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 _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 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 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 _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 _add_dose_rate(compartment, drug_amount, time_unit): """ Adds a dose rate variable to the state variable, which is bound to the dosing regimen. """ # Register a dose rate variable to the compartment and bind it to # pace, i.e. tell myokit that its value is set by the dosing regimen/ # myokit.Protocol compartment = drug_amount.parent() dose_rate = compartment.add_variable_allow_renaming(str('dose_rate')) dose_rate.set_binding('pace') # Set initial value to 0 and unit to unit of drug amount over unit of # time dose_rate.set_rhs(0) dose_rate.set_unit(drug_amount.unit() / time_unit) # Add the dose rate to the rhs of the drug amount variable rhs = drug_amount.rhs() drug_amount.set_rhs(myokit.Plus(rhs, myokit.Name(dose_rate)))
def test_arithmetic_binary(self): # Tests parsing prefix operators # Plus a = myokit.Name('a') b = myokit.Number(1.0) e = myokit.Plus(a, b) x = '<apply><plus/><ci>a</ci><cn>1.0</cn></apply>' self.assertEqual(self.p(x), e) # Minus e = myokit.Minus(a, b) x = '<apply><minus/><ci>a</ci><cn>1.0</cn></apply>' self.assertEqual(self.p(x), e) # Multiply e = myokit.Multiply(a, b) x = '<apply><times/><ci>a</ci><cn>1.0</cn></apply>' self.assertEqual(self.p(x), e) # Divide e = myokit.Divide(a, b) x = '<apply><divide/><ci>a</ci><cn>1.0</cn></apply>' self.assertEqual(self.p(x), e) # No operands self.assertRaisesRegex( mathml.MathMLError, 'at least one operand', self.p, '<apply><times/></apply>') # Only one operand self.assertRaisesRegex( mathml.MathMLError, 'at least two operands', self.p, '<apply><times/><cn>1.0</cn></apply>') # Several operands e = myokit.Multiply( myokit.Multiply(myokit.Multiply(a, b), myokit.Number(2)), myokit.Number(3)) x = '<apply><times/><ci>a</ci><cn>1</cn><cn>2</cn><cn>3</cn></apply>' self.assertEqual(self.p(x), e)
def test_arithmetic_binary(self): # Tests writing basic arithmetic operators a = myokit.Name(self.avar) b = myokit.Number('12', 'pF') ca = '<mi>c.a</mi>' cb = '<mn>12.0</mn>' # Plus x = myokit.Plus(a, b) self.assertWrite(x, '<mrow>' + ca + '<mo>+</mo>' + cb + '</mrow>') # Minus x = myokit.Minus(a, b) self.assertWrite(x, '<mrow>' + ca + '<mo>-</mo>' + cb + '</mrow>') # Multiply x = myokit.Multiply(a, b) self.assertWrite(x, '<mrow>' + ca + '<mo>*</mo>' + cb + '</mrow>') # Divide x = myokit.Divide(a, b) self.assertWrite(x, '<mfrac>' + ca + cb + '</mfrac>')
def test_arithmetic_binary(self): # Tests writing basic arithmetic operators # Plus a = myokit.Name('a') b = myokit.Number(1) e = myokit.Plus(a, b) x = '<apply><plus/><ci>a</ci><cn>1.0</cn></apply>' self.assertWrite(e, x) # Minus e = myokit.Minus(a, b) x = '<apply><minus/><ci>a</ci><cn>1.0</cn></apply>' self.assertWrite(e, x) # Multiply e = myokit.Multiply(a, b) x = '<apply><times/><ci>a</ci><cn>1.0</cn></apply>' self.assertWrite(e, x) # Divide e = myokit.Divide(a, b) x = '<apply><divide/><ci>a</ci><cn>1.0</cn></apply>' self.assertWrite(e, x)
def test_move_variable(self): # Test the method to move component variables to another component. # Create a model m = myokit.Model('LotkaVolterra') X = m.add_component('X') a = X.add_variable('a') a.set_rhs(3) b = X.add_variable('b') b1 = b.add_variable('b1') b2 = b.add_variable('b2') b1.set_rhs(1) b2.set_rhs( myokit.Minus(myokit.Minus(myokit.Name(a), myokit.Name(b1)), myokit.Number(1))) b.set_rhs(myokit.Plus(myokit.Name(b1), myokit.Name(b2))) x = X.add_variable('x') x.promote() Y = m.add_component('Y') c = Y.add_variable('c') c.set_rhs(myokit.Minus(myokit.Name(a), myokit.Number(1))) d = Y.add_variable('d') d.set_rhs(2) y = Y.add_variable('y') y.promote() x.set_rhs( myokit.Minus( myokit.Multiply(myokit.Name(a), myokit.Name(x)), myokit.Multiply( myokit.Multiply(myokit.Name(b), myokit.Name(x)), myokit.Name(y)))) x.set_state_value(10) y.set_rhs( myokit.Plus( myokit.Multiply(myokit.PrefixMinus(myokit.Name(c)), myokit.Name(y)), myokit.Multiply( myokit.Multiply(myokit.Name(d), myokit.Name(x)), myokit.Name(y)))) y.set_state_value(5) Z = m.add_component('Z') t = Z.add_variable('total') t.set_rhs(myokit.Plus(myokit.Name(x), myokit.Name(y))) E = m.add_component('engine') time = E.add_variable('time') time.set_rhs(0) time.set_binding('time') # Move time variable into X m.validate() # If not valid, this will raise an exception E.move_variable(time, Z) m.validate() # Can't do it a second time self.assertRaises(ValueError, E.move_variable, time, Z) # Move to self Z.move_variable(time, Z) m.validate() Z.move_variable(time, Z) m.validate() # Duplicate variable name E.add_variable('time') self.assertRaises(myokit.DuplicateName, Z.move_variable, time, E) # Create a nested variable by moving m = myokit.Model() c = m.add_component('c') v = c.add_variable('v') w = c.add_variable('w') self.assertFalse(w.is_nested()) c.move_variable(w, v) self.assertTrue(w.is_nested()) v.move_variable(w, c) self.assertFalse(w.is_nested()) # State variables can't be made nested w.promote(0) self.assertRaisesRegex(Exception, 'State variables', c.move_variable, w, v)
