# From the validation errors printed above you'll see that none of the
# units we need are built-in. The good news is that we can create the ones
# we need from the set of built-in units, we just need to define the
# relationship. NB: Even though units are used by Variables, which sit
# 'inside' Components, Units sit inside the Model itself. This helps you to
# reuse Units when you have more than one component (more on that in
# Tutorial 5)
# 3.a
# Define the relationship between our custom units and the built-in
# units. There is a list of built-in units and their definitions
# available in section 19.2 of the CellML2 specification.
# First we create the "month" units, which will be equivalent to
# 60*60*24*30 = 2,592,000 seconds.
month = Units("month")
month.addUnit("second", 1,
2592000) # Setting a month to be 2592000 seconds.
model.addUnits(month)
# "second" is a built-in unit, used with a multiplier of 2592000.
# Note that this could have been written:
# month.addUnit("second", "mega", 1, 2.592)
# month.addUnit("second", 5, 25.92)
# 3.b
# Create units which represent "per_month", which
# is simply the inverse of the "month" unit above.
per_month = Units()
per_month.setName("per_month")
per_month.addUnit("month", -1)
def test_set_units(self):
from libcellml import Issue, Units
# void setUnits(const UnitsPtr &units)
e = Issue()
e.setUnits(Units())
def test_replace_units(self):
from libcellml import Model, Units
# bool replaceUnits(size_t index, const UnitsPtr &units)
m = Model()
u1 = Units()
u1.setName('a')
m.addUnits(u1)
u2 = Units()
u2.setName('b')
self.assertTrue(m.replaceUnits(0, u2))
self.assertFalse(m.replaceUnits(1, u1))
self.assertFalse(m.replaceUnits(-1, u1))
self.assertEqual(m.units(0).name(), 'b')
del [m, u1, u2]
# bool replaceUnits(const std::string &name, const UnitsPtr &units)
m = Model()
a = Units()
a.setName('a')
m.addUnits(a)
b = Units()
b.setName('b')
self.assertFalse(m.replaceUnits('b', a))
self.assertTrue(m.replaceUnits('a', b))
self.assertTrue(m.replaceUnits('b', a))
self.assertFalse(m.replaceUnits('b', a))
del [m, a, b]
# bool replaceUnits(const UnitsPtr &oldUnits, const UnitsPtr &newUnits)
m = Model()
a = Units()
m.addUnits(a)
b = Units()
self.assertFalse(m.replaceUnits(b, a))
self.assertFalse(m.replaceUnits(a, b))
self.assertFalse(m.replaceUnits(b, a))
del [m, a, b]
def test_set_units(self):
from libcellml import Error, Units
# void setUnits(const UnitsPtr &units)
e = Error()
e.setUnits(Units())
# The messages below indicate that we're missing a Units item named 'mS_per_cm2'.
# Issue 1: Variable 'Na_conductance' in component 'sodiumChannelEquations' has a units reference 'mS_per_cm2' which is neither standard nor defined in the parent model.
# reference: 2.8.1.2
# see: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB08.html?issue=2.8.1.2
# Issue 2: Variable 'g_Na' in component 'sodiumChannelEquations' has a units reference 'mS_per_cm2' which is neither standard nor defined in the parent model.
# reference: 2.8.1.2
# see: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB08.html?issue=2.8.1.2
# Issue 3: Variable 'g_Na' in component 'sodiumChannelParameters' has a units reference 'mS_per_cm2' which is neither standard nor defined in the parent model.
