pygff 1.0.0

A package to read and write Grace Format files (.gff)

PyGFF

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A Python package to read and write Grace Format Files (.gff).

Easiest way to install PyGFF:

pip install pygff

Basic usage:

1. Loading a .gff file:

   from pygff import load
   data = load('image.gff')
   

2. Saving a numpy array np_arr as a .gff file:

   from pygff import GFF, save
   save('image.gff', GFF(np_arr))
   

What is GFF?

GFF is an open source file format for multimodal biomedical images. The format supports datasets with up to five dimensions (three spatial dimensions, time-variant, and multi-channel) and a rich set of metadata key-value pairs. By default, the implementation uses a lossless compression algorithm to reduce file size and cryptographic hashing for secure writing. Multithreading is also used if possible to speed up reading and writing of .gff files.

The PyGFF package is developed by Gremse-IT GmbH (Aachen, Germany) as a Python interface for Imalytics Preclinical 3.0 which utilizes .gff by default for underlay, overlay, segmentation, and project files.

For more details, please check out this publication:

Yamoah, Grace Gyamfuah et al. “Data Curation for Preclinical and Clinical Multimodal Imaging Studies.” Molecular imaging and biology vol. 21,6 (2019): 1034-1043. doi:10.1007/s11307-019-01339-0

Full text: https://pubmed.ncbi.nlm.nih.gov/30868426/

How to build the package yourself:

1. Clone the repository: git clone [e-mail]:felixgremse/gff_file_format.git
2. Make sure you have the Python build package installed: py -m pip install --upgrade build
3. Then, install pygff in editable mode using: py -m pip install -e .

Examples:

Example notebooks can be found in the /examples/ directory of the repository. They are not included with the PyGFF package. We recommed that you to start with 01_load_and_save.ipynb to learn more about loading, saving, and GFF objects. More tutorials will be added in the future.

Running the examples requires the packages jupyter, matplotlib, numpy, and scipy to be installed. Also, please download the required example datasets if you have not cloned the repository yet.

How to run package tests:

1. Go to the ./test/ directory and simply run pytest

License:

The PyGFF package is licensed under the terms of the MIT license.

All .gff files and Jupyter notebooks contained in the /examples/ directory of the repository are licensed under CC BY-NC-SA 4.0.