def _make_multidim_atom_plane_marker_list(atom_plane_zone_list,
scale=1.,
color='red',
add_numbers=True):
marker_list = []
for i, atom_plane_list in enumerate(atom_plane_zone_list):
for index_atom_plane, atom_plane in enumerate(atom_plane_list):
for j in range(len(atom_plane.atom_list[1:])):
x1 = [-1000] * len(atom_plane_zone_list)
y1 = [-1000] * len(atom_plane_zone_list)
x2 = [-1000] * len(atom_plane_zone_list)
y2 = [-1000] * len(atom_plane_zone_list)
x1[i] = atom_plane.atom_list[j].pixel_x * scale
y1[i] = atom_plane.atom_list[j].pixel_y * scale
x2[i] = atom_plane.atom_list[j + 1].pixel_x * scale
y2[i] = atom_plane.atom_list[j + 1].pixel_y * scale
marker = LineSegment(x1=x1, y1=y1, x2=x2, y2=y2, color=color)
marker_list.append(marker)
if add_numbers:
x = [-1000] * len(atom_plane_zone_list)
y = [-1000] * len(atom_plane_zone_list)
x[i] = atom_plane.atom_list[0].pixel_x * scale
y[i] = atom_plane.atom_list[0].pixel_y * scale
marker = Text(x=x,
y=y,
text=str(index_atom_plane),
color=color,
va='top',
ha='right')
marker_list.append(marker)
return marker_list
def _make_zone_vector_text_marker_list(
zone_vector_list, x=1, y=1, scale=1., color='red'):
number = len(zone_vector_list)
marker_list = []
if len(zone_vector_list) == 1:
marker_list.append(
Text(
x, y,
text=str(zone_vector_list[0]), size=20, color=color))
else:
for index, zone_vector in enumerate(zone_vector_list):
xP, yP = [-1000] * number, [-1000] * number
xP[index] = x
yP[index] = y
marker = Text(xP, yP, text=str(zone_vector), size=20, color=color)
marker_list.append(marker)
return marker_list
def _make_atom_planes_marker_list(
atom_plane_list, scale=1., add_numbers=True, color='red'):
marker_list = []
for i, atom_plane in enumerate(atom_plane_list):
atom_plane_markers = _make_single_atom_plane_marker_list(
atom_plane, scale=scale, color='red')
marker_list.extend(atom_plane_markers)
if add_numbers:
marker = Text(
x=atom_plane.start_atom.pixel_x * scale,
y=atom_plane.start_atom.pixel_y * scale,
text=str(i),
color=color,
va='top',
ha='right')
marker_list.append(marker)
return marker_list
def _make_atom_position_marker_list(atom_position_list,
scale=1.,
markersize=20,
add_numbers=True,
color='red'):
marker_list = []
for i, atom_position in enumerate(atom_position_list):
x = atom_position.pixel_x * scale
y = atom_position.pixel_y * scale
marker = Point(x=x, y=y, color=color, size=markersize)
marker_list.append(marker)
if add_numbers:
marker = Text(x=x,
y=y,
text=str(i),
color=color,
va='top',
ha='right')
marker_list.append(marker)
return marker_list
def plot_grid(
self,
pattern_idx: Optional[Tuple[int, ...]] = None,
rgb_channels: Union[None, List[Tuple], List[List[Tuple]]] = None,
visible_indices: bool = True,
**kwargs,
) -> EBSD:
"""Plot a pattern with the detector grid superimposed,
potentially coloring the edges of three grid tiles red, green
and blue.
Parameters
----------
pattern_idx
A tuple of integers defining the pattern to superimpose the
grid on. If None (default), the first pattern is used.
rgb_channels
A list of tuple indices defining three or more detector grid
tiles which edges to color red, green and blue. If None (default),
no tiles' edges are colored.
visible_indices
Whether to show grid indices. Default is True.
kwargs
Keyword arguments passed to
:func:`matplotlib.pyplot.axhline` and `axvline`, used by
HyperSpy to draw lines.
Returns
-------
pattern : kikuchipy.signals.EBSD
A single pattern with the markers added.
"""
# Get detector scales (column, row)
axes_manager = self.signal.axes_manager
dc, dr = [i.scale for i in axes_manager.signal_axes]
rows = self.grid_rows
cols = self.grid_cols
# Set grid tile indices
markers = []
if visible_indices:
color = kwargs.pop("color", "r")
for row, col in np.ndindex(self.grid_shape):
markers.append(
Text(
x=cols[col] * dc,
y=(rows[row] + (0.1 * rows[1])) * dr,
text=f"{row,col}",
color=color,
))
# Set lines
kwargs.setdefault("color", "w")
markers += [HorizontalLine((i - 0.5) * dr, **kwargs) for i in rows]
markers += [VerticalLine((j - 0.5) * dc, **kwargs) for j in cols]
# Color RGB tiles
if rgb_channels is not None:
for channels, color in zip(rgb_channels, ["r", "g", "b"]):
if isinstance(channels, tuple):
channels = (channels, )
for (row, col) in channels:
kwargs.update({
"color": color,
"zorder": 3,
"linewidth": 2
})
roi = self.roi_from_grid((row, col))
markers += [
Rectangle(
x1=(roi.left - 0.5) * dc,
y1=(roi.top - 0.5) * dc,
x2=(roi.right - 0.5) * dr,
y2=(roi.bottom - 0.5) * dr,
**kwargs,
)
]
# Get pattern and add list of markers
if pattern_idx is None:
pattern_idx = (0, ) * axes_manager.navigation_dimension
pattern = self.signal.inav[pattern_idx]
pattern.add_marker(markers, permanent=True)
return pattern