Usage

Installation

Basic Installation

For local installations, the required packages can be installed with pip:

>>> pip install astropy numpy matplotlib
>>> pip install cripser connected-components-3d jax

To install perch from source:

git clone https://github.com/theo-oneill/perch.git
cd perch
pip install -e .

This will install the core dependencies:

  • numpy

  • matplotlib

  • tqdm

  • jax

Perch requires the following external libraries for the PH computation and structure segmentation:

pip install cripser connected-components-3d

  • cripser: Fast C++ library (cubical ripser) for PH computation

  • cc3d (connected-components-3d): Connected components for structure segmentation

Note

cripser is currently pinned to >=0.0.16,<=0.0.24. Newer releases have not yet been validated against perch; the upper bound will be relaxed once compatibility is confirmed.

Optional Dependencies

For additional functionality, install these optional packages:

Astronomical Data Support:

pip install astropy

This enables FITS file I/O and World Coordinate System (WCS) support.

Data Analysis:

pip install pandas scikit-image

  • pandas: Export structures to DataFrame for analysis

  • scikit-image: Advanced geometric property calculations

For detailed workflow and examples, see the Quickstart Guide guide.