e_ophtha_MA眼底数据集—根据微血管瘤标注Mask绘制Contour轮廓图

眼底医学图像处理：微血管瘤Microaneurysm检测分割

采用数据集e_ophtha中的e_ophtha_MA，此数据集可从互联网下载

实现根据微血管瘤标注Mask，在原图绘制轮廓图，以直观了解微血管瘤，以便检测分割微血管瘤

1. 可展示数据集中原图和绘制轮廓图的并列拼接图

2. 可保存Mask，原图，根据标注绘制轮廓图的眼底图的拼接图

1. 原图和绘制轮廓图的并列拼接图

2. 保存Mask，原图，根据标注绘制轮廓图的眼底图的拼接图

3. 代码

# -*- coding: utf-8 -*-
'''
@Time    : 2020.03.28 12:18
@Author  : Shibing Xiang
@FileName: MaskinFundus.py
@Software: PyCharm
'''

import numpy as np
import cv2,os,imageio
from skimage import measure

def Union_Masks(rst, annotation):
    print(type(rst))

def zh(string):
	return string.encode("gbk").decode(errors="ignore")

def CVShow(img, title = None):
    img = np.array(img)
    if(len(img.shape) == 3):
        h, w, d = img.shape
    else:h, w = img.shape
    fscale = 1800/w
    cv2.namedWindow(title,0)
    cv2.resizeWindow(title, np.int(w * fscale), np.int(h * fscale))
    cv2.imshow(title, img)
    key = cv2.waitKey(0)
    if key == 27:  # wait for ESC key to exit
        cv2.destroyAllWindows()
        return False
    elif key == ord('s'):
        cv2.destroyAllWindows()
        return True

def read_directory(root_path,mask = False):
    images = []
    filepaths = []
    names = os.listdir(root_path)
    for filename in names:
        if filename != 'Thumbs.db':
            filepath = os.path.normpath(root_path + "/" + filename)
            if mask:
                img = cv2.imread(filepath, 0)
            else:
                img = cv2.imread(filepath)
            filepaths.append(filepath)
            images.append(img)
        else: pass
    return names, filepaths, np.array(images)

def CVdrawContour(mask,img, rect = False):
    _, contours, hierarchy = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
    if rect:
        cv2.drawContours(img, contours, -1, (255, 0, 0), 1, hierarchy = hierarchy)
        for cnt in contours:
            x, y, w, h = cv2.boundingRect(cnt)
            cv2.rectangle(img, (x, y), (x + w, y + h), (0, 255, 0), 1)
    else: cv2.drawContours(img, contours, -1, (0, 255, 0), 1, hierarchy = hierarchy)

def skimContour(mask,img, color = (0, 176, 80)):
    contours = measure.find_contours(mask, 0.5)
    for c in contours:
        c = np.around(c).astype(np.int)
        img[c[:, 0], c[:, 1]] = np.array(color)

def MaskinFundus(masks, images, filenames, method = 'CV', show = False):
    MaskedImages = images.copy() # 即使这样也会修改 images 的值
    if method == 'CV':
        for i in range(len(masks)):
            CVdrawContour(masks[i], MaskedImages[i])
            if show:
                I_merge = np.hstack((images[i], MaskedImages[i]))  # 水平拼接
                CVShow(I_merge, 'The ' + str(i+1) + ' th - '+ filenames[i])
    elif method == 'skimage':
        for i in range(len(masks)):
            skimContour(masks[i], MaskedImages[i])
            if show:
                I_merge = np.hstack((images[i], MaskedImages[i]))  # 水平拼接
                CVShow(I_merge, 'The ' + str(i + 1) + ' th - ' + filenames[i])
    else: return None
    return MaskedImages

if __name__ == '__main__':
    root_path = r'J:\Image Projects\Microaneurysm Detection\Datasets\2013_e_ophtha\e_ophtha_MA'
    for temp in os.listdir(root_path+'/'+'MA'):
        Annotation_MA = os.path.normpath(root_path + '/Annotation_MA/' + temp)
        MA = os.path.normpath(root_path + '/MA/' + temp)
        _, _, masks = read_directory(Annotation_MA, mask=True)
        filenames, _, images = read_directory(MA)
        MaskedImages = MaskinFundus(masks, images, filenames, 'CV')
        for i in range(len(masks)):
            hmerge  = np.hstack((images[i], MaskedImages[i]))  # 水平拼接
            save = CVShow(hmerge ,  temp + ' - '  + str(i + 1) + ' - ' + filenames[i])
            if save:
                hmerge0 = np.hstack((masks[i], masks[i]))  # 水平拼接
                hmerge0 = cv2.merge([hmerge0,hmerge0,hmerge0])
                I_merge = np.vstack((hmerge0, hmerge))  # 垂直拼接
                savepath = root_path + '/Sample Images/' + temp + '-' + filenames[i]
                cv2.imwrite(savepath, I_merge)

    # MA_masks = r'J:\Image Projects\Microaneurysm Detection\Datasets\2013_e_ophtha\e_ophtha_MA\Annotation_MA\E0001520'
    # MA_imges = r'J:\Image Projects\Microaneurysm Detection\Datasets\2013_e_ophtha\e_ophtha_MA\MA\E0001520'
    # _, masks = read_directory(MA_masks, mask=True)
    # paths, images = read_directory(MA_imges)
    # MaskinFundus(masks, images, 'CV')