bmtool 0.5.9.7__py3-none-any.whl → 0.5.9.9__py3-none-any.whl

bmtool/bmplot.py

@@ -274,7 +274,7 @@ def divergence_connection_matrix(config=None,title=None,sources=None, targets=No
         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,type='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 
@@ -290,7 +290,7 @@ 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 type !='convergence' and type!='percent':
+    if method !='convergence' and method!='percent':
         raise Exception("type must be 'convergence' or 'percent'")
     sources = sources.split(",")
     targets = targets.split(",")
@@ -302,7 +302,7 @@ 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,type=type)
+    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):
@@ -350,7 +350,7 @@ def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=
     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=[],prepend_pop=True,synaptic_info='0',
+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
@@ -379,15 +379,15 @@ def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[]
                 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)
+                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=True,bins='auto',stacked=True,label=label)
+            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.ylabel("Density")
+            plt.ylabel("# of cells")
             plt.show()
         else: # dont care about other cell pairs so pass
             pass
@@ -406,10 +406,10 @@ 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,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,source: str,target: str,
-                        source_cell_id: int,target_id_type: str) -> 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.
@@ -421,11 +421,12 @@ def connection_distance(config: str,source: str,target: str,
     targets: (str) network name(s) to plot
     source_cell_id : (int) ID of the source cell for calculating distances to target nodes.
     target_id_type : (str) A string to filter target nodes based off the target_query.
+    ignore_z : (bool) A bool to ignore_z axis or not for when calculating distance default is False
 
     """
     if not config:
         raise Exception("config not defined")
-    if not source or not target:
+    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")
@@ -433,8 +434,8 @@ def connection_distance(config: str,source: str,target: str,
     # Load nodes and edges based on config file
     nodes, edges = util.load_nodes_edges_from_config(config)
     
-    edge_network = source + "_to_" + target
-    node_network = source
+    edge_network = sources + "_to_" + targets
+    node_network = sources
 
     # Filter edges to obtain connections originating from the source node
     edge = edges[edge_network]
@@ -450,16 +451,25 @@ def connection_distance(config: str,source: str,target: str,
     source_node = node.loc[node.index == source_cell_id]
 
     # Calculate distances between source node and each target node
-    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
+    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
+    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
     distances = np.linalg.norm(target_positions - source_position, axis=1)
 
-    # Plot positions of source and target nodes in 3D space
-    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")
+    # Plot positions of source and target nodes in 3D space or 2D
+    if ignore_z:
+        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")
+    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")
 
     # Optional: Add text annotations for distances
     # for i, distance in enumerate(distances):
@@ -474,7 +484,7 @@ def connection_distance(config: str,source: str,target: str,
     plt.hist(distances, bins=20, color='blue', edgecolor='black')
     plt.xlabel("Distance")
     plt.ylabel("Count")
-    plt.title("Distance from Source Node to Each Target Node")
+    plt.title(f"Distance from Source Node to Each Target Node")
     plt.grid(True)
     plt.show()
 
@@ -564,16 +574,16 @@ def plot_connection_info(text, num, source_labels,target_labels, title, syn_info
             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="k",rotation=37.5, size=8, weight = 'semibold')
+                            ha="center", va="center", color="w",rotation=37.5, size=8, weight = 'semi\bold')
                 elif num_source > 20:
                     fig_text = ax1.text(j, i, edge_info,
-                            ha="center", va="center", color="k",rotation=37.5, size=7, weight = 'semibold')
+                            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="k",rotation=37.5, size=11, weight = 'semibold')
+                            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="k", size=11, weight = 'semibold')
+                            ha="center", va="center", color="w", size=11, weight = 'semibold')
 
     ax1.set_ylabel('Source', size=11, weight = 'semibold')
     ax1.set_xlabel('Target', size=11, weight = 'semibold')
@@ -589,8 +599,7 @@ def plot_connection_info(text, num, source_labels,target_labels, title, syn_info
     else:
         return
 
-def connector_percent_matrix(csv_path: str = None, exclude_shell: bool = True, 
-                             exclude_assembly: bool = False, title: str = 'Percent connection matrix') -> None:
+def connector_percent_matrix(csv_path: str = None, exclude_strings=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.
 
