bmtool 0.7.0.6.2__py3-none-any.whl → 0.7.1__py3-none-any.whl

bmtool/bmplot/connections.py

@@ -2,40 +2,37 @@
 Want to be able to take multiple plot names in and plot them all at the same time, to save time
 https://stackoverflow.com/questions/458209/is-there-a-way-to-detach-matplotlib-plots-so-that-the-computation-can-continue
 """
-from ..util import util
-import numpy as np
+import re
+import statistics
+
 import matplotlib
-import matplotlib.pyplot as plt
 import matplotlib.cm as cmx
 import matplotlib.colors as colors
-from IPython import get_ipython
-from IPython.display import display, HTML
-import statistics
+import matplotlib.pyplot as plt
+import numpy as np
 import pandas as pd
-import os
-import sys
-import re
-
-from ..util.util import CellVarsFile,load_nodes_from_config,load_templates_from_config #, missing_units
-from bmtk.analyzer.utils import listify
+from IPython import get_ipython
 from neuron import h
 
+from ..util import util
+
 use_description = """
 
 Plot BMTK models easily.
 
-python -m bmtool.plot 
+python -m bmtool.plot
 """
 
+
 def is_notebook() -> bool:
     """
     Detect if code is running in a Jupyter notebook environment.
-    
+
     Returns:
     --------
     bool
         True if running in a Jupyter notebook, False otherwise.
-        
+
     Notes:
     ------
     This is used to determine whether to call plt.show() explicitly or
@@ -43,20 +40,31 @@ def is_notebook() -> bool:
     """
     try:
         shell = get_ipython().__class__.__name__
-        if shell == 'ZMQInteractiveShell':
-            return True   # Jupyter notebook or qtconsole
-        elif shell == 'TerminalInteractiveShell':
+        if shell == "ZMQInteractiveShell":
+            return True  # Jupyter notebook or qtconsole
+        elif shell == "TerminalInteractiveShell":
             return False  # Terminal running IPython
         else:
             return False  # Other type (?)
     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', include_gap=True):
+        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",
+    include_gap=True,
+):
     """
     Generate a plot displaying total connections or other synaptic statistics.
-    
+
     Parameters:
     -----------
     config : str
@@ -84,7 +92,7 @@ def total_connection_matrix(config=None, title=None, sources=None, targets=None,
     include_gap : bool, optional
         If True, include gap junctions and chemical synapses in the analysis.
         If False, only include chemical synapses.
-        
+
     Returns:
     --------
     None
@@ -104,27 +112,53 @@ def total_connection_matrix(config=None, title=None, sources=None, targets=None,
         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,include_gap=include_gap)
+    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=="":
+    if title is None or title == "":
         title = "Total Connections"
-    if synaptic_info=='1':
-        title = "Mean and Stdev # of Conn on Target"    
-    if synaptic_info=='2':
+    if synaptic_info == "1":
+        title = "Mean and Stdev # of Conn on Target"
+    if synaptic_info == "2":
         title = "All Synapse .mod Files Used"
-    if synaptic_info=='3':
+    if synaptic_info == "3":
         title = "All Synapse .json Files Used"
-    plot_connection_info(text,num,source_labels,target_labels,title, syn_info=synaptic_info, save_file=save_file)
+    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',include_gap=True):
+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 
+    config: A BMTK simulation config
     sources: network name(s) to plot
     targets: network name(s) to plot
-    sids: source node identifier 
+    sids: source node identifier
     tids: target node identifier
     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
@@ -135,7 +169,7 @@ def percent_connection_matrix(config=None,nodes=None,edges=None,title=None,sourc
         raise Exception("config not defined")
     if not sources or not targets:
         raise Exception("Sources or targets not defined")
-    
+
     sources = sources.split(",")
     targets = targets.split(",")
     if sids:
@@ -146,17 +180,44 @@ 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,include_gap=include_gap)
-    if title == None or title=="":
+    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 is None or title == "":
         title = "Percent Connectivity"
 
-
-    plot_connection_info(text,num,source_labels,target_labels,title, save_file=save_file)
+    plot_connection_info(text, num, source_labels, target_labels, title, save_file=save_file)
     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,include_gap=True):
+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,
+    include_gap=True,
+):
     """
     Generates probability graphs
     need to look into this more to see what it does
@@ -179,41 +240,53 @@ def probability_connection_matrix(config=None,nodes=None,edges=None,title=None,s
     else:
         tids = []
 
-    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,include_gap=include_gap)
+    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,
+        include_gap=include_gap,
+    )
     if not data.any():
         return
-    if data[0][0]==-1:
+    if data[0][0] == -1:
         return
-    #plot_connection_info(data,source_labels,target_labels,title, save_file=save_file)
+    # plot_connection_info(data,source_labels,target_labels,title, save_file=save_file)
 
-    #plt.clf()# clears previous plots
-    np.seterr(divide='ignore', invalid='ignore')
+    # plt.clf()# clears previous plots
+    np.seterr(divide="ignore", invalid="ignore")
     num_src, num_tar = data.shape
-    fig, axes = plt.subplots(nrows=num_src, ncols=num_tar, figsize=(12,12))
+    fig, axes = plt.subplots(nrows=num_src, ncols=num_tar, figsize=(12, 12))
     fig.subplots_adjust(hspace=0.5, wspace=0.5)
 
     for x in range(num_src):
         for y in range(num_tar):
             ns = data[x][y]["ns"]
             bins = data[x][y]["bins"]
-            
+
             XX = bins[:-1]
-            YY = ns[0]/ns[1]
+            YY = ns[0] / ns[1]
 
             if line_plot:
-                axes[x,y].plot(XX,YY)
+                axes[x, y].plot(XX, YY)
             else:
-                axes[x,y].bar(XX,YY)
+                axes[x, y].bar(XX, YY)
 
-            if x == num_src-1:
-                axes[x,y].set_xlabel(target_labels[y])
+            if x == num_src - 1:
+                axes[x, y].set_xlabel(target_labels[y])
             if y == 0:
-                axes[x,y].set_ylabel(source_labels[x])
+                axes[x, y].set_ylabel(source_labels[x])
 
             if verbose:
-                print("Source: [" + source_labels[x] + "] | Target: ["+ target_labels[y] +"]")
+                print("Source: [" + source_labels[x] + "] | Target: [" + target_labels[y] + "]")
                 print("X:")
                 print(XX)
                 print("Y:")
@@ -223,41 +296,80 @@ def probability_connection_matrix(config=None,nodes=None,edges=None,title=None,s
     if title:
         tt = title
     st = fig.suptitle(tt, fontsize=14)
-    fig.text(0.5, 0.04, 'Target', ha='center')
-    fig.text(0.04, 0.5, 'Source', va='center', rotation='vertical')
+    fig.text(0.5, 0.04, "Target", ha="center")
+    fig.text(0.04, 0.5, "Source", va="center", rotation="vertical")
     notebook = is_notebook
-    if notebook == False:
+    if not notebook:
         fig.show()
 
