X-ray image classification
Unbalanced data
import os
import tensorflow as tf
from tensorflow.keras import regularizers
from tensorflow.keras import layers
from tensorflow.keras import Model
from tensorflow import keras
import matplotlib.pyplot as plt
base_dir = 'chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train/'
train_dir = os.path.join(base_dir, 'train')
validation_dir = os.path.join(base_dir, 'test')
train_NORMAL_dir = os.path.join(train_dir, 'NORMAL')
train_PNEUMONIA_dir = os.path.join(train_dir, 'PNEUMONIA')
validation_NORMAL_dir = os.path.join(validation_dir, 'NORMAL')
validation_PNEUMONIA_dir = os.path.join(validation_dir, 'PNEUMONIA')
train_NORMAL_fnames = os.listdir( train_NORMAL_dir )
train_PNEUMONIA_fnames = os.listdir( train_PNEUMONIA_dir )
print(train_NORMAL_fnames[:10])
print(train_PNEUMONIA_fnames[:10])
print('total training NORMAL images :', len(os.listdir( train_NORMAL_dir ) ))
print('total training PNEUMONIA images :', len(os.listdir( train_PNEUMONIA_dir ) ))
print('total validation NORMAL images :', len(os.listdir( validation_NORMAL_dir ) ))
print('total validation PNEUMONIA images :', len(os.listdir( validation_PNEUMONIA_dir ) ))
import matplotlib.image as mpimg
import matplotlib.pyplot as plt
# Parameters for our graph; we'll output images in a 4x4 configuration
nrows = 4
ncols = 4
pic_index = 0 # Index for iterating over images
# Set up matplotlib fig, and size it to fit 4x4 pics
fig = plt.gcf()
fig.set_size_inches(ncols*4, nrows*4)
pic_index+=8
next_NORMAL_pix = [os.path.join(train_NORMAL_dir, fname)
for fname in train_NORMAL_fnames[ pic_index-8:pic_index]
]
next_PNEUMONIA_pix = [os.path.join(train_PNEUMONIA_dir, fname)
for fname in train_PNEUMONIA_fnames[ pic_index-8:pic_index]
]
for i, img_path in enumerate(next_NORMAL_pix+next_PNEUMONIA_pix):
sp = plt.subplot(nrows, ncols, i + 1)
sp.axis('Off')
img = mpimg.imread(img_path)
plt.imshow(img)
class Conv(tf.keras.Model):
def __init__(self, filters, kernel_size):
super(Conv, self).__init__()
self.conv = tf.keras.layers.Conv2D(filters=filters, kernel_size=kernel_size)
self.bn = tf.keras.layers.BatchNormalization()
self.relu = tf.keras.layers.ReLU()
self.pool = tf.keras.layers.MaxPool2D(pool_size=(2, 2))
def call(self, inputs, training=True):
x = self.conv(inputs)
x = self.bn(x, training=training)
x = self.relu(x)
x = self.pool(x)
return x
model = tf.keras.Sequential(name='X-ray_CNN')
model.add(Conv(filters=32, kernel_size=(3, 3)))
model.add(Conv(filters=64, kernel_size=(3, 3)))
model.add(Conv(filters=128, kernel_size=(3, 3)))
model.add(Conv(filters=128, kernel_size=(3, 3)))
model.add(tf.keras.layers.Flatten())
model.add(tf.keras.layers.Dense(units=512, activation=tf.keras.activations.relu))
model.add(tf.keras.layers.Dense(units=2, activation=tf.keras.activations.softmax))
model.compile(optimizer=tf.keras.optimizers.Adam(learning_rate=1e-4),
loss=tf.keras.losses.SparseCategoricalCrossentropy(),
metrics=['accuracy'])
from glob import glob
base_dir = 'chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train/'
# train_len = len(glob(os.path.join(base_dir, 'train', 'NORMAL', '*.jpeg'))) * 2
val_len = len(glob(os.path.join(base_dir, 'val', 'NORMAL', '*.jpeg'))) * 2
test_len = len(glob(os.path.join(base_dir, 'test', 'NORMAL', '*.jpeg'))) * 2
train_len = 750
from tensorflow.keras.optimizers import RMSprop
from tensorflow.keras.optimizers import SGD
from tensorflow.keras.preprocessing.image import ImageDataGenerator
train_datagen = ImageDataGenerator( rescale = 1.0/255,
rotation_range=40,
width_shift_range=0.2,
height_shift_range=0.2,
shear_range=0.2,
zoom_range=0.2,
horizontal_flip=True,
fill_mode='nearest'
)
validation_datagen = ImageDataGenerator( rescale = 1.0/255,
rotation_range=40,
width_shift_range=0.2,
