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Update app.py
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app.py
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@@ -1,384 +1,384 @@
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import torch
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import gradio as gr
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from PIL import Image
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import cv2
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from AV.models.network import PGNet
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from AV.Tools.AVclassifiation import AVclassifiation
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from AV.Tools.utils_test import paint_border_overlap, extract_ordered_overlap_big, Normalize, sigmoid, recompone_overlap, \
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kill_border
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from AV.config import config_test_general as cfg
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import torch.autograd as autograd
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import numpy as np
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import os
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from datetime import datetime
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def creatMask(Image, threshold=5):
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##This program try to creat the mask for the filed-of-view
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##Input original image (RGB or green channel), threshold (user set parameter, default 10)
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##Output: the filed-of-view mask
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if len(Image.shape) == 3: ##RGB image
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gray = cv2.cvtColor(Image, cv2.COLOR_BGR2GRAY)
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Mask0 = gray >= threshold
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else: # for green channel image
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Mask0 = Image >= threshold
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# ######get the largest blob, this takes 0.18s
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cvVersion = int(cv2.__version__.split('.')[0])
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Mask0 = np.uint8(Mask0)
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contours, hierarchy = cv2.findContours(Mask0, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
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areas = [cv2.contourArea(c) for c in contours]
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max_index = np.argmax(areas)
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Mask = np.zeros(Image.shape[:2], dtype=np.uint8)
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cv2.drawContours(Mask, contours, max_index, 1, -1)
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ResultImg = Image.copy()
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if len(Image.shape) == 3:
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ResultImg[Mask == 0] = (255, 255, 255)
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else:
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ResultImg[Mask == 0] = 255
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Mask[Mask > 0] = 255
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kernel = cv2.getStructuringElement(cv2.MORPH_CROSS, (3, 3))
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Mask = cv2.morphologyEx(Mask, cv2.MORPH_OPEN, kernel, iterations=3)
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return ResultImg, Mask
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def shift_rgb(img, *args):
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result_img = np.empty_like(img)
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shifts = args
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max_value = 255
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# print(shifts)
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for i, shift in enumerate(shifts):
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lut = np.arange(0, max_value + 1).astype("float32")
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lut += shift
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lut = np.clip(lut, 0, max_value).astype(img.dtype)
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if len(img.shape) == 2:
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print(f'=========grey image=======')
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result_img = cv2.LUT(img, lut)
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else:
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result_img[..., i] = cv2.LUT(img[..., i], lut)
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return result_img
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def CAM(x, img_path, rate=0.8, ind=0):
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"""
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:param dataset_path: 计算整个训练数据集的平均RGB通道值
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:param image: array, 单张图片的array 形式
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:return: array形式的cam后的结果
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"""
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# 每次使用新数据集时都需要重新计算前面的RBG平均值
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# RGB-->Rshift-->CLAHE
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x = np.uint8(x)
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_, Mask0 = creatMask(x, threshold=10)
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Mask = np.zeros((x.shape[0], x.shape[1]), np.float32)
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Mask[Mask0 > 0] = 1
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resize = False
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R_mea_num, G_mea_num, B_mea_num = [], [], []
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dataset_path = img_path
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image = np.array(Image.open(dataset_path))
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R_mea_num.append(np.mean(image[:, :, 0]))
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G_mea_num.append(np.mean(image[:, :, 1]))
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B_mea_num.append(np.mean(image[:, :, 2]))
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mea2stand = int((np.mean(R_mea_num) - np.mean(x[:, :, 0])) * rate)
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mea2standg = int((np.mean(G_mea_num) - np.mean(x[:, :, 1])) * rate)
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mea2standb = int((np.mean(B_mea_num) - np.mean(x[:, :, 2])) * rate)
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y = shift_rgb(x, mea2stand, mea2standg, mea2standb)
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y[Mask == 0, :] = 0
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return y
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def modelEvalution_out_big(net, use_cuda=False, dataset='', is_kill_border=True, input_ch=3,
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config=None, output_dir='', evaluate_metrics=False):
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# path for images to save
