Installation and test

  1. Add conda-forge to anaconda channels

(base)$ conda config --add channels conda-forge

  1. Create environment with installed tomocupy

(base)$ conda create -n tomocupy tomocupy

  1. Activate tomocupy environment

(base)$ conda activate tomocupy

  1. Test installation

(tomocupy)$ tomocupy recon -h

Installation for development

  1. Add conda-forge to anaconda channels

(base)$ conda config --add channels conda-forge

  1. Create environment with necessary dependencies

(base)$ conda create -n tomocupy -c conda-forge cupy scikit-build swig pywavelets numexpr opencv tifffile h5py python=3.9

Warning

Conda has a built-in mechanism to determine and install the latest version of cudatoolkit supported by your driver. However, if for any reason you need to force-install a particular CUDA version (say 11.0), you can do:

conda install -c conda-forge cupy cudatoolkit=11.0

  1. Activate tomocupy environment

(base)$ conda activate tomocupy

4*. (If needed) Install meta for supporting hdf meta data writer used by option: –save-format h5

(tomocupy)$ git clone https://github.com/xray-imaging/meta.git
(tomocupy)$ cd meta
(tomocupy)$ pip install .
(tomocupy)$ cd -

  1. Make sure that the path to nvcc compiler is set (or set it by e.g. ‘export CUDACXX=/local/cuda-11.7/bin/nvcc’) and install tomocupy

(tomocupy)$ git clone https://github.com/tomography/tomocupy
(tomocupy)$ cd tomocupy
(tomocupy)$ pip install .

Unit tests

Check the library path to cuda or set it by ‘export LD_LIBRARY_PATH=/local/cuda-11.7/lib64’

Run the following to check all functionality

(tomocupy)$ cd tests; bash test_all.sh

Update

tomocupy is constantly updated to include new features. To update your locally installed version

(tomocupy)$ cd tomocupy
(tomocupy)$ git pull
(tomocupy)$ pip install .