def test_model_creation(self): # Create a model m = myokit.Model('LotkaVolterra') # Add the first component X = m.add_component('X') self.assertEqual(X.qname(), 'X') self.assertEqual(X.parent(), m) self.assertIsInstance(X, myokit.Component) self.assertIn(X.qname(), m) self.assertEqual(len(m), 1) # Add variable a self.assertFalse(X.has_variable('a')) a = X.add_variable('a') self.assertTrue(X.has_variable('a')) self.assertEqual(a, a) self.assertIsInstance(a, myokit.Variable) self.assertEqual(len(X), 1) self.assertIn(a.name(), X) a.set_rhs(3) self.assertFalse(a.is_state()) self.assertFalse(a.is_intermediary()) self.assertTrue(a.is_constant()) self.assertEqual(a.lhs(), myokit.Name(a)) self.assertEqual(a.rhs(), myokit.Number(3)) self.assertEqual(a.rhs().eval(), 3) self.assertEqual(a.code(), 'a = 3\n') self.assertEqual(a.eq().code(), 'X.a = 3') self.assertEqual(a.lhs().code(), 'X.a') self.assertEqual(a.rhs().code(), '3') self.assertEqual( a.eq(), myokit.Equation(myokit.Name(a), myokit.Number(3))) # Check lhs a_name1 = myokit.Name(a) a_name2 = myokit.Name(a) self.assertEqual(a_name1, a_name1) self.assertEqual(a_name2, a_name2) self.assertEqual(a_name1, a_name2) self.assertEqual(a_name2, a_name1) # Add variable b with two temporary variables b = X.add_variable('b') self.assertIsInstance(b, myokit.Variable) self.assertEqual(len(X), 2) self.assertIn(b.name(), X) self.assertFalse(b.has_variable('b1')) b1 = b.add_variable('b1') self.assertTrue(b.has_variable('b1')) self.assertEqual(len(b), 1) self.assertIn(b1.name(), b) self.assertIsInstance(b1, myokit.Variable) b2 = b.add_variable('b2') self.assertEqual(len(b), 2) self.assertIn(b2.name(), b) self.assertIsInstance(b2, myokit.Variable) b1.set_rhs(1) b2.set_rhs( myokit.Minus( myokit.Minus(myokit.Name(a), myokit.Name(b1)), myokit.Number(1)) ) b.set_rhs(myokit.Plus(myokit.Name(b1), myokit.Name(b2))) self.assertEqual(b.rhs().eval(), 2) self.assertFalse(b.is_state()) self.assertFalse(b.is_intermediary()) self.assertTrue(b.is_constant()) self.assertEqual(b.lhs(), myokit.Name(b)) # Add state variable x x = X.add_variable('x') x.set_rhs(10) x.promote() self.assertNotEqual(x, X) self.assertIsInstance(x, myokit.Variable) self.assertEqual(len(X), 3) self.assertIn(x.name(), X) self.assertTrue(x.is_state()) self.assertFalse(x.is_intermediary()) self.assertFalse(x.is_constant()) self.assertEqual(x.lhs(), myokit.Derivative(myokit.Name(x))) self.assertEqual(x.indice(), 0) # Test demoting, promoting x.demote() self.assertFalse(x.is_state()) self.assertFalse(x.is_intermediary()) self.assertTrue(x.is_constant()) self.assertEqual(x.lhs(), myokit.Name(x)) x.promote() self.assertTrue(x.is_state()) self.assertFalse(x.is_intermediary()) self.assertFalse(x.is_constant()) self.assertEqual(x.lhs(), myokit.Derivative(myokit.Name(x))) x.demote() x.promote() x.demote() x.promote() self.assertTrue(x.is_state()) self.assertFalse(x.is_intermediary()) self.assertFalse(x.is_constant()) self.assertEqual(x.lhs(), myokit.Derivative(myokit.Name(x))) # Add second component, variables Y = m.add_component('Y') self.assertNotEqual(X, Y) self.assertEqual(len(m), 2) c = Y.add_variable('c') c.set_rhs(myokit.Minus(myokit.Name(a), myokit.Number(1))) d = Y.add_variable('d') d.set_rhs(2) y = Y.add_variable('y') y.promote() # Set rhs for x and y x.set_rhs(myokit.Minus( myokit.Multiply(myokit.Name(a), myokit.Name(x)), myokit.Multiply( myokit.Multiply(myokit.Name(b), myokit.Name(x)), myokit.Name(y) ) )) x.set_state_value(10) self.assertEqual(x.rhs().code(), 'X.a * X.x - X.b * X.x * Y.y') y.set_rhs(myokit.Plus( myokit.Multiply( myokit.PrefixMinus(myokit.Name(c)), myokit.Name(y) ), myokit.Multiply( myokit.Multiply(myokit.Name(d), myokit.Name(x)), myokit.Name(y) ) )) y.set_state_value(5) self.assertEqual(y.rhs().code(), '-Y.c * Y.y + Y.d * X.x * Y.y') # Add ano component, variables Z = m.add_component('Z') self.assertNotEqual(X, Z) self.assertNotEqual(Y, Z) self.assertEqual(len(m), 3) t = Z.add_variable('total') self.assertEqual(t.name(), 'total') self.assertEqual(t.qname(), 'Z.total') self.assertEqual(t.qname(X), 'Z.total') self.assertEqual(t.qname(Z), 'total') t.set_rhs(myokit.Plus(myokit.Name(x), myokit.Name(y))) self.assertFalse(t.is_state()) self.assertFalse(t.is_constant()) self.assertTrue(t.is_intermediary()) self.assertEqual(t.rhs().code(), 'X.x + Y.y') self.assertEqual(t.rhs().code(X), 