# reference: 2.8.1.2
# see: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB08.html?issue=2.8.1.2
# 3.b
# Create an appropriate Units item (note that S stands for 'siemens'), and add it to your model.
mS_per_cm2 = Units('mS_per_cm2')
mS_per_cm2.addUnit('siemens', 'milli')
mS_per_cm2.addUnit('metre', 'centi', -2)
model.addUnits(mS_per_cm2)
# end 3.b
# As with 3.a, here we have more than one issue generated from the same cause: in this case,
# we haven't specified units for a variable.
# Issue 4: Variable 'V' in component 'sodiumChannel' does not have a valid units attribute. The attribute given is ''.
# reference: 2.8.1.2
# see: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB08.html?issue=2.8.1.2
# Issue 8: Variable 'V' in component 'sodiumChannel' has units of '' and an equivalent variable 'V' in component 'sodiumChannelEquations' with non-matching units of 'mV'. The mismatch is:
# reference:
# see:
# end 4
print('----------------------------------------------------------')
print(' STEP 5: Add the units ')
print('----------------------------------------------------------')
# The validator has reported that the four variables are missing units attributes.
# In this example none of the units exist yet, so we need to create all of them.
# The variables' units should be:
# - t, time has units of *milliseconds*
# - X, gate status has units of *dimensionless*
# - alpha_X and beta_X, rates, have units of *per millisecond*.
# 5.a
# Create the units which will be needed by your variables and add them to the model.
ms = Units('ms')
per_ms = Units('per_ms')
# 5.b
# Add Unit items to the units you created to define them.
ms.addUnit('second', 'milli')
per_ms.addUnit('second', 'milli', -1)
# 5.c
# Add the Units to the model (not the component) so that other components can make
# use of them too.
model.addUnits(ms)
model.addUnits(per_ms)
# 5.d
# Use the setUnits function to associate them with the appropriate variables.
def test_standard_unit(self):
from libcellml import Units
u = Units()
u.addUnit(Units.StandardUnit.AMPERE)
u.addUnit(Units.StandardUnit.BECQUEREL)
u.addUnit(Units.StandardUnit.CANDELA)
u.addUnit(Units.StandardUnit.COULOMB)
u.addUnit(Units.StandardUnit.DIMENSIONLESS)
u.addUnit(Units.StandardUnit.FARAD)
u.addUnit(Units.StandardUnit.GRAM)
u.addUnit(Units.StandardUnit.GRAY)
u.addUnit(Units.StandardUnit.HENRY)
u.addUnit(Units.StandardUnit.HERTZ)
u.addUnit(Units.StandardUnit.JOULE)
u.addUnit(Units.StandardUnit.KATAL)
u.addUnit(Units.StandardUnit.KELVIN)
u.addUnit(Units.StandardUnit.KILOGRAM)
u.addUnit(Units.StandardUnit.LITRE)
u.addUnit(Units.StandardUnit.LUMEN)
u.addUnit(Units.StandardUnit.LUX)
u.addUnit(Units.StandardUnit.METRE)
u.addUnit(Units.StandardUnit.MOLE)
u.addUnit(Units.StandardUnit.NEWTON)
u.addUnit(Units.StandardUnit.OHM)
u.addUnit(Units.StandardUnit.PASCAL)
u.addUnit(Units.StandardUnit.RADIAN)
u.addUnit(Units.StandardUnit.SECOND)
u.addUnit(Units.StandardUnit.SIEMENS)
u.addUnit(Units.StandardUnit.SIEVERT)
u.addUnit(Units.StandardUnit.STERADIAN)
u.addUnit(Units.StandardUnit.TESLA)
u.addUnit(Units.StandardUnit.VOLT)
u.addUnit(Units.StandardUnit.WATT)
u.addUnit(Units.StandardUnit.WEBER)
