Download MedEvalKit/utils/utils.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/utils.py
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hf download hf://datasets/Master-Shi/ExplainableVQA/MedEvalKit/utils/utils.py
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curl -L -o utils.py https://huggingface.co/datasets/Master-Shi/ExplainableVQA/resolve/main/MedEvalKit/utils/utils.py
13.1 kB
| import json | |
| import math | |
| import sys | |
| import copy | |
| import re | |
| import os | |
| import json | |
| import difflib | |
| import asyncio | |
| import random | |
| from google import genai | |
| from tqdm import tqdm | |
| from tqdm.asyncio import tqdm_asyncio | |
| from nltk.translate.meteor_score import single_meteor_score | |
| from nltk.translate.bleu_score import sentence_bleu | |
| from rouge import Rouge | |
| from mathruler.grader import extract_boxed_content | |
| from collections import defaultdict, Counter | |
| from openai import AzureOpenAI, OpenAI,AsyncAzureOpenAI,AsyncOpenAI | |
| from tenacity import ( | |
| retry, | |
| stop_after_attempt, | |
| wait_fixed, | |
| ) | |
| def tokenize(text): | |
| text = text.lower().replace(".", " .").split(" ") | |
| return text | |
| def bleu(pred,target,n): | |
| weights=[1/n for _ in range(n)] | |
| tokenized_target = tokenize(target) | |
| tokenized_pred = tokenize(pred) | |
| return sentence_bleu([tokenized_target], tokenized_pred, weights=weights) | |
| def rouge(pred,target): | |
| rouge_scorer = Rouge() | |
| rouge_scores = rouge_scorer.get_scores(pred.lower(), target.lower()) | |
| return rouge_scores | |
| def get_compare_messages(question,response,answer): | |
| prompt = f""" | |
| Your task is to determine whether the user's answer is correct based on the provided questions and standard answers (for example, if the user expresses a similar meaning to the standard answer, or another interpretation of the standard answer, it is considered correct.) | |
| The question is: {question} | |
| The standard answer: {answer} | |
| The user's answer: {response} | |
| Please strictly follow the following format for output(0 represents correct, 1 represents incorrect): | |
| <think>{{your concise think step}}</think> | |
| <judge>{{0/1}}</judge> | |
| for example: | |
| <think>The standard answer is right, and the user's answer is right frontal lobe, they express the same meaning, so it is correct.</think> | |
| <judge>0</judge> | |
| """ | |
| messages = [{"role":"user","content":prompt}] | |
| return messages | |
| def str_similarity(str1, str2): | |
| seq = difflib.SequenceMatcher(None, str1, str2) | |
| return seq.ratio() | |
| def find_most_similar_index(str_list, target_str): | |
| """ | |
| Given a list of strings and a target string, returns the index of the most similar string in the list. | |
| """ | |
| # Initialize variables to keep track of the most similar string and its index | |
| most_similar_str = None | |
| most_similar_index = 0 | |
| highest_similarity = 0 | |
| # Iterate through each string in the list | |
| for i, str in enumerate(str_list): | |
| # Calculate the similarity between the current string and the target string | |
| similarity = str_similarity(str, target_str) | |
| # If the current string is more similar than the previous most similar string, update the variables | |
| if similarity > highest_similarity: | |
| most_similar_str = str | |
| most_similar_index = i | |
| highest_similarity = similarity | |
| # Return the index of the most similar string | |
| return most_similar_index | |
| def judge_multi_choice(choices,answer,response,alphas = None): | |
| response = response.lower() | |
| if response.split("\n\n")[0] in [chr(ord('a') + i) for i in range(len(choices))]: | |
| response = response.split("\n\n")[0] | |
| elif response.split("\n\n")[-1].split(".")[0] in [chr(ord('a') + i) for i in range(len(choices))]: | |
| response = response.split("\n\n")[-1].split(".")[0] | |
| response = parse_response(response) | |
| alphas = [chr(ord('a') + i) for i in range(len(choices))] | |
| choices = [choice.lower() for choice in choices] | |
| flag = False | |
| response = response.strip().lower() | |
| response = response.replace("\n","") | |
| split_response = response.split(".")[0] | |
| split_response = split_response.split(":")[-1] | |
| answer = answer.strip().lower() | |
