Changeset 1003 for trunk

Timestamp:

10/31/11 14:42:54 (7 months ago)

Author:

apdavison

Message:

Removed _simulator attribute from Connector classes. The simulator kernel is now only used within connect(projection), via the _simulator attribute of Projection. This changes means: (i) it should now be possible to run more than one simulator at the same time, without cross-talk via the common Connector classes; (ii) checking for valid delays no longer happens on Connector construction, but is delayed until connect() is called

Location:

trunk

Files:

• src/brian/connectors.py (modified) (2 diffs)
• src/connectors.py (modified) (23 diffs)
• src/nemo/connectors.py (modified) (1 diff)
• src/nest/connectors.py (modified) (2 diffs)
• src/neuron/connectors.py (modified) (1 diff)
• src/pcsim/connectors.py (modified) (1 diff)
• test/unittests/test_connectors.py (modified) (1 diff)
• test/unittests/test_simulation_control.py (modified) (7 diffs)

trunk/src/brian/connectors.py

@@ -24 +24 @@
                             WeightGenerator, \
                             DelayGenerator, \
-                            ProbaGenerator, Connector
-from pyNN.brian import simulator
-
-Connector._simulator = simulator
+                            ProbaGenerator
 
 
@@ -122 +119 @@
     
     def connect(self, projection):
-        """Connect-up a Projection."""        
+        """Connect-up a Projection."""
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
         if projection.pre.size == projection.post.size:
             N                 = projection.post.size

trunk/src/connectors.py

@@ -66 +66 @@
         self.safe       = safe
         if self.safe:
-            self.get = self.get_safe    
+            self.get = self.get_safe
+        if isinstance(self.source, list):
+            self.source = numpy.array(self.source)
         if isinstance(self.source, numpy.ndarray):
             self.source_iterator = iter(self.source)
@@ -131 +133 @@
             return values
         else:
-            raise Exception("Invalid source")
+            raise Exception("Invalid source (%s)" % type(self.source))
 
     def get_safe(self, N, distance_matrix=None, sub_mask=None):
@@ -190 +192 @@
         if not (all_negative and all_positive):
             raise errors.ConnectionError("delay (%s) is out of range [%s,%s]" % (delay, min_delay, max_delay))
-        return delay    
+        return delay
 
 
@@ -234 +236 @@
         self.safe    = safe
         self.verbose = verbose
-        min_delay    = self._simulator.state.min_delay
-        if delays is None:
-            self.delays = min_delay
-        else:
-            if core.is_listlike(delays):
-                if min(delays) < min_delay:
-                    raise errors.ConnectionError("smallest delay (%g) is smaller than minimum delay (%g)" % (min(delays), min_delay))
-            elif not (isinstance(delays, basestring) or isinstance(delays, RandomDistribution)):
-                if delays < min_delay:
-                    raise errors.ConnectionError("delay (%g) is smaller than minimum delay (%g)" % (delays, min_delay))
-            self.delays = delays        
-        
+        self.delays = delays
+    
     def connect(self, projection):
         raise NotImplementedError()
@@ -252 +244 @@
         self.prog = utility.ProgressBar(0, N, 20, mode='fixed')        
     
-    def progression(self, count):
+    def progression(self, count, mpi_rank):
         self.prog.update_amount(count)
-        if self.verbose and self._simulator.state.mpi_rank == 0:           
+        if self.verbose and mpi_rank == 0:           
             print self.prog, "\r",
             sys.stdout.flush()
@@ -291 +283 @@
         else:
             self.rng = projection.rng
-        
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
         self.local             = projection.post._mask_local
         self.N                 = projection.post.size
         self.weights_generator = WeightGenerator(weights, self.local, projection, safe)
-        self.delays_generator  = DelayGenerator(delays, self.local, kernel=projection._simulator.state, safe=safe)
+        self.delays_generator  = DelayGenerator(self.delays, self.local, kernel=projection._simulator.state, safe=safe)
         self.probas_generator  = ProbaGenerator(RandomDistribution('uniform', (0,1), rng=self.rng), self.local)
         self._distance_matrix  = None
@@ -385 +378 @@
         for count, src in enumerate(projection.pre.all()):
             connector._probabilistic_connect(src, 1)
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
             