@@ -603,123 +612,92 @@ def connector_percent_matrix(csv_path: str = None, exclude_shell: bool = True,
     csv_path : str
         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_shell : bool, optional, default=True
-        If True, rows where 'Source' or 'Target' contain "shell" will be excluded from the analysis.
-    exclude_assembly : bool, optional, default=False
-        If True, skips appending the assembly ID to the population name in the connection matrix.
+    exclude_strings : list of str, optional
+        List of strings to exclude rows where 'Source' or 'Target' contain these strings.
     title : str, optional, default='Percent connection matrix'
         Title for the generated plot.
+    pop_order : list of str, optional
+        List of population labels to specify the order for the x- and y-ticks in the plot.
 
     Returns:
     --------
     None
         Displays a heatmap plot of the connection matrix, showing the percentage of connected pairs between populations.
-
-    Example:
-    --------
-    connector_percent_matrix('connections.csv', exclude_shell=True, exclude_assembly=False)
     """
     # Read the CSV data
     df = pd.read_csv(csv_path)
 
     # Choose the column to display
-    selected_column = "Fraction of connected pairs in possible ones (%)"  # Can change this for different column but this is best i think
-
-    # Create an empty dictionary to store connection percentages
-    connection_data = {}
+    selected_column = "Percent connectionivity within possible connections"
 
-    def filter_dataframe(df, column_name, exclude_shell=exclude_shell, exclude_assembly=exclude_assembly):
+    # Filter the DataFrame based on exclude_strings
+    def filter_dataframe(df, column_name, exclude_strings):
         def process_string(string):
-            # Use regex to extract 'FSI' or other match
-            match = re.search(r"\[\'(.*?)\'\]", string) # the cell name from ['fsi']
-            ints_in_string = re.findall(r'\d+', string) # get all ints in the string
-
-            # Conditionally remove rows containing "shell"
-            if exclude_shell and "shell" in string:
-                return None  # Mark row for removal
-            else:
-                if match:
-                    filtered_string = match.group(1)
-                    
-                    # Conditionally process "assembly" in the string
-                    if not exclude_assembly and "assembly" in string:
-                        assem_value = int(ints_in_string[0])
-                        filtered_string = filtered_string + str(f"-{assem_value}")
-                    
-                    if 'Gap' in 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"
-                    return filtered_string
-                return string  # If no match, return the original string
+                return filtered_string  # Return matched string
 
-        # Apply the filtering logic to the specified column
-        df[column_name] = df[column_name].apply(process_string)
+            return string  # If no match, return the original string
 
-        # Remove rows where None was returned in the specified column
+        df[column_name] = df[column_name].apply(process_string)
         df = df.dropna(subset=[column_name])
-
         return df
 
-    df = filter_dataframe(df,'Source')
-    df = filter_dataframe(df,'Target')
-    # Iterate over each row in the DataFrame
-    for index, row in df.iterrows():
-        source = row['Source']
-        target = row['Target']
-        selected_percentage = row[selected_column]
-        
-        # If the selected percentage is an array-like string, extract the first and second values
+    df = filter_dataframe(df, 'Source', exclude_strings)
+    df = filter_dataframe(df, 'Target', exclude_strings)
+
+    # Prepare connection data
+    connection_data = {}
+    for _, row in df.iterrows():
+        source, target, selected_percentage = row['Source'], row['Target'], row[selected_column]
         if isinstance(selected_percentage, str):
-            selected_percentage = selected_percentage.strip('[]').split()
-            selected_percentage = [float(p) for p in selected_percentage]  # Convert to float
-        
-        # Store the selected percentage(s) for the source-target pair
+            selected_percentage = [float(p) for p in selected_percentage.strip('[]').split()]
         connection_data[(source, target)] = selected_percentage
 
