Installation

To install as a system library and executable "coresi"

pip install .
# or with the whell
pip install dist/coresi-0.0.X-py3-none-any.whl

Setup python environment

conda env create -f conda-env.yaml
conda activate coresi

CORESI is known to work with pytorch version 2.4.1.

Run

python3 -m coresi.main
# OR if coresi is installed
coresi

CORESI can run on GPU or CPU.

Make use the environment variable CUDA_VISIBLE_DEVICES to tell which GPU PyTorch should use.

The batch_scripts folder contains scripts that can be used to run CoReSi on the CREATIS and Jean Zay clusters.

CUDA_VISIBLE_DEVICES="1" python -m coresi.main

Supported flags:

coresi --help
usage: main.py [-h] [-v] [-c CONFIG] [--sensitivity] [--simulation] [--display]

CORESI - Code for Compton camera image reconstruction (default action)

options:
  -h, --help            show this help message and exit
  -v, --verbose         Enable debug output (default: False)
  -c CONFIG, --config CONFIG
                        Path to the configuration file (default: config.yaml)
  --sensitivity         Compute the sensitivity and quits (default: False)
  --simulation          Do a simulation and quit (default: False)
  --display             Display the reconstructed image after the reconstruction (default: False)

See the config.yaml file for configuring CORESI.

Display an image

python -m coresi.display_image --help
usage: display_image.py [-h] -f FILE [-c CONFIG] [-s SLICE] [-a AXIS] [--cpp | --no-cpp]

CORESI - image display

options:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  File path to the volume to display (default: None)
  -c CONFIG, --config CONFIG
                        Path to the configuration file (default: config.yaml)
  -s SLICE, --slice SLICE
                        Slice number (default: 0)
  -a AXIS, --axis AXIS  Axis x, y or z (default: z)
  --cpp, --no-cpp       Use this if the file comes from the C++ version of CORESI (default: None)

Run tests

make tests

Packaging

python3 -m build

This creates an installable wheel in the dist/ folder.