height_shift_range=0.2,
shear_range=0.2,
zoom_range=0.2,
horizontal_flip=True,
fill_mode='nearest'
)
# --------------------
train_generator = train_datagen.flow_from_directory(train_dir,
batch_size=20,
class_mode='binary',
target_size=(150, 150))
# --------------------
# Flow validation images in batches of 20 using test_datagen generator
# --------------------
validation_generator = validation_datagen.flow_from_directory(validation_dir,
batch_size=20,
class_mode = 'binary',
target_size = (150, 150))
checkpoint_path = "training_1/cp.ckpt"
checkpoint_dir = os.path.dirname(checkpoint_path)
# Create a callback that saves the model's weights
callback = tf.keras.callbacks.ModelCheckpoint(filepath=checkpoint_path, save_best_only=True,
save_weights_only=False,
verbose=1)
import numpy as np
def load(f, label):
# load the file into tensor
image = tf.io.read_file(f)
# Decode it to JPEG format
image = tf.image.decode_jpeg(image)
# Convert it to tf.float32
image = tf.cast(image, tf.float32)
return image, label
def resize(input_image, size):
return tf.image.resize(input_image, size)
def random_crop(input_image):
return tf.image.random_crop(input_image, size=[150, 150, 1])
def central_crop(input_image):
image = resize(input_image, [176, 176])
return tf.image.central_crop(image, central_fraction=0.84)
def random_rotation(input_image):
angles = np.random.randint(0, 3, 1)
return tf.image.rot90(input_image, k=angles[0])
def random_jitter(input_image):
# Resize it to 176 x 176 x 3
image = resize(input_image, [176, 176])
# Randomly Crop to 150 x 150 x 3
image = random_crop(image)
# Randomly rotation
image = random_rotation(image)
# Randomly mirroring
image = tf.image.random_flip_left_right(image)
return image
def normalize(input_image):
mid = (tf.reduce_max(input_image) + tf.reduce_min(input_image)) / 2
input_image = input_image / mid - 1
return input_image
def load_image_train(image_file, label):
image, label = load(image_file, label)
image = random_jitter(image)
image = normalize(image)
return image, label
def load_image_val(image_file, label):
image, label = load(image_file, label)
image = central_crop(image)
image = normalize(image)
return image, label
temp_ds = tf.data.Dataset.list_files(os.path.join("chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train", 'train', 'NORMAL', '*.jpeg'))
temp_ds = temp_ds.map(lambda x: (x, 0))
temp2_ds = tf.data.Dataset.list_files(os.path.join("chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train", 'train', 'PNEUMONIA', '*.jpeg'))
temp2_ds = temp2_ds.map(lambda x: (x, 1))
train_ds = temp_ds.concatenate(temp2_ds)
buffer_size = tf.data.experimental.cardinality(train_ds).numpy()
train_ds = train_ds.shuffle(buffer_size)\
.map(load_image_train, num_parallel_calls=16)\
.batch(20)\
.repeat()
temp_ds = tf.data.Dataset.list_files(os.path.join("chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train", 'val', 'NORMAL', '*.jpeg'))
temp_ds = temp_ds.map(lambda x: (x, 0))
temp2_ds = tf.data.Dataset.list_files(os.path.join("chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train", 'val', 'PNEUMONIA', '*.jpeg'))
temp2_ds = temp2_ds.map(lambda x: (x, 1))
val_ds = temp_ds.concatenate(temp2_ds)
val_ds = val_ds.map(load_image_val, num_parallel_calls=16)\
.batch(20)\
.repeat()
temp_ds = tf.data.Dataset.list_files(os.path.join("chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train", 'test', 'NORMAL', '*.jpeg'))
temp_ds = temp_ds.map(lambda x: (x, 0))
temp2_ds = tf.data.Dataset.list_files(os.path.join("chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train", 'test', 'PNEUMONIA', '*.jpeg'))
temp2_ds = temp2_ds.map(lambda x: (x, 1))
test_ds = temp_ds.concatenate(temp2_ds)
batch_size = 10
test_ds = test_ds.map(load_image_val, num_parallel_calls=16)\
.batch(batch_size)\
