from move_file import move_file from random import shuffle import numpy as np import os from PIL import Image import shutil Image.MAX_IMAGE_PIXELS = None def filter_mask(img_names): new_img_name = [] for img_name in img_names: if 'mask' not in img_name: new_img_name.append(img_name) return new_img_name def checkBlank(patch): patch = np.array(patch.convert("RGB")) m = patch.mean() if 200 <= m <= 255: return False else: return True def slide_window_inference(image, model): pass def slide_crop(img_dataroot,mask_dataroot,img_save_root,mask_save_root): # clean if not os.path.exists(img_save_root): os.mkdir(img_save_root) os.mkdir(mask_save_root) else: shutil.rmtree(img_save_root) shutil.rmtree(mask_save_root) os.mkdir(img_save_root) os.mkdir(mask_save_root) img_names = os.listdir(img_dataroot) img_names = filter_mask(img_names) for img_name in img_names[:]: # images img = Image.open(img_dataroot + img_name).convert("RGB") mask = Image.open(mask_dataroot + img_name[:-4]+'_mask.png') # params img_shape = img.size img_dim = len(img_shape) window_size = [256, 256] window_stride = [256, 256] for d in range(img_dim): if (window_size[d] is None) or window_size[d] > img_shape[d]: window_size[d] = img_shape[d] if (window_stride[d] is None) or window_stride[d] > window_size[d]: window_stride[d] = window_size[d] crop_start_list = [] for w in range(0, img_shape[-1], window_stride[-1]): w_min = min(w, img_shape[-1] - window_size[-1]) for h in range(0, img_shape[-2], window_stride[-2]): h_min = min(h, img_shape[-2] - window_size[-2]) if img_dim == 2: crop_start_list.append([h_min, w_min]) else: for d in range(0, img_shape[0], window_stride[0]): d_min = min(d, img_shape[0] - window_size[0]) crop_start_list.append([d_min, h_min, w_min]) i = 0 for c0 in crop_start_list: c1 = [c0[d] + window_size[d] for d in range(img_dim)] img_patch = img.crop((c0[0], c0[1], c1[0], c1[1])) # here, we check the blank patch if checkBlank(img_patch): img_patch.save( img_save_root + img_name[:-4] + f"_{i}.jpg" ) mask_patch = mask.crop((c0[0], c0[1], c1[0], c1[1])) mask_patch.save( mask_save_root + img_name[:-4] + f"_{i}_mask.png" ) i += 1 print("done!") if __name__ == "__main__": # img_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-2/images/" # mask_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-2/labels_v2/" # img_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-2-patch/images/' # mask_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-2-patch/labels_v2/' # slide_crop(img_dataroot, mask_dataroot, img_save_root, mask_save_root) img_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-50/images/" mask_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-50/labels/" img_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-50-patch/images/' mask_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-50-patch/labels/' slide_crop(img_dataroot, mask_dataroot, img_save_root, mask_save_root) # img_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-10/images/" # mask_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-10/labels_v2/" # img_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-10-patch/images/' # mask_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-10-patch/labels_v2/' # slide_crop(img_dataroot, mask_dataroot, img_save_root, mask_save_root) # img_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-20/images/" # mask_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-20/labels_v2/" # img_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-20-patch/images/' # mask_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-20-patch/labels_v2/' # slide_crop(img_dataroot, mask_dataroot, img_save_root, mask_save_root) # img_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-100/images/" # mask_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-100/labels_v2/" # img_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-100-patch/images/' # mask_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-train-100-patch/labels_v2/' # slide_crop(img_dataroot, mask_dataroot, img_save_root, mask_save_root) # img_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-val/images/" # mask_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-val/labels_v2/" # img_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-val-patch/images/' # mask_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-val-patch/labels_v2/' # slide_crop(img_dataroot, mask_dataroot, img_save_root, mask_save_root) # img_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-test/images/" # mask_dataroot = "/mnt/data2/lanfz/datasets/digestpath2019/tissue-test/labels/" # img_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-test-patch/images/' # mask_save_root = '/mnt/data2/lanfz/datasets/digestpath2019/tissue-test-patch/labels/' # slide_crop(img_dataroot, mask_dataroot, img_save_root, mask_save_root)