Representing Brian objects

__repr__ and __str__

Every class should specify or inherit useful __repr__ and __str__ methods. The __repr__ method should give the “official” representation of the object; if possible, this should be a valid Python expression, ideally allowing for eval(repr(x)) == x. The __str__ method on the other hand, gives an “informal” representation of the object. This can be anything that is helpful but does not have to be Python code. For example:

>>> import numpy as np
>>> ar = np.array([1, 2, 3]) * mV
>>> print(ar)  # uses __str__
[ 1.  2.  3.] mV
>>> ar  # uses __repr__
array([ 1.,  2.,  3.]) * mvolt

If the representation returned by __repr__ is not Python code, it should be enclosed in <...>, e.g. a Synapses representation might be <Synapses object with 64 synapses>.

If you don’t want to make the distinction between __repr__ and __str__, simply define only a __repr__ function, it will be used instead of __str__ automatically (no need to write __str__ = __repr__). Finally, if you include the class name in the representation (which you should in most cases), use self.__class__.__name__ instead of spelling out the name explicitly – this way it will automatically work correctly for subclasses. It will also prevent you from forgetting to update the class name in the representation if you decide to rename the class.

LaTeX representations with sympy

Brian objects dealing with mathematical expressions and equations often internally use sympy. Sympy’s latex function does a nice job of converting expressions into LaTeX code, using fractions, root symbols, etc. as well as converting greek variable names into corresponding symbols and handling sub- and superscripts. For the conversion of variable names to work, they should use an underscore for subscripts and two underscores for superscripts:

>>> from sympy import latex, Symbol
>>> tau_1__e = Symbol('tau_1__e')
>>> print latex(tau_1__e)

Sympy’s printer supports formatting arbitrary objects, all they have to do is to implement a _latex method (no trailing underscore). For most Brian objects, this is unnecessary as they will never be formatted with sympy’s LaTeX printer. For some core objects, in particular the units, is is useful, however, as it can be reused in LaTeX representations for ipython (see below). Note that the _latex method should not return $ or \begin{equation} (sympy’s method includes a mode argument that wraps the output automatically).

Representations for ipython

“Old” ipython console

In particular for representations involing arrays or lists, it can be useful to break up the representation into chunks, or indent parts of the representation. This is supported by the ipython console’s “pretty printer”. To make this work for a class, add a _repr_pretty_(self, p, cycle) (note the single underscores) method. You can find more information in the ipython documentation .

“New” ipython console (qtconsole and notebook)

The new ipython consoles, the qtconsole and the ipython notebook support a much richer set of representations for objects. As Brian deals a lot with mathematical objects, in particular the LaTeX and to a lesser extent the HTML formatting capabilities of the ipython notebook are interesting. To support LaTeX representation, implement a _repr_latex_ method returning the LaTeX code (including $, \begin{equation} or similar). If the object already has a _latex method (see LaTeX representations with sympy above), this can be as simple as:

def _repr_latex_(self):
    return sympy.latex(self, mode='inline')  # wraps the expression in $ .. $

The LaTeX rendering only supports a single mathematical block. For complex objects, e.g. NeuronGroup it might be useful to have a richer representation. This can be achieved by returning HTML code from _repr_html_ – this HTML code is processed by MathJax so it can include literal LaTeX code that will be transformed before it is rendered as HTML. An object containing two equations could therefore be represented with a method like this:

def _repr_html_(self):
    return '''
    <h3> Equation 1 </h3>
    <h3> Equation 2 </h3>
    {eq_2}'''.format(eq_1=sympy.latex(self.eq_1, mode='equation'),
                     eq_2=sympy.latex(self.eq_2, mode='equation'))