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n_classes = 3
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Net = PGNet(use_global_semantic=config.use_global_semantic, input_ch=input_ch,
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num_classes=n_classes, use_cuda=use_cuda, pretrained=False, centerness=config.use_centerness,
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centerness_map_size=config.centerness_map_size)
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msg = Net.load_state_dict(net, strict=False)
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if use_cuda:
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Net.cuda()
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Net.eval()
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image_basename = dataset
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# if not os.path.exists(output_dir):
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# os.makedirs(output_dir)
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step = 1
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# every step of between star and end for loop until len(image_basename)
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# for start_end in start_end_list:
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image0 = cv2.imread(image_basename)
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test_image_height = image0.shape[0]
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test_image_width = image0.shape[1]
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if config.use_resize:
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if min(test_image_height, test_image_width) <= 256:
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scaling = 512 / min(test_image_height, test_image_width)
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new_width = int(test_image_width * scaling)
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new_height = int(test_image_height * scaling)
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test_image_width, test_image_height = new_width, new_height
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# 大尺寸处理:确保最长边≤1536
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elif max(test_image_height, test_image_width) >= 2048:
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scaling = 2048 / max(test_image_height, test_image_width)
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new_width = int(test_image_width * scaling)
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new_height = int(test_image_height * scaling)
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test_image_width, test_image_height = new_width, new_height
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ArteryPredAll = np.zeros((1, 1, test_image_height, test_image_width), np.float32)
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VeinPredAll = np.zeros((1, 1, test_image_height, test_image_width), np.float32)
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VesselPredAll = np.zeros((1, 1, test_image_height, test_image_width), np.float32)
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ProMap = np.zeros((1, 3, test_image_height, test_image_width), np.float32)
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MaskAll = np.zeros((1, 1, test_image_height, test_image_width), np.float32)
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ArteryPred, VeinPred, VesselPred, Mask, LabelArtery, LabelVein, LabelVessel = GetResult_out_big(Net, 0,
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use_cuda=use_cuda,
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dataset=image_basename,
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is_kill_border=is_kill_border,
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config=config,
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resize_w_h=(
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test_image_width,
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test_image_height)
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)
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ArteryPredAll[0 % step, :, :, :] = ArteryPred
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VeinPredAll[0 % step, :, :, :] = VeinPred
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VesselPredAll[0 % step, :, :, :] = VesselPred
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MaskAll[0 % step, :, :, :] = Mask
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image_color = AVclassifiation(output_dir, ArteryPredAll, VeinPredAll, VesselPredAll, 1, image_basename)
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return image_color
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def GetResult_out_big(Net, k, use_cuda=False, dataset='', is_kill_border=False, config=None,
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resize_w_h=None):
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ImgName = dataset
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Img0 = cv2.imread(ImgName)
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_, Mask0 = creatMask(Img0, threshold=-1)
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Mask = np.zeros((Img0.shape[0], Img0.shape[1]), np.float32)
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Mask[Mask0 > 0] = 1
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if config.use_resize:
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Img0 = cv2.resize(Img0, resize_w_h)
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Mask = cv2.resize(Mask, resize_w_h, interpolation=cv2.INTER_NEAREST)
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Img = Img0
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height, width = Img.shape[:2]
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n_classes = 3
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patch_height = config.patch_size
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patch_width = config.patch_size
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stride_height = config.stride_height
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stride_width = config.stride_width
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Img = cv2.cvtColor(Img, cv2.COLOR_BGR2RGB)
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if cfg.dataset == 'all':
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# # # 将图像转换为 LAB 颜色空间
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lab = cv2.cvtColor(Img, cv2.COLOR_RGB2LAB)
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# 拆分 LAB 通道
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l, a, b = cv2.split(lab)
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# 创建 CLAHE 对象并应用到 L 通道
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clahe = cv2.createCLAHE(clipLimit=2, tileGridSize=(8, 8))
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l_clahe = clahe.apply(l)
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# 将 CLAHE 处理后的 L 通道与原始的 A 和 B 通道合并
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lab_clahe = cv2.merge((l_clahe, a, b))
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# 将图像转换回 BGR 颜色空间
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Img = cv2.cvtColor(lab_clahe, cv2.COLOR_LAB2RGB)
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if cfg.use_CAM:
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Img = CAM(Img, dataset)
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Img = np.float32(Img / 255.)
