This workshop took place Monday to Friday (May 22nd to 26th) 2023 on Zoom.

Speakers:

Carter Francis (University of Wisconsin-Madison)
Jacob Madsen (University of Vienna)
Kate MacArthur (Oxford Instruments)
Magnus Nord (NTNU, Norway)
Francisco de la Peña (University of Lille)
Eric Prestat (UKAEA)
Stephanie Ribet (LBL)
Thomas Slater (Cardiff University)

Joining also as panellists:

Tara Mishra (LBL)
Steven Zeltmann (Cornell University)

Diamond’s Events Page: https://www.diamond.ac.uk/Home/Events/2023/HyperSpy_2023.html

Agenda

BYOD Session Organiser

If you would like to have a more focussed discussion with one of the Speakers about your own data please express interest via this link:

BYOD_Session.docx

Add to the table your name, a brief description of the type of data analysis and relevant packages, plus links to any existing code / example datasets, if possible. These will then be assigned to Speakers and we will have break-out rooms on Friday’s BYOD session.

Workshop Software Platform

We will be running the workshop on your local python installations [Instructions below]. It is crucial that you check your installation ahead of the week of workshop and if you have any issues to get in touch with us.

Installation guide- Using the bundle (Preferred route!)

You can use this bundle installer to get all the packages needed for the workshop all at once:

https://hyperspy.org/hyperspy-bundle/download.html

For testing the installation, write click on a location on your machine and select Jupyter lab here and open a Python 3 notebook and try importing the packages as below in testing section.

Installation guide- Using Miniforge / Mamba (Potentially not as stable as above)

These instructions are provided to enable you to have your personalised hyperspy (and other packages covered in this workshop) installed on you local machine. Having the installation done through this route allows you to have these packages updated independent of each other, in case there is a new release in future.

Please follow the steps below for the installation:

• Install Python from Mambaforge

• Open a Miniforge terminal. This should look like a regular terminal but with the prompt set to (base)

• Create a new environment by running:
  

  Code Block
  conda create --name hyperspy_env python=3.10

• Activate the above environment by:
  

  Code Block
  WINDOWS: activate hyperspy_env LINUX, macOS: source activate hyperspy_env

  Now your prompt should read: (hyperspy_env)

• Install the packages by running the following commands:

  Code Block
  mamba install hyperspy mamba install abtem nglview mamba install pyxem mamba install atomap mamba install particlespy mamba install jupyterlab notebook ipympl mamba install py4dstem pymatgen

Testing your installation

To test your installation, from the same prompt, run:

jupyter lab

This would open a Jupyter lab launcher in your web browser (You can choose the default browser here). If you have installed using the Bundle you can right click and select Jupyter Lab here! Under Notebook select Python 3 (ipykernel) button to open a new notebook. Copy this code to the first cell and run (press shift + enter). If the installation is correct you should not get any error messages (Note that you may get a Warning about pyOpenCl that can be ignored.).

%matplotlib qt5
import hyperspy.api as hs
import pyxem as pxm
import atomap.api as am
import particlespy.api as ps
import py4DSTEM

Workshop Notebooks and Presentations

We will gradually make the Jupyter notebooks, example datasets and presentations available here to download. In the meantime, we will be updating this github repository:

https://github.com/ePSIC-DLS/Hyperspy_Workshop_2023

Large Data Download links

Link to download Big Data practical.

Link to download py4DSTEM practical demo data.

Slides shared from Speakers

Kate’s EDX talk

Eric’s HyperSpy community talk

Online Resources

HyperSpy webpage - HyperSpy Demos

HyperSpy Gitter chat

Atomap

PyXem - PyXem Demos

ParticleSpy

abTEM

py4DSTEM