def plot_slices(self):
# remove all slice patches
for i in range(len(self.mplWidget.axes.patches))[::-1]:
patch = self.mplWidget.axes.patches[i]
if patch.get_label() == "Slice":
patch.remove()
axes = self.comboBox_plt.currentText()
# for overlays
alpha = 0.3
colors = ("r", "b", "g")
# add scan area to xy plot
patches = []
labels = []
if axes == "xy":
x_min = float(self.lineEdit_scan_x_min.text())
x_max = float(self.lineEdit_scan_x_max.text())
y_min = float(self.lineEdit_scan_y_min.text())
y_max = float(self.lineEdit_scan_y_max.text())
rectangle = Rectangle(
(x_min, y_min),
x_max - x_min,
y_max - y_min,
color="r",
alpha=alpha,
ec="k",
label="Slice",
)
self.mplWidget.axes.add_patch(rectangle)
patches.append(rectangle)
labels.append("Scan Area")
self.mplWidget.axes.legend(patches, labels)
# plot multislice layers
elif axes == "xz" or axes == "yz":
positions = self.atoms.get_positions()
if axes == "xz":
x_min = float(self.lineEdit_scan_x_min.text())
x_max = float(self.lineEdit_scan_x_max.text())
z_min = positions[:, 2].min()
z_max = positions[:, 2].max()
if axes == "yz":
x_min = float(self.lineEdit_scan_y_min.text())
x_max = float(self.lineEdit_scan_y_max.text())
z_min = positions[:, 2].min()
z_max = positions[:, 2].max()
# in Angstrom
slice_thickness = float(self.lineEdit_slice_thickness.text())
# from stemCL code
nslices = math.ceil((z_max - z_min) / slice_thickness)
patches = []
labels = []
for i in range(nslices):
rectangle = Rectangle(
(x_min, z_min + slice_thickness * i),
x_max - x_min,
slice_thickness,
color=colors[i % len(colors)],
alpha=alpha,
ec="k",
label="Slice",
)
self.mplWidget.axes.add_patch(rectangle)
self.mplWidget.axes.text(
self.mplWidget.axes.get_xlim()[0],
z_min + slice_thickness * i,
str(i),
size=12,
color=rectangle.get_facecolor(),
bbox=dict(boxstyle="round", color="w", alpha=0.5),
ha="left",
va="bottom",
)
patches.append(rectangle)
labels.append(f"Slice {i}")
self.mplWidget.draw()