     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+std',include_gap=True,return_dict=None):
+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+std",
+    include_gap=True,
+    return_dict=None,
+):
     """
     Generates connection plot displaying convergence data
-    config: A BMTK simulation config 
+    config: A BMTK simulation config
     sources: network name(s) to plot
     targets: network name(s) to plot
-    sids: source node identifier 
+    sids: source node identifier
     tids: target node identifier
     no_prepend_pop: dictates if population name is displayed before sid or tid when displaying graph
     save_file: If plot should be saved
-    method: 'mean','min','max','stdev' or 'mean+std' connvergence plot 
+    method: 'mean','min','max','stdev' or 'mean+std' connvergence plot
     """
     if not config:
         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,include_gap=include_gap,return_dict=return_dict)
+    return divergence_connection_matrix(
+        config,
+        title,
+        sources,
+        targets,
+        sids,
+        tids,
+        no_prepend_pop,
+        save_file,
+        convergence,
+        method,
+        include_gap=include_gap,
+        return_dict=return_dict,
+    )
 
 
-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+std',include_gap=True,return_dict=None):
+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+std",
+    include_gap=True,
+    return_dict=None,
+):
     """
     Generates connection plot displaying divergence data
-    config: A BMTK simulation config 
+    config: A BMTK simulation config
     sources: network name(s) to plot
     targets: network name(s) to plot
-    sids: source node identifier 
+    sids: source node identifier
     tids: target node identifier
     no_prepend_pop: dictates if population name is displayed before sid or tid when displaying graph
     save_file: If plot should be saved
@@ -278,43 +390,73 @@ 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,include_gap=include_gap)
-
-    
-    #data, labels = util.connection_divergence_average(config=config,nodes=nodes,edges=edges,populations=populations)
+    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,
+    )
 
-    if title == None or title=="":
+    # data, labels = util.connection_divergence_average(config=config,nodes=nodes,edges=edges,populations=populations)
 
-        if method == 'min':
+    if title is None or title == "":
+        if method == "min":
             title = "Minimum "
-        elif method == 'max':
+        elif method == "max":
             title = "Maximum "
-        elif method == 'std':
+        elif method == "std":
             title = "Standard Deviation "
-        elif method == 'mean':
+        elif method == "mean":
             title = "Mean "
-        else: 
-            title = 'Mean + Std '
+        else:
+            title = "Mean + Std "
 
         if convergence:
             title = title + "Synaptic Convergence"
         else:
             title = title + "Synaptic Divergence"
     if return_dict:
-        dict = plot_connection_info(syn_info,data,source_labels,target_labels,title, save_file=save_file,return_dict=return_dict)
+        dict = plot_connection_info(
+            syn_info,
+            data,
+            source_labels,
+            target_labels,
+            title,
+            save_file=save_file,
+            return_dict=return_dict,
+        )
         return dict
     else:
-        plot_connection_info(syn_info,data,source_labels,target_labels,title, save_file=save_file)
+        plot_connection_info(
+            syn_info, data, source_labels, target_labels, title, save_file=save_file
+        )
         return
 
 
-def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=None,tids=None, no_prepend_pop=False,save_file=None,method='convergence'):
+def gap_junction_matrix(
+    config=None,
+    title=None,
+    sources=None,
+    targets=None,
+    sids=None,
+    tids=None,
+    no_prepend_pop=False,
+    save_file=None,
+    method="convergence",
+):
     """
     Generates connection plot displaying gap junction data.
-    config: A BMTK simulation config 
+    config: A BMTK simulation config
     sources: network name(s) to plot
     targets: network name(s) to plot
-    sids: source node identifier 
+    sids: source node identifier
     tids: target node identifier
     no_prepend_pop: dictates if population name is displayed before sid or tid when displaying graph
     save_file: If plot should be saved
@@ -324,7 +466,7 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
         raise Exception("config not defined")
     if not sources or not targets:
         raise Exception("Sources or targets not defined")
-    if method !='convergence' and method!='percent':
+    if method != "convergence" and method != "percent":
         raise Exception("type must be 'convergence' or 'percent'")
     sources = sources.split(",")
     targets = targets.split(",")
@@ -336,16 +478,25 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
         tids = tids.split(",")
     else:
         tids = []
-    syn_info, data, source_labels, target_labels = util.gap_junction_connections(config=config,nodes=None,edges=None,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,method=method)
-    
-    
+    syn_info, data, source_labels, target_labels = util.gap_junction_connections(
+        config=config,
+        nodes=None,
+        edges=None,
+        sources=sources,
+        targets=targets,
+        sids=sids,
+        tids=tids,
+        prepend_pop=not no_prepend_pop,
+        method=method,
+    )
+
     def filter_rows(syn_info, data, source_labels, target_labels):
         """
         Filters out rows in a connectivity matrix that contain only NaN or zero values.
-        
+
         This function is used to clean up connection matrices by removing rows that have no meaningful data,
         which helps create more informative visualizations of network connectivity.
-        
+
         Parameters:
         -----------
         syn_info : numpy.ndarray
@@ -356,7 +507,7 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
             List of labels for the source populations corresponding to rows in the data matrix.
         target_labels : list
             List of labels for the target populations corresponding to columns in the data matrix.
-        
+
         Returns:
         --------
         tuple
@@ -375,11 +526,11 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
     def filter_rows_and_columns(syn_info, data, source_labels, target_labels):
         """
         Filters out both rows and columns in a connectivity matrix that contain only NaN or zero values.
-        
+
         This function performs a two-step filtering process: first removing rows with no data,
         then transposing the matrix and removing columns with no data (by treating them as rows).
         This creates a cleaner, more informative connectivity matrix visualization.
-        
+
         Parameters:
         -----------
         syn_info : numpy.ndarray
@@ -390,7 +541,7 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
             List of labels for the source populations corresponding to rows in the data matrix.
         target_labels : list
             List of labels for the target populations corresponding to columns in the data matrix.
-        
+
         Returns:
         --------
         tuple
@@ -398,7 +549,9 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
             invalid rows and columns removed.
         """
         # Filter rows first
-        syn_info, data, source_labels, target_labels = filter_rows(syn_info, data, source_labels, target_labels)
+        syn_info, data, source_labels, target_labels = filter_rows(
+            syn_info, data, source_labels, target_labels
+        )
 
         # Transpose data to filter columns
         transposed_syn_info = np.transpose(syn_info)
@@ -407,7 +560,12 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
         transposed_target_labels = source_labels
 
         # Filter columns (by treating them as rows in transposed data)
-        transposed_syn_info, transposed_data, transposed_source_labels, transposed_target_labels = filter_rows(
+        (
+            transposed_syn_info,
+            transposed_data,
+            transposed_source_labels,
+            transposed_target_labels,
+        ) = filter_rows(
             transposed_syn_info, transposed_data, transposed_source_labels, transposed_target_labels
         )
 
@@ -419,40 +577,54 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
 
         return filtered_syn_info, filtered_data, filtered_source_labels, filtered_target_labels
 
-    
-    syn_info, data, source_labels, target_labels = filter_rows_and_columns(syn_info, data, source_labels, target_labels)
+    syn_info, data, source_labels, target_labels = filter_rows_and_columns(
+        syn_info, data, source_labels, target_labels
+    )
 
