Sampling image segmentations with Gaussian process
Project description
gpssi
This repository provides code for the paper:
Lê, Matthieu, et al. "Sampling image segmentations for uncertainty quantification." Medical image analysis 34 (2016): 42-51. doi:10.1016/j.media.2016.04.005
Note that this is not an official implementation by the authors and was motivated by the lack of publicly available code. Be aware that there might be difference to the original implementation.
Implementation Details
Geodesic map
To produce the geodesic maps, this project relies on the GeodisTK packages. This package can be installed via pip or via source code (https://github.com/taigw/GeodisTK). Due to observed issues when installing the package via pip, we suggest to install it from the github link (see installation).
Factorization via Kronecker
The authors use a Kronecker matrix representation of the covariance matrix to overcome the issue of large covariance matrices.
This project implements the kronecker matrix-vector product based on following reference:
- Saatçi, Yunus. Scalable inference for structured Gaussian process models. Diss. University of Cambridge, 2012.
- Gilboa, Elad, Yunus Saatçi, and John P. Cunningham. "Scaling multidimensional inference for structured Gaussian processes." IEEE transactions on pattern analysis and machine intelligence 37.2 (2013): 424-436.
Installation
This projects is available as python package and can be installed by
pip install gpssi
Otherwise, the package can also from the source code via
git clone https://github.com/alainjungo/gpssi.git
cd gpssi
pip install .
The GeodisTK package is not installed automatically and has to be installed manually. We propose to use the direct installation via source code:
pip install git+https://github.com/taigw/GeodisTK.git
Alternatively, you can try installing it from pypi (pip install GeodisTK
)
Usage
See gpssi_example.py for an example usage.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.