Add connectivity tutorial.

doc/cpp/remote.rst

@@ -24,7 +24,7 @@ Control Messages
 
     Request termination, giving the reason as a message.
 
-    .. cpp:member:: char[512] reason
+    .. cpp:member:: char reason[512]
 
 .. cpp:class:: msg_epoch
 

doc/tutorial/connectivity.rst

@@ -0,0 +1,237 @@
+.. _tutorial_connectivity:
+
+Declarative Connectivity in Arbor
+=================================
+
+.. admonition:: Concepts and Requirements
+
+    We will assume that you have read the basic recipe and network tutorials.
+
+    In addition to Arbor and its requirements ``matplotlib`` and ``networkx``
+    need to be installed.
+
+In this tutorial, we are going to demonstrate how to leverage Arbor's
+declarative connection description facilities to generate a few common network
+types. We will gradually build up complexity and generally show the full recipe
+first before discussing some of the relevant parts. High-level connectivity
+descriptions can be more intuitive for some types of networks as well as more
+performant in Python simulations, as the construction is handled entirely in C++.
+
+Prelude: Unconnected Cells
+--------------------------
+
+Before we start building actual networks, we will set up the trivial network,
+which has no connections at all. This will be written as a recipe class, as
+discussed in other tutorials, and later examples will derive from this class to
+build upon. If you want, you can skip this part and come back as needed.
+
+Our cells comprise a simple leaky integrate and fire model, not a cable cell, as
+we want to emphasize building networks. We begin by defining the global settings:
+
+.. literalinclude:: ../../python/example/connectivity/unconnected.py
+  :language: python
+  :lines: 7-13
+
+- ``N`` is the cell count of the simulation.
+- ``T`` is the total runtime of the simulation in ``ms``.
+- ``dt`` is the numerical timestep on which cells evolve.
+
+These parameters are used here:
+
+.. literalinclude:: ../../python/example/connectivity/unconnected.py
+  :language: python
+  :lines: 50-
+
+where we run the simulation. Before we discuss the relevant details, the recipe
+reads in full
+
+.. literalinclude:: ../../python/example/connectivity/unconnected.py
+  :language: python
+  :lines: 16-47
+
+In the recipe, we set a prototypical LIF cell:
+
+.. literalinclude:: ../../python/example/connectivity/unconnected.py
+  :language: python
+  :lines: 21
+
+and deliver it for all ``gid``:
+
+.. literalinclude:: ../../python/example/connectivity/unconnected.py
+  :language: python
+  :lines: 43-44
+
+With large and complicated cells this can sometimes help with performance, here,
+it's just a convenient way to structure our recipe. Also, the *first cell* has
+an event generator attached, a Poisson point process seeded with the
+cell's ``gid``.
+
+.. literalinclude:: ../../python/example/connectivity/unconnected.py
+  :language: python
+  :lines: 31-41
+
+All other parameters are set in the constructor:
+
+.. literalinclude:: ../../python/example/connectivity/unconnected.py
+  :language: python
+  :lines: 17-26
+
+We also proceed to add spike recording and generate raster plots using a helper
+function ``plot_spikes`` from ``util.py``, which results in
+
+.. figure:: ../../python/example/connectivity/01-raster.svg
+    :width: 400
+    :align: center
+
+As only the first cell receives spiking inputs, only it will show up on the plot.
+
+Ring Network
+------------
+
+Starting from an unconnected set of cells, we can now start building a simple
+network. A ring structure is defined by connecting each cell to its predecessor,
+i.e. the cell with ``gid = i`` is connected to the cell with ``gid = i - 1`` and
+the cell ``gid = 0`` is connected to the last cell ``gid = N - 1``.
+
+We construct such a network by defining a new recpi ``ring`` deriving from the
+unconnected network
+
+.. literalinclude:: ../../python/example/connectivity/ring.py
+  :language: python
+
+The idiomatic way of extending classes with new functionality is to use
+inheritance. Importantly, the burden of initializing the base class falls on the
+derived class:
+
+.. literalinclude:: ../../python/example/connectivity/ring.py
+  :language: python
+  :lines: 18-20
+
+Next, we add a new method that is responsible for the network. Note that this
+--- in contrast to most other methods on recipe --- does not have an argument of
+``gid``, since it is definining the *global* network.
+
+.. literalinclude:: ../../python/example/connectivity/ring.py
+  :language: python
+  :lines: 22-31
+
+Similar to the construction of a ``decor`` or ``cv_policy``, a light-weight
+language inspired by LISP or Scheme is used here. For this tutorial, we use
+Python format strings to compose expressions. Networks comprise a structure and
+parameters --- ``weight`` and ``delay``, which can be scalars as shown, or more
+elaborate expressions, such a drawing from a random distribution.
+
+The structure is defined in terms of combinators reminiscent of relational
+algebra queries operating on abstract sets of source and target identifiers.
+
+- ``source-cell`` and ``target-cell`` construct a set of eligble sources and targets from a single ``gid``.
+- ``gid-range`` defines a contiguous range of gids ``[start, end)``
+- ``intersect`` constructs the connections between the ``source`` and ``target`` arguments.
