def gen_patches(imgs_dir, patch_dir, img_list, dset, patch_size=256):
for ind, ele in enumerate(img_list):
if ind > 0 and ind % 10 == 0:
print("processing {}/{}".format(ind, len(img_list)))
img_path = os.path.join(imgs_dir, ele)
img_name = os.path.splitext(ele)[0]
json_path = os.path.join(imgs_dir, img_name+".json")
if not (os.path.exists(img_path) and os.path.exists(json_path)):
print("File not available")
img = io.imread(img_path)
anno_dict = format.json_to_dict(json_path)
for cur_r in anno_dict:
cur_anno = anno_dict[cur_r]
x_coors, y_coors = cur_anno['w'], cur_anno['h']
cnt_arr = np.zeros((2, len(x_coors)), np.int32)
cnt_arr[0], cnt_arr[1] = y_coors, x_coors
poly_cnt = poly_transform.np_arr_to_poly(cnt_arr)
start_x, start_y = min(x_coors), min(y_coors)
cnt_w = max(x_coors) - start_x + 1
cnt_h = max(y_coors) - start_y + 1
coors_arr = patch.wsi_coor_splitting(cnt_h, cnt_w, patch_size, overlap_flag=True)
for cur_h, cur_w in coors_arr:
patch_start_w, patch_start_h = cur_w+start_x, cur_h + start_y
patch_center = Point(patch_start_w+patch_size/2, patch_start_h+patch_size/2)
if patch_center.within(poly_cnt) == True:
patch_img = img[patch_start_h:patch_start_h+patch_size, patch_start_w:patch_start_w+patch_size, :]
patch_img = transform.resize(patch_img, (256, 256))
patch_cat_dir = os.path.join(patch_dir, dset, str(label_map[cur_anno['label']]))
if os.path.exists(patch_cat_dir) == False:
os.makedirs(patch_cat_dir)
patch_path = os.path.join(patch_cat_dir, str(uuid.uuid4())[:8] + '.png')
io.imsave(patch_path, patch_img)
def check_contour_valid(slides_dir, annotation_dir):
slide_list = [ele for ele in os.listdir(slides_dir) if "tiff" in ele]
json_list = [ele for ele in os.listdir(annotation_dir) if "json" in ele]
if len(slide_list) != len(json_list):
raise AssertionError("Annotation not complete")
for ele in slide_list:
# slide_path = os.path.join(slides_dir, ele)
json_path = os.path.join(annotation_dir,
os.path.splitext(ele)[0] + ".json")
anno_dict = format.json_to_dict(json_path)
region_annos = anno_dict["regions"]
if len(region_annos) <= 0:
print("Not annotated regions in {}".format(ele))
for cur_r in region_annos:
cur_cnt = region_annos[cur_r]['cnts']
num_ps = len(cur_cnt['h'])
cnt_arr = np.zeros((2, num_ps))
cnt_arr[0] = cur_cnt['h']
cnt_arr[1] = cur_cnt['w']
poly_cnt = poly_transform.np_arr_to_poly(cnt_arr)
center_point = Point(np.mean(cnt_arr[1]), np.mean(cnt_arr[0]))
if center_point.within(poly_cnt) == False:
print("{} in {}".format(cur_r, ele))
def gen_gist_features(roi_dir, fea_dir, mode, args):
fea_dir = os.path.join(fea_dir, args.model_name, mode)
data_dir = os.path.join(roi_dir, mode)
img_list = [ele for ele in os.listdir(data_dir) if "png" in ele]
for ind, ele in enumerate(img_list):
if ind > 0 and ind % 10 == 0:
print("processing {}/{}".format(ind, len(img_list)))
cur_img_path = os.path.join(data_dir, ele)
img_name = os.path.splitext(ele)[0]
cur_anno_path = os.path.join(data_dir, img_name + ".json")
if not (os.path.exists(cur_img_path)
and os.path.exists(cur_anno_path)):
print("File not available")
img = io.imread(cur_img_path)
anno_dict = format.json_to_dict(cur_anno_path)
for cur_r in anno_dict:
cur_anno = anno_dict[cur_r]
region_label = str(label_map[cur_anno['label']])
region_name = "_".join([img_name, 'r' + cur_r])
x_coors, y_coors = cur_anno['w'], cur_anno['h']
cnt_arr = np.zeros((2, len(x_coors)), np.int32)
