def cell_sampling(xml_file, save_path, size):
labels = get_labels(xml_file)
# print(labels)
filename = os.path.splitext(xml_file)[0]
if (not os.path.isfile(filename + ".tif")) and (
not os.path.isfile(filename + ".kfb")):
print(filename + " doesn't exist")
return
try:
slide = openslide.OpenSlide(filename + ".tif")
except:
slide = TSlide(filename + ".kfb")
size_x, size_y = slide.dimensions
points_xy = get_windows(labels, size_x, size_y, size)
# print(points_xy)
# generate jpg files
for (x, y) in points_xy:
cell = slide.read_region((x, y), 0, (size, size)).convert("RGB")
cell.save(save_path + "/" + os.path.basename(filename) + "_" + str(x) +
"_" + str(y) + ".jpg")
slide.close()
# generate xml files
new_xmls = Xml(os.path.basename(filename), save_path, points_xy, labels,
size)
new_xmls.gen_xml()
print("processed ", xml_file)
def cell_sampling(label_file, wsi_path, save_path, size):
labels = get_labels(label_file)
if len(labels) == 0:
return
print("PROCESSING %s ..." % wsi_path)
scale = 20
reader = kr.reader()
kr.reader.ReadInfo(reader, wsi_path, scale, True)
points_xy = get_windows_new(labels, size)
filename, _ = os.path.splitext(os.path.basename(wsi_path))
# generate img files
points_num = len(points_xy)
for i, (x, y) in enumerate(points_xy):
if ((i % 100) == 0):
print(filename, "processed #", i)
cell = reader.ReadRoi(x, y, size, size, scale)
image_file_name = save_path + "/" + filename + "_" + str(x) + "_" + str(y) + ".bmp"
# change l and s of image
# cell = hls_trans_smart(cell)
cv2.imwrite(image_file_name, cell)
# generate xml files
print(filename, "generating xml")
new_xmls = Xml(filename, save_path, points_xy, labels, size)
new_xmls.gen_xml()
print("[INFO]", "processed ", filename)
def cellSampling(files_list, save_path, size):
for txt_file in files_list:
# from .txt filename, get .jpg filename
filename = os.path.splitext(txt_file)[0]
# open .txt file
labels = get_labels(txt_file)
print(labels)
# open .jpg file
img_file = filename + ".jpg"
img = Image.open(img_file)
size_x, size_y = img.size
points_xy = get_windows(labels, size_x, size_y, size)
print(points_xy)
# generate jpg files
for (x, y) in points_xy:
img.crop(
(x, y, x + size,
y + size)).save(save_path + "/" + os.path.basename(filename) +
"_" + str(x) + "_" + str(y) + ".jpg")
img.close()
# generate xml files
new_xmls = Xml(os.path.basename(filename), save_path, points_xy,
labels, size)
new_xmls.gen_xml()
def cell_sampling(xml_file, tiff_path, save_path, size, scale):
# print("#INFO# ", "start cp file")
# copy remote file to local
# local_xml_file = cp_originfile_from_remote(xml_file, path_temp)
# xml_file = local_xml_file
# print("#INFO# ", "end cp file")
labels = get_labels(xml_file)
# filename = os.path.splitext(xml_file)[0]
# if (not os.path.isfile(filename+".tif")) and (not os.path.isfile(filename+".kfb")):
# print(filename + " doesn't exist")
# return
print("PROCESSING %s ..." % tiff_path)
try:
try:
slide = openslide.OpenSlide(tiff_path)
except:
slide = TSlide(tiff_path)
except:
print("ERROR #", "can not open pic ", tiff_path)
exit()
size_x, size_y = slide.dimensions
# points_xy = get_windows(labels, size_x, size_y, size)
# new gen method for cell base instead list all pic
points_xy = get_windows_new(labels, size_x, size_y, size, tiff_path)
# print("labels: ", labels)
# print("points_xy: ", points_xy)
# print("size_x: ", size_x, " size_y:", size_y, " size:", size)
# generate jpg files
# print(filename)
points_num = len(points_xy)
for i, (x, y) in enumerate(points_xy):
if ((i % 100) == 0):
print("# process # ", i, '/', points_num - 1, x, y, size, size)
cell = slide.read_region((x, y), 0, (size, size)).convert("RGB")
filename, _ = os.path.splitext(os.path.basename(tiff_path))
image_file_name = save_path + "/" + filename + "_" + str(
x) + "_" + str(y) + ".jpg"
# need scale pic from 1216 to 608
cell = cell.resize((int(size * scale + 0.5), int(size * scale + 0.5)))
cell.save(image_file_name)
# print("#INFO# ", "get one region cost time is ", (end_get_region - start_get_region).microseconds)
# print("#INFO# ", "save one region cost time is ", (end_save_region - end_get_region).microseconds)
slide.close()
# generate xml files
new_xmls = Xml(os.path.basename(filename), save_path, points_xy, labels,
size, scale)
new_xmls.gen_xml()
#end_one_big_pic = datetime.utcnow()
print("INFO# ", "small pics num is ", i)
# rm temp local file
# rm_tempfile_from_local(local_xml_file, path_temp)
print("INFO# ", "processed ", xml_file)