Changeset 2116

Timestamp:

08/10/10 17:18:06 (18 months ago)

Author:

thesamovar

Message:

** Brian 1.2.2dev-2010-08-10 **

Fixed problems with STDP separating equations for triplet rule
Fixed sparse matrix problem with scipy 0.8.0

Location:

trunk/brian

Files:

• __init__.py (modified) (1 diff)
• experimental/c_stdp.py (modified) (1 diff)
• new_features.txt (modified) (1 diff)
• stdp.py (modified) (1 diff)
• tests/testutils/test_sparse.py (modified) (2 diffs)
• utils/sparse_patch/0_7_1.py (modified) (1 diff)

trunk/brian/__init__.py

@@ -74 +74 @@
 
 __version__ = '1.2.2dev'
-__release_date__ = '2010-07-26'
+__release_date__ = '2010-08-10'
 
 ### Define global preferences which are not defined anywhere else

trunk/brian/experimental/c_stdp.py

@@ -59 +59 @@
         vars_post = [var for var in vars if var in modified_variables(post)]
 
-        # additional dependencies on the set of equations are induced by the
-        # interactions in pre and post code
-        additional_deps = pre.split('\n')+post.split('\n')
+        # additional dependencies are used to ensure that if there are multiple
+        # pre/post separated equations they are grouped together as one
+        additional_deps = ['__pre_deps='+'+'.join(vars_pre),
+                           '__post_deps='+'+'.join(vars_post)]
         separated_equations = separate_equations(eqs_obj, additional_deps)
         if not len(separated_equations) == 2:
+            print separated_equations
             raise ValueError('Equations should separate into pre and postsynaptic variables.')
         sep_pre, sep_post = separated_equations

trunk/brian/new_features.txt

@@ -10 +10 @@
 
 * Equations/aliases now work correctly in STDP (ticket #56)
+* Bug in sparse matrices introduced in scipy 0.8.0 fixed
 
 New features since 1.2.0

trunk/brian/stdp.py

@@ -221 +221 @@
         vars_post = [var for var in vars if var in modified_variables(post)]
 
-        # Additional check TODO: modification of presynaptic variables should not depend on postsynaptic
-        #   variables
-
-        # additional dependencies on the set of equations are induced by the
-        # interactions in pre and post code
-        additional_deps = pre.split('\n')+post.split('\n')
+        # additional dependencies are used to ensure that if there are multiple
+        # pre/post separated equations they are grouped together as one
+        additional_deps = ['__pre_deps='+'+'.join(vars_pre),
+                           '__post_deps='+'+'.join(vars_post)]
         separated_equations = separate_equations(eqs_obj, additional_deps)
         if not len(separated_equations) == 2:

trunk/brian/tests/testutils/test_sparse.py

@@ -1 +1 @@
 from brian.connection import SparseMatrix
+from numpy import zeros, array
 from nose.tools import *
 
 def test_sparse_matrix():
     x = SparseMatrix((10, 10))
+    z = zeros((10, 10), dtype=int)
     x[0, 4] = 3
     x[1, :] = 5
@@ -11 +13 @@
     x[5, 2:4] = [1, 2]
     x[6:8, 4:7] = 1
+    # same thing with z to compare
+    z[0, 4] = 3
+    z[1, :] = 5
+    z[2, []] = []
+    z[3, [0]] = [6]
+    z[4, [0, 1]] = [7, 8]
+    z[5, 2:4] = [1, 2]
+    z[6:8, 4:7] = 1
+    # check the values are correct
+    y = array(x.todense(), dtype=int)
+    assert (y==z).all()
 
 if __name__ == '__main__':

trunk/brian/utils/sparse_patch/0_7_1.py

@@ -62 +62 @@
             sparse.lil_matrix.__setitem__(self, index, [W] * len(xrange(*j.indices(self.shape[1]))))
         elif isinstance(i, slice) and isinstance(j, slice) and isNumberType(W):
-            n = len(xrange(*j.indices(self.shape[0])))
+            n = len(xrange(*i.indices(self.shape[0])))
             m = len(xrange(*j.indices(self.shape[1])))
+            print index
+            print n, m
             sparse.lil_matrix.__setitem__(self, index, W * numpy.ones((n, m)))
         else: