Kaggle competition: RSNA Pneumonia Detection Challenge
<SOS> metric: RSNAObjectDetectionAP Kaggle data source: rsna-pneumonia-detection-challenge<compute_test_metric>
import os
import csv
import random
import pydicom
import numpy as np
import pandas as pd
from skimage import measure
from skimage.transform import resize
import tensorflow as tf
from tensorflow import keras
from matplotlib import pyplot as plt
sigma_opt = mean_absolute_error(y, pred[:, 1])
 unc = pred[:,2] - pred[:, 0]
sigma_mean = np.mean(unc)
 print(sigma_opt, sigma_mean )<prepare_output>
pneumonia_locations = {}
with open(os.path.join('.. /input/stage_1_train_labels.csv'), mode='r')as infile:
reader = csv.reader(infile)
 next(reader, None)
 for rows in reader:
filename = rows[0]
location = rows[1:5]
pneumonia = rows[5]
if pneumonia == '1':
location = [int(float(i)) for i in location]
if filename in pneumonia_locations:
pneumonia_locations[filename].append(location)
 else:
pneumonia_locations[filename] = [location]
sub['FVC1'] = 1.*pe[:, 1]
sub['Confidence1'] = pe[:, 2] - pe[:, 0]
subm = sub[['Patient_Week','FVC','Confidence','FVC1','Confidence1']].copy()
subm.loc[~subm.FVC1.isnull() ].head(10 )<feature_engineering>
folder = '.. /input/stage_1_train_images'
filenames = os.listdir(folder)
 random.shuffle(filenames)
 n_valid_samples = 2560
train_filenames = filenames[n_valid_samples:]
valid_filenames = filenames[:n_valid_samples]
print('n train samples', len(train_filenames))
print('n valid samples', len(valid_filenames))
n_train_samples = len(filenames)- n_valid_samples
subm.loc[~subm.FVC1.isnull() ,'FVC'] = subm.loc[~subm.FVC1.isnull() ,'FVC1']
if sigma_mean<70:
subm['Confidence'] = sigma_opt
else:
subm.loc[~subm.FVC1.isnull() ,'Confidence'] = subm.loc[~subm.FVC1.isnull() ,'Confidence1']<load_from_csv>
class generator(keras.utils.Sequence):
def __init__(self, folder, filenames, pneumonia_locations=None, batch_size=32, image_size=512, shuffle=True, augment=False, predict=False):
self.folder = folder
self.filenames = filenames
self.pneumonia_locations = pneumonia_locations
self.batch_size = batch_size
self.image_size = image_size
self.shuffle = shuffle
self.augment = augment
self.predict = predict
self.on_epoch_end()
def __load__(self, filename):
img = pydicom.dcmread(os.path.join(self.folder, filename)).pixel_array
msk = np.zeros(img.shape)
 filename = filename.split('.')[0]
if filename in pneumonia_locations:
for location in pneumonia_locations[filename]:
x, y, w, h = location
msk[y:y+h, x:x+w] = 1
if self.augment and random.random() > 0.6:
img = np.fliplr(img)
 msk = np.fliplr(msk)
 img = resize(img,(self.image_size, self.image_size), mode='reflect')
 msk = resize(msk,(self.image_size, self.image_size), mode='reflect')> 0.55
img = np.expand_dims(img, -1)
 msk = np.expand_dims(msk, -1)
 return img, msk
def __loadpredict__(self, filename):
img = pydicom.dcmread(os.path.join(self.folder, filename)).pixel_array
img = resize(img,(self.image_size, self.image_size), mode='reflect')
 img = np.expand_dims(img, -1)
 return img
def __getitem__(self, index):
filenames = self.filenames[index*self.batch_size:(index+1)*self.batch_size]
if self.predict:
imgs = [self.__loadpredict__(filename)for filename in filenames]
imgs = np.array(imgs)
 return imgs, filenames
else:
items = [self.__load__(filename)for filename in filenames]
imgs, msks = zip(*items)
 imgs = np.array(imgs)
 msks = np.array(msks)
 return imgs, msks
def on_epoch_end(self):
if self.shuffle:
random.shuffle(self.filenames)
 def __len__(self):
if self.predict:
return int(np.ceil(len(self.filenames)/ self.batch_size))
else:
return int(len(self.filenames)/ self.batch_size )
otest = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/test.csv')
 for i in range(len(otest)) :
subm.loc[subm['Patient_Week']==otest.Patient[i]+'_'+str(otest.Weeks[i]), 'FVC'] = otest.FVC[i]
subm.loc[subm['Patient_Week']==otest.Patient[i]+'_'+str(otest.Weeks[i]), 'Confidence'] = 0.1<save_to_csv>
