Use Chest X-rays Images in Azure Machine Learning Studio to predict Covid-19 and deploy a web service to Azure Kubernetes Service (AKS).

In addition, consume the model to predict through Microsoft Power Apps.

In this lab, I will walk you through on how to apply machine learning to predict COVID-19 cases from chest X-rays. By following the steps in this lab, you will be able to understand get started. I am hoping to reach individuals who are able to contribute their skills to this effort.

You can use this url to try it out Covid Chestxray image upload web service

Reference Architecture

Deploy Required Resources

Click the below button to upload the provided ARM template to the Azure portal, which is written to automatically deploy and configure the following resources:

An Azure Machine Learning Workspace set to Basic
Azure Key Vault
Application Insights
Storage Account (general purpose v2) with LRS (Locally-redundant storage)
Container Registry
Kubernetes Services

Dataset

Using AML to create a new .ipynb and train a model:

Before you begin make sure to create a folder called "data" with subfolders "covid & Normal" and upload all the images from the dataeset folder from this Github repo.

Import Python libraries

import warnings
warnings.filterwarnings("ignore") 

import os
import math
from PIL import Image
import seaborn as sns
from mlxtend.plotting import plot_confusion_matrix
from sklearn.model_selection import train_test_split
from sklearn.metrics import classification_report, confusion_matrix
import numpy as np
import pandas as pd
import cv2
import glob
import matplotlib.pyplot as plt

Loading Covid X-ray Images

dataset_folder = 'project/dataset/covid/'

Some random Images Covid X-ray

image_id = '1-s2.0-S1684118220300682-main.pdf-003-b2.png'
img_data = Image.open(dataset_folder + image_id)
img_data

image_id = '03BF7561-A9BA-4C3C-B8A0-D3E585F73F3C.jpeg'
img_data = Image.open(dataset_folder + image_id)
img_data

image_id = '6C94A287-C059-46A0-8600-AFB95F4727B7.jpeg'
img_data = Image.open(dataset_folder + image_id)
img_data

image_id = '16660_1_1.jpg'
img_data = Image.open(dataset_folder + image_id)
img_data

Loading Covid dataset all images and reshaping into 300*300 because all images have different sizes

Images=[]
Covid_data = 'project/dataset/covid/'

for img in os.listdir(Covid_data):
    img_array = cv2.imread(os.path.join(Covid_data,img), cv2.IMREAD_GRAYSCALE)
    img_pil = Image.fromarray(img_array)
    img_300x300 = np.array(img_pil.resize((300, 300), Image.ANTIALIAS))
    img_array = (img_300x300.flatten())
    img_array  = img_array.reshape(-1,1).T
    with open('Covid_Images.csv', 'ab') as f:
        np.savetxt(f, img_array, delimiter=",")

Loading Covid images data in csv file that we saved above

Covid_data = pd.read_csv('Covid_Images.csv', header=None)

Covid_data

Data Analysis and Preprocessing

First five records

Covid_data.head()

last five records

Covid_data.tail()

Lenght of data

len(Covid_data)

Data information

Covid_data.info()

Giving class 0 to Covid images

Covid_data['class']=0
Covid_data_X=Covid_data.drop(columns=['class'])
Covid_data_y=Covid_data['class']

Rescalling the pixel values in the range of 0 and 1

Covid_data_X=Covid_data_X/255
Covid_data_X=np.array(Covid_data_X)
Covid_data_y=np.array(Covid_data_y)
print(Covid_data_X.shape)
Covid_data_y.shape

Loading Covid data

dataset_folder = 'project/dataset/Normal/'

Some random Images of NORMAL X-ray Images

image_id = 'IM-0115-0001.jpeg'
img_data = Image.open(dataset_folder + image_id)
img_data

image_id = 'IM-0168-0001.jpeg'
img_data = Image.open(dataset_folder + image_id)
img_data

image_id = 'IM-0187-0001.jpeg'
img_data = Image.open(dataset_folder + image_id)
img_data

image_id = 'IM-0207-0001.jpeg'
img_data = Image.open(dataset_folder + image_id)
img_data

