Merge branch 'main' of https://gitty.informatik.hs-mannheim.de/1826514/DSA_SS24

scripts/data_helper.py

@@ -13,7 +13,7 @@ import cv2 as cv
 TODO create overall description
 """
 
-def load_data(only_demographic:bool=False, path_settings:str="../settings.json"):
+def load_data(only_demographic:bool=False, only_diagnosis_ids=False, path_settings:str="../settings.json"):
     """
     Loads data from pickle files based on the specified settings.
 
@@ -28,6 +28,10 @@ def load_data(only_demographic:bool=False, path_settings:str="../settings.json")
     path_data = settings["data_path"] 
     labels = settings["labels"]
 
+    if only_diagnosis_ids:
+        with open(f'{path_data}/diagnosis.pkl', 'rb') as f:
+            return pickle.load(f)
+
     data = {}
     if only_demographic:
         data = {'age': [], 'diag': [], 'gender': []}

scripts/feature_extraction.py

@@ -5,6 +5,7 @@ import math
 import time
 from multiprocessing import Pool
 import sqlite3
+import random
 
 def get_y_value(ecg_cleaned, indecies):
     """
@@ -213,7 +214,6 @@ def extract_features_parallel(data_dict, num_processes, sampling_rate=500, used_
     c = conn.cursor()
     # get unique data
     data_dict = exclude_already_extracted(data_dict, conn)
-
     for label, data in data_dict.items():
         print(f"Extracting features for {label} with {len(data)} data entries.")
         with Pool(processes=num_processes) as pool:
@@ -239,7 +239,7 @@ def extract_features_parallel(data_dict, num_processes, sampling_rate=500, used_
 
 
 
-def extract_features(data_dict, sampling_rate=500, used_channels=[0, 1, 2, 3, 4, 5]):
+def extract_features(data_dict, sampling_rate=500, used_channels=[0, 1, 2, 3, 4, 5], limit=1000):
     """
     Extracts the features from the data.
     Args:
@@ -266,6 +266,8 @@ def extract_features(data_dict, sampling_rate=500, used_channels=[0, 1, 2, 3, 4,
         print("No last file in DB")
 
     for label, data in data_dict.items():
+        # get limit amount of radom samples out of data
+        data = random.sample(data, min(len(data), limit))
         print(f"Extracting features for {label} with {len(data)} data entries.")
         for data_idx, record in enumerate(data):
             # Skip the records that are already in the database

scripts/generate_data.py

@@ -30,7 +30,7 @@ def get_diagnosis_ids(record):
     list_diagnosis = [int(x.strip()) for x in diagnosis.split(',')]
     return list_diagnosis
 
-def generate_raw_data(path_to_data, settings, max_counter=100_000):
+def generate_raw_data(path_to_data, settings, max_counter=100_000, only_ids=False):
     """
     Generates the raw data from the WFDB records.
     Args:
@@ -43,7 +43,10 @@ def generate_raw_data(path_to_data, settings, max_counter=100_000):
     failed_records = []
     categories = settings["labels"]
 
-    diag_dict = {k: [] for k in categories.keys()}
+    if only_ids:
+        diag_dict = {}
+    else:
+        diag_dict = {k: [] for k in categories.keys()}
     # Loop through the records
     for dir_th in os.listdir(path_to_data):
         path_to_1000_records = path_to_data + '/' + dir_th
@@ -60,12 +63,15 @@ def generate_raw_data(path_to_data, settings, max_counter=100_000):
                     record = wfdb.rdrecord(path_to_100_records + '/' + record_name)
                     # Get the diagnosis
                     diagnosis = np.array(get_diagnosis_ids(record))
-                    # check if diagnosis is a subset of one of the categories
+                    if only_ids: 
-                    for category_name, category_codes in categories.items():
+                        diag_dict[record_name] = diagnosis
-                        # if any of the diagnosis codes is in the category_codes
+                    else:
-                        if any(i in category_codes for i in diagnosis):
+                        # check if diagnosis is a subset of one of the categories
-                            diag_dict[category_name].append(record)
+                        for category_name, category_codes in categories.items():
-                            break
+                            # if any of the diagnosis codes is in the category_codes
+                            if any(i in category_codes for i in diagnosis):
+                                diag_dict[category_name].append(record)
+                                break
                     # Increment the counter of how many records we have read
                     counter += 1
                     counter_bool = counter >= max_counter
@@ -83,7 +89,7 @@ def generate_raw_data(path_to_data, settings, max_counter=100_000):
             break
     return diag_dict
 