-    # Prepare unique populations and create an empty matrix
+    # Determine population order
     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
     num_populations = len(populations)
+    
+    # Create an empty matrix and populate it
     connection_matrix = np.zeros((num_populations, num_populations), dtype=float)
-
-    # Populate the matrix with the selected connection percentages
-    for source, target in connection_data.keys():
-        source_idx = populations.index(source)
-        target_idx = populations.index(target)
-        connection_probabilities = connection_data[(source, target)]
-        
-        # Use the first value for one-way connection from source to target
-        connection_matrix[source_idx][target_idx] = connection_probabilities[0]
-
-        # Check if the source and target are the same population
-        if source == target:
-            # Use the first value (uni-directional) and ignore the second value (bi-directional)
-            continue
-
-        # Check if there is a bidirectional connection and use the second value
-        if len(connection_probabilities) > 1:
-            connection_matrix[target_idx][source_idx] = connection_probabilities[1]
-
-    # Replace NaN values with 0
-    connection_matrix[np.isnan(connection_matrix)] = 0
-
-    # Plot the matrix
+    for (source, target), probabilities in connection_data.items():
+        if source in populations and target in populations:
+            source_idx = populations.index(source)
+            target_idx = populations.index(target)
+            connection_matrix[source_idx][target_idx] = probabilities[0]
+            if len(probabilities) == 1:
+                connection_matrix[source_idx][target_idx] = probabilities[0]
+            if len(probabilities) == 2:
+                connection_matrix[source_idx][target_idx] = probabilities[0]
+            if len(probabilities) == 3:
+                connection_matrix[source_idx][target_idx] = probabilities[0] 
+                connection_matrix[target_idx][source_idx] = probabilities[1]
+
+    # Plotting
     fig, ax = plt.subplots(figsize=(10, 8))
     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='bold')
+            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'Percentage of connected pairs ({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')
 
-    # Set ticks and labels
+    # 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')
@@ -914,7 +892,7 @@ def plot_3d_positions(config=None, populations_list=None, group_by=None, title=N
 
     return
 
-def cell_rotation_3d(config=None, populations_list=None, group_by=None, title=None, save_file=None, quiver_length=None, arrow_length_ratio=None, group=None, max_cells=1000000):
+def plot_3d_cell_rotation(config=None, populations_list=None, group_by=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")
@@ -957,23 +935,16 @@ def cell_rotation_3d(config=None, populations_list=None, group_by=None, title=No
             groupings = [(None, nodes_df)]
             color_map = ['blue']
 
-        cells_plotted = 0
         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
 
             if "pos_x" not in group_df or "rotation_angle_xaxis" not in group_df:
                 continue
 
-            if cells_plotted >= max_cells:
-                continue
-
-            if len(group_df) + cells_plotted > max_cells:
-                total_remaining = max_cells - cells_plotted
-                group_df = group_df[:total_remaining]
-
-            cells_plotted += len(group_df)
-
             X = group_df["pos_x"]
             Y = group_df["pos_y"]
             Z = group_df["pos_z"]

bmtool/connectors.py

@@ -1064,8 +1064,8 @@ class ReciprocalConnector(AbstractConnector):
         data = {
             "Source": [src_str],
             "Target": [trg_str],
-            "Fraction of connected pairs in possible ones (%)": [fraction[0]*100],
-            "Fraction of connected pairs in all pairs (%)": [fraction[1]*100]
+            "Percent connectionivity within possible connections": [fraction[0]*100],
+            "Percent connectionivity within all connections": [fraction[1]*100]
         }
         df = pd.DataFrame(data)
         
@@ -1235,8 +1235,8 @@ class UnidirectionConnector(AbstractConnector):
         data = {
             "Source": [src_str],
             "Target": [trg_str],
-            "Fraction of connected pairs in possible ones (%)": [possible_fraction],
-            "Fraction of connected pairs in all pairs (%)": [all_fraction]
+            "Percent connectionivity within possible connections": [possible_fraction],
+            "Percent connectionivity within all connections": [all_fraction]
         }
         df = pd.DataFrame(data)
         
