JSR 17 Task 002 Aiforhealthandhealthcare12122017

19/10/2018 U-Net lung segmentation (Montgomery + Shenzhen) | Kaggle
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Eduardo Mineo 
2
U-Net lung segmentation (Montgomery + Shenzhen)
voters
last run 6 hours ago · IPython Notebook HTML · 126 views

using data from multiple data sources ·  Public
Notebook Code Data (3) Output Comments (1) Log Versions (11) Forks Fork Notebook
Tags multiple data sources
Notebook
https://www.kaggle.com/eduardomineo/u-net-lung-segmentation-montgomery-shenzhen 1/32
RSNA Pneumonia Detection Challenge
Sociedade Beneficente de Senhoras - Hospital Sírio-

Libanês - Brazil
Contents
1. Overview
2. Data preparation
3. Segmentation training
4. Results
1. Overview
This notebook follows the work of Kevin Mader (https://www.kaggle.com/kmader/training-u-net-on-
tb-images-to-segment-lungs/notebook) for lung segmentation. Our motivation is to automatically
identify lung opacities in chest x-rays for the RSNA Pneumonia Detection Challenge
(https://www.kaggle.com/c/rsna-pneumonia-detection-challenge/leaderboard).
Medical Image Segmentation is the process of automatic detection of boundaries within images. In
this exercise, we train a convolutional neural network with U-Net (https://arxiv.org/abs/1505.04597)
architecture, which training strategy relies on the strong use of data augmentation to improve the
efficiency of available annotated samples.
The training is done with two chest x-rays datasets: Montgomery County and Shenzhen Hospital
(https://ceb.nlm.nih.gov/repositories/tuberculosis-chest-x-ray-image-data-sets/). The Montgomery
County dataset includes manually segmented lung masks, whereas Shenzhen Hospital dataset was
manually segmented by Stirenko et al (https://arxiv.org/abs/1803.01199). The lung segmentation
masks were dilated to load lung boundary information within the training net and the images were
resized to 512x512 pixels.
2. Data preparation
Prepare the input segmentation directory structure.
In [1]:
!mkdir ../input/segmentation
!mkdir ../input/segmentation/test
!mkdir ../input/segmentation/train
!mkdir ../input/segmentation/train/augmentation
!mkdir ../input/segmentation/train/image
!mkdir ../input/segmentation/train/mask
!mkdir ../input/segmentation/train/dilate
Import required Python libraries
In [2]:
import os
import numpy as np
import cv2
import matplotlib.pyplot as plt
from keras.models import *

from keras.layers import *
from keras.optimizers import *
from keras import backend as keras
from keras.preprocessing.image import ImageDataGenerator
from keras.callbacks import ModelCheckpoint, LearningRateScheduler
from glob import glob

from tqdm import tqdm
Using TensorFlow backend.
Define appropriate constants for directory paths and training parameters
In [3]:
INPUT_DIR = os.path.join("..", "input")
SEGMENTATION_DIR = os.path.join(INPUT_DIR, "segmentation")

SEGMENTATION_TEST_DIR = os.path.join(SEGMENTATION_DIR, "test")
SEGMENTATION_TRAIN_DIR = os.path.join(SEGMENTATION_DIR, "train")
SEGMENTATION_AUG_DIR = os.path.join(SEGMENTATION_TRAIN_DIR, "augmentat
ion")
SEGMENTATION_IMAGE_DIR = os.path.join(SEGMENTATION_TRAIN_DIR, "image")
SEGMENTATION_MASK_DIR = os.path.join(SEGMENTATION_TRAIN_DIR, "mask")
SEGMENTATION_DILATE_DIR = os.path.join(SEGMENTATION_TRAIN_DIR, "dilat
e")
SEGMENTATION_SOURCE_DIR = os.path.join(INPUT_DIR, \
"pulmonary-chest-xray-abnormali
ties")
ties )
SHENZHEN_TRAIN_DIR = os.path.join(SEGMENTATION_SOURCE_DIR, "ChinaSet_A

