bmtool 0.5.9.7__py3-none-any.whl → 0.5.9.8__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()
 
@@ -914,7 +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")
@@ -957,23 +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/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-0.5.9.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.9.7
+Version: 0.5.9.8
 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 +397,53 @@ 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
 
 
@@ -553,252 +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)
@@ -806,7 +465,6 @@ bmplot.plot_basic_cell_info(config_file='config.json')
 
 ### Generate Graph
 
-
 ```python
 from bmtool import graphs
 import networkx as nx

{bmtool-0.5.9.7.dist-info → bmtool-0.5.9.8.dist-info}/RECORD

@@ -1,8 +1,8 @@
 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=otTOwFwOY9TTX5jaOcaTzari4wx6hVI_Is0GrezD_2Y,52717
-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
@@ -13,12 +13,12 @@ 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-0.5.9.7.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.5.9.7.dist-info/METADATA,sha256=DgDwAN9aw0lw6DXI312P-Bi2nP6OTdo-4CNEnAfQJtA,24455
-bmtool-0.5.9.7.dist-info/WHEEL,sha256=a7TGlA-5DaHMRrarXjVbQagU3Man_dCnGIWMJr5kRWo,91
-bmtool-0.5.9.7.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.5.9.7.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.5.9.7.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-0.5.9.7.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