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sbb_binarization
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update binarization tool

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b-vr103 5 years ago
parent 5209dcf46e
commit e4715b88fa
1 changed files with 130 additions and 382 deletions
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sbb_binarize/sbb_binarize.py
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@ -7,18 +7,10 @@ import sys
import os import os
import numpy as np import numpy as np
import warnings import warnings
import xml.etree.ElementTree as et
import pandas as pd
from tqdm import tqdm
import csv
import cv2 import cv2
import seaborn as sns
import matplotlib.pyplot as plt
from keras.models import load_model from keras.models import load_model
import tensorflow as tf import tensorflow as tf
from keras import backend as K
from skimage.filters import threshold_otsu
import keras.losses
with warnings.catch_warnings(): with warnings.catch_warnings():
@ -30,147 +22,23 @@ Tool to load model and binarize a given image.
""" """
class sbb_binarize: class sbb_binarize:
def __init__(self,image,model, patches='false',save=None, ground_truth=None,weights_dir=None ): def __init__(self,image,model, patches='false',save=None ):
self.image=image self.image=image
self.patches=patches self.patches=patches
self.save=save self.save=save
self.model_dir=model self.model_dir=model
self.ground_truth=ground_truth
self.weights_dir=weights_dir
def resize_image(self,img_in,input_height,input_width): def resize_image(self,img_in,input_height,input_width):
return cv2.resize( img_in, ( input_width,input_height) ,interpolation=cv2.INTER_NEAREST) return cv2.resize( img_in, ( input_width,input_height) ,interpolation=cv2.INTER_NEAREST)
def color_images(self,seg):
ann_u=range(self.n_classes)
if len(np.shape(seg))==3:
seg=seg[:,:,0]
seg_img=np.zeros((np.shape(seg)[0],np.shape(seg)[1],3)).astype(np.uint8)
colors=sns.color_palette("hls", self.n_classes)
for c in ann_u:
c=int(c)
segl=(seg==c)
seg_img[:,:,0][seg==c]=c
seg_img[:,:,1][seg==c]=c
seg_img[:,:,2][seg==c]=c
return seg_img
def otsu_copy_binary(self,img):
img_r=np.zeros((img.shape[0],img.shape[1],3))
img1=img[:,:,0]
#print(img.min())
#print(img[:,:,0].min())
#blur = cv2.GaussianBlur(img,(5,5))
#ret3,th3 = cv2.threshold(blur,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
retval1, threshold1 = cv2.threshold(img1, 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
img_r[:,:,0]=threshold1
img_r[:,:,1]=threshold1
img_r[:,:,2]=threshold1
#img_r=img_r/float(np.max(img_r))*255
return img_r
def otsu_copy(self,img):
img_r=np.zeros((img.shape[0],img.shape[1],3))
#img1=img[:,:,0]
#print(img.min())
#print(img[:,:,0].min())
#blur = cv2.GaussianBlur(img,(5,5))
#ret3,th3 = cv2.threshold(blur,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
_, threshold1 = cv2.threshold(img[:,:,0], 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
_, threshold2 = cv2.threshold(img[:,:,1], 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
_, threshold3 = cv2.threshold(img[:,:,2], 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
img_r[:,:,0]=threshold1
img_r[:,:,1]=threshold2
img_r[:,:,2]=threshold3
###img_r=img_r/float(np.max(img_r))*255
return img_r
def otsu_org(self,img):
binary_global = img > threshold_otsu(img)
binary_global=binary_global*255
#plt.imshow(binary_sauvola*255,cmap=plt.cm.gray)
#plt.imshow(binary_global)
#plt.show()
#print(np.unique(binary_global))
binary_global=np.repeat(binary_global[:, :, np.newaxis], 3, axis=2)
plt.imshow(binary_global)
plt.show()
print(binary_global.shape)
return binary_global
def soft_dice_loss(self,y_true, y_pred, epsilon=1e-6):
axes = tuple(range(1, len(y_pred.shape)-1))
numerator = 2. * K.sum(y_pred * y_true, axes)
denominator = K.sum(K.square(y_pred) + K.square(y_true), axes)
return 1.00 - K.mean(numerator / (denominator + epsilon)) # average over classes and batch
def weighted_categorical_crossentropy(self,weights=None):
def loss(y_true, y_pred):
labels_floats = tf.cast(y_true, tf.float32)
per_pixel_loss = tf.nn.sigmoid_cross_entropy_with_logits(labels=labels_floats,logits=y_pred)