llFiles", \
"ChinaSet_AllFiles")
SHENZHEN_IMAGE_DIR = os.path.join(SHENZHEN_TRAIN_DIR, "CXR_png")
SHENZHEN_MASK_DIR = os.path.join(INPUT_DIR, "shcxr-lung-mask", "mask",
"mask")
MONTGOMERY_TRAIN_DIR = os.path.join(SEGMENTATION_SOURCE_DIR, \
"Montgomery", "MontgomerySet")
MONTGOMERY_IMAGE_DIR = os.path.join(MONTGOMERY_TRAIN_DIR, "CXR_png")
MONTGOMERY_LEFT_MASK_DIR = os.path.join(MONTGOMERY_TRAIN_DIR, \
"ManualMask", "leftMask")
MONTGOMERY_RIGHT_MASK_DIR = os.path.join(MONTGOMERY_TRAIN_DIR, \
"ManualMask", "rightMask")
DILATE_KERNEL = np.ones((15, 15), np.uint8)
#Prod
STEPS_PER_EPOC=512
EPOCHS=48
#Desv
#STEPS_PER_EPOC=64
#EPOCHS=16
1. Combine left and right lung segmentation masks of Montgomery chest x-rays
2. Resize images to 512x512 pixels
3. Dilate masks to gain more information on the edge of lungs
4. Split images into training and test datasets
5. Write images to /segmentation directory
In [4]:
montgomery_left_mask_dir = glob(os.path.join(MONTGOMERY_LEFT_MASK_DIR,
'*.png'))
montgomery_test = montgomery_left_mask_dir[0:50]
montgomery_train= montgomery_left_mask_dir[50:]
for left_image_file in tqdm(montgomery_left_mask_dir):

base_file = os.path.basename(left_image_file)
image_file = os.path.join(MONTGOMERY_IMAGE_DIR, base_file)
right_image_file = os.path.join(MONTGOMERY_RIGHT_MASK_DIR, base_fi
le)
image = cv2.imread(image_file)
left_mask = cv2.imread(left_image_file, cv2.IMREAD_GRAYSCALE)
right_mask = cv2.imread(right_image_file, cv2.IMREAD_GRAYSCALE)
image = cv2.resize(image, (512, 512))

left_mask = cv2.resize(left_mask, (512, 512))
right_mask = cv2.resize(right_mask, (512, 512))
mask = np.maximum(left_mask, right_mask)

mask_dilate = cv2.dilate(mask, DILATE_KERNEL, iterations=1)
if (left_image_file in montgomery_train):
cv2.imwrite(os.path.join(SEGMENTATION_IMAGE_DIR, base_file), \
image)
cv2.imwrite(os.path.join(SEGMENTATION_MASK_DIR, base_file), \
mask)
cv2.imwrite(os.path.join(SEGMENTATION_DILATE_DIR, base_file),
\
mask_dilate)
else:
filename, fileext = os.path.splitext(base_file)
cv2.imwrite(os.path.join(SEGMENTATION_TEST_DIR, base_file), \
image)
cv2.imwrite(os.path.join(SEGMENTATION_TEST_DIR, \
"%s_mask%s" % (filename, fileext)), m
ask)
"%s_dilate%s" % (filename, fileext)),
mask_dilate)
100%|██████████| 138/138 [01:00<00:00, 2.23it/s]
Define some useful functions to display images with segmentation as overlays
In [5]:
def add_colored_dilate(image, mask_image, dilate_image):
mask_image_gray = cv2.cvtColor(mask_image, cv2.COLOR_BGR2GRAY)
dilate_image_gray = cv2.cvtColor(dilate_image, cv2.COLOR_BGR2GRAY)
mask = cv2.bitwise_and(mask_image, mask_image, mask=mask_image_gra

y)
dilate = cv2.bitwise_and(dilate_image, dilate_image, mask=dilate_i
mage_gray)
mask_coord = np.where(mask!=[0,0,0])
dilate_coord = np.where(dilate!=[0,0,0])
mask[mask coord[0] mask coord[1] :]=[255 0 0]

mask[mask_coord[0],mask_coord[1],:]=[255,0,0]
dilate[dilate_coord[0],dilate_coord[1],:] = [0,0,255]
ret = cv2.addWeighted(image, 0.7, dilate, 0.3, 0)

ret = cv2.addWeighted(ret, 0.7, mask, 0.3, 0)
return ret
def add_colored_mask(image, mask_image):


y)
ret = cv2.addWeighted(image, 0.7, mask, 0.3, 0)
return ret
def diff_mask(ref_image, mask_image):


y)
ret = cv2.addWeighted(ref_image, 0.7, mask, 0.3, 0)

return ret
Show some Montgomery chest x-rays and its lung segmentation masks from training and test dataset
to verify the procedure above. In merged image it is possible to see the difference between the dilated
mask in blue and the original mask in red.
In [6]:
base_file = os.path.basename(montgomery_train[0])
image_file = os.path.join(SEGMENTATION_IMAGE_DIR, base_file)

