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Visualisation

Overview

Teaching: 20 min
Exercises: 10 min
Questions
  • How does an image with pleural effusion differ from one without?

  • How is image data represented in a NumPy array?

Objectives
  • Visually compare normal X-rays with those labelled with pleural effusion.

  • Understand how to use NumPy to store and manipulate image data.

  • Compare a slice of numerical data to its corresponding image.

Visualising the X-rays

In the previous section, we set up a dataset comprising 700 chest X-rays. Half of the X-rays are labelled “normal” and half are labelled as “pleural effusion”. Let’s take a look at some of the images.

# cv2 is openCV, a popular computer vision library
import cv2
from matplotlib import pyplot as plt 
import random

def plot_example(example, label, loc):
    image = cv2.imread(example)
    im = ax[loc].imshow(image)
    title = f"Class: {label}\n{example}"
    ax[loc].set_title(title)

fig, ax = plt.subplots(1, 2)
fig.set_size_inches(10, 10)

# Plot a "normal" record
plot_example(random.choice(normal_list), "Normal", 0)

# Plot a record labelled with effusion
plot_example(random.choice(effusion_list), "Effusion", 1)

Example X-rays

Can we detect effusion?

Run the following code to flip a coin to select an x-ray from our collection.

print("Effusion or not?")

# flip a coin
coin_flip = random.choice(["Effusion", "Normal"])
if coin_flip == "Normal":
    fn = random.choice(normal_list)
else:
    fn = random.choice(effusion_list)

# plot the image
image = cv2.imread(fn)
plt.imshow(image)

Show the answer:

# Jupyter doesn't allow us to print the image until the cell has run,
# so we'll print in a new cell.
print(f"The answer is: {coin_flip}!")

Exercise

A) Manually classify 10 X-rays using the coin flip code. Make a note of your predictive accuracy (hint: for a reminder of the formula for accuracy, check the solution below).

Solution

A) Accuracy is the fraction of predictions that were correct (correct predictions / total predictions). If you made 10 predictions and 5 were correct, your accuracy is 50%.

How does a computer see an image?

Consider an image as a matrix in which the value of each pixel corresponds to a number that determines a tone or color. Let’s load one of our images:

import numpy as np 

file_idx = 56
example = normal_list[file_idx]
image = cv2.imread(example)

print(image.shape)
(512, 512, 3)

Here we see that the image has 3 dimensions. The first dimension is height (512 pixels) and the second is width (also 512 pixels). The presence of a third dimension indicates that we are looking at a color image (“RGB”, or Red, Green, Blue).

For more detail on image representation in Python, take a look at the Data Carpentry course on Image Processing with Python. The following image is reproduced from the section on Image Representation.

RGB image

For simplicity, we’ll instead load the images in greyscale. A greyscale image has two dimensions: height and width. Each value in the matrix represents a tone between black (0) and white (255).

image = cv2.imread(example, cv2.IMREAD_GRAYSCALE)
print(image.shape)
(512, 512)

Let’s briefly display the matrix of values, and then see how these same values are rendered as an image.

# Print a 10 by 10 chunk of the matrix
print(image[35:45, 30:40])

Example greyscale numpy array

# Plot the same chunk as an image
plt.imshow(image[35:45, 30:40], cmap='gray', vmin=0, vmax=255)

Example greyscale image

Image pre-processing

In the next episode, we’ll be building and training a model. Let’s prepare our data for the modelling phase. For convenience, we’ll begin by loading all of the images and corresponding labels and assigning them to a list.

# create a list of effusion images and labels
dataset_effusion = [cv2.imread(fn, cv2.IMREAD_GRAYSCALE) for fn in effusion_list]
label_effusion = np.ones(len(dataset_effusion))

# create a list of normal images and labels
dataset_normal = [cv2.imread(fn, cv2.IMREAD_GRAYSCALE) for fn in normal_list]
label_normal = np.zeros(len(dataset_normal))

# Combine the lists
dataset = dataset_effusion + dataset_normal
labels = np.concatenate([label_effusion, label_normal])

Let’s also downsample the images, reducing the size from (512, 512) to (256,256).

# Downsample the images from (512,512) to (256,256)
dataset = [cv2.resize(img, (256,256)) for img in dataset]

# Check the size of the reshaped images
print(dataset[0].shape)

# Normalize the data
# Subtract the mean, divide by the standard deviation.
for i in range(len(dataset)):
  dataset[i] = (dataset[i] - np.average(dataset[i], axis= (0, 1))) / np.std(dataset[i], axis= (0, 1)) 
(256, 256)

Finally, we’ll convert our dataset from a list to an array. We are expecting it to be (700, 256, 256). That is 700 images (350 effusion cases and 350 normal), each with a dimension of 256 by 256.

dataset = np.asarray(dataset, dtype=np.float32)
print(f"Matrix Dimensions: {dataset.shape}")
(700, 256, 256)

We could plot the images by indexing them on dataset, e.g., we can plot the first image in the dataset with:

idx = 0
vals = dataset[idx].flatten()
plt.imshow(dataset[idx], cmap='gray', vmin=min(vals), vmax=max(vals))

Example greyscale image

Key Points

  • In NumPy, RGB images are usually stored as 3-dimensional arrays.