#! /usr/bin/env python3 __version__= '1.0' import argparse import sys import os import numpy as np import warnings import cv2 from keras.models import load_model import tensorflow as tf with warnings.catch_warnings(): warnings.simplefilter("ignore") __doc__=\ """ Tool to load model and binarize a given image. """ class sbb_binarize: def __init__(self,image,model, patches='false',save=None ): self.image=image self.patches=patches self.save=save self.model_dir=model def resize_image(self,img_in,input_height,input_width): return cv2.resize( img_in, ( input_width,input_height) ,interpolation=cv2.INTER_NEAREST) def start_new_session_and_model(self): config = tf.ConfigProto() config.gpu_options.allow_growth=True self.session =tf.Session(config=config)# tf.InteractiveSession() def load_model(self,model_name): self.model = load_model(self.model_dir+'/'+model_name , compile=False) self.img_height=self.model.layers[len(self.model.layers)-1].output_shape[1] self.img_width=self.model.layers[len(self.model.layers)-1].output_shape[2] self.n_classes=self.model.layers[len(self.model.layers)-1].output_shape[3] def end_session(self): self.session.close() del self.model del self.session def predict(self,model_name): self.load_model(model_name) img=cv2.imread(self.image) img_width_model=self.img_width img_height_model=self.img_height if self.patches=='true' or self.patches=='True': margin = int(0.1 * img_width_model) width_mid = img_width_model - 2 * margin height_mid = img_height_model - 2 * margin img = img / float(255.0) img_h = img.shape[0] img_w = img.shape[1] prediction_true = np.zeros((img_h, img_w, 3)) mask_true = np.zeros((img_h, img_w)) nxf = img_w / float(width_mid) nyf = img_h / float(height_mid) if nxf > int(nxf): nxf = int(nxf) + 1 else: nxf = int(nxf) if nyf > int(nyf): nyf = int(nyf) + 1 else: nyf = int(nyf) for i in range(nxf): for j in range(nyf): if i == 0: index_x_d = i * width_mid index_x_u = index_x_d + img_width_model elif i > 0: index_x_d = i * width_mid index_x_u = index_x_d + img_width_model if j == 0: index_y_d = j * height_mid index_y_u = index_y_d + img_height_model elif j > 0: index_y_d = j * height_mid index_y_u = index_y_d + img_height_model if index_x_u > img_w: index_x_u = img_w index_x_d = img_w - img_width_model if index_y_u > img_h: index_y_u = img_h index_y_d = img_h - img_height_model img_patch = img[index_y_d:index_y_u, index_x_d:index_x_u, :] label_p_pred = self.model.predict( img_patch.reshape(1, img_patch.shape[0], img_patch.shape[1], img_patch.shape[2])) seg = np.argmax(label_p_pred, axis=3)[0] seg_color = np.repeat(seg[:, :, np.newaxis], 3, axis=2) if i==0 and j==0: seg_color = seg_color[0:seg_color.shape[0] - margin, 0:seg_color.shape[1] - margin, :] seg = seg[0:seg.shape[0] - margin, 0:seg.shape[1] - margin] mask_true[index_y_d + 0:index_y_u - margin, index_x_d + 0:index_x_u - margin] = seg prediction_true[index_y_d + 0:index_y_u - margin, index_x_d + 0:index_x_u - margin, :] = seg_color elif i==nxf-1 and j==nyf-1: seg_color = seg_color[margin:seg_color.shape[0] - 0, margin:seg_color.shape[1] - 0, :] seg = seg[margin:seg.shape[0] - 0, margin:seg.shape[1] - 0] mask_true[index_y_d + margin:index_y_u - 0, index_x_d + margin:index_x_u - 0] = seg prediction_true[index_y_d + margin:index_y_u - 0, index_x_d + margin:index_x_u - 0, :] = seg_color elif i==0 and j==nyf-1: seg_color = seg_color[margin:seg_color.shape[0] - 0, 0:seg_color.shape[1] - margin, :] seg = seg[margin:seg.shape[0] - 0, 0:seg.shape[1] - margin] mask_true[index_y_d + margin:index_y_u - 0, index_x_d + 0:index_x_u - margin] = seg prediction_true[index_y_d + margin:index_y_u - 0, index_x_d + 0:index_x_u - margin, :] = seg_color elif i==nxf-1 and j==0: seg_color = seg_color[0:seg_color.shape[0] - margin, margin:seg_color.shape[1] - 0, :] seg = seg[0:seg.shape[0] - margin, margin:seg.shape[1] - 0] mask_true[index_y_d + 0:index_y_u - margin, index_x_d + margin:index_x_u - 0] = seg prediction_true[index_y_d + 0:index_y_u - margin, index_x_d + margin:index_x_u - 0, :] = seg_color elif i==0 and j!