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This workshop will take 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

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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: 

    conda create --name hyperspy_env python=3.7

  • Activate the above environment by:

    WINDOWS: activate hyperspy_env
LINUX, macOS: source activate hyperspy_env

  • Install the packages by running the following commands:

    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 ipympl
python -m ipykernel install --user --name=hyperspy_env

Please note that given the number of participants in this year’s workshop we may not be able to provide technical support for local installations.

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

HyperSpy Talk

getting started

notebook:

talk:

Introduction to Data Analysis

talk:

Curve Fitting

notebook

Machine Learning

Big Data & Lazy Signals

EELS Analysis

EDX Data Analysis

PyXem

ParticleSpy

HyperSpy Community

talk

Online Resources

HyperSpy webpage - HyperSpy Demos

HyperSpy Gitter chat

Atomap

PyXem - PyXem Demos

ParticleSpy

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