bmtool 0.6.9.16__py3-none-any.whl → 0.6.9.18__py3-none-any.whl

bmtool/bmplot.py

@@ -35,7 +35,17 @@ python -m bmtool.plot
 
 def is_notebook() -> bool:
     """
-    Used to tell if inside jupyter notebook or not. This is used to tell if we should use plt.show or not
+    Detect if code is running in a Jupyter notebook environment.
+    
+    Returns:
+    --------
+    bool
+        True if running in a Jupyter notebook, False otherwise.
+        
+    Notes:
+    ------
+    This is used to determine whether to call plt.show() explicitly or
+    rely on Jupyter's automatic display functionality.
     """
     try:
         shell = get_ipython().__class__.__name__
@@ -48,18 +58,42 @@ def is_notebook() -> bool:
     except NameError:
         return False      # Probably standard Python interpreter
 
-def total_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None,no_prepend_pop=False,save_file=None,synaptic_info='0',include_gap=True):
+def total_connection_matrix(config=None, title=None, sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False, save_file=None, synaptic_info='0', include_gap=True):
     """
-    Generates connection plot displaying total connection or other stats
-    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
-    synaptic_info: '0' for total connections, '1' for mean and stdev connections, '2' for all synapse .mod files used, '3' for all synapse .json files used
-    include_gap: Determines if connectivity shown should include gap junctions + chemical synapses. False will only include chemical
+    Generate a plot displaying total connections or other synaptic statistics.
+    
+    Parameters:
+    -----------
+    config : str
+        Path to a BMTK simulation config file.
+    title : str, optional
+        Title for the plot. If None, a default title will be used.
+    sources : str
+        Comma-separated string of network names to use as sources.
+    targets : str
+        Comma-separated string of network names to use as targets.
+    sids : str, optional
+        Comma-separated string of source node identifiers to filter.
+    tids : str, optional
+        Comma-separated string of target node identifiers to filter.
+    no_prepend_pop : bool, optional
+        If True, don't display population name before sid or tid in the plot.
+    save_file : str, optional
+        Path to save the plot. If None, plot is not saved.
+    synaptic_info : str, optional
+        Type of information to display:
+        - '0': Total connections (default)
+        - '1': Mean and standard deviation of connections
+        - '2': All synapse .mod files used
+        - '3': All synapse .json files used
+    include_gap : bool, optional
+        If True, include gap junctions and chemical synapses in the analysis.
+        If False, only include chemical synapses.
+        
+    Returns:
+    --------
+    None
+        The function generates and displays a plot.
     """
     if not config:
         raise Exception("config not defined")
@@ -596,7 +630,7 @@ def edge_histogram_matrix(config=None,sources = None,targets=None,sids=None,tids
     report : str, optional
         Name of the report to analyze.
     title : str, optional
-        Custom title for the plot. If None, defaults to "{edge_property} Histogram Matrix".
+        Custom title for the plot.
     save_file : str, optional
         Path to save the generated plot.
     

bmtool/connectors.py

@@ -17,7 +17,21 @@ report_name = 'conn.csv'
 
 # Utility Functions
 def num_prop(ratio, N):
-    """Calculate numbers of total N in proportion to ratio"""
+    """
+    Calculate numbers of total N in proportion to ratio.
+    
+    Parameters:
+    -----------
+    ratio : array-like
+        Proportions to distribute N across.
+    N : int
+        Total number to distribute.
+        
+    Returns:
+    --------
+    numpy.ndarray
+        Array of integers that sum to N, proportionally distributed according to ratio.
+    """
     ratio = np.asarray(ratio)
     p = np.cumsum(np.insert(ratio.ravel(), 0, 0))  # cumulative proportion
     return np.diff(np.round(N / p[-1] * p).astype(int)).reshape(ratio.shape)
@@ -25,9 +39,20 @@ def num_prop(ratio, N):
 
 def decision(prob, size=None):
     """
-    Make single random decision based on input probability.
-    prob: scalar input
-    Return bool array if size specified, otherwise scalar
+    Make random decision(s) based on input probability.
+    
+    Parameters:
+    -----------
+    prob : float
+        Probability threshold between 0 and 1.
+    size : int or tuple, optional
+        Size of the output array. If None, a single decision is returned.
+        
+    Returns:
+    --------
+    bool or numpy.ndarray
+        Boolean result(s) of the random decision(s). True if the random number
+        is less than prob, False otherwise.
     """
     return rng.random(size) < prob
 
