Data preparation

Overview

Questions

• What is the purpose of data augmentation?
• What types of transform can be applied in data augmentation?

Objectives

• Generate an augmented dataset
• Partition data into training and test sets.

Partitioning into training and test sets

---

As we have done in previous projects, we will want to split our data into subsets for training and testing. The training set is used for building our model and our test set is used for evaluation.

To ensure reproducibility, we should set the random state of the splitting method. This means that Python’s random number generator will produce the same “random” split in future.

PYTHON

from sklearn.model_selection import train_test_split

# Our Tensorflow model requires the input to be:
# [batch, height, width, n_channels]
# So we need to add a dimension to the dataset and labels.
# 
# Ellipsis (...) is shorthand for selecting with ":" across dimensions. 
# np.newaxis expands the selection by one dimension.
dataset = dataset[..., np.newaxis]
labels = labels[..., np.newaxis]

# Create training and test sets
dataset_train, dataset_test, labels_train, labels_test = train_test_split(dataset, labels, test_size=0.15, random_state=42)

# Create a validation set
dataset_train, dataset_val, labels_train, labels_val = train_test_split(dataset_train, labels_train, test_size=0.15, random_state=42)

print("No. images, x_dim, y_dim, colors) (No. labels, 1)\n")
print(f"Train: {dataset_train.shape}, {labels_train.shape}")
print(f"Validation: {dataset_val.shape}, {labels_val.shape}")
print(f"Test: {dataset_test.shape}, {labels_test.shape}")

OUTPUT

No. images, x_dim, y_dim, colors) (No. labels, 1)

Train: (505, 256, 256, 1), (505, 1)
Validation: (90, 256, 256, 1), (90, 1)
Test: (105, 256, 256, 1), (105, 1)

Data Augmentation

---

We have a small dataset, which increases the chance of overfitting our model. If our model is overfitted, it becomes less able to generalize to data outside the training data.

To artificially increase the size of our training set, we can use ImageDataGenerator. This function generates new data by applying random transformations to our source images while our model is training.

PYTHON

from tensorflow.keras.preprocessing.image import ImageDataGenerator

# Define what kind of transformations we would like to apply
# such as rotation, crop, zoom, position shift, etc
datagen = ImageDataGenerator(
    rotation_range=0,
    width_shift_range=0,
    height_shift_range=0,
    zoom_range=0,
    horizontal_flip=False)

For the sake of interest, let’s take a look at some examples of the augmented images!

PYTHON

# specify path to source data
path = os.path.join("chest_xrays")
batch_size=5

val_generator = datagen.flow_from_directory(
        path, color_mode="rgb",
        target_size=(256, 256),
        batch_size=batch_size)

def plot_images(images_arr):
    fig, axes = plt.subplots(1, 5, figsize=(20,20))
    axes = axes.flatten()
    for img, ax in zip(images_arr, axes):
        ax.imshow(img.astype('uint8'))
    plt.tight_layout()
    plt.show()

augmented_images = [val_generator[0][0][0] for i in range(batch_size)]
plot_images(augmented_images)

The images look a little strange, but that’s the idea! When our model sees something unusual in real-life, it will be better adapted to deal with it.

Now we have some data to work with, let’s start building our model.

Key Points

• Data augmentation can help to avoid overfitting.