bmtool 0.5.9.8__tar.gz → 0.5.9.9__tar.gz

{bmtool-0.5.9.8 → bmtool-0.5.9.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.9.8
+Version: 0.5.9.9
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -401,6 +401,7 @@ net.add_edges(**connector.edge_params())
 ### for a demo please see the notebook [here](examples/bmplot/bmplot.ipynb) 
 - [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)
@@ -416,6 +417,9 @@ net.add_edges(**connector.edge_params())
 ### 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

{bmtool-0.5.9.8 → bmtool-0.5.9.9}/README.md

@@ -367,6 +367,7 @@ net.add_edges(**connector.edge_params())
 ### for a demo please see the notebook [here](examples/bmplot/bmplot.ipynb) 
 - [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)
@@ -382,6 +383,9 @@ net.add_edges(**connector.edge_params())
 ### 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

{bmtool-0.5.9.8 → bmtool-0.5.9.9}/bmtool/bmplot.py

@@ -574,16 +574,16 @@ def plot_connection_info(text, num, source_labels,target_labels, title, syn_info
             if syn_info =='2' or syn_info =='3':
                 if num_source > 8 and num_source <20:
                     fig_text = ax1.text(j, i, edge_info,
-                            ha="center", va="center", color="k",rotation=37.5, size=8, weight = 'semibold')
+                            ha="center", va="center", color="w",rotation=37.5, size=8, weight = 'semi\bold')
                 elif num_source > 20:
                     fig_text = ax1.text(j, i, edge_info,
-                            ha="center", va="center", color="k",rotation=37.5, size=7, weight = 'semibold')
+                            ha="center", va="center", color="w",rotation=37.5, size=7, weight = 'semibold')
                 else:
                     fig_text = ax1.text(j, i, edge_info,
-                            ha="center", va="center", color="k",rotation=37.5, size=11, weight = 'semibold')
+                            ha="center", va="center", color="w",rotation=37.5, size=11, weight = 'semibold')
             else:
                 fig_text = ax1.text(j, i, edge_info,
-                            ha="center", va="center", color="k", size=11, weight = 'semibold')
+                            ha="center", va="center", color="w", size=11, weight = 'semibold')
 
     ax1.set_ylabel('Source', size=11, weight = 'semibold')
     ax1.set_xlabel('Target', size=11, weight = 'semibold')
@@ -599,8 +599,7 @@ def plot_connection_info(text, num, source_labels,target_labels, title, syn_info
     else:
         return
 
-def connector_percent_matrix(csv_path: str = None, exclude_shell: bool = True, 
-                             exclude_assembly: bool = False, title: str = 'Percent connection matrix') -> None:
+def connector_percent_matrix(csv_path: str = None, exclude_strings=None, title: str = 'Percent connection matrix', pop_order=None) -> None:
     """
     Generates and plots a connection matrix based on connection probabilities from a CSV file produced by bmtool.connector.
 
@@ -613,123 +612,92 @@ def connector_percent_matrix(csv_path: str = None, exclude_shell: bool = True,
     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.
+    exclude_strings : list of str, optional
+        List of strings to exclude rows where 'Source' or 'Target' contain these strings.
     title : str, optional, default='Percent connection matrix'
         Title for the generated plot.
+    pop_order : list of str, optional
+        List of population labels to specify the order for the x- and y-ticks in the 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 (%)"  # Can change this for different column but this is best i think
-
-    # Create an empty dictionary to store connection percentages
-    connection_data = {}
+    selected_column = "Percent connectionivity within possible connections"
 
-    def filter_dataframe(df, column_name, exclude_shell=exclude_shell, exclude_assembly=exclude_assembly):
+    # Filter the DataFrame based on exclude_strings
+    def filter_dataframe(df, column_name, exclude_strings):
         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:
+            match = re.search(r"\[\'(.*?)\'\]", string)
+            if exclude_strings and any(ex_string in string for ex_string in exclude_strings):
+                return None
+            elif match:
+                filtered_string = match.group(1)
+                if 'Gap' in string:
                         filtered_string = filtered_string + "-Gap"
-                    return filtered_string
-                return string  # If no match, return the original string
+                return filtered_string  # Return matched string
 
-        # Apply the filtering logic to the specified column
-        df[column_name] = df[column_name].apply(process_string)
+            return string  # If no match, return the original string
 
-        # Remove rows where None was returned in the specified column
+        df[column_name] = df[column_name].apply(process_string)
         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']
-        target = row['Target']
-        selected_percentage = row[selected_column]
-        
-        # If the selected percentage is an array-like string, extract the first and second values
+    df = filter_dataframe(df, 'Source', exclude_strings)
+    df = filter_dataframe(df, 'Target', exclude_strings)
+
+    # Prepare connection data
+    connection_data = {}
+    for _, row in df.iterrows():
+        source, target, selected_percentage = row['Source'], row['Target'], row[selected_column]
         if isinstance(selected_percentage, str):
-            selected_percentage = selected_percentage.strip('[]').split()
-            selected_percentage = [float(p) for p in selected_percentage]  # Convert to float
-        
-        # Store the selected percentage(s) for the source-target pair
+            selected_percentage = [float(p) for p in selected_percentage.strip('[]').split()]
         connection_data[(source, target)] = selected_percentage
 