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Img_enlarged = paint_border_overlap(Img, patch_height, patch_width, stride_height, stride_width)
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patch_size = config.patch_size
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batch_size = 2
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patches_imgs, global_images = extract_ordered_overlap_big(Img_enlarged, patch_height, patch_width,
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stride_height,
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stride_width)
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patches_imgs = np.transpose(patches_imgs, (0, 3, 1, 2))
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patches_imgs = Normalize(patches_imgs)
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global_images = np.transpose(global_images, (0, 3, 1, 2))
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global_images = Normalize(global_images)
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patchNum = patches_imgs.shape[0]
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max_iter = int(np.ceil(patchNum / float(batch_size)))
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pred_patches = np.zeros((patchNum, n_classes, patch_size, patch_size), np.float32)
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for i in range(max_iter):
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begin_index = i * batch_size
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end_index = (i + 1) * batch_size
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patches_temp1 = patches_imgs[begin_index:end_index, :, :, :]
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patches_input_temp1 = torch.FloatTensor(patches_temp1)
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global_input_temp1 = patches_input_temp1
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if config.use_global_semantic:
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global_temp1 = global_images[begin_index:end_index, :, :, :]
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global_input_temp1 = torch.FloatTensor(global_temp1)
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if use_cuda:
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patches_input_temp1 = autograd.Variable(patches_input_temp1.cuda())
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if config.use_global_semantic:
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global_input_temp1 = autograd.Variable(global_input_temp1.cuda())
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else:
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patches_input_temp1 = autograd.Variable(patches_input_temp1)
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if config.use_global_semantic:
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global_input_temp1 = autograd.Variable(global_input_temp1)
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output_temp, _1, = Net(patches_input_temp1, global_input_temp1)
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pred_patches_temp = np.float32(output_temp.data.cpu().numpy())
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pred_patches_temp_sigmoid = sigmoid(pred_patches_temp)
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pred_patches[begin_index:end_index, :, :, :] = pred_patches_temp_sigmoid[:, :, :patch_size, :patch_size]
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del patches_input_temp1
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del pred_patches_temp
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del patches_temp1
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del output_temp
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del pred_patches_temp_sigmoid
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new_height, new_width = Img_enlarged.shape[0], Img_enlarged.shape[1]
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pred_img = recompone_overlap(pred_patches, new_height, new_width, stride_height, stride_width) # predictions
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pred_img = pred_img[:, 0:height, 0:width]
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if is_kill_border:
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pred_img = kill_border(pred_img, Mask)
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ArteryPred = np.float32(pred_img[0, :, :])
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VeinPred = np.float32(pred_img[2, :, :])
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VesselPred = np.float32(pred_img[1, :, :])
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ArteryPred = ArteryPred[np.newaxis, :, :]
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VeinPred = VeinPred[np.newaxis, :, :]
