A simple rest api that classifies pneumonia infection weather it is Normal, Pneumonia Virus or Pneumonia Bacteria from a chest-x-ray image.

Last update: Jan 08, 2022

Overview

Pneumonia Classification

This is a simple REST api that is served to classify pneumonia given an X-ray image of a chest of a human being. The following are expected results when the model does it's classification.

pneumonia bacteria
pneumonia virus
normal

Starting the server

To run this server and make prediction on your own images follow the following steps

create a virtual environment and activate it
run the following command to install packages

pip install -r requirements.txt

navigate to the app.py file and run

python app.py

Model

We are using a simple Multi Layer Perceptron (MLP) achitecture to do the categorical image classification on chest-x-ray images which looks simply as follows:

class MLP(nn.Module):
    def __init__(self, input_dim, output_dim, dropout=.5):
        super(MLP, self).__init__()
        self.input_fc = nn.Linear(input_dim, 250)
        self.hidden_fc = nn.Linear(250, 100)
        self.output_fc = nn.Linear(100, output_dim)
        self.dropout = nn.Dropout(dropout)

    def forward(self, x):
        batch_size = x.shape[0]
        x = x.view(batch_size, -1)
        x = F.relu(self.input_fc(x))
        x = self.dropout(x)
        x = F.relu(self.hidden_fc(x))
        x = self.dropout(x)
        outputs = self.output_fc(x)
        return outputs, x

All images are transformed to grayscale.

Model Metrics

The following table shows all the metrics summary we get after training the model for few 10 epochs.

model name	model description	test accuracy	validation accuracy	train accuracy	test loss	validation loss	train loss
chest-x-ray.pt	pneumonia classification using Multi Layer Perceprton (MLP)	73.73%	73.73%	72.47%	0.621	0.621	0.639

Classification report

This classification report is based on the first batch of the test dataset i used which consist of 64 images in a batch.

#	precision	recall	f1-score	support
micro avg	100%	81%	90%	4096
macro avg	100%	81%	90%	4096
weighted avg	100%	81%	90%	4096

Confusion matrix

The following image represents a confusion matrix for the first batch in the validation set which contains 64 images in a batch:

Pneumonia classification

If you hit the server at http://localhost:3001/api/pneumonia you will be able to get the following expected response that is if the request method is POST and you provide the file expected by the server.

Expected Response

The expected response at http://localhost:3001/api/pneumonia with a file image of the right format will yield the following json response to the client.

{
  "predictions": {
    "class_label": "PNEUMONIA VIRAL",
    "label": 2,
    "meta": {
      "description": "given a medical chest-x-ray image of a human being we are going to classify weather a person have pneumonia virus, pneumonia bacteria or none of those(normal).",
      "language": "python",
      "library": "pytorch",
      "main": "computer vision (cv)",
      "programmer": "@crispengari"
    },
    "predictions": [
      {
        "class_label": "NORMAL",
        "label": 0,
        "probability": 0.15000000596046448
      },
      {
        "class_label": "PNEUMONIA BACTERIA",
        "label": 1,
        "probability": 0.10000000149011612
      },
      { "class_label": "PNEUMONIA VIRAL", "label": 2, "probability": 0.75 }
    ],
    "probability": 0.75
  },
  "success": true
}

Using `curl`

Make sure that you have the image named normal.jpeg in the current folder that you are running your cmd otherwise you have to provide an absolute or relative path to the image.

To make a curl POST request at http://localhost:3001/api/pneumonia with the file normal.jpeg we run the following command.

curl -X POST -F [email protected] http://127.0.0.1:3001/api/pneumonia

Using Postman client

To make this request with postman we do it as follows:

Change the request method to POST
Click on form-data
Select type to be file on the KEY attribute
For the KEY type image and select the image you want to predict under value
Click send

If everything went well you will get the following response depending on the face you have selected:

{
  "predictions": {
    "class_label": "NORMAL",
    "label": 0,
    "meta": {
      "description": "given a medical chest-x-ray image of a human being we are going to classify weather a person have pneumonia virus, pneumonia bacteria or none of those(normal).",
      "language": "python",
      "library": "pytorch",
      "main": "computer vision (cv)",
      "programmer": "@crispengari"
    },
    "predictions": [
      {
        "class_label": "NORMAL",
        "label": 0,
        "probability": 0.8500000238418579
      },
      {
        "class_label": "PNEUMONIA BACTERIA",
        "label": 1,
        "probability": 0.07000000029802322
      },
      {
        "class_label": "PNEUMONIA VIRAL",
        "label": 2,
        "probability": 0.07999999821186066
      }
    ],
    "probability": 0.8500000238418579
  },
  "success": true
}

Using JavaScript `fetch` api.

