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<div class="section" id="brian-package-structure">
<h1>Brian package structure<a class="headerlink" href="#brian-package-structure" title="Permalink to this headline">¶</a></h1>
<p>List of modules with descriptions of contents:</p>
<p><strong>Root package</strong></p>
<dl class="docutils">
<dt><tt class="docutils literal"><span class="pre">base</span></tt></dt>
<dd>Shared base classes for some Brian clases. At the moment, just the
<tt class="xref py py-class docutils literal"><span class="pre">ObjectContainer</span></tt> class used to implement the <tt class="docutils literal"><span class="pre">contained_objects</span></tt>
protocol.</dd>
<dt><tt class="docutils literal"><span class="pre">clock</span></tt></dt>
<dd>The <tt class="xref py py-class docutils literal"><span class="pre">Clock</span></tt> object, <tt class="xref py py-func docutils literal"><span class="pre">guess_clock()</span></tt> function, and other clock
manipulation functions.</dd>
<dt><tt class="docutils literal"><span class="pre">compartments</span></tt></dt>
<dd>A class used in compartmental modelling (see user documentation).</dd>
<dt><tt class="docutils literal"><span class="pre">connection</span></tt></dt>
<dd>Everything to do with connections, including the <tt class="xref py py-class docutils literal"><span class="pre">Connection</span></tt> and
<tt class="xref py py-class docutils literal"><span class="pre">DelayConnection</span></tt> classes, but also construction/connection matrices
and connection vector code. One of the longest and most technical parts of
Brian.</dd>
<dt><tt class="docutils literal"><span class="pre">correlatedspikes</span></tt></dt>
<dd>A tool for producing correlated spike trains.</dd>
<dt><tt class="docutils literal"><span class="pre">directcontrol</span></tt></dt>
<dd>Classes for producing groups which fire spikes at user specified times.</dd>
<dt><tt class="docutils literal"><span class="pre">equations</span></tt></dt>
<dd>Everything to do with the <tt class="xref py py-class docutils literal"><span class="pre">Equations</span></tt> class.</dd>
<dt><tt class="docutils literal"><span class="pre">globalprefs</span></tt></dt>
<dd>Global preferences for Brian, a few routines for getting and setting.</dd>
<dt><tt class="docutils literal"><span class="pre">group</span></tt></dt>
<dd>A base class for <tt class="xref py py-class docutils literal"><span class="pre">NeuronGroup</span></tt> which creates an <tt class="docutils literal"><span class="pre">_S</span></tt> attribute from
an <tt class="xref py py-class docutils literal"><span class="pre">Equations</span></tt> object with the appropriate dynamical variables, and
allows these variables to be accessed by e.g. <tt class="docutils literal"><span class="pre">grp.V</span></tt> by overriding the
<tt class="docutils literal"><span class="pre">__getattr__</span></tt> and <tt class="docutils literal"><span class="pre">__setattr__</span></tt> methods.</dd>
<dt><tt class="docutils literal"><span class="pre">inspection</span></tt></dt>
<dd>Utility functions for inspecting namespaces, checking consistency of
equations, some code manipulation, etc.</dd>
<dt><tt class="docutils literal"><span class="pre">log</span></tt></dt>
<dd>Brian’s somewhat under-developed logging capabilities.</dd>
<dt><tt class="docutils literal"><span class="pre">magic</span></tt></dt>
<dd>Classes and functions for tracking and finding instances of classes.</dd>
<dt><tt class="docutils literal"><span class="pre">membrane_equations</span></tt></dt>
<dd>More code for compartmental modelling (see user docs).</dd>
<dt><tt class="docutils literal"><span class="pre">monitor</span></tt></dt>
<dd>All the monitors, including <tt class="xref py py-class docutils literal"><span class="pre">SpikeMonitor</span></tt> and <tt class="xref py py-class docutils literal"><span class="pre">StateMonitor</span></tt>.</dd>
<dt><tt class="docutils literal"><span class="pre">network</span></tt></dt>
<dd>The <tt class="xref py py-class docutils literal"><span class="pre">Network</span></tt> and <tt class="xref py py-class docutils literal"><span class="pre">MagicNetwork</span></tt> classes as well as the
<tt class="xref py py-class docutils literal"><span class="pre">NetworkOperation</span></tt> class. Also includes the <tt class="xref py py-func docutils literal"><span class="pre">run()</span></tt>, etc.