     
@@ -428 +421 @@
         for count, src in enumerate(projection.pre.all()):
             connector._probabilistic_connect(src, self.p_connect)
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
             
 
@@ -479 +472 @@
                 proba = proba.astype(float)
             connector._probabilistic_connect(src, proba, self.n_connections)
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
     
 
@@ -500 +493 @@
         """
         # needs extending for dynamic synapses.
-        Connector.__init__(self, 0.0, self._simulator.state.min_delay, safe=safe, verbose=verbose)
+        Connector.__init__(self, 0.0, None, safe=safe, verbose=verbose)
         self.conn_list  = numpy.array(conn_list)               
         
@@ -531 +524 @@
             #projection._divergent_connect(src, tgts[idx].tolist(), weights[idx], delays[idx])
             projection._divergent_connect(src, tgts.tolist(), weights, delays)
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
             count += 1
 
@@ -552 +545 @@
                          distributed simulations.
         """
-        Connector.__init__(self, 0.0, self._simulator.state.min_delay, safe=safe, verbose=verbose)
+        Connector.__init__(self, 0.0, None, safe=safe, verbose=verbose)
         
         if isinstance(file, basestring):
@@ -613 +606 @@
         
     def connect(self, projection):
-        """Connect-up a Projection."""        
+        """Connect-up a Projection."""
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
         local             = numpy.ones(len(projection.post), bool)
         weights_generator = WeightGenerator(self.weights, local, projection, self.safe)
@@ -651 +646 @@
                 projection._divergent_connect(src, targets.tolist(), weights, delays)
             
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
 
 
@@ -700 +695 @@
     def connect(self, projection):
         """Connect-up a Projection."""
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
         local             = numpy.ones(len(projection.pre), bool)
         weights_generator = WeightGenerator(self.weights, local, projection, self.safe)
@@ -736 +733 @@
                 projection._divergent_connect(src, tgt, w, d)
             
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
             
 
@@ -762 +759 @@
     
     def connect(self, projection):
-        """Connect-up a Projection."""        
+        """Connect-up a Projection."""
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
         if projection.pre.size == projection.post.size:
             N                 = projection.post.size
@@ -780 +779 @@
                 # the float is in case the values are of type numpy.float64, which NEST chokes on
                 projection._divergent_connect(src, [tgt], [float(w)], [float(d)])
-                self.progression(count)
+                self.progression(count, projection._simulator.state.mpi_rank)
                 count += 1
         else:
@@ -866 +865 @@
     def connect(self, projection):
         """Connect-up a Projection."""
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
         local                  = numpy.ones(len(projection.post), bool)
         self.N                 = projection.post.size        
@@ -885 +886 @@
             proba = proba_generator.get(self.N, self.distance_matrix).astype(float)
             self._smallworld_connect(src, proba, self.n_connections)
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
 
 
@@ -895 +896 @@
             """
             """
-            min_delay = self._simulator.state.min_delay
             Connector.__init__(self, None, None, safe=safe, verbose=verbose)
             self.cset = cset
@@ -905 +905 @@
                     self.weights = DEFAULT_WEIGHT
                 self.delays = delays
-                if delays is None:
-                    self.delays = self._simulator.state.min_delay
             else:
                 assert cset.arity == 2, 'must specify mask or connection-set with arity 2'
@@ -926 +924 @@
     def connect(self, projection):
         """Connect-up a Projection."""
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
         i0 = projection.pre.first_id
         size1 = projection.pre.last_id - i0

trunk/src/nemo/connectors.py

@@ -21 +21 @@
                             FixedNumberPostConnector, \
                             SmallWorldConnector, \
-                            CSAConnector, \
-                            WeightGenerator, \
-                            DelayGenerator, \
-                            ProbaGenerator, \
-                            Connector
-from pyNN.nemo import simulator
-
-Connector._simulator = simulator
+                            CSAConnector

trunk/src/nest/connectors.py

@@ -13 +13 @@
                             FromListConnector, FromFileConnector, WeightGenerator, \
                             DelayGenerator, ProbaGenerator, DistanceMatrix, CSAConnector
-from pyNN.nest import simulator
+
 import numpy
 from pyNN.space import Space
 