-    if title == None or title=="":
-        title = 'Gap Junction'
-        if method == 'convergence':
-            title+=' Syn Convergence'
-        elif method == 'percent':
-            title+=' Percent Connectivity'
-    plot_connection_info(syn_info,data,source_labels,target_labels,title, save_file=save_file)
+    if title is None or title == "":
+        title = "Gap Junction"
+        if method == "convergence":
+            title += " Syn Convergence"
+        elif method == "percent":
+            title += " Percent Connectivity"
+    plot_connection_info(syn_info, data, source_labels, target_labels, title, save_file=save_file)
     return
 
 
-def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],no_prepend_pop=True,synaptic_info='0',
-                      source_cell = None,target_cell = None,include_gap=True):
+def connection_histogram(
+    config=None,
+    nodes=None,
+    edges=None,
+    sources=[],
+    targets=[],
+    sids=[],
+    tids=[],
+    no_prepend_pop=True,
+    synaptic_info="0",
+    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 
+    config: A BMTK simulation config
     sources: network name(s) to plot
     targets: network name(s) to plot
-    sids: source node identifier 
+    sids: source node identifier
     tids: target node identifier
     no_prepend_pop: dictates if population name is displayed before sid or tid when displaying graph
     source_cell: where connections are coming from
     target_cell: where connections on coming onto
     save_file: If plot should be saved
     """
+
     def connection_pair_histogram(**kwargs):
         """
         Creates a histogram showing the distribution of connection counts between a specific source and target cell type.
-        
+
         This function is designed to be used with the relation_matrix utility and will only create histograms
         for the specified source and target cell types, ignoring all other combinations.
-        
+
         Parameters:
         -----------
         kwargs : dict
@@ -462,7 +634,7 @@ def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[]
             - tid: Column name for target ID type in the edges DataFrame
             - source_id: Value to filter edges by source ID type
             - target_id: Value to filter edges by target ID type
-        
+
         Global parameters used:
         ---------------------
         source_cell : str
@@ -471,37 +643,41 @@ def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[]
             The target cell type to plot.
         include_gap : bool
             Whether to include gap junctions in the analysis. If False, gap junctions are excluded.
-        
+
         Returns:
         --------
         None
             Displays a histogram showing the distribution of connection counts.
         """
-        edges = kwargs["edges"] 
+        edges = kwargs["edges"]
         source_id_type = kwargs["sid"]
         target_id_type = kwargs["tid"]
         source_id = kwargs["source_id"]
         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()
+            temp = edges[
+                (edges[source_id_type] == source_id) & (edges[target_id_type] == target_id)
+            ]
+            if not include_gap:
+                temp = temp[~temp["is_gap_junction"]]
+            node_pairs = temp.groupby("target_node_id")["source_node_id"].count()
             try:
                 conn_mean = statistics.mean(node_pairs.values)
                 conn_std = statistics.stdev(node_pairs.values)
                 conn_median = statistics.median(node_pairs.values)
-                label = "mean {:.2f} std {:.2f} median {:.2f}".format(conn_mean,conn_std,conn_median)
-            except: # lazy fix for std not calculated with 1 node
+                label = "mean {:.2f} std {:.2f} median {:.2f}".format(
+                    conn_mean, conn_std, conn_median
+                )
+            except:  # lazy fix for std not calculated with 1 node
                 conn_mean = statistics.mean(node_pairs.values)
                 conn_median = statistics.median(node_pairs.values)
-                label = "mean {:.2f} median {:.2f}".format(conn_mean,conn_median)
-            plt.hist(node_pairs.values,density=False,bins='auto',stacked=True,label=label)
+                label = "mean {:.2f} median {:.2f}".format(conn_mean, conn_median)
+            plt.hist(node_pairs.values, density=False, bins="auto", stacked=True, label=label)
             plt.legend()
-            plt.xlabel("# of conns from {} to {}".format(source_cell,target_cell))
+            plt.xlabel("# of conns from {} to {}".format(source_cell, target_cell))
             plt.ylabel("# of cells")
             plt.show()
-        else: # dont care about other cell pairs so pass
+        else:  # dont care about other cell pairs so pass
             pass
 
     if not config:
@@ -518,18 +694,35 @@ def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[]
         tids = tids.split(",")
     else:
         tids = []
-    util.relation_matrix(config,nodes,edges,sources,targets,sids,tids,not no_prepend_pop,relation_func=connection_pair_histogram,synaptic_info=synaptic_info)
+    util.relation_matrix(
+        config,
+        nodes,
+        edges,
+        sources,
+        targets,
+        sids,
+        tids,
+        not no_prepend_pop,
+        relation_func=connection_pair_histogram,
+        synaptic_info=synaptic_info,
+    )
 
 
-def connection_distance(config: str,sources: str,targets: str,
-                        source_cell_id: int,target_id_type: str,ignore_z:bool=False) -> None:
+def connection_distance(
+    config: str,
+    sources: str,
+    targets: str,
+    source_cell_id: int,
+    target_id_type: str,
+    ignore_z: bool = False,
+) -> None:
     """
     Plots the 3D spatial distribution of target nodes relative to a source node
     and a histogram of distances from the source node to each target node.
 
     Parameters:
     ----------
-    config: (str) A BMTK simulation config 
+    config: (str) A BMTK simulation config
     sources: (str) network name(s) to plot
     targets: (str) network name(s) to plot
     source_cell_id : (int) ID of the source cell for calculating distances to target nodes.
@@ -541,22 +734,22 @@ def connection_distance(config: str,sources: str,targets: str,
         raise Exception("config not defined")
     if not sources or not targets:
         raise Exception("Sources or targets not defined")
-    #if source != target:
-        #raise Exception("Code is setup for source and target to be the same! Look at source code for function to add feature")
-    
+    # if source != target:
+    # raise Exception("Code is setup for source and target to be the same! Look at source code for function to add feature")
+
     # Load nodes and edges based on config file
     nodes, edges = util.load_nodes_edges_from_config(config)
-    
+
     edge_network = sources + "_to_" + targets
     node_network = sources
 
     # Filter edges to obtain connections originating from the source node
     edge = edges[edge_network]
-    edge = edge[edge['source_node_id'] == source_cell_id]
+    edge = edge[edge["source_node_id"] == source_cell_id]
     if target_id_type:
-        edge = edge[edge['target_query'].str.contains(target_id_type, na=False)]
+        edge = edge[edge["target_query"].str.contains(target_id_type, na=False)]
 
-    target_node_ids = edge['target_node_id']
+    target_node_ids = edge["target_node_id"]
 
     # Filter nodes to obtain only the target and source nodes
     node = nodes[node_network]
@@ -565,24 +758,40 @@ def connection_distance(config: str,sources: str,targets: str,
 
