Skip to content

Commit

Permalink
Update interconnectivity.rst (#2353)
Browse files Browse the repository at this point in the history
<!-- Please make sure your PR follows our [contribution
guidelines](https://github.com/arbor-sim/arbor/tree/master/doc/contrib)
and agree to the terms outlined in the [PR
procedure](https://github.com/arbor-sim/arbor/tree/master/doc/contrib/pr.rst).
-->

---------

Co-authored-by: Thorsten Hater <[email protected]>
  • Loading branch information
ErbB4 and thorstenhater authored Aug 8, 2024
1 parent 16c8687 commit 2c6da98
Showing 1 changed file with 26 additions and 17 deletions.
43 changes: 26 additions & 17 deletions doc/cpp/interconnectivity.rst
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ Interconnectivity
a cell or a spike source. The target is a synapse on the post-synaptic cell.

The :cpp:member:`target` does not include the gid of a cell, this is because a
:cpp:class:`cell_connection` is bound to the target cell which means that the gid
:cpp:class:`cell_connection` is bound to the target cell, which means that the gid
is implicitly known.

.. cpp:member:: cell_global_label_type source
Expand Down Expand Up @@ -45,13 +45,22 @@ Interconnectivity
a cell or a spike source. The target is a synapse on the post-synaptic cell.

The :cpp:member:`target` does not include the gid of a cell, this is because a
:cpp:class:`ext_cell_connection` is bound to the target cell which means that the gid
:cpp:class:`ext_cell_connection` is bound to the target cell, which means that the ``gid``
is implicitly known.

.. cpp:member:: cell_remote_label_type source

Source end point, represented by a :cpp:type:`cell_remote_label_type` which packages
a cell gid, integral tag of a group of sources on the cell, and source selection policy.
Source end point, comprising

- global id, uniquely identifying the source object inside the remote simulation,
- local id, uniquely identifying the location of the source on the source object,
- selection policy, how to map sources `(gid, lid)` to the targets in Arbor.

.. Note::
The tuple ``(gid, lid)`` must be unique for each source. This addressing scheme follows Arbor's model of multiple
sources (threshold detectors) per cell. If the remote simulation does not provide multiple items per
source object, ``lid`` can be ignored and set to zero.


.. cpp:member:: cell_local_label_type target

Expand All @@ -76,7 +85,7 @@ Interconnectivity

Describes a gap junction connection between two gap junction sites. The :cpp:member:`local` site does
not include the gid of a cell, this is because a :cpp:class:`gap_junction_connection` is bound to the local
cell which means that the gid is implicitly known.
cell, which means that the gid is implicitly known.

.. note::

Expand Down Expand Up @@ -140,11 +149,11 @@ Interconnectivity

.. cpp:class:: network_value

A network value, describing the its calculation for each connection.
A network value, describing the calculation for each connection.

.. cpp:function:: network_value scalar(double value)

A fixed scalar valaue.
A fixed scalar value.

.. cpp:function:: network_value named(std::string name)

Expand All @@ -160,11 +169,11 @@ Interconnectivity

.. cpp:function:: network_value normal_distribution(unsigned seed, double mean, double std_deviation)

A normal random distribution with given mean and standard deviation.
A normal random distribution with a given mean and standard deviation.

.. cpp:function:: network_value truncated_normal_distribution(unsigned seed, double mean, double std_deviation, const std::array<double, 2>& range)

A truncated normal random distribution with given mean and standard deviation. Sampled through accept-reject method to only returns values in [range_0, range_1)
A truncated normal random distribution with a given mean and standard deviation. Sampled through an accept-reject method to only return values in [range_0, range_1)

.. cpp:function:: network_value custom(custom_func_type func)

Expand Down Expand Up @@ -196,11 +205,11 @@ Interconnectivity

.. cpp:function:: network_value exp(network_value v)

Exponential of given value.
Exponential of a given value.

.. cpp:function:: network_value log(network_value v)

Logarithm of given value.
Logarithm of a given value.

.. cpp:function:: if_else(network_selection cond, network_value true_value, network_value false_value)

Expand Down Expand Up @@ -293,7 +302,7 @@ Interconnectivity

.. cpp:function:: network_selection random(unsigned seed, network_value p);

Random selection using the bernoulli random distribution with probability "p" between 0.0 and 1.0
Random selection using the Bernoulli random distribution with probability "p" between 0.0 and 1.0

.. cpp:function:: network_selection custom(custom_func_type func);

Expand All @@ -303,12 +312,12 @@ Interconnectivity

.. cpp:function:: network_selection distance_lt(double d);

Only select within given distance. This may enable more efficient sampling through an
Only select within a given distance. This may enable more efficient sampling through an
internal spatial data structure.

.. cpp:function:: network_selection distance_gt(double d);

Only select if distance greater then given distance. This may enable more efficient sampling
Only select if the distance is greater than a given distance. This may enable more efficient sampling
through an internal spatial data structure.


Expand Down Expand Up @@ -359,14 +368,14 @@ Interconnectivity

.. cpp:member:: network_label_dict dict

Label dictionary for named selecations and values.
Label dictionary for named selections and values.


.. function:: generate_network_connections(recipe, context, decomp)

Generate network connections from the network description in the recipe. Only generates connections
with local gids in the domain composition as target. Does not include connections from
the "connections_on" recipe function.
with local gids in the domain composition as the target. Does not include connections from
the ``connections_on`` recipe function.

.. function:: generate_network_connections(recipe)

Expand Down

0 comments on commit 2c6da98

Please sign in to comment.