Re-organise tripartite connectivity generation to support multiple primary connection rules

doc/htmldoc/examples/index.rst

@@ -60,7 +60,8 @@ PyNEST examples
            * :doc:`../auto_examples/astrocytes/astrocyte_single`
            * :doc:`../auto_examples/astrocytes/astrocyte_interaction`
            * :doc:`../auto_examples/astrocytes/astrocyte_small_network`
-           * :doc:`../auto_examples/astrocytes/astrocyte_brunel`
+           * :doc:`../auto_examples/astrocytes/astrocyte_brunel_bernoulli`
+           * :doc:`../auto_examples/astrocytes/astrocyte_brunel_fixed_indegree`
 
 
 .. grid:: 1 1 2 3

doc/htmldoc/model_details/astrocyte_model_implementation.ipynb

@@ -170,7 +170,7 @@
     "    y[0, 1] = 1.0\n",
     "    y[0, 2] = 1.0\n",
     "    fos = []  # full output dict from odeint()\n",
-    "    delta_ip3 = 5.0  # parameter determining the increase in IP3 induced by synaptic input\n",
+    "    delta_ip3 = p.delta_IP3  # parameter determining the increase in IP3 induced by synaptic input\n",
     "\n",
     "    # update time-step by time-step\n",
     "    for k in range(1, n):\n",
@@ -211,7 +211,7 @@
     "    \"Kd_IP3_2\": 0.9434,\n",
     "    \"Km_SERCA\": 0.1,\n",
     "    \"ratio_ER_cyt\": 0.185,\n",
-    "    \"delta_IP3\": 5.0,\n",
+    "    \"delta_IP3\": 0.0002,\n",
     "    \"k_IP3R\": 0.0002,\n",
     "    \"rate_L\": 0.00011,\n",
     "    \"tau_IP3\": 7142.0,\n",
@@ -318,7 +318,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.12.1"
   }
  },
  "nbformat": 4,

doc/htmldoc/synapses/connectivity_concepts.rst

@@ -500,18 +500,25 @@ As multapses are per default allowed and possible with this rule, you can disall
 
 .. _tripartite_connectivity:
 
-Tripartite Bernoulli with pool
-------------------------------
+Third-factor Bernoulli with pool
+--------------------------------
 
 For each possible pair of nodes from a source ``NodeCollection`` (e.g., a neuron population ``S``)
 and a target ``NodeCollection`` (e.g., a neuron population ``T``), a connection is
-created with probability ``p_primary``, and these connections are
-called 'primary' connections. For each primary connection, a
+created according to the ``conn_spec`` parameter passed to
+``TripariteConnect``; any one-directional connection specification can
+be used. The connections created between ``S`` and ``T`` are the
+*primary* connections.
+
+For each primary connection, a
 third-party connection pair involving a node from a third ``NodeCollection``
-(e.g., an astrocyte population ``A``) is created with the conditional probability
-``p_third_if_primary``. This connection pair includes a connection
+(e.g., an astrocyte population ``A``) is created according to the
+``third_factor_conn_spec`` provided. This connection pair includes a connection
 from the ``S`` node to the ``A`` node, and a connection from the ``A`` node to the
-``T`` node. The ``A`` node to connect to is chosen
+``T`` node.
+
+At present, ``third_factor_bernoulli_with_pool`` is the only connection rule
+available for third-factor connectivity. It chooses the ``A`` node to connect
 at random from a pool, a subset of the nodes in ``A``. By default,
 this pool is all of ``A``.
 
@@ -548,55 +555,41 @@ up to two randomly selected nodes in ``A`` (given ``pool_size == 2``).
     S = nest.Create('aeif_cond_alpha_astro', N_S)
     T = nest.Create('aeif_cond_alpha_astro', N_T)
     A = nest.Create('astrocyte_lr_1994', N_A)
-    conn_spec = {'rule': 'tripartite_bernoulli_with_pool',
-                      'p_primary': p_primary,
-		      'p_third_if_primary': p_third_if_primary,
-                      'pool_type': pool_type,
-		      'pool_size': pool_size}
+    conn_spec = {'rule': 'pairwise_bernoulli',
+                      'p': p_primary}
+    third_factor_conn_spec = {'rule': 'third_factor_bernoulli_with_pool',
+		                   'p': p_third_if_primary,
+                                   'pool_type': pool_type,
+		                   'pool_size': pool_size}
     syn_specs = {'third_out': 'sic_connection'}
-    nest.TripartiteConnect(S, T, A, conn_spec, syn_specs)
+    nest.TripartiteConnect(S, T, A, conn_spec, third_factor_conn_spec, syn_specs)
 
 (B) In
 the first example of ``'block'`` pool type, let ``N_T/N_A`` = 2,
 then each node in ``T`` can be connected with one node in ``A``
 (``pool_size == 1`` is required because ``N_A < N_T``), and each node in
 ``A`` can be connected with up to two nodes in ``T``.
 
+The code for this example is identical to the code for example (A),
+except for the choice of pool type and size:
+
 .. code-block:: python
 
-    N_S, N_T, N_A, p_primary, p_third_if_primary = 6, 6, 3, 0.2, 1.0
     pool_type, pool_size = 'block', 1
-    S = nest.Create('aeif_cond_alpha_astro', N_S)
-    T = nest.Create('aeif_cond_alpha_astro', N_T)
-    A = nest.Create('astrocyte_lr_1994', N_A)
-    conn_spec = {'rule': 'tripartite_bernoulli_with_pool',
-                 'p_primary': p_primary,
-                 'p_third_if_primary': p_third_if_primary,
-                 'pool_type': pool_type,
-                 'pool_size': pool_size}
-    syn_specs = {'third_out': 'sic_connection'}
-    nest.TripartiteConnect(S, T, A, conn_spec, syn_specs)
 
 (C) In the second example
 of ``'block'`` pool type, let ``N_A/N_T`` = 2, then each node in
 ``T`` can be connected with up to two nodes in ``A`` (``pool_size == 2`` is
 required because ``N_A/N_T`` = 2), and each node in ``A`` can be
 connected to one node in ``T``.
 
+In this example, we have different values for ``N_T`` and ``N_A`` than
+in examples (A) and (B), and a different pool size than in example (B):
+
 .. code-block:: python
 
     N_S, N_T, N_A, p_primary, p_third_if_primary = 6, 3, 6, 0.2, 1.0
     pool_type, pool_size = 'block', 2
-    S = nest.Create('aeif_cond_alpha_astro', N_S)
-    T = nest.Create('aeif_cond_alpha_astro', N_T)
-    A = nest.Create('astrocyte_lr_1994', N_A)
-    conn_spec = {'rule': 'tripartite_bernoulli_with_pool',
-                 'p_primary': p_primary,
-                 'p_third_if_primary': p_third_if_primary,
-                 'pool_type': pool_type,
-                 'pool_size': pool_size}
-    syn_specs = {'third_out': 'sic_connection'}
-    nest.TripartiteConnect(S, T, A, conn_spec, syn_specs)
 
 
 References

models/astrocyte_lr_1994.cpp

@@ -123,7 +123,7 @@ nest::astrocyte_lr_1994::Parameters_::Parameters_()
   , Km_SERCA_( 0.1 )    // µM
   , SIC_scale_( 1.0 )
   , SIC_th_( 0.19669 )    // µM
-  , delta_IP3_( 5.0 )     // µM
+  , delta_IP3_( 0.0002 )  // µM
   , k_IP3R_( 0.0002 )     // 1/(µM*ms)
   , rate_IP3R_( 0.006 )   // 1/ms
   , rate_L_( 0.00011 )    // 1/ms