pyUSID

Python framework for storing and processing scientific data formatted according to the USID model

Attention

If your data has a clear N-dimensional form, consider using NSID and pyNSID as simpler and more user-friendly alternatives to USID and pyUSID.

  • The Universal Spectroscopic and Imaging Data (USID) model:

    • facilitates the representation of any spectroscopic or imaging data regardless of its origin, modality, size, or dimensionality.

    • enables the development of instrument- and modality- agnostic data processing and analysis algorithms.

    • is just a definition or a blueprint rather than something tangible and readily usable.

  • pyUSID is a python package that currently provides two pieces of functionality:

    1. io: Primarily, it enables the storage and access of USID in hierarchical data format (HDF5) files (referred to as h5USID files) using python

    2. processing: It provides a framework for formulating scientific problems into computational problems. See pycroscopy - a sister project that uses pyUSID for analysis of microscopy data.

  • pyUSID uses a data-centric approach wherein the raw data collected from the instrument, results from analysis and processing routines can all written to the same h5USID file for traceability and reproducibility.

  • Just as scipy uses numpy underneath, scientific packages like pycroscopy use pyUSID for all file-handling, data processing, and generating plots for journal publications

  • pyUSID uses popular packages such as numpy, h5py, joblib, matplotlib, etc. for most of the storage, computation, and visualization.

  • For more information, please see our recent Arxiv paper

  • See a high-level overview of pyUSID in this presentation

  • Jump to our GitHub project

  • While pyUSID was originally a part of pycroscopy up to 2017, it has since been serving as an independent, science-agnostic data handling package. pyUSID was born so that it can integrate with other existing mature packages in any domain. If you are interested in integrating our data model with your existing package, please get in touch with us.

  • Note - As of 2020, pyUSID has transitioned to maintenance mode.