+- ``chain`` constructs the set of connections between adjacent neighbours.
+- ``join`` takes two sub-structures ``A`` and ``B`` and returns their union.
+
+Upon close inspection, these combinators directly spell out the prose
+description of the ring network given above: Connect adjacent cells and close
+the ring by connecting the beginning and end! Running the network and plotting
+the spikes we find cells deeper into the ring spiking now
+
+.. figure:: ../../python/example/connectivity/02-raster.svg
+    :width: 400
+    :align: center
+
+The network structure is rendered via ``networkx``
+
+.. figure:: ../../python/example/connectivity/02-graph.svg
+    :width: 400
+    :align: center
+
+Excercise: All-to-all Network
+-----------------------------
+
+Using the ``unconnected`` recipe and the
+`network documentation <https://docs.arbor-sim.org/en/stable/concepts/interconnectivity.html#network-selection-expressions>`_
+define a fully connected network, i.e. where each cell is connected to every other cell except itself.
+
+.. hint::
+
+   1. ``source-cell`` and ``target-cell`` can take a range of ids
+   2. Use and intersection with ``inter-cell`` to remove self connections
+
+Our solution produces the following output
+
+.. figure:: ../../python/example/connectivity/03-raster.svg
+    :width: 400
+    :align: center
+
+The network should look like this
+
+.. figure:: ../../python/example/connectivity/03-graph.svg
+    :width: 400
+    :align: center
+
+For reference, we reproduce it here:
+
+.. literalinclude:: ../../python/example/connectivity/all-to-all.py
+  :language: python
+
+Brunel Network
+--------------
+
+The Brunel network, or in other words, a inhibition-dominated randomly connected
+recurrent network, is a common network structure used in computational
+neuroscience proposed by Nicolas Brunel in 2000. It contains sparsely connected
+inhibitory and excitatory neurons where a critical balance between inhibition
+and excitation inputs to each neuron is maintained to ensure a brain-realistic
+network-wide dynamics. It entails a few typical dynamics of cortical circuits.
+
+Practically, we can describe this network by two populations, called the
+excitatory and inhibitory populations, such that
+
+1. Each cell is connected to each other with some probablity :math:`0 < p < 1`
+   - There no self-connections
+2. If the pre-synaptic cell is in the excitatory population, the weight is :math:`w_{exc} > 0`
+3. If the pre-synaptic cell is in the inhitatory population, the weight is :math:`w_{inh} < 0`
+   - :math:`|w_{inh}| < |w_{exc}|`
+
+The Brunel network simulation can be implemented like this
+
+.. literalinclude:: ../../python/example/connectivity/brunel.py
+  :language: python
+  :lines: 18-32
+
+again using the base class ``unconnected`` to define everything except the
+network. We implement these by writing down the rules above in the recipe
+
+.. literalinclude:: ../../python/example/connectivity/brunel.py
+  :language: python
+  :lines: 34-42
+
+The ``rand`` structure encodes the random connectivity and removes any potential
+self-connections by ``intersect`` with ``inter-cell``, as before. Next, we
+define the weight according the population of the pre-synaptic neuron. The
+population is defined by the ``gid`` of the neuron; the first 80% of cells is
+considered excitatory and the remainder inhibitory. The predicate ``inh``
+reifies this description. The weight function ``weight`` then dispatches to one
+of two values based on the predicate.
+
+Rendering the structure becomes slow and frankly unusable, but showing the
+adjacency matrix might be helpful
+
+.. figure:: ../../python/example/connectivity/04-matrix.svg
+    :width: 400
+    :align: center
+
+Note that rendering can be disabled, if things get too slow.
+
+
+Final Thoughts
+--------------
+
+Using a few examples we have shown how Arbor's high-level network description
+method can be leveraged to generate common structures. The key insight is to
+build complex layouts from atomic blocks by using set operators like ``join``,
+``difference``, and ``intersect``. There are more to explore in the
+documentation, be especially aware of stochastic distributions. We have also
+seen how to produce weights and by extension delays using the same, declarative
+approach. This functionality is quite young and if any useful additions come to
+mind, do not hesitate to request or implement them!

doc/tutorial/index.rst

@@ -45,6 +45,7 @@ Networks
    network_ring
    network_two_cells_gap_junctions
    brunel
+
 
 Probes
 ------
@@ -72,17 +73,19 @@ Hardware
    network_ring_gpu
 
 Advanced
--------
+--------
 
 .. toctree::
    :maxdepth: 1
 
    nmodl
    plasticity
+   connectivity
 
 Demonstrations
 --------------
 
-We try to collect models scientists have built in our `contributor space <https://github.com/arbor-contrib/>`_.
-In addition to the tutorials, browsing these models should give you a good idea of what's possible with Arbor
-and find get in contact with other Arbor users.
+We try to collect models scientists have built in our `contributor space
+<https://github.com/arbor-contrib/>`_. In addition to the tutorials, browsing
+these models should give you a good idea of what's possible with Arbor and find
+get in contact with other Arbor users.