Classes
class	Colourable

class	NotifyHandler

class	OnlyDebugFilter

class	OnlyTheseSourcesFilter

class	OnlyWarningsFilter

class	Sentinel

class	unitary_iterator

Functions
def	DEBUG (facility, *args)

def	LOG (facility, level, *args)

def	amara_parse (source, uri=None, rules=None, binderobj=None, prefixes=None)

def	element_path (elt)

def	element_path_cmp (e1, e2)

def	element_xpath (elt)

def	brief_xml (elt)

def	call_if (tf, callable, args, *kwargs)

def	max_i (it)

def	prid (obj, show_cls=False)

def	add_dicts (r, *ds)

def	open_output_stream (fname)

def	close_output_stream (stream)

Variables
list	__all__

	DFS = Enum('White', 'Gray', 'Black')

Detailed Description

Copyright (c) 2005-2016, University of Oxford.
All rights reserved.

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Function Documentation

◆ add_dicts()

def CellMLToNektar.utilities.add_dicts	(		r,
		*	ds
	)

Add multiple dictionaries together.

Updates the first input dictionary by adding values from
subsequent inputs.  Produces a dictionary with keys taken from the
input dictionaries, and values being the sum of the corresponding
values in all inputs.
Assumes values are numeric.

Definition at line 284 of file utilities.py.

def add_dicts(r, *ds):
    """Add multiple dictionaries together.
 
    Updates the first input dictionary by adding values from
    subsequent inputs.  Produces a dictionary with keys taken from the
    input dictionaries, and values being the sum of the corresponding
    values in all inputs.
    Assumes values are numeric.
    """
    for d in ds:
        for k, v in d.iteritems():
            r[k] = r.get(k, 0) + v
 
 

Referenced by CellMLToNektar.pycml.mathml_apply.tree_complexity(), and CellMLToNektar.pycml.mathml_piecewise.tree_complexity().

◆ amara_parse()

def CellMLToNektar.utilities.amara_parse	(	source,
		uri = `None`,
		rules = `None`,
		binderobj = `None`,
		prefixes = `None`
	)

Convenience function for parsing XML.

Works just as amara.parse, except that if source is '-' then
it reads from standard input.

Definition at line 191 of file utilities.py.

                prefixes=None):
    """Convenience function for parsing XML.
    
    Works just as amara.parse, except that if source is '-' then
    it reads from standard input.
    """
    if source == '-':
        return amara.parse(sys.stdin, uri=uri, rules=rules,
                           binderobj=binderobj, prefixes=prefixes)
    else:
        return amara.parse(source, uri=uri, rules=rules,
                           binderobj=binderobj, prefixes=prefixes)
 
 

Referenced by CellMLToNektar.pycml.amara_parse_cellml(), and CellMLToNektar.translators.ConfigurationStore.read_configuration_file().

◆ brief_xml()

def CellMLToNektar.utilities.brief_xml ( elt )

Print a more concise version of elt.xml() that omits all attributes.

Definition at line 232 of file utilities.py.

def brief_xml(elt):
    """Print a more concise version of elt.xml() that omits all attributes."""
    s = ''
    if getattr(elt, 'nodeType', None) == Node.ELEMENT_NODE:
        children = getattr(elt, 'xml_children', [])
        if children:
            s += '<' + elt.localName + '>'
            for child in children:
                s += brief_xml(child)
            s += '</' + elt.localName + '>'
        else:
            s += '<' + elt.localName + '/>'
    else:
        s += str(elt)
    return s
 
 

References CellMLToNektar.utilities.brief_xml().

Referenced by CellMLToNektar.utilities.brief_xml().

◆ call_if()

def CellMLToNektar.utilities.call_if	(		tf,
			callable,
		*	args,
		**	kwargs
	)

Miscellaneous functions # #

Call the given callable with the given arguments iff tf is True.

Definition at line 255 of file utilities.py.

def call_if(tf, callable, *args, **kwargs):
    """Call the given callable with the given arguments iff tf is True."""
    if tf:
        return callable(*args, **kwargs)
 
 

Referenced by CellMLToNektar.translators.ConfigurationStore._find_transmembrane_currents_from_voltage_ode().

◆ close_output_stream()

def CellMLToNektar.utilities.close_output_stream ( stream )

Close the given output stream, unless it's one of the standard streams
(i.e. sys.stdout or sys.stderr).
Note that closing a stream multiple times is safe.

Definition at line 314 of file utilities.py.

def close_output_stream(stream):
    """
    Close the given output stream, unless it's one of the standard streams
    (i.e. sys.stdout or sys.stderr).
    Note that closing a stream multiple times is safe.
    """
    if not stream is sys.stdout and not stream is sys.stderr:
        stream.close()

Referenced by CellMLToNektar.translators.run(), and CellMLToNektar.validator.run().

◆ DEBUG()

def CellMLToNektar.utilities.DEBUG	(		facility,
		*	args
	)

Log a debug message to facility.

Arguments are treated as for the print statement.

Definition at line 95 of file utilities.py.

def DEBUG(facility, *args):
    """Log a debug message to facility.
 
    Arguments are treated as for the print statement.
    """
    logger = logging.getLogger(facility)
    if logger.isEnabledFor(logging.DEBUG):
        logger.debug(' '.join(map(str, args)))
 
 

◆ element_path()

def CellMLToNektar.utilities.element_path ( elt )

Find the path from the root element to this element.

