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Small typo, docstring update, and fixed a bug. #706

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Small typo, docstring update, and fixed a bug. #706

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c8c8646
Small typo, docstring update, and fixed a bug.
tcpekin Jan 29, 2025
f260337
format with black
sezelt Jan 29, 2025
4e7d000
change branch behavior
tcpekin Feb 3, 2025
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8 changes: 4 additions & 4 deletions py4DSTEM/process/diffraction/crystal_viz.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,15 +34,15 @@ def plot_structure(
returnfig: bool = False,
):
"""
Quick 3D plot of the untit cell /atomic structure.
Quick 3D plot of the unit cell/atomic structure.

Args:
orientation_matrix (array): (3,3) orientation matrix, where columns represent projection directions.
zone_axis_lattice (array): (3,) projection direction in lattice indices
proj_x_lattice (array): (3,) x-axis direction in lattice indices
zone_axis_cartesian (array): (3,) cartesian projection direction
proj_x_cartesian (array): (3,) cartesian projection direction
scale_markers (float): Size scaling for markers
size_marker (float): Size scaling for markers
tol_distance (float): Tolerance for repeating atoms on edges on cell boundaries.
plot_limit (float): (2,3) numpy array containing x y z plot min and max in columns.
Default is 1.1* unit cell dimensions.
Expand Down Expand Up @@ -150,7 +150,7 @@ def plot_structure(

# atoms
ID_all = np.unique(ID)
if occ is None:
if np.all(np.asarray(occ) == 1):
for ID_plot in ID_all:
sub = ID == ID_plot
ax.scatter(
Expand All @@ -166,7 +166,7 @@ def plot_structure(
# init
tol = 1e-4
num_seg = 180
radius = 0.7
radius = size_marker / 800
zp = np.zeros(num_seg + 1)

mark = np.ones(xyz.shape[0], dtype="bool")
Expand Down