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LLM_extraction
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Delete q25_14_ins_int8.py

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      import os
      import re
      import torch
      import json
      # import time
      # import pynvml
      from tqdm import tqdm
      import torch.distributed as dist
      from vllm import LLM, SamplingParams
      os.environ["NCCL_P2P_DISABLE"] = "1"
      torch.cuda.empty_cache()
      os.environ["TRANSFORMERS_OFFLINE"] = "1"
      os.environ["HF_DATASETS_OFFLINE"] = "1"
      os.environ["PYTORCH_CUDA_ALLOC_CONF"] = "expandable_segments:True"
      texts_path = "/home/limeng/NLP/LLM/data/jcza/record_text2.txt"
      model_path = "/home/limeng/NLP/LLM/model/Qwen2.5-14B-Instruct-GPTQ-Int8"
      output_path = "/home/limeng/NLP/LLM/code/0220/result"
      llm = LLM(model=model_path, dtype="half",gpu_memory_utilization=0.9)
      sampling_params = SamplingParams(temperature=0.3, top_p=0.3, max_tokens = 1500)
      with open(texts_path, "r", encoding="utf-8") as file:
      for i,line in enumerate(file):
      medical_record = line.strip() # 处理每一行，去除首尾空白字符
      prompt = f"""
      你是一个专业的医疗信息抽取助手。请从以下病历数据中严格按照#### 示例 JSON 提取字段信息，并确保：
      1. **字段必须完整**，与示例 JSON 结构完全一致，不可缺失/新增/改动任何字段
      2. **重点字段精确**：
      - 手术史需抽提所有手术名称+时间（格式："手术名称": "时间"）
      - 化疗方案需按"方案名": {{时间+具体用药列表}} 格式提取
      - 放疗方案需按"方案描述": {{时间+次数+剂量}} 格式提取
      3. **严格空值处理**：
      - 字符串字段填"无"
      - 列表/字典字段填空列表[]/空字典{{}}
      - 嵌套结构需保持完整（如肿瘤患病史必须含"肿瘤类型"/"肿瘤结局"字段）
      4. **严格JSON格式**：
      - 保持与示例完全相同的缩进/标点格式
      - 确保所有括号闭合，逗号正确
      - 生成第一个完整JSON后立即停止，禁止解释性文字
      #### 病历数据
      {medical_record}
      #### 示例 JSON
      {{
      "消瘦": "有",
      "呕吐": "有",
      "恶心": "有",
      "腹部肿块": "有",
      "腹胀": "有",
      "腹痛": "有",
      "里急后重": "有",
      "腹泻": "有",
      "大便形状改变": "有",
      "排便困难": "有",
      "黑便": "有",
      "便血": "有",
      "大便习惯和性状改变": "有",
      "肠梗阻": "有",
      "肠穿孔": "有",
      "手术史": {{
      "直肠癌经腹前切除+末端回肠造口术": "2017-01-11日",
      "冠脉支架置入术":" 2019年",
      }},
      "肝转移": "有",
      "肺转移": "有",
      "腹膜转移": "有",
      "骨转移": "有",
      "远处转移": "有",
      "锁骨上转移": "有",
      "腹股沟转移": "有",
      "腹膜后淋巴结转移": "有",
      "其他远处淋巴转移": "无",
      "化疗方案": {{
      "2011-1-12行XELOX方案":
      {{"时间": "2011-1-12"
      "具体用药": [
      "卡培他宾1.5g 2/日d1-14",
      "奥沙利铂200mg d1"
      ]
      }},
      "2022-7-17、8-9行FOLFOX+西妥昔单抗方案":
      {{ "时间": "2022-7-17、8-9"
      "具体用药": [
      "奥沙利铂140mg 静滴D1",
      "亚叶酸钙0.6g 静滴D1",
      "5-FU 0.4g 静滴D1",
      "5-FU 4.0g 化疗泵入44h",
      "西妥昔单抗800mg 静滴D1"
      ]}}
      }},
      "放疗方案":
      {{
      "盆腔复发灶": {{
      "时间": "2023-04-20至2023-05-30",
      "次数": "25",
      "单次剂量":"2Gy",
      "总剂量":"50Gy"
      }},
      "照射方法为适形调强放疗IMRT，分割方法为常规分割，疗效评估为PR": {{
      "时间": "2021年11月15日开始，2021年12月24日结束",
      "次数": "25",
      "单次剂量":"2Gy",
