MEDfl 0.2.1__py3-none-any.whl → 2.0.0__py3-none-any.whl

Medfl/LearningManager/utils.py

@@ -0,0 +1,331 @@
+#!/usr/bin/env python3
+
+import pkg_resources
+import torch
+import yaml
+from sklearn.metrics import *
+from yaml.loader import SafeLoader
+
+
+from MEDfl.NetManager.database_connector import DatabaseManager
+
+# from scripts.base import *
+import json
+
+
+import pandas as pd
+import numpy as np
+
+import os
+import configparser
+
+import subprocess
+import ast
+
+from sqlalchemy import text
+
+
+# Get the directory of the current script
+current_directory = os.path.dirname(os.path.abspath(__file__))
+
+# Load configuration from the config file
+yaml_path = os.path.join(current_directory, 'params.yaml')
+
+with open(yaml_path) as g:
+    params = yaml.load(g, Loader=SafeLoader)
+
+# global_yaml_path = pkg_resources.resource_filename(__name__, "../../global_params.yaml")
+# with open(global_yaml_path) as g:
+#     global_params = yaml.load(g, Loader=SafeLoader)
+
+
+# Default path for the config file
+DEFAULT_CONFIG_PATH = 'db_config.ini'
+
+
+def load_db_config_dep():
+    config = os.environ.get('MEDfl_DB_CONFIG')
+
+    if config:
+        return ast.literal_eval(config)
+    else:
+        raise ValueError(f"MEDfl db config not found")
+
+# Function to allow users to set config path programmatically
+
+
+def set_db_config_dep(config_path):
+    config = configparser.ConfigParser()
+    config.read(config_path)
+    if (config['sqllite']):
+        os.environ['MEDfl_DB_CONFIG'] = str(dict(config['sqllite']))
+    else:
+        raise ValueError(f"mysql key not found in file '{config_path}'")
+
+
+
+def load_db_config():
+    """Read a dictionary from an environment variable."""
+    obj_str = os.getenv("MEDfl_DB_CONFIG")
+    if obj_str is not None:
+        return ast.literal_eval(obj_str)
+    else:
+        raise ValueError(f"Environment variable MEDfl_DB_CONFIG not found")
+
+# Function to allow users to set config path programmatically
+
+
+def set_db_config(config_path):
+    obj = {"database" : config_path}
+
+    """Store a dictionary as a string in an environment variable."""
+    obj_str = str(obj)
+    os.environ['MEDfl_DB_CONFIG'] = obj_str
+
+    
+
+
+
+
+# Create databas
+
+
+def create_MEDfl_db():
+    script_path = os.path.join(os.path.dirname(
+        __file__), 'scripts', 'create_db.sh')
+    subprocess.run(['sh', script_path], check=True)
+
+
+def custom_classification_report(y_true, y_pred_prob):
+    """
+    Compute custom classification report metrics including accuracy, sensitivity, specificity, precision, NPV,
+    F1-score, false positive rate, and true positive rate.
+
+    Args:
+        y_true (array-like): True labels.
+        y_pred (array-like): Predicted labels.
+
+    Returns:
+        dict: A dictionary containing custom classification report metrics.
+    """
+    y_pred = (y_pred_prob).round(
+    )  # Round absolute values of predicted probabilities to the nearest integer
+
+    auc = roc_auc_score(y_true, y_pred_prob)  # Calculate AUC
+
+    tn, fp, fn, tp = confusion_matrix(y_true, y_pred).ravel()
+
+    # Accuracy
+    denominator_acc = tp + tn + fp + fn
+    acc = (tp + tn) / denominator_acc if denominator_acc != 0 else 0.0
+
+    # Sensitivity/Recall
+    denominator_sen = tp + fn
+    sen = tp / denominator_sen if denominator_sen != 0 else 0.0
