def save_slide_cutting(file_path, save_location, level):
slide = OpenSlide(file_path)
print('==> saving slide_lv_' + str(level) + ' at ' + save_location)
x_lv_, y_lv_ = 0, 0
w_lv_, h_lv_ = slide.level_dimensions[level]
wsi_pil_lv_ = slide.read_region((0,0), level,\
(w_lv_, h_lv_))
wsi_ary_lv_ = np.array(wsi_pil_lv_)
wsi_bgr_lv_ = cv2.cvtColor(wsi_ary_lv_, cv2.COLOR_RGBA2BGR)
margin_top = int(round(h_lv_ / 12.))
margin_bottom = int(round(h_lv_ / 32.))
wsi_bgr_lv_[0:margin_top, :] = 255
wsi_bgr_lv_[h_lv_ - margin_bottom:h_lv_, :] = 255
cv2.imwrite(save_location, wsi_bgr_lv_)
# plt.subplot(1,1,1), plt.imshow(wsi_bgr_lv_)
# plt.xticks([]), plt.yticks([])
# plt.show()
python类COLOR_RGBA2BGR的实例源码
def save_slide_as_jpg_with_level(file_path, save_location, level):
slide_tif = OpenSlide(file_path)
print(('==> saving slide_lv_%s at ' + save_location) % level)
wsi_pil_lv_ = slide_tif.read_region((0, 0), level,\
slide_tif.level_dimensions[level])
wsi_ary_lv_ = np.array(wsi_pil_lv_)
wsi_bgr_lv_ = cv2.cvtColor(wsi_ary_lv_, cv2.COLOR_RGBA2BGR)
cv2.imwrite(save_location, wsi_bgr_lv_)
def _exportVideoThread(self):
ww = self.display.widget
n = None
if self.pAnnotate.value():
n = self.display.layerNames()
videoWrite(self.pPath.value(), ww.image,
levels=ww.item.levels,
shape=(self.pHeight.value(), self.pWidth.value()),
frames=self.pFrames.value(),
annotate_names=n,
lut=ww.item.lut, updateFn=self._thread.sigUpdate)
#
# fourcc = cv2.VideoWriter_fourcc(*'XVID')
# ww = self.display.widget
# im = ww.image
# if self.pResize.value():
# w, h = (self.pWidth.value(), self.pHeight.value())
# im = [cv2.resize(i, (w, h)) for i in im]
# else:
# h, w = im.shape[1:3]
# fr = self.pFrames.value()
# pa = self.pPath.value()
# assert pa[-3:] in ('avi',
# 'png'), 'video export only supports *.avi or *.png'
# isVideo = pa[-3:] == 'avi'
# if isVideo:
# cap = cv2.VideoCapture(0)
# # im.ndim==4)
# out = cv2.VideoWriter(pa, fourcc, fr, (w, h), isColor=1)
#
# times = np.linspace(0, len(im), len(im) * fr)
# interpolator = LinearInterpolateImageStack(im)
#
# lut = ww.item.lut
# if lut is not None:
# lut = lut(im[0])
#
# for n, time in enumerate(times):
# # update progress:
# self._thread.sigUpdate.emit(100 * n / len(times))
# image = interpolator(time)
#
# argb = makeRGBA(image, lut=lut,
# levels=ww.item.levels)[0]
# cimg = cv2.cvtColor(argb, cv2.COLOR_RGBA2BGR)
#
# if isVideo:
# out.write(cimg)
# else:
# cv2.imwrite('%s_%i_%.3f.png' % (pa[:-4], n, time), cimg)
#
# if isVideo:
# cap.release()
# out.release()
def save_patch(\
file_path_tif,
save_location_path_patch,
patch_level,
size_patch):
print('=> Making patch ..')
