pycemrg-image-analysis

A high-level framework for cardiac image segmentation post-processing and model creation, built on SimpleITK. Maintained by the Cardiac Electromechanics Research Group (CEMRG) at Imperial College London.

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Installation

This library depends on pycemrg, which provides the core label management and configuration scaffolding utilities. Both packages should be installed together.

1. Clone both repositories

git clone https://github.com/OpenHeartDevelopers/pycemrg.git
git clone https://github.com/OpenHeartDevelopers/pycemrg-image-analysis.git

2. Create and activate a virtual environment

Preferred: Conda

conda create -n pycemrg-image-analysis python=3.10 -y 
conda activate pycemrg-image-analysis

Or via python's venv

python -m venv .venv
source .venv/bin/activate   # on Windows: .venv\Scripts\activate

3. Install both packages in editable mode

Install pycemrg first, then pycemrg-image-analysis:

pip install -e pycemrg/
pip install -e pycemrg-image-analysis/

Why editable (-e)? Editable installs link directly to the source tree so changes to either package take effect immediately without reinstalling.

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Running the tests

# Unit tests (no data required)
pytest pycemrg-image-analysis/tests/unit/

# Integration tests (requires segmentation data)
PYCEMRG_TEST_DATA_ROOT=/path/to/your/data pytest pycemrg-image-analysis/tests/integration/

# All tests
pytest pycemrg-image-analysis/

Integration tests are skipped automatically when PYCEMRG_TEST_DATA_ROOT is not set.

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Requirements

• Python ≥ 3.10
• SimpleITK ≥ 2.4.0
• pycemrg ≥ 0.1.0 (see above)

All other dependencies are declared in pyproject.toml and installed automatically by pip.