cnt_arr[0], cnt_arr[1] = y_coors, x_coors
poly_cnt = poly_transform.np_arr_to_poly(cnt_arr)
start_x, start_y = min(x_coors), min(y_coors)
cnt_w = max(x_coors) - start_x + 1
cnt_h = max(y_coors) - start_y + 1
coors_arr = patch.wsi_coor_splitting(cnt_h,
cnt_w,
args.patch_size,
overlap_flag=True)
Feas, BBoxes = [], []
for cur_h, cur_w in coors_arr:
patch_start_w, patch_start_h = cur_w + start_x, cur_h + start_y
patch_center = Point(patch_start_w + args.patch_size / 2,
patch_start_h + args.patch_size / 2)
if patch_center.within(poly_cnt) == True:
patch_img = img[patch_start_h:patch_start_h +
args.patch_size,
patch_start_w:patch_start_w +
args.patch_size, :]
patch_desp = gist.extract(patch_img)
Feas.append(patch_desp)
BBoxes.append([
patch_start_h, patch_start_w, args.patch_size,
args.patch_size
])
fea_dict = {'feat': np.asarray(Feas), 'bbox': np.asarray(BBoxes)}
# save features
cat_fea_dir = os.path.join(fea_dir, region_label)
if not os.path.exists(cat_fea_dir):
os.makedirs(cat_fea_dir)
dd.io.save(os.path.join(cat_fea_dir, region_name + ".h5"),
fea_dict)
def test_poly_transform():
np_arr = np.array([[1., 2., 4., 5., 3.], [1., 3., 4., 2., 0.]])
poly1 = np_arr_to_poly(np_arr)
print("Bounds of poly1 is: ", poly1.exterior.bounds)
point_list = np_arr_to_point_list(np_arr)
poly2 = point_list_to_poly(point_list)
print("Bounds of poly2 is: ", poly2.exterior.bounds)
if poly1 != poly2:
raise AssertionError("Conversion error")
min_h, max_h = np.min(np_arr[0]), np.max(np_arr[0])
min_w, max_w = np.min(np_arr[1]), np.max(np_arr[1])
poly3 = bbox_to_poly(min_h, min_w, max_h, max_w)
print("Bounds of poly3 is: ", poly3.exterior.bounds)
# poly3.exterior.coords.xy
poly1_arr = poly_to_np_arr(poly1)
print("Numpy coordinates of poly1 is:")
if not np.array_equal(np_arr, poly1_arr):
raise AssertionError("Conversion error")
def contour_valid(cnt_arr):
""" Check contour is valid or not.
Parameters
-------
cnt_arr: np.array
contour with standard numpy 2d array format
Returns
-------
valid: boolean
True if valid, else False
"""
poly = np_arr_to_poly(cnt_arr)
valid = True if poly.is_valid else False
return valid
def locate_tissue(slides_dir):
slide_list = []
svs_file_list = filesystem.find_ext_files(slides_dir, "svs")
slide_list.extend(svs_file_list)
SVS_file_list = filesystem.find_ext_files(slides_dir, "SVS")
slide_list.extend(SVS_file_list)
tissue_dir = os.path.join(os.path.dirname(slides_dir), "Visualization/TissueLoc")
filesystem.overwrite_dir(tissue_dir)
for ind, slide_path in enumerate(slide_list):
print("processing {}/{}".format(ind+1, len(slide_list)))
# locate tissue contours with default parameters
cnts, d_factor = tl.locate_tissue_cnts(slide_path, max_img_size=2048, smooth_sigma=13,
thresh_val=0.88, min_tissue_size=120000)
cnts = sorted(cnts, key=lambda x: cv2.contourArea(x), reverse=True)
# if len(cnts) != 1:
# print("There are {} contours in {}".format(len(cnts), os.path.basename(slide_path)))
# load slide
select_level, select_factor = tl.select_slide_level(slide_path, max_size=2048)
wsi_head = pyramid.load_wsi_head(slide_path)
slide_img = wsi_head.read_region((0, 0), select_level, wsi_head.level_dimensions[select_level])
slide_img = np.asarray(slide_img)[:,:,:3]
slide_img = np.ascontiguousarray(slide_img, dtype=np.uint8)
# change not valid poly to convex_hull
cnt_arr = cv_cnt_to_np_arr(cnts[0])
cnt_poly = np_arr_to_poly(cnt_arr)
if cnt_poly.is_valid == True:
valid_cnt = cnts[0].astype(int)
