Virus Xray Image Classification with Tensorflow Keras Python and Apache Spark Scala

George Jen, Jen Tek LLC

Disclaimer:

This writing is exclusively and entirely for educational purpose in the field of computer science. Only government medical board-certified radiologist can and should perform diagnosis from an Xray image.

Introduction

Can average person tell the difference from a picture of cat or dog? Probably yes. Can average person tell the difference from looking at an Xray photo and tells the difference between normal or virus caused pneumonia? Not unless that person is a board-certified medical professional.

For educational purpose in computer science on machine learning, can a computer after it is trained by a given dataset (labeled Xray pictures) that are empirically true to differentiate an Xray photo and tells the difference between normal and virus caused pneumonia from Xray images?

Data Preparation

To begin with, I downloaded the Xray image dataset from Kaggle (Coronahack chest Xray dataset)

https://www.kaggle.com/praveengovi/coronahack-chest-xraydataset

and build a neural network with Tensorflow Keras train the machine.

Generally, dataset to be used in image recognition is usually stored the following way, because the dataset is not a single file, with features and label, but many image files such as jpegs and a csv file telling the label and file name for each image file.

For image classification, common practice would be creating a folder, name the folder with label name, and place all the image files belong to that label inside that folder.

Therefore, I placed the files in below directory structure:

Train:
./
├── normal
└── virus
Validation:
./
├── normal
└── virus

Data Preprocessing

Apache Spark SQL API Image Read API Scala code to explore the image size

First, determine the image size by the following Scala code invoking Apache Spark Image read API:

val df = spark.read.format("image").option("dropInvalid", true).load("file:///home/bigdata2/dataset/Coronahack-Chest-XRay-Dataset/Coronahack-Chest-XRay-Dataset/train/normal")
df.select("image.origin", "image.width", "image.height").show(3)
+--------------------+-----+------+
|              origin|width|height|
+--------------------+-----+------+
|file:///home/bigd...| 2619|  2628|
|file:///home/bigd...| 2510|  2543|
|file:///home/bigd...| 2633|  2578|
+--------------------+-----+------+
only showing top 3 rows

Scala code to resize the jpeg image

The images are large, around 2500*2500, about 6 MP. This means, each pixel is a feature, or a column, this is like a table that has 6 million columns.

Therefore, I need to downsize to smaller image. I wrote the following Scala code to resize the image from about 2500*2500 to about 300*350, about one MP.

import java.awt.image.BufferedImage
import java.io.File
import javax.imageio.ImageIO
import javax.swing.ImageIcon;
import java.awt.Image;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
//Get the Image path of the training image files, both normal and virus
val normal=new java.io.File("/home/bigdata2/dataset/Coronahack-Chest-XRay-Dataset/Coronahack-Chest-XRay-Dataset/train/normal/").listFiles
//val bacteria=new java.io.File("/home/bigdata2/dataset/Coronahack-Chest-XRay-Dataset/Coronahack-Chest-XRay-Dataset/train/bacteria/").listFiles
val virus=new java.io.File("/home/bigdata2/dataset/Coronahack-Chest-XRay-Dataset/Coronahack-Chest-XRay-Dataset/train/virus/").listFiles
/*
Write a helper function to resize each image file to desired width and height
and save the resize image file into desired path
*/
def resizeImage(image:Array[java.io.File],base:String,width:Int,height:Int):Unit=
{
//val width = 300
//val height = 350
for (filePath<-image){
// Load image from disk
var originalImage: BufferedImage = ImageIO.read(new File(filePath.toString))
//var originalImage: BufferedImage = ImageIO.read(new File("/home/bigdata2/dataset/Coronahack-Chest-XRay-Dataset/Coronahack-Chest-XRay-Dataset/train/normal/IM-0419-0001.jpeg"))
// Resize
var resized = originalImage.getScaledInstance(width, height, Image.SCALE_DEFAULT)
// saving image back to disk
var bufferedImage = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB)
bufferedImage.getGraphics.drawImage(resized, 0, 0, null)
//println(base+filePath.toString.split("/").last)
ImageIO.write(bufferedImage, "JPEG", new File(base+filePath.toString.split("/").last))
}
}
//resize the train/normal images to 300*350 and saved into target path
resizeImage(normal,"/mnt/common/20200510/train/normal/",300,350)
//resize the train/virus images to 300*350 and saved into target path
//Get the Image path of the validation image files, both normal and virus
val normalV=new java.io.File("/home/bigdata2/dataset/Coronahack-Chest-XRay-Dataset/Coronahack-Chest-XRay-Dataset/validation/normal/").listFiles
val virusV=new java.io.File("/home/bigdata2/dataset/Coronahack-Chest-XRay-Dataset/Coronahack-Chest-XRay-Dataset/validation/virus/").listFiles
//resize the validation/normal images to 300*350 and saved into target path
resizeImage(normalV,"/mnt/common/20200510/validation/normal/",300,350)
//resize the validation/virus images to 300*350 and saved into target path
resizeImage(virusV,"/mnt/common/20200510/validation/virus/",300,350)

After resizing images to 300*350, the new location of the image files are in /mnt/common/20200510

./
├── train
│   ├── normal
│   └── virus
└── validation
├── normal
└── virus

Algorithm Selection

Image classification is typically by convolutional neural network. I use Tensorflow/Keras. Now I need to switch language from Scala to Python to invoke Keras APIs.

