bmtool 0.5.0__tar.gz → 0.5.1__tar.gz

{bmtool-0.5.0 → bmtool-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.0
+Version: 0.5.1
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.5.0 → bmtool-0.5.1}/bmtool/bmplot.py

@@ -14,6 +14,7 @@ import matplotlib.colors as colors
 import matplotlib.gridspec as gridspec
 from mpl_toolkits.mplot3d import Axes3D
 from IPython import get_ipython
+from IPython.display import display, HTML
 import statistics
 import pandas as pd
 import os
@@ -44,7 +45,7 @@ def is_notebook() -> bool:
     except NameError:
         return False      # Probably standard Python interpreter
 
-def total_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None,no_prepend_pop=False,save_file=None,synaptic_info='0'):
+def total_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None,no_prepend_pop=False,save_file=None,synaptic_info='0',include_gap=True):
     """
     Generates connection plot displaying total connection or other stats
     config: A BMTK simulation config 
@@ -55,6 +56,7 @@ def total_connection_matrix(config=None,title=None,sources=None, targets=None, s
     no_prepend_pop: dictates if population name is displayed before sid or tid when displaying graph
     save_file: If plot should be saved
     synaptic_info: '0' for total connections, '1' for mean and stdev connections, '2' for all synapse .mod files used, '3' for all synapse .json files used
+    include_gap: Determines if connectivity shown should include gap junctions + chemical synapses. False will only include chemical
     """
     if not config:
         raise Exception("config not defined")
@@ -70,7 +72,7 @@ def total_connection_matrix(config=None,title=None,sources=None, targets=None, s
         tids = tids.split(",")
     else:
         tids = []
-    text,num, source_labels, target_labels = util.connection_totals(config=config,nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,synaptic_info=synaptic_info)
+    text,num, source_labels, target_labels = util.connection_totals(config=config,nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,synaptic_info=synaptic_info,include_gap=include_gap)
 
     if title == None or title=="":
         title = "Total Connections"
@@ -84,7 +86,7 @@ def total_connection_matrix(config=None,title=None,sources=None, targets=None, s
     plot_connection_info(text,num,source_labels,target_labels,title, syn_info=synaptic_info, save_file=save_file)
     return
     
-def percent_connection_matrix(config=None,nodes=None,edges=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,method = 'total'):
+def percent_connection_matrix(config=None,nodes=None,edges=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,method = 'total',include_gap=True):
     """
     Generates a plot showing the percent connectivity of a network
     config: A BMTK simulation config 
@@ -95,6 +97,7 @@ def percent_connection_matrix(config=None,nodes=None,edges=None,title=None,sourc
     no_prepend_pop: dictates if population name is displayed before sid or tid when displaying graph
     method: what percent to displace on the graph 'total','uni',or 'bi' for total connections, unidirectional connections or bidirectional connections
     save_file: If plot should be saved
+    include_gap: Determines if connectivity shown should include gap junctions + chemical synapses. False will only include chemical
     """
     if not config:
         raise Exception("config not defined")
@@ -111,7 +114,7 @@ def percent_connection_matrix(config=None,nodes=None,edges=None,title=None,sourc
         tids = tids.split(",")
     else:
         tids = []
-    text,num, source_labels, target_labels = util.percent_connections(config=config,nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,method=method)
+    text,num, source_labels, target_labels = util.percent_connections(config=config,nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,method=method,include_gap=include_gap)
     if title == None or title=="":
         title = "Percent Connectivity"
 
@@ -120,7 +123,7 @@ def percent_connection_matrix(config=None,nodes=None,edges=None,title=None,sourc
     return
 
 def probability_connection_matrix(config=None,nodes=None,edges=None,title=None,sources=None, targets=None, sids=None, tids=None, 
-                            no_prepend_pop=False,save_file=None, dist_X=True,dist_Y=True,dist_Z=True,bins=8,line_plot=False,verbose=False):
+                            no_prepend_pop=False,save_file=None, dist_X=True,dist_Y=True,dist_Z=True,bins=8,line_plot=False,verbose=False,include_gap=True):
     """
     Generates probability graphs
     need to look into this more to see what it does
@@ -145,7 +148,7 @@ def probability_connection_matrix(config=None,nodes=None,edges=None,title=None,s
 
