Getting Started

  • Follow these instructions to install pyUSID

  • We have compiled a list of handy tutorials on basic / prerequisite topics such as programming in python, hdf5 handling, etc.

  • See our examples to get started on using and writing your own pyUSID functions.

  • Details regarding the definition, implementation, and guidelines for Universal Spectroscopy and Imaging Data (USID) and its implementation in HDF5 (h5USID) are available in this document.

  • If you are interested in contributing your code to pyUSID, please look at our guidelines

  • We also have a handy document for converting your matlab code to python.

  • If you need detailed documentation on what is where and why, all our classes, functions, etc., please visit our API

  • For a concise change-log, please see the release history.

  • Please get in touch if you would like to use USID and pyUSID for other new or mature scientific packages.

  • Have questions? See our FAQ to see if we have already answered them.

  • Need more information? Please see our Arxiv paper.

  • Need help or need to get in touch with us? See our contact information.

Guide for python novices

For the python novices by a python novice - Nick Mostovych, Brown University

  1. Learn about the philosophy, purpose, etc. of pyUSID.

  2. Get an idea of the different resources available by reading the getting started section

  3. Watch the video on installing Anaconda from the Tutorials on Basics page

  4. Follow instructions on the installation page to install Anaconda.

  5. Watch the video tutorial from the Jupyter Notebooks section in the Tutorials on Basics page

  6. Read the whole Tutorial on Basics page. Do NOT proceed unless you are familiar with basic python programming and usage.

  7. Read the document on the USID model and h5USID. This is very important and highlights the advantages of using USID. New users should not jump to the examples until they have a good understanding of the data format.

  8. Depending on your needs, go through the recommended sequence of tutorials and examples

Tips and pitfalls

For the python novices by a python novice - Nick Mostovych, Brown University

  • Documentation and examples on this website are for the latest version of pyUSID. If something does not work as shown on this website, chances are that you may be using an older version of pyUSID. Follow the instructions to update pyUSID to the latest version

  • pyUSID has excellent documentation (+ examples too) for all functions. If you are ever confused with the usage of a function or class, you can get help in numerous ways:

    • If you are using jupyter notebooks, just hit the Shift+Tab keys after typing the name of your function. See this quick video for a demo. E.g. - type px.USIDataset(. Hit Shift+Tab twice or four times. You should be able to see the documentation for the class / function to learn how to supply inputs / extract outputs

    • Use the search function and reference the source code in the API section for detailed comments. Most detailed questions are answered there.

  • Use the USIDataset everywhere possible to simplify your tasks.

  • Many functions in pyUSID have a verbose keyword argument that can be set to True to get detailed print logs of intermediate steps in the function. This is very handy for debugging code

If there are tips or pitfalls you would like to add to this list, please get in touch to us