'x + Y.y') self.assertEqual(t.rhs().code(Y), 'X.x + y') self.assertEqual(t.rhs().code(Z), 'X.x + Y.y') # Add engine component E = m.add_component('engine') self.assertNotEqual(X, E) self.assertNotEqual(Y, E) self.assertNotEqual(Z, E) self.assertEqual(len(m), 4) time = E.add_variable('time') time.set_rhs(0) self.assertIsNone(time.binding()) time.set_binding('time') self.assertIsNotNone(time.binding()) # Check state state = [i for i in m.states()] self.assertEqual(len(state), 2) self.assertIn(x, state) self.assertIn(y, state) # Test variable iterators def has(*v): for var in v: self.assertIn(var, vrs) self.assertEqual(len(vrs), len(v)) vrs = [i for i in m.variables()] has(a, b, c, d, x, y, t, time) vrs = [i for i in m.variables(deep=True)] has(a, b, c, d, x, y, t, b1, b2, time) vrs = [i for i in m.variables(const=True)] has(a, b, c, d) vrs = [i for i in m.variables(const=True, deep=True)] has(a, b, c, d, b1, b2) vrs = [i for i in m.variables(const=False)] has(x, y, t, time) vrs = [i for i in m.variables(const=False, deep=True)] has(x, y, t, time) vrs = [i for i in m.variables(state=True)] has(x, y) vrs = [i for i in m.variables(state=True, deep=True)] has(x, y) vrs = [i for i in m.variables(state=False)] has(a, b, c, d, t, time) vrs = [i for i in m.variables(state=False, deep=True)] has(a, b, c, d, t, b1, b2, time) vrs = [i for i in m.variables(inter=True)] has(t) vrs = [i for i in m.variables(inter=True, deep=True)] has(t) vrs = [i for i in m.variables(inter=False)] has(a, b, c, d, x, y, time) vrs = [i for i in m.variables(inter=False, deep=True)] has(a, b, c, d, x, y, b1, b2, time) vrs = list(m.variables(const=True, state=True)) has() vrs = list(m.variables(const=True, state=False)) has(a, b, c, d) # Test sorted variable iteration names = [v.name() for v in m.variables(deep=True, sort=True)] self.assertEqual(names, [ 'a', 'b', 'b1', 'b2', 'x', 'c', 'd', 'y', 'total', 'time']) # Test equation iteration # Deeper testing is done when testing the ``variables`` method. eq = [eq for eq in X.equations(deep=False)] self.assertEqual(len(eq), 3) self.assertEqual(len(eq), X.count_equations(deep=False)) eq = [eq for eq in X.equations(deep=True)] self.assertEqual(len(eq), 5) self.assertEqual(len(eq), X.count_equations(deep=True)) eq = [eq for eq in Y.equations(deep=False)] self.assertEqual(len(eq), 3) self.assertEqual(len(eq), Y.count_equations(deep=False)) eq = [eq for eq in Y.equations(deep=True)] self.assertEqual(len(eq), 3) self.assertEqual(len(eq), Y.count_equations(deep=True)) eq = [eq for eq in Z.equations(deep=False)] self.assertEqual(len(eq), 1) self.assertEqual(len(eq), Z.count_equations(deep=False)) eq = [eq for eq in Z.equations(deep=True)] self.assertEqual(len(eq), 1) self.assertEqual(len(eq), Z.count_equations(deep=True)) eq = [eq for eq in E.equations(deep=False)] self.assertEqual(len(eq), 1) eq = [eq for eq in E.equations(deep=True)] self.assertEqual(len(eq), 1) eq = [eq for eq in m.equations(deep=False)] self.assertEqual(len(eq), 8) eq = [eq for eq in m.equations(deep=True)] self.assertEqual(len(eq), 10) # Test dependency mapping def has(var, *dps): lst = vrs[m.get(var).lhs() if isinstance(var, basestring) else var] self.assertEqual(len(lst), len(dps)) for d in dps: d = m.get(d).lhs() if isinstance(d, basestring) else d self.assertIn(d, lst) vrs = m.map_shallow_dependencies(omit_states=False) self.assertEqual(len(vrs), 12) has('X.a') has('X.b', 'X.b.b1', 'X.b.b2') has('X.b.b1') has('X.b.b2', 'X.a', 'X.b.b1') has('X.x', 'X.a', 'X.b', myokit.Name(x), myokit.Name(y)) has(myokit.Name(x)) has('Y.c', 'X.a') has('Y.d') has('Y.y', 'Y.c', 'Y.d', myokit.Name(x), myokit.Name(y)) has(myokit.Name(y)) has('Z.total', myokit.Name(x), myokit.Name(y)) vrs = m.map_shallow_dependencies() self.assertEqual(len(vrs), 10) has('X.a') has('X.b', 'X.b.b1', 'X.b.b2') has('X.b.b1') has('X.b.b2', 'X.a', 'X.b.b1') has('X.x', 'X.a', 'X.b') has('Y.c', 'X.a') has('Y.d') has('Y.y', 'Y.c', 'Y.d') has('Z.total') vrs = m.map_shallow_dependencies(collapse=True) self.assertEqual(len(vrs), 8) has('X.a') has('X.b', 'X.a') has('X.x', 'X.a', 'X.b') has('Y.c', 'X.a') has('Y.d') has('Y.y', 'Y.c', 'Y.d') has('Z.total') # Validate m.validate() # Get solvable order order = m.solvable_order() self.assertEqual(len(order), 5) self.assertIn('*remaining*', order) self.assertIn('X', order) self.assertIn('Y', order) self.assertIn('Z', order) # Check that X comes before Y pos = dict([(name, k) for k, name in enumerate(order)]) self.assertLess(pos['X'], pos['Y']) self.assertEqual(pos['*remaining*'], 4) # Check component equation lists eqs = order['*remaining*'] self.assertEqual(len(eqs), 0) eqs = order['Z'] self.assertEqual(len(eqs), 1) self.assertEqual(eqs[0].code(), 'Z.total = X.x + Y.y') eqs = order['Y'] self.assertEqual(len(eqs), 3) self.assertEqual( eqs[2].code(), 'dot(Y.y) = -Y.c * Y.y + Y.d * X.x * Y.y') eqs = order['X'] self.assertEqual(len(eqs), 5) self.assertEqual(eqs[0].code(), 'X.a = 3') self.assertEqual(eqs[1].code(), 'b1 = 1') self.assertEqual(eqs[2].code(), 'b2 = X.a - b1 - 1') self.assertEqual(eqs[3].code(), 'X.b = b1 + b2') # Test model export and cloning code1 = m.code() code2 = m.clone().code() self.assertEqual(code1, code2)
