CellMLToNektar.pycml.mathml Class Reference

Inheritance diagram for CellMLToNektar.pycml.mathml:

Public Member Functions
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	__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	clone (expr)

Properties
	component = property(get_component)

Private Member Functions
def	_unset_cached_links (self, elt=None)
def	_ensure_units_exist (self, units=None, no_act=False)

Private Attributes
	_cml_component
	_cml_model
	_cml_source_expr_for_clone

Additional Inherited Members
Public Attributes inherited from CellMLToNektar.pycml.element_base
	xml_attributes

Detailed Description

Base class for MathML elements.

Definition at line 3682 of file pycml.py.

Constructor & Destructor Documentation

__init__()

def CellMLToNektar.pycml.mathml.__init__

(

self

)

Reimplemented from CellMLToNektar.pycml.element_base.

Reimplemented in CellMLToNektar.pycml.mathml_plus, CellMLToNektar.pycml.mathml_piecewise, CellMLToNektar.pycml.mathml_apply, CellMLToNektar.pycml.mathml_ci, CellMLToNektar.pycml.mathml_cn, CellMLToNektar.pycml.mathml_constructor, and CellMLToNektar.pycml.mathml_math.

Definition at line 3684 of file pycml.py.

    def __init__(self):
        super(mathml, self).__init__()
        self._cml_component = None
        self._cml_model = None
        self._cml_source_expr_for_clone = None
        return
    

Member Function Documentation

__deepcopy__()

def CellMLToNektar.pycml.mathml.__deepcopy__	(		self,
			memo
	)

Customise copying of MathML expressions.

When copying an expression tree, we only want to deepcopy the
XML, not the additional info that we have attached to it -
these should be copied as references to the originals.

Definition at line 3694 of file pycml.py.

    def __deepcopy__(self, memo):
        """Customise copying of MathML expressions.
 
        When copying an expression tree, we only want to deepcopy the
        XML, not the additional info that we have attached to it -
        these should be copied as references to the originals.
        """
        new_elt = copy.copy(self)
        # Children may refer to us, so need to update memo before copying children
        assert id(self) not in memo
        memo[id(self)] = new_elt
        new_dict = {}
        for name, value in self.__dict__.iteritems():
            name_copy = copy.deepcopy(name, memo)
            if not name.startswith('_cml'):
                new_dict[name_copy] = copy.deepcopy(value, memo)
            else:
                new_dict[name_copy] = value
        new_elt.__dict__.update(new_dict)
        return new_elt
 

__repr__()

def CellMLToNektar.pycml.mathml.__repr__

(

self

)

Definition at line 3691 of file pycml.py.

    def __repr__(self):
        return '<%s (%s) at 0x%x>' % (self.__class__.__name__, str(self), id(self))
 

_ensure_units_exist()

def CellMLToNektar.pycml.mathml._ensure_units_exist (   self,   units = None,   no_act = False  )

private

Ensure that there is an element in the XML tree giving this
expression's units.

Add a new <units> element if this expression has generated units.

If units is not None, use the given units rather than those of
this expression.

Return an attribute dictionary with the appropriate units
attribute.

Definition at line 3807 of file pycml.py.

    def _ensure_units_exist(self, units=None, no_act=False):
        """Ensure that there is an element in the XML tree giving this
        expression's units.
 
        Add a new <units> element if this expression has generated units.
 
        If units is not None, use the given units rather than those of
        this expression.
 
        Return an attribute dictionary with the appropriate units
        attribute."""
        if no_act:
            # Doesn't matter what we return, as it wont be used
            return {(u'cml:units', NSS[u'cml']): u'#UNUSED#'}
        try:
            if units is None:
                units = self.get_units().extract()

References CellMLToNektar.pycml.extract(), CellMLToNektar.pycml.cellml_variable.get_units(), CellMLToNektar.pycml.mathml_apply.get_units(), CellMLToNektar.pycml.mathml_piecewise.get_units(), CellMLToNektar.pycml.mathml_cn.get_units(), and CellMLToNektar.pycml.mathml_ci.get_units().

Referenced by CellMLToNektar.pycml.mathml_constructor._eval_self().

_unset_cached_links()

def CellMLToNektar.pycml.mathml._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 in CellMLToNektar.pycml.mathml_ci.

Definition at line 3767 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.
        """
        if elt is None:
            elt = self
        if isinstance(elt, mathml):
            elt._cml_component = None
        for child in self.xml_element_children(elt):
            if hasattr(child, '_unset_cached_links'):
                child._unset_cached_links()
            else:
                self._unset_cached_links(child)
        return
 

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

Referenced by CellMLToNektar.pycml.mathml._unset_cached_links().

clone()

def CellMLToNektar.pycml.mathml.clone (   expr )

static

Properly clone a MathML sub-expression.