-def write_data(data_dict, path='./data', file_prefix=''):
+def write_data(data_dict, path='./data', file_prefix='', only_ids=False):
     """
     Writes the data to a pickle file.
     Args:
@@ -93,6 +99,13 @@ def write_data(data_dict, path='./data', file_prefix=''):
     # if path not exists create it
     if not os.path.exists(path):
             os.makedirs(path)
+
+    if only_ids:
+        # write to pickle
+        print(f"Writing diagnosis IDs to pickle with {len(data_dict)} data entries.")
+        with open(f'{path}/{file_prefix}.pkl', 'wb') as f:
+            pickle.dump(data_dict, f)
+        return
     # write to pickle
     for cat_name, data in data_dict.items():
         print(f"Writing {cat_name} to pickle with {len(data)} data entries.")
@@ -114,7 +127,7 @@ def generate_feature_data(input_data_path, settings, parallel=False, split_ratio
         split_ratio = settings['split_ratio']
     print(list(os.listdir(input_data_path)))
     for file in os.listdir(input_data_path):
-        if file.endswith(".pkl"):
+        if file.endswith(".pkl") and not file.startswith("diagnosis"):
             print(f"Reading {file}")
             with open(f'{input_data_path}/{file}', 'rb') as f:
                 data = pickle.load(f)
@@ -127,13 +140,14 @@ def generate_feature_data(input_data_path, settings, parallel=False, split_ratio
                 print(f"Using {max_processes} processes to extract features.")
                 feature_extraction.extract_features_parallel(data_dict, num_processes=max_processes)
             else:
-                feature_extraction.extract_features(data_dict)
+                print(f"For even distribution of data, the limit is set to the smallest size: 1000.")
+                feature_extraction.extract_features(data_dict, limit=1000)
     # Split the data
     feature_extraction.split_and_shuffle_data(split_ratio=split_ratio)
 
 
 
-def main(gen_data=True, gen_features=True, split_ratio=None, parallel=False, settings_path='./settings.json', num_process_files=-1):
+def main(gen_data=True, gen_features=True, gen_diag_ids=True, split_ratio=None, parallel=False, settings_path='./settings.json', num_process_files=-1):
     """
     Main function to generate the data.
     Args:
@@ -159,6 +173,11 @@ def main(gen_data=True, gen_features=True, split_ratio=None, parallel=False, set
     if gen_features:
         feature_data_dict = generate_feature_data(settings["data_path"], settings, split_ratio=split_ratio, parallel=parallel)
         ret_data = feature_data_dict
+    if gen_diag_ids:
+        raw_data_dir = settings["wfdb_path"] + '/WFDBRecords'
+        data_dict = generate_raw_data(raw_data_dir, settings, max_counter=num_process_files, only_ids=True)
+        write_data(data_dict, path=settings["data_path"], file_prefix='diagnosis', only_ids=True)
+        ret_data = data_dict
 
     return ret_data
         
@@ -178,6 +197,7 @@ if __name__ == '__main__':
     # SB, AFIB, GSVT, SR
     # new GSVT, AFIB, SR, SB
     # Generate the data
-    main(gen_data=True, gen_features=False, num_process_files=100_000)
+    #main(gen_data=True, gen_features=False, gen_diag_ids=False, num_process_files=100_000)
-    #main(gen_data=False, gen_features=True, split_ratio=[0.8, 0.1, 0.1], parallel=False, num_process_files=100_000)
+    #main(gen_data=False, gen_features=True, gen_diag_ids=False, split_ratio=[0.8, 0.1, 0.1])
+    main(gen_data=False, gen_features=False, gen_diag_ids=True)
     print("Data generation completed.")