mask_image_file = os.path.join(SEGMENTATION_MASK_DIR, base_file)
dilate_image_file = os.path.join(SEGMENTATION_DILATE_DIR, base_file)
g ( g )
mask_image = cv2.imread(mask_image_file)
dilate_image = cv2.imread(dilate_image_file)
merged_image = add_colored_dilate(image, mask_image, dilate_image)
fig, axs = plt.subplots(2, 4, figsize=(15, 8))
axs[0, 0].set_title("X-Ray")
axs[0, 0].imshow(image)
axs[0, 1].set_title("Mask")
axs[0, 1].imshow(mask_image)
axs[0, 2].set_title("Dilate")
axs[0, 2].imshow(dilate_image)
axs[0, 3].set_title("Merged")
axs[0, 3].imshow(merged_image)
base_file = os.path.basename(montgomery_test[0])
image_file = os.path.join(SEGMENTATION_TEST_DIR, base_file)
mask_image_file = os.path.join(SEGMENTATION_TEST_DIR, \
"%s_mask%s" % (filename, fileext))
dilate_image_file = os.path.join(SEGMENTATION_TEST_DIR, \
"%s_dilate%s" % (filename, fileext))
Out[6]:
<matplotlib.image.AxesImage at 0x7f7a1f0ed5c0>
1. Resize Shenzhen Hospital chest x-ray images to 512x512 pixels

2. Dilate masks to gain more information on the edge of lungs
3. Split images into training and test datasets
4. Write images to /segmentation directory
In [7]:
shenzhen_mask_dir = glob(os.path.join(SHENZHEN_MASK_DIR, '*.png'))
shenzhen_test = shenzhen_mask_dir[0:50]
shenzhen_train= shenzhen_mask_dir[50:]
for mask_file in tqdm(shenzhen_mask_dir):

base_file = os.path.basename(mask_file).replace("_mask", "")
image_file = os.path.join(SHENZHEN_IMAGE_DIR, base_file)
mask = cv2.imread(mask_file, cv2.IMREAD_GRAYSCALE)
image = cv2.resize(image, (512, 512))

mask = cv2.resize(mask, (512, 512))
mask_dilate = cv2.dilate(mask, DILATE_KERNEL, iterations=1)
if (mask_file in shenzhen_train):
cv2.imwrite(os.path.join(SEGMENTATION_IMAGE_DIR, base_file), \
image)
cv2.imwrite(os.path.join(SEGMENTATION_MASK_DIR, base_file), \
mask)
cv2.imwrite(os.path.join(SEGMENTATION_DILATE_DIR, base_file),
\
mask_dilate)
else:
cv2 imwrite(os path join(SEGMENTATION TEST DIR base file) \

cv2.imwrite(os.path.join(SEGMENTATION_TEST_DIR, base_file), \
image)
"%s_mask%s" % (filename, fileext)), m
ask)
"%s_dilate%s" % (filename, fileext)),
mask_dilate)
100%|██████████| 566/566 [01:49<00:00, 5.18it/s]
Show some Shenzhen Hospital chest x-rays and its lung segmentation masks from training and test
dataset to verify the procedure above. In merged image it is possible to see the difference between the
dilated mask in blue and the original mask in red.
In [8]:
base_file = os.path.basename(shenzhen_train[0].replace("_mask", ""))
image_file = os.path.join(SEGMENTATION_IMAGE_DIR, base_file)

mask_image_file = os.path.join(SEGMENTATION_MASK_DIR, base_file)
dilate_image_file = os.path.join(SEGMENTATION_DILATE_DIR, base_file)
base_file = os.path.basename(shenzhen_test[0].replace("_mask", ""))


dilate_image_file = os.path.join(SEGMENTATION_TEST_DIR, \
"%s_dilate%s" % (filename, fileext))
Out[8]:
<matplotlib.image.AxesImage at 0x7f7a1c5d5908>
Print the count of images and segmentation lung masks available to test and train the model
In [9]:
In [9]:
(len(glob(os.path.join(SEGMENTATION_TEST_DIR, "*.png"))), \
len(glob(os.path.join(SEGMENTATION_IMAGE_DIR, "*.png"))), \
len(glob(os.path.join(SEGMENTATION_MASK_DIR, "*.png"))), \
len(glob(os.path.join(SEGMENTATION_DILATE_DIR, "*.png"))))
Out[9]:
(300, 604, 604, 604)
3. Segmentation training
References: https://github.com/zhixuhao/unet/ (https://github.com/zhixuhao/unet/),
https://github.com/jocicmarko/ultrasound-nerve-segmentation
(https://github.com/jocicmarko/ultrasound-nerve-segmentation)
Data augmentation helper function for training the net
In [10]:
# From: https://github.com/zhixuhao/unet/blob/master/data.py
def train_generator(batch_size, train_path, image_folder, mask_folder,
aug_dict,
image_color_mode="grayscale",
mask_color_mode="grayscale",
image_save_prefix="image",
mask_save_prefix="mask",
save_to_dir=None,
target_size=(256,256),
seed=1):
'''
can generate image and mask at the same time use the same seed for
image_datagen and mask_datagen to ensure the transformation for ima
ge
and mask is the same if you want to visualize the results of genera
tor,
set save_to_dir = "your path"
'''
image_datagen = ImageDataGenerator(**aug_dict)
mask_datagen = ImageDataGenerator(**aug_dict)
image_generator = image_datagen.flow_from_directory(
train_path,
classes = [image_folder],
class_mode = None,
color_mode = image_color_mode,
target_size = target_size,
batch_size = batch_size,
save_to_dir = save_to_dir,
save_prefix = image_save_prefix,
seed = seed)
mask_generator = mask_datagen.flow_from_directory(
train_path,
classes = [mask_folder],
class_mode = None,
color_mode = mask_color_mode,
target_size = target_size,
batch_size = batch_size,
save_to_dir = save_to_dir,
save_prefix = mask_save_prefix,
seed = seed)
train_gen = zip(image_generator, mask_generator)
for (img, mask) in train_gen:

