bmtool 0.5.9.6__py3-none-any.whl → 0.5.9.8__py3-none-any.whl

bmtool/bmplot.py

@@ -12,6 +12,7 @@ import matplotlib.cm as cmx
 import matplotlib.colors as colors
 import matplotlib.gridspec as gridspec
 from mpl_toolkits.mplot3d import Axes3D
+from matplotlib.axes import Axes
 from IPython import get_ipython
 from IPython.display import display, HTML
 import statistics
@@ -19,8 +20,10 @@ import pandas as pd
 import os
 import sys
 import re
+from typing import Optional, Dict
+from .analysis.spikes import load_spikes_to_df
 
-from .util.util import CellVarsFile #, missing_units
+from .util.util import CellVarsFile,load_nodes_from_config #, missing_units
 from bmtk.analyzer.utils import listify
 
 use_description = """
@@ -271,7 +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 
@@ -287,7 +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(",")
@@ -299,7 +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):
@@ -347,7 +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
@@ -376,15 +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
@@ -403,10 +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.
@@ -418,11 +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")
@@ -430,8 +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]
@@ -447,16 +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):
@@ -471,7 +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()
 
@@ -725,82 +738,92 @@ def connector_percent_matrix(csv_path: str = None, exclude_shell: bool = True,
     plt.tight_layout()
     plt.show()
 
-def raster_old(config=None,title=None,populations=['hippocampus']):
-    """
-    old function probs dep
-    """
-    conf = util.load_config(config)
-    spikes_path = os.path.join(conf["output"]["output_dir"],conf["output"]["spikes_file"])
-    nodes = util.load_nodes_from_config(config)
-    plot_spikes(nodes,spikes_path)
-    return
-
-def raster(config=None,title=None,population=None,group_key='pop_name'):
-    """
-    old function probs dep or more to new spike module?
+def raster(spikes_df: Optional[pd.DataFrame] = None, config: Optional[str] = None, network_name: Optional[str] = None, 
+           ax: Optional[Axes] = None,tstart: Optional[float] = None,tstop: Optional[float] = None,
+           color_map: Optional[Dict[str, str]] = None) -> Axes:
     """
-    conf = util.load_config(config)
+    Plots a raster plot of neural spikes, with different colors for each population.
     
-    cells_file = conf["networks"]["nodes"][0]["nodes_file"]
-    cell_types_file = conf["networks"]["nodes"][0]["node_types_file"]
-    spikes_path = os.path.join(conf["output"]["output_dir"],conf["output"]["spikes_file"])
-
-    from bmtk.analyzer.visualization import spikes
-    spikes.plot_spikes(cells_file,cell_types_file,spikes_path,population=population,group_key=group_key)
-    return
-
-def plot_spikes(nodes, spikes_file,save_file=None):   
-    """
-    old function probs dep
+    Parameters:
+    ----------
+    spikes_df : pd.DataFrame, optional
+        DataFrame containing spike data with columns 'timestamps', 'node_ids', and optional 'pop_name'.
+    config : str, optional
+        Path to the configuration file used to load node data.
+    network_name : str, optional
+        Specific network name to select from the configuration; if not provided, uses the first network.
+    ax : matplotlib.axes.Axes, optional
+        Axes on which to plot the raster; if None, a new figure and axes are created.
+    tstart : float, optional
+        Start time for filtering spikes; only spikes with timestamps greater than `tstart` will be plotted.
+    tstop : float, optional
+        Stop time for filtering spikes; only spikes with timestamps less than `tstop` will be plotted.
+    color_map : dict, optional
+        Dictionary specifying colors for each population. Keys should be population names, and values should be color values.
+    
+    Returns:
+    -------
+    matplotlib.axes.Axes
+        Axes with the raster plot.
+    
+    Notes:
+    -----
+    - If `config` is provided, the function merges population names from the node data with `spikes_df`.
+    - Each unique population (`pop_name`) in `spikes_df` will be represented by a different color if `color_map` is not specified.
+    - If `color_map` is provided, it should contain colors for all unique `pop_name` values in `spikes_df`.
     """
-    import h5py
-
-    spikes_h5 = h5py.File(spikes_file, 'r')
-    spike_gids = np.array(spikes_h5['/spikes/gids'], dtype=np.uint)
-    spike_times = np.array(spikes_h5['/spikes/timestamps'], dtype=np.float)
+    # Initialize axes if none provided
+    if ax is None:
+        _, ax = plt.subplots(1, 1)
+
+    # Filter spikes by time range if specified
+    if tstart is not None:
+        spikes_df = spikes_df[spikes_df['timestamps'] > tstart]
+    if tstop is not None:
+        spikes_df = spikes_df[spikes_df['timestamps'] < tstop]
+
+    # Load and merge node population data if config is provided
+    if config:
+        nodes = load_nodes_from_config(config)
+        if network_name:
+            nodes = nodes.get(network_name, {})
+        else:
+            nodes = list(nodes.values())[0] if nodes else {}
+            print("Grabbing first network; specify a network name to ensure correct node population is selected.")
         
