import os
import shutil
import pandas as pd

# 讀取 Excel 文件
file_path = '/home/onlylian/patient_modalities_files.xlsx'
df = pd.read_excel(file_path)

# 定義來源和目標資料夾
source_dir = '/home/onlylian/Complete_NEW_ORGAN_Target_Files'
target_dir = '/home/onlylian/sorted_OAR_Target_files'
modalities = ['CT', 'CTC', 'T1', 'T1C', 'T2', 'FLAIR', 'CT+CTC']

# 創建目標資料夾結構
for modality in modalities:
    modality_path = os.path.join(target_dir, modality)
    os.makedirs(modality_path, exist_ok=True)

# 遍歷每個病人ID和日期
for _, row in df.iterrows():
    modality = row['Modalities']
    patient_id = row['patient_id']
    date = str(row['date'])
    
    if modality in modalities:
        # 構建來源資料夾路徑
        source_path = os.path.join(source_dir, patient_id, date)
        print(f"Checking source path: {source_path}")  # 檢查路徑
        if os.path.exists(source_path):
            # 分別處理 ORGAN 和 RT 目錄
            organ_path = os.path.join(source_path, 'ORGAN')
            rt_path = os.path.join(source_path, 'RT')
            
            # 構建目標資料夾路徑
            modality_path = os.path.join(target_dir, modality, patient_id, date)
            os.makedirs(modality_path, exist_ok=True)

            # 遍歷 ORGAN 目錄中的所有檔案
            if os.path.exists(organ_path):
                for file_name in os.listdir(organ_path):
                    if file_name.endswith('.nii.gz'):  # 檢查檔案格式
                        source_file = os.path.join(organ_path, file_name)
                        target_file = os.path.join(modality_path, file_name)
                        print(f"Copying {source_file} to {target_file}")
                        shutil.copy2(source_file, target_file)
            else:
                print(f"ORGAN folder not found: {organ_path}")
            
            # 遍歷 RT 目錄中的所有檔案
            if os.path.exists(rt_path):
                for file_name in os.listdir(rt_path):
                    if file_name.endswith('.nii.gz'):  # 檢查檔案格式
                        source_file = os.path.join(rt_path, file_name)
                        target_file = os.path.join(modality_path, file_name)
                        print(f"Copying {source_file} to {target_file}")
                        shutil.copy2(source_file, target_file)
            else:
                print(f"RT folder not found: {rt_path}")
        else:
            print(f"Source path not found: {source_path}")
    else:
        print(f"Unknown modality {modality} for patient {patient_id} on {date}")