SETUP.md

Polyp Localization

Polyp localization Using Fully Convolutional Networks

Link to Slack [https://mlmi1819.slack.com/messages/CDSAF4ENA/]

1. Python Setup

Prerequisites:

• Unix system (Linux or MacOS)
• Python version 3
• Integrated development environment (IDE) (e.g. PyCharm or Sublime Text)

which virtualenv

to point to the installed location.

Also, installing with pip should work (the virtualenv executable should be added to your search path automatically):

pip3 install virtualenv

Execute virtualenv -p python3.5 --no-site-packages venv

Basically, this installs a sandboxed Python in the directory .venv. The additional argument ensures that sandboxed packages are used even if they had already been installed globally before.

Whenever you want to use this virtualenv in a shell you have to first activate it by calling:

source .venv/bin/activate

To test whether your virtualenv activation has worked, call:

which python

This should now point to .venv/bin/python.

Installing required packages:

pip3 install -r requirements.txt

2. Tensorflow

(Current release for CPU-only)

pip install tensorflow

pip install tensorboard

GPU package for CUDA-enabled GPU cards

pip install tensorflow-gpu

pip install tensorboard

3. Pytorch

Install pytorch (MAC CPU-only / Linux GPU Cuda 9.0)

pip3 install torch torchvision

Install IPython

pip install Ipython

Install Tensorboard for pytorch

pip3 install tensorboard-pytorch --no-cache-dir