bmtool 0.5.1__tar.gz → 0.5.3__tar.gz

{bmtool-0.5.1 → bmtool-0.5.3}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.1
+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
 
@@ -230,8 +232,8 @@ X, Y = run_and_plot(sim)
 plt.show()
 ```
 
-    Injection location: Cell_Cf[23].soma[0](0.5)
-    Recording: Cell_Cf[23].soma[0](0.5)._ref_v
+    Injection location: Cell_Cf[22].soma[0](0.5)
+    Recording: Cell_Cf[22].soma[0](0.5)._ref_v
     ZAP current simulation running...
     
     Chirp current injection with frequency changing from 0 to 15 Hz over 15 seconds
@@ -350,21 +352,21 @@ background = NetworkBuilder('background')
 background.add_nodes(N=300,pop_name='tON',potential='exc',model_type='virtual')
 ```
 
-#### Unidirectional connector - unidirectional connections in bmtk network model with given probability within a single population (or between two populations)
+#### Unidirectional connector - Object for building unidirectional connections in bmtk network model with given probability within a single population (or between two populations).
 ```python
 from bmtool.connectors  import UnidirectionConnector
 connector = UnidirectionConnector(p=0.15, n_syn=1)
 connector.setup_nodes(source=net.nodes(pop_name = 'PopA'), target=net.nodes(pop_name = 'PopB'))
 net.add_edges(**connector.edge_params())
 ```
-#### Recipical connector - buiilding connections in bmtk network model with reciprocal probability within a single population (or between two populations
+#### Recipical connector - Object for building connections in bmtk network model with reciprocal probability within a single population (or between two populations)
 ```python
 from bmtool.connectors  import ReciprocalConnector
 connector = ReciprocalConnector(p0=0.15, pr=0.06767705087, n_syn0=1, n_syn1=1,estimate_rho=False)
 connector.setup_nodes(source=net.nodes(pop_name = 'PopA'), target=net.nodes(pop_name = 'PopA'))
 net.add_edges(**connector.edge_params())
 ```
-#### CorrelatedGapJunction
+#### CorrelatedGapJunction - Object for building gap junction connections in bmtk network model with given probabilities within a single population which could be correlated with the recurrent chemical synapses in this population.
 ```python
 from bmtool.connectors import ReciprocalConnector, CorrelatedGapJunction
 connector = ReciprocalConnector(p0=0.15, pr=0.06, n_syn0=1, n_syn1=1, estimate_rho=False)
@@ -376,7 +378,7 @@ conn = net.add_edges(is_gap_junction=True, syn_weight=0.0000495, target_sections
 **gap_junc.edge_params())
 ```
 
-#### OneToOneSequentialConnector
+#### OneToOneSequentialConnector - Object for building one to one correspondence connections in bmtk network model with between two populations. One of the population can consist of multiple sub-populations.
 ```python
 from bmtool.connectors  import OneToOneSequentialConnector
 connector = OneToOneSequentialConnector()
@@ -391,10 +393,12 @@ 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)
 - [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
@@ -402,7 +406,7 @@ net.add_edges(**connector.edge_params())
 
 ```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)
+bmplot.total_connection_matrix(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',no_prepend_pop=True,include_gap=False)
 ```
 
 
@@ -412,11 +416,11 @@ bmplot.total_connection_matrix(config='config.json',sources='LA',targets='LA',ti
 
 
 ### Percent connection plot
-#### Generates a table of the percent connectivity of neuron populations.Method can change if you want the table to be total percent connectivity or only unidirectional connectivity or only bi directional connectvity 
+#### 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')
+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)
 ```
 
 
@@ -426,11 +430,11 @@ bmplot.percent_connection_matrix(config='config.json',sources='LA',targets='LA',
 
 
 ### Convergence plot
-#### Generates a table of the mean convergence of neuron populations. Method can be changed to show max,and min convergence a cell recieves and also changed to show standard deviation of convergence
+#### 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)
+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')
 ```
 
 
@@ -440,17 +444,28 @@ bmplot.convergence_connection_matrix(config='config.json',sources='LA',targets='
 
 
 ### Divergence plot
-#### Generates a table of the mean divergence of neuron populations. Method can be changed to show max,and min divergence a cell recieves and also changed to show standard deviation of divergence
+#### 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')
+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)
+![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 
@@ -458,7 +473,7 @@ bmplot.divergence_connection_matrix(config='config.json',sources='LA',targets='L
 
 
 ```python
-bmplot.connection_histogram(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',source_cell='PNa',target_cell='PV')
+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)
 ```
 
 
@@ -476,17 +491,14 @@ bmplot.probability_connection_matrix(config='config.json',sources='LA',targets='
 ```
 
 
-
-
-
     
-![png](readme_figures/output_29_1.png)
+![png](readme_figures/output_29_0.png)
     
 
 
 
     
-![png](readme_figures/output_29_2.png)
+![png](readme_figures/output_29_1.png)
     
 
 
@@ -517,3 +529,388 @@ bmplot.cell_rotation_3d(config='config2.json',populations_list='all',group_by='p
 ![png](readme_figures/output_33_0.png)
     
 
+
+### Plot Connection Diagram
+
+
+```python
+bmplot.plot_network_graph(config='config.json',sources='LA',targets='LA',tids='pop_name',sids='pop_name',no_prepend_pop=True)
+```
+
+
+    
+![png](readme_figures/output_35_0.png)
+    
+
+
+
+
+
+```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)
+- [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>
+
+