@@ -35,8 +60,17 @@ def decision(prob, size=None):
 def decisions(prob):
     """
     Make multiple random decisions based on input probabilities.
-    prob: iterable
-    Return bool array of the same shape
+    
+    Parameters:
+    -----------
+    prob : array-like
+        Array of probability thresholds between 0 and 1.
+        
+    Returns:
+    --------
+    numpy.ndarray
+        Boolean array with the same shape as prob, containing results of 
+        the random decisions.
     """
     prob = np.asarray(prob)
     return rng.random(prob.shape) < prob
@@ -130,26 +164,36 @@ def gaussian(x, mean=0., stdev=1., pmax=NORM_COEF):
 
 class GaussianDropoff(DistantDependentProbability):
     """
-    Object for calculating connection probability following a Gaussian function
-    of the distance between cells, using spherical or cylindrical distance.
-
+    Connection probability class that follows a Gaussian function of distance.
+    
+    This class calculates connection probabilities using a Gaussian function
+    of the distance between cells, with options for spherical or cylindrical metrics.
+    
     Parameters:
-        mean, stdev: Parameters for the Gaussian function.
-        min_dist, max_dist: Distance range for any possible connection,
-            the support of the Gaussian function.
-        pmax: The maximum value of the Gaussian function at its mean parameter.
-        ptotal: Overall probability within distance range. If specified, ignore
-            input pmax, and calculate pmax. See calc_pmax_from_ptotal() method.
-        ptotal_dist_range: Distance range for calculating pmax when ptotal is
-        specified. If not specified, set to range (min_dist, max_dist).
-        dist_type: 'spherical' or 'cylindrical' for distance metric.
-            Used when ptotal is specified.
-
-    Returns:
-        A callable object. When called with a single distance input,
-        returns the probability value.
-
-    TODO: Accept convergence and cell density information for calculating pmax.
+    -----------
+    mean : float, optional
+        Mean parameter of the Gaussian function, typically 0 for peak at origin.
+    stdev : float, optional
+        Standard deviation parameter controlling the width of the Gaussian.
+    min_dist : float, optional
+        Minimum distance for connections. Below this distance, probability is zero.
+    max_dist : float, optional
+        Maximum distance for connections. Above this distance, probability is zero.
+    pmax : float, optional
+        Maximum probability value at the peak of the Gaussian function.
+    ptotal : float, optional
+        Overall connection probability within the specified distance range.
+        If provided, pmax is calculated to achieve this overall probability.
+    ptotal_dist_range : tuple, optional
+        Distance range (min_dist, max_dist) for calculating pmax when ptotal is provided.
+    dist_type : str, optional
+        Distance metric to use, either 'spherical' (default) or 'cylindrical'.
+        
+    Notes:
+    ------
+    When ptotal is specified, the maximum probability (pmax) is calculated to achieve
+    the desired overall connection probability within the specified distance range,
+    assuming homogeneous cell density.
     """
 
     def __init__(self, mean=0., stdev=1., min_dist=0., max_dist=np.inf,

bmtool/graphs.py

@@ -4,12 +4,24 @@ import bmtool.util.util as u
 import pandas as pd
 
 
-def generate_graph(config,source,target):
+def generate_graph(config, source, target):
     """
-    returns a graph object
-    config: A BMTK simulation config 
-    source: network name 
-    target: network name
+    Generate a NetworkX graph from BMTK network configuration.
+    
+    Parameters:
+    -----------
+    config : str
+        Path to a BMTK simulation config file.
+    source : str
+        Network name for source nodes.
+    target : str
+        Network name for target nodes.
+        
+    Returns:
+    --------
+    nx.DiGraph
+        A directed graph representing the network with nodes containing 
+        position and population information.
     """
     nodes,edges = u.load_nodes_edges_from_config(config)
     nodes_source = nodes[source]
@@ -131,11 +143,24 @@ def generate_graph(config,source,target):
 
 def export_node_connections_to_csv(Graph, filename):
     """
-    Generates a CSV file with node type and all outgoing connections that node has.
+    Generate a CSV file with node type and all incoming connections that node has.
     