     # Calculate distances between source node and each target node
     if ignore_z:
-        target_positions = target_nodes[['pos_x', 'pos_y']].values
-        source_position = np.array([source_node['pos_x'], source_node['pos_y']]).ravel()  # Ensure 1D shape
+        target_positions = target_nodes[["pos_x", "pos_y"]].values
+        source_position = np.array(
+            [source_node["pos_x"], source_node["pos_y"]]
+        ).ravel()  # Ensure 1D shape
     else:
-        target_positions = target_nodes[['pos_x', 'pos_y', 'pos_z']].values
-        source_position = np.array([source_node['pos_x'], source_node['pos_y'], source_node['pos_z']]).ravel()  # Ensure 1D shape
+        target_positions = target_nodes[["pos_x", "pos_y", "pos_z"]].values
+        source_position = np.array(
+            [source_node["pos_x"], source_node["pos_y"], source_node["pos_z"]]
+        ).ravel()  # Ensure 1D shape
     distances = np.linalg.norm(target_positions - source_position, axis=1)
 
     # Plot positions of source and target nodes in 3D space or 2D
     if ignore_z:
-        fig = plt.figure(figsize=(8, 6)) 
+        fig = plt.figure(figsize=(8, 6))
         ax = fig.add_subplot(111)
-        ax.scatter(target_nodes['pos_x'], target_nodes['pos_y'], c='blue', label="target cells")
-        ax.scatter(source_node['pos_x'], source_node['pos_y'], c='red', label="source cell")
+        ax.scatter(target_nodes["pos_x"], target_nodes["pos_y"], c="blue", label="target cells")
+        ax.scatter(source_node["pos_x"], source_node["pos_y"], c="red", label="source cell")
     else:
-        fig = plt.figure(figsize=(8, 6)) 
-        ax = fig.add_subplot(111, projection='3d')
-        ax.scatter(target_nodes['pos_x'], target_nodes['pos_y'], target_nodes['pos_z'], c='blue', label="target cells")
-        ax.scatter(source_node['pos_x'], source_node['pos_y'], source_node['pos_z'], c='red', label="source cell")
+        fig = plt.figure(figsize=(8, 6))
+        ax = fig.add_subplot(111, projection="3d")
+        ax.scatter(
+            target_nodes["pos_x"],
+            target_nodes["pos_y"],
+            target_nodes["pos_z"],
+            c="blue",
+            label="target cells",
+        )
+        ax.scatter(
+            source_node["pos_x"],
+            source_node["pos_y"],
+            source_node["pos_z"],
+            c="red",
+            label="source cell",
+        )
 
     # Optional: Add text annotations for distances
     # for i, distance in enumerate(distances):
@@ -593,23 +802,36 @@ def connection_distance(config: str,sources: str,targets: str,
     plt.show()
 
     # Plot distances in a separate 2D plot
-    plt.figure(figsize=(8, 6)) 
-    plt.hist(distances, bins=20, color='blue', edgecolor='black')
+    plt.figure(figsize=(8, 6))
+    plt.hist(distances, bins=20, color="blue", edgecolor="black")
     plt.xlabel("Distance")
     plt.ylabel("Count")
-    plt.title(f"Distance from Source Node to Each Target Node")
+    plt.title("Distance from Source Node to Each Target Node")
     plt.grid(True)
     plt.show()
 
 
-def edge_histogram_matrix(config=None,sources = None,targets=None,sids=None,tids=None,no_prepend_pop=None,edge_property = None,time = None,time_compare = None,report=None,title=None,save_file=None):
+def edge_histogram_matrix(
+    config=None,
+    sources=None,
+    targets=None,
+    sids=None,
+    tids=None,
+    no_prepend_pop=None,
+    edge_property=None,
+    time=None,
+    time_compare=None,
+    report=None,
+    title=None,
+    save_file=None,
+):
     """
     Generates a matrix of histograms showing the distribution of edge properties between different populations.
-    
-    This function creates a grid of histograms where each cell in the grid represents the distribution of a 
-    specific edge property (e.g., synaptic weights, delays) between a source population (row) and 
+
+    This function creates a grid of histograms where each cell in the grid represents the distribution of a
+    specific edge property (e.g., synaptic weights, delays) between a source population (row) and
     target population (column).
-    
+
     Parameters:
     -----------
     config : str
@@ -636,13 +858,13 @@ def edge_histogram_matrix(config=None,sources = None,targets=None,sids=None,tids
         Custom title for the plot.
     save_file : str, optional
         Path to save the generated plot.
-    
+
     Returns:
     --------
     None
         Displays a matrix of histograms.
     """
-    
+
     if not config:
         raise Exception("config not defined")
     if not sources or not targets:
@@ -660,34 +882,48 @@ def edge_histogram_matrix(config=None,sources = None,targets=None,sids=None,tids
     if time_compare:
         time_compare = int(time_compare)
 
-    data, source_labels, target_labels = util.edge_property_matrix(edge_property,nodes=None,edges=None,config=config,sources=sources,targets=targets,sids=sids,tids=tids,prepend_pop=not no_prepend_pop,report=report,time=time,time_compare=time_compare)
+    data, source_labels, target_labels = util.edge_property_matrix(
+        edge_property,
+        nodes=None,
+        edges=None,
+        config=config,
+        sources=sources,
+        targets=targets,
+        sids=sids,
+        tids=tids,
+        prepend_pop=not no_prepend_pop,
+        report=report,
+        time=time,
+        time_compare=time_compare,
+    )
 
     # Fantastic resource
-    # https://stackoverflow.com/questions/7941207/is-there-a-function-to-make-scatterplot-matrices-in-matplotlib 
+    # https://stackoverflow.com/questions/7941207/is-there-a-function-to-make-scatterplot-matrices-in-matplotlib
     num_src, num_tar = data.shape
-    fig, axes = plt.subplots(nrows=num_src, ncols=num_tar, figsize=(12,12))
+    fig, axes = plt.subplots(nrows=num_src, ncols=num_tar, figsize=(12, 12))
     fig.subplots_adjust(hspace=0.5, wspace=0.5)
 
     for x in range(num_src):
         for y in range(num_tar):
-            axes[x,y].hist(data[x][y])
+            axes[x, y].hist(data[x][y])
 
-            if x == num_src-1:
-                axes[x,y].set_xlabel(target_labels[y])
+            if x == num_src - 1:
+                axes[x, y].set_xlabel(target_labels[y])
             if y == 0:
-                axes[x,y].set_ylabel(source_labels[x])
+                axes[x, y].set_ylabel(source_labels[x])
 
     tt = edge_property + " Histogram Matrix"
     if title:
         tt = title
     st = fig.suptitle(tt, fontsize=14)
-    fig.text(0.5, 0.04, 'Target', ha='center')
-    fig.text(0.04, 0.5, 'Source', va='center', rotation='vertical')
+    fig.text(0.5, 0.04, "Target", ha="center")
+    fig.text(0.04, 0.5, "Source", va="center", rotation="vertical")
     plt.draw()
 
 
-def distance_delay_plot(simulation_config: str,source: str,target: str,
-    group_by: str,sid: str,tid: str) -> None:
+def distance_delay_plot(
+    simulation_config: str, source: str, target: str, group_by: str, sid: str, tid: str
+) -> None:
     """
     Plots the relationship between the distance and delay of connections between nodes in a neural network simulation.
 
