Pneumonia_Classifier/How_To_Run.txt at master · rmcnew/Pneumonia_Classifier · GitHub

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Pneumonia_Classifier was developed using Python 3.5.3 on Linux.

It should be able to run under on other platforms that support Python
3, but it has not been tested exhaustively.

These instructions assume that you have little to no Python
background, but should enable you to get the Pneumonia_Classifier
running.

0.  Download zip or 'git clone' Pneumonia_Classifier from GitHub.

Go to 'https://github.com/rmcnew/Pneumonia_Classifier' and click the
"Clone or Download" button and then click download Zip.  Unzip the
resulting file.

OR

If you have git installed, run 'git clone https://github.com/rmcnew/Pneumonia_Classifier.git'

1.  Install Python 3 on your platform.

If you are using Linux or macOS, there's a good chance that you might
have Python already installed.  Open a terminal and try running
"python3 --version".  If you are on another platform, point your web
browser to https://www.python.org, download the latest release for
your platform and follow the installation instructions for your
platform.

2.  Install virtualenv.

virtualenv is a localized Python package management system that allows
Python packages to be installed locally for Python projects.  Follow
the virtualenv installation instructions at

https://packaging.python.org/guides/installing-using-pip-and-virtualenv/

3.  Create a virtualenv environment

In the Pneumonia_Classifier directory from step 0, run the following
command:

python3 -m venv .venv

This will create an empty virtualenv environment in the ".venv"
directory.  This allows the Pneumonia_Classifier Python requirements
to be installed locally.

4.  Activate the virtualenv environment

In the Pneumonia_Classifier directory, run the following command:

source .venv/bin/activate

This should prepend "(.venv)" to your shell prompt, letting you know
that you are in the virtualenv.

5.  Install Python requirements

While inside the virtualenv environment and in the
Pneumonia_Classifier directory, run the following command:

pip install -r requirements.txt

This will install the Python packages needed to run
Pneumonia_Classifer in the virtualenv.

6.  Run Pneumonia_Classifer scripts (note that you will need a machine
with 16 GB RAM or more for the scripts to run in a reasonable amount
of time).

python pneumonia_classifier.py

will run the current main function of pneumonia_classifier.py.  By
default this will run the pneumonia_classifier_model.m5 against the
Validate dataset subset.  You can edit the last few lines of
pneumonia_classifier.py to change what action is performed.  This
includes: 1) Training the model from scratch, 2) Training the current
model more, 3) Running the pneumonia_classifier_model.m5 against the
Test dataset subset, and 4) Running the pneumonia_classifier_model.m5
against the Validate dataset subset.

python predict_xray.py XRAY_IMAGE_FILE

where XRAY_IMAGE_FILE is an arbitrary chest X-ray image file.  This
will run the pneumonia_classifier_model.m5 against the XRAY_IMAGE_FILE
that you provide.  You can use X-ray images from the Validate dataset
subset that are found in the dataset/validate directories.  For
example:

python predict_xray.py ./dataset/validate/NORMAL/NORMAL2-IM-1431-0001.jpeg

OR

python predict_xray.py ./dataset/validate/PNEUMONIA/person1949_bacteria_4880.jpeg


Images that are not part of the dataset should also work.  Some sample
chest X-ray images are in the other_xrays directory.