bmtool 0.5.2__tar.gz → 0.5.4__tar.gz

{bmtool-0.5.2/bmtool.egg-info → bmtool-0.5.4}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.2
+Version: 0.5.4
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
-Author: Tyler Banks
-Author-email: tbanks@mail.missouri.edu
+Author: Neural Engineering Laboratory at the University of Missouri
+Author-email: gregglickert@mail.missouri.edu
 License: MIT
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Education
@@ -28,6 +28,7 @@ Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: questionary
 Requires-Dist: pynmodlt
+Requires-Dist: plotly
 
 # bmtool
 A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
@@ -40,6 +41,7 @@ A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/
 - [Single Cell](#Single-Cell-Module)
 - [Connectors](#Connectors-Module)
 - [Bmplot](#bmplot-Module)
+- [Graphs](#graphs-module)
 
 ## Getting Started
 
@@ -391,6 +393,7 @@ net.add_edges(**connector.edge_params())
 - [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)
@@ -452,6 +455,17 @@ bmplot.divergence_connection_matrix(config='config.json',sources='LA',targets='L
     
 ![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')
+```
+
+
+    
+![png](output_gap.png)
 
 
 ### Connection histogram 
@@ -776,5 +790,127 @@ bmplot.plot_basic_cell_info(config_file='config.json')
 
 
     'LA'
+## Graphs Module
+- [Generate graph](#generate-graph)
+- [Plot Graph](#plot-graph)
+- [Connectioon table](#generate-graph-connection-table)
+
+### Generate Graph
+
+
+```python
+from bmtool import graphs
+import networkx as nx
+
+Graph = graphs.generate_graph(config='config.json',source='LA',target='LA')
+print("Number of nodes:", Graph.number_of_nodes())
+print("Number of edges:", Graph.number_of_edges())
+print("Node labels:", set(nx.get_node_attributes(Graph, 'label').values()))
+```
+
+    Number of nodes: 2000
+    Number of edges: 84235
+    Node labels: {'SOM', 'PNc', 'PNa', 'PV'}
+
+
+### Plot Graph
+#### Generates an interactive plot showing nodes, edges and # of connections
+
+
+```python
+graphs.plot_graph(Graph)
+```
+
+
+
+### Generate graph connection table
+#### Generates a CSV of all cells and the number of connections each individual cell receives
+
+
+```python
+import pandas as pd
+graphs.export_node_connections_to_csv(Graph, 'node_connections.csv')
+df = pd.read_csv('node_connections.csv')
+df.head()
+```
+
+
+
+
+<div>
+<style scoped>
+    .dataframe tbody tr th:only-of-type {
+        vertical-align: middle;
+    }
+
+    .dataframe tbody tr th {
+        vertical-align: top;
+    }
+
+    .dataframe thead th {
+        text-align: right;
+    }
+</style>
+<table border="1" class="dataframe">
+  <thead>
+    <tr style="text-align: right;">
+      <th></th>
+      <th>Unnamed: 0</th>
+      <th>Node Label</th>
+      <th>PNc Connections</th>
+      <th>PV Connections</th>
+      <th>SOM Connections</th>
+      <th>PNa Connections</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <th>0</th>
+      <td>0</td>
+      <td>PNa</td>
+      <td>15</td>
+      <td>11</td>
+      <td>9</td>
+      <td>6</td>
+    </tr>
+    <tr>
+      <th>1</th>
+      <td>1</td>
+      <td>PNa</td>
+      <td>24</td>
+      <td>25</td>
+      <td>6</td>
+      <td>21</td>
+    </tr>
+    <tr>
+      <th>2</th>
+      <td>2</td>
+      <td>PNa</td>
+      <td>27</td>
+      <td>28</td>
+      <td>12</td>
+      <td>25</td>
+    </tr>
+    <tr>
+      <th>3</th>
+      <td>3</td>
+      <td>PNa</td>
+      <td>19</td>
+      <td>27</td>
+      <td>15</td>
+      <td>35</td>
+    </tr>
+    <tr>
+      <th>4</th>
+      <td>4</td>
+      <td>PNa</td>
+      <td>25</td>
+      <td>11</td>
+      <td>8</td>
+      <td>16</td>
+    </tr>
+  </tbody>
+</table>
+</div>
 
 

bmtool-0.5.2/PKG-INFO → bmtool-0.5.4/README.md

@@ -1,34 +1,3 @@
-Metadata-Version: 2.1
-Name: bmtool
-Version: 0.5.2
-Summary: BMTool
-Home-page: https://github.com/cyneuro/bmtool
-Download-URL: 
-Author: Tyler Banks
-Author-email: tbanks@mail.missouri.edu
-License: MIT
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Education
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Classifier: Operating System :: OS Independent
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: bmtk
-Requires-Dist: click
-Requires-Dist: clint
-Requires-Dist: h5py
-Requires-Dist: matplotlib
-Requires-Dist: networkx
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: questionary
-Requires-Dist: pynmodlt
-
 # bmtool
 A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
 
