update plot-dataframe readout

kirchhoff/circuit_flow.py

@@ -341,6 +341,7 @@ class flow_circuit(circuit,object):
         E=self.get_edges_data()
         V=self.get_nodes_data()
 
+        self.set_pos()
         fig=dx.plot_networkx(   self.G, edge_list=self.list_graph_edges, node_list=self.list_graph_nodes, edge_data=E,  node_data=V )
 
         return fig

kirchhoff/circuit_flux.py

@@ -42,7 +42,7 @@ def initialize_flux_circuit_from_crystal(crystal_type='default',periods=1):
 def setup_default_flux_circuit(dict_pars):
 
     kirchhoff_graph=initialize_flux_circuit_from_networkx(dict_pars['plexus'])
-    kirchhoff_graph.set_source_landscape(mode='dipole_border')
+    kirchhoff_graph.set_source_landscape(mode='dipole_point')
     kirchhoff_graph.set_solute_landscape()
 
     kirchhoff_graph.scales['diffusion']=dict_pars['diffusion']
@@ -236,7 +236,7 @@ class flux_circuit(flow_circuit,object):
 
     def get_edges_data(self):
 
-        de=pd.DataFrame(self.edges[['conductivity','flow_rate','absorption','peclet','length']])
+        de=pd.DataFrame(self.edges[['conductivity','flow_rate','absorption','uptake','peclet','length']])
         de['weight']=np.power(self.edges['conductivity'].to_numpy(),0.25)*self.draw_weight_scaling
 
         return de

kirchhoff/circuit_init.py

@@ -231,21 +231,24 @@ class circuit:
 
         return pos
 
-    def set_pos(self,pos_data):
+    def set_pos(self,pos_data={}):
 
         pos_key='pos'
         reset_layout=False
+        nodata=False
+        if len(pos_data.values())==0:
+            nodata=True
+
         for j,n in enumerate(self.G.nodes()):
             if pos_key not in self.G.nodes[n]:
                 reset_layout=True
-        if reset_layout:
+        if reset_layout and nodata:
             print('set networkx.spring_layout()')
             pos = nx.spring_layout(self.G)
-            for j,n in enumerate(self.G.nodes()):
-                self.G.nodes[n]=pos[n]
+            nx.set_node_attributes(self.G, pos, 'pos')
         else:
-            for j,n in enumerate(self.G.nodes()):
-                self.G.nodes[n]=pos_data[n]
+            nx.set_node_attributes(self.G, pos_data, 'pos')
+
 
     def set_scale_pars(self, new_parameters):
 
@@ -258,6 +261,7 @@ class circuit:
     # output
     def plot_circuit(self):
 
+        self.set_pos()
         fig=dx.plot_networkx(   self.G, edge_list=self.list_graph_edges, node_list=self.list_graph_nodes )
 
         return fig

notebook/test_init_graphs.ipynb

@@ -148,7 +148,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

notebook/test_plot_networkx.ipynb

@@ -26925,7 +26925,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,