CellMLToNektar.pycml.mathml_ci Class Reference

Inheritance diagram for CellMLToNektar.pycml.mathml_ci:

Public Member Functions
def	__init__ (self)
def	variable (self)
def	get_units (self, return_set=True)
def	evaluate (self)
def	classify_variables (self, dependencies_only=False, needs_special_treatment=lambda n:None)
Public Member Functions inherited from CellMLToNektar.pycml.mathml
def	__init__ (self)
def	__repr__ (self)
def	__deepcopy__ (self, memo)
def	clone_self (self, register=False)
def	get_original_of_clone (self)
def	get_component (self)
def	model (self)
def	eval (self, elt)
Public Member Functions inherited from CellMLToNektar.pycml.element_base
def	__init__ (self)
def	__delattr__ (self, key)
def	__setattr__ (self, key, value)
def	rootNode (self)
def	cmeta_id (self)
def	xml_remove_child_at (self, index=-1)
def	xml_doc (self)
def	xml_properties (self)

Static Public Member Functions
def	create_new (elt, variable_name)
Static Public Member Functions inherited from CellMLToNektar.pycml.mathml
def	clone (expr)

Private Member Functions
def	_unset_cached_links (self, elt=None)
def	_set_variable_obj (self, var)
def	_get_binding_time (self)
def	_rename (self, new_name=None)
def	_reduce (self)

Private Attributes
	_cml_variable
	_cml_units

Additional Inherited Members
Public Attributes inherited from CellMLToNektar.pycml.element_base
	xml_attributes
Properties inherited from CellMLToNektar.pycml.mathml
	component = property(get_component)

Detailed Description

Definition at line 4219 of file pycml.py.

Constructor & Destructor Documentation

__init__()

def CellMLToNektar.pycml.mathml_ci.__init__

(

self

)

Reimplemented from CellMLToNektar.pycml.mathml.

Definition at line 4220 of file pycml.py.

    def __init__(self):
        super(mathml_ci, self).__init__()
        self._cml_variable = None
        self._cml_units = None
        return
    

References CellMLToNektar.pycml.mathml_ci.__init__().

Referenced by CellMLToNektar.pycml.mathml_ci.__init__().

Member Function Documentation

_get_binding_time()

def CellMLToNektar.pycml.mathml_ci._get_binding_time (   self )

private

Return the binding time of this expression.

The binding time of a <ci> element is that of the variable it
represents.

Definition at line 4266 of file pycml.py.

    def _get_binding_time(self):
        """Return the binding time of this expression.
 
        The binding time of a <ci> element is that of the variable it
        represents.
        """
        return self.variable._get_binding_time()
 

References CellMLToNektar.pycml.mathml_ci._get_binding_time(), Nektar::LibUtilities::Interpreter::ExpressionEvaluator::AnalyticExpression::definition< ScannerT >.variable, and CellMLToNektar.pycml.mathml_ci.variable().

Referenced by CellMLToNektar.pycml.mathml_ci._get_binding_time(), CellMLToNektar.pycml.mathml_ci._reduce(), CellMLToNektar.pycml.mathml_apply._reduce(), CellMLToNektar.pycml.mathml_piecewise._reduce(), CellMLToNektar.pycml.cellml_variable.get_value(), and CellMLToNektar.pycml.cellml_variable.is_statically_const().

_reduce()

def CellMLToNektar.pycml.mathml_ci._reduce (   self )

private

Reduce this expression by evaluating its static parts.

If this is a static variable, replace by its value (as a <cn> element).

Otherwise the behaviour depends on the number of uses of this
variable.  If there is only one, instantiate the definition of
this variable here in place of the <ci> element, otherwise
leave the element unchanged to avoid code duplication.

Definition at line 4282 of file pycml.py.

    def _reduce(self):
        """Reduce this expression by evaluating its static parts.
 
        If this is a static variable, replace by its value (as a <cn> element).
 
