Changeset 467

Timestamp:

10/02/08 16:58:17 (2 months ago)

Author:

apdavison

Message:

pcsim Connectors now handle arrays of weights/delays (see ticket:116).

Files:

• trunk/src/__init__.py (modified) (1 diff)
• trunk/src/pcsim/__init__.py (modified) (6 diffs)
• trunk/src/pcsim/connectors.py (modified) (2 diffs)
• trunk/test/unittests/pcsimtests_population.py (modified) (2 diffs)

trunk/src/__init__.py

@@ -2 +2 @@
-__all__ = ["common", "random", "nest1", "nest2", "neuron", "neuron2", "pcsim", 'brian' ]
-
+#

trunk/src/pcsim/__init__.py

@@ -997 +997 @@
-        
-        weight = self.getWeight(weight)
-
-
+self.
+ or hasattr(weight, '__len__')
-            w = 1.
-        else:
-
+self.
-        
-        delay  = self.getDelay(delay)
-
+ or hasattr(delay, '__len__')
-            d = pcsim_globals.minDelay/1000.
-        else:
@@ -1033 +1033 @@
-        if isinstance(weight, pyNN.random.RandomDistribution):
-            self.randomizeWeights(weight)
+        elif hasattr(weight, '__len__'):
+            assert len(weight) == len(self), "Weight array does not have the same number of elements as the Projection %d != %d" % (len(weight),len(self))
+            self.setWeights(weight)
-        
-        if isinstance(delay, pyNN.random.RandomDistribution):
-            self.randomizeDelays(delay)
+        elif hasattr(delay, '__len__'):
+            assert len(delay) == len(self), "Weight array does not have the same number of elements as the Projection %d != %d" % (len(weight),len(self))
+            self.setDelays(delay)
-        
-        if not label:
@@ -1061 +1067 @@
-        synapses.
-        """
-
-
+
-        if isinstance(w, float) or isinstance(w, int):
-            for i in range(len(self)):
@@ -1077 +1082 @@
-        # argument type. It could make for easier-to-read simulation code to
-        # give it a separate name, though. Comments?
-
-
+
-        weights = rand_distr.next(len(self))
-        for i in range(len(self)):
@@ -1094 +1098 @@
-                pcsim_globals.net.object(self.pcsim_projection[i]).delay = d
-        else:
+            assert 1000.0*min(d) >= pcsim_globals.minDelay, "Smallest delay %g ms must be smaller than %g ms" % (min(d), pcsim_globals.minDelay)
-            for i in range(len(self)):
-                pcsim_globals.net.object(self.pcsim_projection[i]).delay = d[i]
@@ -1105 +1110 @@
-        for i in range(len(self)):
-            pcsim_globals.net.object(self.pcsim_projection[i]).delay = delays[i]
+    
+    def getWeights(self, format='list', gather=True):
+        """
+        Possible formats are: a list of length equal to the number of connections
+        in the projection, a 2D weight array (with zero or None for non-existent
+        connections).
+        """
+        if format == 'list':
+            if self.is_conductance:
+                A = 1e6 # S --> uS
+            else:
+                A = 1e9 # A --> nA
+            return [A*self.pcsim_projection.object(i).W for i in xrange(self.pcsim_projection.size())]
+        elif format == 'array':
+            raise Exception("Not yet implemented")
+        else:
+            raise Exception("Valid formats are 'list' and 'array'")
+    
+    def getDelays(self, format='list', gather=True):
+        """
+        Possible formats are: a list of length equal to the number of connections
+        in the projection, a 2D weight array (with zero or None for non-existent
+        connections).
+        """
+        if format == 'list':
+            A = 1e3 # s --> ms
+            return [A*self.pcsim_projection.object(i).delay for i in xrange(self.pcsim_projection.size())]
+        elif format == 'array':
+            raise Exception("Not yet implemented")
+        else:
+            raise Exception("Valid formats are 'list' and 'array'")
-    
-    # --- Methods for writing/reading information to/from file. ----------------

trunk/src/pcsim/connectors.py

@@ -90 +90 @@
-        # pcsim does not yet deal with having lists of weights, delays, so for now we just return 0 values
-        # and will set the weights, delays later
-0.0, 0.0
+self.weights, self.delays
-
-class FromFileConnector(common.FromFileConnector):
@@ -114 +114 @@
-        # pcsim does not yet deal with having lists of weights, delays, so for now we just return 0 values
-        # and will set the weights, delays later
-0.0, 0.0
+self.weights, self.delays

trunk/test/unittests/pcsimtests_population.py

@@ -16 +16 @@
-import numpy.random
-
+def arrays_almost_equal(a, b, threshold):
+    return (abs(a-b) < threshold).all()
+
+def max_array_diff(a, b):
+    return max(abs(a-b))
-
-class PopulationInitTest(unittest.TestCase):
@@ -341 +346 @@
-        
-    def testWithWeightArray(self):
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
-#     def testSaveAndLoad(self):
-#         prj1 = neuron.Projection(self.source33, self.target33, 'oneToOne')