img, mask = adjust_data(img, mask)
yield (img,mask)
def adjust_data(img,mask):
img = img / 255
mask = mask / 255
mask[mask > 0.5] = 1
mask[mask <= 0.5] = 0
return (img, mask)
U-net architecture
In [11]:
# From: https://github.com/jocicmarko/ultrasound-nerve-segmentation/blo
b/master/train.py
def dice_coef(y_true, y_pred):
y_true_f = keras.flatten(y_true)
y_pred_f = keras.flatten(y_pred)
intersection = keras.sum(y_true_f * y_pred_f)
return (2. * intersection + 1) / (keras.sum(y_true_f) + keras.sum(
y_pred_f) + 1)
def dice_coef_loss(y_true, y_pred):

return -dice_coef(y_true, y_pred)
def unet(input_size=(256,256,1)):
inputs = Input(input_size)
conv1 = Conv2D(32, (3, 3), activation='relu', padding='same')(inpu

ts)
conv1 = Conv2D(32, (3, 3), activation='relu', padding='same')(conv
1)
pool1 = MaxPooling2D(pool_size=(2, 2))(conv1)
conv2 = Conv2D(64, (3, 3), activation='relu', padding='same')(pool

1)
2)
conv3 = Conv2D(128, (3, 3), activation='relu', padding='same')(poo

l2)
conv3 = Conv2D(128, (3, 3), activation='relu', padding='same')(con
v3)

l3)
v4)

l4)
v5)
up6 = concatenate([Conv2DTranspose(256, (2, 2), strides=(2, 2), pa

dding='same')(conv5), conv4], axis=3)
conv6 = Conv2D(256, (3, 3), activation='relu', padding='same')(up6
)
v6)
up7 = concatenate([Conv2DTranspose(128, (2, 2), strides=(2, 2), pa

dding='same')(conv6), conv3], axis=3)
conv7 = Conv2D(128, (3, 3), activation='relu', padding='same')(up7
)
v7)
up8 = concatenate([Conv2DTranspose(64, (2, 2), strides=(2, 2), pad

ding='same')(conv7), conv2], axis=3)
conv8 = Conv2D(64, (3, 3), activation='relu', padding='same')(up8)
8)
8)
up9 = concatenate([Conv2DTranspose(32, (2, 2), strides=(2, 2), pad

ding='same')(conv8), conv1], axis=3)
conv9 = Conv2D(32, (3, 3), activation='relu', padding='same')(up9)
9)
conv10 = Conv2D(1, (1, 1), activation='sigmoid')(conv9)
return Model(inputs=[inputs], outputs=[conv10])
Helper functions to load test chest x-ray images
In [12]:
# From: https://github.com/zhixuhao/unet/blob/master/data.py
def test_load_image(test_file, target_size=(256,256)):
img = cv2.imread(test_file, cv2.IMREAD_GRAYSCALE)
img = img / 255
img = cv2.resize(img, target_size)
img = np.reshape(img, img.shape + (1,))
img = np.reshape(img,(1,) + img.shape)
return img
def test_generator(test_files, target_size=(256,256)):

for test_file in test_files:
yield test_load_image(test_file, target_size)
def save_result(save_path, npyfile, test_files):

for i, item in enumerate(npyfile):
result_file = test_files[i]
img = (item[:, :, 0] * 255.).astype(np.uint8)
filename, fileext = os.path.splitext(os.path.basename(result_f

ile))
result_file = os.path.join(save_path, "%s_predict%s" % (filena

me, fileext))
cv2.imwrite(result_file, img)
Select test and validation files
In [13]:
def add suffix(base file suffix):
def add_suffix(base_file, suffix):
return "%s_%s%s" % (filename, suffix, fileext)
test_files = [test_file for test_file in glob(os.path.join(SEGMENTATIO

N_TEST_DIR, "*.png")) \
if ("_mask" not in test_file \
and "_dilate" not in test_file \
and "_predict" not in test_file)]
validation_data = (test_load_image(test_files[0], target_size=(512, 51

