator))
elif name == 'log':
return self._parse_log(element, iterator)
elif name == 'root':
return self._parse_root(element, iterator)
elif name == 'power':
return myokit.Power(*self._eat(element, iterator, 2))
elif name == 'floor':
return myokit.Floor(*self._eat(element, iterator))
elif name == 'ceiling':
return myokit.Ceil(*self._eat(element, iterator))
elif name == 'abs':
return myokit.Abs(*self._eat(element, iterator))
elif name == 'quotient':
return myokit.Quotient(*self._eat(element, iterator, 2))
elif name == 'rem':
return myokit.Remainder(*self._eat(element, iterator, 2))
# Logic
elif name == 'and':
return self._parse_nary(element, iterator, myokit.And)
elif name == 'or':
return self._parse_nary(element, iterator, myokit.Or)
elif name == 'xor':
# Becomes ``(x or y) and not(x and y)``
x, y = self._eat(element, iterator, 2)
return myokit.And(myokit.Or(x, y), myokit.Not(myokit.And(x, y)))
elif name == 'not':
return myokit.Not(*self._eat(element, iterator))
elif name == 'eq' or name == 'equivalent':
return myokit.Equal(*self._eat(element, iterator, 2))
elif name == 'neq':
return myokit.NotEqual(*self._eat(element, iterator, 2))
elif name == 'gt':
return myokit.More(*self._eat(element, iterator, 2))
elif name == 'lt':
return myokit.Less(*self._eat(element, iterator, 2))
elif name == 'geq':
return myokit.MoreEqual(*self._eat(element, iterator, 2))
elif name == 'leq':
return myokit.LessEqual(*self._eat(element, iterator, 2))
# Trigonometry
elif name == 'sin':
return myokit.Sin(*self._eat(element, iterator))
elif name == 'cos':
return myokit.Cos(*self._eat(element, iterator))
elif name == 'tan':
return myokit.Tan(*self._eat(element, iterator))
elif name == 'arcsin':
return myokit.ASin(*self._eat(element, iterator))
elif name == 'arccos':
return myokit.ACos(*self._eat(element, iterator))
elif name == 'arctan':
return myokit.ATan(*self._eat(element, iterator))
# Redundant trigonometry (CellML includes this)
elif name == 'csc':
# Cosecant: csc(x) = 1 / sin(x)
return myokit.Divide(self._const(1),
myokit.Sin(*self._eat(element, iterator)))
elif name == 'sec':
# Secant: sec(x) = 1 / cos(x)
return myokit.Divide(self._const(1),
myokit.Cos(*self._eat(element, iterator)))
elif name == 'cot':
# Contangent: cot(x) = 1 / tan(x)
return myokit.Divide(self._const(1),
myokit.Tan(*self._eat(element, iterator)))
elif name == 'arccsc':
# ArcCosecant: acsc(x) = asin(1/x)
return myokit.ASin(
myokit.Divide(self._const(1), *self._eat(element, iterator)))
elif name == 'arcsec':
# ArcSecant: asec(x) = acos(1/x)
return myokit.ACos(
myokit.Divide(self._const(1), *self._eat(element, iterator)))
elif name == 'arccot':
# ArcCotangent: acot(x) = atan(1/x)
return myokit.ATan(
myokit.Divide(self._const(1), *self._eat(element, iterator)))
# Hyperbolic trig
elif name == 'sinh':
# Hyperbolic sine: sinh(x) = 0.5 * (e^x - e^-x)
x = self._eat(element, iterator)[0]
return myokit.Multiply(
self._const(0.5),
myokit.Minus(myokit.Exp(x), myokit.Exp(myokit.PrefixMinus(x))))
elif name == 'cosh':
# Hyperbolic cosine: cosh(x) = 0.5 * (e^x + e^-x)
x = self._eat(element, iterator)[0]
return myokit.Multiply(
self._const(0.5),
myokit.Plus(myokit.Exp(x), myokit.Exp(myokit.PrefixMinus(x))))
elif name == 'tanh':
# Hyperbolic tangent: tanh(x) = (e^2x - 1) / (e^2x + 1)
x = self._eat(element, iterator)[0]