def 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 model(self, E=-88, g=1, component='ikr', current='IKr'): m = myokit.Model() # Add time variable ce = m.add_component('engine') t = ce.add_variable('time') t.set_rhs(0) t.set_binding('time') p = ce.add_variable('pace') p.set_rhs(0) p.set_binding('pace') # Add membrane potential variable cm = m.add_component('membrane') v = cm.add_variable('V') v.set_rhs(-80)#-80 v.set_label('membrane_potential') # Add current component cc = m.add_component(component) cc.add_alias('V', v) # Add parameters i = 0 pvars = [] for rate in self.rates: i += 1 p = cc.add_variable('p' + str(i)) p.set_rhs(rate.alpha) pvars.append(p) i += 1 p = cc.add_variable('p' + str(i)) p.set_rhs(rate.beta) pvars.append(p) i += 1 p = cc.add_variable('p' + str(i)) p.set_rhs(myokit.Number(g)) pvars.append(p) # Add rates, store in map from names to variables rvars = {} for i, rate in enumerate(self.rates): var = cc.add_variable(rate.name) rvars[rate.name] = var # Generate term a * exp(+-b * V) alpha = myokit.Name(pvars[2 * i]) beta = myokit.Name(pvars[1 + 2 * i]) if not rate.positive: beta = myokit.PrefixMinus(beta) var.set_rhs(myokit.Multiply( alpha, myokit.Exp(myokit.Multiply(beta, myokit.Name(v))))) # Add reversal potential variable e = cc.add_variable('E') e.set_rhs(myokit.Number(E)) # Add maximum conductance variable g = cc.add_variable('g') g.set_rhs(myokit.Name(p)) # Create states, store in map from names to variables svars = {} for i, state in enumerate(self.states): var = cc.add_variable(state.name) if i==0: # Add initial condition of all probability in first state. var.promote(1) else: var.promote(0) svars[state.name] = var # Set equations for states for state in self.states: incoming = [] outgoing = [] for edge in self.edges: # Gather info if state == edge.state_from: # Edge from this state to other state state2 = edge.state_to rate_in = edge.backward_rate rate_out = edge.forward_rate mult_in = edge.backward_multiplier mult_out = edge.forward_multiplier elif state == edge.state_to: # Edge from other state to this state state2 = edge.state_from rate_in = edge.forward_rate rate_out = edge.backward_rate mult_in = edge.forward_multiplier mult_out = edge.backward_multiplier else: continue # Add incoming term term = myokit.Name(svars[state2.name]) term = myokit.Multiply( myokit.Name(rvars[rate_in.name]), term) if mult_in != 1: term = myokit.Multiply(myokit.Number(mult_in), term) incoming.append(term) # Add outgoing term term = myokit.Name(rvars[rate_out.name]) if mult_out != 1: term = myokit.Multiply(myokit.Number(mult_out), term) outgoing.append(term) # Start with outgoing terms (grouped) outgoing = iter(outgoing) rhs = next(outgoing) for term in outgoing: rhs = myokit.Plus(rhs, term) rhs = myokit.PrefixMinus(rhs) rhs = myokit.Multiply(rhs, myokit.Name(svars[state.name])) # Add incoming terms (one by one) incoming = iter(incoming) for term in incoming: rhs = myokit.Plus(rhs, term) # Set rhs svars[state.name].set_rhs(rhs) # Add current variable var = cc.add_variable(current) rhs = myokit.Name(g) for state in self.states: if state.conducting: rhs = myokit.Multiply(rhs, myokit.Name(svars[state.name])) rhs = myokit.Multiply( rhs, myokit.Minus(myokit.Name(v), myokit.Name(e))) var.set_rhs(rhs) print(m.code()) return m
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.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_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.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 convert_hh_states_to_inf_tau_form(model, v=None): """ Scans a :class:`myokit.Model` for Hodgkin-Huxley style states written in "alpha-beta form", and converts them to "inf-tau form". For any state ``x`` written in the form ``dot(x) = alpha * (1 - x) - beta * x`` this method will calculate the steady state and time constant, and add variables for both. Next, the state RHS will be replaced by an expression of the form ``dot(x) = (x_inf - x) / tau_x``, where ``x_inf`` and ``tau_x`` are the new variables. See also: :meth:`get_alpha_and_beta()`. Arguments: ``model`` A :class:`myokit.Model` object to convert. ``v`` An optional :class:`myokit.Variable`` representing the membrane potential. If not given, the method will search for a variable labelled ``membrane_potential``. An error is raised if no membrane potential variable can be found. Returns an updated copy