Definition at line 206 of file utilities.py.

def element_path(elt):
    """Find the path from the root element to this element."""
    if hasattr(elt, 'xml_parent'):
        idx = 0
        for child in elt.xml_parent.xml_children:
            if getattr(child, 'nodeType', None) == Node.ELEMENT_NODE:
                idx += 1
                if child is elt:
                    break
        return element_path(elt.xml_parent) + [idx]
    else:
        return []
    
 

References CellMLToNektar.utilities.element_path().

Referenced by CellMLToNektar.utilities.element_path(), CellMLToNektar.utilities.element_path_cmp(), and CellMLToNektar.utilities.element_xpath().

◆ element_path_cmp()

def CellMLToNektar.utilities.element_path_cmp	(	e1,
		e2
	)

Compare 2 elements by comparing their paths from the root element.

Definition at line 220 of file utilities.py.

def element_path_cmp(e1, e2):
    """Compare 2 elements by comparing their paths from the root element."""
    return cmp(element_path(e1), element_path(e2))
 
 

References CellMLToNektar.utilities.element_path().

◆ element_xpath()

def CellMLToNektar.utilities.element_xpath ( elt )

Return an xpath expression that will select this element.

Definition at line 225 of file utilities.py.

def element_xpath(elt):
    """Return an xpath expression that will select this element."""
    indices = element_path(elt)
    xpath = u'/*[' + u']/*['.join(map(str, indices)) + u']'
    return xpath
 
 

References CellMLToNektar.utilities.element_path().

Referenced by CellMLToNektar.pycml.mathml_units_mixin._add_units_conversion(), and CellMLToNektar.pycml.MathsError._generate_message().

◆ LOG()

def CellMLToNektar.utilities.LOG	(		facility,
			level,
		*	args
	)

Log a message to facility with the given level.

Arguments are treated as for the print statement.

Definition at line 105 of file utilities.py.

def LOG(facility, level, *args):
    """Log a message to facility with the given level.
 
    Arguments are treated as for the print statement.
    """
    logger = logging.getLogger(facility)
    if logger.isEnabledFor(level):
        logger.log(level, ' '.join(map(str, args)))
 

Referenced by CellMLToNektar.translators.ConfigurationStore.find_lookup_variables().

◆ max_i()

def CellMLToNektar.utilities.max_i ( it )

Find the maximum entry of an iterable, and return it with its index.

Returns (i, m) where i is the index of m, the maximum entry of `it`.

Definition at line 261 of file utilities.py.

def max_i(it):
    """Find the maximum entry of an iterable, and return it with its index.
 
    Returns (i, m) where i is the index of m, the maximum entry of `it`.
    """
    idx, m = None, None
    for i, val in enumerate(it):
        if m is None or val > m:
            m, idx = val, i
    return idx, m
 
 

Referenced by CellMLToNektar.pycml.mathml_piecewise.tree_complexity().

◆ open_output_stream()

def CellMLToNektar.utilities.open_output_stream ( fname )

Open fname for output.

fname should be a local filename, or '-' for standard output.
Additionally, the names 'stdout' and 'stderr' have the usual
special meanings.

Definition at line 298 of file utilities.py.

def open_output_stream(fname):
    """Open fname for output.
    
    fname should be a local filename, or '-' for standard output.
    Additionally, the names 'stdout' and 'stderr' have the usual
    special meanings.
    """
    if fname == '-' or fname == 'stdout':
        stream = sys.stdout
    elif fname == 'stderr':
        stream = sys.stderr
    else:
        stream = open(fname, 'w')
    return stream
 
 

Referenced by CellMLToNektar.translators.run(), and CellMLToNektar.validator.run().

◆ prid()

def CellMLToNektar.utilities.prid	(	obj,
		show_cls = `False`
	)

Get the id of an object as a hex string, optionally with its class/type.

Definition at line 273 of file utilities.py.

def prid(obj, show_cls=False):
    """Get the id of an object as a hex string, optionally with its class/type."""
    if obj is None:
        s = 'None'
    else:
        s = hex(id(obj))
        if show_cls:
            s += str(type(obj))
    return s
 
 

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

Variable Documentation

◆ all

list CellMLToNektar.utilities.__all__

private

Initial value:

=  ['OnlyWarningsFilter', 'OnlyDebugFilter', 'OnlyTheseSourcesFilter', 'NotifyHandler',
           'DEBUG', 'LOG',
           'Colourable', 'DFS', 'Sentinel', 'unitary_iterator',
           'amara_parse', 'element_path', 'element_path_cmp', 'element_xpath', 'brief_xml',
           'call_if', 'max_i', 'prid', 'add_dicts',
           'open_output_stream', 'close_output_stream']

Definition at line 45 of file utilities.py.

◆ DFS

CellMLToNektar.utilities.DFS = Enum('White', 'Gray', 'Black')

Miscellaneous classes # #

Definition at line 121 of file utilities.py.

Classes

Functions

Variables

Detailed Description

Function Documentation

◆ add_dicts()

◆ amara_parse()

◆ brief_xml()

◆ call_if()

◆ close_output_stream()

◆ DEBUG()

◆ element_path()

◆ element_path_cmp()

◆ element_xpath()

◆ LOG()

◆ max_i()

◆ open_output_stream()

◆ prid()

Variable Documentation

◆ __all__

◆ DFS

◆ all