        Otherwise the behaviour depends on the number of uses of this
        variable.  If there is only one, instantiate the definition of
        this variable here in place of the <ci> element, otherwise
        leave the element unchanged to avoid code duplication.
        """
        bt = self._get_binding_time()
        DEBUG('partial-evaluator', "Reducing", self.variable.fullname(),
              "which is", bt)
        if bt is BINDING_TIMES.static:
            value = self.evaluate()
            attrs = {(u'cml:units', NSS[u'cml']): self.variable.units}
            cn = self.xml_create_element(u'cn', NSS[u'm'],
                                         content=unicode("%.17g" % value),
                                         attributes=attrs)
            DEBUG('partial-evaluator', "  value =", unicode(cn))
            self._xfer_complexity(cn)
            self.xml_parent.xml_insert_after(self, cn)
            self.xml_parent.xml_remove_child(self)
            self.variable._decrement_usage_count()
        else:
            defns = self.variable.get_dependencies()
            if defns:
                defn = defns[0]
            else:
                # Just need to update the name to be canonical - done in later pass
                defn = None
            if isinstance(defn, cellml_variable):
                if self.variable.pe_keep:
                    # Don't remove this var, just reduce its source
                    DEBUG('partial-evaluator', "Keeping",
                          self.variable.fullname())
                    self.variable._reduce(update_usage=True)
                else:
                    # Create a new <ci> element
                    ci = self.xml_create_element(
                        u'ci', NSS[u'm'], content=defn.fullname(cellml=True))
                    self._xfer_complexity(ci)
                    ci._set_variable_obj(defn)
                    DEBUG('partial-evaluator', "  to", defn.fullname())
                    self.xml_parent.xml_insert_after(self, ci)
                    self.xml_parent.xml_remove_child(self)
                    # Decrement the usage count of just us, not source vars
                    self.variable._decrement_usage_count(follow_maps=False)
                    # May need to recurse down maps
                    ci._reduce()
            elif isinstance(defn, mathml_apply):
                if (not self.variable.pe_keep and
                    (self.variable.get_usage_count() == 1 or
                     self.rootNode.partial_evaluator.is_instantiable(defn))):
                    # defn is defining expression, so will be a MathML element already,
                    # and should be reduced already as well due to topological sort.
                    # Clone the RHS and instantiate it here.
                    rhs = mathml.clone(list(defn.operands())[1])
                    DEBUG('partial-evaluator', "  to", rhs)
                    parent = self.xml_parent
                    parent.xml_insert_after(self, rhs)
                    parent.xml_remove_child(self)
                    parent._adjust_complexity(self, rhs)
                    # Flag the defining expression for removal
                    defn._pe_process = u'remove'
                    self.variable._decrement_usage_count()
            elif defn is not None:
                raise ValueError("Unexpected variable definition: " + defn.xml())
        return
    

References CellMLToNektar.pycml.cellml_variable._get_binding_time(), CellMLToNektar.pycml.mathml_cn._get_binding_time(), CellMLToNektar.pycml.mathml_ci._get_binding_time(), CellMLToNektar.pycml.mathml_piecewise._get_binding_time(), CellMLToNektar.pycml.mathml_diff._get_binding_time(), CellMLToNektar.pycml.mathml_and._get_binding_time(), CellMLToNektar.pycml.mathml_or._get_binding_time(), CellMLToNektar.pycml.mathml_eq._get_binding_time(), CellMLToNektar.pycml.mathml_apply._get_binding_time(), CellMLToNektar.pycml.mathml_ci._reduce(), CellMLToNektar.utilities.DEBUG(), CellMLToNektar.pycml.mathml_cn.evaluate(), CellMLToNektar.pycml.mathml_ci.evaluate(), CellMLToNektar.pycml.mathml_apply.evaluate(), CellMLToNektar.pycml.mathml_piecewise.evaluate(), CellMLToNektar.pycml.mathml_plus.evaluate(), CellMLToNektar.pycml.mathml_minus.evaluate(), CellMLToNektar.pycml.mathml_times.evaluate(), CellMLToNektar.pycml.mathml_divide.evaluate(), CellMLToNektar.pycml.mathml_exp.evaluate(), CellMLToNektar.pycml.mathml_ln.evaluate(), CellMLToNektar.pycml.mathml_log.evaluate(), CellMLToNektar.pycml.mathml_abs.evaluate(), CellMLToNektar.pycml.mathml_power.evaluate(), CellMLToNektar.pycml.mathml_root.evaluate(), CellMLToNektar.pycml.mathml_and.evaluate(), CellMLToNektar.pycml.mathml_or.evaluate(), CellMLToNektar.pycml.mathml_leq.evaluate(), CellMLToNektar.pycml.mathml_lt.evaluate(), CellMLToNektar.pycml.mathml_geq.evaluate(), CellMLToNektar.pycml.mathml_gt.evaluate(), CellMLToNektar.pycml.mathml_neq.evaluate(), CellMLToNektar.pycml.mathml_eq.evaluate(), CellMLToNektar.pycml.mathml_rem.evaluate(), CellMLToNektar.pycml.mathml_logbase.evaluate(), CellMLToNektar.pycml.mathml_degree.evaluate(), CellMLToNektar.pycml.mathml_sin.evaluate(), CellMLToNektar.pycml.mathml_cos.evaluate(), CellMLToNektar.pycml.mathml_tan.evaluate(), CellMLToNektar.pycml.mathml_arcsin.evaluate(), CellMLToNektar.pycml.mathml_arccos.evaluate(), CellMLToNektar.pycml.mathml_arctan.evaluate(), CellMLToNektar.pycml.element_base.rootNode(), Nektar::LibUtilities::Interpreter::ExpressionEvaluator::AnalyticExpression::definition< ScannerT >.variable, and CellMLToNektar.pycml.mathml_ci.variable().