of the given model. """ # Clone the model before editing if not isinstance(model, myokit.Model): raise ValueError('Given `model` must be a myokit.Model.') model = model.clone() # Check membrane potential variable is known. if v is None: v = model.label('membrane_potential') if v is None: raise ValueError( 'Membrane potential must be given as `v` or by setting the' ' label `membrane_potential` in the model.') else: # Ensure v is a variable, and from the cloned model if isinstance(v, myokit.Variable): v = v.qname() v = model.get(v) # Loop over states # - If they're in alpha-beta form, add new (nested) variables inf and tau for x in model.states(): res = get_alpha_and_beta(x, v) if res is not None: # Create variabless for inf and tau a = myokit.Name(res[0]) b = myokit.Name(res[1]) tau = x.add_variable_allow_renaming('tau') tau.set_rhs(myokit.Divide(myokit.Number(1), myokit.Plus(a, b))) inf = x.add_variable_allow_renaming('inf') inf.set_rhs(myokit.Multiply(a, myokit.Name(tau))) # Update RHS expression for state x.set_rhs( myokit.Divide(myokit.Minus(myokit.Name(inf), myokit.Name(x)), myokit.Name(tau))) return model
def test_split_factor(self): # Tests _split_factor # Load model, to create interesting RHS fname = os.path.join(DIR_DATA, 'clancy-1999-fitting.mmt') model = myokit.load_model(fname) v1 = model.get('ina.C1') v2 = model.get('ina.C2') v3 = model.get('ina.C3') v4 = model.get('ina.IF') # Test simplest cases v4.set_rhs('C1') self.assertEqual(markov._split_factor(v4.rhs(), [v1]), (myokit.Name(v1), myokit.Number(1))) v4.set_rhs('+++C1') self.assertEqual(markov._split_factor(v4.rhs(), [v1]), (myokit.Name(v1), myokit.Number(1))) v4.set_rhs('--C1') self.assertEqual(markov._split_factor(v4.rhs(), [v1]), (myokit.Name(v1), myokit.Number(1))) v4.set_rhs('---C1') self.assertEqual( markov._split_factor(v4.rhs(), [v1]), (myokit.Name(v1), myokit.PrefixMinus(myokit.Number(1)))) # Test multiplication v4.set_rhs('C1 * 3') self.assertEqual(markov._split_factor(v4.rhs(), [v1]), (myokit.Name(v1), myokit.Number(3))) v4.set_rhs('C1 * (sqrt(C2) + C3)') self.assertEqual( markov._split_factor(v4.rhs(), [v1]), (myokit.Name(v1), myokit.Plus(myokit.Sqrt(myokit.Name(v2)), myokit.Name(v3)))) # Test division v4.set_rhs('C1 / (sqrt(C2) + C3)') self.assertEqual( markov._split_factor(v4.rhs(), [v1]), (myokit.Name(v1), myokit.Divide( myokit.Number(1), myokit.Plus(myokit.Sqrt(myokit.Name(v2)), myokit.Name(v3))))) # Test division that's not allowed v4.set_rhs('(sqrt(C2) + C3) / C1') self.assertRaisesRegex(ValueError, r'Non-linear function \(division\)', markov._split_factor, v4.rhs(), [v1]) # Test with list of variables v4.set_rhs('C2 * 3') self.assertEqual(markov._split_factor(v4.rhs(), [v1, v2, v3]), (myokit.Name(v2), myokit.Number(3))) # Multiple variables is not allowed v4.set_rhs('C2 * C1') self.assertRaisesRegex(ValueError, 'must reference exactly one variable', markov._split_factor, v4.rhs(), [v1, v2, v3]) # Zero variables is not allowed v4.set_rhs('C3') self.assertRaisesRegex(ValueError, 'must reference exactly one variable', markov._split_factor, v4.rhs(), [v1, v2]) # Non-linear term is not allowed v4.set_rhs('sqrt(C1)') self.assertRaisesRegex(ValueError, 'Non-linear function', markov._split_factor, v4.rhs(), [v1, v2]) # Multiple terms is not allowed v4.set_rhs('C2 - C2') self.assertRaisesRegex(ValueError, 'must be a single term', markov._split_factor, v4.rhs(), [v1, v2, v3])
def _ex_plus(self, e): a, b = e.as_two_terms() return myokit.Plus(self.ex(a), self.ex(b))
def test_remove_variable(self): # Test the removal of a variable. # Create a model m = myokit.Model('LotkaVolterra') # Add a variable 'a' X = m.add_component('X') # Simplest case a = X.add_variable('a') self.assertEqual(X.count_variables(), 1) X.remove_variable(a) self.assertEqual(X.count_variables(), 0) self.assertRaises(Exception, X.remove_variable, a) # Test re-adding a = X.add_variable('a') a.set_rhs(myokit.Number(5)) self.assertEqual(X.count_variables(), 1) # Test deleting dependent variables b = X.add_variable('b') self.assertEqual(X.count_variables(), 2) b.set_rhs(myokit.Plus(myokit.Number(3), myokit.Name(a))) # Test blocking of removal self.assertRaises(myokit.IntegrityError, X.remove_variable, a) self.assertEqual(X.count_variables(), 2) # Test removal in the right order X.remove_variable(b) self.assertEqual(X.count_variables(), 1) X.remove_variable(a) self.assertEqual(X.count_variables(), 0) # Test reference to current state variable values a = X.add_variable('a') a.set_rhs(myokit.Number(5)) a.promote() b = X.add_variable('b') b.set_rhs(myokit.Plus(myokit.Number(3), myokit.Name(a))) self.assertRaises(myokit.IntegrityError, X.remove_variable, a) X.remove_variable(b) X.remove_variable(a) self.assertEqual(X.count_variables(), 0) # Test reference to current