Download MedEvalKit/utils/base_dataset.py from Master-Shi/ExplainableVQA: direct link, hf CLI and curl.
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https://huggingface.co/datasets/Master-Shi/ExplainableVQA/resolve/main/MedEvalKit/utils/base_dataset.py
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hf download hf://datasets/Master-Shi/ExplainableVQA/MedEvalKit/utils/base_dataset.py
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curl -L -o base_dataset.py https://huggingface.co/datasets/Master-Shi/ExplainableVQA/resolve/main/MedEvalKit/utils/base_dataset.py
5.28 kB
| import torch | |
| import os | |
| import json | |
| from tqdm import tqdm | |
| import gc | |
| from .utils import save_json | |
| class BaseDataset: | |
| def __init__(self): | |
| self.chunk_idx = int(os.environ.get("chunk_idx",0)) | |
| self.num_chunks = int(os.environ.get("num_chunks",1)) | |
| def run(self,samples,model,batch_size = 2000): | |
| out_samples = [] | |
| with torch.no_grad(): | |
| messages_list = [] | |
| current_messages = [] | |
| current_samples = [] | |
| for sample in tqdm(samples): | |
| messages = sample["messages"] | |
| current_messages.append(messages) | |
| current_samples.append(sample) | |
| if len(current_messages) >= batch_size: | |
| messages_list.append([current_messages,current_samples]) | |
| current_messages = [] | |
| current_samples = [] | |
| if current_messages: | |
| messages_list.append([current_messages,current_samples]) | |
| for current_messages,current_samples in tqdm(messages_list): | |
| outputs = model.generate_outputs(current_messages) | |
| try: | |
| for sample,response in zip(current_samples,outputs): | |
| del sample["messages"] | |
| sample["response"] = response | |
| out_samples.append(sample) | |
| except Exception as e: | |
| from pdb import set_trace;set_trace() | |
| print(e) | |
| gc.collect() | |
| return out_samples | |
| def cal_matrics(self): | |
| pass | |
| def init_dataset(self): | |
| pass | |
| def construct_messages(self): | |
| pass | |
| def eval(self): | |
| model = self.model | |
| dataset_path = self.dataset_path | |
| output_path = self.output_path | |
| num_chunks = self.num_chunks | |
| chunk_idx = self.chunk_idx | |
| if num_chunks == 1: | |
| results_path = os.path.join(output_path,"results.json") | |
| matric_path = os.path.join(output_path,"metrics.json") | |
| out_samples = self.run(self.samples,model) | |
| save_json(results_path,out_samples) | |
| metrics,out_samples = self.cal_metrics(out_samples) | |
| save_json(matric_path,metrics) | |
| save_json(results_path,out_samples) | |
| return metrics | |
| elif num_chunks > 1: | |
| results_path = os.path.join(output_path,f"results_{chunk_idx}.json") | |
| final_results_path = os.path.join(output_path,"results.json") | |
| out_samples = self.run(self.samples,model) | |
| save_json(results_path,out_samples) | |
| total_results_path = os.listdir(output_path) | |
| total_results_path = [result for result in total_results_path if result.startswith("results_")] | |
| if len(total_results_path) == num_chunks: | |
| total_results = [] | |
| for result in total_results_path: | |
| results_path = os.path.join(output_path,result) | |
| with open(results_path,"r") as f: | |
| total_results.extend(json.load(f)) | |
| save_json(final_results_path,total_results) | |
| metrics,out_samples = self.cal_metrics(total_results) | |
| matric_path = os.path.join(output_path,"metrics.json") | |
| save_json(matric_path,metrics) | |
| save_json(final_results_path,out_samples) | |
| return metrics | |
| else: | |
| return None | |
| else: | |
| raise ValueError("num_chunks must be greater than 0") | |
| def _download_file_local(self,local_path,url): | |
| # download the specific file to local_path | |
| os.makedirs(local_path,exist_ok=True) | |
| # Extract filename from URL | |
| filename = url.split("/")[-1] | |
| file_path = os.path.join(local_path, filename) | |
| # Check if wget or curl is available | |
| if os.system("which wget > /dev/null 2>&1") == 0: | |
| download_cmd = f"wget {url} -O {file_path}" | |
| elif os.system("which curl > /dev/null 2>&1") == 0: | |
| download_cmd = f"curl -L {url} -o {file_path}" | |
| else: | |
| raise RuntimeError("Neither wget nor curl is available for downloading") | |
| # Download with error handling | |
| if os.system(download_cmd) != 0: | |
| if os.path.exists(file_path): | |
| os.remove(file_path) | |
| raise RuntimeError("Failed to download dataset") | |
| def _unzip_img_zip_local(self, local_path, zip_filename): | |
| # suppose zip_filename is like 'images.zip' or 'data.tgz' | |
| zip_file_path = os.path.join(local_path, zip_filename) | |
| if zip_filename.endswith('.zip'): | |
| if os.system(f"unzip -q {zip_file_path} -d {local_path}") != 0: | |
| if os.path.exists(zip_file_path): | |
| os.remove(zip_file_path) | |
| raise RuntimeError("Failed to extract dataset") | |
| elif zip_filename.endswith('.tgz') or zip_filename.endswith('.tar.gz'): | |
| if os.system(f"tar -xzf {zip_file_path} -C {local_path}") != 0: | |
| if os.path.exists(zip_file_path): | |
| os.remove(zip_file_path) | |
| raise RuntimeError("Failed to extract dataset") | |
| else: | |
| if os.path.exists(zip_file_path): | |
| os.remove(zip_file_path) | |
| raise RuntimeError(f"Unsupported file format: {zip_filename}") | |
| if os.path.exists(zip_file_path): | |
| os.remove(zip_file_path) |