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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)