Referenced by CellMLToNektar.pycml.mathml_ci._reduce().

_rename()

def CellMLToNektar.pycml.mathml_ci._rename (   self,   new_name = None  )

private

Update the variable reference to use a canonical name.

Definition at line 4274 of file pycml.py.

    def _rename(self, new_name=None):
        """Update the variable reference to use a canonical name."""
        self.xml_remove_child(unicode(self))
        if new_name is None:
            new_name = self.variable.fullname(cellml=True)
        self.xml_append(unicode(new_name))
        return
 

References Nektar::LibUtilities::Interpreter::ExpressionEvaluator::AnalyticExpression::definition< ScannerT >.variable, and CellMLToNektar.pycml.mathml_ci.variable().

Referenced by CellMLToNektar.pycml.mathml_ci.variable().

_set_variable_obj()

def CellMLToNektar.pycml.mathml_ci._set_variable_obj (   self,   var  )

private

Set the variable object referred to by this element.

Definition at line 4244 of file pycml.py.

    def _set_variable_obj(self, var):
        """Set the variable object referred to by this element."""
        self._cml_variable = var
 

References CellMLToNektar.pycml.mathml_ci._cml_variable.

_unset_cached_links()

def CellMLToNektar.pycml.mathml_ci._unset_cached_links (   self,   elt = None  )

private

Forget cached component and variable references in this MathML tree.

Used by partial evaluator when moving maths to a new component, and by
simulation protocols.

Reimplemented from CellMLToNektar.pycml.mathml.

Definition at line 4226 of file pycml.py.

    def _unset_cached_links(self, elt=None):
        """Forget cached component and variable references in this MathML tree.
        
        Used by partial evaluator when moving maths to a new component, and by
        simulation protocols.
        """
        self._cml_variable = None
        super(mathml_ci, self)._unset_cached_links()
 

References CellMLToNektar.pycml.mathml_ci._cml_variable, and CellMLToNektar.pycml.mathml_ci._unset_cached_links().

Referenced by CellMLToNektar.pycml.mathml._unset_cached_links(), and CellMLToNektar.pycml.mathml_ci._unset_cached_links().

classify_variables()

def CellMLToNektar.pycml.mathml_ci.classify_variables	(		self,
			dependencies_only = False,
			needs_special_treatment = lambda n: None
	)

Classify variables in this expression according to how they are used.

For ci elements we just return a set containing the referenced variable
as the single dependency.  If dependencies_only is False, we also mark
the variable as used.

Definition at line 4352 of file pycml.py.

                           needs_special_treatment=lambda n: None):
        """Classify variables in this expression according to how they are used.
        
        For ci elements we just return a set containing the referenced variable
        as the single dependency.  If dependencies_only is False, we also mark
        the variable as used.
        """
        var = self.variable
        if not dependencies_only:
            var._used()
        return set([var])
 

References Nektar::LibUtilities::Interpreter::ExpressionEvaluator::AnalyticExpression::definition< ScannerT >.variable, and CellMLToNektar.pycml.mathml_ci.variable().

create_new()

def CellMLToNektar.pycml.mathml_ci.create_new (   elt,   variable_name  )

static

Create a new <ci> element with the given variable name.

Definition at line 4366 of file pycml.py.

    def create_new(elt, variable_name):
        """Create a new <ci> element with the given variable name."""
        new_elt = elt.xml_create_element(u'ci', NSS[u'm'],
                                         content=unicode(variable_name))
        return new_elt
 

evaluate()

def CellMLToNektar.pycml.mathml_ci.evaluate

(

self

)

Evaluate this expression by returning the value of the
variable it represents.

Definition at line 4259 of file pycml.py.

    def evaluate(self):
        """
        Evaluate this expression by returning the value of the
        variable it represents.
        """
        return self.variable.get_value()
 

References Nektar::LibUtilities::Interpreter::ExpressionEvaluator::AnalyticExpression::definition< ScannerT >.variable, and CellMLToNektar.pycml.mathml_ci.variable().