def create_downsample(channels, inputs):
x = keras.layers.BatchNormalization(momentum=0.9 )(inputs)
 x = keras.layers.LeakyReLU(0 )(x)
 x = keras.layers.Conv2D(channels, 1, padding='same', use_bias=False )(x)
 x = keras.layers.MaxPool2D(( 2, 2))(x)
 return x
def create_resblock(channels, inputs):
x = keras.layers.BatchNormalization(momentum=0.95 )(inputs)
 x = keras.layers.LeakyReLU(0 )(x)
 x = keras.layers.Conv2D(channels, 3, padding='same', use_bias=False )(x)
 x = keras.layers.BatchNormalization(momentum=0.95 )(x)
 x = keras.layers.LeakyReLU(0 )(x)
 x = keras.layers.Conv2D(channels, 3, padding='same', use_bias=False )(x)
 return keras.layers.add([x, inputs])
 def create_network(input_size, channels, n_blocks=2, depth=3):
inputs = keras.Input(shape=(input_size, input_size, 1))
x = keras.layers.Conv2D(channels, 3, padding='same', use_bias=False )(inputs)
 for d in range(depth):
channels = channels * 2
x = create_downsample(channels, x)
 for b in range(n_blocks):
x = create_resblock(channels, x)
 x = keras.layers.BatchNormalization(momentum=0.9 )(x)
 x = keras.layers.LeakyReLU(0 )(x)
 x = keras.layers.Conv2D(1, 1, activation='sigmoid' )(x)
 outputs = keras.layers.UpSampling2D(2**depth )(x)
 model = keras.Model(inputs=inputs, outputs=outputs)
 return model
subm[["Patient_Week","FVC","Confidence"]].to_csv("submission_regression.csv", index=False )<prepare_output>
def iou_loss(y_true, y_pred):
y_true = tf.reshape(y_true, [-1])
 y_pred = tf.reshape(y_pred, [-1])
 intersection = tf.reduce_sum(y_true * y_pred)
 score =(intersection + 1.) /(tf.reduce_sum(y_true)+ tf.reduce_sum(y_pred)- intersection + 1.)
return 1 - score
def iou_bce_loss(y_true, y_pred):
return 0.5 * keras.losses.binary_crossentropy(y_true, y_pred)+ 0.5 * iou_loss(y_true, y_pred)
 def mean_iou(y_true, y_pred):
y_pred = tf.round(y_pred)
 intersect = tf.reduce_sum(y_true * y_pred, axis=[1, 2, 3])
 union = tf.reduce_sum(y_true, axis=[1, 2, 3])+ tf.reduce_sum(y_pred, axis=[1, 2, 3])
 smooth = tf.ones(tf.shape(intersect))
return tf.reduce_mean(( intersect + smooth)/(union - intersect + smooth))
model = create_network(input_size=256, channels=32, n_blocks=2, depth=4)
 model.compile(optimizer='adam',
loss=iou_bce_loss,
metrics=['accuracy', mean_iou])
 def cosine_annealing(x):
lr = 0.001
epochs = 25
return lr*(np.cos(np.pi*x/epochs)+1.) /2
learning_rate = tf.keras.callbacks.LearningRateScheduler(cosine_annealing)
 folder = '.. /input/stage_1_train_images'
train_gen = generator(folder, train_filenames, pneumonia_locations, batch_size=32, image_size=256, shuffle=True, augment=True, predict=False)
 valid_gen = generator(folder, valid_filenames, pneumonia_locations, batch_size=32, image_size=256, shuffle=False, predict=False)
 history = model.fit_generator(train_gen, validation_data=valid_gen, callbacks=[learning_rate], epochs=25, shuffle=True )
<sort_values><EOS> 
folder = '.. /input/stage_1_test_images'
test_filenames = os.listdir(folder)
 print('n test samples:', len(test_filenames))
test_gen = generator(folder, test_filenames, None, batch_size=25, image_size=256, shuffle=False, predict=True)
 submission_dict = {}
for imgs, filenames in test_gen:
preds = model.predict(imgs)
 for pred, filename in zip(preds, filenames):
pred = resize(pred,(1024, 1024), mode='reflect')
 comp = pred[:, :, 0] > 0.5
comp = measure.label(comp)
 predictionString = ''
for region in measure.regionprops(comp):
y, x, y2, x2 = region.bbox
height = y2 - y
width = x2 - x
conf = np.mean(pred[y:y+height, x:x+width])
 predictionString += str(conf)+ ' ' + str(x)+ ' ' + str(y)+ ' ' + str(width)+ ' ' + str(height)+ ' '
filename = filename.split('.')[0]
submission_dict[filename] = predictionString
if len(submission_dict)>= len(test_filenames):
break
sub = pd.DataFrame.from_dict(submission_dict,orient='index')
 sub.index.names = ['patientId']
sub.columns = ['PredictionString']
sub.to_csv('submission.csv' )