.repeat()
for images, labels in train_ds.take(1):
fig, ax = plt.subplots(1, 10, figsize=(20, 6))
for j in range(10):
image = images[j].numpy()
image = image / np.amax(image)
image = np.clip(image, 0, 1)
ax[j].imshow(image)
ax[j].set_title(labels[j].numpy())
plt.show()
checkpoint_path = "./train/x-ray/unbalanced/cp-{epoch:04d}.ckpt"
checkpoint_dir = os.path.dirname(checkpoint_path)
cp_callback = tf.keras.callbacks.ModelCheckpoint(filepath=checkpoint_path,
save_best_only=True,
save_weights_only=True,
verbose=1)
base_dir = "chest_xray/reduced size - unbalanced/unbalanced_more_normal_in_train/"
train_len = len(glob(os.path.join(base_dir, 'train', 'NORMAL', '*.jpeg'))) * 2
val_len = len(glob(os.path.join(base_dir, 'val', 'NORMAL', '*.jpeg'))) * 2
test_len = len(glob(os.path.join(base_dir, 'test', 'NORMAL', '*.jpeg'))) * 2
train_len = 750
history = model.fit(train_ds,
steps_per_epoch=train_len/20,
validation_data=val_ds,
validation_steps=val_len/20,
epochs=50,
verbose=1,
callbacks=[cp_callback]
)
from matplotlib.pyplot import figure
colors = plt.rcParams['axes.prop_cycle'].by_key()['color']
def plot_metrics(history):
metrics = ['loss', 'accuracy']
for n, metric in enumerate(metrics):
name = metric.replace("_"," ").capitalize()
figure(figsize=(20, 8))
plt.subplot(1,2,n+1)
plt.plot(history.epoch, history.history[metric], color=colors[0], label='Train')
plt.plot(history.epoch, history.history['val_'+metric],
color=colors[0], linestyle="--", label='Val')
plt.xlabel('Epoch')
plt.ylabel(name)
if metric == 'loss':
plt.ylim([0, plt.ylim()[1]])
elif metric == 'auc':
plt.ylim([0.8,1])
else:
plt.ylim([0,1])
plt.legend()
plot_metrics(history)
model.summary()
test_ds
model.evaluate(test_ds, steps=int(test_len/batch_size))
# divided by batch size"""
# batch_size = 10
# predictions = model.predict(test_ds, steps=int(test_len/batch_size))
# predictions
# for i in range(predictions.shape[0]):
# if float(predictions[i][0]) > float(predictions[i][1]):
# pred[i] = 0
# else:
# pred[i] = 1
# pred
# predictions
i=0
p = []
gnd = []
prob = []
"""test_ds.take method takes samles from the test_ds n times when n is the number provided
as argument. When all the samples are taken, it starts repeating from the first position"""
for images, labels in test_ds.take(int(test_len/batch_size)):
i+=1
predictions = model(images)
p.append(predictions)
fig, ax = plt.subplots(1, batch_size, figsize=(20, 6))
"""Here the second argument in plt.subplots is different from the test_ds.take method's argument
plt.plot's second argument should be equalto the batch size whereas test_ds's argument indicates
how many times the script will enter test_ds"""
for j in range(batch_size):
"""This argument is for loop is also equal to batch size"""
image = images[j].numpy()
image = image / np.amax(image)
image = np.clip(image, 0, 1)
ax[j].imshow(image)
normal_prob = predictions[j][0]
normal_prob = round(float(normal_prob),2)
pneumonia_prob = predictions[j][1]
pneumonia_prob = round(float(pneumonia_prob),2)
ax[j].set_title(" gnd = {},\n n = {},\n p = {}".format(labels[j].numpy(),\
normal_prob,pneumonia_prob))
gnd.append(labels[j].numpy())
if (normal_prob>pneumonia_prob):
prob_temp = 0
else:
prob_temp = 1
prob.append(prob_temp)
# ax[j].set_title(labels[j].numpy())
plt.show()
predictions
from sklearn.metrics import accuracy_score
from sklearn.metrics import precision_score
from sklearn.metrics import recall_score
from sklearn.metrics import f1_score
accuracy_score(gnd, prob)
precision_score(gnd, prob, average = None)
recall_score(gnd, prob, average = None)
f1_score(gnd, prob, average = None)
from sklearn.metrics import classification_report
print(classification_report(gnd, prob))
from sklearn.metrics import confusion_matrix
print(confusion_matrix(gnd, prob))