@@ -40,6 +9,7 @@ A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/
 - [Single Cell](#Single-Cell-Module)
 - [Connectors](#Connectors-Module)
 - [Bmplot](#bmplot-Module)
+- [Graphs](#graphs-module)
 
 ## Getting Started
 
@@ -391,6 +361,7 @@ net.add_edges(**connector.edge_params())
 - [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)
@@ -452,6 +423,17 @@ bmplot.divergence_connection_matrix(config='config.json',sources='LA',targets='L
     
 ![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')
+```
+
+
+    
+![png](output_gap.png)
 
 
 ### Connection histogram 
@@ -776,5 +758,127 @@ bmplot.plot_basic_cell_info(config_file='config.json')
 
 
     'LA'
+## Graphs Module
+- [Generate graph](#generate-graph)
+- [Plot Graph](#plot-graph)
+- [Connectioon table](#generate-graph-connection-table)
+
+### Generate Graph
+
+
+```python
+from bmtool import graphs
+import networkx as nx
+
+Graph = graphs.generate_graph(config='config.json',source='LA',target='LA')
+print("Number of nodes:", Graph.number_of_nodes())
+print("Number of edges:", Graph.number_of_edges())
+print("Node labels:", set(nx.get_node_attributes(Graph, 'label').values()))
+```
+
+    Number of nodes: 2000
+    Number of edges: 84235
+    Node labels: {'SOM', 'PNc', 'PNa', 'PV'}
+
+
+### Plot Graph
+#### Generates an interactive plot showing nodes, edges and # of connections
+
+
+```python
+graphs.plot_graph(Graph)
+```
+
+
+
+### Generate graph connection table
+#### Generates a CSV of all cells and the number of connections each individual cell receives
+
+
+```python
+import pandas as pd
+graphs.export_node_connections_to_csv(Graph, 'node_connections.csv')
+df = pd.read_csv('node_connections.csv')
+df.head()
+```
+
+
+
+
+<div>
+<style scoped>
+    .dataframe tbody tr th:only-of-type {
+        vertical-align: middle;
+    }
+
+    .dataframe tbody tr th {
+        vertical-align: top;
+    }
+
+    .dataframe thead th {
+        text-align: right;
+    }
+</style>
+<table border="1" class="dataframe">
+  <thead>
+    <tr style="text-align: right;">
+      <th></th>
+      <th>Unnamed: 0</th>
+      <th>Node Label</th>
+      <th>PNc Connections</th>
+      <th>PV Connections</th>
+      <th>SOM Connections</th>
+      <th>PNa Connections</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <th>0</th>
+      <td>0</td>
+      <td>PNa</td>
+      <td>15</td>
+      <td>11</td>
+      <td>9</td>
+      <td>6</td>
+    </tr>
+    <tr>
+      <th>1</th>
+      <td>1</td>
+      <td>PNa</td>
+      <td>24</td>
+      <td>25</td>
+      <td>6</td>
+      <td>21</td>
+    </tr>
+    <tr>
+      <th>2</th>
+      <td>2</td>
+      <td>PNa</td>
+      <td>27</td>
+      <td>28</td>
+      <td>12</td>
+      <td>25</td>
+    </tr>
+    <tr>
+      <th>3</th>
+      <td>3</td>
+      <td>PNa</td>
+      <td>19</td>
+      <td>27</td>
+      <td>15</td>
+      <td>35</td>
+    </tr>
+    <tr>
+      <th>4</th>
+      <td>4</td>
+      <td>PNa</td>
+      <td>25</td>
+      <td>11</td>
+      <td>8</td>
+      <td>16</td>
+    </tr>
+  </tbody>
+</table>
+</div>
 
 

{bmtool-0.5.2 → bmtool-0.5.4}/bmtool/bmplot.py

@@ -3,7 +3,6 @@ Want to be able to take multiple plot names in and plot them all at the same tim
 https://stackoverflow.com/questions/458209/is-there-a-way-to-detach-matplotlib-plots-so-that-the-computation-can-continue
 """
 from .util import util
-
 import argparse,os,sys
 
