malwarebo / carcinet

Basic breast cancer detection using Machine Learning

Cancer Detect

This was a Hackathon project which uses machine learning to detect breast cancer at early stage.

Tools and Setup (Linux)

Install virtual environment

Install pip first

sudo apt-get install python3-pip

Then install virtualenv using pip3

sudo pip3 install virtualenv

Now create a virtual environment

virtualenv venv

you can use any name insted of venv

You can also use a Python interpreter of your choice

virtualenv -p /usr/bin/python3.6 venv

Active your virtual environment:

source venv/bin/activate

Using fish shell:

source venv/bin/activate.fish

To deactivate:

deactivate

Create virtualenv using Python3

virtualenv -p python3 myenv

Instead of using virtualenv you can use this command in Python3

python3 -m venv myenv

Installation without sudo

curl https://bootstrap.pypa.io/get-pip.py | python3.6 - --user

This may sometimes give a warning such as:

WARNING: The script wheel is installed in '/home/ubuntu/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

Verification

After this, pip, pip3, and pip3.6 can all be expected to point to the same target:

$ (pip -V && pip3 -V && pip3.6 -V) | uniq pip 18.0 from /usr/local/lib/python3.6/dist-packages (python 3.6)

Of course you can alternatively use python3.6 -m pip as well.

$ python3.6 -m pip -V pip 18.0 from /usr/local/lib/python3.6/dist-packages (python 3.6)

Install virtualenvwrapper

pip3.6 install virtualenvwrapper

Working!!

python3.6 -m virtualenv venv

Install Tensorflow

$ pip install --upgrade tensorflow $ pip install numpy scipy $ pip install scikit-learn $ pip install pillow $ pip install h5py $ pip install keras

sudo apt-get install python-scipy or sudo pip3.6 install scipy --upgrade

Install other tools

$ pip install numpy opencv-contrib-python $ pip install pillow $ pip install tensorflow keras $ pip install imutils $ pip install scikit-learn matplotlib

Configuration

Inside the src config.py change the path for ORIG_INPUT_DATASET and BASE_PATH to the directories where you have stored the image data. I recommened putting the images in datasets/orig and datasets/idc.