diff --git a/py4DSTEM/process/diffraction/crystal_viz.py b/py4DSTEM/process/diffraction/crystal_viz.py index 5bc16c1bc..93a9ad3e8 100644 --- a/py4DSTEM/process/diffraction/crystal_viz.py +++ b/py4DSTEM/process/diffraction/crystal_viz.py @@ -34,7 +34,7 @@ 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. @@ -42,7 +42,7 @@ def plot_structure( 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. @@ -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( @@ -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")