state variable values with "self"-ref a = X.add_variable('a') a.promote() a.set_rhs(myokit.Name(a)) X.remove_variable(a) # Test it doesn't interfere with normal workings a = X.add_variable('a') a.promote() a.set_rhs(myokit.Name(a)) b = X.add_variable('b') b.set_rhs(myokit.Name(a)) self.assertRaises(myokit.IntegrityError, X.remove_variable, a) X.remove_variable(b) X.remove_variable(a) # Test reference to dot a = X.add_variable('a') a.set_rhs(myokit.Number(5)) a.promote() b = X.add_variable('b') b.set_rhs(myokit.Derivative(myokit.Name(a))) self.assertRaises(myokit.IntegrityError, X.remove_variable, a) X.remove_variable(b) X.remove_variable(a) # Test if orphaned self.assertIsNone(b.parent()) # Test deleting variable with nested variables a = X.add_variable('a') b = a.add_variable('b') b.set_rhs(myokit.Plus(myokit.Number(2), myokit.Number(2))) a.set_rhs(myokit.Multiply(myokit.Number(3), myokit.Name(b))) self.assertRaises(myokit.IntegrityError, X.remove_variable, a) self.assertEqual(a.count_variables(), 1) self.assertEqual(X.count_variables(), 1) # Test recursive deleting X.remove_variable(a, recursive=True) self.assertEqual(a.count_variables(), 0) self.assertEqual(X.count_variables(), 0) # Test deleting variable with nested variables that depend on each # other a = X.add_variable('a') b = a.add_variable('b') c = a.add_variable('c') d = a.add_variable('d') a.set_rhs('b + c - d') a.promote(0.1) b.set_rhs('2 * a - d') c.set_rhs('a + b + d') d.set_rhs('3 * a') self.assertRaises(myokit.IntegrityError, X.remove_variable, a) self.assertEqual(a.count_variables(), 3) self.assertEqual(X.count_variables(), 1) X.remove_variable(a, recursive=True) self.assertEqual(a.count_variables(), 0) self.assertEqual(X.count_variables(), 0) # Test if removed from model's label and binding lists m = myokit.Model() c = m.add_component('c') x = c.add_variable('x') y = c.add_variable('y') x.set_rhs(0) y.set_rhs(0) x.set_binding('time') y.set_label('membrane_potential') self.assertIs(m.binding('time'), x) self.assertIs(m.label('membrane_potential'), y) c.remove_variable(x) self.assertIs(m.binding('time'), None) self.assertIs(m.label('membrane_potential'), y) c.remove_variable(y) self.assertIs(m.binding('time'), None) self.assertIs(m.label('membrane_potential'), None)
def set_roa(self, dose_comp, indirect): """ Sets route of administration. Arguments: dose_comp -- Compartment that is either infused with drug (direct) or connected to the depot compartment (indirect). indirect -- Flag whether dose is administered directly (False) into the dose compartment or indriectly (True) through a depot. """ # Check that model contains dose_comp if not self._model.has_component(dose_comp): raise ValueError # Check that dose compartment has a variable called amount amount = dose_comp + '.amount' if not self._model.has_variable(amount): raise ValueError # Check that amount is a state variable amount = self._model.var(amount) if not amount.is_state(): raise ValueError # Check that model has time bound variable time = self._model.binding(binding='time') if time is None: raise ValueError # Get amount and time unit from dose compartment amount_unit = amount.unit() time_unit = time.unit() # TODO: Remove previously set roa compartments, variables and # expressions. # Remember name of dose_comp self._dose_comp = dose_comp # Get dose compartment object dose_comp = self._model.get(dose_comp) # Add depot compartment if dose is administered indirectly if indirect: # Add depot compartment depot_comp = self._model.add_component_allow_renaming('depot') # Remember name of depot compartment self._depot_comp = depot_comp.name() # Add drug amount and absorption rate to the depot compartment amount_de = depot_comp.add_variable('amount') k_a = depot_comp.add_variable('k_a') # Set default values for amount and absorption rate amount_de.set_rhs(0) k_a.set_rhs(0) # Set units amount_de.set_unit(amount_unit) k_a.set_unit(1 / time_unit) # Promote amount to state variable amount_de.promote() # Add outflow expression to depot compartment amount_de.set_rhs( myokit.Multiply(myokit.PrefixMinus(myokit.Name(k_a)), myokit.Name(amount_de))) # Add inflow expression to dose compartment expr = amount.rhs() amount.set_rhs( myokit.Plus( expr, myokit.Multiply(myokit.Name(k_a), myokit.Name(amount_de)))) # Set the depot to the dose compartment dose_comp = depot_comp amount = amount_de del depot_comp del amount_de # Add dose rate and regimen variables dose_rate = dose_comp.add_variable_allow_renaming('dose_rate') regimen = dose_comp.add_variable_allow_renaming('regimen') # Remember dose rate variable name comp_name = dose_comp.name() self._dose_rate = comp_name + '.' + dose_rate.name() # Set default values for dose_rate and regimen dose_rate.set_rhs(0) regimen.set_rhs(0) # Set units dose_rate.set_unit(amount_unit / time_unit) regimen.set_unit('dimensionless') # Bind regimen to myokit pacer (so regimen can be adjusted with # myokit.Protocol) regimen.set_binding('pace') # Add dose infusion expression to dose compartment expr = amount.rhs() amount.set_rhs( myokit.Plus( expr, myokit.Multiply(myokit.Name(dose_rate), myokit.Name(regimen)))) # Flag route of administration to be set self._roa_set = True # Check whether a valid model has been created self.validate()