functions.</dd>
<dt><tt class="docutils literal"><span class="pre">neurongroup</span></tt></dt>
<dd>The <tt class="xref py py-class docutils literal"><span class="pre">NeuronGroup</span></tt> definition and some related stuff, including linked
variables (the <tt class="xref py py-class docutils literal"><span class="pre">LinkedVar</span></tt> class) and <tt class="xref py py-class docutils literal"><span class="pre">PoissonGroup</span></tt>.</dd>
<dt><tt class="docutils literal"><span class="pre">optimiser</span></tt></dt>
<dd>Some tools for freezing expressions (converting e.g. <tt class="docutils literal"><span class="pre">3*ms</span></tt> into 0.003) and
simplifying some equations (e.g. <tt class="docutils literal"><span class="pre">a/(10*ms)</span></tt> converted to <tt class="docutils literal"><span class="pre">a*100</span></tt>).</dd>
<dt><tt class="docutils literal"><span class="pre">plotting</span></tt></dt>
<dd>Plotting tools, mostly <tt class="docutils literal"><span class="pre">raster_plot</span></tt>.</dd>
<dt><tt class="docutils literal"><span class="pre">quantityarray</span></tt></dt>
<dd>A leftover from the day when Brian had support for arrays with units, will
be removed when practical.</dd>
<dt><tt class="docutils literal"><span class="pre">reset</span></tt></dt>
<dd>Reset classes.</dd>
<dt><tt class="docutils literal"><span class="pre">stateupdater</span></tt></dt>
<dd>State update classes and the <tt class="xref py py-func docutils literal"><span class="pre">magic_state_updater()</span></tt> function.</dd>
<dt><tt class="docutils literal"><span class="pre">stdp</span></tt></dt>
<dd>STDP features.</dd>
<dt><tt class="docutils literal"><span class="pre">stdunits</span></tt></dt>
<dd>Standard unit names such as <tt class="docutils literal"><span class="pre">mV</span></tt> for <tt class="docutils literal"><span class="pre">mvolt</span></tt>, etc.</dd>
<dt><tt class="docutils literal"><span class="pre">stp</span></tt></dt>
<dd>Short term plasticity features.</dd>
<dt><tt class="docutils literal"><span class="pre">threshold</span></tt></dt>
<dd>Threshold classes.</dd>
<dt><tt class="docutils literal"><span class="pre">timedarray</span></tt></dt>
<dd>The <tt class="xref py py-class docutils literal"><span class="pre">TimedArray</span></tt> class and related functions.</dd>
<dt><tt class="docutils literal"><span class="pre">units</span></tt></dt>
<dd>The Brian units package, including the <tt class="xref py py-class docutils literal"><span class="pre">Quantity</span></tt> class.</dd>
<dt><tt class="docutils literal"><span class="pre">unitsafefunctions</span></tt></dt>
<dd>Some functions which override the numpy ones which are safe to use with
units, e.g. <tt class="docutils literal"><span class="pre">sin(3*volt)</span></tt> raises a dimensionality error.</dd>
</dl>
<p><strong>``library`` subpackage</strong></p>
<dl class="docutils">
<dt><tt class="docutils literal"><span class="pre">electrophysiology</span></tt></dt>
<dd>Electrophysiology library with electrode and amplifier models.</dd>
<dt><tt class="docutils literal"><span class="pre">IF</span></tt></dt>
<dd>Integrate-and-fire models (leaky, quadratic, exponential...).</dd>
<dt><tt class="docutils literal"><span class="pre">ionic_currents</span></tt></dt>
<dd>Ionic current models (K+, Na+...).</dd>
<dt><tt class="docutils literal"><span class="pre">random_processes</span></tt></dt>
<dd>Currently only Ornstein-Uhlenbeck.</dd>
<dt><tt class="docutils literal"><span class="pre">synapses</span></tt></dt>
<dd>Synaptic models (exponential, alpha and biexponential models).</dd>
</dl>
<p><strong>``utils`` subpackage</strong></p>
<dl class="docutils">
<dt><tt class="docutils literal"><span class="pre">approximatecomparisons</span></tt></dt>
<dd>Some tools for doing approximate comparisons with floating point numbers
(because they are inexact).</dd>
<dt><tt class="docutils literal"><span class="pre">autodiff</span></tt></dt>
<dd>Automatic differentiation routines (for single-valued functions).</dd>
<dt><tt class="docutils literal"><span class="pre">circular</span></tt> and the <tt class="docutils literal"><span class="pre">ccircular</span></tt> subpackage</dt>
<dd>The important <tt class="xref py py-class docutils literal"><span class="pre">SpikeContainer</span></tt> and related classes. The <tt class="docutils literal"><span class="pre">C</span></tt> version
uses SWIG and is much faster but requires the user to compile themselves
at the moment (this will be addressed at some point in the future).</dd>
<dt><tt class="docutils literal"><span class="pre">documentation</span></tt></dt>
<dd>Some utility functions related to documentation.</dd>
<dt><tt class="docutils literal"><span class="pre">information_theory</span></tt></dt>
<dd>Entropy and mutual information estimators. Requires the ANN wrapper in scikits.</dd>
<dt><tt class="docutils literal"><span class="pre">parallelpython</span></tt></dt>
<dd>A utility function for using the Parallel Python module.</dd>
<dt><tt class="docutils literal"><span class="pre">parameters</span></tt></dt>
<dd>The <tt class="xref py py-class docutils literal"><span class="pre">Parameters</span></tt> class, basically independent of Brian but
potentially useful.</dd>
<dt><tt class="docutils literal"><span class="pre">progressreporting</span></tt></dt>
<dd>A progress reporting framework which <tt class="xref py py-meth docutils literal"><span class="pre">Network.run()</span></tt> can use to report
how long it is taking to run, with text or graphical options.</dd>
<dt><tt class="docutils literal"><span class="pre">statistics</span></tt></dt>
<dd>Statistics of spike trains (CV, vector strength, correlograms...).</dd>
<dt><tt class="docutils literal"><span class="pre">tabulate</span></tt></dt>
<dd>Tabulation of numerical functions (precalculation).</dd>
</dl>
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