self.assertRaises(RuntimeError, u.addUnit,
Units.StandardUnit.AMPERE - 1)
self.assertRaises(RuntimeError, u.addUnit,
Units.StandardUnit.WEBER + 1)
def test_inheritance(self):
import libcellml
from libcellml import Units
x = Units()
self.assertIsInstance(x, libcellml.ImportedEntity)
self.assertIsInstance(x, libcellml.NamedEntity)
self.assertIsInstance(x, libcellml.Entity)
# Test access to inherited methods
x = Units()
idx = 'test'
self.assertEqual(x.getId(), '')
x.setId(idx)
self.assertEqual(x.getId(), idx)
y = Units(x)
self.assertEqual(y.getId(), idx)
def test_remove_all_units(self):
from libcellml import Units
# void removeAllUnits()
u = Units()
self.assertEqual(u.unitCount(), 0)
u.addUnit('')
self.assertEqual(u.unitCount(), 1)
u.addUnit('')
self.assertEqual(u.unitCount(), 2)
u.removeAllUnits()
self.assertEqual(u.unitCount(), 0)
def test_requires_imports(self):
from libcellml import Units
u = Units("Volt")
self.assertFalse(u.requiresImports())
def test_remove_unit(self):
from libcellml import Units
# bool removeUnit(size_t index)
u = Units()
self.assertFalse(u.removeUnit(0))
self.assertFalse(u.removeUnit(1))
self.assertFalse(u.removeUnit(-1))
u.addUnit('hello')
self.assertFalse(u.removeUnit(1))
self.assertFalse(u.removeUnit(-1))
self.assertTrue(u.removeUnit(0))
self.assertFalse(u.removeUnit(0))
del [u]
# bool removeUnit(const std::string &reference)
u = Units()
self.assertFalse(u.removeUnit('hello'))
u.addUnit('hello')
self.assertFalse(u.removeUnit('hi'))
self.assertTrue(u.removeUnit('hello'))
self.assertFalse(u.removeUnit('hello'))
del [u]
def test_unit_attributes(self):
from libcellml import Units
# void unitAttributes(size_t index, std::string &reference,
# std::string &prefix, double &exponent, double &multiplier, std::string &id)
u = Units()
x = u.unitAttributes(0)
self.assertIsInstance(x, list)
self.assertEqual(x, ['', '', 1.0, 1.0, ''])
u.addUnit('blabla', 'hello', 1.2, 3.4, 'unitid')
x = u.unitAttributes(0)
self.assertIsInstance(x, list)
self.assertEqual(x, ['blabla', 'hello', 1.2, 3.4, 'unitid'])
x = u.unitAttributes(1)
self.assertIsInstance(x, list)
self.assertEqual(x, ['', '', 1.0, 1.0, ''])
del [u, x]
# void unitAttributes(const std::string &reference,
# std::string &prefix, double &exponent, double &multiplier) const;
u = Units()
x = u.unitAttributes('newton')
self.assertIsInstance(x, list)
self.assertEqual(x, ['newton', '', 1.0, 1.0, ''])
u.addUnit('few', 'bars', 4.3, 2.1, 'job')
x = u.unitAttributes('newton')
self.assertIsInstance(x, list)
self.assertEqual(x, ['newton', '', 1.0, 1.0, ''])
x = u.unitAttributes('few')
self.assertIsInstance(x, list)
self.assertEqual(x, ['few', 'bars', 4.3, 2.1, 'job'])
del [u, x]
def test_prefix(self):
from libcellml import Units
u = Units()
u.addUnit('test', Units.Prefix.YOTTA)
u.addUnit('test', Units.Prefix.ZETTA)
u.addUnit('test', Units.Prefix.EXA)
u.addUnit('test', Units.Prefix.PETA)
u.addUnit('test', Units.Prefix.TERA)
u.addUnit('test', Units.Prefix.GIGA)
u.addUnit('test', Units.Prefix.MEGA)
u.addUnit('test', Units.Prefix.KILO)
u.addUnit('test', Units.Prefix.HECTO)
u.addUnit('test', Units.Prefix.DECA)
u.addUnit('test', Units.Prefix.DECI)
u.addUnit('test', Units.Prefix.CENTI)