Loading Normal dataset all images and reshaping into 300*300 because all images have different sizes

Images=[]
Normal_data = 'project/dataset/Normal/'

for img in os.listdir(Normal_data):
    img_array = cv2.imread(os.path.join(Normal_data,img), cv2.IMREAD_GRAYSCALE)
    img_pil = Image.fromarray(img_array)
    img_300x300 = np.array(img_pil.resize((300, 300), Image.ANTIALIAS))
    img_array = (img_300x300.flatten())
    img_array  = img_array.reshape(-1,1).T
    with open('Normal_Images.csv', 'ab') as f:
        np.savetxt(f, img_array, delimiter=",")

Loading Normal images data in csv file that we saved aboved

Normal_data = pd.read_csv('Normal_Images.csv', header=None)

Data Analysis and Preprocessing

First five records

Normal_data.head()

last five records

Normal_data.tail()

Lenght of data

len(Normal_data)

Data information

Normal_data.info()

Giving class 1 to Normal images

Normal_data['class']=1
Normal_data_X=Normal_data.drop(columns=['class'])
Normal_data_y=Normal_data['class']

Rescalling the pixel values in the range of 0 and 1

Normal_data_X=Normal_data_X/255
Normal_data_X=np.array(Normal_data_X)
Normal_data_y=np.array(Normal_data_y)
print(Normal_data_X.shape)
Normal_data_y.shape

Combining the Covid and Normal images data

X=np.concatenate((Covid_data_X,Normal_data_X), axis=0)
y=np.concatenate((Covid_data_y,Normal_data_y), axis=0)
print("The Feature data has the shape ", X.shape)
print("The Label data has the shape ", y.shape)
unique, counts = np.unique(y, return_counts=True)
plt.figure(figsize=(8,6))
sns.barplot(x=unique, y=counts)
plt.title('Counts of X-ray images of Covid and Normal')
plt.ylabel('Count')
plt.xlabel('Class (0:Covid, 1:Normal)')

Spliting Dataset into 70% Training and 30% Testing

from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.30, random_state=2)

SVM Support Vector Machine Algorithm

from sklearn.svm import LinearSVC

svc=LinearSVC(C=1, max_iter=500)
svc= svc.fit(X_train , y_train)
svc

Accuracy

y_pred1 = svc.predict(X_test)
dm=svc.score(X_test, y_test)
print('Accuracy score= {:.2f}'.format(svc.score(X_test, y_test)))

Precision, Recall, F1

from sklearn.metrics import classification_report, confusion_matrix


print('\n')
print("Precision, Recall, F1")
print('\n')
CR=classification_report(y_test, y_pred1)
print(CR)
print('\n')

Confusion Matrix

from sklearn.metrics import classification_report, confusion_matrix
from mlxtend.plotting import plot_confusion_matrix


print('\n')
print("confusion matrix")
print('\n')
CR=confusion_matrix(y_test, y_pred1)
print(CR)
print('\n')

fig, ax = plot_confusion_matrix(conf_mat=CR,figsize=(10, 10),
                                show_absolute=True,
                                show_normed=True,
                                colorbar=True)
plt.show()

Graph comparison of predictions and true

y_pred = svc.predict(X_test)
a=pd.DataFrame()
a['true']=y_test
a['predictions']=y_pred

plt.figure(figsize=(25, 10))
plt.subplot(1,1,1)
plt.plot(a.true.values,color='red',label='True Cases')
plt.plot(a.predictions.values,color='green',label='Predictions')

plt.title('Comparison of true and predictions')
plt.xlabel('Counts of images')
plt.ylabel('Class as 0 cobid or 1 as normal')
plt.legend(bbox_to_anchor=(1, 1))
plt.show()

Random Forest Algorithm

from sklearn.ensemble import RandomForestClassifier

raf=RandomForestClassifier(min_samples_leaf=20, min_samples_split=20,random_state=100)
raf= raf.fit(X_train , y_train)
raf