@@ -708,25 +944,27 @@ def distance_delay_plot(simulation_config: str,source: str,target: str,
     """
     nodes, edges = util.load_nodes_edges_from_config(simulation_config)
     nodes = nodes[target]
-    #node id is index of nodes df
+    # node id is index of nodes df
     node_id_source = nodes[nodes[group_by] == sid].index
     node_id_target = nodes[nodes[group_by] == tid].index
 
-    edges = edges[f'{source}_to_{target}']
-    edges = edges[edges['source_node_id'].isin(node_id_source) & edges['target_node_id'].isin(node_id_target)]
+    edges = edges[f"{source}_to_{target}"]
+    edges = edges[
+        edges["source_node_id"].isin(node_id_source) & edges["target_node_id"].isin(node_id_target)
+    ]
 
     stuff_to_plot = []
     for index, row in edges.iterrows():
         try:
-            source_node = row['source_node_id']
-            target_node = row['target_node_id']
-            
-            source_pos = nodes.loc[[source_node], ['pos_x', 'pos_y', 'pos_z']]
-            target_pos = nodes.loc[[target_node], ['pos_x', 'pos_y', 'pos_z']]
-            
+            source_node = row["source_node_id"]
+            target_node = row["target_node_id"]
+
+            source_pos = nodes.loc[[source_node], ["pos_x", "pos_y", "pos_z"]]
+            target_pos = nodes.loc[[target_node], ["pos_x", "pos_y", "pos_z"]]
+
             distance = np.linalg.norm(source_pos.values - target_pos.values)
 
-            delay = row['delay']  # This line may raise KeyError
+            delay = row["delay"]  # This line may raise KeyError
             stuff_to_plot.append([distance, delay])
 
         except KeyError as e:
@@ -737,9 +975,9 @@ def distance_delay_plot(simulation_config: str,source: str,target: str,
             print(f"Unexpected error at edge index {index}: {e}")
 
     plt.scatter([x[0] for x in stuff_to_plot], [x[1] for x in stuff_to_plot])
-    plt.xlabel('Distance')
-    plt.ylabel('Delay')
-    plt.title(f'Distance vs Delay for edge between {sid} and {tid}')
+    plt.xlabel("Distance")
+    plt.ylabel("Delay")
+    plt.title(f"Distance vs Delay for edge between {sid} and {tid}")
     plt.show()
 
 
@@ -748,7 +986,7 @@ def plot_synapse_location_histograms(config, target_model, source=None, target=N
     generates a histogram of the positions of the synapses on a cell broken down by section
     config: a BMTK config
     target_model: the name of the model_template used when building the BMTK node
-    source: The source BMTK network 
+    source: The source BMTK network
     target: The target BMTK network
     """
     # Load mechanisms and template
@@ -758,37 +996,36 @@ def plot_synapse_location_histograms(config, target_model, source=None, target=N
     # Load node and edge data
     nodes, edges = util.load_nodes_edges_from_config(config)
     nodes = nodes[source]
-    edges = edges[f'{source}_to_{target}']
+    edges = edges[f"{source}_to_{target}"]
 
     # Map target_node_id to model_template
-    edges['target_model_template'] = edges['target_node_id'].map(nodes['model_template'])
+    edges["target_model_template"] = edges["target_node_id"].map(nodes["model_template"])
 
     # Map source_node_id to pop_name
-    edges['source_pop_name'] = edges['source_node_id'].map(nodes['pop_name'])
+    edges["source_pop_name"] = edges["source_node_id"].map(nodes["pop_name"])
 
-    edges = edges[edges['target_model_template'] == target_model]
+    edges = edges[edges["target_model_template"] == target_model]
 
     # Create the cell model from target model
-    cell = getattr(h, target_model.split(':')[1])()
- 
+    cell = getattr(h, target_model.split(":")[1])()
+
     # Create a mapping from section index to section name
     section_id_to_name = {}
     for idx, sec in enumerate(cell.all):
         section_id_to_name[idx] = sec.name()
 
     # Add a new column with section names based on afferent_section_id
-    edges['afferent_section_name'] = edges['afferent_section_id'].map(section_id_to_name)
+    edges["afferent_section_name"] = edges["afferent_section_id"].map(section_id_to_name)
 
     # Get unique sections and source populations
-    unique_pops = edges['source_pop_name'].unique()
+    unique_pops = edges["source_pop_name"].unique()
 
     # Filter to only include sections with data
-    section_counts = edges['afferent_section_name'].value_counts()
+    section_counts = edges["afferent_section_name"].value_counts()
     sections_with_data = section_counts[section_counts > 0].index.tolist()
 
-
     # Create a figure with subplots for each section
-    plt.figure(figsize=(8,12))
+    plt.figure(figsize=(8, 12))
 
     # Color map for source populations
     color_map = plt.cm.tab10(np.linspace(0, 1, len(unique_pops)))
@@ -796,30 +1033,37 @@ def plot_synapse_location_histograms(config, target_model, source=None, target=N
 
     # Create a histogram for each section
     for i, section in enumerate(sections_with_data):
-        ax = plt.subplot(len(sections_with_data), 1, i+1)
-        
+        ax = plt.subplot(len(sections_with_data), 1, i + 1)
+
         # Get data for this section
-        section_data = edges[edges['afferent_section_name'] == section]
-        
+        section_data = edges[edges["afferent_section_name"] == section]
+
         # Group by source population
-        for pop_name, pop_group in section_data.groupby('source_pop_name'):
+        for pop_name, pop_group in section_data.groupby("source_pop_name"):
             if len(pop_group) > 0:
-                ax.hist(pop_group['afferent_section_pos'], bins=15, alpha=0.7, 
-                    label=pop_name, color=pop_colors[pop_name])
-        
+                ax.hist(
+                    pop_group["afferent_section_pos"],
+                    bins=15,
+                    alpha=0.7,
+                    label=pop_name,
+                    color=pop_colors[pop_name],
+                )
+
         # Set title and labels
         ax.set_title(f"{section}", fontsize=10)
-        ax.set_xlabel('Section Position', fontsize=8)
-        ax.set_ylabel('Frequency', fontsize=8)
+        ax.set_xlabel("Section Position", fontsize=8)
+        ax.set_ylabel("Frequency", fontsize=8)
         ax.tick_params(labelsize=7)
         ax.grid(True, alpha=0.3)
-        
+
         # Only add legend to the first plot
         if i == 0:
             ax.legend(fontsize=8)
 
     plt.tight_layout()
-    plt.suptitle('Connection Distribution by Cell Section and Source Population', fontsize=16, y=1.02)
+    plt.suptitle(
+        "Connection Distribution by Cell Section and Source Population", fontsize=16, y=1.02
+    )
     if is_notebook:
         plt.show()
     else:
@@ -828,105 +1072,147 @@ def plot_synapse_location_histograms(config, target_model, source=None, target=N
     # Create a summary table
     print("Summary of connections by section and source population:")
     pivot_table = edges.pivot_table(
-        values='afferent_section_id', 
-        index='afferent_section_name',
-        columns='source_pop_name',
-        aggfunc='count',
-        fill_value=0
+        values="afferent_section_id",
+        index="afferent_section_name",
+        columns="source_pop_name",
+        aggfunc="count",
+        fill_value=0,
     )
     print(pivot_table)
 