      "总剂量":""
      }},
      }},
      "仍需治疗的其他疾病情况": ["高血压", "糖尿病"],
      "入院前仍在服用的治疗药物": ["硝苯地平缓释片", "达格列净", "格列齐特"],
      "高血压史": "有",
      "伤寒史": "有",
      "结核史": "有",
      "病毒性肝炎史": "有",
      "糖尿病史": "有",
      "冠心病史": "有",
      "冠脉支架放置": "有",
      "脑卒中史": "有",
      "其他非肿瘤疾病": [
      "慢性乙型病毒性肝炎",
      ],
      "肿瘤患病史": {{
      "肿瘤类型": "左肺腺癌",
      "肿瘤结局": "治愈"
      }}
      "吸烟史": {{
      "吸烟年数": "25年",
      "日吸烟量": "10支/天",
      "是否戒烟": "已戒烟15年"
      }},
      "饮酒史": "有"
      "婚育史": {{
      "是否已婚": "已婚",
      "是否已育": "已育",
      "已育数量": "1女"
      }},
      "结直肠癌家族史": {{
      "遗传性结直肠癌类型": "无",
      "亲属类型": "弟弟",
      "其他遗传性肿瘤": "结肠癌"
      }},
      "体温": "36.0℃",
      "呼吸": "18次/分",
      "心率": "80次/分",
      "血压": "120/80mmHg",
      "BMI": "19.6"
      "直肠指诊": {{
      "直肠指诊姿势": "膝胸位",
      "直肠指诊是否触及肿块": "有",
      "直肠指诊肿块下缘到肛缘距离": "5cm",
      "直肠指诊肿块下缘到齿状线距离": "无",
      "直肠指诊肿块活动度": "尚可",
      "直肠指诊指套推出是否染血": "有"
      }},
      "贫血貌": "有",
      "巩膜黄染": "有",
      "锁骨上淋巴结肿大": "有",
      "腹壁静脉曲张": "有",
      "肠形": "有",
      "腹部压痛": "有",
      }}
      """
      try:
      # 调用模型生成结果
      outputs = llm.generate(prompt, sampling_params)
      model_output = outputs[0].outputs[0].text
      print(model_output)
      # 尝试提取 JSON 部分
      json_str = re.search(r'```json\n(.*?)\n```', model_output, re.DOTALL)
      if json_str:
      json_str = json_str.group(1)
      result_json = json.loads(json_str)
      else:
      # 如果未找到 JSON 部分，直接保存原始文本
      json_str = re.search(r'#### JSON 提取结果\n(.*?)\n#### JSON 提取结果', model_output, re.DOTALL)
      if json_str:
      result_json = json.loads(json_str.group(1))
      else:
      # 如果未找到 #### JSON 提取结果 格式，尝试提取 #### JSON 输出 格式
      json_str = re.search(r'#### JSON 输出\n(.*?)\n#### JSON 输出', model_output, re.DOTALL)
      if json_str:
      result_json = json.loads(json_str.group(1))
      else:
      json_str = re.search(r'#### JSON 提取结果\n(.*?) 根据提', model_output, re.DOTALL)
      if json_str:
      result_json = json.loads(json_str.group(1))
      else:
      result_json = {"error": "Invalid model output format", "original_text": medical_record, "model_output": model_output}
      # 保存结果到 JSON 文件
      file_name = f"long_txt{i}.json"
      file_path = os.path.join(output_path, file_name)
      with open(file_path, 'w', encoding='utf-8') as f:
      json.dump({"text_record": medical_record, "extracted_info": result_json}, f, ensure_ascii=False, indent=4)
      except Exception as e:
      # 捕获异常并记录错误
      print(f"Error processing record {i}: {e}")
      # 保存原始文本
      file_name = f"long_txt{i}_error.json"
      file_path = os.path.join(output_path, file_name)
      with open(file_path, 'w', encoding='utf-8') as f:
      json.dump({"text_record": medical_record, "error": str(e)}, f, ensure_ascii=False, indent=4)
      \ No newline at end of file
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