dragon-ml-toolbox 1.3.2__tar.gz → 1.4.1__tar.gz

{dragon_ml_toolbox-1.3.2/dragon_ml_toolbox.egg-info → dragon_ml_toolbox-1.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dragon-ml-toolbox
-Version: 1.3.2
+Version: 1.4.1
 Summary: A collection of tools for data science and machine learning projects
 Author-email: Karl Loza <luigiloza@gmail.com>
 License-Expression: MIT
@@ -27,6 +27,7 @@ Requires-Dist: ipython
 Requires-Dist: ipykernel
 Requires-Dist: notebook
 Requires-Dist: jupyterlab
+Requires-Dist: ipywidgets
 Requires-Dist: joblib
 Requires-Dist: xgboost
 Requires-Dist: lightgbm<=4.5.0
@@ -79,7 +80,7 @@ Clone the repository and install in editable mode with optional dependencies:
 ```bash
 git clone https://github.com/DrAg0n-BoRn/ML_tools.git
 cd ML_tools
-pip install -e '.[pytorch]'
+pip install -e .
 ```
 
 ## Usage
@@ -90,3 +91,19 @@ After installation, import modules like this:
 from ml_tools.utilities import sanitize_filename
 from ml_tools.logger import custom_logger
 ```
+
+## Available modules
+
+```bash
+data_exploration
+datasetmaster
+ensemble_learning
+handle_excel
+logger
+MICE_imputation
+particle_swarm_optimization
+trainer
+utilities
+VIF_factor
+vision_helpers
+```

{dragon_ml_toolbox-1.3.2 → dragon_ml_toolbox-1.4.1}/README.md

@@ -40,7 +40,7 @@ Clone the repository and install in editable mode with optional dependencies:
 ```bash
 git clone https://github.com/DrAg0n-BoRn/ML_tools.git
 cd ML_tools
-pip install -e '.[pytorch]'
+pip install -e .
 ```
 
 ## Usage
@@ -51,3 +51,19 @@ After installation, import modules like this:
 from ml_tools.utilities import sanitize_filename
 from ml_tools.logger import custom_logger
 ```
+
+## Available modules
+
+```bash
+data_exploration
+datasetmaster
+ensemble_learning
+handle_excel
+logger
+MICE_imputation
+particle_swarm_optimization
+trainer
+utilities
+VIF_factor
+vision_helpers
+```

{dragon_ml_toolbox-1.3.2 → dragon_ml_toolbox-1.4.1/dragon_ml_toolbox.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dragon-ml-toolbox
-Version: 1.3.2
+Version: 1.4.1
 Summary: A collection of tools for data science and machine learning projects
 Author-email: Karl Loza <luigiloza@gmail.com>
 License-Expression: MIT
@@ -27,6 +27,7 @@ Requires-Dist: ipython
 Requires-Dist: ipykernel
 Requires-Dist: notebook
 Requires-Dist: jupyterlab
+Requires-Dist: ipywidgets
 Requires-Dist: joblib
 Requires-Dist: xgboost
 Requires-Dist: lightgbm<=4.5.0
@@ -79,7 +80,7 @@ Clone the repository and install in editable mode with optional dependencies:
 ```bash
 git clone https://github.com/DrAg0n-BoRn/ML_tools.git
 cd ML_tools
-pip install -e '.[pytorch]'
+pip install -e .
