bmtool 0.5.5__py3-none-any.whl → 0.5.6.1__py3-none-any.whl

bmtool/bmplot.py

@@ -18,6 +18,7 @@ import statistics
 import pandas as pd
 import os
 import sys
+import re
 
 from .util.util import CellVarsFile #, missing_units
 from bmtk.analyzer.utils import listify
@@ -500,22 +501,78 @@ 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):
+def connector_percent_matrix(csv_path: str = None, exclude_shell: bool = True, 
+                             exclude_assembly: bool = False, title: str = 'Percent connection matrix') -> 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
+    Generates and plots a connection matrix based on connection probabilities from a CSV file produced by bmtool.connector.
+
+    This function is useful for visualizing percent connectivity while factoring in population distance and other parameters. 
+    It processes the connection data by filtering the 'Source' and 'Target' columns in the CSV, and displays the percentage of 
+    connected pairs for each population combination in a matrix.
+
+    Parameters:
+    -----------
+    csv_path : str
+        Path to the CSV file containing the connection data. The CSV should be an output from the bmtool.connector 
+        classes, specifically generated by the `save_connection_report()` function.
+    exclude_shell : bool, optional, default=True
+        If True, rows where 'Source' or 'Target' contain "shell" will be excluded from the analysis.
+    exclude_assembly : bool, optional, default=False
+        If True, skips appending the assembly ID to the population name in the connection matrix.
+    title : str, optional, default='Percent connection matrix'
+        Title for the generated plot.
+
+    Returns:
+    --------
+    None
+        Displays a heatmap plot of the connection matrix, showing the percentage of connected pairs between populations.
+
+    Example:
+    --------
+    connector_percent_matrix('connections.csv', exclude_shell=True, exclude_assembly=False)
     """
     # 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
+    selected_column = "Fraction of connected pairs in possible ones (%)"  # Can change this for different column but this is best i think
 
     # Create an empty dictionary to store connection percentages
     connection_data = {}
 
+    def filter_dataframe(df, column_name, exclude_shell=exclude_shell, exclude_assembly=exclude_assembly):
+        def process_string(string):
+            # Use regex to extract 'FSI' or other match
+            match = re.search(r"\[\'(.*?)\'\]", string) # the cell name from ['fsi']
+            ints_in_string = re.findall(r'\d+', string) # get all ints in the string
+
+            # Conditionally remove rows containing "shell"
+            if exclude_shell and "shell" in string:
+                return None  # Mark row for removal
+            else:
+                if match:
+                    filtered_string = match.group(1)
+                    
+                    # Conditionally process "assembly" in the string
+                    if not exclude_assembly and "assembly" in string:
+                        assem_value = int(ints_in_string[0])
+                        filtered_string = filtered_string + str(f"-{assem_value}")
+                    
+                    if 'Gap' in string:
+                        filtered_string = filtered_string + "-Gap"
+                    return filtered_string
+                return string  # If no match, return the original string
+
+        # Apply the filtering logic to the specified column
+        df[column_name] = df[column_name].apply(process_string)
+
+        # Remove rows where None was returned in the specified column
+        df = df.dropna(subset=[column_name])
+
+        return df
+
+    df = filter_dataframe(df,'Source')
+    df = filter_dataframe(df,'Target')
     # Iterate over each row in the DataFrame
     for index, row in df.iterrows():
         source = row['Source']
@@ -570,7 +627,7 @@ def connector_percent_matrix(csv_path = None):
     plt.colorbar(im, label=f'Percentage of connected pairs ({selected_column})')
 
     # Set title and axis labels
-    ax.set_title('Neuronal Connection Matrix')
+    ax.set_title(title)
     ax.set_xlabel('Target Population')
     ax.set_ylabel('Source Population')
 

bmtool/connectors.py

@@ -10,6 +10,8 @@ import re
 
 rng = np.random.default_rng()
 
+report_name = 'conn.csv'
+
 ##############################################################################
 ############################## CONNECT CELLS #################################
 
@@ -534,7 +536,7 @@ class ReciprocalConnector(AbstractConnector):
                  pr=0., pr_arg=None, estimate_rho=True, rho=None,
                  dist_range_forward=None, dist_range_backward=None,
                  n_syn0=1, n_syn1=1, autapses=False,
-                 quick_pop_check=False, cache_data=True, verbose=True,save_report=True,report_name='connection_report.csv'):
+                 quick_pop_check=False, cache_data=True, verbose=True,save_report=True,report_name=None):
         args = locals()
         var_set = ('p0', 'p0_arg', 'p1', 'p1_arg',
                    'pr', 'pr_arg', 'n_syn0', 'n_syn1')
@@ -553,6 +555,9 @@ class ReciprocalConnector(AbstractConnector):
         self.cache = self.ConnectorCache(cache_data and self.estimate_rho)
         self.verbose = verbose
         self.save_report = save_report
+
+        if report_name is None:
+            report_name = globals().get('report_name', 'default_report.csv')
         self.report_name = report_name
 
         self.conn_prop = [{}, {}]
@@ -1104,14 +1109,17 @@ class UnidirectionConnector(AbstractConnector):
             This is useful in similar manner as in ReciprocalConnector.
     """
 