2)),
test_load_image(add_suffix(test_files[0], "dilate"
), target_size=(512, 512)))
len(test_files), len(validation_data)
Out[13]:
(100, 2)
Prepare the U-Net model and train the model. It will take a while...
In [14]:
train_generator_args = dict(rotation_range=0.2,
width_shift_range=0.05,
height_shift_range=0.05,
shear_range=0.05,
zoom_range=0.05,
horizontal_flip=True,
fill_mode='nearest')
train_gen = train_generator(2,
SEGMENTATION_TRAIN_DIR,
'image',
'dilate',
train_generator_args,
target_size=(512,512),
save_to_dir=os.path.abspath(SEGMENTATION_A
UG_DIR))
model = unet(input_size=(512,512,1))
model.compile(optimizer=Adam(lr=1e-5), loss=dice_coef_loss, \
metrics=[dice_coef, 'binary_accuracy'])
model.summary()
model_checkpoint = ModelCheckpoint('unet_lung_seg.hdf5',
monitor='loss',
verbose=1,
save_best_only=True)
history = model.fit_generator(train_gen,
steps_per_epoch=STEPS_PER_EPOC,
epochs=EPOCHS,
callbacks=[model_checkpoint],
validation_data = validation_data)
_____________________________________________________________________
_____________________________
Layer (type) Output Shape Param # Conn
ected to
=====================================================================
=============================
input_1 (InputLayer) (None, 512, 512, 1) 0
_____________________________________________________________________
_____________________________
conv2d_1 (Conv2D) (None, 512, 512, 32) 320 inpu
t_1[0][0]
_____________________________________________________________________
_____________________________
conv2d_2 (Conv2D) (None, 512, 512, 32) 9248 conv
2d_1[0][0]
_____________________________________________________________________
_____________________________
max_pooling2d_1 (MaxPooling2D) (None, 256, 256, 32) 0 conv
2d_2[0][0]
_____________________________________________________________________
_____________________________
conv2d_3 (Conv2D) (None, 256, 256, 64) 18496 max_
pooling2d_1[0][0]
_____________________________________________________________________
_____________________________
2d_3[0][0]
_____________________________________________________________________
_____________________________
2d_4[0][0]
_____________________________________________________________________
_____________________________
conv2d_5 (Conv2D) (None, 128, 128, 128 73856 max_
pooling2d_2[0][0]
_____________________________________________________________________
_____________________________
conv2d_6 (Conv2D) (None, 128, 128, 128 147584 conv
( ) ( , , ,
2d_5[0][0]
_____________________________________________________________________
_____________________________
2d_6[0][0]
_____________________________________________________________________
_____________________________
pooling2d_3[0][0]
_____________________________________________________________________
_____________________________
2d_7[0][0]
_____________________________________________________________________
_____________________________
2d_8[0][0]
_____________________________________________________________________
_____________________________
pooling2d_4[0][0]
_____________________________________________________________________
_____________________________
2d_9[0][0]
_____________________________________________________________________
_____________________________
conv2d_transpose_1 (Conv2DTrans (None, 64, 64, 256) 524544 conv
2d_10[0][0]
_____________________________________________________________________
_____________________________
concatenate_1 (Concatenate) (None, 64, 64, 512) 0 conv
2d_transpose_1[0][0]
conv
2d_8[0][0]
_____________________________________________________________________
_____________________________
conv2d_11 (Conv2D) (None, 64, 64, 256) 1179904 conc
atenate_1[0][0]
_____________________________________________________________________
_____________________________
2d_11[0][0]
_____________________________________________________________________
_____________________________
conv2d_transpose_2 (Conv2DTrans (None, 128, 128, 128 131200 conv
2d_12[0][0]
_____________________________________________________________________
_____________________________
concatenate_2 (Concatenate) (None, 128, 128, 256 0 conv
conv
2d_6[0][0]
_____________________________________________________________________
_____________________________
conv2d_13 (Conv2D) (None, 128, 128, 128 295040 conc
atenate_2[0][0]
_____________________________________________________________________
_____________________________
conv2d_14 (Conv2D) (None, 128, 128, 128 147584 conv
2d_13[0][0]
_____________________________________________________________________
_____________________________
2d_14[0][0]
_____________________________________________________________________
_____________________________
concatenate_3 (Concatenate) (None, 256, 256, 128 0 conv
conv
2d_4[0][0]
_____________________________________________________________________
_____________________________
atenate_3[0][0]
_____________________________________________________________________
_____________________________
2d_15[0][0]
_____________________________________________________________________
_____________________________
2d_16[0][0]
_____________________________________________________________________
_____________________________
concatenate_4 (Concatenate) (None, 512, 512, 64) 0 conv
conv
2d_2[0][0]
_____________________________________________________________________
_____________________________
atenate_4[0][0]
_____________________________________________________________________
_____________________________
2d_17[0][0]
_____________________________________________________________________
_____________________________
2d_18[0][0]
=====================================================================
=============================
Total params: 7,759,521
Trainable params: 7,759,521
Non-trainable params: 0
_____________________________________________________________________
_____________________________
Epoch 1/48
Found 604 images belonging to 1 classes.
Found 604 images belonging to 1 classes.
512/512 [==============================] - 196s 384ms/step - loss: -
0.4672 - dice_coef: 0.4672 - binary_accuracy: 0.4820 - val_loss: -0.4
817 - val_dice_coef: 0.4817 - val_binary_accuracy: 0.6168
Epoch 00001: loss improved from inf to -0.46716, saving model to unet
_lung_seg.hdf5
Epoch 2/48
512/512 [==============================] - 186s 364ms/step - loss: -
Epoch 00002: loss improved from -0.46716 to -0.65851, saving model to