e2x = myokit.Exp(myokit.Multiply(self._const(2), x))
return myokit.Divide(myokit.Minus(e2x, self._const(1)),
myokit.Plus(e2x, self._const(1)))
elif name == 'arcsinh':
# Inverse hyperbolic sine: asinh(x) = log(x + sqrt(x*x + 1))
x = self._eat(element, iterator)[0]
return myokit.Log(
myokit.Plus(
x,
myokit.Sqrt(
myokit.Plus(myokit.Multiply(x, x), self._const(1)))))
elif name == 'arccosh':
# Inverse hyperbolic cosine:
# acosh(x) = log(x + sqrt(x*x - 1))
x = self._eat(element, iterator)[0]
return myokit.Log(
myokit.Plus(
x,
myokit.Sqrt(
myokit.Minus(myokit.Multiply(x, x), self._const(1)))))
elif name == 'arctanh':
# Inverse hyperbolic tangent:
# atanh(x) = 0.5 * log((1 + x) / (1 - x))
x = self._eat(element, iterator)[0]
return myokit.Multiply(
self._const(0.5),
myokit.Log(
myokit.Divide(myokit.Plus(self._const(1), x),
myokit.Minus(self._const(1), x))))
# Hyperbolic redundant trig
elif name == 'csch':
# Hyperbolic cosecant: csch(x) = 2 / (exp(x) - exp(-x))
x = self._eat(element, iterator)[0]
return myokit.Divide(
self._const(2),
myokit.Minus(myokit.Exp(x), myokit.Exp(myokit.PrefixMinus(x))))
elif name == 'sech':
# Hyperbolic secant: sech(x) = 2 / (exp(x) + exp(-x))
x = self._eat(element, iterator)[0]
return myokit.Divide(
self._const(2),
myokit.Plus(myokit.Exp(x), myokit.Exp(myokit.PrefixMinus(x))))
elif name == 'coth':
# Hyperbolic cotangent:
# coth(x) = (exp(2*x) + 1) / (exp(2*x) - 1)
x = self._eat(element, iterator)[0]
e2x = myokit.Exp(myokit.Multiply(self._const(2), x))
return myokit.Divide(myokit.Plus(e2x, self._const(1)),
myokit.Minus(e2x, self._const(1)))
elif name == 'arccsch':
# Inverse hyperbolic cosecant:
# arccsch(x) = log(1 / x + sqrt(1 / x^2 + 1))
x = self._eat(element, iterator)[0]
return myokit.Log(
myokit.Plus(
myokit.Divide(self._const(1), x),
myokit.Sqrt(
myokit.Plus(
myokit.Divide(self._const(1),
myokit.Multiply(x, x)),
self._const(1)))))
elif name == 'arcsech':
# Inverse hyperbolic secant:
# arcsech(x) = log(1 / x + sqrt(1 / x^2 - 1))
x = self._eat(element, iterator)[0]
return myokit.Log(
myokit.Plus(
myokit.Divide(self._const(1), x),
myokit.Sqrt(
myokit.Minus(
myokit.Divide(self._const(1),
myokit.Multiply(x, x)),
self._const(1)))))
elif name == 'arccoth':
# Inverse hyperbolic cotangent:
# arccoth(x) = 0.5 * log((x + 1) / (x - 1))
x = self._eat(element, iterator)[0]
return myokit.Multiply(
self._const(0.5),
myokit.Log(
myokit.Divide(myokit.Plus(x, self._const(1)),
myokit.Minus(x, self._const(1)))))
# Last option: A single atomic inside an apply
# Do this one last to stop e.g. <apply><times /></apply> returning the
# error 'Unsupported element' (which is what parse_atomic would call).
elif len(apply_element) == 1:
return self._parse_atomic(element)
# Unexpected element
else:
raise MathMLError(
'Unsupported element in apply: ' + str(element.tag) + '.',
element)
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 parsex(node):
"""
Parses a mathml expression.
"""
def chain(kind, node, unary=None):
"""
Parses operands for chained operators (for example plus, minus,
times and division).
The argument ``kind`` must be the myokit expression type being
parsed, ``node`` is a DOM node and ``unary``, if given, should be
the unary expression type (unary Plus or unary Minus).