-    def __init__(self, p=1., p_arg=None, n_syn=1, verbose=True,save_report=True,report_name='connection_report.csv'):
+    def __init__(self, p=1., p_arg=None, n_syn=1, verbose=True,save_report=True,report_name=None):
         args = locals()
         var_set = ('p', 'p_arg', 'n_syn')
         self.vars = {key: args[key] for key in var_set}
 
         self.verbose = verbose
         self.save_report = save_report
+        if report_name is None:
+            report_name = globals().get('report_name', 'default_report.csv')
         self.report_name = report_name
+
         self.conn_prop = {}
         self.iter_count = 0
 
@@ -1214,14 +1222,16 @@ class UnidirectionConnector(AbstractConnector):
     def save_connection_report(self):
         """Save connections into a CSV file to be read from later"""
         src_str, trg_str = self.get_nodes_info()
-        n_conn, n_poss, n_pair, fraction = self.connection_number()
+        
+        possible_fraction = (100. * self.n_conn / self.n_poss)
+        all_fraction = (100. * self.n_conn / self.n_pair)
 
         # Extract the population name from source_str and target_str
         data = {
             "Source": [src_str],
             "Target": [trg_str],
-            "Fraction of connected pairs in possible ones (%)": [fraction[0]*100],
-            "Fraction of connected pairs in all pairs (%)": [fraction[1]*100]
+            "Fraction of connected pairs in possible ones (%)": [possible_fraction],
+            "Fraction of connected pairs in all pairs (%)": [all_fraction]
         }
         df = pd.DataFrame(data)
         
@@ -1257,8 +1267,9 @@ class GapJunction(UnidirectionConnector):
         Similar to `UnidirectionConnector`.
     """
 
-    def __init__(self, p=1., p_arg=None, verbose=True,report_name='connection_report.csv'):
-        super().__init__(p=p, p_arg=p_arg, verbose=verbose,report_name=report_name)
+    def __init__(self, p=1., p_arg=None, verbose=True,report_name=None):
+        super().__init__(p=p, p_arg=p_arg, verbose=verbose,report_name=None)
+
 
     def setup_nodes(self, source=None, target=None):
         super().setup_nodes(source=source, target=target)

{bmtool-0.5.5.dist-info → bmtool-0.5.6.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.5
+Version: 0.5.6.1
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.5.5.dist-info → bmtool-0.5.6.1.dist-info}/RECORD

@@ -1,8 +1,8 @@
 bmtool/SLURM.py,sha256=8XbzNLIQfE_lNRd_Z8ya2PEDT4TqhVnDZkil-ckLUCU,11508
 bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
 bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
-bmtool/bmplot.py,sha256=p39s3SwXvG1D7ujYwY5zCmeUql2epnzLKqXZMBn_vjo,43511
-bmtool/connectors.py,sha256=RPQGFfefKxJxu5sM6uge-RKHvLAE96EVFh8xXj8HR0A,71560
+bmtool/bmplot.py,sha256=-kw4VOcTnA22JVQi1PzH2E308pcmY1Xo7oqgCnm0cC8,46260
+bmtool/connectors.py,sha256=d5Pt66f9UHm8YY2qJ0mtYbASimczOzfviFxZQWkazjs,71804
 bmtool/graphs.py,sha256=K8BiughRUeXFVvAgo8UzrwpSClIVg7UfmIcvtEsEsk0,6020
 bmtool/manage.py,sha256=_lCU0qBQZ4jSxjzAJUd09JEetb--cud7KZgxQFbLGSY,657
 bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
@@ -16,9 +16,9 @@ bmtool/util/commands.py,sha256=zJF-fiLk0b8LyzHDfvewUyS7iumOxVnj33IkJDzux4M,64396
 bmtool/util/util.py,sha256=24E5rUoDU86nqypDF4uZJkuJKO1BrwrQE8lZzAxu1kw,56770
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=xSRpRN6DhPFz4q5buq_W8UmsD7BbUrkzYBEbKVloYss,87194
-bmtool-0.5.5.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.5.5.dist-info/METADATA,sha256=aRwr0X8bt33WJDcPh6Js-YULLKSfTlD_nPsMn1bSZTs,24105
-bmtool-0.5.5.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-bmtool-0.5.5.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.5.5.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.5.5.dist-info/RECORD,,
+bmtool-0.5.6.1.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.5.6.1.dist-info/METADATA,sha256=8LEjuoxY62XgrDbHqCvPhn67mAnj18aAlKilm1A3Mv0,24107
+bmtool-0.5.6.1.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+bmtool-0.5.6.1.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.5.6.1.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.5.6.1.dist-info/RECORD,,