unet_lung_seg.hdf5
Epoch 3/48
512/512 [==============================] - 187s 364ms/step - loss: -

unet_lung_seg.hdf5
Epoch 4/48
512/512 [==============================] - 186s 364ms/step - loss: -

unet_lung_seg.hdf5
Epoch 5/48
512/512 [==============================] - 186s 364ms/step - loss: -

unet_lung_seg.hdf5
Epoch 6/48
512/512 [==============================] - 186s 364ms/step - loss: -

unet_lung_seg.hdf5
Epoch 7/48
512/512 [==============================] - 186s 363ms/step - loss: -

unet_lung_seg.hdf5
Epoch 8/48
512/512 [==============================] - 186s 363ms/step - loss: -
Epoch 00008: loss did not improve from -0.90660

Epoch 9/48
512/512 [==============================] - 186s 363ms/step - loss: -

unet_lung_seg.hdf5
Epoch 10/48
512/512 [==============================] - 186s 363ms/step - loss: -

unet_lung_seg.hdf5
Epoch 11/48
512/512 [==============================] - 186s 363ms/step - loss: -

unet_lung_seg.hdf5
Epoch 12/48
512/512 [==============================] - 186s 362ms/step - loss: -

l hdf
unet_lung_seg.hdf5
Epoch 13/48
512/512 [==============================] - 186s 362ms/step - loss: -

unet_lung_seg.hdf5
Epoch 14/48
512/512 [==============================] - 185s 362ms/step - loss: -

unet_lung_seg.hdf5
Epoch 15/48
512/512 [==============================] - 185s 362ms/step - loss: -

unet_lung_seg.hdf5
Epoch 16/48
512/512 [==============================] - 186s 362ms/step - loss: -

unet_lung_seg.hdf5
Epoch 17/48
512/512 [==============================] - 186s 362ms/step - loss: -

unet_lung_seg.hdf5
Epoch 18/48
512/512 [==============================] - 186s 363ms/step - loss: -

unet_lung_seg.hdf5
Epoch 19/48
512/512 [==============================] - 186s 362ms/step - loss: -
Epoch 00019: loss did not improve from 0 95237

Epoch 00019: loss did not improve from -0.95237
Epoch 20/48
484/512 [===========================>..] - ETA: 10s - loss: -0.9504 -
dice_coef: 0.9504 - binary_accuracy: 0.9699
Show some results from model fitting history
In [15]:
fig, axs = plt.subplots(1, 2, figsize = (15, 4))
training_loss = history.history['loss']
validation_loss = history.history['val_loss']
training_accuracy = history.history['binary_accuracy']
validation_accuracy = history.history['val_binary_accuracy']
epoch_count = range(1, len(training_loss) + 1)
axs[0].plot(epoch_count, training_loss, 'r--')

axs[0].plot(epoch_count, validation_loss, 'b-')
axs[0].legend(['Training Loss', 'Validation Loss'])
axs[1].plot(epoch_count, training_accuracy, 'r--')