u.addUnit('test', Units.Prefix.MILLI)
u.addUnit('test', Units.Prefix.MICRO)
u.addUnit('test', Units.Prefix.NANO)
u.addUnit('test', Units.Prefix.PICO)
u.addUnit('test', Units.Prefix.FEMTO)
u.addUnit('test', Units.Prefix.ATTO)
u.addUnit('test', Units.Prefix.ZEPTO)
u.addUnit('test', Units.Prefix.YOCTO)
self.assertRaises(RuntimeError, u.addUnit, 'test',
Units.Prefix.YOTTA - 1)
self.assertRaises(RuntimeError, u.addUnit, 'test',
Units.Prefix.YOCTO + 1)
def test_item(self):
from libcellml import Component, Issue, ImportSource, Model, Unit
from libcellml import Reset, Units, Variable, CellmlElementType, VariablePair
i = Issue()
item = i.item()
self.assertEqual(CellmlElementType.UNDEFINED, item[0])
self.assertIsNone(item[1])
i.setItem(CellmlElementType.VARIABLE, Variable("v"))
vItem = i.item()
self.assertEqual(CellmlElementType.VARIABLE, vItem[0])
self.assertEqual("v", vItem[1].name())
i.setItem(CellmlElementType.UNITS, Units("u"))
uItem = i.item()
self.assertEqual(CellmlElementType.UNITS, uItem[0])
self.assertEqual("u", uItem[1].name())
u = Units("ui")
u.addUnit("volt")
u.addUnit("second")
u.addUnit("metre")
i.setItem(CellmlElementType.UNIT, Unit(u, 2))
uiItem = i.item()
self.assertEqual(CellmlElementType.UNIT, uiItem[0])
self.assertEqual("ui", uiItem[1].units().name())
self.assertEqual(2, uiItem[1].index())
v1 = Variable("v1")
v2 = Variable("v2")
i.setItem(CellmlElementType.CONNECTION, VariablePair(v1, v2))
vpItem = i.item()
self.assertEqual(CellmlElementType.CONNECTION, vpItem[0])
self.assertEqual("v1", vpItem[1].variable1().name())
self.assertEqual("v2", vpItem[1].variable2().name())
v3 = Variable("v3")
v4 = Variable("v4")
i.setItem(CellmlElementType.MAP_VARIABLES, VariablePair(v3, v4))
vpItem = i.item()
self.assertEqual(CellmlElementType.MAP_VARIABLES, vpItem[0])
self.assertEqual("v3", vpItem[1].variable1().name())
self.assertEqual("v4", vpItem[1].variable2().name())
r = Reset()
r.setId("r")
i.setItem(CellmlElementType.RESET, r)
rItem = i.item()
self.assertEqual(CellmlElementType.RESET, rItem[0])
self.assertEqual("r", rItem[1].id())
r.setId("r1")
i.setItem(CellmlElementType.RESET_VALUE, r)
rItem = i.item()
self.assertEqual(CellmlElementType.RESET_VALUE, rItem[0])
self.assertEqual("r1", rItem[1].id())
r.setId("r2")
i.setItem(CellmlElementType.TEST_VALUE, r)
rItem = i.item()
self.assertEqual(CellmlElementType.TEST_VALUE, rItem[0])
self.assertEqual("r2", rItem[1].id())
i.setItem(CellmlElementType.MODEL, Model("m"))
mItem = i.item()
self.assertEqual(CellmlElementType.MODEL, mItem[0])
self.assertEqual("m", mItem[1].name())
i.setItem(CellmlElementType.ENCAPSULATION, Model("e"))
mItem = i.item()
self.assertEqual(CellmlElementType.ENCAPSULATION, mItem[0])
self.assertEqual("e", mItem[1].name())
iS = ImportSource()
iS.setId("is")
i.setItem(CellmlElementType.IMPORT, iS)
isItem = i.item()
self.assertEqual(CellmlElementType.IMPORT, isItem[0])
self.assertEqual("is", isItem[1].id())
i.setItem(CellmlElementType.COMPONENT, Component("c"))
cItem = i.item()
self.assertEqual(CellmlElementType.COMPONENT, cItem[0])
self.assertEqual("c", cItem[1].name())
i.setItem(CellmlElementType.COMPONENT_REF, Component("c1"))
cItem = i.item()