else:
valid_arr = poly_to_np_arr(cnt_poly.convex_hull)
valid_cnt = np_arr_to_cv_cnt(valid_arr).astype(int)
cv2.drawContours(slide_img, [valid_cnt], 0, (0, 255, 0), 8)
# overlay and save
# cv2.drawContours(slide_img, cnts, 0, (0, 255, 0), 8)
tissue_save_name = os.path.splitext(os.path.basename(slide_path))[0] + ".png"
tissue_save_path = os.path.join(tissue_dir, tissue_save_name)
io.imsave(tissue_save_path, slide_img)
def contour_to_poly_valid(cnt_arr):
""" Convert contour to poly valid if not poly valid
Parameters
-------
cnt_arr: np.array
contour with standard numpy 2d array format
Returns
-------
cnt_valid_arr: np.array
contour with standard numpy 2d array format
"""
poly = np_arr_to_poly(cnt_arr)
if poly.is_valid == True:
cnt_valid_arr = cnt_arr
else:
cnt_valid_arr = poly_to_np_arr(poly.convex_hull)
return cnt_valid_arr
def gen_slide_patches(slide_dir, slide_name, patch_dir, patch_size=256):
img_path = os.path.join(slide_dir, slide_name + ".png")
json_path = os.path.join(slide_dir, slide_name + ".json")
if not (os.path.exists(img_path) and os.path.exists(json_path)):
print("File not available")
img = io.imread(img_path)
anno_dict = format.json_to_dict(json_path)
for cur_r in anno_dict:
cur_anno = anno_dict[cur_r]
x_coors, y_coors = cur_anno['w'], cur_anno['h']
cnt_arr = np.zeros((2, len(x_coors)), np.int32)
cnt_arr[0], cnt_arr[1] = y_coors, x_coors
poly_cnt = poly_transform.np_arr_to_poly(cnt_arr)
start_x, start_y = min(x_coors), min(y_coors)
cnt_w = max(x_coors) - start_x + 1
cnt_h = max(y_coors) - start_y + 1
coors_arr = patch.wsi_coor_splitting(cnt_h,
cnt_w,
patch_size,
overlap_flag=True)
for cur_h, cur_w in coors_arr:
patch_start_w, patch_start_h = cur_w + start_x, cur_h + start_y
patch_center = Point(patch_start_w + patch_size / 2,
patch_start_h + patch_size / 2)
if patch_center.within(poly_cnt) == True:
patch_img = img[patch_start_h:patch_start_h + patch_size,
patch_start_w:patch_start_w + patch_size, :]
patch_cat_dir = os.path.join(patch_dir,
str(label_map[cur_anno['label']]))
if os.path.exists(patch_cat_dir) == False:
os.makedirs(patch_cat_dir)
patch_path = os.path.join(patch_cat_dir,
str(uuid.uuid4())[:8] + '.png')
io.imsave(patch_path, patch_img)
def gen_l2_data(slides_dir, annotation_dir, level_dir, level=2, size=256):
slide_list = [ele for ele in os.listdir(slides_dir) if "tiff" in ele]
json_list = [ele for ele in os.listdir(annotation_dir) if "json" in ele]
if len(slide_list) != len(json_list):
raise AssertionError("Annotation not complete")
for ind, ele in enumerate(slide_list):
if ind > 0 and ind % 20 == 0:
print("Processing {:3d}/{}".format(ind, len(slide_list)))
slide_name = os.path.splitext(ele)[0]
json_path = os.path.join(annotation_dir, slide_name + ".json")
anno_dict = format.json_to_dict(json_path)
region_annos = anno_dict["regions"]
if len(region_annos) <= 0:
continue
slide_path = os.path.join(slides_dir, ele)
slide_head = openslide.OpenSlide(slide_path)
level_dim = slide_head.level_dimensions[level]
img_w, img_h = level_dim
new_anno_dict = {}
for cur_r in region_annos:
cur_cnt = region_annos[cur_r]['cnts']
cur_desp = region_annos[cur_r]['desp']
num_ps = len(cur_cnt['h'])
cnt_arr = np.zeros((2, num_ps), np.int32)
cnt_arr[0] = [ele / np.power(2, level) for ele in cur_cnt['h']]
cnt_arr[1] = [ele / np.power(2, level) for ele in cur_cnt['w']]
if np.min(cnt_arr[0]) < 0 or np.min(cnt_arr[1]) < 0:
continue