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VesselPred = VesselPred[np.newaxis, :, :]
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Mask = Mask[np.newaxis, :, :]
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return ArteryPred, VeinPred, VesselPred, Mask, ArteryPred, VeinPred, VesselPred,
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def out_test(cfg, output_dir='', evaluate_metrics=False, img_name='out_test'):
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device = torch.device("cuda" if cfg.use_cuda else "cpu")
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model_root = cfg.model_path_pretrained_G
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model_path = os.path.join(model_root, 'G_' + str(cfg.model_step_pretrained_G) + '.pkl')
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net = torch.load(model_path, map_location=device)
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image_color = modelEvalution_out_big(net,
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use_cuda=cfg.use_cuda,
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dataset=img_name,
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input_ch=cfg.input_nc,
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config=cfg,
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output_dir=output_dir, evaluate_metrics=evaluate_metrics)
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return image_color
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def segment_by_out_test(image,model_name):
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print("✅ 传到后端的模型名:", model_name)
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cfg.set_dataset(model_name)
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if image is None:
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raise gr.Error("
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os.makedirs("./examples", exist_ok=True)
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timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
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temp_path = f"./examples/tmp_upload_{timestamp}.png"
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image.save(temp_path)
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image_color = out_test(cfg, output_dir='', evaluate_metrics=False, img_name=temp_path)
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return Image.fromarray(image_color)
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def gradio_interface():
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model_info_md = """
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### 📘 模型说明
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| 模型 | 数据集 | patch size |running time |
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|------|--------|------------|--------|
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| DRIVE | 小分辨率血管图像 | 256 |30s以内|
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| HRF |
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| LES | 视盘中心图像适配 | 256 |2min以内|
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| UKBB | UKBB图像 | 256 |2min以内 |
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| 通用模型(512) | 超清图像,适配性强 | 512 |2min以内|
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"""
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model_choices = [
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("1: DRIVE专用模型", "DRIVE"),
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("2: HRF专用模型", "hrf"),
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("3: LES专用模型","LES"),
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("4: UKBB专用模型", "ukbb"),
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("5: 通用模型", "all"),
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]
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with gr.Blocks(theme=gr.themes.Soft()) as demo:
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gr.Markdown("# 👁️ 眼底图像动静脉血管分割")
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gr.Markdown("上传眼底图像,选择一个模型开始处理,结果将自动生成。")
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with gr.Row():
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image_input = gr.Image(type="pil", label="📤 上传图像",height=300)
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with gr.Row():
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with gr.Column():
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model_select = gr.Radio(
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choices=model_choices,
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label="🎯 选择模型",
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value="DRIVE",
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interactive = True
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)
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submit_btn = gr.Button("🚀 开始分割")