"""
ops = []
node = dom_next(node)
while node:
ops.append(parsex(node))
node = dom_next(node)
n = len(ops)
if n < 1:
raise MathMLError('Operator needs at least one operand.')
if n < 2:
if unary:
return unary(ops[0])
else:
raise MathMLError('Operator needs at least two operands')
ex = kind(ops[0], ops[1])
for i in range(2, n):
ex = kind(ex, ops[i])
return ex
# Start parsing
name = node.tagName
if name == 'apply':
# Brackets, can be ignored in an expression tree.
return parsex(dom_child(node))
elif name == 'ci':
# Reference
var = str(node.firstChild.data).strip()
if var_table is not None:
try:
var = var_table[var]
except KeyError:
if logger:
logger.warn('Unable to resolve reference to <' +
str(var) + '>.')
return myokit.Name(var)
elif name == 'diff':
# Derivative
# Check time variable
bvar = dom_next(node, 'bvar')
if derivative_post_processor:
derivative_post_processor(parsex(dom_child(bvar, 'ci')))
# Check degree, if given
d = dom_child(bvar, 'degree')
if d is not None:
d = parsex(dom_child(d, 'cn')).eval()
if not d == 1:
raise MathMLError(
'Only derivatives of degree one are supported.')
# Create derivative and return
x = dom_next(node, 'ci')
if x is None:
raise MathMLError(
'Derivative of an expression found: only derivatives of'
' variables are supported.')
return myokit.Derivative(parsex(x))
elif name == 'cn':
# Number
number = parse_mathml_number(node, logger)
if number_post_processor:
return number_post_processor(node, number)
return number
#
# Algebra
#
elif name == 'plus':
return chain(myokit.Plus, node, myokit.PrefixPlus)
elif name == 'minus':
return chain(myokit.Minus, node, myokit.PrefixMinus)
elif name == 'times':
return chain(myokit.Multiply, node)
elif name == 'divide':
return chain(myokit.Divide, node)
#
# Functions
#
elif name == 'exp':
return myokit.Exp(parsex(dom_next(node)))
elif name == 'ln':
return myokit.Log(parsex(dom_next(node)))
elif name == 'log':
if dom_next(node).tagName != 'logbase':
return myokit.Log10(parsex(dom_next(node)))
else:
return myokit.Log(parsex(dom_next(dom_next(node))),
parsex(dom_child(dom_next(node))))
elif name == 'root':
# Check degree, if given
nxt = dom_next(node)
if nxt.tagName == 'degree':
# Degree given, return x^(1/d) unless d is 2
d = parsex(dom_child(nxt))
x = parsex(dom_next(nxt))
if d.is_literal() and d.eval() == 2:
return myokit.Sqrt(x)
return myokit.Power(x, myokit.Divide(myokit.Number(1), d))
else:
return myokit.Sqrt(parsex(nxt))
elif name == 'power':
n2 = dom_next(node)
return myokit.Power(parsex(n2), parsex(dom_next(n2)))
elif name == 'floor':
return myokit.Floor(parsex(dom_next(node)))
elif name == 'ceiling':
return myokit.Ceil(parsex(dom_next(node)))
elif name == 'abs':
return myokit.Abs(parsex(dom_next(node)))
elif name == 'quotient':
n2 = dom_next(node)
return myokit.Quotient(parsex(n2), parsex(dom_next(n2)))
elif name == 'rem':
n2 = dom_next(node)
return myokit.Remainder(parsex(n2), parsex(dom_next(n2)))
#
# Trigonometry
#
elif name == 'sin':
return myokit.Sin(parsex(dom_next(node)))
elif name == 'cos':
return myokit.Cos(parsex(dom_next(node)))
elif name == 'tan':
return myokit.Tan(parsex(dom_next(node)))
elif name == 'arcsin':
return myokit.ASin(parsex(dom_next(node)))
elif name == 'arccos':