if np.max(cnt_arr[0]) > img_h or np.max(cnt_arr[1]) > img_w:
continue
poly_cnt = poly_transform.np_arr_to_poly(cnt_arr)
start_h, start_w = np.min(cnt_arr[0]), np.min(cnt_arr[1])
cnt_h = np.max(cnt_arr[0]) - start_h + 1
cnt_w = np.max(cnt_arr[1]) - start_w + 1
coors_arr = patch.wsi_coor_splitting(cnt_h,
cnt_w,
size,
overlap_flag=True)
for cur_h, cur_w in coors_arr:
patch_center = Point(cur_w + start_w + size / 2,
cur_h + start_h + size / 2)
if patch_center.within(poly_cnt) == True:
new_anno_dict[cur_r] = {
'label': cur_desp,
'h': cnt_arr[0].tolist(),
'w': cnt_arr[1].tolist()
}
break
if len(new_anno_dict) > 0:
wsi_img = slide_head.read_region((0, 0), level, level_dim)
wsi_img = np.array(wsi_img)[:, :, :3]
io.imsave(os.path.join(level_dir, slide_name + ".png"), wsi_img)
format.dict_to_json(new_anno_dict,
os.path.join(level_dir, slide_name + ".json"))
else:
print("---{} have no proper regions---".format(slide_name))
def gen_patches(slide_path, annotation_dict, args):
""" Generate patch images and masks based on annotations as well as slide information.
"""
# load slide header information
slide_head = openslide.OpenSlide(slide_path) # 读取图像
slide_name = os.path.basename(slide_path) # slide id
# level_count——幻灯片中的级别数。级别从0（最高分辨率）到level_count - 1（最低分辨率）编号。
if args.slide_level < 0 or args.slide_level >= slide_head.level_count: # slide_head.level_count = 4
print("level {} not availabel in {}".format(args.slide_level,
slide_name))
sys.exit()
img_save_dir, mask_save_dir = get_save_dirs(args)
for cur_reg in annotation_dict:
# slide_head.level_downsamples[args.slide_level = 1.0
# 原始坐标是(w,h)
coords = (annotation_dict[cur_reg] /
slide_head.level_downsamples[args.slide_level]).astype(
np.int32)
coords = np.transpose(np.array(coords)) # (2,428)
coords[[0, 1]] = coords[[1, 0]] # swap width and height
min_h, max_h = np.min(coords[0, :]), np.max(
coords[0, :]) # 0 is height (22,20464)
min_w, max_w = np.min(coords[1, :]), np.max(
coords[1, :]) # 1 is width (6119,33036)
num = 0
# 使用numpy二维数组([0]-h， [1]-w)构造多边形, 需要注意的是，高度是第一维，宽度是第二维
cur_poly = poly_transform.np_arr_to_poly(np.asarray(coords)) # 生成多边形
# 一个图片滑动10次
while num < 10:
rand_h = np.random.randint(min_h, max_h)
rand_w = np.random.randint(min_w, max_w)
# 原始坐标是(w,h)
h_over_flag = rand_h + args.crop_size >= slide_head.level_dimensions[
args.slide_level][1]
w_over_flag = rand_w + args.crop_size >= slide_head.level_dimensions[
args.slide_level][0]
if h_over_flag or w_over_flag:
continue
cen_h = int(rand_h + args.crop_size / 2) # (5385)
cen_w = int(rand_w + args.crop_size / 2) # (14173)
cen_point = Point(cen_w, cen_h) # 构造几何图形中心点 (14173,5385)
patch_in_flag = cen_point.within(cur_poly) # 判断中心点是否在多边形之中
if not patch_in_flag:
num += 1
continue
# 将(1024,1024)的区域按随机生成的(rand_h,rand_w)裁剪出来
cur_patch = slide_head.read_region(
(rand_w, rand_h), args.slide_level,
(args.crop_size, args.crop_size)) # shape : (1024,1024)
cur_patch = np.asarray(cur_patch)[:, :, :
3] # (1024,1024)-->(1024,1024,3)
# correct patch mask on ignore pixels
## very slow, need to speed this ignore part 1024x1024次迭代
patch_mask = gen_patch_mask(args)
for pw in range(rand_w, rand_w + args.crop_size):
for ph in range(rand_h, rand_h + args.crop_size):
cur_p = Point(pw, ph) # 当前坐标点
# 如果坐标点不在多边形曲线内，则mask置为0
if not cur_p.within(cur_poly):
patch_mask[ph - rand_h, pw - rand_w] = 0
save_img = transform.resize(
cur_patch, (args.save_size, args.save_size)) # (256,256,3)