-    # Prepare unique populations and create an empty matrix
+    # Determine population order
     populations = sorted(list(set(df['Source'].unique()) | set(df['Target'].unique())))
+    if pop_order:
+        populations = [pop for pop in pop_order if pop in populations]  # Order according to pop_order, if provided
     num_populations = len(populations)
+    
+    # Create an empty matrix and populate it
     connection_matrix = np.zeros((num_populations, num_populations), dtype=float)
-
-    # Populate the matrix with the selected connection percentages
-    for source, target in connection_data.keys():
-        source_idx = populations.index(source)
-        target_idx = populations.index(target)
-        connection_probabilities = connection_data[(source, target)]
-        
-        # Use the first value for one-way connection from source to target
-        connection_matrix[source_idx][target_idx] = connection_probabilities[0]
-
-        # Check if the source and target are the same population
-        if source == target:
-            # Use the first value (uni-directional) and ignore the second value (bi-directional)
-            continue
-
-        # Check if there is a bidirectional connection and use the second value
-        if len(connection_probabilities) > 1:
-            connection_matrix[target_idx][source_idx] = connection_probabilities[1]
-
-    # Replace NaN values with 0
-    connection_matrix[np.isnan(connection_matrix)] = 0
-
-    # Plot the matrix
+    for (source, target), probabilities in connection_data.items():
+        if source in populations and target in populations:
+            source_idx = populations.index(source)
+            target_idx = populations.index(target)
+            connection_matrix[source_idx][target_idx] = probabilities[0]
+            if len(probabilities) == 1:
+                connection_matrix[source_idx][target_idx] = probabilities[0]
+            if len(probabilities) == 2:
+                connection_matrix[source_idx][target_idx] = probabilities[0]
+            if len(probabilities) == 3:
+                connection_matrix[source_idx][target_idx] = probabilities[0] 
+                connection_matrix[target_idx][source_idx] = probabilities[1]
+
+    # Plotting
     fig, ax = plt.subplots(figsize=(10, 8))
     im = ax.imshow(connection_matrix, cmap='viridis', interpolation='nearest')
 
     # Add annotations
     for i in range(num_populations):
         for j in range(num_populations):
-            text = ax.text(j, i, f"{connection_matrix[i, j]:.2f}%",
-                        ha="center", va="center", color="w", size=10, weight='bold')
+            text = ax.text(j, i, f"{connection_matrix[i, j]:.2f}%", ha="center", va="center", color="w", size=10, weight='semibold')
 
     # Add colorbar
-    plt.colorbar(im, label=f'Percentage of connected pairs ({selected_column})')
+    plt.colorbar(im, label=f'{selected_column}')
 
     # Set title and axis labels
     ax.set_title(title)
     ax.set_xlabel('Target Population')
     ax.set_ylabel('Source Population')
 
-    # Set ticks and labels
+    # Set ticks and labels based on populations in specified order
     ax.set_xticks(np.arange(num_populations))
     ax.set_yticks(np.arange(num_populations))
     ax.set_xticklabels(populations, rotation=45, ha="right", size=12, weight='semibold')

{bmtool-0.5.9.8 → bmtool-0.5.9.9}/bmtool/connectors.py

@@ -1064,8 +1064,8 @@ class ReciprocalConnector(AbstractConnector):
         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]
+            "Percent connectionivity within possible connections": [fraction[0]*100],
+            "Percent connectionivity within all connections": [fraction[1]*100]
         }
         df = pd.DataFrame(data)
         
@@ -1235,8 +1235,8 @@ class UnidirectionConnector(AbstractConnector):
         data = {
             "Source": [src_str],
             "Target": [trg_str],
-            "Fraction of connected pairs in possible ones (%)": [possible_fraction],
-            "Fraction of connected pairs in all pairs (%)": [all_fraction]
+            "Percent connectionivity within possible connections": [possible_fraction],
+            "Percent connectionivity within all connections": [all_fraction]
         }
         df = pd.DataFrame(data)
         
@@ -1336,8 +1336,8 @@ class GapJunction(UnidirectionConnector):
         data = {
             "Source": [src_str+"Gap"],
             "Target": [trg_str+"Gap"],
-            "Fraction of connected pairs in possible ones (%)": [fraction_0*100],
-            "Fraction of connected pairs in all pairs (%)": [fraction_1*100]
+            "Percent connectionivity within possible connections": [fraction_0*100],
+            "Percent connectionivity within all connections": [fraction_1*100]
         }
         df = pd.DataFrame(data)
         

{bmtool-0.5.9.8 → bmtool-0.5.9.9}/bmtool/synapses.py

@@ -649,6 +649,4 @@ class SynapseTuner:
         display(ui)
 
 
-
-
     

{bmtool-0.5.9.8 → bmtool-0.5.9.9}/bmtool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.9.8
+Version: 0.5.9.9
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -401,6 +401,7 @@ net.add_edges(**connector.edge_params())
 ### for a demo please see the notebook [here](examples/bmplot/bmplot.ipynb) 
 - [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)
@@ -416,6 +417,9 @@ net.add_edges(**connector.edge_params())
 ### 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

{bmtool-0.5.9.8 → bmtool-0.5.9.9}/setup.py

@@ -6,7 +6,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name="bmtool",
-    version='0.5.9.8',
+    version='0.5.9.9',
     author="Neural Engineering Laboratory at the University of Missouri",
     author_email="gregglickert@mail.missouri.edu",
     description="BMTool",