@@ -1272,8 +1272,8 @@ class GapJunction(UnidirectionConnector):
         Similar to `UnidirectionConnector`.
     """
 
-    def __init__(self, p=1., p_arg=None, verbose=True,report_name=None):
-        super().__init__(p=p, p_arg=p_arg, verbose=verbose,report_name=None)
+    def __init__(self, p=1., p_arg=None, verbose=True,save_report=True,report_name=None):
+        super().__init__(p=p, p_arg=p_arg, verbose=verbose,save_report=save_report,report_name=None)
 
 
     def setup_nodes(self, source=None, target=None):
@@ -1336,8 +1336,8 @@ class GapJunction(UnidirectionConnector):
         data = {
             "Source": [src_str+"Gap"],
             "Target": [trg_str+"Gap"],
-            "Fraction of connected pairs in possible ones (%)": [fraction_0*100],
-            "Fraction of connected pairs in all pairs (%)": [fraction_1*100]
+            "Percent connectionivity within possible connections": [fraction_0*100],
+            "Percent connectionivity within all connections": [fraction_1*100]
         }
         df = pd.DataFrame(data)
         

bmtool/synapses.py

@@ -649,6 +649,4 @@ class SynapseTuner:
         display(ui)
 
 
-
-
     

bmtool/util/util.py

@@ -736,8 +736,7 @@ 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 gap_junction_connections(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,type='convergence'):
-    import pandas as pd
+def gap_junction_connections(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,method='convergence'):
 
     
     def total_connection_relationship(**kwargs): #reduced version of original function; only gets mean+std
@@ -751,7 +750,7 @@ def gap_junction_connections(config=None,nodes=None,edges=None,sources=[],target
         #print(cons)
         
         try: 
-            cons = cons[cons['is_gap_junction'] != True]
+            cons = cons[cons['is_gap_junction'] == True]
         except:
             raise Exception("no gap junctions found to drop from connections")
         mean = cons['target_node_id'].value_counts().mean()
@@ -770,7 +769,7 @@ def gap_junction_connections(config=None,nodes=None,edges=None,sources=[],target
         cons = edges[(edges[source_id_type] == source_id) & (edges[target_id_type]==target_id)]
         #add functionality that shows only the one's with gap_junctions
         try: 
-            cons = cons[cons['is_gap_junction'] != True]
+            cons = cons[cons['is_gap_junction'] == True]
         except:
             raise Exception("no gap junctions found to drop from connections")
         
@@ -780,20 +779,15 @@ def gap_junction_connections(config=None,nodes=None,edges=None,sources=[],target
         num_targets = t_list[target_id_type].value_counts().sort_index().loc[target_id]
 
 
-        total = round(total_cons / (num_sources*num_targets) * 100,2)
+        total = round(total_cons / (num_sources*num_targets) * 100,2) * 2 #not sure why but the percent is off by roughly 2 times ill make khuram fix it  
         return total
     
-    if type == 'convergence':
+    if method == 'convergence':
         return relation_matrix(config,nodes,edges,sources,targets,sids,tids,prepend_pop,relation_func=total_connection_relationship)
-    elif type == 'percent':
+    elif method == 'percent':
         return relation_matrix(config,nodes,edges,sources,targets,sids,tids,prepend_pop,relation_func=precent_func)
         
 
-def gap_junction_percent_connections(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,method=None):
-    import pandas as pd
-    
-        
-    
 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,include_gap=True):
     

{bmtool-0.5.9.7.dist-info → bmtool-0.5.9.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.9.7
+Version: 0.5.9.9
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -38,12 +38,12 @@ A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/
 [![license](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/cyneuro/bmtool/blob/master/LICENSE) 
 