+
+    # Specificity
+    denominator_sp = tn + fp
+    sp = tn / denominator_sp if denominator_sp != 0 else 0.0
+
+    # PPV/Precision
+    denominator_ppv = tp + fp
+    ppv = tp / denominator_ppv if denominator_ppv != 0 else 0.0
+
+#     NPV
+    denominator_npv = tn + fn
+    npv = tn / denominator_npv if denominator_npv != 0 else 0.0
+
+    # F1 Score
+    denominator_f1 = sen + ppv
+    f1 = 2 * (sen * ppv) / denominator_f1 if denominator_f1 != 0 else 0.0
+
+    # False Positive Rate
+    denominator_fpr = fp + tn
+    fpr = fp / denominator_fpr if denominator_fpr != 0 else 0.0
+
+    # True Positive Rate
+    denominator_tpr = tp + fn
+    tpr = tp / denominator_tpr if denominator_tpr != 0 else 0.0
+
+    return {
+        "confusion matrix": {"TP": tp, "FP": fp, "FN": fn, "TN": tn},
+        "Accuracy": round(acc, 3),
+        "Sensitivity/Recall": round(sen, 3),
+        "Specificity": round(sp, 3),
+        "PPV/Precision": round(ppv, 3),
+        "NPV": round(npv, 3),
+        "F1-score": round(f1, 3),
+        "False positive rate": round(fpr, 3),
+        "True positive rate": round(tpr, 3),
+        "auc": auc
+    }
+
+
+def test(model, test_loader, device=torch.device("cpu")):
+    """
+    Evaluate a model using a test loader and return a custom classification report.
+
+    Args:
+        model (torch.nn.Module): PyTorch model to evaluate.
+        test_loader (torch.utils.data.DataLoader): DataLoader for the test dataset.
+        device (torch.device, optional): Device for model evaluation. Default is "cpu".
+
+    Returns:
+        dict: A dictionary containing custom classification report metrics.
+    """
+
+    model.eval()
+    with torch.no_grad():
+        X_test, y_test = test_loader.dataset[:][0].to(
+            device), test_loader.dataset[:][1].to(device)
+        y_hat_prob = torch.squeeze(model(X_test), 1).cpu()
+
+    return custom_classification_report(y_test.cpu().numpy(), y_hat_prob.cpu().numpy())
+
+
+column_map = {"object": "VARCHAR(255)", "int64": "INT", "float64": "FLOAT"}
+
+
+def empty_db():
+    """
+    Empty the database by deleting records from multiple tables and resetting auto-increment counters.
+
+    Returns:
+        None
+    """
+    db_manager = DatabaseManager()
+    db_manager.connect()
+    my_eng = db_manager.get_connection()
+
+    # my_eng.execute(text(f"DELETE FROM  {'DataSets'}"))
+    my_eng.execute(text(f"DELETE FROM {'Nodes'}"))
+    my_eng.execute(text(f"DELETE FROM {'FedDatasets'}"))
+    my_eng.execute(text(f"DELETE FROM {'Networks'}"))
+    my_eng.execute(text(f"DELETE FROM {'FLsetup'}"))
+
+    my_eng.execute(text(f"DELETE FROM {'FLpipeline'}"))
+    my_eng.execute(text(f"ALTER TABLE {'Nodes'} AUTO_INCREMENT = 1"))
+    my_eng.execute(text(f"ALTER TABLE {'Networks'} AUTO_INCREMENT = 1"))
+    my_eng.execute(text(f"ALTER TABLE {'FedDatasets'} AUTO_INCREMENT = 1"))
+    my_eng.execute(text(f"ALTER TABLE {'FLsetup'} AUTO_INCREMENT = 1"))
+    my_eng.execute(text(f"ALTER TABLE {'FLpipeline'} AUTO_INCREMENT = 1"))
+    my_eng.execute(text(f"DELETE FROM {'testResults'}"))
+    my_eng.execute(text(f"DROP TABLE IF EXISTS {'MasterDataset'}"))
+    my_eng.execute(text(f"DROP TABLE IF EXISTS {'DataSets'}"))
+
+
+def get_pipeline_from_name(name):
+    """
+    Get the pipeline ID from its name in the database.
+