     Parameters:
-    Graph: a DiGraph object (directed graph)
-    filename: A string for the name of output, must end in .csv
+    -----------
+    Graph : nx.DiGraph
+        A directed graph object from NetworkX.
+    filename : str
+        Path and filename for the output CSV file (must end in .csv).
+        
+    Returns:
+    --------
+    None
+        The function saves the results to the specified CSV file.
+        
+    Notes:
+    ------
+    The resulting CSV file will have the node label as the first column,
+    followed by columns for each type of incoming connection.
     """
     # Create an empty dictionary to store the connections for each node
     node_connections = {}

bmtool-0.6.9.18.dist-info/METADATA

@@ -0,0 +1,79 @@
+Metadata-Version: 2.4
+Name: bmtool
+Version: 0.6.9.18
+Summary: BMTool
+Home-page: https://github.com/cyneuro/bmtool
+Download-URL: 
+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
+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
+Requires-Dist: xarray
+Requires-Dist: fooof
+Requires-Dist: requests
+Requires-Dist: pyyaml
+Requires-Dist: PyWavelets
+Requires-Dist: numba
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
+
+# bmtool
+A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
+
+[![license](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/cyneuro/bmtool/blob/master/LICENSE) 
+
+## In depth documentation and examples can be found [here](https://cyneuro.github.io/bmtool/)
+
+## Getting Started
+
+**Installation**
+```bash
+pip install bmtool
+```
+For developers who will be pulling down additional updates to this repository regularly use the following instead.
+```bash
+git clone https://github.com/cyneuro/bmtool.git
+cd bmtool
+python setup.py develop
+```
+Then download updates (from this directory) with
+```bash
+git pull
+```
+
+BMTool provides several modules to simplify the development of computational neuroscience models with NEURON and the Brain Modeling Toolkit (BMTK). It offers functionality for:
+
+- **Single Cell Modeling**: Analyze passive properties, current injection, FI curves, and impedance profiles
+- **Synapse Development**: Tools for tuning synaptic properties and gap junctions
+- **Network Construction**: Connectors for building complex network structures
+- **Visualization**: Plot connection matrices, network positions, and more
+- **Simulation Management**: Run simulations on SLURM clusters with parameter sweeps
+- **Analysis**: Process simulation results efficiently