Referenced by CellMLToNektar.pycml.mathml_constructor._eval_self(), and CellMLToNektar.pycml.mathml_ci._reduce().

get_units()

def CellMLToNektar.pycml.mathml_ci.get_units	(		self,
			return_set = True
	)

Return the units of the variable represented by this element.

Definition at line 4248 of file pycml.py.

    def get_units(self, return_set=True):
        """Return the units of the variable represented by this element."""
        if not self._cml_units:
            self._cml_units = UnitsSet([self.component.get_units_by_name(self.variable.units)],
                                       expression=self)
        if not return_set:
            u = self._cml_units.extract()
        else:
            u = self._cml_units
        return u
    

References CellMLToNektar.pycml.cellml_model._cml_units, CellMLToNektar.pycml.cellml_component._cml_units, CellMLToNektar.pycml.mathml_units_mixin_tokens._cml_units, CellMLToNektar.pycml.mathml_units_mixin_container._cml_units, CellMLToNektar.pycml.mathml_cn._cml_units, CellMLToNektar.pycml.mathml_ci._cml_units, CellMLToNektar.pycml.mathml_apply._cml_units, CellMLToNektar.pycml.mathml_piecewise._cml_units, CellMLToNektar.pycml.cellml_variable.component, CellMLToNektar.pycml.mathml.component, CellMLToNektar.pycml.extract(), CellMLToNektar.pycml.get_units_by_name(), Nektar::LibUtilities::Interpreter::ExpressionEvaluator::AnalyticExpression::definition< ScannerT >.variable, and CellMLToNektar.pycml.mathml_ci.variable().

Referenced by CellMLToNektar.pycml.mathml._ensure_units_exist(), CellMLToNektar.pycml.mathml_units_mixin_tokens._set_in_units(), and CellMLToNektar.pycml.mathml_apply._set_in_units().

variable()

def CellMLToNektar.pycml.mathml_ci.variable

(

self

)

Cache & return the variable object refered to by this element.

Definition at line 4236 of file pycml.py.

    def variable(self):
        """Cache & return the variable object refered to by this element."""
        if self._cml_variable is None:
            vname = unicode(self).strip()
            self._rename(vname) # Remove excess whitespace from our text content
            self._cml_variable = self.component.get_variable_by_name(vname)
        return self._cml_variable
    

References CellMLToNektar.pycml.mathml_ci._cml_variable, CellMLToNektar.pycml.mathml_ci._rename(), CellMLToNektar.pycml.cellml_variable.component, and CellMLToNektar.pycml.mathml.component.

Referenced by CellMLToNektar.pycml.mathml_ci._get_binding_time(), CellMLToNektar.pycml.mathml_ci._reduce(), CellMLToNektar.pycml.mathml_ci._rename(), CellMLToNektar.pycml.mathml_ci.classify_variables(), CellMLToNektar.pycml.mathml_ci.evaluate(), and CellMLToNektar.pycml.mathml_ci.get_units().

Member Data Documentation

_cml_units

CellMLToNektar.pycml.mathml_ci._cml_units

private

Definition at line 4223 of file pycml.py.

Referenced by CellMLToNektar.pycml.cellml_model._build_units_dictionary(), CellMLToNektar.pycml.cellml_component._build_units_dictionary(), CellMLToNektar.pycml.mathml_apply._set_in_units(), CellMLToNektar.pycml.mathml_piecewise._set_in_units(), CellMLToNektar.pycml.cellml_model.add_units(), CellMLToNektar.pycml.cellml_component.add_units(), CellMLToNektar.pycml.cellml_model.get_all_units(), CellMLToNektar.pycml.cellml_component.get_all_units(), CellMLToNektar.pycml.mathml_apply.get_units(), CellMLToNektar.pycml.mathml_piecewise.get_units(), CellMLToNektar.pycml.mathml_cn.get_units(), CellMLToNektar.pycml.mathml_ci.get_units(), CellMLToNektar.pycml.cellml_model.get_units_by_name(), CellMLToNektar.pycml.cellml_component.get_units_by_name(), and CellMLToNektar.pycml.cellml_model.has_units().

_cml_variable

CellMLToNektar.pycml.mathml_ci._cml_variable

private

Definition at line 4222 of file pycml.py.

Referenced by CellMLToNektar.pycml.mathml_ci._set_variable_obj(), CellMLToNektar.pycml.mathml_ci._unset_cached_links(), and CellMLToNektar.pycml.mathml_ci.variable().