     throwaway, data, source_labels, target_labels = util.connection_probabilities(config=config,nodes=None,
         edges=None,sources=sources,targets=targets,sids=sids,tids=tids,
-        prepend_pop=not no_prepend_pop,dist_X=dist_X,dist_Y=dist_Y,dist_Z=dist_Z,num_bins=bins)
+        prepend_pop=not no_prepend_pop,dist_X=dist_X,dist_Y=dist_Y,dist_Z=dist_Z,num_bins=bins,include_gap=include_gap)
     if not data.any():
         return
     if data[0][0]==-1:
@@ -195,7 +198,7 @@ def probability_connection_matrix(config=None,nodes=None,edges=None,title=None,s
 
     return
 
-def convergence_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,convergence=True,method='mean'):
+def convergence_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,convergence=True,method='mean',include_gap=True):
     """
     Generates connection plot displaying convergence data
     config: A BMTK simulation config 
@@ -211,9 +214,9 @@ def convergence_connection_matrix(config=None,title=None,sources=None, targets=N
         raise Exception("config not defined")
     if not sources or not targets:
         raise Exception("Sources or targets not defined")
-    return divergence_connection_matrix(config,title ,sources, targets, sids, tids, no_prepend_pop, save_file ,convergence, method)
+    return divergence_connection_matrix(config,title ,sources, targets, sids, tids, no_prepend_pop, save_file ,convergence, method,include_gap=include_gap)
 
-def divergence_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,convergence=False,method='mean'):
+def divergence_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,convergence=False,method='mean',include_gap=True):
     """
     Generates connection plot displaying divergence data
     config: A BMTK simulation config 
@@ -240,7 +243,7 @@ def divergence_connection_matrix(config=None,title=None,sources=None, targets=No
     else:
         tids = []
 
-    syn_info, data, source_labels, target_labels = util.connection_divergence(config=config,nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,convergence=convergence,method=method)
+    syn_info, data, source_labels, target_labels = util.connection_divergence(config=config,nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,convergence=convergence,method=method,include_gap=include_gap)
 
     
     #data, labels = util.connection_divergence_average(config=config,nodes=nodes,edges=edges,populations=populations)
@@ -265,7 +268,7 @@ def divergence_connection_matrix(config=None,title=None,sources=None, targets=No
     return
 
 def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,synaptic_info='0',
-                      source_cell = None,target_cell = None):
+                      source_cell = None,target_cell = None,include_gap=True):
     """
     Generates histogram of number of connections individual cells in a population receieve from another population
     config: A BMTK simulation config 
@@ -286,6 +289,8 @@ def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[]
         target_id = kwargs["target_id"]
         if source_id == source_cell and target_id == target_cell:
             temp = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)]
+            if include_gap == False:
+                temp = temp[temp['is_gap_junction'] != True]
             node_pairs = temp.groupby('target_node_id')['source_node_id'].count()
             conn_mean = statistics.mean(node_pairs.values)
             conn_std = statistics.stdev(node_pairs.values)
@@ -684,7 +689,7 @@ def plot_network_graph(config=None,nodes=None,edges=None,title=None,sources=None
         tids = tids.split(",")
     else:
         tids = []
-    data, source_labels, target_labels = util.connection_graph_edge_types(nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,edge_property=edge_property)
+    throw_away, data, source_labels, target_labels = util.connection_graph_edge_types(config=config,nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,edge_property=edge_property)
 
     if title == None or title=="":
         title = "Network Graph"
@@ -800,7 +805,7 @@ def sim_setup(config_file='simulation_config.json',network=None):
     # Plot spike train info
     plot_inspikes(config_file)
     # Using bmtool, print total number of connections between cell groups
-    connection_matrix(config=config_file,sources='all',targets='all',sids='pop_name',tids='pop_name',title='All Connections found', size_scalar=2, no_prepend_pop=True, synaptic_info='0')
+    total_connection_matrix(config=config_file,sources='all',targets='all',sids='pop_name',tids='pop_name',title='All Connections found', size_scalar=2, no_prepend_pop=True, synaptic_info='0')
     # Plot 3d positions of the network
     plot_3d_positions(populations='all',config=config_file,group_by='pop_name',title='3D Positions',save_file=None)
 