return myokit.ACos(parsex(dom_next(node)))
elif name == 'arctan':
return myokit.ATan(parsex(dom_next(node)))
#
# Redundant trigonometry (CellML includes this)
#
elif name == 'csc':
# Cosecant: csc(x) = 1 / sin(x)
return myokit.Divide(myokit.Number(1),
myokit.Sin(parsex(dom_next(node))))
elif name == 'sec':
# Secant: sec(x) = 1 / cos(x)
return myokit.Divide(myokit.Number(1),
myokit.Cos(parsex(dom_next(node))))
elif name == 'cot':
# Contangent: cot(x) = 1 / tan(x)
return myokit.Divide(myokit.Number(1),
myokit.Tan(parsex(dom_next(node))))
elif name == 'arccsc':
# ArcCosecant: acsc(x) = asin(1/x)
return myokit.ASin(
myokit.Divide(myokit.Number(1), parsex(dom_next(node))))
elif name == 'arcsec':
# ArcSecant: asec(x) = acos(1/x)
return myokit.ACos(
myokit.Divide(myokit.Number(1), parsex(dom_next(node))))
elif name == 'arccot':
# ArcCotangent: acot(x) = atan(1/x)
return myokit.ATan(
myokit.Divide(myokit.Number(1), parsex(dom_next(node))))
#
# Hyperbolic trigonometry (CellML again)
#
elif name == 'sinh':
# Hyperbolic sine: sinh(x) = 0.5 * (e^x - e^-x)
x = parsex(dom_next(node))
return myokit.Multiply(
myokit.Number(0.5),
myokit.Minus(myokit.Exp(x), myokit.Exp(myokit.PrefixMinus(x))))
elif name == 'cosh':
# Hyperbolic cosine: cosh(x) = 0.5 * (e^x + e^-x)
x = parsex(dom_next(node))
return myokit.Multiply(
myokit.Number(0.5),
myokit.Plus(myokit.Exp(x), myokit.Exp(myokit.PrefixMinus(x))))
elif name == 'tanh':
# Hyperbolic tangent: tanh(x) = (e^2x - 1) / (e^2x + 1)
x = parsex(dom_next(node))
e2x = myokit.Exp(myokit.Multiply(myokit.Number(2), x))
return myokit.Divide(myokit.Minus(e2x, myokit.Number(1)),
myokit.Plus(e2x, myokit.Number(1)))
#
# Inverse hyperbolic trigonometry (CellML...)
#
elif name == 'arcsinh':
# Inverse hyperbolic sine: asinh(x) = log(x + sqrt(1 + x*x))
x = parsex(dom_next(node))
return myokit.Log(
myokit.Plus(
x,
myokit.Sqrt(
myokit.Plus(myokit.Number(1), myokit.Multiply(x, x)))))
elif name == 'arccosh':
# Inverse hyperbolic cosine:
# acosh(x) = log(x + sqrt(x + 1) * sqrt(x - 1))
x = parsex(dom_next(node))
return myokit.Log(
myokit.Plus(
x,
myokit.Multiply(
myokit.Sqrt(myokit.Plus(x, myokit.Number(1))),
myokit.Sqrt(myokit.Minus(x, myokit.Number(1))))))
elif name == 'arctanh':
# Inverse hyperbolic tangent:
# atanh(x) = 0.5 * (log(1 + x) - log(1 - x))
x = parsex(dom_next(node))
return myokit.Multiply(
myokit.Number(0.5),
myokit.Minus(myokit.Log(myokit.Plus(myokit.Number(1), x)),
myokit.Log(myokit.Minus(myokit.Number(1), x))))
#
# Hyperbolic redundant trigonometry (CellML...)
#
elif name == 'csch':
# Hyperbolic cosecant: csch(x) = 2 / (exp(x) - exp(-x))
x = parsex(dom_next(node))
return myokit.Divide(
myokit.Number(2),
myokit.Minus(myokit.Exp(x), myokit.Exp(myokit.PrefixMinus(x))))
elif name == 'sech':
# Hyperbolic secant: sech(x) = 2 / (exp(x) + exp(-x))
x = parsex(dom_next(node))
return myokit.Divide(
myokit.Number(2),
myokit.Plus(myokit.Exp(x), myokit.Exp(myokit.PrefixMinus(x))))
elif name == 'coth':
# Hyperbolic cotangent:
# coth(x) = (exp(2*x) + 1) / (exp(2*x) - 1)
x = parsex(dom_next(node))
e2x = myokit.Exp(myokit.Multiply(myokit.Number(2), x))
return myokit.Divide(myokit.Plus(e2x, myokit.Number(1)),
myokit.Minus(e2x, myokit.Number(1)))