 import numpy as np
@@ -267,6 +266,82 @@ 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'):
+    """
+    Generates connection plot displaying gap junction data.
+    config: A BMTK simulation config 
+    sources: network name(s) to plot
+    targets: network name(s) to plot
+    sids: source node identifier 
+    tids: target node identifier
+    no_prepend_pop: dictates if population name is displayed before sid or tid when displaying graph
+    save_file: If plot should be saved
+    type:'convergence' or 'percent' connections
+    """
+    if not config:
+        raise Exception("config not defined")
+    if not sources or not targets:
+        raise Exception("Sources or targets not defined")
+    if type !='convergence' and type!='percent':
+        raise Exception("type must be 'convergence' or 'percent'")
+    sources = sources.split(",")
+    targets = targets.split(",")
+    if sids:
+        sids = sids.split(",")
+    else:
+        sids = []
+    if tids:
+        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)
+    
+    
+    def filter_rows(syn_info, data, source_labels, target_labels):
+        new_syn_info = syn_info
+        new_data = data
+        new_source_labels = source_labels
+        new_target_labels = target_labels
+        for row in new_data:
+            row_index = -1
+            try:
+                if((np.isnan(row).all())): #checks if all of a row is nan
+                    row_index = np.where(np.isnan(new_data)==np.isnan(row))[0][0]  
+            except:
+                row_index = -1
+            finally:          
+                if(all(x==0 for x in row)): #checks if all of a row is zeroes
+                    row_index = np.where(new_data==row)[0][0] 
+                if row_index!=-1:   #deletes corresponding row accordingly in all relevant variables.
+                    new_syn_info = np.delete(new_syn_info,row_index,0) 
+                    new_data = np.delete(new_data,row_index,0)
+                    new_source_labels = np.delete(new_source_labels,row_index)
+        return new_syn_info, new_data,new_source_labels,new_target_labels
+
+    def filter_rows_and_columns(syn_info,data,source_labels,target_labels):
+        syn_info, data, source_labels, target_labels = filter_rows(syn_info, data, source_labels, target_labels)
+        transposed_syn_info = np.transpose(syn_info) #transpose everything and put it in to make sure columns get filtered
+        transposed_data = np.transpose(data)
+        transposed_source_labels = target_labels
+        transposed_target_labels = source_labels
+        syn_info, data, source_labels, target_labels = filter_rows(transposed_syn_info, transposed_data, transposed_source_labels, transposed_target_labels)
+        filtered_syn_info = np.transpose(syn_info) #transpose everything back to original order after filtering.
+        filtered_data = np.transpose(data)
+        filtered_source_labels = target_labels
+        filtered_target_labels = source_labels
+        return filtered_syn_info,filtered_data,filtered_source_labels,filtered_target_labels
+    
+    syn_info, data, source_labels, target_labels = filter_rows_and_columns(syn_info, data, source_labels, target_labels)
+
+    if title == None or title=="":
+        title = 'Gap Junction'
+        if type == 'convergence':
+            title+=' Syn Convergence'
+        elif type == 'percent':
+            title+=' Percent Connectivity'
+    plot_connection_info(syn_info,data,source_labels,target_labels,title, save_file=save_file)
+    return
+    
 def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[],sids=[],tids=[],prepend_pop=True,synaptic_info='0',
                       source_cell = None,target_cell = None,include_gap=True):
     """
@@ -292,10 +367,15 @@ def connection_histogram(config=None,nodes=None,edges=None,sources=[],targets=[]
             if include_gap == False:
                 temp = temp[temp['is_gap_junction'] != True]
             node_pairs = temp.groupby('target_node_id')['source_node_id'].count()
-            conn_mean = statistics.mean(node_pairs.values)
-            conn_std = statistics.stdev(node_pairs.values)
-            conn_median = statistics.median(node_pairs.values)
-            label = "mean {:.2f} std ({:.2f}) median {:.2f}".format(conn_mean,conn_std,conn_median)
+            try:
+                conn_mean = statistics.mean(node_pairs.values)
+                conn_std = statistics.stdev(node_pairs.values)
+                conn_median = statistics.median(node_pairs.values)
+                label = "mean {:.2f} std ({:.2f}) median {:.2f}".format(conn_mean,conn_std,conn_median)
+            except: # lazy fix for std not calculated with 1 node
+                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.legend()
             plt.xlabel("# of conns from {} to {}".format(source_cell,target_cell))
@@ -420,6 +500,89 @@ def plot_connection_info(text, num, source_labels,target_labels, title, syn_info
         plt.savefig(save_file)
     return
 
+def connector_percent_matrix(csv_path = None):
+    """
+    useful because can display percent connectivity factoring in distance easily 
+    Generates a connection matrix from the output of bmtool.connector
+    csv: An output csv from the bmtool.connector classes see function save_connection_report() in that module
+    returns: connection matrix plot
+    """
+    # Read the CSV data
+    df = pd.read_csv(csv_path)
+
+    # Choose the column to display
+    selected_column = "Fraction of connected pairs in possible ones (%)"  # Change this to the desired column name
+
+    # Create an empty dictionary to store connection percentages
+    connection_data = {}
+
+    # 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
+        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
+        connection_data[(source, target)] = selected_percentage
+
+    # Prepare unique populations and create an empty matrix
+    populations = sorted(list(set(df['Source'].unique()) | set(df['Target'].unique())))
+    num_populations = len(populations)
+    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
+    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')
+
+    # Add colorbar
+    plt.colorbar(im, label=f'Percentage of connected pairs ({selected_column})')
+
+    # Set title and axis labels
+    ax.set_title('Neuronal Connection Matrix')
+    ax.set_xlabel('Target Population')
+    ax.set_ylabel('Source Population')
+
+    # Set ticks and labels
+    ax.set_xticks(np.arange(num_populations))
+    ax.set_yticks(np.arange(num_populations))
+    ax.set_xticklabels(populations, rotation=45, ha="right", size=12, weight='semibold')
+    ax.set_yticklabels(populations, size=12, weight='semibold')
+
+    plt.tight_layout()
+    plt.show()
+
 def raster_old(config=None,title=None,populations=['hippocampus']):
     """
     old function probs dep