From c8c8646a3bc0d372fa4e92dfc55d97ec78bf075c Mon Sep 17 00:00:00 2001 From: tcpekin Date: Wed, 29 Jan 2025 23:31:12 +0100 Subject: [PATCH 1/3] Small typo, docstring update, and fixed a bug. --- py4DSTEM/process/diffraction/crystal_viz.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/py4DSTEM/process/diffraction/crystal_viz.py b/py4DSTEM/process/diffraction/crystal_viz.py index 5bc16c1bc..9afbbdd87 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. @@ -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") From f2603378a88a2f49b9ebab1373d2424493d0dfe9 Mon Sep 17 00:00:00 2001 From: Steven Zeltmann Date: Wed, 29 Jan 2025 18:17:37 -0500 Subject: [PATCH 2/3] format with black --- py4DSTEM/process/diffraction/crystal_viz.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/py4DSTEM/process/diffraction/crystal_viz.py b/py4DSTEM/process/diffraction/crystal_viz.py index 9afbbdd87..ab0641964 100644 --- a/py4DSTEM/process/diffraction/crystal_viz.py +++ b/py4DSTEM/process/diffraction/crystal_viz.py @@ -166,7 +166,7 @@ def plot_structure( # init tol = 1e-4 num_seg = 180 - radius = size_marker/800 + radius = size_marker / 800 zp = np.zeros(num_seg + 1) mark = np.ones(xyz.shape[0], dtype="bool") From 4e7d0003c5d1719a288120c93eb31f6d2bc89630 Mon Sep 17 00:00:00 2001 From: tcpekin Date: Mon, 3 Feb 2025 22:04:32 +0100 Subject: [PATCH 3/3] change branch behavior --- py4DSTEM/process/diffraction/crystal_viz.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/py4DSTEM/process/diffraction/crystal_viz.py b/py4DSTEM/process/diffraction/crystal_viz.py index ab0641964..93a9ad3e8 100644 --- a/py4DSTEM/process/diffraction/crystal_viz.py +++ b/py4DSTEM/process/diffraction/crystal_viz.py @@ -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(