Changeset 728

Timestamp:

03/11/10 17:41:37 (2 years ago)

Author:

pierre

Message:

Minor modification in the test to be able to pass the tests for connectors2.py. Still in testing phase, but you can try it if you want, and report bugs if any. Seems to work. I'll add also a progressbar I think to all those Connector, to be able to visualize the status of the connections. Can be useful maybe, to have an idea of the building time

Location:

trunk

Files:

• src/connectors2.py (modified) (11 diffs)
• test/unittests/generictests.py (modified) (2 diffs)

trunk/src/connectors2.py

@@ -3 +3 @@
 from pyNN.space import Space
 from pyNN.random import RandomDistribution
-from numpy import exp
+from numpy import arccos, arcsin, arctan, arctan2, ceil, cos, cosh, e, exp, \
+                    fabs, floor, fmod, hypot, ldexp, log, log10, modf, pi, power, \
+                    sin, sinh, sqrt, tan, tanh, maximum, minimum
 
 class ConnectionAttributeGenerator(object):
@@ -27 +29 @@
             return values
         elif isinstance(self.source, RandomDistribution):
-            values = self.source.next(N, mask_local=self.local_mask)
-            if sub_mask is not None:
-                values = values[sub_mask]
+            if sub_mask is None:
+                values = self.source.next(N, mask_local=self.local_mask)
+            else:
+                values = self.source.next(len(sub_mask), mask_local=self.local_mask)
             return values
         elif isinstance(self.source, numpy.ndarray):
@@ -44 +47 @@
       ConnectionAttributeGenerator.__init__(self, source, local_mask, safe)
       self.projection     = projection
-      self.is_conductance = common.is_conductance(projection.post.local_cells[0])
-
+      self.is_conductance = common.is_conductance(projection.post.all_cells[0])
+      
     def check(self, weight):
         if weight is None:
@@ -167 +170 @@
         self.projection        = projection
         self.allow_self_connections = allow_self_connections
-
+        
     def _probabilistic_connect(self, src, p):
         """
@@ -178 +181 @@
             create = numpy.arange(self.local.sum())
         else:
-            rarr   = self.probas_generator.get(self.N, self.distance_matrix)
-            create = numpy.where(rarr < p)[0]
-        
-        if isinstance(self.weights, basestring) or isinstance(self.delays, basestring):      
-            self.distance_matrix.set_source(src.position)
-        
+            rarr   = self.probas_generator.get(self.N)
+            if not core.is_listlike(rarr) and numpy.isscalar(rarr): # if N=1, rarr will be a single number
+                rarr = numpy.array([rarr])
+            create = numpy.where(rarr < p)[0]  
+        self.distance_matrix.set_source(src.position)        
         targets = self.projection.post.local_cells[create]
         weights = self.weights_generator.get(self.N, self.distance_matrix, create)
@@ -226 +228 @@
         
     def connect(self, projection):
-        connector = ProbabilisticConnector(projection, self.weights, self.delays, self.allow_self_connections, self.space, safe=self.safe)
-        for src in projection.pre.all():
+        connector = ProbabilisticConnector(projection, self.weights, self.delays, self.allow_self_connections, self.space, safe=self.safe)        
+        for count, src in enumerate(projection.pre.all()):
             connector._probabilistic_connect(src, 1)
+
 
     
@@ -430 +433 @@
         weights_generator = WeightGenerator(self.weights, local, projection, self.safe)
         delays_generator  = DelayGenerator(self.delays, local, self.safe)
-        distance_matrix   = DistanceMatrix(projection.post.positions, self.space, local)
+        distance_matrix   = DistanceMatrix(projection.post.positions, self.space, numpy.arange(len(projection.post)))
         candidates        = projection.post.all_cells.flatten()            
         
@@ -443 +446 @@
                 n = self.n
             
-            targets     = numpy.zeros(0, int)
-            loc_targets = []
-            create      = []
-            
+            targets     = numpy.zeros(0, int)            
             while len(targets) < n: # if the number of requested cells is larger than the size of the
                                     # postsynaptic population, we allow multiple connections for a given cell                
@@ -455 +455 @@
                     targets = numpy.delete(targets, idx)
             
-            targets = targets[:n]            
-            if isinstance(self.weights, basestring) or isinstance(self.delays, basestring):      
-                distance_matrix.set_source(src.position)
-            
-            # We need to keep only the local cells, because then distances will be computed only
-            # by the nodes that will established the connections. create is just a mask with all 
-            # the id of the cells that are local and that need to be used. Same id could be repeted
-            # but this is not a problem.
-            for id in targets:
-                pos = numpy.where(id == projection.post.local_cells)[0]
-                N   = len(pos)
-                if N > 0:
-                    loc_targets += N*[id]
-                    create      += [pos[0]]
-            
+            distance_matrix.set_source(src.position)
+            targets = targets[:n].astype(int)                        
+            create  = targets - projection.post.first_id            
             weights = weights_generator.get(n, distance_matrix, create)
             delays  = delays_generator.get(n, distance_matrix, create)            
                         
-            if len(loc_targets) > 0:
-                projection.connection_manager.connect(src, loc_targets, weights, delays)
+            if len(targets) > 0:
+                projection.connection_manager.connect(src, targets.tolist(), weights, delays)
                     
 
@@ -538 +526 @@
                 n = self.n
             
-            sources = []
+            sources = numpy.zeros(0, int)
             while len(sources) < n: # if the number of requested cells is larger than the size of the
                                     # presynaptic population, we allow multiple connections for a given cell
@@ -547 +535 @@
                     sources = numpy.delete(sources, i)
             
+            distance_matrix.set_source(tgt.position)        
             sources = sources[:n].astype(int)
-            
-            if isinstance(self.weights, basestring) or isinstance(self.delays, basestring):      
-                distance_matrix.set_source(tgt.position)
-            
             create  = sources - projection.pre.first_id
             weights = weights_generator.get(n, distance_matrix, create)

trunk/test/unittests/generictests.py

@@ -886 +886 @@
             for tgtP in [self.target6, self.target33]:
                 for conn in connectors:
-                    print conn.w_expr
+                    #print conn.w_expr
                     prj = sim.Projection(srcP, tgtP, conn)
                     first_connection = prj.connections[0]
@@ -892 +892 @@
                     for c in first_connection, last_connection:
                        d = space.distance(c.source, c.target)
-                       self.assertAlmostEqual(c.weight, eval(conn.w_expr), 10)
+                       self.assertAlmostEqual(c.weight, eval(conn.weights), 10)
 
 class ProjectionSetTest(unittest.TestCase):