{bmtool-0.6.9.16.dist-info → bmtool-0.6.9.18.dist-info}/RECORD

@@ -1,9 +1,9 @@
 bmtool/SLURM.py,sha256=PST_jOD5ZmwbJj15Tgq3UIvdq4FYN4EkPuDt66P8OXU,20136
 bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
 bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
-bmtool/bmplot.py,sha256=TPkdqenzY_ovAISSiGFk98pmoe6Q5_2WoZg9o7nKNWI,61873
-bmtool/connectors.py,sha256=hWkUUcJ4tmas8NDOFPPjQT-TgTlPcpjuZsYyAW2WkPA,72242
-bmtool/graphs.py,sha256=K8BiughRUeXFVvAgo8UzrwpSClIVg7UfmIcvtEsEsk0,6020
+bmtool/bmplot.py,sha256=gJY1frsYXiR5XxbSDdzHpIfnE1TPFuuknmUBsl6Bohs,62714
+bmtool/connectors.py,sha256=7IKsUZNEiiojzTzNL67zqQCMrQEk_qKE7x_u4SqqsbM,73495
+bmtool/graphs.py,sha256=ShBgJr1iZrM3ugU2wT6hbhmBAkc3mmf7yZQfPuPEqPM,6691
 bmtool/manage.py,sha256=_lCU0qBQZ4jSxjzAJUd09JEetb--cud7KZgxQFbLGSY,657
 bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
 bmtool/singlecell.py,sha256=imcdxIzvYVkaOLSGDxYp8WGGssGwXXBCRhzhlqVp7hA,44267
@@ -19,9 +19,9 @@ bmtool/util/commands.py,sha256=zJF-fiLk0b8LyzHDfvewUyS7iumOxVnj33IkJDzux4M,64396
 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-0.6.9.16.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.6.9.16.dist-info/METADATA,sha256=Zmwi4JuYibdyYvc9l8RLeiKPiFqrRU-XAf850kY_cx4,20479
-bmtool-0.6.9.16.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-bmtool-0.6.9.16.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.6.9.16.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.6.9.16.dist-info/RECORD,,
+bmtool-0.6.9.18.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.6.9.18.dist-info/METADATA,sha256=spdS9_tiyimQL_IyZT52Osm15hNSWPqa6LLWiVW0j44,2769
+bmtool-0.6.9.18.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+bmtool-0.6.9.18.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.6.9.18.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.6.9.18.dist-info/RECORD,,