# 经过resize后变为了0或1的矩阵 (256,256)
save_mask = transform.resize(
patch_mask, (args.save_size, args.save_size),
order=0) # order=0: Nearest-neighbor interpolation
save_mask = (save_mask * 255).astype(np.uint8)
img_fullname = str(uuid.uuid4())[:8] + ".png" # 随机生成8位唯一的id
save_img_path = os.path.join(img_save_dir, img_fullname)
save_mask_path = os.path.join(mask_save_dir, img_fullname)
io.imsave(save_img_path, save_img)
io.imsave(save_mask_path, save_mask)
num = num + 1
def _slide_patch_generator(slide_path, annotation_dict, annotation_label):
"""
generates the image and mask patch from slide, and save them.
:param slide_path:
:param annotation_dict:
:param annotation_label:
:return:
"""
slide = openslide.OpenSlide(slide_path)
slide_name = os.path.basename(slide_path)
if opt.slide_level < 0 or opt.slide_level >= slide.level_count:
raise Exception(
f'level {opt.slide_level} is not available in the {slide_name}')
if annotation_label not in annotation_label_dict:
raise Exception(
f"a value of an annotation '{annotation_label}' is not set")
for curr_annotation_region in annotation_dict:
annotation_coords = \
(annotation_dict[curr_annotation_region] / slide.level_downsamples[opt.slide_level]).astype(np.int32)
annotation_coords = np.transpose(np.array(annotation_coords))
# swap width and height
annotation_coords[[0, 1]] = annotation_coords[[1, 0]]
min_h, max_h = np.min(annotation_coords[0, :]), np.max(
annotation_coords[0, :])
min_w, max_w = np.min(annotation_coords[1, :]), np.max(
annotation_coords[1, :])
try:
annotation_polygon = poly_transform.np_arr_to_poly(
np.asarray(annotation_coords))
except ValueError as e:
logging.error(
f'Failed to transform coordinates to polygon, this will be skipped,'
f' slide_name: {slide_name}, region: {curr_annotation_region}')
logging.error(f'Exception: {e}')
continue
patch_generate_try_cnt = 0
while patch_generate_try_cnt < opt.patch_gen_try_num:
rand_h = np.random.randint(min_h, max_h)
rand_w = np.random.randint(min_w, max_w)
is_height_exceeds = rand_h + opt.crop_size >= slide.level_dimensions[
opt.slide_level][1]
is_width_exceeds = rand_w + opt.crop_size >= slide.level_dimensions[
opt.slide_level][0]
if is_width_exceeds or is_height_exceeds:
continue
patch_center_coord_h = int(rand_h + opt.crop_size / 2)
patch_center_coord_w = int(rand_w + opt.crop_size / 2)
patch_center_point = Point(patch_center_coord_w,
patch_center_coord_h)
if not patch_center_point.within(annotation_polygon):
patch_generate_try_cnt += 1
continue
curr_patch = slide.read_region((rand_w, rand_h), opt.slide_level,
(opt.crop_size, opt.crop_size))
curr_patch = np.asarray(curr_patch)[:, :, :3]
curr_patch_ground_truth = _generate_ground_truth(
rand_w,
rand_h,
crop_size=opt.crop_size,
annotation_polygon=annotation_polygon,
pixel_annotation_value=annotation_label_dict[annotation_label])
curr_patch = transform.resize(curr_patch,
(opt.save_size, opt.save_size))
# order=0: Nearest-neighbor interpolation
curr_patch_ground_truth = transform.resize(
curr_patch_ground_truth, (opt.save_size, opt.save_size),
order=0,
anti_aliasing=False)
curr_patch = (curr_patch * 255).astype(np.uint8)
curr_patch_ground_truth = curr_patch_ground_truth.astype(np.uint8)
yield curr_patch, curr_patch_ground_truth
patch_generate_try_cnt += 1
def gen_patches(slide_path, annotation_dict, args):
""" Generate patch images and masks based on annotations as well as slide information.
