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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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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 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:
/opt/conda/lib/python3.8/site-packages/hyperspy/drawing/utils.py:163: MatplotlibDeprecationWarning:
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
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.
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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 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