 
-def plot_connection_info(text, num, source_labels, target_labels, title, syn_info='0', save_file=None, return_dict=None):
+def plot_connection_info(
+    text, num, source_labels, target_labels, title, syn_info="0", save_file=None, return_dict=None
+):
     """
     Function to plot connection information as a heatmap, including handling missing source and target values.
     If there is no source or target, set the value to 0.
     """
-    
+
     # Ensure text dimensions match num dimensions
     num_source = len(source_labels)
     num_target = len(target_labels)
-    
+
     # Set color map
-    matplotlib.rc('image', cmap='viridis')
-    
+    matplotlib.rc("image", cmap="viridis")
+
     # Create figure and axis for the plot
     fig1, ax1 = plt.subplots(figsize=(num_source, num_target))
-    num = np.nan_to_num(num, nan=0) # replace NaN with 0
+    num = np.nan_to_num(num, nan=0)  # replace NaN with 0
     im1 = ax1.imshow(num)
-    
+
     # Set ticks and labels for source and target
     ax1.set_xticks(list(np.arange(len(target_labels))))
     ax1.set_yticks(list(np.arange(len(source_labels))))
     ax1.set_xticklabels(target_labels)
-    ax1.set_yticklabels(source_labels, size=12, weight='semibold')
-    
+    ax1.set_yticklabels(source_labels, size=12, weight="semibold")
+
     # Rotate the tick labels for better visibility
-    plt.setp(ax1.get_xticklabels(), rotation=45, ha="right",
-             rotation_mode="anchor", size=12, weight='semibold')
-    
+    plt.setp(
+        ax1.get_xticklabels(),
+        rotation=45,
+        ha="right",
+        rotation_mode="anchor",
+        size=12,
+        weight="semibold",
+    )
+
     # Dictionary to store connection information
     graph_dict = {}
-    
+
     # Loop over data dimensions and create text annotations
     for i in range(num_source):
         for j in range(num_target):
             # Get the edge info, or set it to '0' if it's missing
             edge_info = text[i, j] if text[i, j] is not None else 0
-            
+
             # Initialize the dictionary for the source node if not already done
             if source_labels[i] not in graph_dict:
                 graph_dict[source_labels[i]] = {}
-            
+
             # Add edge info for the target node
             graph_dict[source_labels[i]][target_labels[j]] = edge_info
-            
+
             # Set text annotations based on syn_info type
-            if syn_info == '2' or syn_info == '3':
+            if syn_info == "2" or syn_info == "3":
                 if num_source > 8 and num_source < 20:
-                    fig_text = ax1.text(j, i, edge_info,
-                                        ha="center", va="center", color="w", rotation=37.5, size=8, weight='semibold')
+                    fig_text = ax1.text(
+                        j,
+                        i,
+                        edge_info,
+                        ha="center",
+                        va="center",
+                        color="w",
+                        rotation=37.5,
+                        size=8,
+                        weight="semibold",
+                    )
                 elif num_source > 20:
-                    fig_text = ax1.text(j, i, edge_info,
-                                        ha="center", va="center", color="w", rotation=37.5, size=7, weight='semibold')
+                    fig_text = ax1.text(
+                        j,
+                        i,
+                        edge_info,
+                        ha="center",
+                        va="center",
+                        color="w",
+                        rotation=37.5,
+                        size=7,
+                        weight="semibold",
+                    )
                 else:
-                    fig_text = ax1.text(j, i, edge_info,
-                                        ha="center", va="center", color="w", rotation=37.5, size=11, weight='semibold')
+                    fig_text = ax1.text(
+                        j,
+                        i,
+                        edge_info,
+                        ha="center",
+                        va="center",
+                        color="w",
+                        rotation=37.5,
+                        size=11,
+                        weight="semibold",
+                    )
             else:
-                fig_text = ax1.text(j, i, edge_info,
-                                    ha="center", va="center", color="w", size=11, weight='semibold')
-    
+                fig_text = ax1.text(
+                    j, i, edge_info, ha="center", va="center", color="w", size=11, weight="semibold"
+                )
+
     # Set labels and title for the plot
-    ax1.set_ylabel('Source', size=11, weight='semibold')
-    ax1.set_xlabel('Target', size=11, weight='semibold')
-    ax1.set_title(title, size=20, weight='semibold')
-    
+    ax1.set_ylabel("Source", size=11, weight="semibold")
+    ax1.set_xlabel("Target", size=11, weight="semibold")
+    ax1.set_title(title, size=20, weight="semibold")
+
     # Display the plot or save it based on the environment and arguments
     notebook = is_notebook()  # Check if running in a Jupyter notebook
-    if notebook == False:
+    if not notebook:
         fig1.show()
-    
+
     if save_file:
         plt.savefig(save_file)
-    
+
     if return_dict:
         return graph_dict
     else:
         return
 
 
-def connector_percent_matrix(csv_path: str = None, exclude_strings=None, assemb_key=None, title: str = 'Percent connection matrix', pop_order=None) -> None:
+def connector_percent_matrix(
+    csv_path: str = None,
+    exclude_strings=None,
+    assemb_key=None,
+    title: str = "Percent connection matrix",
+    pop_order=None,
+) -> None:
     """
     Generates and plots a connection matrix based on connection probabilities from a CSV file produced by bmtool.connector.
 
-    This function is useful for visualizing percent connectivity while factoring in population distance and other parameters. 
-    It processes the connection data by filtering the 'Source' and 'Target' columns in the CSV, and displays the percentage of 
+    This function is useful for visualizing percent connectivity while factoring in population distance and other parameters.
+    It processes the connection data by filtering the 'Source' and 'Target' columns in the CSV, and displays the percentage of
     connected pairs for each population combination in a matrix.
 
     Parameters:
     -----------
     csv_path : str
-        Path to the CSV file containing the connection data. The CSV should be an output from the bmtool.connector 
+        Path to the CSV file containing the connection data. The CSV should be an output from the bmtool.connector
         classes, specifically generated by the `save_connection_report()` function.
     exclude_strings : list of str, optional
         List of strings to exclude rows where 'Source' or 'Target' contain these strings.
@@ -949,15 +1235,14 @@ def connector_percent_matrix(csv_path: str = None, exclude_strings=None, assemb_
     # Filter the DataFrame based on exclude_strings
     def filter_dataframe(df, column_name, exclude_strings):
         def process_string(string):
-            
             match = re.search(r"\[\'(.*?)\'\]", string)
             if exclude_strings and any(ex_string in string for ex_string in exclude_strings):
                 return None
             elif match:
                 filtered_string = match.group(1)
-                if 'Gap' in string:
-                        filtered_string = filtered_string + "-Gap"
-                
+                if "Gap" in string:
+                    filtered_string = filtered_string + "-Gap"
+
                 if assemb_key:
                     if assemb_key in string:
                         filtered_string = filtered_string + assemb_key
@@ -965,65 +1250,73 @@ def connector_percent_matrix(csv_path: str = None, exclude_strings=None, assemb_
                 return filtered_string  # Return matched string
 
             return string  # If no match, return the original string
-        
+
         df[column_name] = df[column_name].apply(process_string)
         df = df.dropna(subset=[column_name])
-        
+
         return df
 
