SAM_ca17_04_no_level0_tumor_mask_for_kaili

在这里插入代码片
import os
import numpy as np
import cv2
import json
from PIL import Image
import openslide
from tqdm import tqdm
#export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libffi.so.7
os.environ['LD_PRELOAD'] = '/usr/lib/x86_64-linux-gnu/libffi.so.7'

def run(wsi_path,level,json_path):
    # get the level * dimensions e.g. tumor0.tif level 6 shape (1589, 7514)
    slide = openslide.OpenSlide(wsi_path)
    w, h = slide.level_dimensions[level]
    mask_tumor = np.zeros((h, w)) # the init mask, and all the value is 0
    # get the factor of level * e.g. level 6 is 2^6
    factor = slide.level_downsamples[level]
    with open(json_path) as f:
        dicts = json.load(f)
    tumor_polygons = dicts['positive']
    for tumor_polygon in tumor_polygons:
        name = tumor_polygon["name"]
        vertices = np.array(tumor_polygon["vertices"]) / factor
        vertices = vertices.astype(np.int32)
        cv2.fillPoly(mask_tumor, [vertices], (255))
    mask_tumor = mask_tumor[:] > 127
    return mask_tumor

def mask_show(npy_path,wsi_path,mask_save_path):
    wsi_name = wsi_path.split('/')[-1]
    mask = np.load(npy_path)
    num = np.zeros((mask.shape[0], (mask.shape[1])), dtype=np.int32)
    num[mask] = 1
    img_mask = num * 255
    cv2.imwrite(mask_save_path,img_mask)

def wsi_png(wsi_path,level,slide_save_path):
    wsi_name = wsi_path.split('/')[-1]
    slide = openslide.OpenSlide(wsi_path)
    downsamples = slide.level_downsamples
    [w, h] = slide.level_dimensions[0]
    # size1=int(w*(downsamples[0]/downsamples[4]))
    # size2=int(h*(downsamples[0]/downsamples[4]))
    size_w = round(w * (downsamples[0] / downsamples[level]))
    size_h = round(h * (downsamples[0] / downsamples[level]))
    region = np.array(slide.read_region((0, 0), level, (size_w, size_h)))
    im = Image.fromarray(region.astype('uint8')).convert('RGB')
    #save_path = os.path.join(slide_save_path,wsi_name)
    im.save(slide_save_path, quality=100)

def main():
    level = 3
    # json_route = '/media/wagnchogn/data_2tb/path_sam/dataset/camleyon17/label/json'
    # wsi_route = '/media/wagnchogn/data_16t/camelyon/CAMELYON17/training_wsi/center_4'
    # #npy_route = r'D:\code\pre_code\wsi_prepocessing\dataset\camelyon\tumor4'
    # #mask_save_route = r'D:\code\pre_code\wsi_prepocessing\dataset\camelyon\tumor4_show'
    # save_route = '/media/wagnchogn/data_2tb/path_sam/dataset/camleyon17_10x/center_4/tumor'


    json_route = '/media/dell/data_4t/SAM_withmag/data/17/labels/json_1'
    wsi_route = '/media/dell/data_4t/SAM_withmag/data/17/train'
    #npy_route = r'D:\code\pre_code\wsi_prepocessing\dataset\camelyon\tumor4'
    #mask_save_route = r'D:\code\pre_code\wsi_prepocessing\dataset\camelyon\tumor4_show'
    save_route = '/media/dell/data_4t/SAM_withmag/data/17/train/level_3_v2'

    mask_save_route = os.path.join(save_route,'mask')
    crop_save_route = os.path.join(save_route, 'img')
    if not os.path.exists(mask_save_route):
        os.makedirs(mask_save_route)
    if not os.path.exists(crop_save_route):
        os.makedirs(crop_save_route)
    label_files = os.listdir(json_route)

    wsi_files = os.listdir(wsi_route)
    for wsi_file in tqdm(wsi_files):
        json_path = os.path.join(json_route, wsi_file.replace('.tif', '.json'))
        wsi_path = os.path.join(wsi_route, wsi_file)

        if wsi_file.replace('.tif','.json') in label_files:
            print(wsi_file)
            mask_tumor = run(wsi_path, level, json_path)
        else:
            continue
        slide = openslide.OpenSlide(wsi_path)
        level_downsample = slide.level_downsamples[level]

        tumor_img = np.uint8(mask_tumor*255)
        contours, _ = cv2.findContours(tumor_img, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
        bounding_rects = [cv2.boundingRect(contour) for contour in contours] #(x,y,width,height)
        for i in range(len(bounding_rects)):
            ###
            # x_ori,y_ori,width_ori,height_ori = bounding_rects[i]
            # '''
            # x = x_ori - 50
            # y = y_ori - 50
            # width = width_ori + 100
            # height = height_ori + 100
            # '''
            # width = (width_ori + 255) // 256 * 256
            # height = (height_ori + 255) // 256 * 256
            #
            # # 计算增量
            # delta_width = width - width_ori
            # delta_height = height - height_ori
            #
            # # 调整 x 和 y 以保持中心不变
            # x = x_ori - delta_width // 2
            # y = y_ori - delta_height // 2
            #

            ###
            x_ori, y_ori, width_ori, height_ori = bounding_rects[i]
            # 1. 计算高和宽能否被1024整除，求商的最大值
            ####?
            factor_width = (width_ori // 1024) + (1 if width_ori % 1024 != 0 else 0)
            factor_height = (height_ori // 1024) + (1 if height_ori % 1024 != 0 else 0)

            # 2. 新的宽度和高度
            factor_all = max(factor_width, factor_height)

            width = factor_all * 1024
            height = factor_all * 1024

            # 3. 计算增量并调整x和y，以保持中心不变
            delta_width = width - width_ori
            delta_height = height - height_ori
            x = x_ori - delta_width // 2
            y = y_ori - delta_height // 2

            ###

            #cv2.rectangle(tumor_img, (x, y), (x + width, y + height), (0, 255, 0), 2) #显示裁剪区域
            mask = tumor_img[y:y + height, x:x + width]

            x_level_0 = int(x * level_downsample)
            y_level_0 = int(y * level_downsample)
            sel_wsi = slide.read_region((x_level_0, y_level_0), level, (width, height))
            sel_wsi = sel_wsi.convert('RGB')

            mask_path = os.path.join(mask_save_route, wsi_file.split('.tif')[0] + '_' + str(x) + '_' + str(y) + '_' + str(width) + '_' + str(height) + '_' + str(level) + f'level_mask' + '.png')
            sel_wsi_path = os.path.join(crop_save_route,
                                        wsi_file.split('.tif')[0] + '_' + str(x) + '_' + str(y) + '_' + str(
                                            width) + '_' + str(height) + '_' + str(level) + 'level' + '.png')

            try:
                cv2.imwrite(mask_path, mask)
                sel_wsi.save(sel_wsi_path)

            except Exception as e:
                print(e)
                print(f'{wsi_file} {x}x {y}y {width}width {height}height {level}level')
                # continue





            #print(bounding_rects)

if __name__ == "__main__":
    main()


####   level=3 one bug