def create_tumour_growth_model(): r""" Returns a tumour growth myokit model. .. math:: \frac{\text{d}V^s_T}{\text{d}t} = \frac{2\lambda _0\lambda _1 V^s_T} {2\lambda _0 V^s_T + \lambda _1}, where the tumour volume :math:`V^s_T` is measured in :math:`\text{cm}^3`, the exponential growth rate :math:`\lambda _0` is mesured in :math:`\text{day}` and the linear growth rate :math:`\lambda _1` is measured in :math:`\text{cm}^3/\text{day}`. """ # 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') lambda_0 = central_comp.add_variable('lambda_0') lambda_1 = central_comp.add_variable('lambda_1') # bind time time = central_comp.add_variable('time') time.set_binding('time') # set preferred representation of units # time in days unit = myokit.parse_unit('day') myokit.Unit.register_preferred_representation('day', unit) # rates in 1 / day unit = myokit.parse_unit('1/day') myokit.Unit.register_preferred_representation('1/day', unit) # tumor volume unit = myokit.parse_unit('cm^3') myokit.Unit.register_preferred_representation('cm^3', unit) # linear growth unit = myokit.parse_unit('cm^3/day') myokit.Unit.register_preferred_representation('cm^3/day', unit) # set intial values (some default values) and units time.set_rhs(0) volume_t.set_rhs(0) lambda_0.set_rhs(0) lambda_1.set_rhs(1) # avoid ZeroDivisionError # set units time.set_unit('day') # time in days volume_t.set_unit('cm^3') # milimeter cubed lambda_0.set_unit('1 / day') # per day lambda_1.set_unit('cm^3 / day') # milimiter cubed per day # set rhs of tumor volume # dot(volume_t) = # (2 * lambda_0 * lambda_1 * volume_t) / # (2 * lambda_0 * volume_t + lambda_1) volume_t.promote() volume_t.set_rhs( myokit.Divide( myokit.Multiply( myokit.Number(2), myokit.Multiply( myokit.Name(lambda_0), myokit.Multiply(myokit.Name(lambda_1), myokit.Name(volume_t)))), myokit.Plus( myokit.Multiply( myokit.Number(2), myokit.Multiply(myokit.Name(lambda_0), myokit.Name(volume_t))), myokit.Name(lambda_1)))) # Validate model model.validate() # TODO: Check units # model.check_units() return model
def create_pktgi_model(): """ Returns 1 compartmental PK model. """ # Instantiate model model = Model() # Add central compartment central_comp = model.add_compartment('central') # Add PK variables and constants to central compartment amount = central_comp.add_variable('amount') volume_c = central_comp.add_variable('volume_c') k_e = central_comp.add_variable('k_e') conc = central_comp.add_variable('conc') # add PD variables to central compartment volume_t = central_comp.add_variable('volume_t') lambda_0 = central_comp.add_variable('lambda_0') lambda_1 = central_comp.add_variable('lambda_1') kappa = central_comp.add_variable('kappa') # bind time time = central_comp.add_variable('time') time.set_binding('time') # set intial values (some default values) time.set_rhs(0) amount.set_rhs(0) volume_c.set_rhs(1) # avoid ZeroDivisionError k_e.set_rhs(0) conc.set_rhs(0) volume_t.set_rhs(0) lambda_0.set_rhs(0) lambda_1.set_rhs(1) # avoid ZeroDivisionError kappa.set_rhs(0) # set units time.set_unit('day') # time in days amount.set_unit('mg') # miligram volume_c.set_unit('L') # liter k_e.set_unit('1 / day') # 1 / day conc.set_unit('mg / L') # miligram / liter volume_t.set_unit('cm^3') # milimeter cubed lambda_0.set_unit('1 / day') # per day lambda_1.set_unit('cm^3 / day') # milimiter cubed per day kappa.set_unit('L / mg / day') # in reference L / ug / day, # set preferred representation of units # time days unit = myokit.parse_unit('day') myokit.Unit.register_preferred_representation('day', unit) # rates in 1 / day unit = myokit.parse_unit('1/day') myokit.Unit.register_preferred_representation('1/day', unit) # amount in mg unit = myokit.parse_unit('mg') myokit.Unit.register_preferred_representation('mg', unit) # dose rate in mg / day unit = myokit.parse_unit('mg/day') myokit.Unit.register_preferred_representation('mg/day', unit) # concentration mg / L unit = myokit.parse_unit('mg/L') myokit.Unit.register_preferred_representation('mg/L', unit) # tumor volume unit = myokit.parse_unit('cm^3') myokit.Unit.register_preferred_representation('cm^3', unit) # linear growth unit = myokit.parse_unit('cm^3/day') myokit.Unit.register_preferred_representation('cm^3/day', unit) # potency unit = myokit.parse_unit('L/mg/day') myokit.Unit.register_preferred_representation('L/mg/day', unit) # set