"""
# load slide header information
slide_head = openslide.OpenSlide(slide_path)
slide_name = os.path.basename(slide_path)
if args.slide_level < 0 or args.slide_level >= slide_head.level_count:
print("level {} not availabel in {}".format(args.slide_level,
slide_name))
sys.exit()
img_save_dir, mask_save_dir = get_save_dirs(args)
for cur_reg in annotation_dict:
coords = (annotation_dict[cur_reg] /
slide_head.level_downsamples[args.slide_level]).astype(
np.int32)
coords = np.transpose(np.array(coords))
coords[[0, 1]] = coords[[1, 0]] # swap width and height
min_h, max_h = np.min(coords[0, :]), np.max(coords[0, :])
min_w, max_w = np.min(coords[1, :]), np.max(coords[1, :])
num = 0
cur_poly = poly_transform.np_arr_to_poly(np.asarray(coords))
while num < 10:
rand_h = np.random.randint(min_h, max_h)
rand_w = np.random.randint(min_w, max_w)
h_over_flag = rand_h + args.crop_size >= slide_head.level_dimensions[
args.slide_level][1]
w_over_flag = rand_w + args.crop_size >= slide_head.level_dimensions[
args.slide_level][0]
if h_over_flag or w_over_flag:
continue
cen_h = int(rand_h + args.crop_size / 2)
cen_w = int(rand_w + args.crop_size / 2)
cen_point = Point(cen_w, cen_h)
patch_in_flag = cen_point.within(cur_poly)
if not patch_in_flag:
num += 1
continue
# crop patch image
cur_patch = slide_head.read_region(
(rand_w, rand_h), args.slide_level,
(args.crop_size, args.crop_size))
cur_patch = np.asarray(cur_patch)[:, :, :3]
# correct patch mask on ignore pixels
## very slow, need to speed this ignore part
patch_mask = gen_patch_mask(args)
for pw in range(rand_w, rand_w + args.crop_size):
for ph in range(rand_h, rand_h + args.crop_size):
cur_p = Point(pw, ph)
if not cur_p.within(cur_poly):
patch_mask[ph - rand_h, pw - rand_w] = 0
save_img = transform.resize(cur_patch,
(args.save_size, args.save_size))
save_mask = transform.resize(
patch_mask, (args.save_size, args.save_size),
order=0) # order=0: Nearest-neighbor interpolation
save_mask = (save_mask * 255).astype(np.uint8)
img_fullname = str(uuid.uuid4())[:8] + ".png"
save_img_path = os.path.join(img_save_dir, img_fullname)
save_mask_path = os.path.join(mask_save_dir, img_fullname)
io.imsave(save_img_path, save_img)
io.imsave(save_mask_path, save_mask)
num = num + 1
def gen_samples(slides_dir, patch_level, patch_size, tumor_type, slide_list, dset, overlap_mode):
# prepare saving directory
patch_path = os.path.join(os.path.dirname(slides_dir), "Patches", tumor_type)
patch_img_dir = os.path.join(patch_path, dset, "imgs")
if not os.path.exists(patch_img_dir):
os.makedirs(patch_img_dir)
patch_mask_dir = os.path.join(patch_path, dset, "masks")
if not os.path.exists(patch_mask_dir):
os.makedirs(patch_mask_dir)
# processing slide one-by-one
ttl_patch = 0
slide_list.sort()
for ind, ele in enumerate(slide_list):
print("Processing {} {}/{}".format(ele, ind+1, len(slide_list)))