 ```
 
 ## Usage
@@ -90,3 +91,19 @@ After installation, import modules like this:
 from ml_tools.utilities import sanitize_filename
 from ml_tools.logger import custom_logger
 ```
+
+## Available modules
+
+```bash
+data_exploration
+datasetmaster
+ensemble_learning
+handle_excel
+logger
+MICE_imputation
+particle_swarm_optimization
+trainer
+utilities
+VIF_factor
+vision_helpers
+```

{dragon_ml_toolbox-1.3.2 → dragon_ml_toolbox-1.4.1}/dragon_ml_toolbox.egg-info/SOURCES.txt

@@ -8,6 +8,7 @@ dragon_ml_toolbox.egg-info/dependency_links.txt
 dragon_ml_toolbox.egg-info/requires.txt
 dragon_ml_toolbox.egg-info/top_level.txt
 ml_tools/MICE_imputation.py
+ml_tools/VIF_factor.py
 ml_tools/__init__.py
 ml_tools/data_exploration.py
 ml_tools/datasetmaster.py

{dragon_ml_toolbox-1.3.2 → dragon_ml_toolbox-1.4.1}/dragon_ml_toolbox.egg-info/requires.txt

@@ -13,6 +13,7 @@ ipython
 ipykernel
 notebook
 jupyterlab
+ipywidgets
 joblib
 xgboost
 lightgbm<=4.5.0

{dragon_ml_toolbox-1.3.2 → dragon_ml_toolbox-1.4.1}/ml_tools/MICE_imputation.py

@@ -3,9 +3,20 @@ import miceforest as mf
 import os
 import matplotlib.pyplot as plt
 import numpy as np
-from ml_tools.utilities import load_dataframe, list_csv_paths, sanitize_filename
+from ml_tools.utilities import load_dataframe, list_csv_paths, sanitize_filename, _script_info
 from plotnine import ggplot, labs, theme, element_blank # type: ignore
 
+
+__all__ = [
+    "apply_mice",
+    "save_imputed_datasets",
+    "get_na_column_names",
+    "get_convergence_diagnostic",
+    "get_imputed_distributions",
+    "run_mice_pipeline"
+]
+
+
 def apply_mice(df: pd.DataFrame, df_name: str, resulting_datasets: int=1, iterations: int=20, random_state: int=101):
     
     # Initialize kernel with number of imputed datasets to generate
@@ -120,7 +131,7 @@ def get_imputed_distributions(kernel: mf.ImputationKernel, df_name: str, root_di
     '''
     # Check path
     os.makedirs(root_dir, exist_ok=True)
-    local_save_dir = os.path.join(root_dir, f"Distribution_Metrics_{df_name}")
+    local_save_dir = os.path.join(root_dir, f"Distribution_Metrics_{df_name}_imputed")
     if not os.path.isdir(local_save_dir):
         os.makedirs(local_save_dir)
     
@@ -169,8 +180,12 @@ def get_imputed_distributions(kernel: mf.ImputationKernel, df_name: str, root_di
         # Adjust layout and save
         # fig.tight_layout()
         # fig.subplots_adjust(bottom=0.2, left=0.2)  # Optional, depending on overflow
+        
+        # sanitize savename
+        feature_save_name = sanitize_filename(filename)
+        
         fig.savefig(
-            os.path.join(local_save_dir, filename + ".svg"),
+            os.path.join(local_save_dir, feature_save_name + ".svg"),
             format='svg',
             bbox_inches='tight',
             pad_inches=0.1
@@ -185,8 +200,7 @@ def get_imputed_distributions(kernel: mf.ImputationKernel, df_name: str, root_di
     else:
         for feature in column_names:
             fig = kernel.plot_imputed_distributions(variables=[feature])
-            feature_save_name = sanitize_filename(feature)
-            _process_figure(fig, feature_save_name)
+            _process_figure(fig, feature)
 
     print("\tImputed distributions saved successfully.")
 
@@ -207,7 +221,7 @@ def run_mice_pipeline(df_path_or_dir: str, save_datasets_dir: str, save_metrics_
     if os.path.isfile(df_path_or_dir):
         all_file_paths = [df_path_or_dir]
     elif os.path.isdir(df_path_or_dir):
-        all_file_paths, _ = list_csv_paths(df_path_or_dir)
+        all_file_paths = list(list_csv_paths(df_path_or_dir).values())
     else:
         raise ValueError(f"Invalid path or directory: {df_path_or_dir}")
     
@@ -223,3 +237,7 @@ def run_mice_pipeline(df_path_or_dir: str, save_datasets_dir: str, save_metrics_
         get_convergence_diagnostic(kernel=kernel, imputed_dataset_names=imputed_dataset_names, column_names=imputed_column_names, root_dir=save_metrics_dir)
         
         get_imputed_distributions(kernel=kernel, df_name=df_name, root_dir=save_metrics_dir, column_names=imputed_column_names)
+
+
+def info():
+    _script_info(__all__)

dragon_ml_toolbox-1.4.1/ml_tools/VIF_factor.py

@@ -0,0 +1,224 @@
+
+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+from typing import Optional
+from statsmodels.stats.outliers_influence import variance_inflation_factor
+from statsmodels.tools.tools import add_constant
+import warnings
+import os
+from .utilities import sanitize_filename, yield_dataframes_from_dir, save_dataframe, _script_info
+
+
+__all__ = [
+    "compute_vif",
+    "drop_vif_based",
+    "compute_vif_multi"
+]
+
+
+def compute_vif(
+    df: pd.DataFrame,
+    use_columns: Optional[list[str]] = None,
+    ignore_columns: Optional[list[str]] = None,
+    max_features_to_plot: int = 20,
+    save_dir: Optional[str] = None,
+    filename: Optional[str] = None,
+    fontsize: int = 14,
+    show_plot: bool = True,
+) -> pd.DataFrame:
+    """
+    Computes Variance Inflation Factors (VIF) for numeric columns in a DataFrame. Optionally, generates a bar plot of VIF values.
