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This workshop took place on Monday and Tuesday (March 2nd and 3rd) 2020 in Room G53/54 in Diamond House.

Duncan Johnstone (University of Cambridge)
Magnus Nord (EMAT, Antwerp)
Francisco de la Peña (University of Lille)
Eric Prestat (University of Manchester- SuperSTEM)
Paul Quinn (Diamond Light Source)
Thomas Slater (ePSIC - Diamond Light Source)

Table of Contents


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Installation guide- Bundle installation

During the workshop we will have Windows PC workstations prepared with the packages installed and the example notebooks / datasets on disk. We do however encourage the participants to install these packages on their own laptops / workstations and acquaint themselves with the Jupyter Lab environment before the workshop to benefit the most form the presented material.

The easiest way to install hyperspy and other hyperspy extensions (pyxem and atomap) presented in the workshop is to install using the bundles here.

The detailed bundle installation instructions for Windows and MAC can be found through the provided links (courtesy of Eric Prestat).

ParticleSpy is not included in this bundle and should be installed separately following the instructions here.

For this year’s workshop we will be using the bundle above for the workshop workstations.

Installation guide- Conda installation

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. The bundle install is a more rigid package but is guaranteed to work in one step, so it is simpler.

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
    jupyter labextension install @jupyter-widgets/jupyterlab-manager
    conda install -c conda-forge pyxem
    conda install -c conda-forge atomap

ParticleSpy is not included in this bundle and should be installed separately following the instructions here.

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

Code Block
jupyter lab

This would open a Jupyter Lab 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.

Code Block
%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 Lab notebooks, example datasets and presentations available here for download.

Notebooks and Presentations

HyperSpy Talk

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name2020-03-02_HyperSpy_ePSIC workshop.pdf

getting started


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name01 Getting_Started_completed.ipynb


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Introduction to Data Analysis


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Curve Fitting


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name02 Fitting_tutorial_completed.ipynb

Machine Learning

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Big Data & Lazy Signals

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name06 Lazy_completed.ipynb

EELS Analysis

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EDX Data Analysis

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nameSTEM EDX Data Analysis - Workshop.ipynb


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name01 GaAs Nanowire - Data Inspection - Preprocessing - Unsupervised Machine Learning.ipynb


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HyperSpy Community


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