=0 and j!=nyf-1: seg_color = seg_color[margin:seg_color.shape[0] - margin, 0:seg_color.shape[1] - margin, :] seg = seg[margin:seg.shape[0] - margin, 0:seg.shape[1] - margin] mask_true[index_y_d + margin:index_y_u - margin, index_x_d + 0:index_x_u - margin] = seg prediction_true[index_y_d + margin:index_y_u - margin, index_x_d + 0:index_x_u - margin, :] = seg_color elif i==nxf-1 and j!=0 and j!=nyf-1: seg_color = seg_color[margin:seg_color.shape[0] - margin, margin:seg_color.shape[1] - 0, :] seg = seg[margin:seg.shape[0] - margin, margin:seg.shape[1] - 0] mask_true[index_y_d + margin:index_y_u - margin, index_x_d + margin:index_x_u - 0] = seg prediction_true[index_y_d + margin:index_y_u - margin, index_x_d + margin:index_x_u - 0, :] = seg_color elif i!=0 and i!=nxf-1 and j==0: seg_color = seg_color[0:seg_color.shape[0] - margin, margin:seg_color.shape[1] - margin, :] seg = seg[0:seg.shape[0] - margin, margin:seg.shape[1] - margin] mask_true[index_y_d + 0:index_y_u - margin, index_x_d + margin:index_x_u - margin] = seg prediction_true[index_y_d + 0:index_y_u - margin, index_x_d + margin:index_x_u - margin, :] = seg_color elif i!=0 and i!=nxf-1 and j==nyf-1: seg_color = seg_color[margin:seg_color.shape[0] - 0, margin:seg_color.shape[1] - margin, :] seg = seg[margin:seg.shape[0] - 0, margin:seg.shape[1] - margin] mask_true[index_y_d + margin:index_y_u - 0, index_x_d + margin:index_x_u - margin] = seg prediction_true[index_y_d + margin:index_y_u - 0, index_x_d + margin:index_x_u - margin, :] = seg_color else: seg_color = seg_color[margin:seg_color.shape[0] - margin, margin:seg_color.shape[1] - margin, :] seg = seg[margin:seg.shape[0] - margin, margin:seg.shape[1] - margin] mask_true[index_y_d + margin:index_y_u - margin, index_x_d + margin:index_x_u - margin] = seg prediction_true[index_y_d + margin:index_y_u - margin, index_x_d + margin:index_x_u - margin, :] = seg_color prediction_true = prediction_true.astype(np.uint8) else: img_h_page=img.shape[0] img_w_page=img.shape[1] img = img /float( 255.0) img = self.resize_image(img, img_height_model, img_width_model) label_p_pred = self.model.predict( img.reshape(1, img.shape[0], img.shape[1], img.shape[2])) seg = np.argmax(label_p_pred, axis=3)[0] seg_color =np.repeat(seg[:, :, np.newaxis], 3, axis=2) prediction_true = self.resize_image(seg_color, img_h_page, img_w_page) prediction_true = prediction_true.astype(np.uint8) return prediction_true[:,:,0] def run(self): self.start_new_session_and_model() models_n=os.listdir(self.model_dir) img_last=0 for model_in in models_n: res=self.predict(model_in) img_fin=np.zeros((res.shape[0],res.shape[1],3) ) res[:,:][res[:,:]==0]=2 res=res-1 res=res*255 img_fin[:,:,0]=res img_fin[:,:,1]=res img_fin[:,:,2]=res img_fin=img_fin.astype(np.uint8) img_fin=(res[:,:]==0)*255 img_last=img_last+img_fin kernel = np.ones((5,5),np.uint8) img_last[:,:][img_last[:,:]>0]=255 img_last=(img_last[:,:]==0)*255 if self.save is not None: cv2.imwrite(self.save,img_last) def main(): parser=argparse.ArgumentParser() parser.add_argument('-i','--image', dest='inp1', default=None, help='image.') parser.add_argument('-p','--patches', dest='inp3', default=False, help='by setting this parameter to true you let the model to see the image in patches.') parser.add_argument('-s','--save', dest='inp4', default=False, help='save prediction with a given name here. The name and format should be given (outputname.tif).') parser.add_argument('-m','--model', dest='inp2', default=None, help='models directory.') options=parser.parse_args() possibles=globals() possibles.update(locals()) x=sbb_binarize(options.inp1,options.inp2,options.inp3,options.inp4) x.run() if __name__=="__main__": main()