+
+    Args:
+        df (pd.DataFrame): The input DataFrame.
+        use_columns (list[str] | None): Optional list of columns to include. Defaults to all numeric columns.
+        ignore_columns (list[str] | None): Optional list of columns to exclude from the VIF computation. Skipped if `target_columns` is provided.
+        max_features_to_plot (int): Adjust the number of features shown in the plot.
+        save_dir (str | None): Directory to save the plot as SVG. If None, the plot is not saved.
+        filename (str | None): Optional filename for saving the plot. Defaults to "VIF_plot.svg".
+        fontsize (int): Base fontsize to scale title and labels on the plot.
+        show_plot (bool): Display plot.
+
+    Returns:
+        pd.DataFrame: DataFrame with features and their corresponding VIF values.
+        
+    NOTE:
+    **Variance Inflation Factor (VIF)** quantifies the degree of multicollinearity among features in a dataset. 
+    A VIF value indicates how much the variance of a regression coefficient is inflated due to linear dependence with other features. 
+    A VIF of 1 suggests no correlation, values between 1 and 5 indicate moderate correlation, and values greater than 10 typically signal high multicollinearity, which may distort model interpretation and degrade performance.
+    """
+    ground_truth_cols = df.columns.to_list()
+    if use_columns is None:
+        sanitized_columns = df.select_dtypes(include='number').columns.tolist()
+        missing_features = set(ground_truth_cols) - set(sanitized_columns)
+        if missing_features:
+            print(f"⚠️ These columns are not Numeric:\n{missing_features}")
+    else:
+        sanitized_columns = list()
+        for feature in use_columns:
+            if feature not in ground_truth_cols:
+                print(f"⚠️ The provided column '{feature}' is not in the DataFrame.")
+            else:
+                sanitized_columns.append(feature)
+    
+    if ignore_columns is not None and use_columns is None:
+        missing_ignore = set(ignore_columns) - set(ground_truth_cols)
+        if missing_ignore:
+            print(f"⚠️ Warning: The following 'columns to ignore' are not in the Dataframe:\n{missing_ignore}")
+        sanitized_columns = [f for f in sanitized_columns if f not in ignore_columns]
+
+    X = df[sanitized_columns].copy()
+    X = add_constant(X, has_constant='add')
+
+    vif_data = pd.DataFrame()
+    vif_data["feature"] = X.columns # type: ignore
+    
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", category=RuntimeWarning)
+
+        vif_data["VIF"] = [
+            variance_inflation_factor(X.values, i) for i in range(X.shape[1]) # type: ignore
+        ]
+
+    # Replace infinite values (perfect multicollinearity)
+    vif_data["VIF"] = vif_data["VIF"].replace([np.inf, -np.inf], 999.0)
+
+    # Drop the constant column
+    vif_data = vif_data[vif_data["feature"] != "const"]
+
+    # Add color coding
+    def vif_color(v: float) -> str:
+        if v >= 10:
+            return "red"
+        elif v >= 5:
+            return "gold"
+        else:
+            return "green"
+
+    vif_data["color"] = vif_data["VIF"].apply(vif_color)
+
+    # Sort by VIF descending
+    vif_data = vif_data.sort_values(by="VIF", ascending=False).reset_index(drop=True)
+
+    # Filter for plotting
+    plot_data = vif_data.head(max_features_to_plot)
+    
+    if save_dir or show_plot:
+        if not plot_data.empty:
+            plt.figure(figsize=(10, 6))
+            plt.barh(
+                plot_data["feature"],
+                plot_data["VIF"],
+                color=plot_data["color"],
+                edgecolor='black'
+            )
+            plt.title("Variance Inflation Factor (VIF) per Feature", fontsize=fontsize+1)
+            plt.xlabel("VIF value", fontsize=fontsize)
+            plt.xticks(fontsize=fontsize)
+            plt.yticks(fontsize=fontsize)
+            plt.axvline(x=5, color='gold', linestyle='--', label='VIF = 5')
+            plt.axvline(x=10, color='red', linestyle='--', label='VIF = 10')
+            plt.xlim(0, 12)
+            plt.legend(loc='lower right', fontsize=fontsize-1)
+            plt.gca().invert_yaxis()
+            plt.grid(axis='x', linestyle='--', alpha=0.5)
+            plt.tight_layout()
+
+            if save_dir:
+                os.makedirs(save_dir, exist_ok=True)
+                if filename is None:
+                    filename = "VIF_plot.svg"
+                else:
+                    filename = sanitize_filename(filename)
+                    if not filename.endswith(".svg"):
+                        filename += ".svg"
+                save_path = os.path.join(save_dir, "VIF_" + filename)
+                plt.savefig(save_path, format='svg', bbox_inches='tight')
+                print(f"\tSaved VIF plot: '{filename}'")
+            
+            if show_plot:
+                plt.show()
+            plt.close()
+
+    return vif_data.drop(columns="color")
+
+
+def drop_vif_based(df: pd.DataFrame, vif_df: pd.DataFrame, threshold: float = 10.0) -> tuple[pd.DataFrame, list[str]]:
+    """
+    Drops columns from the original DataFrame based on their VIF values exceeding a given threshold.
