Strain Anisotropy and Magnetic Domains in Embedded Nanomagnets

Transmission electron microscopy data and processing scripts related to the journal article "Strain Anisotropy and Magnetic Domains in Embedded Nanomagnets": https://doi.org/10.1002/smll.201904738

Data files

The data is contained within the 00N_....hdf5 files, which can be accessed using an HDF5 reader. Note that these datasets are very large, and trying to load one of them directly will most likely lead to your computer crashing.

Loading the data in python with h5py:

import h5py
f = h5py.File('003_stripe1.hdf5', mode='r')
data = f['fpd_expt/fpd_data/data']
data_subset = data[0:16, 0:16, :, :]

Exploring the datasets lazily, i.e. without loading the whole dataset into memory at the same time. Using pixStem:

import pixstem.api as ps
s = ps.load_ps_signal("003_stripe1.hdf5", lazy=True)
s.plot()

Processing files

All the TEM data has been processed using python scripts, which is named based on the type of processing:

d00N_...: STEM-DPC processing

l00N_...: lattice size processing

s00N_...: rotation "simulations" to find the relation between the scan and detector rotation

Several of the scripts generate intermediate files, which are saved in folders with the same prefix as the scripts. So the d001_... script makes a folder named d001_... . These intermediate files are included here as zip-files, since Zenodo doesn't support folder structures.

The python libraries required to run the scripts are listed in requirements.txt. Newer versions of the libraries will most likely also work.

To setup the python environment with the required libraries, and run all the scripts:

pip3 install -r requirements.txt
python3 run_all_scripts.py

This will most likely take several hours to complete.