+    Args:
+        name (str): Name of the pipeline.
+
+    Returns:
+        int: ID of the pipeline.
+    """
+    db_manager = DatabaseManager()
+    db_manager.connect()
+    my_eng = db_manager.get_connection()
+
+    NodeId = int(
+        pd.read_sql(
+            text(f"SELECT id FROM FLpipeline WHERE name = '{name}'"), my_eng
+        ).iloc[0, 0]
+    )
+    return NodeId
+
+
+def get_pipeline_confusion_matrix(pipeline_id):
+    """
+    Get the global confusion matrix for a pipeline based on test results.
+
+    Args:
+        pipeline_id (int): ID of the pipeline.
+
+    Returns:
+        dict: A dictionary representing the global confusion matrix.
+    """
+    db_manager = DatabaseManager()
+    db_manager.connect()
+    my_eng = db_manager.get_connection()
+
+    data = pd.read_sql(
+        text(
+            f"SELECT confusionmatrix FROM testResults WHERE pipelineid = '{pipeline_id}'"), my_eng
+    )
+
+    # Convert the column of strings into a list of dictionaries representing confusion matrices
+    confusion_matrices = [
+        json.loads(matrix.replace("'", "\"")) for matrix in data['confusionmatrix']
+    ]
+
+    # Initialize variables for global confusion matrix
+    global_TP = global_FP = global_FN = global_TN = 0
+
+    # Iterate through each dictionary and sum the corresponding values for each category
+    for matrix in confusion_matrices:
+        global_TP += matrix['TP']
+        global_FP += matrix['FP']
+        global_FN += matrix['FN']
+        global_TN += matrix['TN']
+
+    # Create a global confusion matrix as a dictionary
+    global_confusion_matrix = {
+        'TP': global_TP,
+        'FP': global_FP,
+        'FN': global_FN,
+        'TN': global_TN
+    }
+    # Return the list of dictionaries representing confusion matrices
+    return global_confusion_matrix
+
+
+def get_node_confusion_matrix(pipeline_id, node_name):
+    """
+    Get the confusion matrix for a specific node in a pipeline based on test results.
+
+    Args:
+        pipeline_id (int): ID of the pipeline.
+        node_name (str): Name of the node.
+
+    Returns:
+        dict: A dictionary representing the confusion matrix for the specified node.
+    """
+    db_manager = DatabaseManager()
+    db_manager.connect()
+    my_eng = db_manager.get_connection()
+
+    data = pd.read_sql(
+        text(
+            f"SELECT confusionmatrix FROM testResults WHERE pipelineid = '{pipeline_id}' AND nodename = '{node_name}'"), my_eng
+    )
+
+    # Convert the column of strings into a list of dictionaries representing confusion matrices
+    confusion_matrices = [
+        json.loads(matrix.replace("'", "\"")) for matrix in data['confusionmatrix']
+    ]
+
+    # Return the list of dictionaries representing confusion matrices
+    return confusion_matrices[0]
+
+
+def get_pipeline_result(pipeline_id):
+    """
+    Get the test results for a pipeline.
+
+    Args:
+        pipeline_id (int): ID of the pipeline.
+
+    Returns:
+        pandas.DataFrame: DataFrame containing test results for the specified pipeline.
+    """
+    db_manager = DatabaseManager()
+    db_manager.connect()
+    my_eng = db_manager.get_connection()
+
+    data = pd.read_sql(
+        text(
+            f"SELECT * FROM testResults WHERE pipelineid = '{pipeline_id}'"), my_eng
+    )
+    return data

