Blame for MedEvalKit/utils/utils.py

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
            )
    
    @retry(wait=wait_fixed(10), stop=stop_after_attempt(1000), before=before_retry_fn)
    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
    

    
    @retry(wait=wait_fixed(10), stop=stop_after_attempt(1000), before=before_retry_fn)
    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)
    
    @retry(wait=wait_fixed(10), stop=stop_after_attempt(3), before=before_retry_fn)
    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()