if weights is not None:
weight_mask = tf.maximum(tf.reduce_max(tf.constant(
np.array(weights, dtype=np.float32)[None, None, None])
* labels_floats, axis=-1), 1.0)
per_pixel_loss = per_pixel_loss * weight_mask[:, :, :, None]
return tf.reduce_mean(per_pixel_loss)
return self.loss
def IoU(self,Yi,y_predi):
## mean Intersection over Union
## Mean IoU = TP/(FN + TP + FP)
IoUs = []
Nclass = np.unique(Yi)
for c in Nclass:
TP = np.sum( (Yi == c)&(y_predi==c) )
FP = np.sum( (Yi != c)&(y_predi==c) )
FN = np.sum( (Yi == c)&(y_predi != c))
IoU = TP/float(TP + FP + FN)
if self.n_classes>2:
print("class {:02.0f}: #TP={:6.0f}, #FP={:6.0f}, #FN={:5.0f}, IoU={:4.3f}".format(c,TP,FP,FN,IoU))
IoUs.append(IoU)
if self.n_classes>2:
mIoU = np.mean(IoUs)
print("_________________")
print("Mean IoU: {:4.3f}".format(mIoU))
return mIoU
elif self.n_classes==2:
mIoU = IoUs[1]
print("_________________")
print("IoU: {:4.3f}".format(mIoU))
return mIoU
def start_new_session_and_model(self): def start_new_session_and_model(self):
config = tf.ConfigProto() config = tf.ConfigProto()
config.gpu_options.allow_growth=True config.gpu_options.allow_growth=True
self.session =tf.Session(config=config)# tf.InteractiveSession() self.session =tf.Session(config=config)# tf.InteractiveSession()
#keras.losses.custom_loss = self.weighted_categorical_crossentropy
def load_model(self,model_name): def load_model(self,model_name):
self.model = load_model(self.model_dir+'/'+model_name , compile=False) self.model = load_model(self.model_dir+'/'+model_name , compile=False)
#if self.weights_dir!=None:
# print('man burdayammmmaaa')
# self.model.load_weights(self.weights_dir)
self.img_height=self.model.layers[len(self.model.layers)-1].output_shape[1] 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.img_width=self.model.layers[len(self.model.layers)-1].output_shape[2]
@ -183,287 +51,170 @@ class sbb_binarize:
del self.model del self.model
del self.session del self.session
def predict(self,model_name): def predict(self,model_name):
#self.start_new_session_and_model(model_name)
self.load_model(model_name) self.load_model(model_name)
if self.patches=='true' or self.patches=='True':
print(self.patches,'gadaaiikk')
#def textline_contours(img,input_width,input_height,n_classes,model):
img=cv2.imread(self.image) 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)
if img.shape[0]<self.img_height: width_mid = img_width_model - 2 * margin
img=cv2.resize( img, ( img.shape[1],self.img_width) ,interpolation=cv2.INTER_NEAREST) height_mid = img_height_model - 2 * margin
if img.shape[1]<self.img_width:
img=cv2.resize( img, ( self.img_height,img.shape[0]) ,interpolation=cv2.INTER_NEAREST)
margin=True
if margin:
kernel = np.ones((5,5),np.uint8)
width=self.img_width
height=self.img_height
#offset=int(.1*width)
offset=int(0.1*width)
width_mid=width-2*offset
height_mid=height-2*offset
#img= cv2.medianBlur(img, 5)
#img = cv2.GaussianBlur(img,(5,5),0)
#img= cv2.medianBlur(img, 5)
#img= cv2.medianBlur(img, 5)
#img= cv2.medianBlur(img, 5)
#img= cv2.medianBlur(img, 5)
#img=self.otsu_copy_binary(img)
#img=self.otsu_org(img)
img=img.astype(np.uint8)
#for i in range(10):
# img= cv2.medianBlur(img, 3)
img=img/255.0
img = img / float(255.0)
img_h=img.shape[0] img_h = img.shape[0]
img_w=img.shape[1] img_w = img.shape[1]
prediction_true=np.zeros((img_h,img_w,3)) prediction_true = np.zeros((img_h, img_w, 3))
mask_true=np.zeros((img_h,img_w)) mask_true = np.zeros((img_h, img_w))
nxf=img_w/float(width_mid) nxf = img_w / float(width_mid)
nyf=img_h/float(height_mid) nyf = img_h / float(height_mid)
if nxf>int(nxf): if nxf > int(nxf):
nxf=int(nxf)+1 nxf = int(nxf) + 1
else: else:
nxf=int(nxf) nxf = int(nxf)
if nyf>int(nyf): if nyf > int(nyf):
nyf=int(nyf)+1 nyf = int(nyf) + 1
else: else:
nyf=int(nyf) nyf = int(nyf)
for i in range(nxf): for i in range(nxf):
for j in range(nyf): for j in range(nyf):
if i==0: if i == 0:
index_x_d=i*width_mid index_x_d = i * width_mid
index_x_u=index_x_d+width#(i+1)*width index_x_u = index_x_d + img_width_model
elif i>0: elif i > 0:
index_x_d=i*width_mid index_x_d = i * width_mid
index_x_u=index_x_d+width#(i+1)*width index_x_u = index_x_d + img_width_model