Accuracy

y_pred1 = raf.predict(X_test)
rf=raf.score(X_test, y_test)
print('Accuracy score= {:.2f}'.format(raf.score(X_test, y_test)))

Precision, Recall, F1

from sklearn.metrics import classification_report, confusion_matrix


print('\n')
print("Precision, Recall, F1")
print('\n')
CR=classification_report(y_test, y_pred1)
print(CR)
print('\n')

Confusion Matrix

from sklearn.metrics import classification_report, confusion_matrix
from mlxtend.plotting import plot_confusion_matrix


print('\n')
print("confusion matrix")
print('\n')
CR=confusion_matrix(y_test, y_pred1)
print(CR)
print('\n')

fig, ax = plot_confusion_matrix(conf_mat=CR,figsize=(10, 10),
                                show_absolute=True,
                                show_normed=True,
                                colorbar=True)
plt.show()

Comparison of all algorithms Results

pip install PrettyTable
from prettytable import PrettyTable
x = PrettyTableprg()
print('\n')
print("Comparison of all algorithm results")
x.field_names = ["Model", "Accuracy"]


x.add_row(["SVM Algorithm", round(dm,2)])
x.add_row(["Random Forest Algorithm", round(rf,2)])

print(x)
print('\n')

Best Model is SVM algorithm with higest accuracy

x = PrettyTable()
print('\n')
print("Best Model.")
x.field_names = ["Model", "Accuracy"]
x.add_row(["SVM",round(dm,2)])
print(x)
print('\n')

Now, as we know SVM working good so going to train on all data

svc=LinearSVC(C=1, max_iter=500)
svc= svc.fit(X , y)
svc

Saving Trained model

import pickle

Train_model='Trained_model'
with open(Train_model, 'wb') as file:
    pickle.dump(svc, file)

Loading saved model

import pickle
Train_model='Trained_model'
with open(Train_model, 'rb') as file:
    Train_model_loaded = pickle.load(file)

Loading X-ray image from X_ray_Image_for_prediction

Images=[]
data = 'project/X_ray_Image_for_prediction/'

for img in os.listdir(data):
    img_array = cv2.imread(os.path.join(data,img), cv2.IMREAD_GRAYSCALE)
    img_pil = Image.fromarray(img_array)
    img_300x300 = np.array(img_pil.resize((300, 300), Image.ANTIALIAS))
    img_array = (img_300x300.flatten())
    img_array  = img_array.reshape(-1,1).T
img_array.shape

The image is from the Covid x-ray so the model should predict Covid as well

from IPython.display import display
from PIL import Image
covid="project/covid.jpg"
healthy="project/healthy.jpg"
aa=Train_model_loaded.predict(img_array)
if aa==0:
    print("Covid X-ray")
    display(Image.open(covid))
else:
    print("Normal X-ray")
    display(Image.open(healthy))

Deploying a web service to Azure Kubernetes Service (AKS)

Step 1:- Create an Azure Machine Learning workspace

Sign in to the Azure portal by using the credentials for your Azure subscription.
In the upper-left corner of Azure portal, select + Create a resource.
Use the search bar to find Machine Learning.
Select Machine Learning.
In the Machine Learning pane, select Create to begin.
Provide the required information to configure your new workspace

Step 2: Create a notebook

After creation of Azure Machine learning workspace, now open the azure ML workspace and go to the “compute” section and create new instances of compute. Now launch the studio, and go to the “New” section for creation of the notebook and type the name of the notebook and select the file type as Notebook. Gave name as “CovidXrayNote.ipynb”

Step 3: Upload the Data in zip format

Go to the root folder of your user or project, click the upload icon and select the zip file of data for using your project. Now open your notebook, which we have created already and provide the script for the extraing the zip file into the required path.

Import zipfile
import os
datafile = "CovidXRAY Dataset.zip"
datafile_dbfs = os.path.join("/Data/" + mountname, datafile)

print ("unzipping takes approximatelly 2 minutes")
zip_ref = zipfile.ZipFile(datafile_dbfs, 'r')
zip_ref.extractall("/Data/" + mountname)
zip_ref.close()

Step 4: Import the libraries(CovidXrayNote.ipynb)

Import the required libraries. CovidXrayNote file is used to train and test the model classification of images. And check the accuracy of the model.