-    spikes = np.rot90(np.vstack((spike_gids,spike_times))) # Make array [[gid spiketime],[gid2 spiketime2]]
+        # Find common columns, but exclude the join key from the list
+        common_columns = spikes_df.columns.intersection(nodes.columns).tolist()
+        common_columns = [col for col in common_columns if col != 'node_ids']  # Remove our join key from the common list
 
-    #spikes = spikes[spikes[:,0].argsort()] # Sort by cell number
+        # Drop all intersecting columns except the join key column from df2
+        spikes_df = spikes_df.drop(columns=common_columns)
+        # merge nodes and spikes df
+        spikes_df = spikes_df.merge(nodes['pop_name'], left_on='node_ids', right_index=True, how='left')
 
-    """
-    Author: Tyler Banks
-    Loop through all spike files, create a list of when each cell spikes, plot.
-    """
-   
-    cell_types = ['EC','CA3e','CA3o','CA3b','DGg','DGh','DGb']
-    cell_nums = [30,63,8,8,384,32,32]
-    d = [[] for _ in range(sum(cell_nums))]
-    
-    color_picker=['red','orange','yellow','green','blue','purple','black']
-    colors = []
-    offset=0
-    
-    for i, row in enumerate(spikes):
-        d[int(row[0])+offset].append(row[1])
-            
-    for i, n in enumerate(cell_nums):
-        for _ in range(n):
-            colors.append(color_picker[i])
-        
-    fig, axs = plt.subplots(1,1)
-    axs.eventplot(d,colors=colors)
-    axs.set_title('Hipp BMTK')
-    axs.set_ylabel('Cell Number')
-    axs.set_xlabel('Time (ms)')
-    axs.legend(cell_types[::-1])
-    
-    leg = axs.get_legend()
-    for i,c in enumerate(color_picker):
-        leg.legendHandles[-i-1].set_color(c)
+
+    # Get unique population names
+    unique_pop_names = spikes_df['pop_name'].unique()
     
-    #splt.savefig('raster3_after_pycvode_fixes.png')
-    if save_file:
-        plt.savefig(save_file)
+    # Generate colors if no color_map is provided
+    if color_map is None:
+        cmap = plt.get_cmap('tab10')  # Default colormap
+        color_map = {pop_name: cmap(i / len(unique_pop_names)) for i, pop_name in enumerate(unique_pop_names)}
+    else:
+        # Ensure color_map contains all population names
+        missing_colors = [pop for pop in unique_pop_names if pop not in color_map]
+        if missing_colors:
+            raise ValueError(f"color_map is missing colors for populations: {missing_colors}")
     
-    plt.draw()
+    # Plot each population with its specified or generated color
+    for pop_name, group in spikes_df.groupby('pop_name'):
+        ax.scatter(group['timestamps'], group['node_ids'], label=pop_name, color=color_map[pop_name], s=0.5)
+
+    # Label axes
+    ax.set_xlabel("Time")
+    ax.set_ylabel("Node ID")
+    ax.legend(title="Population", loc='upper right', framealpha=0.9, markerfirst=False)
     
-    return
+    return ax
     
 def plot_3d_positions(config=None, populations_list=None, group_by=None, title=None, save_file=None, subset=None):
     """
@@ -901,7 +924,7 @@ 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")
@@ -944,23 +967,16 @@ 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

@@ -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):

bmtool/synapses.py

@@ -115,7 +115,7 @@ class SynapseTuner:
         - `set_up_cell()` should be called before setting up the synapse.
         - Synapse location, type, and properties are specified within `spec_syn_param` and `spec_settings`.
         """
-        self.syn = getattr(h, self.conn['spec_syn_param']['level_of_detail'])(list(self.cell.all)[self.conn['spec_settings']['sec_id']](self.conn['spec_settings']['sec_x']))
+        self.syn = getattr(h, self.conn['spec_settings']['level_of_detail'])(list(self.cell.all)[self.conn['spec_settings']['sec_id']](self.conn['spec_settings']['sec_x']))
         for key, value in self.conn['spec_syn_param'].items():
             if isinstance(value, (int, float)):  # Only create sliders for numeric values
                 if hasattr(self.syn, key):

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-0.5.9.6.dist-info → bmtool-0.5.9.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.9.6
+Version: 0.5.9.8
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -38,11 +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)
-- [Connectors](#Connectors-Module)
-- [Bmplot](#bmplot-Module)
+- [Getting Started](#getting-started)
+- [CLI](#cli)
+- [Single Cell](#single-cell-module)
+- [Synapses](#synapses-module)
+- [Connectors](#connectors-module)
+- [Bmplot](#bmplot-module)
 - [Graphs](#graphs-module)
 