@@ -823,7 +828,7 @@ def plot_I_clamps(fp):
         plt.legend()
         num_clamps=num_clamps+1
 
-def plot_basic_cell_info(config_file,notebook=0):
+def plot_basic_cell_info(config_file):
     print("Network and node info:")
     nodes=util.load_nodes_from_config(config_file)
     if not nodes:
@@ -857,7 +862,11 @@ def plot_basic_cell_info(config_file,notebook=0):
                 count=1
             df1 = pd.DataFrame(CELLS, columns = ["node_type","pop_name","model_type","count"])
             print(j+':')
-            print(df1)
+            notebook = is_notebook()
+            if notebook == True:
+                display(HTML(df1.to_html()))
+            else:
+                print(df1)
         elif node['model_type'][0]=='biophysical':
             CELLS=[]
             count=1
@@ -871,7 +880,7 @@ def plot_basic_cell_info(config_file,notebook=0):
                     pop_name=node['pop_name'][i]
                     model_type=node['model_type'][i]
                     model_template=node['model_template'][i]
-                    morphology=node['morphology'][i] if node.get('morphology') else ''
+                    morphology=node['morphology'][i] if node['morphology'][i] else ''
                     CELLS.append([node_type,pop_name,model_type,model_template,morphology,count])
                     count=1
             else:
@@ -879,17 +888,20 @@ def plot_basic_cell_info(config_file,notebook=0):
                 pop_name=node['pop_name'][i]
                 model_type=node['model_type'][i]
                 model_template=node['model_template'][i]
-                morphology=node['morphology'][i] if node.get('morphology') else ''
+                morphology=node['morphology'][i] if node['morphology'][i] else ''
                 CELLS.append([node_type,pop_name,model_type,model_template,morphology,count])
                 count=1
             df2 = pd.DataFrame(CELLS, columns = ["node_type","pop_name","model_type","model_template","morphology","count"])
             print(j+':')
             bio.append(j)
-            print(df2)
+            notebook = is_notebook()
+            if notebook == True:
+                display(HTML(df2.to_html()))
+            else:
+                print(df2)
     if len(bio)>0:      
         return bio[0]        
 
-
 def plot_inspikes(fp):
     
     print("Plotting spike Train info...")

{bmtool-0.5.0 → bmtool-0.5.1}/bmtool/connectors.py

@@ -303,7 +303,7 @@ def rho_2_pr(p0, p1, rho):
 
 class ReciprocalConnector(AbstractConnector):
     """
-    Object for buiilding connections in bmtk network model with reciprocal
+    Object for building connections in bmtk network model with reciprocal
     probability within a single population (or between two populations).
 
     Algorithm:
@@ -949,7 +949,7 @@ class ReciprocalConnector(AbstractConnector):
 
 class UnidirectionConnector(AbstractConnector):
     """
-    Object for buiilding unidirectional connections in bmtk network model with
+    Object for building unidirectional connections in bmtk network model with
     given probability within a single population (or between two populations).
 
     Parameters:
@@ -1083,7 +1083,7 @@ class UnidirectionConnector(AbstractConnector):
 
 class CorrelatedGapJunction(UnidirectionConnector):
     """
-    Object for buiilding gap junction connections in bmtk network model with
+    Object for building gap junction connections in bmtk network model with
     given probabilities within a single population which could be correlated
     with the recurrent chemical synapses in this population.
 
@@ -1190,7 +1190,7 @@ class CorrelatedGapJunction(UnidirectionConnector):
 
 
 class OneToOneSequentialConnector(AbstractConnector):
-    """Object for buiilding one to one correspondence connections in bmtk
+    """Object for building one to one correspondence connections in bmtk
     network model with between two populations. One of the population can
     consist of multiple sub-populations. These sub-populations need to be added
     sequentially using setup_nodes() and edge_params() methods followed by BMTK

