Changeset 1015

Timestamp:

11/25/11 14:53:10 (6 months ago)

Author:

apdavison

Message:

Implemented (together with Jochen and Mikael) NEST-specific version of the CSAConnector, which uses the NEST connection-generator interface currently available in the csanest branch of NEST.

Location:

trunk

Files:

• examples/VAbenchmarks2-csa.py (modified) (1 diff)
• src/connectors.py (modified) (4 diffs)
• src/nest/connectors.py (modified) (2 diffs)

trunk/examples/VAbenchmarks2-csa.py

@@ -126 +126 @@
 inh_cells = all_cells[n_exc:]
 if benchmark == "COBA":
-    ext_stim = Population(20, SpikeSourcePoisson,{'rate' : rate, 'duration' : stim_dur},"expoisson")
+    ext_stim = Population(20, SpikeSourcePoisson, {'rate' : rate, 'duration' : stim_dur}, label="expoisson")
     rconn = 0.01
     ext_conn = FixedProbabilityConnector(rconn, weights=0.1)
 
 print "%s Initialising membrane potential to random values..." % node_id
-rng = NumpyRNG(seed=rngseed, parallel_safe=parallel_safes)
+rng = NumpyRNG(seed=rngseed, parallel_safe=parallel_safe)
 uniformDistr = RandomDistribution('uniform', [v_reset,v_thresh], rng=rng)
 all_cells.initialize('v', uniformDistr)

trunk/src/connectors.py

@@ -898 +898 @@
             Connector.__init__(self, None, None, safe=safe, verbose=verbose)
             self.cset = cset
-            if cset.arity == 0:
+            if csa.arity(cset) == 0:
                 #assert weights is not None and delays is not None, \
                 #       'must specify weights and delays in addition to a CSA mask'
@@ -906 +906 @@
                 self.delays = delays
             else:
-                assert cset.arity == 2, 'must specify mask or connection-set with arity 2'
+                assert csa.arity(cset) == 2, 'must specify mask or connection-set with arity 2'
                 assert weights is None and delays is None, \
                        "weights or delays specified both in connection-set and as CSAConnector argument"
@@ -926 +926 @@
         if self.delays is None:
             self.delays = projection._simulator.state.min_delay
-        i0 = projection.pre.first_id
-        size1 = projection.pre.last_id - i0
-        j0 = projection.post.first_id
-        targets = [j - j0 for j in projection.post]
-
-        # Cut out finite part and shift to global ids
-        c = csa.shift (i0, j0) * csa.cross ((0, size1), targets) * self.cset
-        
-        if csa.arity (self.cset) == 2:
+        # Cut out finite part
+        c = csa.cross((0, projection.pre.size-1), (0, projection.post.size-1)) * self.cset
+        
+        if csa.arity(self.cset) == 2:
             # Connection-set with arity 2
             for (i, j, weight, delay) in c:
-                projection._divergent_connect (i, [j], weight, delay)
+                projection._divergent_connect(projection.pre[i], [projection.post[j]], weight, delay)
         elif CSAConnector.isConstant (self.weights) \
              and CSAConnector.isConstant (self.delays):
             # Mask with constant weights and delays
             for (i, j) in c:
-                projection._divergent_connect (i, [j], self.weights, self.delays)
+                projection._divergent_connect (projection.pre[i], [projection.post[j]], self.weights, self.delays)
         else:
             # Mask with weights and/or delays iterable
@@ -952 +947 @@
                 delays = CSAConnector.constantIterator (delays)
             for (i, j), weight, delay in zip (c, weights, delays):
-                projection._divergent_connect (i, [j], weight, delay)
+                projection._divergent_connect (projection.pre[i], [projection.post[j]], weight, delay)

trunk/src/nest/connectors.py

@@ -16 +16 @@
 import numpy
 from pyNN.space import Space
-
-
-
+from pyNN.common.populations import Population
+try:
+    import csa
+    have_csa = True
+except ImportError:
+    have_csa = False
+import nest
 
 class FastProbabilisticConnector(Connector):
@@ -209 +213 @@
             connector._probabilistic_connect(tgt, proba, self.n_connections, self.rewiring)
             self.progression(count, projection._simulator.state.mpi_rank)
+
+
+class CSAConnector(CSAConnector):
+    
+    def connect(self, projection):
+        """Connect-up a Projection."""
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
+
+        def connect_csa(cset, pre, post, syn_type):
+            print "connecting using cset"
+            if isinstance(pre, Population) and isinstance(post, Population):
+                # contiguous IDs, so just pass first_id and size
+                nest.sli_func("Connect_cg_i_i_i_i_D_l",
+                              self.cset,
+                              pre.first_id, pre.size,
+                              post.first_id, post.size,
+                              {'weight': 0, 'delay': 1}, # ignored if arity==0
+                              syn_type)
+            else: # PopulationViews or Assemblies
+                # IDs may be non-contiguous, so need to pass entire arrays
+                nest.sli_func("Connect_cg_a_a_D_l",
+                              self.cset,
+                              pre.all_cells,
+                              post.all_cells,
+                              {'weight': 0, 'delay': 1}, # ignored if arity==0
+                              syn_type)
+        # TODO: fix weights units
+        if csa.arity(self.cset) == 2:
+            # Connection-set with arity 2
+            connect_csa(self.cset, projection.pre,
+                        projection.post, projection.synapse_model)
+        elif CSAConnector.isConstant(self.weights) \
+            and CSAConnector.isConstant(self.delays):
+            # Mask with constant weights and delays
+            assert csa.arity(self.cset) == 0
+            nest.SetDefaults(projection.synapse_model, {'weight': self.weights, 'delay': self.delays})
+            connect_csa(self.cset, projection.pre,
+                        projection.post, projection.synapse_model)
+        projection._sources = projection.pre.all_cells