我们从Python开源项目中，提取了以下5个代码示例，用于说明如何使用cv2.COLOR_RGBA2BGR。
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()
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