bmtool-0.6.9.16.dist-info/METADATA

@@ -1,610 +0,0 @@
-Metadata-Version: 2.4
-Name: bmtool
-Version: 0.6.9.16
-Summary: BMTool
-Home-page: https://github.com/cyneuro/bmtool
-Download-URL: 
-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
-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
-Requires-Dist: xarray
-Requires-Dist: fooof
-Requires-Dist: requests
-Requires-Dist: pyyaml
-Requires-Dist: PyWavelets
-Requires-Dist: numba
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license
-Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: summary
-
-# bmtool
-A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
-
-[![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)
-- [Synapses](#synapses-module)
-- [Connectors](#connectors-module)
-- [Bmplot](#bmplot-module)
-- [Analysis](#analysis-module)
-- [SLURM](#slurm-module)
-- [Graphs](#graphs-module)
-
-## Getting Started
-
-**Installation**
-```bash
-pip install bmtool
-```
-For developers who will be pulling down additional updates to this repository regularly use the following instead.
-```bash
-git clone https://github.com/cyneuro/bmtool.git
-cd bmtool
-python setup.py develop
-```
-Then download updates (from this directory) with
-```bash
-git pull
-```
-
-## CLI
-#### Many of modules available can be accesed using the command line 
-```bash
-> cd your_bmtk_model_directory
-> bmtool
-Usage: bmtool [OPTIONS] COMMAND [ARGS]...
-
-Options:
-  --verbose  Verbose printing
-  --help     Show this message and exit.
-
-Commands:
-  debug
-  plot
-  util
-
->  
-> bmtool plot 
-Usage: bmtool plot [OPTIONS] COMMAND [ARGS]...
-
-Options:
-  --config PATH  Configuration file to use, default: "simulation_config.json"
-  --no-display   When set there will be no plot displayed, useful for saving
-                 plots
-  --help         Show this message and exit.
-
-Commands:
-  connection  Display information related to neuron connections
-  positions   Plot cell positions for a given set of populations
-  raster      Plot the spike raster for a given population
-  report      Plot the specified report using BMTK's default report plotter
->
-```
-
-## Single Cell Module
-- [Passive properties](#passive-properties)
-- [Current injection](#current-clamp)
-- [FI curve](#fi-curve)
-- [ZAP](#zap)
-- [Tuner](#single-cell-tuning)
-- [VHalf Segregation](#vhalf-segregation-module)
-#### Jupyter Notebook for how to use passive properties, current injection, FI curve, and ZAP can be found [here](examples/single_cell/). There are versions with example how to use single cells in HOC format and in the Allen Database format. 
-
-#### The single cell module can take any neuron HOC object and calculate passive properties, run a current clamp, calculate FI curve, or run a ZAP. The module is designed to work with HOC template files and can also turn Allen database SWC and json files into HOC objects and use those. The examples below uses "Cell_Cf" which is the name of a HOC templated loaded by the profiler. E
-
-#### First step is it initialize the profiler.
-
-
-```python
-from bmtool.singlecell import Profiler
-profiler = Profiler(template_dir='templates', mechanism_dir = 'mechanisms', dt=0.1)
-```
-
-#### Can provide any single cell module with either name of Hoc template or a HOC object. If you are wanted to use Allen database SWC and json files you can use the following function
-
-
-```python
-from bmtool.singlecell import load_allen_database_cells
-cell = load_allen_database_cells(path_to_SWC_file,path_to_json_file)
-```
-
-### Passive properties
-#### Calculates the passive properties(V-rest, Rin and tau) of a HOC object
-
-
-```python
-from bmtool.singlecell import Passive,run_and_plot
-import matplotlib.pyplot as plt
-sim = Passive('Cell_Cf', inj_amp=-100., inj_delay=1500., inj_dur=1000., tstop=2500., method='exp2')
-title = 'Passive Cell Current Injection'
-xlabel = 'Time (ms)'
-ylabel = 'Membrane Potential (mV)'
-X, Y = run_and_plot(sim, title, xlabel, ylabel, plot_injection_only=True)
-plt.gca().plot(*sim.double_exponential_fit(), 'r:', label='double exponential fit')
-plt.legend()
-plt.show()
-```
-
-    Injection location: Cell_Cf[0].soma[0](0.5)
-    Recording: Cell_Cf[0].soma[0](0.5)._ref_v
-    Running simulation for passive properties...
-    
-    V Rest: -70.21 (mV)
-    Resistance: 128.67 (MOhms)
-    Membrane time constant: 55.29 (ms)
-    
-    V_rest Calculation: Voltage taken at time 1500.0 (ms) is
-    -70.21 (mV)
-    
-    R_in Calculation: dV/dI = (v_final-v_rest)/(i_final-i_start)
-    (-83.08 - (-70.21)) / (-0.1 - 0)
-    12.87 (mV) / 0.1 (nA) = 128.67 (MOhms)
-    
-    Tau Calculation: Fit a double exponential curve to the membrane potential response
-    f(t) = a0 + a1*exp(-t/tau1) + a2*exp(-t/tau2)