| if len(split_response) > 300: | |
| flag = False | |
| # letter,letter. choice,choice | |
| if split_response == answer: | |
| flag = True | |
| # letter,choice | |
| elif split_response in alphas: | |
| if choices[ord(split_response)-ord("a")]== answer: | |
| flag = True | |
| # choice letter | |
| elif split_response in choices: | |
| if answer in alphas and split_response == choices[ord(answer)-ord("a")]: | |
| flag = True | |
| # unparsed | |
| else: | |
| index = find_most_similar_index(choices,response) | |
| if alphas[index] == answer or choices[index] == answer: | |
| flag = True | |
| return flag | |
| def parse_response(response): | |
| response = response.lower() | |
| if "boxed" in response: | |
| response = extract_boxed_content(response) | |
| elif "<answer>" in response: | |
| response = extract(response,"answer") | |
| answer_patterns = [ | |
| "**answer**:", | |
| "**answer**", | |
| "*answer*:", | |
| "**answer:**", | |
| "answer is", | |
| "answer:", | |
| "答案:", | |
| "final answer", | |
| "final answer is" | |
| ] | |
| for answer_pattern in answer_patterns: | |
| if answer_pattern in response: | |
| response = response.split(answer_pattern)[-1] | |
| return response | |
| def judge_close_end_vqa(answer,response): | |
| answer = answer.lower() | |
| response = parse_response(response) | |
| response = response.replace("\n","").replace(".","") | |
| if response == answer: | |
| return True | |
| else: | |
| return False | |
| def judge_judgement(answer,response): | |
| answer = answer.lower() | |
| response = parse_response(response) | |
| response = response.replace("\n","").replace(".","") | |
| if ('yes' in response) ^ ('no' in response): | |
| if answer in response: | |
| return True | |
| return False | |
| def judge_open_end_vqa(answer,response): | |
| answer = answer.lower() | |
| response = parse_response(response) | |
| bleu1 = bleu(response,answer,1) | |
| bleu2 = bleu(response,answer,2) | |
| bleu3 = bleu(response,answer,3) | |
| bleu4 = bleu(response,answer,4) | |
| em = response == answer | |
| rouge_scores = rouge(response,answer) | |
| rouge_1 = rouge_scores[0]["rouge-1"]["f"] | |
| rouge_2 = rouge_scores[0]["rouge-2"]["f"] | |
| rouge_l = rouge_scores[0]["rouge-l"]["f"] | |
| precision,recall,f1 = calculate_f1(response,answer) | |
| return { | |
| "em" : em, | |
| "bleu1" : bleu1, | |
| "bleu2" : bleu2, | |
| "bleu3" : bleu3, | |
| "bleu4" : bleu4, | |
| "rouge1" : rouge_1, | |
| "rouge2" : rouge_2, | |
| "rougel" : rouge_l, | |
| "precision": precision, | |
| "recall": recall, | |
| "f1" :f1 | |
| } | |
| def calculate_f1(prediction, ground_truth): | |
| prediction_tokens = set(prediction.lower().split()) | |
| ground_truth_tokens = set(ground_truth.lower().split()) | |
| common = prediction_tokens & ground_truth_tokens | |
| if len(prediction_tokens) == 0 or len(ground_truth_tokens) == 0: | |
| return 0 | |
| precision = len(common) / len(prediction_tokens) | |
| recall = len(common) / len(ground_truth_tokens) | |
| if precision + recall == 0: | |
| return 0,0,0 | |
| f1 = 2 * (precision * recall) / (precision + recall) | |
| return f1,precision,recall | |
| def get_content_between_a_b(start_tag, end_tag, text): | |
| extracted_text = "" | |
| start_index = text.find(start_tag) | |
| while start_index != -1: | |
| end_index = text.find(end_tag, start_index + len(start_tag)) | |
| if end_index != -1: | |
| extracted_text += text[start_index + len(start_tag) : end_index] + " " | |
| start_index = text.find(start_tag, end_index + len(end_tag)) | |
| else: | |
| break | |
| return extracted_text.strip() | |
| def extract(text, type,hard = True): | |
| if text: | |
| target_str = get_content_between_a_b(f"<{type}>", f"</{type}>", text) | |
| if target_str: | |
| return target_str | |
| elif hard: | |
| return text | |
| else: | |
| return "" | |
| else: | |
| return "" | |
| # DATA SAVING | |
| class _NumpyEncoder(json.JSONEncoder): | |
| """将 numpy 整数/浮点/数组 转为 Python 原生类型,避免 JSON 序列化报错。""" | |
| def default(self, obj): | |
| import numpy as np | |
| if isinstance(obj, np.integer): | |
| return int(obj) | |
| if isinstance(obj, np.floating): | |
| return float(obj) | |
| if isinstance(obj, np.ndarray): | |
| return obj.tolist() | |
| return super().default(obj) | |
| def save_json(filename, ds): | |
| with open(filename, 'w', encoding='utf-8') as f: | |