-    df = filter_dataframe(df, 'Source', exclude_strings)
-    df = filter_dataframe(df, 'Target', exclude_strings)
-    
-    #process assem rows and combine them into one prob per assem type
+    df = filter_dataframe(df, "Source", exclude_strings)
+    df = filter_dataframe(df, "Target", exclude_strings)
+
+    # process assem rows and combine them into one prob per assem type
     if assemb_key:
-        assems = df[df['Source'].str.contains(assemb_key)]
-        unique_sources = assems['Source'].unique()
+        assems = df[df["Source"].str.contains(assemb_key)]
+        unique_sources = assems["Source"].unique()
 
         for source in unique_sources:
-            source_assems = assems[assems['Source'] == source]
-            unique_targets = source_assems['Target'].unique()  # Filter targets for the current source
+            source_assems = assems[assems["Source"] == source]
+            unique_targets = source_assems[
+                "Target"
+            ].unique()  # Filter targets for the current source
 
             for target in unique_targets:
                 # Filter the assemblies with the current source and target
-                unique_assems = source_assems[source_assems['Target'] == target]
-                
+                unique_assems = source_assems[source_assems["Target"] == target]
+
                 # find the prob of a conn
                 forward_probs = []
-                for _,row in unique_assems.iterrows():
+                for _, row in unique_assems.iterrows():
                     selected_percentage = row[selected_column]
-                    selected_percentage = [float(p) for p in selected_percentage.strip('[]').split()]
+                    selected_percentage = [
+                        float(p) for p in selected_percentage.strip("[]").split()
+                    ]
                     if len(selected_percentage) == 1 or len(selected_percentage) == 2:
                         forward_probs.append(selected_percentage[0])
                     if len(selected_percentage) == 3:
                         forward_probs.append(selected_percentage[0])
                         forward_probs.append(selected_percentage[1])
-                        
+
                 mean_probs = np.mean(forward_probs)
                 source = source.replace(assemb_key, "")
                 target = target.replace(assemb_key, "")
-                new_row = pd.DataFrame({
-                    'Source': [source],
-                    'Target': [target],
-                    'Percent connectionivity within possible connections': [mean_probs],
-                    'Percent connectionivity within all connections': [0]
-                })
+                new_row = pd.DataFrame(
+                    {
+                        "Source": [source],
+                        "Target": [target],
+                        "Percent connectionivity within possible connections": [mean_probs],
+                        "Percent connectionivity within all connections": [0],
+                    }
+                )
 
                 df = pd.concat([df, new_row], ignore_index=False)
-            
+
     # Prepare connection data
     connection_data = {}
     for _, row in df.iterrows():
-        source, target, selected_percentage = row['Source'], row['Target'], row[selected_column]
+        source, target, selected_percentage = row["Source"], row["Target"], row[selected_column]
         if isinstance(selected_percentage, str):
-            selected_percentage = [float(p) for p in selected_percentage.strip('[]').split()]
+            selected_percentage = [float(p) for p in selected_percentage.strip("[]").split()]
         connection_data[(source, target)] = selected_percentage
 
     # Determine population order
-    populations = sorted(list(set(df['Source'].unique()) | set(df['Target'].unique())))
+    populations = sorted(list(set(df["Source"].unique()) | set(df["Target"].unique())))
     if pop_order:
-        populations = [pop for pop in pop_order if pop in populations]  # Order according to pop_order, if provided
+        populations = [
+            pop for pop in pop_order if pop in populations
+        ]  # Order according to pop_order, if provided
     num_populations = len(populations)
-    
+
     # Create an empty matrix and populate it
     connection_matrix = np.zeros((num_populations, num_populations), dtype=float)
     for (source, target), probabilities in connection_data.items():
@@ -1031,40 +1324,49 @@ def connector_percent_matrix(csv_path: str = None, exclude_strings=None, assemb_
             source_idx = populations.index(source)
             target_idx = populations.index(target)
 
-            if type(probabilities) == float:
+            if isinstance(probabilities, float):
                 connection_matrix[source_idx][target_idx] = probabilities
             elif len(probabilities) == 1:
                 connection_matrix[source_idx][target_idx] = probabilities[0]
             elif len(probabilities) == 2:
                 connection_matrix[source_idx][target_idx] = probabilities[0]
             elif len(probabilities) == 3:
-                connection_matrix[source_idx][target_idx] = probabilities[0] 
+                connection_matrix[source_idx][target_idx] = probabilities[0]
                 connection_matrix[target_idx][source_idx] = probabilities[1]
             else:
                 raise Exception("unsupported format")
 
     # Plotting
     fig, ax = plt.subplots(figsize=(10, 8))
-    im = ax.imshow(connection_matrix, cmap='viridis', interpolation='nearest')
+    im = ax.imshow(connection_matrix, cmap="viridis", interpolation="nearest")
 
     # Add annotations
     for i in range(num_populations):
         for j in range(num_populations):
-            text = ax.text(j, i, f"{connection_matrix[i, j]:.2f}%", ha="center", va="center", color="w", size=10, weight='semibold')
+            text = ax.text(
+                j,
+                i,
+                f"{connection_matrix[i, j]:.2f}%",
+                ha="center",
+                va="center",
+                color="w",
+                size=10,
+                weight="semibold",
+            )
 
     # Add colorbar
-    plt.colorbar(im, label=f'{selected_column}')
+    plt.colorbar(im, label=f"{selected_column}")
 
     # Set title and axis labels
     ax.set_title(title)
-    ax.set_xlabel('Target Population')
-    ax.set_ylabel('Source Population')
+    ax.set_xlabel("Target Population")
+    ax.set_ylabel("Source Population")
 
     # Set ticks and labels based on populations in specified order
     ax.set_xticks(np.arange(num_populations))
     ax.set_yticks(np.arange(num_populations))
-    ax.set_xticklabels(populations, rotation=45, ha="right", size=12, weight='semibold')
-    ax.set_yticklabels(populations, size=12, weight='semibold')
+    ax.set_xticklabels(populations, rotation=45, ha="right", size=12, weight="semibold")
+    ax.set_yticklabels(populations, size=12, weight="semibold")
 
     plt.tight_layout()
     plt.show()
@@ -1073,22 +1375,22 @@ def connector_percent_matrix(csv_path: str = None, exclude_strings=None, assemb_
 def plot_3d_positions(config=None, sources=None, sid=None, title=None, save_file=None, subset=None):
     """
     Plots a 3D graph of all cells with x, y, z location.
-    
+
     Parameters:
-    - config: A BMTK simulation config 
-    - sources: Which network(s) to plot 
+    - config: A BMTK simulation config
+    - sources: Which network(s) to plot
     - sid: How to name cell groups
     - title: Plot title
     - save_file: If plot should be saved
     - subset: Take every Nth row. This will make plotting large network graphs easier to see.
     """
-    
+
     if not config:
         raise Exception("config not defined")
-    
+
     if sources is None:
         sources = "all"
-    
+
     # Set group keys (e.g., node types)
     group_keys = sid
     if title is None:
@@ -1096,66 +1398,75 @@ def plot_3d_positions(config=None, sources=None, sid=None, title=None, save_file
 