+
+    Args:
+        df (pd.DataFrame): Original DataFrame containing the columns to test.
+        vif_df (pd.DataFrame): DataFrame with 'feature' and 'VIF' columns as returned by `compute_vif()`.
+        threshold (float): VIF threshold above which columns will be dropped.
+
+    Returns:
+        (tuple[pd.DataFrame, list[str]]): 
+            - A new DataFrame with high-VIF columns removed.
+            - A list with dropped column names.
+    """
+    # Ensure expected structure
+    if 'feature' not in vif_df.columns or 'VIF' not in vif_df.columns:
+        raise ValueError("`vif_df` must contain 'feature' and 'VIF' columns.")
+    
+    # Identify features to drop
+    to_drop = vif_df[vif_df["VIF"] > threshold]["feature"].tolist()
+    print(f"\tDropping {len(to_drop)} column(s) with VIF > {threshold}: {to_drop}")
+    
+    result_df = df.drop(columns=to_drop)
+    
+    if result_df.empty:
+        print(f"\t⚠️ Warning: All columns were dropped.")
+
+    return result_df, to_drop
+
+
+def compute_vif_multi(input_directory: str,
+                      output_plot_directory: str,
+                      output_dataset_directory: Optional[str] = None,
+                      use_columns: Optional[list[str]] = None,
+                      ignore_columns: Optional[list[str]] = None,
+                      max_features_to_plot: int = 20,
+                      fontsize: int = 14):
+    """
+    Computes Variance Inflation Factors (VIF) for numeric columns in a directory with CSV files (loaded as pandas DataFrames). 
+    Generates a bar plot of VIF values. Optionally drops columns with VIF >= 10 and saves as a new CSV file.
+
+    Args:
+        input_directory (str): Target directory with CSV files able to be loaded as DataFrame.
+        output_plot_directory (str): Save plots to this directory.
+        output_dataset_directory (str | None): If provided, saves new CSV files to this directory.
+        use_columns (list[str] | None): Optional list of columns to include. Defaults to all numeric columns.
+        ignore_columns (list[str] | None): Optional list of columns to exclude from the VIF computation. Skipped if `target_columns` is provided.
+        max_features_to_plot (int): Adjust the number of features shown in the plot.
+        fontsize (int): Base fontsize to scale title and labels on hte plot.
+        
+    NOTE:
+    **Variance Inflation Factor (VIF)** quantifies the degree of multicollinearity among features in a dataset. 
+    A VIF value indicates how much the variance of a regression coefficient is inflated due to linear dependence with other features. 
+    A VIF of 1 suggests no correlation, values between 1 and 5 indicate moderate correlation, and values greater than 10 typically signal high multicollinearity, which may distort model interpretation and degrade performance.
+    """
+    if output_dataset_directory is not None:
+        os.makedirs(output_dataset_directory, exist_ok=True)
+    
+    for df, df_name in yield_dataframes_from_dir(datasets_dir=input_directory):
+        vif_dataframe = compute_vif(df=df,
+                            use_columns=use_columns,
+                            ignore_columns=ignore_columns,
+                            max_features_to_plot=max_features_to_plot,
+                            fontsize=fontsize,
+                            save_dir=output_plot_directory,
+                            filename=df_name,
+                            show_plot=False)
+        
+        if output_dataset_directory is not None:
+            new_filename = 'VIF_' + df_name
+            result_df, dropped_cols = drop_vif_based(df=df, vif_df=vif_dataframe)
+            
+            if len(dropped_cols) > 0:
+                save_dataframe(df=result_df, save_dir=output_dataset_directory, filename=new_filename)
+
+
+def info():
+    _script_info(__all__)