{bmtool-0.5.0 → bmtool-0.5.1}/bmtool/util/util.py

@@ -592,7 +592,7 @@ def relation_matrix(config=None, nodes=None,edges=None,sources=[],targets=[],sid
                                                 
     return syn_info, e_matrix, source_pop_names, target_pop_names
 
-def connection_totals(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,synaptic_info='0'):
+def connection_totals(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,synaptic_info='0',include_gap=True):
     
     def total_connection_relationship(**kwargs):
         edges = kwargs["edges"]
@@ -601,12 +601,15 @@ def connection_totals(config=None,nodes=None,edges=None,sources=[],targets=[],si
         source_id = kwargs["source_id"]
         target_id = kwargs["target_id"]
 
-        total = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)].count()
+        total = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)]
+        if include_gap == False:
+            total = total[total['is_gap_junction'] != True]
+        total = total.count()
         total = total.source_node_id # may not be the best way to pick
         return total
     return relation_matrix(config,nodes,edges,sources,targets,sids,tids,prepend_pop,relation_func=total_connection_relationship,synaptic_info=synaptic_info)
 
-def percent_connections(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,method=None):
+def percent_connections(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,method=None,include_gap=True):
 
     def precent_func(**kwargs): 
         edges = kwargs["edges"]
@@ -618,6 +621,8 @@ def percent_connections(config=None,nodes=None,edges=None,sources=[],targets=[],
         s_list = kwargs["source_nodes"]
 
         cons = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)]
+        if include_gap == False:
+            cons = cons[cons['is_gap_junction'] != True]
         total_cons = cons.count().source_node_id
         # to determine reciprocal connectivity
         # create a copy and flip source/dest
@@ -649,8 +654,7 @@ def percent_connections(config=None,nodes=None,edges=None,sources=[],targets=[],
 
     return relation_matrix(config,nodes,edges,sources,targets,sids,tids,prepend_pop,relation_func=precent_func)
 
-
-def connection_divergence(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,convergence=False,method='mean'):
+def connection_divergence(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,convergence=False,method='mean',include_gap=True):
 
     import pandas as pd
 
@@ -665,6 +669,8 @@ def connection_divergence(config=None,nodes=None,edges=None,sources=[],targets=[
         count = 1
 
         cons = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)]
+        if include_gap == False:
+            cons = cons[cons['is_gap_junction'] != True]
 
         if convergence:
             if method == 'min':
@@ -697,7 +703,10 @@ def connection_divergence(config=None,nodes=None,edges=None,sources=[],targets=[
                 count = vc.loc[source_id]#count = s_list[s_list[source_id_type]==source_id]
 
         # Only executed when mean
-        total = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)].count()
+        total = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)]
+        if include_gap == False:
+            total = total[total['is_gap_junction'] != True]
+        total = total.count()
         total = total.source_node_id # may not be the best way to pick
         ret = round(total/count,1)
         if ret == 0:
@@ -707,7 +716,7 @@ def connection_divergence(config=None,nodes=None,edges=None,sources=[],targets=[
     return relation_matrix(config,nodes,edges,sources,targets,sids,tids,prepend_pop,relation_func=total_connection_relationship)
 
 def connection_probabilities(config=None,nodes=None,edges=None,sources=[],
-    targets=[],sids=[],tids=[],prepend_pop=True,dist_X=True,dist_Y=True,dist_Z=True,num_bins=10):
+    targets=[],sids=[],tids=[],prepend_pop=True,dist_X=True,dist_Y=True,dist_Z=True,num_bins=10,include_gap=True):
     
     import pandas as pd
     from scipy.spatial import distance
@@ -782,7 +791,9 @@ def connection_probabilities(config=None,nodes=None,edges=None,sources=[],
             return ret
 
         relevant_edges = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)]
-        connected_distances = eudist(relevant_edges,dist_X,dist_Y,dist_Z).tolist()
+        if include_gap == False:
+            relevant_edges = relevant_edges[relevant_edges['is_gap_junction'] != True]
+        connected_distances = eudist(relevant_edges,dist_X,dist_Y,dist_Z).values.tolist()
         if len(connected_distances)>0:
             if connected_distances[0]==0:
                 return -1

{bmtool-0.5.0 → bmtool-0.5.1}/bmtool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.0
+Version: 0.5.1
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.5.0 → bmtool-0.5.1}/setup.py

@@ -6,7 +6,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name="bmtool",
-    version="0.5.0",
+    version="0.5.1",
     author="Tyler Banks",
     author_email="tbanks@mail.missouri.edu",
     description="BMTool",