from fastapi import FastAPI, Query from fastapi.responses import JSONResponse import torch import torchvision import numpy as np import requests import skimage.io import cv2 import tempfile import os from PIL import Image from transformers import AutoImageProcessor, AutoModel import joblib from pytorch_grad_cam import GradCAM from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget import torchxrayvision as xrv import requests from io import BytesIO import logging logging.getLogger("uvicorn").setLevel(logging.WARNING) import tempfile temp_dir = tempfile.gettempdir() matplotlib_cache = os.path.join(temp_dir, "matplotlib") torchxrayvision_cache = os.path.join(temp_dir, "torchxrayvision") os.environ["MPLCONFIGDIR"] = matplotlib_cache os.environ["TORCHXrayVISION_CACHE"] = torchxrayvision_cache os.makedirs(matplotlib_cache, exist_ok=True) os.makedirs(torchxrayvision_cache, exist_ok=True) app = FastAPI() cxr_model = xrv.models.DenseNet(weights="densenet121-res224-all") cxr_model.eval() device = torch.device("cuda" if torch.cuda.is_available() else "cpu") tb_processor = AutoImageProcessor.from_pretrained("StanfordAIMI/dinov2-base-xray-224") tb_model = AutoModel.from_pretrained("StanfordAIMI/dinov2-base-xray-224").to(device) logreg = joblib.load("logreg_model.joblib") def preprocess_image(image_path): img = skimage.io.imread(image_path) img = xrv.datasets.normalize(img, 255) if img.ndim == 3: img = img.mean(2)[None, ...] elif img.ndim == 2: img = img[None, ...] transform = torchvision.transforms.Compose([ xrv.datasets.XRayCenterCrop(), xrv.datasets.XRayResizer(224) ]) img = transform(img) return torch.from_numpy(img) def get_predictions(img_tensor, model): with torch.no_grad(): outputs = model(img_tensor[None, ...]) preds = dict(zip(model.pathologies, outputs[0].detach().numpy())) return preds, outputs def get_top_preds(preds, tolerance=0.01, topk=5): sorted_preds = sorted(preds.items(), key=lambda x: -x[1]) top_conf = sorted_preds[0][1] similar_preds = [(i, p, conf) for i, (p, conf) in enumerate(sorted_preds) if abs(conf - top_conf) <= tolerance][:topk] return sorted_preds, similar_preds def get_bounding_boxes(img_tensor, model, similar_preds): boxes = {} target_layer = model.features[-1] for idx, pathology, conf in similar_preds: cam = GradCAM(model=model, target_layers=[target_layer]) pred_index = list(model.pathologies).index(pathology) grayscale_cam = cam(input_tensor=img_tensor[None, ...], targets=[ClassifierOutputTarget(pred_index)])[0] cam_resized = cv2.resize(grayscale_cam, (224, 224)) cam_uint8 = (cam_resized * 255).astype(np.uint8) _, thresh = cv2.threshold(cam_uint8, 100, 255, cv2.THRESH_BINARY) contours, _ = cv2.findContours(thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE) if contours: x, y, w, h = cv2.boundingRect(contours[0]) boxes[pathology] = [[x, y], [x + w, y + h]] return boxes def predict_tb(image_path): image = Image.open(image_path) inputs = tb_processor(images=image, return_tensors="pt").to(device) with torch.no_grad(): outputs = tb_model(**inputs) embeddings = outputs.pooler_output.cpu().numpy() prediction = logreg.predict(embeddings) return int(prediction[0] == "tb") @app.get("/predict") async def predict_cxr(image_url: str = Query(..., description="URL to a chest X-ray image")): try: response = requests.get(image_url) if response.status_code != 200: return JSONResponse(content={"error": "Failed to download image"}, status_code=400) with tempfile.NamedTemporaryFile(delete=False, suffix=".png") as tmp: tmp.write(response.content) tmp_path = tmp.name img_tensor = preprocess_image(tmp_path) preds, _ = get_predictions(img_tensor, cxr_model) sorted_preds, similar_preds = get_top_preds(preds) prediction_result = {k: float(f"{v:.2f}") for k, v in preds.items()} bounding_boxes = get_bounding_boxes(img_tensor, cxr_model, similar_preds) tb_result = predict_tb(tmp_path) os.remove(tmp_path) return JSONResponse(content={ "prediction_result": prediction_result, "bounding_box": bounding_boxes, # top-left , bottom-right coordinates "tb_finding": tb_result }) except Exception as e: return JSONResponse(content={"error": str(e)}, status_code=500)