Partial fix to traub 2005 demo.

Author: subhacom

snippets/nsdf_vec.py

@@ -6,9 +6,9 @@
 # Maintainer: 
 # Created: Sat Dec 19 22:27:27 2015 (-0500)
 # Version: 
-# Last-Updated: Tue Dec 29 12:50:02 2015 (-0500)
+# Last-Updated: Thu Aug 11 11:09:33 2016 (-0400)
 #           By: Subhasis Ray
-#     Update #: 134
+#     Update #: 135
 # URL: 
 # Keywords: 
 # Compatibility: 
@@ -100,7 +100,7 @@ def write_nsdf():
         pulse.delay[0] = 5 * (ii+1)
         pulse.width[0] = 20
         t_lead.threshold = 0.5
-        moose.connect(pulse, 'output', t_lead,'Vm');
+        moose.connect(pulse, 'output', t_lead,'Vm')
         moose.connect(nsdf, 'requestOut', pulse, 'getOutputValue')
         # ei = nsdf.eventInput[ii]
         # moose.connect(t_lead, 'spikeOut', ei, 'input')

traub_2005/py/display_morphology.py

@@ -6,9 +6,9 @@
 # Maintainer: 
 # Created: Fri Mar  8 11:26:13 2013 (+0530)
 # Version: 
-# Last-Updated: Sat Aug  6 15:47:37 2016 (-0400)
-#           By: subha
-#     Update #: 377
+# Last-Updated: Thu Aug 11 11:29:36 2016 (-0400)
+#           By: Subhasis Ray
+#     Update #: 389
 # URL: 
 # Keywords: 
 # Compatibility: 
@@ -76,8 +76,8 @@ def cell_to_graph(cell, label=False):
         msg = 'distalOut'
     else:
         raise Exception('No neighbors on raxial or distal')
-    es = [(c1.path, c2[0].path, {'weight': 2/ (moose.Compartment(c1).Ra + moose.Compartment(c2).Ra)}) \
-              for c1 in moose.wildcardFind('%s/##[ISA=Compartment]' % (cell.path)) \
+    es = [(c1.path, c2[0].path, {'weight': 2/ (c1.Ra + c2[0].Ra)}) \
+              for c1 in moose.wildcardFind('%s/##[ISA=CompartmentBase]' % (cell.path)) \
               for c2 in moose.Compartment(c1).neighbors[msg]]
     g = nx.Graph()
     g.add_edges_from(es)
@@ -109,7 +109,7 @@ def plot_cell_topology(cell, label=False):
     weights = np.array([g.edge[e[0]][e[1]]['weight'] for e in g.edges()])
     try:
         pos = nx.graphviz_layout(g,prog='twopi',root=cell.path + '/comp_1')
-    except NameError, AttributeError:
+    except (NameError, AttributeError) as e:
         # this is the best networkx can do by itself. Its Furchtman
         # Reingold layout ends up with overlapping edges even for a
         # tree. igraph does much better.
@@ -151,7 +151,6 @@ def plot_cell_topology(cell, label=False):
             print('-p  filename (optional) save outputin a pdf file named "filename".')
             print('-h,--help print this help')
             sys.exit(0)
-    print( 'args', optlist, args)
     figures = []
     if len(celltype) > 0:
         try:

traub_2005/py/gui.py

@@ -6,9 +6,9 @@
 # Maintainer: 
 # Created: Fri Jul 12 11:53:50 2013 (+0530)
 # Version: 
-# Last-Updated: Sat Aug  6 14:30:41 2016 (-0400)
-#           By: subha
-#     Update #: 743
+# Last-Updated: Thu Aug 11 11:59:17 2016 (-0400)
+#           By: Subhasis Ray
+#     Update #: 746
 # URL: 
 # Keywords: 
 # Compatibility: 
@@ -195,9 +195,10 @@ def displayGraph(self, g, label=False):
             print('Empty graph for cell. Make sure proto file has `*asymmetric` on top. I cannot handle symmetric compartmental connections')
             return
         weights = np.array([g.edge[e[0]][e[1]]['weight'] for e in g.edges()])
-        #pos = nx.graphviz_layout(g, prog='twopi')
-        from networkx.drawing.nx_agraph import graphviz_layout
-        pos = graphviz_layout(g, prog='twopi')
+        try:
+            pos = nx.graphviz_layout(g, prog='twopi')
+        except (NameError, AttributeError) as e:
+            pos = nx.spectral_layout(g)
         xmin, ymin, xmax, ymax = 1e9, 1e9, -1e9, -1e9
         for p in pos.values():
             if xmin > p[0]:
@@ -211,6 +212,7 @@ def displayGraph(self, g, label=False):
         edge_widths = 10.0 * weights / max(weights)
         node_colors = ['k' if x in axon else 'gray' for x in g.nodes()]
         lw = [1 if n.endswith('comp_1') else 0 for n in g.nodes()]
+        print('Edge widths:', edge_widths)
         self.axes.clear()
         self.axes.set_xlim((xmin-10, xmax+10))
         self.axes.set_ylim((ymin-10, ymax+10))