# Read file name list of slide directory
file_name_list_tif = get_list_file_name(file_path_tif)
for index in range(len(file_name_list_tif)):
file_name_tif = file_name_list_tif[index]
file_name_slide = file_name_tif.split('.')[0]
file_name_csv = file_name_slide + '.csv'
cur_file_path_tif =\
os.path.join(file_path_tif, file_name_tif)
cur_file_path_csv =\
os.path.join(save_location_path_patch, file_name_slide)
cur_file_path_csv =\
os.path.join(cur_file_path_csv, file_name_csv)
# Load slide image
slide = OpenSlide(cur_file_path_tif)
# Read patch position csv file
csv_file = open(cur_file_path_csv, 'rb')
csv_reader = csv.DictReader(csv_file)
csv_data = list(csv_reader)
# Make patch and Save
for i, row in enumerate(csv_data):
x = int(row['X'])
y = int(row['Y'])
patch = slide.read_region((x, y),\
patch_level,\
(size_patch, size_patch))
patch = np.array(patch)
patch = cv2.cvtColor(patch, cv2.COLOR_RGBA2BGR)
file_name_patch_jpg = file_name_slide + '_patch_' + str(i) + '.jpg'
cur_save_path_patch_jpg =\
os.path.join(save_location_path_patch,\
file_name_slide)
cur_save_path_patch_jpg =\
os.path.join(cur_save_path_patch_jpg ,\
file_name_patch_jpg)
cv2.imwrite(cur_save_path_patch_jpg, patch)
csv_file.close()
print('=> Next..')
def patch_generation(tif_dir,mask_dir,save_fdir,save_pdir,save_cdir,slide_level,patch_size,patch_num,tumor_win=False):
"""
save patch image and extraction point with csv, jpg image on the directory
tif_dir : the tif directory
mask_dir : the mask directory
save_fdir : patch saved directory
save_pdir : point jpg directory
save_cdir : Y,X csv directory
slide : slide_level that mask image was applied with
patch_size : patch size square
patch_num : the number of patches in a whole slide
tumor_win : tumor window patch sampling true
tif file and mask file sholud be one to one mached and same ordered
"""
list_tif_name = filelist_in_directory(tif_dir)
list_mask_name = filelist_in_directory(mask_dir)
for slide_idx in range(len(list_tif_name)):
pwd_tif = join(tif_dir,list_tif_name[slide_idx])
pwd_msk = join(mask_dir,list_mask_name[slide_idx])
filename = splitext(list_tif_name[slide_idx])[0]
# open slide, csv, BGR_image, mask
slide = OpenSlide(pwd_tif)
f = open(save_cdir+filename+".csv",'wt')
c_writer = csv.writer(f)
c_writer.writerow(('Y','X'))
rgba_pil = slide.read_region((0,0),slide_level,slide.level_dimensions[slide_level])
bgr_im = cv2.cvtColor(np.array(rgba_pil),cv2.COLOR_RGBA2BGR)
mask = cv2.imread(pwd_msk,cv2.IMREAD_GRAYSCALE)
#if mask tunes 255 change to 1
if np.max(mask) == 255:
mask = mask == 255
mask = mask.astype(int)
# sampling patches
if tumor_win:
patch_list,patch_point = tumor_patch_sampling_using_centerwin(slide,slide_level,mask,patch_size,patch_num)
else:
patch_list,patch_point = patch_sampling_using_integral(slide,slide_level,mask,patch_size,patch_num)
p_l_size = patch_size/ slide.level_downsamples[slide_level]
p_l_size = int(p_l_size)
#image wirte and save patches
for f_th in range(len(patch_list)):
cv2.imwrite(save_fdir+filename+"_patch_"+str(f_th)+"_"+str(patch_point[f_th][1])+"_"+str(patch_point[f_th][0])+"_"+str(patch_size)+".jpg",patch_list[f_th])
c_writer.writerow((patch_point[f_th][1],patch_point[f_th][0]))
cv2.rectangle(bgr_im,(patch_point[f_th][1],patch_point[f_th][0]),(patch_point[f_th][1]+p_l_size,patch_point[f_th][0]+p_l_size),(255,0,0),1)
cv2.imwrite(save_pdir+filename+"_selection_point.jpg",bgr_im)
print "complete patch extraction about "+ list_tif_name[slide_idx]
f.close()
return 0
