Merge pull request #624 from apdavison/issue622

Fix for #622

Author: Andrew Davison

pyNN/brian/projections.py

@@ -11,6 +11,7 @@
 from pyNN import common
 from pyNN.standardmodels.synapses import TsodyksMarkramSynapse
 from pyNN.core import is_listlike
+from .populations import PopulationView
 from pyNN.parameters import ParameterSpace
 from pyNN.space import Space
 from . import simulator
@@ -139,7 +140,7 @@ def _partition(self, indices):
         else:
             partitions = [indices]
         return partitions
-    
+
     def _localize_index(self, index):
         """determine which group the postsynaptic index belongs to """
         if isinstance(self.post, common.Assembly):
@@ -192,7 +193,7 @@ def _set_attributes(self, connection_parameters):
             value = value.T
             filtered_value = value[syn_obj.postsynaptic, syn_obj.presynaptic]
             setattr(syn_obj, name, filtered_value)
-    
+
     def _get_attributes_as_arrays(self, attribute_names, multiple_synapses='sum'):
         if isinstance(self.post, common.Assembly) or isinstance(self.pre, common.Assembly):
             raise NotImplementedError
@@ -215,8 +216,12 @@ def _get_attributes_as_list(self, attribute_names):
         for name in attribute_names:
             if name == "presynaptic_index":
                 value = self._brian_synapses[0][0].presynaptic
+                if isinstance(self.pre, PopulationView):
+                    value = self.pre.id_to_index(value)
             elif name == "postsynaptic_index":
                 value = self._brian_synapses[0][0].postsynaptic
+                if isinstance(self.post, PopulationView):
+                    value = self.post.id_to_index(value)
             else:
                 data_obj = getattr(self._brian_synapses[0][0], name).data
                 if hasattr(data_obj, "tolist"):

pyNN/common/populations.py

@@ -923,6 +923,25 @@ def index_in_grandparent(self, indices):
         else:
             return indices_in_parent
 
+    def __eq__(self, other):
+        """
+        Determine whether two views are the same.
+        """
+        return not self.__ne__(other)
+
+    def __ne__(self, other):
+        """
+        Determine whether two views are different.
+        """
+        # We can't use the self.mask, as different masks can select the same cells
+        # (e.g. slices vs arrays), therefore we have to use self.all_cells
+        if isinstance(other, PopulationView):
+            return self.parent != other.parent or not numpy.array_equal(self.all_cells, other.all_cells)
+        elif isinstance(other, Population):
+            return self.parent != other or not numpy.array_equal(self.all_cells, other.all_cells)
+        else:
+            return True
+
     def describe(self, template='populationview_default.txt', engine='default'):
         """
         Returns a human-readable description of the population view.

pyNN/connectors.py

@@ -191,7 +191,7 @@ def _standard_connect(self, projection, connection_map_generator, distance_map=N
             # `source_mask` - boolean numpy array, indicating which of the pre-synaptic neurons should be connected to,
             #                 or a single boolean, meaning connect to all/none of the pre-synaptic neurons
             #                 It can also be an array of addresses
-            _proceed = False 
+            _proceed = False
             if source_mask is True or source_mask.any():
                 _proceed = True
             elif type(source_mask) == numpy.ndarray:
@@ -206,7 +206,7 @@ def _standard_connect(self, projection, connection_map_generator, distance_map=N
                     source_mask = numpy.arange(projection.pre.size, dtype=int)
                 elif source_mask.dtype == bool:
                     source_mask = source_mask.nonzero()[0]
-            
+
                 # Evaluate the lazy arrays containing the synaptic parameters
                 connection_parameters = {}
                 for name, map in parameter_space.items():
@@ -275,6 +275,10 @@ def __init__(self, allow_self_connections=True, safe=True,
     def connect(self, projection):
         if not self.allow_self_connections and projection.pre == projection.post:
             connection_map = LazyArray(lambda i, j: i != j, shape=projection.shape)
+            # there is a more complicated scenario, where we connect two different
+            # views of the same population. In this case, something other than i != j
+            # will be needed. It should at least be documented that we currently
+            # don't handle this situation.
         elif self.allow_self_connections == 'NoMutual' and projection.pre == projection.post:
             connection_map = LazyArray(lambda i, j: i > j, shape=projection.shape)
         else:
@@ -559,7 +563,7 @@ class FromFileConnector(FromListConnector):
 
                 # columns = ["i", "j", "weight", "delay", "U", "tau_rec"]
 
-            Note that the header requires `#` at the beginning of the line.            
+            Note that the header requires `#` at the beginning of the line.
 
         `distributed`:
             if this is True, then each node will read connections from a file
@@ -1015,7 +1019,7 @@ def connect(self, projection):
 
         # Assume that targets are equally distributed over processes
         targets_per_process = int(len(projection.post) / num_processes)
-            
+
         # Calculate the number of synapses on each process
         bino = RandomDistribution('binomial',
                                   [self.n, targets_per_process / len(projection.post)],
@@ -1031,7 +1035,7 @@ def connect(self, projection):
             sum_dist += targets_per_process
             sum_partitions += num_conns_on_vp[k]
 
-        # Draw random sources and targets 
+        # Draw random sources and targets
         connections = [[] for i in range(projection.post.size)]
         possible_targets = numpy.arange(projection.post.size)[projection.post._mask_local]
         for i in range(num_conns_on_vp[rank]):

test/system/scenarios/test_connectors.py

@@ -201,6 +201,29 @@ def issue309(sim):
     sim.end()
 
 
+@register()
+def issue622(sim):
+    sim.setup()
+    pop = sim.Population(10, sim.IF_cond_exp, {}, label="pop")
+
+    view1 = sim.PopulationView(pop, [2,3,4])
+    view2 = sim.PopulationView(pop, [2,3,4])
+
+    proj1 = sim.Projection(view1, view2, sim.AllToAllConnector(allow_self_connections = False), sim.StaticSynapse(
+        weight=0.015, delay=1.0), receptor_type='excitatory')
+    proj2 = sim.Projection(view1, view1, sim.AllToAllConnector(allow_self_connections = False), sim.StaticSynapse(
+        weight=0.015, delay=1.0), receptor_type='excitatory')
+
+
+    w1 = proj1.get("weight", "list")
+    w2 = proj2.get("weight", "list")
+
+    assert_equal(w1, w2)
+    assert_equal(sorted(w1),
+                 sorted([(0.0, 1.0, 0.015), (0.0, 2.0, 0.015), (1.0, 0.0, 0.015),
+                         (1.0, 2.0, 0.015), (2.0, 0.0, 0.015), (2.0, 1.0, 0.015)]))
+
+
 if __name__ == '__main__':
     from pyNN.utility import get_simulator
     sim, args = get_simulator()