bmtool 0.5.9.8__py3-none-any.whl → 0.6.0__py3-none-any.whl

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')
@@ -922,7 +890,7 @@ def plot_3d_positions(config=None, populations_list=None, group_by=None, title=N
     if not is_notebook:
         plt.show()
 
-    return
+    return ax
 
 def plot_3d_cell_rotation(config=None, populations_list=None, group_by=None, title=None, save_file=None, quiver_length=None, arrow_length_ratio=None, group=None, subset=None):
     from scipy.spatial.transform import Rotation as R

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/synapses.py

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

{bmtool-0.5.9.8.dist-info → bmtool-0.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.9.8
+Version: 0.6.0
 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.dist-info → bmtool-0.6.0.dist-info}/RECORD

@@ -1,13 +1,13 @@
 bmtool/SLURM.py,sha256=AX5MKV7dD-XwS8SROnW1IyesZ3jDwMf0txO6mHxTbuw,13694
 bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
 bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
-bmtool/bmplot.py,sha256=VoX-oXqu6dRb3JEUgGxWiX23JxUy9PeemE7z4f6hVbY,53177
-bmtool/connectors.py,sha256=QEaBGc6mEoQc-H3ltjvjn5-XWyYgnrhcfNRblVOUE2A,72228
+bmtool/bmplot.py,sha256=vIknbCwBSJNsr4m53SymteKdvyE0Omn3Xv8udzroeKc,51825
+bmtool/connectors.py,sha256=2vVUsqYMaCuWZ-4C5eUzqwsFItFM9vm0ytZdRQdWgoc,72243
 bmtool/graphs.py,sha256=K8BiughRUeXFVvAgo8UzrwpSClIVg7UfmIcvtEsEsk0,6020
 bmtool/manage.py,sha256=_lCU0qBQZ4jSxjzAJUd09JEetb--cud7KZgxQFbLGSY,657
 bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
 bmtool/singlecell.py,sha256=Q4poQvG9fw0jlyMmHFzbRPrpcEkPz5MKS8Guuo73Bzs,26849
-bmtool/synapses.py,sha256=CA4mPeLCnyaqhDYphcKz-1s7C2JVknCRW_NoTfHS9MM,27500
+bmtool/synapses.py,sha256=cBa4NAYob8BxCFi04FfVcqDs_LNYJrP4vscgnT8Rk1c,27498
 bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/debug/commands.py,sha256=AwtcR7BUUheM0NxvU1Nu234zCdpobhJv5noX8x5K2vY,583
 bmtool/debug/debug.py,sha256=xqnkzLiH3s-tS26Y5lZZL62qR2evJdi46Gud-HzxEN4,207
@@ -16,9 +16,9 @@ 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-0.5.9.8.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.5.9.8.dist-info/METADATA,sha256=rrR39yoM5X0WSk15L0KZV3KoRFqwt5KAmwMXW-apI_c,18823
-bmtool-0.5.9.8.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
-bmtool-0.5.9.8.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.5.9.8.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.5.9.8.dist-info/RECORD,,
+bmtool-0.6.0.dist-info/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.6.0.dist-info/METADATA,sha256=8qbBKGJWEedc2N_xdm9OYb66bCQScXxb2faMQvdJvsQ,19113
+bmtool-0.6.0.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
+bmtool-0.6.0.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.6.0.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.6.0.dist-info/RECORD,,