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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)
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Agenda
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Workshop Software Platform
We will be running the workshop on Google Cloud Platform. You will receive an invitation to join a Google Group (you will need a Google account to join) which 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 you will need required for the workshop should appear on your /home directory from the start.
Known issues:
With the widget backends, attempting to plot an hs object I just get the buttons on the LHS with no plot showing - And the cell remains busy.
Sometimes getting error:
The set_window_title function was deprecated in Matplotlib 3.4 and will be removed two minor releases later. Use manager.set_window_title or GUI-specific methods instead.
fig.canvas.set_window_title(window_title)
Installation guide- Conda installation
These instructions are provided to enable you to have your personalised hyperspy (and other packages covered in this worshop) 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. 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 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
To test your installation, from the same prompt, run:
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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 (Note that you may get a Warning about pyOpenCl that can be ignored.).
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%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 to download.
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