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with gr.Column():
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output_image = gr.Image(label="🖼️ 分割结果")
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gr.Markdown("### 📁
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gr.Examples(
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examples=[
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["examples/DRIVE.tif", "DRIVE"],
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["examples/LES.png", "LES"],
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356 |
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["examples/hrf.png", "hrf"],
|
357 |
-
["examples/ukbb.png", "ukbb"],
|
358 |
-
["examples/all.jpg", "all"]
|
359 |
-
],
|
360 |
-
inputs=[image_input, model_select],
|
361 |
-
label="示例图像",
|
362 |
-
examples_per_page=5
|
363 |
-
)
|
364 |
-
with gr.Accordion("📖
|
365 |
-
gr.Markdown(model_info_md)
|
366 |
-
|
367 |
-
# 功能连接
|
368 |
-
submit_btn.click(
|
369 |
-
fn=segment_by_out_test,
|
370 |
-
inputs=[image_input, model_select],
|
371 |
-
outputs=[output_image]
|
372 |
-
)
|
373 |
-
gr.Markdown("📚
|
374 |
-
gr.Markdown("📚
|
375 |
-
demo.queue()
|
376 |
-
demo.launch()
|
377 |
-
|
378 |
-
|
379 |
-
if __name__ == '__main__':
|
380 |
-
# cfg.set_dataset('all')
|
381 |
-
# image_color = out_test(cfg = cfg, evaluate_metrics=False, img_name=r'.\AV\data\AV-DRIVE\test\images\01_test.tif')
|
382 |
-
# Image.fromarray(image_color).save('image_color.png')
|
383 |
-
#print(cfg.patch_size)
|
384 |
-
gradio_interface()
|
|
|
1 |
+
import torch
|
2 |
+
import gradio as gr
|
3 |
+
from PIL import Image
|
4 |
+
import cv2
|
5 |
+
from AV.models.network import PGNet
|
6 |
+
from AV.Tools.AVclassifiation import AVclassifiation
|
7 |
+
from AV.Tools.utils_test import paint_border_overlap, extract_ordered_overlap_big, Normalize, sigmoid, recompone_overlap, \
|
8 |
+
kill_border
|
9 |
+
from AV.config import config_test_general as cfg
|
10 |
+
import torch.autograd as autograd
|
11 |
+
import numpy as np
|
12 |
+
import os
|
13 |
+
from datetime import datetime
|
14 |
+
|
15 |
+
def creatMask(Image, threshold=5):
|
16 |
+
##This program try to creat the mask for the filed-of-view
|
17 |
+
##Input original image (RGB or green channel), threshold (user set parameter, default 10)
|
18 |
+
##Output: the filed-of-view mask
|
19 |
+
|
20 |
+
if len(Image.shape) == 3: ##RGB image
|
21 |
+
gray = cv2.cvtColor(Image, cv2.COLOR_BGR2GRAY)
|
22 |
+
Mask0 = gray >= threshold
|
23 |
+
|
24 |
+
else: # for green channel image
|
25 |
+
Mask0 = Image >= threshold
|
26 |
+
|
27 |
+
# ######get the largest blob, this takes 0.18s
|
28 |
+
cvVersion = int(cv2.__version__.split('.')[0])
|
29 |
+
|
30 |
+
Mask0 = np.uint8(Mask0)
|
31 |
+
|
32 |
+
contours, hierarchy = cv2.findContours(Mask0, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
|
33 |
+
|
34 |
+
areas = [cv2.contourArea(c) for c in contours]
|
35 |
+
max_index = np.argmax(areas)
|
36 |
+
Mask = np.zeros(Image.shape[:2], dtype=np.uint8)
|
37 |
+
cv2.drawContours(Mask, contours, max_index, 1, -1)
|
38 |
+
|
39 |
+
ResultImg = Image.copy()
|
40 |
+
if len(Image.shape) == 3:
|
41 |
+
ResultImg[Mask == 0] = (255, 255, 255)
|
42 |
+
else:
|
43 |
+
ResultImg[Mask == 0] = 255
|
44 |
+
Mask[Mask > 0] = 255
|
45 |
+
kernel = cv2.getStructuringElement(cv2.MORPH_CROSS, (3, 3))
|
46 |
+
Mask = cv2.morphologyEx(Mask, cv2.MORPH_OPEN, kernel, iterations=3)
|
47 |
+
return ResultImg, Mask
|
48 |
+
|
49 |
+
|
50 |
+
def shift_rgb(img, *args):
|
51 |
+
result_img = np.empty_like(img)
|
52 |
+
shifts = args
|
53 |
+
max_value = 255
|
54 |
+
# print(shifts)
|
55 |
+
for i, shift in enumerate(shifts):
|
56 |
+
lut = np.arange(0, max_value + 1).astype("float32")
|
57 |
+
lut += shift
|
58 |
+
|
59 |
+
lut = np.clip(lut, 0, max_value).astype(img.dtype)
|
60 |
+
if len(img.shape) == 2:
|
61 |
+
print(f'=========grey image=======')
|
62 |
+
result_img = cv2.LUT(img, lut)
|
63 |
+
else:
|
64 |
+
result_img[..., i] = cv2.LUT(img[..., i], lut)
|
65 |
+
|
66 |
+
return result_img
|
67 |
+
|
68 |
+
|
69 |
+
def CAM(x, img_path, rate=0.8, ind=0):
|
70 |
+
"""
|
71 |
+
:param dataset_path: 计算整个训练数据集的平均RGB通道值
|
72 |
+
:param image: array, 单张图片的array 形式
|
73 |
+
:return: array形式的cam后的结果
|
74 |
+
"""
|
75 |
+
# 每次使用新数据集时都需要重新计算前面的RBG平均值
|
76 |
+
# RGB-->Rshift-->CLAHE
|
77 |
+
|
78 |
+
x = np.uint8(x)
|
79 |
+
_, Mask0 = creatMask(x, threshold=10)
|
80 |
+
Mask = np.zeros((x.shape[0], x.shape[1]), np.float32)
|
81 |
+
Mask[Mask0 > 0] = 1
|
82 |
+
|
83 |
+
resize = False
|
84 |
+
R_mea_num, G_mea_num, B_mea_num = [], [], []
|
85 |
+
|
86 |
+
dataset_path = img_path
|
87 |
+
image = np.array(Image.open(dataset_path))
|
88 |
+
R_mea_num.append(np.mean(image[:, :, 0]))
|
89 |
+
G_mea_num.append(np.mean(image[:, :, 1]))
|
90 |
+