-Connector._simulator = simulator
+
 
 
@@ -29 +29 @@
         else:
             self.rng = projection.rng
-        
+        if self.delays is None:
+            self.delays = projection._simulator.state.min_delay
         self.N                 = projection.pre.size   
         idx                    = numpy.arange(self.N*rank(), self.N*(rank()+1))        

trunk/src/neuron/connectors.py

@@ -18 +18 @@
                             FixedNumberPostConnector, \
                             SmallWorldConnector, \
-                            CSAConnector, \
-                            Connector
-
-Connector._simulator = simulator
+                            CSAConnector

trunk/src/pcsim/connectors.py

@@ -16 +16 @@
                             FixedNumberPreConnector, \
                             FixedNumberPostConnector, \
-                            SmallWorldConnector, \
-                            Connector
-from pyNN.pcsim import simulator
-
-
-Connector._simulator = simulator
+                            SmallWorldConnector

trunk/test/unittests/test_connectors.py

@@ -186 +186 @@
                       (20, 82, 162.0, 0.5)])
 
-    def test_create_with_delays_None(self):
+    def test_connect_with_delays_None(self):
         C = connectors.AllToAllConnector(weights=0.1, delays=None)
         assert_equal(C.weights, 0.1)
-        assert_equal(C.delays, C._simulator.state.min_delay)
+        assert_equal(C.delays, None)
         assert C.safe
         assert C.allow_self_connections
-        
-    def test_create_with_delays_too_small(self):
-        assert_raises(errors.ConnectionError,
-                      connectors.AllToAllConnector,
-                      allow_self_connections=True,
-                      delays=0.0)
-
-    def test_create_with_list_delays_too_small(self):
-        assert_raises(errors.ConnectionError,
-                      connectors.AllToAllConnector,
-                      allow_self_connections=True,
-                      delays=[1.0, 1.0, 0.0])
-    
+        C.connect(self.prj)
+        assert_equal(self.prj.connections[0][3], self.prj._simulator.state.min_delay)
+        
+    def test_connect_with_delays_too_small(self):
+        C = connectors.AllToAllConnector(weights=0.1, delays=0.0)
+        assert_raises(errors.ConnectionError, C.connect, self.prj)
+
+    def test_connect_with_list_delays_too_small(self):
+        C = connectors.AllToAllConnector(weights=0.1, delays=[1.0, 1.0, 0.0, 0.0, 3.0, 1.5, 2.3, 0.9])
+        assert_raises(errors.ConnectionError, C.connect, self.prj)
+
 
 class TestFixedProbabilityConnector(object):

trunk/test/unittests/test_simulation_control.py

@@ -39 +39 @@
 def test_reset():
     simulator = MockSimulator()
-    reset = common.control.build_reset(simulator)
+    reset = common.build_reset(simulator)
     reset()
     assert simulator.reset_called
@@ -51 +51 @@
 def test_current_time():
     simulator = MockSimulator()
-    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.build_state_queries(simulator)
     get_current_time()
     assert_equal(simulator.state.accesses, ['t'])
@@ -57 +57 @@
 def test_time_step():
     simulator = MockSimulator()
-    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.build_state_queries(simulator)
     get_time_step()
     assert_equal(simulator.state.accesses, ['dt'])
@@ -63 +63 @@
 def test_min_delay():
     simulator = MockSimulator()
-    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.build_state_queries(simulator)
     get_min_delay()
     assert_equal(simulator.state.accesses, ['min_delay'])
@@ -69 +69 @@
 def test_max_delay():
     simulator = MockSimulator()
-    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.build_state_queries(simulator)
     get_max_delay()
     assert_equal(simulator.state.accesses, ['max_delay'])
@@ -75 +75 @@
 def test_num_processes():
     simulator = MockSimulator()
-    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.build_state_queries(simulator)
     num_processes()
     assert_equal(simulator.state.accesses, ['num_processes'])
@@ -81 +81 @@
 def test_rank():
     simulator = MockSimulator()
-    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.build_state_queries(simulator)
     rank()
     assert_equal(simulator.state.accesses, ['mpi_rank'])