First you need to get the input from html
Create a formData object
make a POST requests

res.json()) .then((data) => console.log(data));">

const input = document.getElementById("input").files[0];
let formData = new FormData();
formData.append("image", input);
fetch("http://127.0.0.1:3001/api/pneumonia", {
  method: "POST",
  body: formData,
})
  .then((res) => res.json())
  .then((data) => console.log(data));

If everything went well you will be able to get expected response.

{
  "predictions": {
    "class_label": "PNEUMONIA VIRAL",
    "label": 2,
    "meta": {
      "description": "given a medical chest-x-ray image of a human being we are going to classify weather a person have pneumonia virus, pneumonia bacteria or none of those(normal).",
      "language": "python",
      "library": "pytorch",
      "main": "computer vision (cv)",
      "programmer": "@crispengari"
    },
    "predictions": [
      {
        "class_label": "NORMAL",
        "label": 0,
        "probability": 0.15000000596046448
      },
      {
        "class_label": "PNEUMONIA BACTERIA",
        "label": 1,
        "probability": 0.10000000149011612
      },
      { "class_label": "PNEUMONIA VIRAL", "label": 2, "probability": 0.75 }
    ],
    "probability": 0.75
  },
  "success": true
}

Notebooks

The ipynb notebook that i used for training the model and saving an .pt file was can be found:

Model Training And Saving

A simple rest api that classifies pneumonia infection weather it is Normal, Pneumonia Virus or Pneumonia Bacteria from a chest-x-ray image.

Related tags

Overview

Pneumonia Classification

Starting the server

Model

Model Metrics

Classification report

Confusion matrix

Pneumonia classification

Expected Response

Using `curl`

Using Postman client

Using JavaScript `fetch` api.

Notebooks

Owner

crispengari

Weight estimation in CT by multi atlas techniques

Dense Prediction Transformers

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Supporting code for the paper "Dangers of Bayesian Model Averaging under Covariate Shift"

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imbalanced-DL: Deep Imbalanced Learning in Python

Code for paper PairRE: Knowledge Graph Embeddings via Paired Relation Vectors.

Which Style Makes Me Attractive? Interpretable Control Discovery and Counterfactual Explanation on StyleGAN

Tutorial on active learning with the Nvidia Transfer Learning Toolkit (TLT).

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Few-Shot Graph Learning for Molecular Property Prediction

BASH - Biomechanical Animated Skinned Human

A simple rest api that classifies pneumonia infection weather it is Normal, Pneumonia Virus or Pneumonia Bacteria from a chest-x-ray image.

Related tags

Overview

Pneumonia Classification

Starting the server

Model

Model Metrics

Classification report

Confusion matrix

Pneumonia classification

Expected Response

Using curl

Using Postman client

Using JavaScript fetch api.

Notebooks

Owner

crispengari

Weight estimation in CT by multi atlas techniques

Dense Prediction Transformers

Template repository for managing machine learning research projects built with PyTorch-Lightning

Supporting code for the paper "Dangers of Bayesian Model Averaging under Covariate Shift"

Heart Arrhythmia Classification

dualFace: Two-Stage Drawing Guidance for Freehand Portrait Sketching (CVMJ)

The code for Expectation-Maximization Attention Networks for Semantic Segmentation (ICCV'2019 Oral)

Paddle-Skeleton-Based-Action-Recognition - DecoupleGCN-DropGraph, ASGCN, AGCN, STGCN

Docker containers of baseline agents for the Crafter environment

imbalanced-DL: Deep Imbalanced Learning in Python

Code for paper PairRE: Knowledge Graph Embeddings via Paired Relation Vectors.

Which Style Makes Me Attractive? Interpretable Control Discovery and Counterfactual Explanation on StyleGAN

Tutorial on active learning with the Nvidia Transfer Learning Toolkit (TLT).

catch-22: CAnonical Time-series CHaracteristics

MetaBalance: High-Performance Neural Networks for Class-Imbalanced Data

scikit-learn inspired API for CRFsuite

Amazing-Python-Scripts - 🚀 Curated collection of Amazing Python scripts from Basics to Advance with automation task scripts.

Large-Scale Pre-training for Person Re-identification with Noisy Labels (LUPerson-NL)

Few-Shot Graph Learning for Molecular Property Prediction

BASH - Biomechanical Animated Skinned Human

Using `curl`

Using JavaScript `fetch` api.