#
# Inverse hyperbolic redundant trigonometry (CellML has a lot to answer
# for...)
#
elif name == 'arccsch':
# Inverse hyperbolic cosecant:
# arccsch(x) = log(sqrt(1/(x*x) + 1) + 1/x)
x = parsex(dom_next(node))
return myokit.Log(
myokit.Plus(
myokit.Sqrt(
myokit.Plus(
myokit.Divide(myokit.Number(1),
myokit.Multiply(x, x)),
myokit.Number(1))),
myokit.Divide(myokit.Number(1), x)))
elif name == 'arcsech':
# Inverse hyperbolic secant:
# arcsech(x) = log(sqrt(1/(x*x) - 1) + 1/x)
x = parsex(dom_next(node))
return myokit.Log(
myokit.Plus(
myokit.Sqrt(
myokit.Minus(
myokit.Divide(myokit.Number(1),
myokit.Multiply(x, x)),
myokit.Number(1))),
myokit.Divide(myokit.Number(1), x)))
elif name == 'arccoth':
# Inverse hyperbolic cotangent:
# arccoth(x) = 0.5 * (log(3 + 1) - log(3 - 1))
x = parsex(dom_next(node))
return myokit.Multiply(
myokit.Number(0.5),
myokit.Log(
myokit.Divide(myokit.Plus(x, myokit.Number(1)),
myokit.Minus(x, myokit.Number(1)))))
#
# Logic
#
elif name == 'and':
return chain(myokit.And, node)
elif name == 'or':
return chain(myokit.Or, node)
elif name == 'not':
return chain(None, node, myokit.Not)
elif name == 'eq' or name == 'equivalent':
n2 = dom_next(node)
return myokit.Equal(parsex(n2), parsex(dom_next(n2)))
elif name == 'neq':
n2 = dom_next(node)
return myokit.NotEqual(parsex(n2), parsex(dom_next(n2)))
elif name == 'gt':
n2 = dom_next(node)
return myokit.More(parsex(n2), parsex(dom_next(n2)))
elif name == 'lt':
n2 = dom_next(node)
return myokit.Less(parsex(n2), parsex(dom_next(n2)))
elif name == 'geq':
n2 = dom_next(node)
return myokit.MoreEqual(parsex(n2), parsex(dom_next(n2)))
elif name == 'leq':
n2 = dom_next(node)
return myokit.LessEqual(parsex(n2), parsex(dom_next(n2)))
elif name == 'piecewise':
# Piecewise contains at least one piece, optionally contains an
# "otherwise". Syntax doesn't ensure this statement makes sense.
conds = []
funcs = []
other = None
piece = dom_child(node)
while piece:
if piece.tagName == 'otherwise':
if other is None:
other = parsex(dom_child(piece))
elif logger:
logger.warn(
'Multiple <otherwise> tags found in <piecewise>'
' statement.')
elif piece.tagName == 'piece':
n2 = dom_child(piece)
funcs.append(parsex(n2))
conds.append(parsex(dom_next(n2)))
elif logger:
logger.warn('Unexpected tag type in <piecewise>: <' +
piece.tagName + '>.')
piece = dom_next(piece)
if other is None:
if logger:
logger.warn('No <otherwise> tag found in <piecewise>')
other = myokit.Number(0)
# Create string of if statements
args = []
f = iter(funcs)
for c in conds:
args.append(c)
args.append(next(f))
args.append(other)
return myokit.Piecewise(*args)
#
# Constants
#
elif name == 'pi':
return myokit.Number('3.14159265358979323846')
elif name == 'exponentiale':
return myokit.Exp(myokit.Number(1))
elif name == 'true':
# This is corrent, even in Python True == 1 but not True == 2
return myokit.Number(1)
elif name == 'false':
return myokit.Number(0)
#
# Unknown/unhandled elements
#
else:
if logger:
logger.warn('Unknown element: ' + name)
ops = []
node = dom_child(node) if dom_child(node) else dom_next(node)
while node:
ops.append(parsex(node))
node = dom_next(node)
return myokit.UnsupportedFunction(name, ops)
def _ex_quotient(self, e):
# Note that this _must_ round towards minus infinity.
# See myokit.Quotient
# CUDA docs are unclear on convention, so assuming it follows C and
# so we need a custom implementation.
return self.ex(myokit.Floor(myokit.Divide(e[0], e[1])))