B_mea_num.append(np.mean(image[:, :, 2]))
|
91 |
+
|
92 |
+
mea2stand = int((np.mean(R_mea_num) - np.mean(x[:, :, 0])) * rate)
|
93 |
+
mea2standg = int((np.mean(G_mea_num) - np.mean(x[:, :, 1])) * rate)
|
94 |
+
mea2standb = int((np.mean(B_mea_num) - np.mean(x[:, :, 2])) * rate)
|
95 |
+
|
96 |
+
y = shift_rgb(x, mea2stand, mea2standg, mea2standb)
|
97 |
+
|
98 |
+
y[Mask == 0, :] = 0
|
99 |
+
|
100 |
+
return y
|
101 |
+
|
102 |
+
|
103 |
+
def modelEvalution_out_big(net, use_cuda=False, dataset='', is_kill_border=True, input_ch=3,
|
104 |
+
config=None, output_dir='', evaluate_metrics=False):
|
105 |
+
# path for images to save
|
106 |
+
n_classes = 3
|
107 |
+
Net = PGNet(use_global_semantic=config.use_global_semantic, input_ch=input_ch,
|
108 |
+
num_classes=n_classes, use_cuda=use_cuda, pretrained=False, centerness=config.use_centerness,
|
109 |
+
centerness_map_size=config.centerness_map_size)
|
110 |
+
msg = Net.load_state_dict(net, strict=False)
|
111 |
+
|
112 |
+
if use_cuda:
|
113 |
+
Net.cuda()
|
114 |
+
Net.eval()
|
115 |
+
|
116 |
+
image_basename = dataset
|
117 |
+
|
118 |
+
# if not os.path.exists(output_dir):
|
119 |
+
# os.makedirs(output_dir)
|
120 |
+
|
121 |
+
step = 1
|
122 |
+
# every step of between star and end for loop until len(image_basename)
|
123 |
+
|
124 |
+
# for start_end in start_end_list:
|
125 |
+
image0 = cv2.imread(image_basename)
|
126 |
+
test_image_height = image0.shape[0]
|
127 |
+
test_image_width = image0.shape[1]
|
128 |
+
|
129 |
+
if config.use_resize:
|
130 |
+
|
131 |
+
if min(test_image_height, test_image_width) <= 256:
|
132 |
+
scaling = 512 / min(test_image_height, test_image_width)
|
133 |
+
new_width = int(test_image_width * scaling)
|
134 |
+
new_height = int(test_image_height * scaling)
|
135 |
+
test_image_width, test_image_height = new_width, new_height
|
136 |
+
|
137 |
+
# 大尺寸处理:确保最长边≤1536
|
138 |
+
elif max(test_image_height, test_image_width) >= 2048:
|
139 |
+
scaling = 2048 / max(test_image_height, test_image_width)
|
140 |
+
new_width = int(test_image_width * scaling)
|
141 |
+
new_height = int(test_image_height * scaling)
|
142 |
+
test_image_width, test_image_height = new_width, new_height
|
143 |
+
|
144 |
+
ArteryPredAll = np.zeros((1, 1, test_image_height, test_image_width), np.float32)
|
145 |
+
VeinPredAll = np.zeros((1, 1, test_image_height, test_image_width), np.float32)
|
146 |
+
VesselPredAll = np.zeros((1, 1, test_image_height, test_image_width), np.float32)
|
147 |
+
ProMap = np.zeros((1, 3, test_image_height, test_image_width), np.float32)
|
148 |
+
MaskAll = np.zeros((1, 1, test_image_height, test_image_width), np.float32)
|
149 |
+
ArteryPred, VeinPred, VesselPred, Mask, LabelArtery, LabelVein, LabelVessel = GetResult_out_big(Net, 0,
|
150 |
+
use_cuda=use_cuda,
|
151 |
+
dataset=image_basename,
|
152 |
+
is_kill_border=is_kill_border,
|
153 |
+
config=config,
|
154 |
+
resize_w_h=(
|
155 |
+
test_image_width,
|
156 |
+
test_image_height)
|
157 |
+
)
|
158 |
+
ArteryPredAll[0 % step, :, :, :] = ArteryPred
|
159 |
+
VeinPredAll[0 % step, :, :, :] = VeinPred
|
160 |
+
VesselPredAll[0 % step, :, :, :] = VesselPred
|
161 |
+
|
162 |
+
MaskAll[0 % step, :, :, :] = Mask
|
163 |
+
|
164 |
+
image_color = AVclassifiation(output_dir, ArteryPredAll, VeinPredAll, VesselPredAll, 1, image_basename)
|
165 |
+
|
166 |
+
return image_color
|
167 |
+
|
168 |
+
|
169 |
+
def GetResult_out_big(Net, k, use_cuda=False, dataset='', is_kill_border=False, config=None,
|
170 |
+
resize_w_h=None):
|
171 |
+
ImgName = dataset
|
172 |
+
Img0 = cv2.imread(ImgName)
|
173 |
+
|
174 |
+
_, Mask0 = creatMask(Img0, threshold=-1)
|
175 |
+
Mask = np.zeros((Img0.shape[0], Img0.shape[1]), np.float32)
|
176 |
+
Mask[Mask0 > 0] = 1
|
177 |
+
|
178 |
+
if config.use_resize:
|
179 |
+
Img0 = cv2.resize(Img0, resize_w_h)
|
180 |
+
Mask = cv2.resize(Mask, resize_w_h, interpolation=cv2.INTER_NEAREST)
|
181 |
+
|
182 |
+
Img = Img0
|
183 |
+
height, width = Img.shape[:2]
|
184 |
+
n_classes = 3
|
185 |
+
patch_height = config.patch_size
|
186 |
+
patch_width = config.patch_size
|
187 |
+
stride_height = config.stride_height
|
188 |
+
stride_width = config.stride_width
|
189 |
+
|
190 |
+
Img = cv2.cvtColor(Img, cv2.COLOR_BGR2RGB)
|
191 |
+
if cfg.dataset == 'all':
|
192 |
+
# # # 将图像转换为 LAB 颜色空间
|
193 |
+
lab = cv2.cvtColor(Img, cv2.COLOR_RGB2LAB)
|
194 |
+
|
195 |
+
# 拆分 LAB 通道
|
196 |
+
l, a, b = cv2.split(lab)
|
197 |
+
|
198 |
+
# 创建 CLAHE 对象并应用到 L 通道
|
199 |
+
clahe = cv2.createCLAHE(clipLimit=2, tileGridSize=(8, 8))
|
200 |
+
l_clahe = clahe.apply(l)
|
201 |
+
|
202 |
+
# 将 CLAHE 处理后的 L 通道与原始的 A 和 B 通道合并
|
203 |
+
lab_clahe = cv2.merge((l_clahe, a, b))
|
204 |
+
|
205 |
+
# 将图像转换回 BGR 颜色空间
|
206 |
+
Img = cv2.cvtColor(lab_clahe, cv2.COLOR_LAB2RGB)
|
207 |
+
|
208 |
+
if cfg.use_CAM:
|
209 |
+
Img = CAM(Img, dataset)
|
210 |
+
|
211 |
+
Img = np.float32(Img / 255.)
