import os
import shutil
import difflib

def copy_organ_files(source_root, target_root):
    # 確保目標資料夾存在
    if not os.path.exists(target_root):
        os.makedirs(target_root)
        print(f"Created directory {target_root}")

    # 遍歷來源的根資料夾和所有子資料夾，尋找名為 ORGAN 的資料夾
    for root, dirs, files in os.walk(source_root):
        for dir in dirs:
            if dir == 'ORGAN':
                source_folder_path = os.path.join(root, dir)
                # 提取病例資料夾和日期資料夾
                case_folder = os.path.basename(os.path.dirname(os.path.dirname(os.path.dirname(source_folder_path))))
                date_folder = os.path.basename(os.path.dirname(os.path.dirname(source_folder_path)))
                # 組合目標資料夾路徑
                target_folder_path = os.path.join(target_root, case_folder, date_folder)
                
                # 確保目標資料夾存在
                if not os.path.exists(target_folder_path):
                    os.makedirs(target_folder_path)
                    print(f"Created directory {target_folder_path}")
                
                # 複製資料夾中的所有檔案到目標資料夾
                for file_name in os.listdir(source_folder_path):
                    source_file_path = os.path.join(source_folder_path, file_name)
                    target_file_path = os.path.join(target_folder_path, file_name)
                    
                    # 如果目標檔案已經存在，重新命名以避免覆蓋
                    if os.path.exists(target_file_path):
                        base, extension = os.path.splitext(file_name)
                        counter = 1
                        new_file_name = f"{base}_{counter}{extension}"
                        target_file_path = os.path.join(target_folder_path, new_file_name)
                        while os.path.exists(target_file_path):
                            counter += 1
                            new_file_name = f"{base}_{counter}{extension}"
                            target_file_path = os.path.join(target_folder_path, new_file_name)
                    
                    shutil.copy(source_file_path, target_file_path)
                    print(f"Copied {source_file_path} to {target_file_path}")

    print("All ORGAN files have been copied.")

def check_and_copy_files(root_dir, required_file_groups, target_dir, match_cutoff=0.7):
    # 確保目標目錄存在
    os.makedirs(target_dir, exist_ok=True)
    
    # 計算缺少文件的病人數量
    missing_files_patients = 0
    copied_files_patients = 0
    
    # 遍歷根目錄下的每個病人文件夾
    for patient_id in os.listdir(root_dir):
        patient_dir = os.path.join(root_dir, patient_id)
        
        # 確保是目錄
        if os.path.isdir(patient_dir):
            # 遍歷病人目錄下的日期文件夾
            for date_folder in os.listdir(patient_dir):
                date_dir = os.path.join(patient_dir, date_folder)
                existing_files = os.listdir(date_dir)
                
                # 檢查指定的OAR文件是否存在
                missing_files = []
                for file_group in required_file_groups:
                    # 對於左右眼的文件，進行更精確的匹配
                    if 'Left_Eye' in file_group[0]:
                        matches = [f for f in existing_files if 'Left_Eye' in f]
                    elif 'Right_Eye' in file_group[0]:
                        matches = [f for f in existing_files if 'Right_Eye' in f]
                    else:
                        # 對其他文件使用模糊匹配來查找接近的文件名稱
                        matches = difflib.get_close_matches(file_group[0], existing_files, n=1, cutoff=match_cutoff)
                    
                    if not matches:
                        missing_files.append(file_group[0])  # 使用文件組中的第一個文件名作為缺失文件的表示
                    else:
                        print(f"匹配到的文件: {matches[0]} 對應到 {file_group[0]}")
                
                if missing_files:
                    missing_files_patients += 1
                    print(f"病人: {patient_id}, 日期: {date_folder}, 缺失的文件: {missing_files}")
                else:
                    # 沒有缺失文件，複製文件到新目錄
                    new_patient_dir = os.path.join(target_dir, patient_id)
                    new_date_dir = os.path.join(new_patient_dir, date_folder)
                    os.makedirs(new_date_dir, exist_ok=True)
                    
                    for file_name in existing_files:
                        src_file = os.path.join(date_dir, file_name)
                        dst_file = os.path.join(new_date_dir, file_name)
                        shutil.copy(src_file, dst_file)
                    
                    copied_files_patients += 1
                    print(f"病人: {patient_id}, 日期: {date_folder}, 文件已成功複製")
    
    print(f"缺少所需OAR文件的資料總數: {missing_files_patients}")
    print(f"文件完整且已複製的資料總數: {copied_files_patients}")

def count_patients_and_records(target_dir):
    patient_count = 0
    record_count = 0
    
    for patient_id in os.listdir(target_dir):
        patient_dir = os.path.join(target_dir, patient_id)
        
        if os.path.isdir(patient_dir):
            patient_count += 1
            record_count += len(os.listdir(patient_dir))
    
    print(f"完整OAR文件的病人總數: {patient_count}")
    print(f"完整OAR文件的資料總數: {record_count}")

if __name__ == "__main__":
    # 第一部分：複製 ORGAN 文件
    source_root = '/mnt/1218/onlylian/M6_24Q3/nii'
    intermediate_target = '/mnt/1218/onlylian/NEW_ORGAN_Files'
    copy_organ_files(source_root, intermediate_target)

    # 第二部分：檢查並複製完整的 OAR 文件
    required_file_groups = [
        ['Struct_Brain_Stem.nii.gz'],
        ['Struct_Left_Optic_Nerve.nii.gz'],
        ['Struct_Right_Optic_Nerve.nii.gz'],
        ['Struct_Left_Eye.nii.gz'],
        ['Struct_Right_Eye.nii.gz'],
        ['Struct_Optic_Chiasm.nii.gz']
    ]
    final_target = '/mnt/1218/onlylian/Complete_NEW_OAR_Files'
    
    check_and_copy_files(intermediate_target, required_file_groups, final_target)
    
    # 計算總共的病人和記錄數量
    count_patients_and_records(final_target)