UMPIRE

Implementation of the UMPIRE algorithm from the following paper:

Simon Robinson, Horst Schödl, Siegfried Trattnig, 2014 July, "A method for unwrapping highly wrapped multi-echo phase images at very high field: UMPIRE", Magnetic Resonance in Medicine, 72(1):80-92 DOI: 10.1002/mrm.24897

How to use UMPIRE

Check out the jupyter notebooks inside the notebooks folder for some help on how to use this module!

Installation

Depending on wether you want to only use or also contribute to the package, choose the appropriate installation.

Usage

$ git clone https://github.com/DiracKeteering/UMPIRE.git

$ cd UMPIRE

$ pip install -e .

Development

$ git clone https://github.com/DiracKeteering/UMPIRE.git

$ cd UMPIRE

$ pip install -e ".[dev]"

Adding Dependencies

All package handling is done inside the pyproject.toml file. Here are the steps necessary to add dependencies to the package:

0. Before adding a dependency to the package, make sure it is compatible! (See Tox!)

1. Open the file pyproject.toml and go to [project]. Then, add the dependency inside the dependencies-list. You can use the syntax listed here to specify the dependencies.

2. Use the pip-tools command to compile dependencies files:

• Generate usage dependencies file:

$ pip-compile --output-file=requirements.txt --resolver=backtracking

• Generate development dependencies file:

$ pip-compile --extra=dev --output-file=dev-requirements.txt --resolver=backtracking pyproject.toml