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This workshop took place Monday to Friday (April 19th to 23rd) 2021 on Zoom.

Speakers:
Phillip Crout (University of Cambridge)
Magnus Nord (NTNU, Norway)
Francisco de la Peña (University of Lille)
Eric Prestat (University of Manchester- SuperSTEM)
Timothy Poon (Diamond Light Source)
Thomas Slater (ePSIC - Diamond Light Source)

Agenda

Workshop Software Platform

We will be running the workshop on Google Cloud Platform. Please visit the following link:

https://groups.google.com/g/epsic-hyperspy-workshop-2021

and request to join this Google Group (you will need a Google account to join). This would then give you access to the cluster on GCP. Once you start the server, you will have to clone a github repository that contains all the notebooks for the workshop. The data required for the workshop should appear on your /home directory from the start.

For Q&A both before and during the workshop we will be running a Slack channel.

Installation guide- Conda installation

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 3.7 from Anaconda

• Open an Anaconda Prompt Terminal and create a new environment by running:
  

  Code Block
  conda create --name hyperspy_env python=3.7

• Activate the above environment by:
  

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

• Install the packages by running the following commands:

  Code Block
  conda install hyperspy -c conda-forge conda install -c conda-forge pyxem conda install -c conda-forge atomap conda install -c conda-forge particlespy conda install -c conda-forge jupyterlab conda install -c conda-forge notebook conda install -c conda-forge ipympl python -m ipykernel install --user --name=hyperspy_env

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

jupyter notebook

This would open a Jupyter notebook launcher in your web browser. Under Notebook select Python 3 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

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_2021.git

Notebooks and Presentations

Notebooks can ge accessed here: https://github.com/ePSIC-DLS/Hyperspy_Workshop_2021

HyperSpy Talk

Curve Fitting

Machine Learning

EDX Data Analysis

HyperSpy Community

Online Resources

HyperSpy webpage - HyperSpy Demos

HyperSpy Gitter chat

Atomap

PyXem - PyXem Demos

ParticleSpy