 ## Getting Started
@@ -335,6 +336,12 @@ bmtool util cell --hoc segmented_template.hoc vhsegbuild
 ```
 ex: [https://github.com/tjbanks/two-cell-hco](https://github.com/tjbanks/two-cell-hco)
 
+### Synapses Module
+-[SynapticTuner](#synaptictuner)
+
+#### SynapticTuner - Aids in the tuning of synapses by printing out synaptic properties and giving the user sliders in a Jupyter notebook to tune the synapse. For more info view the example [here](examples/synapses/synaptic_tuner.ipynb)
+
+
 ### Connectors Module
 - [UnidirectionConnector](#unidirectional-connector---unidirectional-connections-in-bmtk-network-model-with-given-probability-within-a-single-population-or-between-two-populations)
 - [ReciprocalConnector](#recipical-connector---buiilding-connections-in-bmtk-network-model-with-reciprocal-probability-within-a-single-population-or-between-two-populations)
@@ -390,148 +397,53 @@ 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
-#### 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)
-```
+## 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)
+- [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
 
     
-![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)
-    
-
-
-### 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
-
-
-```python
-bmplot.gap_junction_matrix(config='config.json',sources='LA',targets='LA',sids='pop_name',tids='pop_name',no_prepend_pop=True,type='percent')
-```
+### 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
 
 
-    
-![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
 
 
@@ -546,252 +458,6 @@ 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)
@@ -799,7 +465,6 @@ bmplot.plot_basic_cell_info(config_file='config.json')
 
 ### Generate Graph
 
-
 ```python
 from bmtool import graphs
 import networkx as nx

{bmtool-0.5.9.6.dist-info → bmtool-0.5.9.8.dist-info}/RECORD

@@ -1,24 +1,24 @@
 bmtool/SLURM.py,sha256=AX5MKV7dD-XwS8SROnW1IyesZ3jDwMf0txO6mHxTbuw,13694
 bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
 bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
-bmtool/bmplot.py,sha256=pdwj1BG-NjVKb3sb-Sya2_9AjkqMm_iooQbEOuy5l3w,50931
-bmtool/connectors.py,sha256=8FbQXewdI9Q0Dlx6cVbM3hPKt9ead4WEDkG22tyKa2o,72187
+bmtool/bmplot.py,sha256=VoX-oXqu6dRb3JEUgGxWiX23JxUy9PeemE7z4f6hVbY,53177
+bmtool/connectors.py,sha256=QEaBGc6mEoQc-H3ltjvjn5-XWyYgnrhcfNRblVOUE2A,72228
 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=wKLVGSnsDu_9cJGZoZTeO-RYqRQoZ-Q_LLYHi4fJkmg,27501
+bmtool/synapses.py,sha256=CA4mPeLCnyaqhDYphcKz-1s7C2JVknCRW_NoTfHS9MM,27500
 bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/debug/commands.py,sha256=AwtcR7BUUheM0NxvU1Nu234zCdpobhJv5noX8x5K2vY,583
 bmtool/debug/debug.py,sha256=xqnkzLiH3s-tS26Y5lZZL62qR2evJdi46Gud-HzxEN4,207
 bmtool/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/commands.py,sha256=zJF-fiLk0b8LyzHDfvewUyS7iumOxVnj33IkJDzux4M,64396
-bmtool/util/util.py,sha256=24E5rUoDU86nqypDF4uZJkuJKO1BrwrQE8lZzAxu1kw,56770
+bmtool/util/util.py,sha256=00vOAwTVIifCqouBoFoT0lBashl4fCalrk8fhg_Uq4c,56654
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=xSRpRN6DhPFz4q5buq_W8UmsD7BbUrkzYBEbKVloYss,87194
-bmtool-0.5.9.6.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.5.9.6.dist-info/METADATA,sha256=XtYX2dO9qDsTeqdoaZno_AUR1ZGsqygkz7BI0hnOaxQ,24131
-bmtool-0.5.9.6.dist-info/WHEEL,sha256=a7TGlA-5DaHMRrarXjVbQagU3Man_dCnGIWMJr5kRWo,91
-bmtool-0.5.9.6.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.5.9.6.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.5.9.6.dist-info/RECORD,,
+bmtool-0.5.9.8.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.5.9.8.dist-info/METADATA,sha256=rrR39yoM5X0WSk15L0KZV3KoRFqwt5KAmwMXW-apI_c,18823
+bmtool-0.5.9.8.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
+bmtool-0.5.9.8.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.5.9.8.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.5.9.8.dist-info/RECORD,,

{bmtool-0.5.9.6.dist-info → bmtool-0.5.9.8.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