Medfl/NetManager/__init__.py

@@ -0,0 +1,10 @@
+# # MEDfl/NetworkManager/__init__.py
+
+# # Import modules from this package
+# from .dataset import *
+# from .flsetup import *
+# from .net_helper import *
+# from .net_manager_queries import *
+# from .network import *
+# from .node import *
+# from .database_connector import *

Medfl/NetManager/database_connector.py

@@ -0,0 +1,43 @@
+import os
+import subprocess
+from sqlalchemy import create_engine
+from configparser import ConfigParser
+
+class DatabaseManager:
+    def __init__(self):
+        from MEDfl.LearningManager.utils import load_db_config
+        db_config = load_db_config()
+        if db_config:
+            self.config = db_config
+        else:
+            self.config = None
+        self.engine = None
+
+    def connect(self):
+        if not self.config:
+            raise ValueError("Database configuration not loaded. Use load_db_config() or set_config_path() first.")
+        # Assuming the SQLite database file path is provided in the config with the key 'database'
+        database_path = self.config['database']
+        connection_string = f"sqlite:///{database_path}"
+        self.engine = create_engine(connection_string, pool_pre_ping=True)
+
+    def get_connection(self):
+        if not self.engine:
+            self.connect()
+        return self.engine.connect()
+
+    def create_MEDfl_db(self, path_to_csv):
+        # Get the directory of the current script
+        current_directory = os.path.dirname(__file__)
+
+        # Define the path to the create_db.py script
+        create_db_script_path = os.path.join(current_directory, '..', 'scripts', 'create_db.py')
+
+        # Execute the create_db.py script
+        subprocess.run(['python', create_db_script_path, path_to_csv], check=True)
+
+        return
+
+    def close(self):
+        if self.engine:
+            self.engine.dispose()

Medfl/NetManager/dataset.py

@@ -0,0 +1,92 @@
+import pandas as pd
+from sqlalchemy import text
+
+from .net_helper import *
+from .net_manager_queries import (DELETE_DATASET, INSERT_DATASET,
+                                  SELECT_ALL_DATASET_NAMES)
+from MEDfl.NetManager.database_connector import DatabaseManager
+
+class DataSet:
+    def __init__(self, name: str, path: str, engine=None):
+        """
+        Initialize a DataSet object.
+
+        :param name: The name of the dataset.
+        :type name: str
+        :param path: The file path of the dataset CSV file.
+        :type path: str
+        """
+        self.name = name
+        self.path = path
+        db_manager = DatabaseManager()
+        db_manager.connect()
+        self.engine = db_manager.get_connection()
+
+    def validate(self):
+        """
+        Validate name and path attributes.
+
+        :raises TypeError: If name or path is not a string.
+        """
+        if not isinstance(self.name, str):
+            raise TypeError("name argument must be a string")
+
+        if not isinstance(self.path, str):
+            raise TypeError("path argument must be a string")
+
+    def upload_dataset(self, NodeId=-1):
+        """
+        Upload the dataset to the database.
+
+        :param NodeId: The NodeId associated with the dataset.
+        :type NodeId: int
+
+        Notes:
+        - Assumes the file at self.path is a valid CSV file.
+        - The dataset is uploaded to the 'DataSets' table in the database.
+        """
+
+        data_df = pd.read_csv(self.path)
+        nodeId = NodeId
+        columns = data_df.columns.tolist()
+        
+
+        data_df = process_eicu(data_df)
+        for index, row in data_df.iterrows():
+            query_1 = "INSERT INTO DataSets(DataSetName,nodeId," + "".join(
+                f"{x}," for x in columns
+            )
+            query_2 = f" VALUES ('{self.name}',{nodeId}, " + "".join(
+                f"{is_str(data_df, row, x)}," for x in columns
+            )
+            query = query_1[:-1] + ")" + query_2[:-1] + ")"
+             
+            self.engine.execute(text(query))
+
+    def delete_dataset(self):
+        """
+        Delete the dataset from the database.
+
+        Notes:
+        - Assumes the dataset name is unique in the 'DataSets' table.
+        """
+        self.engine.execute(text(DELETE_DATASET), {"name": self.name})
+
+    def update_data(self):
+        """
+        Update the data in the dataset.
+
+        Not implemented yet.
+        """
+        pass
+
+    @staticmethod
+    def list_alldatasets(engine):
+        """
+        List all dataset names from the 'DataSets' table.
+
+        :returns: A DataFrame containing the names of all datasets in the 'DataSets' table.
+        :rtype: pd.DataFrame
+        """
+        res = pd.read_sql(text(SELECT_ALL_DATASET_NAMES), engine)
+        return res