Changeset 730

Timestamp:

03/12/10 10:14:48 (2 years ago)

Author:

pierre

Message:

Add a method to save Positions into a file. Polish and test the new Connector2 module, by adding a connectors_benchmark script in the unittest that allow to plot graphs of the connections for all the connectors and according to all the parameters. Need to play a bit with, but everything seems to be OK. Andrew, maybe please have a small look, and as soon as you consider that the progress bar, the connections are ok for you, you can commit the new connectors2 module and erase the old one.

Location:

trunk/src

Files:

• common.py (modified) (1 diff)
• connectors2.py (modified) (2 diffs)

trunk/src/common.py

@@ -898 +898 @@
         raise NotImplementedError()
     
+    def savePositions(self, filename, gather=True, compatible_output=True):
+        """
+        Save positions to file. The output format is id x y z
+        """
+        fmt = "%s\t%s\t%s\t%s\n" % ("%d", "%g", "%g", "%g")
+        lines = []
+        for cell in self.all():  
+            x,y,z = cell.position
+            line = fmt  % (cell, x, y, z)
+            lines.append(line)
+        if rank() == 0:
+            f = open(filename, 'w')
+            f.writelines(lines)
+            f.close()
+    
 # ==============================================================================
 

trunk/src/connectors2.py

@@ -24 +24 @@
         
     def extract(self, N, distance_matrix=None, sub_mask=None):
+        #local_mask is supposed to be a mask of booleans, while 
+        #sub_mask is a list of cells ids.
         if isinstance(self.source, basestring):
             assert distance_matrix is not None
@@ -198 +200 @@
         self.distance_matrix.set_source(src.position)        
         targets = self.projection.post.local_cells[create]
+        if not self.allow_self_connections and self.projection.pre == self.projection.post and src in targets:
+            i       = numpy.where(targets == src)[0]
+            targets = numpy.delete(targets, i)
+            create  = numpy.delete(create, i)
+        
         weights = self.weights_generator.get(self.N, self.distance_matrix, create)
         delays  = self.delays_generator.get(self.N, self.distance_matrix, create)
             
-        if not self.allow_self_connections and self.projection.pre == self.projection.post and src in targets:
-            i       = numpy.where(targets == src)[0]
-            weights = numpy.delete(weights, i)
-            delays  = numpy.delete(delays, i)
-            targets = numpy.delete(targets, i)
-        
         if len(targets) > 0:
             self.projection.connection_manager.connect(src, targets.tolist(), weights, delays)