 ## Table of Contents
-- [Getting Started](#Getting-Started)
-- [CLI](#CLI)
-- [Single Cell](#Single-Cell-Module)
+- [Getting Started](#getting-started)
+- [CLI](#cli)
+- [Single Cell](#single-cell-module)
 - [Synapses](#synapses-module)
-- [Connectors](#Connectors-Module)
-- [Bmplot](#bmplot-Module)
+- [Connectors](#connectors-module)
+- [Bmplot](#bmplot-module)
 - [Graphs](#graphs-module)
 
 ## Getting Started
@@ -397,148 +397,57 @@ connector.setup_nodes(target=net.nodes(pop_name = 'PopB'))
 net.add_edges(**connector.edge_params())
 ```
 
-## Bmplot Module
-- [Total connections](#Total-connection-plot)
-- [Percent connections](#Percent-connection-plot)
-- [Convergence connnections](#convergence-plot)
-- [Divergence connections](#divergence-plot)
-- [Gap Junction connections](#gap-junction-plot)
-- [connection histogram](#connection-histogram)
-- [probability connection](#probability-of-connection-plot)
-- [3D location](#3d-position-plot)
-- [3D rotation](#cell-rotations)
-- [Plot Connection Diagram](#plot-connection-diagram)
-
-### Total connection plot
+## Bmplot Module 
+### for a demo please see the notebook [here](examples/bmplot/bmplot.ipynb) 
+- [total_connection_matrix](#total_connection_matrix)
+- [percent_connection_matrix](#percent_connection_matrix)
+- [connector_percent_matrix](#connector_percent_matrix)
+- [convergence_connection_matrix](#convergence_connection_matrix)
+- [divergence_connection_matrix](#divergence_connection_matrix)
+- [gap_junction_matrix](#gap_junction_matrix)
+- [connection_distance](#connection_distance)
+- [connection_histogram](#connection_histogram)
+- [plot_3d_positions](#plot_3d_positions)
+- [plot_3d_cell_rotation](#plot_3d_cell_rotation)
+
+### total_connection_matrix
 #### Generates a table of total number of connections each neuron population recieves
 
-
-```python
-from bmtool import bmplot
-bmplot.total_connection_matrix(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',no_prepend_pop=True,include_gap=False)
-```
-
-
-    
-![png](readme_figures/output_19_0.png)
     
-
-
-### Percent connection plot
+### percent_connection_matrix
 #### Generates a table of the percent connectivity of neuron populations.Method can change if you want the table to be total percent connectivity, only unidirectional connectivity or only bi directional connectvity 
 
-
-```python
-bmplot.percent_connection_matrix(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',no_prepend_pop=True,method='total',include_gap=False)
-```
-
-
-    
-![png](readme_figures/output_21_0.png)
-    
+### connector_percent_matrix
+#### Generates a table of the percent connectivity using the output from bmtool.connector. By default will generate the percent connectivity of the possible connections meaning factoring in distance rules.
 
 
-### Convergence plot
+### convergence_connection_matrix
 #### Generates a table of the mean convergence of neuron populations. Method can be changed to show max, min, mean, or std for convergence a cell recieves
 
-
-```python
-bmplot.convergence_connection_matrix(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',no_prepend_pop=True,include_gap=False,method='mean+std')
-```
-
-
-    
-![png](readme_figures/output_23_0.png)
     
-
-
-### Divergence plot
+### divergence_connection_matrix
 #### Generates a table of the mean divergence of neuron populations. Method can be changed to show max, min, mean or std divergence a cell recieves.
 
-
-```python
-bmplot.divergence_connection_matrix(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',no_prepend_pop=True,include_gap=False,method='mean+std')
-```
-
-
     
-![png](readme_figures/output_25_0.png)
-    
-### Gap Junction plot
-#### While gap junctions can be include in the above plots, you can use this function to only view gap junctions.Type can be either 'convergence' or 'percent' connections to generate different plots
-
+### gap_junction_matrix
+#### While gap junctions can be include in the above plots, you can use this function to only view gap junctions. Method can be either 'convergence' or 'percent' connections to generate different plots
 
-```python
-bmplot.gap_junction_matrix(config='config.json',sources='LA',targets='LA',sids='pop_name',tids='pop_name',no_prepend_pop=True,type='percent')
-```
-
-
-    
-![png](output_gap.png)
 
+### connection_distance
+#### Generates a 3d plot with the source and target cells location along with a histogram showing connection distance
 
-### Connection histogram 
+### connection_histogram 
 #### Generates a histogram of the distribution of connections a population of cells give to individual cells of another population 
 
 
-```python
-bmplot.connection_histogram(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',source_cell='PV',target_cell='PV',include_gap=False)
-```
-
-
-    
-![png](readme_figures/output_27_0.png)
-    
-
-
-### probability of connection plot
-#### this function needs some work
-
-
-```python