-    Constained by initial value: f(0) = a0 + a1 + a2 = v_rest
-    Fit parameters: (a0, a1, a2, tau1, tau2) = (-83.06, -3306.48, 3319.33, 55.29, 55.15)
-    Membrane time constant is determined from the slowest exponential term: 55.29 (ms)
-    
-    Sag potential: v_sag = v_peak - v_final = -0.66 (mV)
-    Normalized sag potential: v_sag / (v_peak - v_rest) = 0.049
-    
-
-
-
-    
-![png](readme_figures/output_8_1.png)
-    
-
-
-### Current clamp
-#### Runs a current clamp on a HOC object
-
-
-```python
-from bmtool.singlecell import CurrentClamp
-sim = CurrentClamp('Cell_Cf', inj_amp=350., inj_delay=1500., inj_dur=1000., tstop=3000., threshold=-15.)
-X, Y = run_and_plot(sim, title='Current Injection', xlabel='Time (ms)',
-                    ylabel='Membrane Potential (mV)', plot_injection_only=True)
-plt.show()
-```
-
-    Injection location: Cell_Cf[1].soma[0](0.5)
-    Recording: Cell_Cf[1].soma[0](0.5)._ref_v
-    Current clamp simulation running...
-    
-    Number of spikes: 19
-    
-
-
-
-    
-![png](readme_figures/output_10_1.png)
-    
-
-
-### FI curve
-#### Calculates the frequency vs current injection plot for a HOC object
-
-
-```python
-from bmtool.singlecell import FI
-sim = FI('Cell_Cf', i_start=0., i_stop=1000., i_increment=50., tstart=1500.,threshold=-15.)
-X, Y = run_and_plot(sim, title='FI Curve', xlabel='Injection (nA)', ylabel='# Spikes')
-plt.show()
-```
-
-    Injection location: Cell_Cf[21].soma[0](0.5)
-    Recording: Cell_Cf[21].soma[0](0.5)._ref_v
-    Running simulations for FI curve...
-    
-    Results
-    Injection (nA): 0, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95
-    Number of spikes: 0, 1, 10, 12, 15, 16, 17, 19, 20, 20, 21, 21, 22, 23, 23, 24, 25, 25, 26, 27
-    
-
-
-
-    
-![png](readme_figures/output_12_1.png)
-    
-
-
-### ZAP
-#### Runs a ZAP on a HOC object
-
-
-```python
-from bmtool.singlecell import ZAP
-sim = ZAP('Cell_Cf')
-X, Y = run_and_plot(sim)
-plt.show()
-```
-
-    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
-    Impedance is calculated as the ratio of FFT amplitude of membrane voltage to FFT amplitude of chirp current
-    
-
-
-
-    
-![png](readme_figures/output_14_1.png)
-    
-
-
-### Single Cell Tuning
-
-#### From a BMTK Model directory containing a `simulation_config.json` file:
-```bash
-bmtool util cell tune --builder
-```
-
-#### For non-BMTK cell tuning:
-```bash
-bmtool util cell --template TemplateFile.hoc --mod-folder ./ tune --builder
-```
-![bmtool](./figures/figure2.png "Tuning Figure")
-
-### VHalf Segregation Module
-
-#### Based on the Alturki et al. (2016) paper.
-
-#### Segregate your channel activation for an easier time tuning your cells.
-
-
-```bash
-> bmtool util cell vhseg --help
-
-Usage: bmtool util cell vhseg [OPTIONS]
-
-  Alturki et al. (2016) V1/2 Automated Segregation Interface, simplify
-  tuning by separating channel activation
-
-Options:
-  --title TEXT
-  --tstop INTEGER
-  --outhoc TEXT         Specify the file you want the modified cell template
-                        written to
-  --outfolder TEXT      Specify the directory you want the modified cell
-                        template and mod files written to (default: _seg)
-  --outappend           Append out instead of overwriting (default: False)
-  --debug               Print all debug statements
-  --fminpa INTEGER      Starting FI Curve amps (default: 0)
-  --fmaxpa INTEGER      Ending FI Curve amps (default: 1000)
-  --fincrement INTEGER  Increment the FI Curve amps by supplied pA (default:
-                        100)
-  --infvars TEXT        Specify the inf variables to plot, skips the wizard.
-                        (Comma separated, eg: inf_mech,minf_mech2,ninf_mech2)
-  --segvars TEXT        Specify the segregation variables to globally set,
-                        skips the wizard. (Comma separated, eg:
-                        mseg_mech,nseg_mech2)
-  --eleak TEXT          Specify the eleak var manually
-  --gleak TEXT          Specify the gleak var manually
-  --othersec TEXT       Specify other sections that a window should be
-                        generated for (Comma separated, eg: dend[0],dend[1])
-  --help                Show this message and exit.
-
-```
-
-### Examples 
-
-#### Wizard Mode (Interactive)
-
-```bash
-> bmtool util cell vhseg
-
-? Select a cell:  CA3PyramidalCell
-Using section dend[0]
-? Show other sections? (default: No)  Yes
-? Select other sections (space bar to select):  done (2 selections)
-? Select inf variables to plot (space bar to select):   done (5 selections)
-? Select segregation variables [OR VARIABLES YOU WANT TO CHANGE ON ALL SEGMENTS at the same time] (space bar to select):  done (2 selections)
