Summary

Licensing

I, the copyright holder of this work, hereby publish it under the following license:

This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license.

You are free:

• to share – to copy, distribute and transmit the work
• to remix – to adapt the work

Under the following conditions:

• attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
• share alike – If you remix, transform, or build upon the material, you must distribute your contributions under the same or compatible license as the original.

https://creativecommons.org/licenses/by-sa/4.0CC BY-SA 4.0 Creative Commons Attribution-Share Alike 4.0 truetrue

Code

from scipy.ndimage import rotate
import matplotlib.pyplot as plt
import matplotlib.patheffects as patheffects
import matplotlib.font_manager as fm
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
from ase.visualize.plot import plot_atoms
from ase.lattice.spacegroup import crystal
import hyperspy.api as hs

# Load, rotate and crop data
s_adf = hs.load("s007_ADF.hdf5")  # From https://zenodo.org/record/3476746
s_adf.data = rotate(s_adf.data, angle=95.4, reshape=False)
s_adf_crop = s_adf.isig[:, 88:-88]

aspect_ratio = s_adf_crop.data.shape[0] / s_adf_crop.data.shape[1]

# Making figure
fig, ax = plt.subplots(figsize=(7, 7 * aspect_ratio))

ax.imshow(s_adf_crop, extent=s_adf_crop.axes_manager.signal_extent)

xmin = s_adf_crop.axes_manager[0].low_value
xmax = s_adf_crop.axes_manager[0].high_value
ymin = s_adf_crop.axes_manager[1].low_value
ymax = s_adf_crop.axes_manager[1].high_value

# Annotations
path_effects = [patheffects.withStroke(linewidth=3, foreground='black', capstyle="round")]
text_kwargs = {'fontsize': 38, 'color': 'white', 'path_effects': path_effects,
               'transform': ax.transAxes}
ax.text(0.05, 0.05, "SrTiO$_3$", ha="left", va="bottom", **text_kwargs)
ax.text(0.05, 0.40, "LaFeO$_3$", ha="left", va="bottom", **text_kwargs)
ax.text(0.05, 0.80, "La$_{0.7}$Sr$_{0.3}$MnO$_3$", ha="left", va="bottom", **text_kwargs)

# Scalebar
fontprops = fm.FontProperties(size=30)
kwargs_sizebar = {'loc': 4, 'frameon': False, 'color': 'white', 'label_top': False}
scalebar = AnchoredSizeBar(transform=ax.transData, size=2, label=u'2 nm',
                           size_vertical=0.15, fontproperties=fontprops, **kwargs_sizebar)
ax.add_artist(scalebar)
scalebar.txt_label._text.set_path_effects(path_effects)

# Plotting atom structure
srtio3 = crystal(
	['Sr','Ti','O'],
	[(0.0, 0.0, 0.0), (0.5, 0.5, 0.5), (0.5, 0.5, 0)],
	spacegroup=221,
	cellpar=3.905,
	size=(4, 4, 4))
plot_atoms(srtio3, ax, radii=0.43, rotation=('45x,0y,35z'), scale=0.100, offset=(7.35, 4.12),
	   show_unit_cell=False)

ax.set_xlim(xmin, xmax)
ax.set_ylim(ymin, ymax)
ax.set_axis_off()

fig.subplots_adjust(0, 0, 1, 1)
fig.savefig("perovskite_oxide_thin_film.jpg", dpi=200)