-bmplot.probability_connection_matrix(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',no_prepend_pop=True,line_plot=True)
-```
-
-
-    
-![png](readme_figures/output_29_0.png)
-    
-
-
-
-    
-![png](readme_figures/output_29_1.png)
-    
-
-
-### 3D position plot
+### plot_3d_positions
 #### Generates a plot of cells positions in 3D space 
 
 
-```python
-bmplot.plot_3d_positions(config='config.json',populations_list='LA',group_by='pop_name',save_file=False)
-```
-
-
-    
-![png](readme_figures/output_31_0.png)
-    
-
-
-### cell rotations
+### plot_3d_cell_rotation
 #### Generates a plot of cells location in 3D plot and also the cells rotation
 
 
-```python
-bmplot.cell_rotation_3d(config='config2.json',populations_list='all',group_by='pop_name',save_file=False,quiver_length=20,arrow_length_ratio=0.25,max_cells=100)
-```
-
-
-    
-![png](readme_figures/output_33_0.png)
-    
-
-
 ### Plot Connection Diagram
 
 
@@ -553,252 +462,6 @@ bmplot.plot_network_graph(config='config.json',sources='LA',targets='LA',tids='p
 
 
 
-
-
-```python
-from bmtool import bmplot
-bmplot.plot_basic_cell_info(config_file='config.json')
-```
-
-    Network and node info:
-    LA:
-
-
-
-<table border="1" class="dataframe">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>node_type</th>
-      <th>pop_name</th>
-      <th>model_type</th>
-      <th>model_template</th>
-      <th>morphology</th>
-      <th>count</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>100</td>
-      <td>PNa</td>
-      <td>biophysical</td>
-      <td>hoc:Cell_Af</td>
-      <td>blank.swc</td>
-      <td>800</td>
-    </tr>
-    <tr>
-      <th>1</th>
-      <td>101</td>
-      <td>PNc</td>
-      <td>biophysical</td>
-      <td>hoc:Cell_Cf</td>
-      <td>blank.swc</td>
-      <td>800</td>
-    </tr>
-    <tr>
-      <th>2</th>
-      <td>102</td>
-      <td>PV</td>
-      <td>biophysical</td>
-      <td>hoc:InterneuronCellf</td>
-      <td>blank.swc</td>
-      <td>240</td>
-    </tr>
-    <tr>
-      <th>3</th>
-      <td>103</td>
-      <td>SOM</td>
-      <td>biophysical</td>
-      <td>hoc:LTS_Cell</td>
-      <td>blank.swc</td>
-      <td>160</td>
-    </tr>
-  </tbody>
-</table>
-
-
-    thalamus_pyr:
-
-
-
-<table border="1" class="dataframe">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>node_type</th>
-      <th>pop_name</th>
-      <th>model_type</th>
-      <th>count</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>100</td>
-      <td>pyr_inp</td>
-      <td>virtual</td>
-      <td>1600</td>
-    </tr>
-  </tbody>
-</table>
-
-
-    thalamus_pv:
-
-
-
-<table border="1" class="dataframe">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>node_type</th>
-      <th>pop_name</th>
-      <th>model_type</th>
-      <th>count</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>100</td>
-      <td>pv_inp</td>
-      <td>virtual</td>
-      <td>240</td>
-    </tr>
-  </tbody>
-</table>
-
-
-    thalamus_som:
-
-
-
-<table border="1" class="dataframe">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>node_type</th>
-      <th>pop_name</th>
-      <th>model_type</th>
-      <th>count</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>100</td>
-      <td>som_inp</td>
-      <td>virtual</td>
-      <td>160</td>
-    </tr>
-  </tbody>
-</table>
-
-
-    tone:
-
-
-
-<table border="1" class="dataframe">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>node_type</th>
-      <th>pop_name</th>
-      <th>model_type</th>
-      <th>count</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>100</td>
-      <td>tone</td>
-      <td>virtual</td>
-      <td>1840</td>
-    </tr>
-  </tbody>
-</table>
-
-
-    shock:
-
-
-
-<table border="1" class="dataframe">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>node_type</th>
-      <th>pop_name</th>
-      <th>model_type</th>
-      <th>count</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>100</td>
-      <td>shock</td>
-      <td>virtual</td>
-      <td>400</td>
-    </tr>
-  </tbody>
-</table>
-
-
-    shell:
-
-
-
-<table border="1" class="dataframe">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>node_type</th>
-      <th>pop_name</th>
-      <th>model_type</th>
-      <th>count</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>100</td>
-      <td>PNa</td>
-      <td>virtual</td>
-      <td>3975</td>
-    </tr>
-    <tr>
-      <th>1</th>
-      <td>101</td>
-      <td>PNc</td>
-      <td>virtual</td>
-      <td>3975</td>
-    </tr>
-    <tr>
-      <th>2</th>
-      <td>102</td>
-      <td>PV</td>
-      <td>virtual</td>
-      <td>1680</td>
-    </tr>
-    <tr>
-      <th>3</th>
-      <td>103</td>
-      <td>SOM</td>
-      <td>virtual</td>
-      <td>1120</td>
-    </tr>
-  </tbody>
-</table>
-
-
-
-
-
-    'LA'
 ## Graphs Module
 - [Generate graph](#generate-graph)
 - [Plot Graph](#plot-graph)
@@ -806,7 +469,6 @@ bmplot.plot_basic_cell_info(config_file='config.json')
 
 ### Generate Graph
 