|
212 |
+
Img_enlarged = paint_border_overlap(Img, patch_height, patch_width, stride_height, stride_width)
|
213 |
+
patch_size = config.patch_size
|
214 |
+
batch_size = 2
|
215 |
+
patches_imgs, global_images = extract_ordered_overlap_big(Img_enlarged, patch_height, patch_width,
|
216 |
+
stride_height,
|
217 |
+
stride_width)
|
218 |
+
|
219 |
+
patches_imgs = np.transpose(patches_imgs, (0, 3, 1, 2))
|
220 |
+
patches_imgs = Normalize(patches_imgs)
|
221 |
+
global_images = np.transpose(global_images, (0, 3, 1, 2))
|
222 |
+
global_images = Normalize(global_images)
|
223 |
+
patchNum = patches_imgs.shape[0]
|
224 |
+
max_iter = int(np.ceil(patchNum / float(batch_size)))
|
225 |
+
|
226 |
+
pred_patches = np.zeros((patchNum, n_classes, patch_size, patch_size), np.float32)
|
227 |
+
|
228 |
+
for i in range(max_iter):
|
229 |
+
begin_index = i * batch_size
|
230 |
+
end_index = (i + 1) * batch_size
|
231 |
+
|
232 |
+
patches_temp1 = patches_imgs[begin_index:end_index, :, :, :]
|
233 |
+
|
234 |
+
patches_input_temp1 = torch.FloatTensor(patches_temp1)
|
235 |
+
global_input_temp1 = patches_input_temp1
|
236 |
+
if config.use_global_semantic:
|
237 |
+
global_temp1 = global_images[begin_index:end_index, :, :, :]
|
238 |
+
global_input_temp1 = torch.FloatTensor(global_temp1)
|
239 |
+
if use_cuda:
|
240 |
+
patches_input_temp1 = autograd.Variable(patches_input_temp1.cuda())
|
241 |
+
if config.use_global_semantic:
|
242 |
+
global_input_temp1 = autograd.Variable(global_input_temp1.cuda())
|
243 |
+
else:
|
244 |
+
patches_input_temp1 = autograd.Variable(patches_input_temp1)
|
245 |
+
if config.use_global_semantic:
|
246 |
+
global_input_temp1 = autograd.Variable(global_input_temp1)
|
247 |
+
|
248 |
+
output_temp, _1, = Net(patches_input_temp1, global_input_temp1)
|
249 |
+
|
250 |
+
pred_patches_temp = np.float32(output_temp.data.cpu().numpy())
|
251 |
+
|
252 |
+
pred_patches_temp_sigmoid = sigmoid(pred_patches_temp)
|
253 |
+
|
254 |
+
pred_patches[begin_index:end_index, :, :, :] = pred_patches_temp_sigmoid[:, :, :patch_size, :patch_size]
|
255 |
+
|
256 |
+
del patches_input_temp1
|
257 |
+
del pred_patches_temp
|
258 |
+
del patches_temp1
|
259 |
+
del output_temp
|
260 |
+
del pred_patches_temp_sigmoid
|
261 |
+
|
262 |
+
new_height, new_width = Img_enlarged.shape[0], Img_enlarged.shape[1]
|
263 |
+
|
264 |
+
pred_img = recompone_overlap(pred_patches, new_height, new_width, stride_height, stride_width) # predictions
|
265 |
+
pred_img = pred_img[:, 0:height, 0:width]
|
266 |
+
|
267 |
+
if is_kill_border:
|
268 |
+
pred_img = kill_border(pred_img, Mask)
|
269 |
+
|
270 |
+
ArteryPred = np.float32(pred_img[0, :, :])
|
271 |
+
VeinPred = np.float32(pred_img[2, :, :])
|
272 |
+
VesselPred = np.float32(pred_img[1, :, :])
|
273 |
+
|
274 |
+
ArteryPred = ArteryPred[np.newaxis, :, :]
|
275 |
+
VeinPred = VeinPred[np.newaxis, :, :]
|
276 |
+
VesselPred = VesselPred[np.newaxis, :, :]
|
277 |
+
Mask = Mask[np.newaxis, :, :]
|
278 |
+
|
279 |
+
return ArteryPred, VeinPred, VesselPred, Mask, ArteryPred, VeinPred, VesselPred,
|
280 |
+
|
281 |
+
|
282 |
+
def out_test(cfg, output_dir='', evaluate_metrics=False, img_name='out_test'):
|
283 |
+
device = torch.device("cuda" if cfg.use_cuda else "cpu")
|
284 |
+
model_root = cfg.model_path_pretrained_G
|
285 |
+
model_path = os.path.join(model_root, 'G_' + str(cfg.model_step_pretrained_G) + '.pkl')
|
286 |
+
net = torch.load(model_path, map_location=device)
|
287 |
+
|
288 |
+
image_color = modelEvalution_out_big(net,
|
289 |
+
use_cuda=cfg.use_cuda,
|
290 |
+
dataset=img_name,
|
291 |
+
input_ch=cfg.input_nc,
|
292 |