Makes sure siblings and parent don't get copied too.

Definition at line 3716 of file pycml.py.

    def clone(expr):
        """Properly clone a MathML sub-expression.
 
        Makes sure siblings and parent don't get copied too.
        """
#        print "Cloning MathML", prid(expr, True)
        next_elem, par = expr.next_elem, getattr(expr, 'xml_parent', None)
        expr.next_elem = None  # Make sure we don't copy siblings...
        expr.xml_parent = None # ...and parent
        new_expr = copy.deepcopy(expr) # Do the clone
        expr.next_elem = next_elem # Restore siblings...
        expr.xml_parent = par      # ...and parent to original
        return new_expr
    

clone_self()

def CellMLToNektar.pycml.mathml.clone_self	(		self,
			register = False
	)

Properly clone this expression.

If register is True, then keep a link to this expression in the clone.

Definition at line 3730 of file pycml.py.

    def clone_self(self, register=False):
        """Properly clone this expression.
        
        If register is True, then keep a link to this expression in the clone.
        """
        clone = mathml.clone(self)
        if register:
            clone._cml_source_expr_for_clone = self
        return clone
    

eval()

def CellMLToNektar.pycml.mathml.eval	(		self,
			elt
	)

Evaluate the given element.

Tries to evaluate the given element, and raises an EvaluationError
if this is not possible.

Definition at line 3791 of file pycml.py.

    def eval(self, elt):
        """Evaluate the given element.
 
        Tries to evaluate the given element, and raises an EvaluationError
        if this is not possible.
        """
        if hasattr(elt, 'evaluate') and callable(elt.evaluate):
            return elt.evaluate()
        elif elt.localName == u'pi':
            return math.pi
        else:
            # No evaluate() method on elt
            raise EvaluationError("Don't know how to evaluate element " +
                                  elt.localName)
        return
 

Referenced by CellMLToNektar.pycml.mathml_piecewise._get_binding_time(), CellMLToNektar.pycml.mathml_and._get_binding_time(), CellMLToNektar.pycml.mathml_or._get_binding_time(), CellMLToNektar.pycml.mathml_power._reduce(), CellMLToNektar.pycml.mathml_piecewise._reduce(), 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(), and CellMLToNektar.pycml.mathml_apply.get_units().

get_component()

def CellMLToNektar.pycml.mathml.get_component

(

self

)

Definition at line 3747 of file pycml.py.

    def get_component(self):
        "Cache & return the enclosing component element."
        if self._cml_component is None:
            def get_ancestor(elt, name):
                while elt and elt.localName != name:
                    elt = elt.parentNode
                return elt
            comp = get_ancestor(self, u'component')
            if comp:
                self._cml_component = comp
            else:
                # It may be in the solver_info section, in which case fake a component
                solver_info = get_ancestor(self, u'solver_info')
                if solver_info:
                    self._cml_component = self.model.get_component_by_name(u'')
                else:
                    raise ValueError("MathML element " + str(self) + " does not occur in a model component!")
        return self._cml_component

References CellMLToNektar.pycml.mathml._cml_component, CellMLToNektar.processors.ModelModifier.model, CellMLToNektar.pycml.cellml_variable.model(), CellMLToNektar.pycml.mathml.model(), and CellMLToNektar.translators.CellMLTranslator.model.

get_original_of_clone()

def CellMLToNektar.pycml.mathml.get_original_of_clone

(

self

)

If this is a clone with a registered original expression, return it.
Otherwise returns None.

Definition at line 3740 of file pycml.py.

    def get_original_of_clone(self):
        """
        If this is a clone with a registered original expression, return it.
        Otherwise returns None.
        """
        return self._cml_source_expr_for_clone
 

References CellMLToNektar.pycml.mathml._cml_source_expr_for_clone.

model()

def CellMLToNektar.pycml.mathml.model

(

self

)

Cache & return the enclosing model element.

Definition at line 3785 of file pycml.py.

    def model(self):
        """Cache & return the enclosing model element."""
        if self._cml_model is None:
            self._cml_model = self.rootNode.model
        return self._cml_model
    

References CellMLToNektar.pycml.mathml._cml_model, and CellMLToNektar.pycml.element_base.rootNode().