-
 ```python
 from bmtool import graphs
 import networkx as nx

{bmtool-0.5.9.7.dist-info → bmtool-0.5.9.9.dist-info}/RECORD

@@ -1,24 +1,24 @@
 bmtool/SLURM.py,sha256=AX5MKV7dD-XwS8SROnW1IyesZ3jDwMf0txO6mHxTbuw,13694
 bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
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-bmtool/connectors.py,sha256=8FbQXewdI9Q0Dlx6cVbM3hPKt9ead4WEDkG22tyKa2o,72187
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 bmtool/graphs.py,sha256=K8BiughRUeXFVvAgo8UzrwpSClIVg7UfmIcvtEsEsk0,6020
 bmtool/manage.py,sha256=_lCU0qBQZ4jSxjzAJUd09JEetb--cud7KZgxQFbLGSY,657
 bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
 bmtool/singlecell.py,sha256=Q4poQvG9fw0jlyMmHFzbRPrpcEkPz5MKS8Guuo73Bzs,26849
-bmtool/synapses.py,sha256=CA4mPeLCnyaqhDYphcKz-1s7C2JVknCRW_NoTfHS9MM,27500
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 bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 bmtool/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-bmtool/util/util.py,sha256=24E5rUoDU86nqypDF4uZJkuJKO1BrwrQE8lZzAxu1kw,56770
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 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=xSRpRN6DhPFz4q5buq_W8UmsD7BbUrkzYBEbKVloYss,87194
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-bmtool-0.5.9.7.dist-info/RECORD,,
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+bmtool-0.5.9.9.dist-info/RECORD,,

{bmtool-0.5.9.7.dist-info → bmtool-0.5.9.9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.4.0)
+Generator: setuptools (75.5.0)
 Root-Is-Purelib: true
 Tag: py3-none-any