import torch import os import json import gc import csv from PIL import Image from datasets import load_dataset from collections import defaultdict from tqdm import tqdm import numpy as np from ..utils import save_json,extract from ..base_dataset import BaseDataset from ..question_formats import get_report_generation_prompt class CheXpert_Plus(BaseDataset): def __init__(self,model,dataset_path,output_path): self.model = model self.output_path = output_path self.dataset_path = dataset_path self.samples = [] self.chunk_idx = int(os.environ.get("chunk_idx",0)) self.num_chunks = int(os.environ.get("num_chunks",1)) def load_data(self): self.maybe_download_dataset() dataset_path = self.dataset_path json_path = os.path.join(dataset_path,"test.json") with open(json_path,"r") as f: dataset = json.load(f) for idx,sample in tqdm(enumerate(dataset)): if idx % self.num_chunks == self.chunk_idx: if sample["findings"].strip() == "" and sample["impression"].strip() == "": continue sample = self.construct_messages(sample) self.samples.append(sample) print("total samples number:", len(self.samples)) return self.samples def construct_messages(self,sample): image_root = os.path.join(self.dataset_path,"images") image = sample["image"] image = Image.open(os.path.join(image_root,image)) findings = sample["findings"] impression = sample["impression"] findings = "None" if findings.strip() == "" else findings impression = "None" if impression.strip() == "" else impression prompt = get_report_generation_prompt() messages = {"prompt":prompt,"image":image} sample["messages"] = messages return sample def cal_metrics(self,out_samples): import pandas as pd predictions_data = [] ground_truth_data = [] for i,sample in enumerate(out_samples): response = sample["response"] findings = sample["findings"] impression = sample["impression"] golden = f"Findings: {findings} Impression: {impression}." # 生成唯一的study_id study_id = f"study_{i+1}" # 添加预测数据 predictions_data.append({ 'study_id': study_id, 'report': response }) # 添加真实标签数据 ground_truth_data.append({ 'study_id': study_id, 'report': golden }) # 创建DataFrame predictions_df = pd.DataFrame(predictions_data) ground_truth_df = pd.DataFrame(ground_truth_data) prediction_path = os.path.join(self.output_path,'predictions.csv') ground_truth_path = os.path.join(self.output_path,'ground_truth.csv') # 保存为CSV文件 predictions_df.to_csv(prediction_path, index=False) ground_truth_df.to_csv(ground_truth_path, index=False) return {"total metrics":"please use cal_report_metrics.py to generate metrics"},out_samples def maybe_download_dataset(self): if not os.path.exists(self.dataset_path): raise ValueError(f"Dataset path {self.dataset_path} does not exist. Please download from https://aimi.stanford.edu/datasets/chexpert-plus and put it under {self.dataset_path}.")