rhs of drug amount # (dot(amount) = - k_e * amount) amount.promote() amount.set_rhs( myokit.Multiply(myokit.PrefixMinus(myokit.Name(k_e)), myokit.Name(amount))) # set rhs of tumor volume # dot(volume_t) = # (2 * lambda_0 * lambda_1 * volume_t) / # (2 * lambda_0 * volume_t + lambda_1) - # kappa * conc * volume_t volume_t.promote() volume_t.set_rhs( myokit.Minus( myokit.Divide( myokit.Multiply( myokit.Number(2), myokit.Multiply( myokit.Name(lambda_0), myokit.Multiply(myokit.Name(lambda_1), myokit.Name(volume_t)))), myokit.Plus( myokit.Multiply( myokit.Number(2), myokit.Multiply(myokit.Name(lambda_0), myokit.Name(volume_t))), myokit.Name(lambda_1))), myokit.Multiply( myokit.Name(kappa), myokit.Multiply(myokit.Name(conc), myokit.Name(volume_t))))) # set algebraic relation between drug and concentration # conc = amount / volume_c conc.set_rhs(myokit.Divide(myokit.Name(amount), myokit.Name(volume_c))) return model
def get_rl_expression(x, dt, v=None): """ For states ``x`` with RHS expressions written in the "inf-tau form" (see :meth:`has_inf_tau_form`) this returns a Rush-Larsen (RL) update expression of the form ``x_inf + (x - x_inf) * exp(-(dt / tau_x))``. If the state does not have the "inf-tau form", ``None`` is returned. Arguments: ``x`` A state variable for which to return the RL update expression. ``dt`` A :class:`myokit.Name` expression to use for the time step in the RL expression. ``v`` An optional variable representing the membrane potential. Returns a :class:`myokit.Expression` if succesful, or ``None`` if not. Example: # Load a Myokit model model = myokit.load_model('example') v = model.get('membrane.V') # Get a copy where all HH-state variables are written in inf-tau form model = myokit.lib.hh.convert_hh_states_to_inf_tau_form(model, v) # Create an expression for the time step dt = myokit.Name('dt') # Show an RL-update for the variable ina.h h = model.get('ina.h') e = myokit.lib.hh.get_rl_expression(h, dt, v) print('h[t + dt] = ' + str(e)) See: [1] Rush, Larsen (1978) A Practical Algorithm for Solving Dynamic Membrane Equations. IEEE Transactions on Biomedical Engineering, https://doi.org/10.1109/TBME.1978.326270 [2] Marsh, Ziaratgahi, Spiteri (2012) The secrets to the success of the Rush-Larsen method and its generalization. IEEE Transactions on Biomedical Engineering, https://doi.org/10.1109/TBME.2012.2205575 """ # Test dt is an expression if not isinstance(dt, myokit.Expression): raise ValueError('Argument `dt` must be a myokit.Expression.') # Get x_inf and tau_x, if possible res = get_inf_and_tau(x, v) if res is None: return None # Create expression for RL update # x_inf + (x - x_inf) * exp(-(dt / tau_x)) x = myokit.Name(x) x_inf = myokit.Name(res[0]) tau_x = myokit.Name(res[1]) return myokit.Plus( x_inf, myokit.Multiply( myokit.Minus(x, x_inf), myokit.Exp(myokit.PrefixMinus(myokit.Divide(dt, tau_x)))))
def test_basic(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') # Name self.assertEqual(ws.ex(a), 'c.a') self.assertEqual(wd.ex(a), 'c.a') self.assertEqual(wn.ex(a), 'c.a') # Number with unit self.assertEqual(ws.ex(b), '12.0f') self.assertEqual(wd.ex(b), '12.0') self.assertEqual(wn.ex(b), '12.0f') # Prefix plus x = myokit.PrefixPlus(b) self.assertEqual(ws.ex(x), '12.0f') self.assertEqual(wd.ex(x), '12.0') self.assertEqual(wn.ex(x), '12.0f') # Prefix minus x = myokit.PrefixMinus(b) self.assertEqual(ws.ex(x), '(-12.0f)') self.assertEqual(wd.ex(x), '(-12.0)') self.assertEqual(wn.ex(x), '(-12.0f)') # Plus x = myokit.Plus(a, b) self.assertEqual(ws.ex(x), 'c.a + 12.0f') self.assertEqual(wd.ex(x), 'c.a + 12.0') self.assertEqual(wn.ex(x), 'c.a + 12.0f') # Minus x = myokit.Minus(a, b) self.assertEqual(ws.ex(x), 'c.a - 12.0f') self.assertEqual(wd.ex(x), 'c.a - 12.0') self.assertEqual(wn.ex(x), 'c.a - 12.0f') # Multiply x = myokit.Multiply(a, b) self.assertEqual(ws.ex(x), 'c.a * 12.0f') self.assertEqual(wd.ex(x), 'c.a * 12.0') self.assertEqual(wn.ex(x), 'c.a * 12.0f') # Divide x = myokit.Divide(a, b) self.assertEqual(ws.ex(x), 'c.a / 12.0f') self.assertEqual(wd.ex(x), 'c.a / 12.0') self.assertEqual(wn.ex(x), 'c.a / 12.0f') # Quotient x = myokit.Quotient(a, b) self.assertEqual(ws.ex(x), 'floor(c.a / 12.0f)') self.assertEqual(wd.ex(x), 'floor(c.a / 12.0)') self.assertEqual(wn.ex(x), 'floor(c.a / 12.0f)') # Remainder x = myokit.Remainder(a, b) self.assertEqual(ws.ex(x), 'c.a - 12.0f * (floor(c.a / 12.0f))') self.assertEqual(wd.ex(x), 'c.a - 12.0 * (floor(c.a / 12.0))') self.assertEqual(wn.ex(x), 'c.a - 12.0f * (floor(c.a / 12.0f))')
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_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 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 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)