if j==0: if j == 0:
index_y_d=j*height_mid index_y_d = j * height_mid
index_y_u=index_y_d+height#(j+1)*height index_y_u = index_y_d + img_height_model
elif j>0: elif j > 0:
index_y_d=j*height_mid index_y_d = j * height_mid
index_y_u=index_y_d+height#(j+1)*height index_y_u = index_y_d + img_height_model
if index_x_u>img_w: if index_x_u > img_w:
index_x_u=img_w index_x_u = img_w
index_x_d=img_w-width index_x_d = img_w - img_width_model
if index_y_u>img_h: if index_y_u > img_h:
index_y_u=img_h index_y_u = img_h
index_y_d=img_h-height index_y_d = img_h - img_height_model
img_patch=img[index_y_d:index_y_u,index_x_d:index_x_u,:]
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]))
label_p_pred=self.model.predict( seg = np.argmax(label_p_pred, axis=3)[0]
img_patch.reshape(1,img_patch.shape[0],img_patch.shape[1],img_patch.shape[2]))
#print(np.unique(label_p_pred)) seg_color = np.repeat(seg[:, :, np.newaxis], 3, axis=2)
th3=label_p_pred[0,:,:,1]
th3=th3*255
th3=th3.astype(np.uint8)
#print(np.unique(th3))
ret3,th3 = cv2.threshold(th3,30,250,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
seg=np.argmax(label_p_pred,axis=3)[0] 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]
seg_color=self.color_images(seg) 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
seg_color=seg_color[offset:seg_color.shape[0]-offset,offset:seg_color.shape[1]-offset,:] elif i==0 and j==nyf-1:
seg=seg[offset:seg.shape[0]-offset,offset:seg.shape[1]-offset] seg_color = seg_color[margin:seg_color.shape[0] - 0, 0:seg_color.shape[1] - margin, :]
th3=th3[offset:th3.shape[0]-offset,offset:th3.shape[1]-offset] seg = seg[margin:seg.shape[0] - 0, 0:seg.shape[1] - margin]
mask_true[index_y_d+offset:index_y_u-offset,index_x_d+offset:index_x_u-offset]=seg mask_true[index_y_d + margin:index_y_u - 0, index_x_d + 0:index_x_u - margin] = seg
prediction_true[index_y_d+offset:index_y_u-offset,index_x_d+offset:index_x_u-offset,:]=seg_color prediction_true[index_y_d + margin:index_y_u - 0, index_x_d + 0:index_x_u - margin,
:] = seg_color
y_predi = mask_true 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]
#print(np.unique(mask_true)) mask_true[index_y_d + 0:index_y_u - margin, index_x_d + margin:index_x_u - 0] = seg
#find_contours(mask_true) prediction_true[index_y_d + 0:index_y_u - margin, index_x_d + margin:index_x_u - 0,
:] = seg_color
#y_testi = label[:,:,0]#np.argmax(label.reshape(1,label.shape[0],label.shape[1],label.shape[2]), axis=3) 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]
#y_predi=cv2.erode(y_predi,kernel,iterations=3) mask_true[index_y_d + margin:index_y_u - margin, index_x_d + margin:index_x_u - 0] = seg
y_predi=cv2.resize( y_predi, ( img.shape[1],img.shape[0]) ,interpolation=cv2.INTER_NEAREST) prediction_true[index_y_d + margin:index_y_u - margin, index_x_d + margin:index_x_u - 0,
return y_predi :] = 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]
if not 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,
kernel = np.ones((5,5),np.uint8) :] = seg_color
width=self.img_width elif i!=0 and i!=nxf-1 and j==nyf-1:
height=self.img_height 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
#img = cv2.medianBlur(img,5)
img=self.otsu_copy_binary(img)
#img=cv2.bilateralFilter(img,9,75,75)
img = cv2.GaussianBlur(img,(5,5),0)
img=img/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)
nyf=img_h/float(height)
if nxf>int(nxf):
nxf=int(nxf)+1
else: else:
nxf=int(nxf) 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]
if nyf>int(nyf):
nyf=int(nyf)+1
else:
nyf=int(nyf)
print(nxf,nyf)
for i in range(nxf):
for j in range(nyf):
index_x_d=i*width
index_x_u=(i+1)*width
index_y_d=j*height
index_y_u=(j+1)*height
if index_x_u>img_w:
index_x_u=img_w
index_x_d=img_w-width
if index_y_u>img_h:
index_y_u=img_h
index_y_d=img_h-height
img_patch=img[index_y_d:index_y_u,index_x_d:index_x_u,:] 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]))
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)
prediction_true = self.resize_image(seg_color, img_h_page, img_w_page)
prediction_true = prediction_true.astype(np.uint8)
seg=np.argmax(label_p_pred,axis=3)[0] return prediction_true[:,:,0]