+
config=cfg,
|
293 |
+
output_dir=output_dir, evaluate_metrics=evaluate_metrics)
|
294 |
+
|
295 |
+
return image_color
|
296 |
+
|
297 |
+
|
298 |
+
def segment_by_out_test(image,model_name):
|
299 |
+
print("✅ 传到后端的模型名:", model_name)
|
300 |
+
|
301 |
+
cfg.set_dataset(model_name)
|
302 |
+
if image is None:
|
303 |
+
raise gr.Error("请上传一张图像(upload a fundus image)。")
|
304 |
+
os.makedirs("./examples", exist_ok=True)
|
305 |
+
timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
|
306 |
+
temp_path = f"./examples/tmp_upload_{timestamp}.png"
|
307 |
+
image.save(temp_path)
|
308 |
+
|
309 |
+
image_color = out_test(cfg, output_dir='', evaluate_metrics=False, img_name=temp_path)
|
310 |
+
return Image.fromarray(image_color)
|
311 |
+
|
312 |
+
def gradio_interface():
|
313 |
+
model_info_md = """
|
314 |
+
### 📘 模型说明
|
315 |
+
|
316 |
+
| 模型(model name) | 数据集(dataset) | patch size |running time |
|
317 |
+
|------|--------|------------|--------|
|
318 |
+
| DRIVE | 小分辨率血管图像 | 256 |30s以内|
|
319 |
+
| HRF | 高分辨率图像(健康、青光眼等)| 256 | 2min以内|
|
320 |
+
| LES | 视盘中心图像适配 | 256 |2min以内|
|
321 |
+
| UKBB | UKBB图像 | 256 |2min以内 |
|
322 |
+
| 通用模型(512) | 超清图像,适配性强 | 512 |2min以内|
|
323 |
+
"""
|
324 |
+
model_choices = [
|
325 |
+
("1: DRIVE专用模型", "DRIVE"),
|
326 |
+
("2: HRF专用模型", "hrf"),
|
327 |
+
("3: LES专用模型","LES"),
|
328 |
+
("4: UKBB专用模型", "ukbb"),
|
329 |
+
("5: 通用模型(general)", "all"),
|
330 |
+
]
|
331 |
+
|
332 |
+
with gr.Blocks(theme=gr.themes.Soft()) as demo:
|
333 |
+
gr.Markdown("# 👁️ 眼底图像动静脉血管分割(Retinal image artery and vein segmentation)")
|
334 |
+
gr.Markdown("上传眼底图像,选择一个模型开始处理,结果将自动生成。(Upload the retinal image, select a model to start processing, and the results will be generated automatically.)")
|
335 |
+
|
336 |
+
with gr.Row():
|
337 |
+
image_input = gr.Image(type="pil", label="📤 上传图像(upload)",height=300)
|
338 |
+
|
339 |
+
with gr.Row():
|
340 |
+
with gr.Column():
|
341 |
+
model_select = gr.Radio(
|
342 |
+
choices=model_choices,
|
343 |
+
label="🎯 选择模型",
|
344 |
+
value="DRIVE",
|
345 |
+
interactive = True
|
346 |
+
)
|
347 |
+
submit_btn = gr.Button("🚀 开始分割(RUN)")
|
348 |
+
with gr.Column():
|
349 |
+
output_image = gr.Image(label="🖼️ 分割结果(Result)")
|
350 |
+
|
351 |
+
gr.Markdown("### 📁 示例图像examples(点击自动加载)")
|
352 |
+
gr.Examples(
|
353 |
+
examples=[
|
354 |
+
["examples/DRIVE.tif", "DRIVE"],
|
355 |
+
["examples/LES.png", "LES"],
|
356 |
+
["examples/hrf.png", "hrf"],
|
357 |
+
["examples/ukbb.png", "ukbb"],
|
358 |
+
["examples/all.jpg", "all"]
|
359 |
+
],
|
360 |
+
inputs=[image_input, model_select],
|
361 |
+
label="示例图像",
|
362 |
+
examples_per_page=5
|
363 |
+
)
|
364 |
+
with gr.Accordion("📖 模型���明desciption(点击展开)", open=False):
|
365 |
+
gr.Markdown(model_info_md)
|
366 |
+
|
367 |
+
# 功能连接
|
368 |
+
submit_btn.click(
|
369 |
+
fn=segment_by_out_test,
|
370 |
+
inputs=[image_input, model_select],
|
371 |
+
outputs=[output_image]
|
372 |
+
)
|
373 |
+
gr.Markdown("📚 **专用模型引用cite**: RIP-AV: Joint Representative Instance Pre-training with Context Aware Network for Retinal Artery/Vein Segmentation")
|
374 |
+
gr.Markdown("📚 **通用模型引用cite**: An Efficient and Interpretable Foundation Model for Retinal Image Analysis in Disease Diagnosis.")
|
375 |
+
demo.queue()
|
376 |
+
demo.launch()
|
377 |
+
|
378 |
+
|
379 |
+
if __name__ == '__main__':
|
380 |
+
# cfg.set_dataset('all')
|
381 |
+
# image_color = out_test(cfg = cfg, evaluate_metrics=False, img_name=r'.\AV\data\AV-DRIVE\test\images\01_test.tif')
|
382 |
+
# Image.fromarray(image_color).save('image_color.png')
|
383 |
+
#print(cfg.patch_size)
|
384 |
+
gradio_interface()
|