Step 5: Get the workspace(DeployNotebook.ipynb)

This file is used to deploy the model in AKS service. Import the libraries. Load existing workspace

ws = Workspace.from_config()
print(ws.name, ws.resource_group, ws.location, ws.subscription_id, sep='\n')
ws.write_config()
ws.get_details()

Step 6: Register the model

## AKS Model Registration 
from azureml.core.model import Model
aksmodel = Model.register(model_path = '/mnt/batch/tasks/shared/LS_root/mounts/clusters/mlcovidcompute/code/Users/harash/Trained_model', # this points to a local file
                       model_name = "aks_covid.pkl", # this is the name the model is registered as
                       tags = {'area': "covid", 'type': "classification"},
                       description = "covid xray",
                       workspace = ws)

print(aksmodel.name, aksmodel.description, aksmodel.version)

Step 7: Create the Environment

Create an environment that the model will be deployed with

#custom Deployment Environment
from azureml.core import Environment
from azureml.core.conda_dependencies import CondaDependencies


environment = Environment('covid-environment')
environment.python.conda_dependencies = CondaDependencies.create(pip_packages=[
    'azureml-defaults',
    'inference-schema[numpy-support]',
    'joblib',
    'numpy',
    'scikit-learn',
    'Pillow',
    'scikit-image==0.15.0',
    'opencv-python==4.2.0.34'
])

Step 8: Write the Entry script(score.py)

Write the script that will be used to predict on your model Now, create a locally “score.py” file and paste the below code and save it. Go to current project or user folder and upload the score.py file in azure workspace.

import json
import joblib
from azureml.core.model import Model
import os
import PIL
from PIL import Image
import numpy as np
import pandas as pd
#import cv2
import flask
import pickle
import werkzeug
from werkzeug.utils import secure_filename
from skimage import io
import requests
from io import BytesIO
import azureml.core
from azureml.core import Workspace

# Called when the service is loaded
print('get dir',os.getcwd())

def init():
    global model
    print(os.getcwd())
    # Get the path to the registered model file and load it
    model_path = Model.get_model_path('covid-xray-model')
    model = joblib.load(model_path)

    # Called when a request is received
def run(url):
    # Get the input data as a numpy array
    img_array = io.imread(url, as_grey=True)
    img_pil = Image.fromarray(img_array)
    img_300x300 = np.array(img_pil.resize((300, 300), Image.ANTIALIAS))
    img_array = (img_300x300.flatten())
    img_array = img_array.reshape(-1, 1).T

    predictions = model.predict(img_array)
    # Return the predictions as any JSON serializable format
    return predictions.tolist()

Step 9: Create the inferenceConfig

Create the inference config that will be used when deploying the model

#inferenceConfig
from azureml.core.model import InferenceConfig
from azureml.core.compute import AksCompute, ComputeTarget
from azureml.core.webservice import Webservice, AksWebservice

inference_config = InferenceConfig(entry_script='./score.py', environment=environment)
#inf_config = InferenceConfig(entry_script='./score.py', environment=environment)

Step 10: AKS Cluster

This is a one time setup. You can reuse this cluster for multiple deployments after it has been created. If you delete the cluster or the resource group that contains it, then you would have to recreate it.

# Use the default configuration (can also provide parameters to customize)
prov_config = AksCompute.provisioning_configuration()

aks_name = 'covid-xray-aks1' 
# Create the cluster
aks_target = ComputeTarget.create(workspace = ws, 
                                  name = aks_name, 
                                  provisioning_configuration = prov_config)

Step 11: Deploy web service to AKS

## Deploy Script
# Set the web service configuration (using default here)
aks_config = AksWebservice.deploy_configuration()

# # Enable token auth and disable (key) auth on the webservice
# aks_config = AksWebservice.deploy_configuration(token_auth_enabled=True, auth_enabled=False)