seg_color=self.color_images(seg)
###seg_color=color_images_diva(seg,n_classes)
mask_true[index_y_d:index_y_u,index_x_d:index_x_u]=seg
prediction_true[index_y_d:index_y_u,index_x_d:index_x_u,:]=seg_color
#mask_true=color_images(mask_true,n_classes)
y_predi = mask_true
#print(np.unique(mask_true))
#find_contours(mask_true)
#y_testi = label[:,:,0]#np.argmax(label.reshape(1,label.shape[0],label.shape[1],label.shape[2]), axis=3)
#y_predi=cv2.erode(y_predi,kernel,iterations=3)
y_predi=cv2.resize( y_predi, ( img.shape[1],img.shape[0]) ,interpolation=cv2.INTER_NEAREST)
#self.end_session()
return y_predi
#def extract_page(img,input_width,input_height,n_classes,model):
if self.patches=='false' or self.patches=='False':
img=cv2.imread(self.image,0)
img_org_height=img.shape[0]
img_org_width=img.shape[1]
#kernel = np.ones((5,5),np.uint8)
width=self.img_width
height=self.img_height
#for _ in range(1):
#img = cv2.medianBlur(img,5)
img=self.otsu_org(img)
#img=img.astype(np.uint8)
img=img.astype(np.uint8)
#img = cv2.medianBlur(img,5)
#img=img.astype(np.uint8)
#img = cv2.GaussianBlur(img,(5,5),0)
#img=self.otsu_copy_binary(img)
img=img.astype(np.uint8)
img=img/255.0
img=self.resize_image(img,self.img_height,self.img_width)
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]
print(np.shape(seg),np.unique(seg))
plt.imshow(seg*255)
plt.show()
seg_color=self.color_images(seg)
print(np.unique(seg_color))
#imgs = seg_color#/np.max(seg_color)*255#np.repeat(seg_color[:, :, np.newaxis], 3, axis=2)
y_predi=cv2.resize( seg_color, ( img_org_width,img_org_height) ,interpolation=cv2.INTER_NEAREST)
return y_predi
def run(self): def run(self):
self.start_new_session_and_model() self.start_new_session_and_model()
models_n=os.listdir(self.model_dir) models_n=os.listdir(self.model_dir)
img_last=0 img_last=0
for model_in in models_n: for model_in in models_n:
res=self.predict(model_in) res=self.predict(model_in)
if self.ground_truth!=None:
gt_img=cv2.imread(self.ground_truth)
print(np.shape(gt_img),np.shape(res))
#self.IoU(gt_img[:,:,0],res)
#print(np.unique(res))
img_fin=np.zeros((res.shape[0],res.shape[1],3) ) img_fin=np.zeros((res.shape[0],res.shape[1],3) )
res[:,:][res[:,:]==0]=2 res[:,:][res[:,:]==0]=2
@ -479,24 +230,21 @@ class sbb_binarize:
kernel = np.ones((5,5),np.uint8) kernel = np.ones((5,5),np.uint8)
img_last[:,:][img_last[:,:]>0]=255 img_last[:,:][img_last[:,:]>0]=255
img_last=(img_last[:,:]==0)*255 img_last=(img_last[:,:]==0)*255
#img_fin= cv2.medianBlur(img_fin, 5)
if self.save is not None: if self.save is not None:
cv2.imwrite('./'+self.save,img_last) cv2.imwrite(self.save,img_last)
def main(): def main():
parser=argparse.ArgumentParser() parser=argparse.ArgumentParser()
parser.add_argument('-i','--image', dest='inp1', default=None, help='directory of alto files which have to be transformed.') parser.add_argument('-i','--image', dest='inp1', default=None, help='image.')
parser.add_argument('-p','--patches', dest='inp3', default=False, help='use patches of image for prediction or should image resize be applied to be fit for model. this parameter should be true or false') 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 agive name in the same directory you are. The name and format should be given (0045.tif).') 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='model directory and name should be provided here.') parser.add_argument('-m','--model', dest='inp2', default=None, help='models directory.')
parser.add_argument('-gt','--groundtruth', dest='inp5', default=None, help='ground truth directory if you want to see the iou of prediction.')
parser.add_argument('-mw','--model_weights', dest='inp6', default=None, help='previous model weights which are saved.')
options=parser.parse_args() options=parser.parse_args()
possibles=globals() possibles=globals()
possibles.update(locals()) possibles.update(locals())
x=sbb_binarize(options.inp1,options.inp2,options.inp3,options.inp4,options.inp5,options.inp6) x=sbb_binarize(options.inp1,options.inp2,options.inp3,options.inp4)
x.run() x.run()
if __name__=="__main__": if __name__=="__main__":

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