axs[1].plot(epoch_count, validation_accuracy, 'b-')
axs[1].legend(['Training Accuracy', 'Validation Accuracy'])
Out[15]:
<matplotlib.legend.Legend at 0x7f7a143ede48>
Make lung segmentation predictions
In [16]:
test_gen = test_generator(test_files, target_size=(512,512))
results = model.predict_generator(test_gen, len(test_files), verbose=1
)
save result(SEGMENTATION TEST DIR results test files)
save_result(SEGMENTATION_TEST_DIR, results, test_files)
100/100 [==============================] - 7s 69ms/step
4. Results
Below, we see some results from our work, presented as Predicted, Gold Standard (manually
segmented) and the difference between segmentations.
The next step will be the selection of lungs area on RSNA images dataset and the generation of a
lungs-only image dataset.
In [17]:
image = cv2.imread("../input/segmentation/test/CHNCXR_0003_0.png")
predict_image = cv2.imread("../input/segmentation/test/CHNCXR_0003_0_p
redict.png")
mask_image = cv2.imread("../input/segmentation/test/CHNCXR_0003_0_dila
te.png")
axs[0, 0].set_title("Predicted")
axs[0, 0].imshow(add_colored_mask(image, predict_image))
axs[0, 1].set_title("Gold Std.")
axs[0, 1].imshow(add_colored_mask(image, mask_image))
axs[0, 2].set_title("Diff.")
axs[0, 2].imshow(diff_mask(mask_image, predict_image))
image = cv2.imread("../input/segmentation/test/MCUCXR_0003_0.png")
predict_image = cv2.imread("../input/segmentation/test/MCUCXR_0003_0_p
redict.png")
mask_image = cv2.imread("../input/segmentation/test/MCUCXR_0003_0_dila
te.png")
image = cv2.imread("../input/segmentation/test/CHNCXR_0020_0.png")
predict_image = cv2.imread("../input/segmentation/test/CHNCXR_0020_0_p
redict.png")
mask_image = cv2.imread("../input/segmentation/test/CHNCXR_0020_0_dila
te.png")
image = cv2.imread("../input/segmentation/test/MCUCXR_0016_0.png")
predict_image = cv2.imread("../input/segmentation/test/MCUCXR_0016_0_p
redict.png")
mask_image = cv2.imread("../input/segmentation/test/MCUCXR_0016_0_dila
te.png")
Out[17]:
<matplotlib.image.AxesImage at 0x7f7a1410acc0>
In [18]:
!tar zcvf results.tgz --directory=../input/segmentation/test .
./
./CHNCXR_0657_1_dilate.png
./MCUCXR_0071_0_dilate.png
./CHNCXR_0283_0_predict.png
./MCUCXR_0367_1.png
./CHNCXR_0020_0.png
./CHNCXR_0030_0_mask.png
./MCUCXR_0006_0_mask.png
./CHNCXR_0649_1.png
./MCUCXR_0046_0.png
./MCUCXR_0188_1.png
./MCUCXR_0350_1.png
./MCUCXR_0017_0.png
./MCUCXR_0188_1_predict.png
./CHNCXR_0460_1.png
./CHNCXR_0572_1.png
./CHNCXR_0462_1.png
./C C _0 6 _ .p g
./MCUCXR_0011_0.png
./CHNCXR_0538_1.png
./CHNCXR_0506_1.png
./CHNCXR_0658_1.png
./MCUCXR_0101_0.png
./CHNCXR_0620_1.png
./MCUCXR_0275_1.png
./CHNCXR_0238_0.png
./CHNCXR_0651_1.png
./MCUCXR_0003_0.png
./CHNCXR_0030_0.png
./MCUCXR_0049_0.png
./MCUCXR_0313_1.png
./CHNCXR_0657_1.png
./CHNCXR_0320_0.png
./CHNCXR_0032_0.png
./MCUCXR_0035_0.png
./CHNCXR_0259_0.png
./CHNCXR_0329_1.png
./MCUCXR_0182_1.png
./MCUCXR_0057_0.png
./MCUCXR_0051_0.png
./MCUCXR_0289_1.png
./MCUCXR_0375_1.png
./MCUCXR_0258_1.png
./CHNCXR_0004_0.png
./CHNCXR_0005_0.png
./CHNCXR_0567_1.png
./CHNCXR_0070_0.png
./MCUCXR_0058_0.png
./MCUCXR_0030_0.png
./CHNCXR_0155_0.png
./MCUCXR_0141_1.png
./MCUCXR_0071_0.png
./MCUCXR_0399_1.png
./MCUCXR_0048_0.png
./MCUCXR_0390_1.png
./MCUCXR_0352_1.png
./CHNCXR_0060_0.png
./CHNCXR_0446_1.png
./CHNCXR_0608_1.png
./MCUCXR_0006_0.png
./CHNCXR_0091_0.png
./MCUCXR_0077_0.png
./MCUCXR_0144_1.png
./CHNCXR_0409_1.png
./CHNCXR_0575_1.png
./MCUCXR_0091_0.png
./MCUCXR_0113_1.png
./MCUCXR_0311_1.png
./CHNCXR_0375_1.png
./MCUCXR_0080_0.png
./CHNCXR_0122_0.png
./CHNCXR_0387_1.png
./CHNCXR_0275_0.png
./CHNCXR_0423_1.png
./MCUCXR_0170_1.png
./MCUCXR_0099_0.png
./CHNCXR_0112_0.png
./CHNCXR_0384_1.png
/CHNCXR 0003 0
./CHNCXR_0003_0.png
./CHNCXR_0628_1.png
./CHNCXR_0283_0.png
./MCUCXR_0150_1.png
./MCUCXR_0255_1.png
./MCUCXR_0266_1.png
./MCUCXR_0102_0.png
./MCUCXR_0096_0.png
./MCUCXR_0059_0.png
./MCUCXR_0042_0.png
./CHNCXR_0152_0.png
./MCUCXR_0016_0.png
/CHNCXR 0462 1 dilate png
./CHNCXR_0408_1.png
./CHNCXR_0510_1.png
./MCUCXR_0301_1.png
/CHNCXR 0004 0 mask png
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JSR 17 Task 002 Aiforhealthandhealthcare12122017