     # Load nodes from the configuration
     nodes = util.load_nodes_from_config(config)
-    
+
     # Get the list of populations to plot
-    if 'all' in sources:
+    if "all" in sources:
         populations = list(nodes)
     else:
         populations = sources.split(",")
-    
-    # Split group_by into list 
+
+    # Split group_by into list
     group_keys = group_keys.split(",")
-    group_keys += (len(populations) - len(group_keys)) * ["node_type_id"]  # Extend the array to default values if not enough given
+    group_keys += (len(populations) - len(group_keys)) * [
+        "node_type_id"
+    ]  # Extend the array to default values if not enough given
     if len(group_keys) > 1:
         raise Exception("Only one group by is supported currently!")
-    
+
     fig = plt.figure(figsize=(10, 10))
-    ax = fig.add_subplot(projection='3d')
+    ax = fig.add_subplot(projection="3d")
     handles = []
 
-    for pop in (list(nodes)):
-        
-        if 'all' not in populations and pop not in populations:
+    for pop in list(nodes):
+        if "all" not in populations and pop not in populations:
             continue
-        
+
         nodes_df = nodes[pop]
-        group_key = group_keys[0] 
-        
+        group_key = group_keys[0]
+
         # If group_key is provided, ensure the column exists in the dataframe
         if group_key is not None:
             if group_key not in nodes_df:
                 raise Exception(f"Could not find column '{group_key}' in {pop}")
-            
+
             groupings = nodes_df.groupby(group_key)
             n_colors = nodes_df[group_key].nunique()
             color_norm = colors.Normalize(vmin=0, vmax=(n_colors - 1))
-            scalar_map = cmx.ScalarMappable(norm=color_norm, cmap='hsv')
+            scalar_map = cmx.ScalarMappable(norm=color_norm, cmap="hsv")
             color_map = [scalar_map.to_rgba(i) for i in range(n_colors)]
         else:
             groupings = [(None, nodes_df)]
-            color_map = ['blue']
+            color_map = ["blue"]
 
         # Loop over groupings and plot
         for color, (group_name, group_df) in zip(color_map, groupings):
             if "pos_x" not in group_df or "pos_y" not in group_df or "pos_z" not in group_df:
-                print(f"Warning: Missing position columns in group '{group_name}' for {pop}. Skipping this group.")
+                print(
+                    f"Warning: Missing position columns in group '{group_name}' for {pop}. Skipping this group."
+                )
                 continue  # Skip if position columns are missing
 
             # Subset the dataframe by taking every Nth row if subset is provided
             if subset is not None:
                 group_df = group_df.iloc[::subset]
 
-            h = ax.scatter(group_df["pos_x"], group_df["pos_y"], group_df["pos_z"], color=color, label=group_name)
+            h = ax.scatter(
+                group_df["pos_x"],
+                group_df["pos_y"],
+                group_df["pos_z"],
+                color=color,
+                label=group_name,
+            )
             handles.append(h)
-    
+
     if not handles:
         print("No data to plot.")
         return
-    
+
     # Set plot title and legend
     plt.title(title)
     plt.legend(handles=handles)
-    
+
     # Draw the plot
     plt.draw()
 
@@ -1170,8 +1481,19 @@ def plot_3d_positions(config=None, sources=None, sid=None, title=None, save_file
     return ax
 
 
-def plot_3d_cell_rotation(config=None, sources=None, sids=None, title=None, save_file=None, quiver_length=None, arrow_length_ratio=None, group=None, subset=None):
+def plot_3d_cell_rotation(
+    config=None,
+    sources=None,
+    sids=None,
+    title=None,
+    save_file=None,
+    quiver_length=None,
+    arrow_length_ratio=None,
+    group=None,
+    subset=None,
+):
     from scipy.spatial.transform import Rotation as R
+
     if not config:
         raise Exception("config not defined")
 
@@ -1185,38 +1507,38 @@ def plot_3d_cell_rotation(config=None, sources=None, sids=None, title=None, save
 
     nodes = util.load_nodes_from_config(config)
 
-    if 'all' in sources:
+    if "all" in sources:
         populations = list(nodes)
     else:
         populations = sources
 
     fig = plt.figure(figsize=(10, 10))
-    ax = fig.add_subplot(111, projection='3d')
+    ax = fig.add_subplot(111, projection="3d")
     handles = []
 
     for nodes_key, group_key in zip(list(nodes), group_keys):
-        if 'all' not in populations and nodes_key not in populations:
+        if "all" not in populations and nodes_key not in populations:
             continue
 
         nodes_df = nodes[nodes_key]
 
         if group_key is not None:
             if group_key not in nodes_df.columns:
-                raise Exception(f'Could not find column {group_key}')
+                raise Exception(f"Could not find column {group_key}")
             groupings = nodes_df.groupby(group_key)
 
             n_colors = nodes_df[group_key].nunique()
             color_norm = colors.Normalize(vmin=0, vmax=(n_colors - 1))
-            scalar_map = cmx.ScalarMappable(norm=color_norm, cmap='hsv')
+            scalar_map = cmx.ScalarMappable(norm=color_norm, cmap="hsv")
             color_map = [scalar_map.to_rgba(i) for i in range(n_colors)]
         else:
             groupings = [(None, nodes_df)]
-            color_map = ['blue']
+            color_map = ["blue"]
 
         for color, (group_name, group_df) in zip(color_map, groupings):
             if subset is not None:
                 group_df = group_df.iloc[::subset]
-            
+
             if group and group_name not in group.split(","):
                 continue
 
@@ -1238,9 +1560,9 @@ def plot_3d_cell_rotation(config=None, sources=None, sids=None, title=None, save
                 W = np.zeros(len(Z))
 
             # Create rotation matrices from Euler angles
-            rotations = R.from_euler('xyz', np.column_stack((U, V, W)), degrees=False)
+            rotations = R.from_euler("xyz", np.column_stack((U, V, W)), degrees=False)
 
-            # Define initial vectors 
+            # Define initial vectors
             init_vectors = np.column_stack((np.ones(len(X)), np.zeros(len(Y)), np.zeros(len(Z))))
 
             # Apply rotations to initial vectors
@@ -1251,7 +1573,18 @@ def plot_3d_cell_rotation(config=None, sources=None, sids=None, title=None, save
             rot_y = rots[:, 1]
             rot_z = rots[:, 2]
 
-            h = ax.quiver(X, Y, Z, rot_x, rot_y, rot_z, color=color, label=group_name, arrow_length_ratio=arrow_length_ratio, length=quiver_length)
+            h = ax.quiver(
+                X,
+                Y,
+                Z,
+                rot_x,
+                rot_y,
+                rot_z,
+                color=color,
+                label=group_name,
+                arrow_length_ratio=arrow_length_ratio,
+                length=quiver_length,
+            )
             ax.scatter(X, Y, Z, color=color, label=group_name)
             ax.set_xlim([min(X), max(X)])
             ax.set_ylim([min(Y), max(Y)])
@@ -1268,5 +1601,5 @@ def plot_3d_cell_rotation(config=None, sources=None, sids=None, title=None, save
     if save_file:
         plt.savefig(save_file)
     notebook = is_notebook
-    if notebook == False:
+    if not notebook:
         plt.show()