bmtool 0.5.2__tar.gz → 0.5.3__tar.gz

{bmtool-0.5.2/bmtool.egg-info → bmtool-0.5.3}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.2
+Version: 0.5.3
 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-0.5.3/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-0.5.3}/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):
     """