cur_slide_path = os.path.join(slides_dir, ele+".svs")
if os.path.exists(cur_slide_path):
cur_slide_path = os.path.join(slides_dir, ele+".svs")
# locate contours and generate batches based on tissue contours
cnts, d_factor = tl.locate_tissue_cnts(cur_slide_path, max_img_size=2048, smooth_sigma=13,
thresh_val=0.88, min_tissue_size=120000)
select_level, select_factor = tl.select_slide_level(cur_slide_path, max_size=2048)
cnts = sorted(cnts, key=lambda x: cv2.contourArea(x), reverse=True)
# scale contour to slide level 2
wsi_head = pyramid.load_wsi_head(cur_slide_path)
cnt_scale = select_factor / int(wsi_head.level_downsamples[patch_level])
tissue_arr = cv_cnt_to_np_arr(cnts[0] * cnt_scale).astype(np.int32)
# convert tissue_arr to convex if poly is not valid
tissue_poly = np_arr_to_poly(tissue_arr)
if tissue_poly.is_valid == False:
tissue_arr = poly_to_np_arr(tissue_poly.convex_hull).astype(int)
coors_arr = None
if overlap_mode == "half_overlap":
level_w, level_h = wsi_head.level_dimensions[patch_level]
coors_arr = contour.contour_patch_splitting_half_overlap(tissue_arr, level_h, level_w, patch_size, inside_ratio=0.80)
elif overlap_mode == "self_overlap":
coors_arr = contour.contour_patch_splitting_self_overlap(tissue_arr, patch_size, inside_ratio=0.80)
else:
raise NotImplementedError("unknown overlapping mode")
wsi_img = wsi_head.read_region((0, 0), patch_level, wsi_head.level_dimensions[patch_level])
wsi_img = np.asarray(wsi_img)[:,:,:3]
mask_path = os.path.join(slides_dir, "_".join([ele, tumor_type+".tif"]))
mask_img = io.imread(mask_path)
wsi_mask = (transform.resize(mask_img, wsi_img.shape[:2], order=0) * 255).astype(np.uint8) * 255
if dset == "val":
test_slides_dir = os.path.join(os.path.dirname(slides_dir), "TestSlides")
if not os.path.exists(os.path.join(test_slides_dir, cur_slide_path)):
shutil.copy(cur_slide_path, test_slides_dir)
if not os.path.exists(os.path.join(test_slides_dir, mask_path)):
shutil.copy(mask_path, test_slides_dir)
for cur_arr in coors_arr:
cur_h, cur_w = cur_arr[0], cur_arr[1]
cur_patch = wsi_img[cur_h:cur_h+patch_size, cur_w:cur_w+patch_size]
if cur_patch.shape[0] != patch_size or cur_patch.shape[1] != patch_size:
continue
cur_mask = wsi_mask[cur_h:cur_h+patch_size, cur_w:cur_w+patch_size]
# background RGB (235, 210, 235) * [0.299, 0.587, 0.114]
if patch.patch_bk_ratio(cur_patch, bk_thresh=0.864) > 0.88:
continue
if overlap_mode == "half_overlap" and tumor_type == "viable":
pixel_ratio = np.sum(cur_mask > 0) * 1.0 / cur_mask.size
if pixel_ratio < 0.05:
continue
patch_name = ele + "_" + str(uuid.uuid1())[:8]
io.imsave(os.path.join(patch_img_dir, patch_name+".jpg"), cur_patch)
io.imsave(os.path.join(patch_mask_dir, patch_name+".png"), cur_mask)
ttl_patch += 1
print("There are {} patches in total.".format(ttl_patch))