-```
-
-#### Command Mode (Non-interactive)
-
-```bash
-bmtool util cell --template CA3PyramidalCell vhseg --othersec dend[0],dend[1] --infvars inf_im --segvars gbar_im --gleak gl_ichan2CA3 --eleak el_ichan2CA3
-```
-
-Example:
-
-![bmtool](./figures/figure4.png "Seg Figure")
-
-#### Simple models can utilize 
-``` bash
-bmtool util cell --hoc cell_template.hoc vhsegbuild --build
-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)
--Gap Junction tuner
-
-#### 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)
-#### GapJunctionTuner - Provides jupyter sliders to tune for coupling coefficient in a similar style to the SynapticTuner. The Gap junction tuner also has an optimizer which can find the best resistance for the desired coupling coefficient. an example can be viewed [here](examples/synapses/gap_junction_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)
-- [CorrelatedGapJunction](#correlatedgapjunction)
-- [OneToOneSequentialConnector](#onetoonesequentialconnector)
-
-#### This module contains helper functions and classes that work with BMTK's NetworkBuilder module in building networks. It facilitates building reciprocal connections, distance dependent connections, afferent connections, etc. See documentation inside the script `connectors.py` for more notes on usage.
-
-#### All connector example below use the following network node structure
-```python
-from bmtk.builder import NetworkBuilder
-net = NetworkBuilder('example_net')
-net.add_nodes(N=100, pop_name='PopA',model_type = 'biophysical')
-net.add_nodes(N=100, pop_name='PopB',model_type = 'biophysical')
-
-background = NetworkBuilder('background')
-background.add_nodes(N=300,pop_name='tON',potential='exc',model_type='virtual')
-```
-
-#### 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 - 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 - 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)
-connector.setup_nodes(source=net.nodes(pop_name='PopA'), target=net.nodes(pop_name='PopA'))
-net.add_edges(**connector.edge_params())
-gap_junc = CorrelatedGapJunction(p_non=0.1228,p_uni=0.56,p_rec=1,connector=connector)
-gap_junc.setup_nodes(source=net.nodes(pop_name='PopA'), target=net.nodes(pop_name='PopA'))
-conn = net.add_edges(is_gap_junction=True, syn_weight=0.0000495, target_sections=None,afferent_section_id=0, afferent_section_pos=0.5,
-**gap_junc.edge_params())
-```
-
-#### 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()
-connector.setup_nodes(source=background.nodes(), target=net.nodes(pop_name = 'PopA'))
-net.add_edges(**connector.edge_params())
-connector.setup_nodes(target=net.nodes(pop_name = 'PopB'))
-net.add_edges(**connector.edge_params())
-```
-
-## Bmplot Module 
-- [total_connection_matrix](#total_connection_matrix)
-- [percent_connection_matrix](#percent_connection_matrix)
-- [connector_percent_matrix](#connector_percent_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)
-### for a demo please see the notebook [here](examples/bmplot/bmplot.ipynb) 
-
-### total_connection_matrix
-#### Generates a table of total number of connections each neuron population recieves
-
-    
-### 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 
-
-### connector_percent_matrix
-#### Generates a table of the percent connectivity using the output from bmtool.connector. By default will generate the percent connectivity of the possible connections meaning factoring in distance rules.
-
-
-### 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
-
-    
-### 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.
-
-    
-### 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
-
-
-### connection_distance
-#### Generates a 3d plot with the source and target cells location along with a histogram showing connection distance
-
-### connection_histogram 
-#### Generates a histogram of the distribution of connections a population of cells give to individual cells of another population 
-
-
-### plot_3d_positions
-#### Generates a plot of cells positions in 3D space 
-
-
-### plot_3d_cell_rotation
-#### Generates a plot of cells location in 3D plot and also the cells rotation
-
-
-### 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)
-
-
-## Analysis Module
-### A notebook example of how to use the spikes module can be found [here](examples/analysis/using_spikes.ipynb)
-
-## SLURM Module
-### This is an extremely helpful module that can simplify using SLURM too submit your models. There is also features to enable doing a seedSweep. This will vary the parameters of the simulation and make tuning the model easier. An example can be found [here](examples/SLURM/using_BlockRunner.ipynb) 
-
-
-## 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>
-
-