#%%time
aks_service_name ='aks-covid-service1'

aks_service = Model.deploy(workspace=ws,
                           name=aks_service_name,
                           models=[model],
                           inference_config=inference_config,
                           deployment_config=aks_config,
                           deployment_target=aks_target)

aks_service.wait_for_deployment(show_output = True)
print(aks_service.state)


Get the aks service URL and Keys

print(aks_service.scoring_uri)

key1, Key2 = aks_service.get_keys()
print(key1)

Step 12: Test the web service(ClientService.ipynb)

import requests

import json
url ='https://qnacovdi19app-bot.azurewebsites.net/image/Normal.jpeg'
url_c ='https://qnacovdi19app-bot.azurewebsites.net/image/Covid.png'

endpoint_aks ='http://52.148.194.176:80/api/v1/service/aks-covid-service1/score'
key1 ='egfG7b8is01WqgDdCvaN0eKohbluGr7y'

# # If (key) auth is enabled, don't forget to add key to the HTTP header.
headers = {'Content-Type':'application/json', 'Authorization': 'Bearer ' + key1}

# # If token auth is enabled, don't forget to add token to the HTTP header.
# headers = {'Content-Type':'application/json', 'Authorization': 'Bearer ' + access_token}

resp = requests.post(endpoint_aks, url_c, headers=headers)
res =''
respose =resp.text
respose = respose.replace('[','').replace(']','')
if (respose == '1'):
    res ='Normal'
else:
    res ='Covid'


print("prediction:", res)

Limitations and Considerations

This is a demo to showcase the capabiliites of Azure machine learning and AKS. It is not intended to be a framework or scalable architecture for all scenarios, though it can give you an idea of what your scenario might end up looking like.

haroon921 / x-raypredictioncovid-19 Goto Github PK

x-raypredictioncovid-19's Introduction

Use Chest X-rays Images in Azure Machine Learning Studio to predict Covid-19 and deploy a web service to Azure Kubernetes Service (AKS).

In addition, consume the model to predict through Microsoft Power Apps.

Reference Architecture

Deploy Required Resources

Dataset

Using AML to create a new .ipynb and train a model:

Import Python libraries

Loading Covid X-ray Images

Some random Images Covid X-ray

Loading Covid dataset all images and reshaping into 300*300 because all images have different sizes

Loading Covid images data in csv file that we saved above

Data Analysis and Preprocessing

First five records

last five records

Lenght of data

Data information

Giving class 0 to Covid images

Rescalling the pixel values in the range of 0 and 1

Loading Covid data

Some random Images of NORMAL X-ray Images

Loading Normal dataset all images and reshaping into 300*300 because all images have different sizes

Loading Normal images data in csv file that we saved aboved

Data Analysis and Preprocessing

First five records

last five records

Lenght of data

Data information

Giving class 1 to Normal images

Rescalling the pixel values in the range of 0 and 1

Combining the Covid and Normal images data

Spliting Dataset into 70% Training and 30% Testing

SVM Support Vector Machine Algorithm

Accuracy

Precision, Recall, F1

Confusion Matrix

Graph comparison of predictions and true

Random Forest Algorithm

Accuracy

Precision, Recall, F1

Confusion Matrix

Comparison of all algorithms Results

Best Model is SVM algorithm with higest accuracy

Now, as we know SVM working good so going to train on all data

Saving Trained model

Loading saved model

Loading X-ray image from X_ray_Image_for_prediction

The image is from the Covid x-ray so the model should predict Covid as well

Deploying a web service to Azure Kubernetes Service (AKS)

Step 1:- Create an Azure Machine Learning workspace

Step 2: Create a notebook

Step 3: Upload the Data in zip format

Step 4: Import the libraries(CovidXrayNote.ipynb)

Step 5: Get the workspace(DeployNotebook.ipynb)

Step 6: Register the model

Step 7: Create the Environment

Step 8: Write the Entry script(score.py)

Step 9: Create the inferenceConfig

Step 10: AKS Cluster

Step 11: Deploy web service to AKS

Step 12: Test the web service(ClientService.ipynb)

Limitations and Considerations

Further reading

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