Installation of TomoSuitePY

TomoSuitePY DOES NOT work with RedHat.

Installing Conda Environment To Jupyter

For each environment below please use the following to add each environment to jupyter. While replacing thre environment name with the appropriate name on your computer.

source activate env_tomosuite

# Installing ipykernel so the environment can be used in jupyter
ipython kernel install --user --name=env_tomosuite

# install where you are running your jupyter lab - allows for interactive viewing
jupyter labextension install @jupyter-widgets/jupyterlab-manager itk-jupyter-widgets

Basic Conda Environment

Basics of tomosuite (excluding RIFE, Noise2Noise, TomoGAN, and Deepfill networks).

# Installing basic packages
conda create -n test_basic python=3.6
conda env update -n basic --file /location/to/tomosuitpy/github/clone/envs/basic.yml

source activate basic

# Initilizing env for Jupyter
ipython kernel install --user --name=basic

TomoGAN and Noise2Noise Conda Environment

Install the required packages to be used for TomoGAN, Noise2Noise, and RIFE networks.

# Installing TomoGAN and Noise2Noise packages
conda create -n test_tomogan python=3.6
conda env update -n test_tomogan --file /location/to/tomosuitpy/github/clone/envs/tomogan_n2n.yml

source activate test_tomogan

pip install pandas
pip install pympler
pip install ipykernel

ipython kernel install --user --name=test_tomogan

RIFE Conda Environment

Install the required packages to be used for RIFE networks.

# Installing RIFE packages
conda create -n rife_tomosuitepy python=3.6
conda env update -n rife_tomosuitepy --file /location/to/tomosuitpy/github/clone/envs/rife.yml

source activate rife_tomosuitepy

ipython kernel install --user --name=rife_tomosuitepy

Installing Through (PyPi)

The PyPi package has no dependencies listed. Users must complete the instructions listed above before installing the PyPi version of TomoSuitePY.

source activate conda_env
pip install tomosuitepy