self.assertEqual(CellmlElementType.COMPONENT_REF, cItem[0])
self.assertEqual("c1", cItem[1].name())
def test_add_unit(self):
from libcellml import Units
# void addUnit(const std::string &reference, const std::string &prefix,
# double exponent=1.0, double multiplier=1.0)
u = Units()
u.addUnit('a', 'b')
u.addUnit('a', 'b', 2.0)
u.addUnit('a', 'b', -1)
u.addUnit('a', 'b', 0)
u.addUnit('a', 'b', 3, 3)
u.addUnit('a', 'b', 0.1, -1.2)
del u
# void addUnit(const std::string &reference, int prefix,
# double exponent, double multiplier=1.0)
u = Units()
u.addUnit('a', 1, -1)
u.addUnit('a', 1, 2.3)
u.addUnit('a', 1, -1, 3)
u.addUnit('a', 1, -1, 2.3)
u.addUnit('a', 1, 1.2, 3.4)
u.addUnit('a', -1, -1)
u.addUnit('a', -1, 2.3)
u.addUnit('a', -1, -1, 3)
u.addUnit('a', -1, -1, 2.3)
u.addUnit('a', -1, 1.2, 3.4)
del u
# void addUnit(const std::string &reference, double exponent)
u = Units()
u.addUnit('a', 1.0)
# TODO Ints get converted to Prefix enum, not to double!
# u.addUnit('a', -1)
del u
# void addUnit(const std::string &reference)
u = Units()
u.addUnit('')
u.addUnit('a')
del u
# void addUnit(StandardUnit standardRef, const std::string &prefix,
# double exponent=1.0, double multiplier=1.0)
u = Units()
u.addUnit(Units.StandardUnit.KATAL, 'pico')
u.addUnit(Units.StandardUnit.KATAL, 'pico', 1.0)
u.addUnit(Units.StandardUnit.KATAL, 'pico', -1)
u.addUnit(Units.StandardUnit.KATAL, 'pico', 1.0, 2.0)
u.addUnit(Units.StandardUnit.KATAL, 'pico', 1, 2.0)
u.addUnit(Units.StandardUnit.KATAL, 'pico', -1, 2)
del u
# void addUnit(StandardUnit standardRef, int prefix,
# double exponent, double multiplier=1.0)
u = Units()
u.addUnit(Units.StandardUnit.KATAL, 1, 1.0)
u.addUnit(Units.StandardUnit.KATAL, -1, -1.0)
u.addUnit(Units.StandardUnit.KATAL, 1, 1.0, 1.0)
u.addUnit(Units.StandardUnit.KATAL, -1, -1.0, 1.0, 'id')
del u
# void addUnit(StandardUnit standardRef, double exponent)
# Hidden to avoid confusion with addUnit(StandardUnit, Prefix, double,
# double)
# void addUnit(StandardUnit standardRef)
u = Units()
u.addUnit(Units.StandardUnit.KATAL)
del u
def test_unit_item_coverage(self):
from libcellml import Units, Unit
u = Units("bob")
ui = Unit(u, 0)
self.assertFalse(ui.isValid())
# 3.d Call the validator and print the messages to the terminal.
# Expected errors refer to units referred to by these variables, but
# which don't (yet) exist in the model.
validator.validateModel(model)
print_errors_to_terminal(validator)
print("-----------------------------------------------")
print(" STEP 4: Define the units and add to the model")
print("-----------------------------------------------")
# 4.a Defining the units of millisecond, millivolt, per_millisecond,
# microA_per_cm2, and milliS_per_cm2. Note that the dimensionless
# units are part of those built-in already, so do not need to be
# defined here.
ms = Units()
ms.setName("millisecond")
ms.addUnit("second", "milli")
mV = Units()
mV.setName("millivolt")
mV.addUnit("volt", "milli")
per_ms = Units()
per_ms.setName("per_millisecond")
per_ms.addUnit("millisecond", -1.0)
microA_per_cm2 = Units()
microA_per_cm2.setName("microA_per_cm2")
microA_per_cm2.addUnit("ampere", "micro")
microA_per_cm2.addUnit("metre", "centi", -2.0)
