bmtool 0.6.9.15__py3-none-any.whl → 0.6.9.17__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-0.6.9.15.dist-info → bmtool-0.6.9.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bmtool
-Version: 0.6.9.15
+Version: 0.6.9.17
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.6.9.15.dist-info → bmtool-0.6.9.17.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-0.6.9.15.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.6.9.15.dist-info/METADATA,sha256=Gfn16YTwe69lfsGLnyJUTUbPd4xBV-sXjJ44J0uLKRI,20479
-bmtool-0.6.9.15.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-bmtool-0.6.9.15.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.6.9.15.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.6.9.15.dist-info/RECORD,,
+bmtool-0.6.9.17.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.6.9.17.dist-info/METADATA,sha256=Z4POeFa5fCmHQ7eWOh9RsT6nSIunWdnzpd9TbeELOqs,20479
+bmtool-0.6.9.17.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+bmtool-0.6.9.17.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.6.9.17.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.6.9.17.dist-info/RECORD,,