Original Xray image

This is the example of the image before resizing:

from IPython.display import Image
Image(filename='/home/bigdata2/dataset/Coronahack-Chest-XRay-Dataset/Coronahack-Chest-XRay-Dataset/validation/normal/NORMAL2-IM-1423-0001.jpeg')

Resized Xray Image

This is the example of resized image that is label as normal

Image(filename=’/mnt/common/20200510/validation/normal/NORMAL2-IM-1423–0001.jpeg’)

This is the example of resized image that is labeled as pneumonia by virus

Image(filename='/mnt/common/20200510/validation/virus/person1609_virus_2791.jpeg')

Xray CNN image classification by Keras

Following is the code to train the machine to classify Xray Images whether normal or pneumonia by virus by convolutional neural network with Keras and Tensorflow on the background

import keras
from keras.models import Sequential
from keras.layers import Conv2D, MaxPooling2D
from keras.layers import Activation, Dropout, Flatten, Dense
from keras.preprocessing.image import ImageDataGenerator, array_to_img, img_to_array, load_img
#Create a convolutional neural network model
model = Sequential()
model.add(Conv2D(32, (2, 2), input_shape=(300, 350,3)))
model.add(Activation('relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Conv2D(32, (2, 2)))
model.add(Activation('relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Conv2D(64, (2, 2)))
model.add(Activation('relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Flatten())  # converts 3D feature maps to 1D feature vectors
model.add(Dense(64))
model.add(Activation('relu'))
model.add(Dropout(0.5))
model.add(Dense(1))
model.add(Activation('sigmoid'))
# Once the model is created, config the model with losses and metrics with model.compile()
model.compile(loss='binary_crossentropy',
optimizer='rmsprop',
metrics=['accuracy'])
batch_size = 16
# augmentation configuration for training
train_datagen = ImageDataGenerator(
rescale=1./255,
shear_range=0.2,
zoom_range=0.2,
horizontal_flip=True)
train_generator = train_datagen.flow_from_directory(
'/mnt/common/20200510/train/',  # this is the target directory
target_size=(300, 350),  # all images will be resized to 150x150
batch_size=batch_size,
class_mode='binary')  # since we use binary_crossentropy loss, we need binary labels
# Found 2016 images belonging to 2 classes.
# generator for validation data
validation_generator = test_datagen.flow_from_directory(
'/mnt/common/20200510/validation/',
target_size=(300, 350),
batch_size=batch_size,
class_mode='binary')
# Found 670 images belonging to 2 classes.
# Fits the model on data yielded batch-by-batch by a Python generator
model.fit_generator(
train_generator,
steps_per_epoch=2000 // batch_size,
epochs=50,
validation_data=validation_generator,
validation_steps=800 // batch_size)
Epoch 1/50
125/125 [==============================] - 37s 293ms/step - loss: 0.7213 - accuracy: 0.6635 - val_loss: 0.4492 - val_accuracy: 0.8208
Epoch 2/50
125/125 [==============================] - 36s 292ms/step - loss: 0.4976 - accuracy: 0.7735 - val_loss: 0.1604 - val_accuracy: 0.8659
...
Epoch 49/50
125/125 [==============================] - 35s 282ms/step - loss: 0.2251 - accuracy: 0.9320 - val_loss: 0.4890 - val_accuracy: 0.8885
Epoch 50/50
125/125 [==============================] - 36s 284ms/step - loss: 0.2067 - accuracy: 0.9340 - val_loss: 0.5270 - val_accuracy: 0.9261
<keras.callbacks.callbacks.History at 0x7f90917a6ef0>
#Always saving model weights
model.save_weights('/mnt/common/20200510/xray.h5')

Hardware Used:

By the way, the machine that runs this exercise is equipped with Intel 8700 8th gen CPU with 6 cores/12 threads, 64GB RAM and a nvidia GTX 1060 GPU with 6GB GPU memory. Both Tensorflow and Keras are GPU enabled version.

Summary

With not many lines of Python code and a few minutes of processing time, deep learning by CNN (Convolutional Neural Network) using Tensorflow/Keras yield training/validation accuracy of about 93%, which means, out of 100 Xray images, the machine tell whether normal or pneumonia by virus correctly on 93 images and wrong on 7 images.

As always, code used in this writing is in my GitHub repo:

https://github.com/geyungjen/jentekllc

Disclaimer again

This writing is exclusively and entirely for educational purpose in the field of computer science. Only government medical board-certified radiologist can and should perform diagnosis from an Xray image.

Thank you for your time viewing this writing.