| json.dump(ds, f, indent=4, ensure_ascii=False, cls=_NumpyEncoder) | |
| class fake_response: | |
| def __init__(self,usage): | |
| self.usage = usage | |
| def before_retry_fn(retry_state): | |
| if retry_state.attempt_number > 1: | |
| print(f"Retrying API call. Attempt #{retry_state.attempt_number}, f{retry_state}") | |
| async def deal_tasks(tasks, max_concurrent_tasks=500): | |
| semaphore = asyncio.Semaphore(max_concurrent_tasks) | |
| results = [] | |
| async def sem_task(task): | |
| async with semaphore: | |
| return await task | |
| sem_tasks = [sem_task(task) for task in tasks] | |
| for coro in tqdm_asyncio.as_completed(sem_tasks, total=len(sem_tasks)): | |
| result = await coro | |
| results.append(result) | |
| return results | |
| class openai_llm: | |
| def __init__(self,model = None): | |
| if model is None: | |
| model = os.environ.get("judge_model","gpt-4.1-2025-04-14") | |
| base_url = os.environ.get("base_url", "https://api.openai.com/v1") | |
| base_url = None if base_url == "None" else base_url | |
| self.model = model | |
| api_key = os.environ["api_key"] | |
| self.client = OpenAI( | |
| api_key=api_key, | |
| base_url=base_url | |
| ) | |
| self.async_client = AsyncOpenAI( | |
| api_key=api_key, | |
| base_url=base_url | |
| ) | |
| def response(self,messages,**kwargs): | |
| response = self.client.chat.completions.create( | |
| # gpt4o-0513 gpt4-turbo-2024-04-29 gpt-4o-2 | |
| model=kwargs.get("model", self.model), | |
| messages=messages, | |
| n = kwargs.get("n", 1), | |
| temperature= kwargs.get("temperature", 0), | |
| max_tokens=kwargs.get("max_tokens", 4000), | |
| timeout=kwargs.get("timeout", 180) | |
| ) | |
| return response.choices[0].message.content | |
| async def response_async(self,messages,**kwargs): | |
| response = await self.async_client.chat.completions.create( | |
| # gpt4o-0513 gpt4-turbo-2024-04-29 gpt-4o-2 | |
| model=kwargs.get("model", self.model), | |
| messages=messages, | |
| n = kwargs.get("n", 1), | |
| temperature= kwargs.get("temperature", 0), | |
| max_tokens=kwargs.get("max_tokens", 4096), | |
| timeout=kwargs.get("timeout", 180) | |
| ) | |
| return response.choices[0].message.content | |
| def generate_output(self,messages,**kwargs): | |
| try: | |
| response = self.response(messages,**kwargs) | |
| except Exception as e: | |
| response = None | |
| print(f"get {kwargs.get('model', self.model)} response failed: {e}") | |
| return response | |
| async def generate_output_async(self,idx, messages,**kwargs): | |
| try: | |
| response = await self.response_async(messages,**kwargs) | |
| except Exception as e: | |
| response = None | |
| print(f"get {kwargs.get('model', self.model)} response failed: {e}") | |
| return idx,response | |
| def generate_outputs(self,messages,**kwargs): | |
| tasks = [self.generate_output_async(i,messages[i],**kwargs) for i in range(len(messages))] | |
| results = asyncio.run(deal_tasks(tasks)) | |
| results = sorted(results, key=lambda x: x[0]) | |
| results = [x[1] for x in results] | |
| return results | |
| class Gemini: | |
| def __init__(self,model = "gemini-2.0-flash") -> None: | |
| self.model = model | |
| self.api_key = os.environ.get("api_key") | |
| self.client = genai.Client(api_key=self.api_key) | |
| def response(self,messages,**kwargs): | |
| response = self.client.models.generate_content( | |
| model=kwargs.get("model", self.model), | |
| contents=messages, | |
| ) | |
| return response.text | |
| def generate_output(self,messages,**kwargs): | |
| try: | |
| response = self.response(messages,**kwargs) | |
| except Exception as e: | |
| response = None | |
| print(f"get {kwargs.get('model', self.model)} response failed: {e}") | |
| return response | |
| def generate_outputs(self,messages,**kwargs): | |
| results = [] | |
| for message in tqdm(messages): | |
| response = self.generate_output(message,**kwargs) | |
| results.append(response) | |
| return results | |
| def init_judger(): | |
| if os.environ.get("judge_model_type", "openai") in ["openai","claude","deepseek"]: | |
| judger = openai_llm() | |
| elif os.environ.get("judge_model_type", "openai") == "gemini": | |
| judger = Gemini() | |
| else: | |
| raise ValueError("Unsupported judge model type. Please set 'judge_model_type' to 'openai', 'gemini', or 'claude'.") | |
| return judger | |
| judger = init_judger() | |