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19/10/2018 U-Net lung segmentation (Montgomery + Shenzhen) | Kaggle

Search kaggle  Competitions Datasets Kernels Discussion Learn Sign In

last run 6 hours ago · IPython Notebook HTML · 126 views

Tags multiple data sources

RSNA Pneumonia Detection Challenge

Sociedade Beneﬁcente de Senhoras - Hospital Sírio-

Import required Python libraries

from keras.models import *

from glob import glob

Using TensorFlow backend.

Deﬁne appropriate constants for directory paths and training parameters

SEGMENTATION_DIR = os.path.join(INPUT_DIR, "segmentation")

SHENZHEN_TRAIN_DIR = os.path.join(SEGMENTATION_SOURCE_DIR, "ChinaSet_A

DILATE_KERNEL = np.ones((15, 15), np.uint8)

for left_image_file in tqdm(montgomery_left_mask_dir):

right_mask = cv2.imread(right_image_file, cv2.IMREAD_GRAYSCALE)

image = cv2.resize(image, (512, 512))

mask = np.maximum(left_mask, right_mask)

100%|██████████| 138/138 [01:00<00:00, 2.23it/s]

Deﬁne some useful functions to display images with segmentation as overlays

mask = cv2.bitwise_and(mask_image, mask_image, mask=mask_image_gra

mask[mask coord[0] mask coord[1] :]=[255 0 0]

ret = cv2.addWeighted(image, 0.7, dilate, 0.3, 0)

def add_colored_mask(image, mask_image):

mask = cv2.bitwise_and(mask_image, mask_image, mask=mask_image_gra

ret = cv2.addWeighted(image, 0.7, mask, 0.3, 0)

def diff_mask(ref_image, mask_image):

mask = cv2.bitwise_and(mask_image, mask_image, mask=mask_image_gra

ret = cv2.addWeighted(ref_image, 0.7, mask, 0.3, 0)

image_file = os.path.join(SEGMENTATION_IMAGE_DIR, base_file)

fig, axs = plt.subplots(2, 4, figsize=(15, 8))

1. Resize Shenzhen Hospital chest x-ray images to 512x512 pixels

for mask_file in tqdm(shenzhen_mask_dir):

image = cv2.resize(image, (512, 512))

cv2 imwrite(os path join(SEGMENTATION TEST DIR base file) \

100%|██████████| 566/566 [01:49<00:00, 5.18it/s]

image_file = os.path.join(SEGMENTATION_IMAGE_DIR, base_file)

fig, axs = plt.subplots(2, 4, figsize=(15, 8))

base_file = os.path.basename(shenzhen_test[0].replace("_mask", ""))

filename, fileext = os.path.splitext(base_file)

Data augmentation helper function for training the net

train_gen = zip(image_generator, mask_generator)

for (img, mask) in train_gen:

return (img, mask)

def dice_coef_loss(y_true, y_pred):

conv1 = Conv2D(32, (3, 3), activation='relu', padding='same')(inpu

conv2 = Conv2D(64, (3, 3), activation='relu', padding='same')(pool

conv3 = Conv2D(128, (3, 3), activation='relu', padding='same')(poo

conv4 = Conv2D(256, (3, 3), activation='relu', padding='same')(poo

conv5 = Conv2D(512, (3, 3), activation='relu', padding='same')(poo

up6 = concatenate([Conv2DTranspose(256, (2, 2), strides=(2, 2), pa

up7 = concatenate([Conv2DTranspose(128, (2, 2), strides=(2, 2), pa

up8 = concatenate([Conv2DTranspose(64, (2, 2), strides=(2, 2), pad

up9 = concatenate([Conv2DTranspose(32, (2, 2), strides=(2, 2), pad

conv10 = Conv2D(1, (1, 1), activation='sigmoid')(conv9)

return Model(inputs=[inputs], outputs=[conv10])

Helper functions to load test chest x-ray images

def test_generator(test_files, target_size=(256,256)):

def save_result(save_path, npyfile, test_files):

filename, fileext = os.path.splitext(os.path.basename(result_f

result_file = os.path.join(save_path, "%s_predict%s" % (filena

Select test and validation ﬁles

test_files = [test_file for test_file in glob(os.path.join(SEGMENTATIO