Referenced by CellMLToNektar.processors.InterfaceGenerator._add_all_odes_to_interface(), CellMLToNektar.processors.ModelModifier._clear_model_caches(), CellMLToNektar.processors.ModelModifier._create_connection_element(), CellMLToNektar.processors.ModelModifier._find_connection_element(), CellMLToNektar.processors.ModelModifier._find_or_create_variable(), CellMLToNektar.processors.ModelModifier._process_operator(), CellMLToNektar.pycml.reduce_commutative_nary._reduce(), CellMLToNektar.pycml.mathml_power._reduce(), CellMLToNektar.pycml.mathml_piecewise._set_in_units(), CellMLToNektar.pycml.cellml_variable._set_source_variable(), CellMLToNektar.processors.InterfaceGenerator._split_ode(), CellMLToNektar.processors.InterfaceGenerator._transform_derivatives_on_rhs(), CellMLToNektar.processors.ModelModifier._update_connections(), CellMLToNektar.processors.UnitsConverter.add_all_conversions(), CellMLToNektar.processors.UnitsConverter.add_conversions_for_component(), CellMLToNektar.processors.ModelModifier.add_expr_to_comp(), CellMLToNektar.processors.InterfaceGenerator.add_output_function(), CellMLToNektar.pycml.cellml_variable.add_rdf_annotation(), CellMLToNektar.processors.ModelModifier.add_units(), CellMLToNektar.processors.ModelModifier.add_variable(), CellMLToNektar.translators.CellMLTranslator.calculate_extended_dependencies(), CellMLToNektar.pycml.mathml_apply.classify_variables(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.code_name(), CellMLToNektar.processors.ModelModifier.connect_variables(), CellMLToNektar.processors.UnitsConverter.convert_assignments(), CellMLToNektar.processors.UnitsConverter.convert_connections(), CellMLToNektar.processors.UnitsConverter.convert_constant(), CellMLToNektar.processors.UnitsConverter.convert_mapping(), CellMLToNektar.processors.ModelModifier.create_new_component(), CellMLToNektar.processors.ModelModifier.finalize(), CellMLToNektar.pycml.mathml.get_component(), CellMLToNektar.processors.InterfaceGenerator.get_interface_component(), CellMLToNektar.pycml.cellml_variable.get_rdf_annotation(), CellMLToNektar.pycml.cellml_variable.get_rdf_annotations(), CellMLToNektar.pycml.mathml_apply.get_units(), CellMLToNektar.pycml.mathml_piecewise.get_units(), CellMLToNektar.pycml.cellml_variable.is_statically_const(), CellMLToNektar.processors.InterfaceGenerator.make_var_computed_constant(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_backward_euler_mathematics(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_constructor(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_default_stimulus(), CellMLToNektar.translators.CellMLTranslator.output_equations(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_equations(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_get_i_ionic(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_includes(), CellMLToNektar.translators.CellMLTranslator.output_mathematics(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_model_attributes(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_top_boilerplate(), CellMLToNektar.translators.CellMLTranslator.output_top_boilerplate(), CellMLToNektar.CellMLToNektarTranslator.CellMLToNektarTranslator.output_verify_state_variables(), CellMLToNektar.processors.ModelModifier.remove_connections(), CellMLToNektar.pycml.cellml_variable.remove_rdf_annotations(), CellMLToNektar.translators.CellMLTranslator.var_display_name(), and CellMLToNektar.translators.CellMLTranslator.varobj().

Member Data Documentation

_cml_component

CellMLToNektar.pycml.mathml._cml_component

private

Definition at line 3686 of file pycml.py.

Referenced by CellMLToNektar.pycml.mathml.get_component().

_cml_model

CellMLToNektar.pycml.mathml._cml_model

private

Definition at line 3687 of file pycml.py.

Referenced by CellMLToNektar.pycml.mathml.model().

_cml_source_expr_for_clone

CellMLToNektar.pycml.mathml._cml_source_expr_for_clone

private

Definition at line 3688 of file pycml.py.

Referenced by CellMLToNektar.pycml.mathml.get_original_of_clone().

Property Documentation

component

CellMLToNektar.pycml.mathml.component = property(get_component)

static

Definition at line 3765 of file pycml.py.

Referenced by CellMLToNektar.pycml.mathml_constructor._get_element_units(), CellMLToNektar.pycml.mathml_units_mixin._set_element_in_units(), CellMLToNektar.pycml.cellml_variable.fullname(), CellMLToNektar.pycml.cellml_variable.get_units(), CellMLToNektar.pycml.mathml_ci.get_units(), CellMLToNektar.pycml.cellml_model.get_variable_by_name(), CellMLToNektar.pycml.cellml_variable.model(), and CellMLToNektar.pycml.mathml_ci.variable().