pyTEMlib 0.2023.4.0__tar.gz → 0.2023.8.0__tar.gz

{pyTEMlib-0.2023.4.0/pyTEMlib.egg-info → pyTEMlib-0.2023.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: pyTEMlib
-Version: 0.2023.4.0
+Version: 0.2023.8.0
 Summary: pyTEM: TEM Data Quantification library through a model-based approach
 Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
 Author: Gerd Duscher
@@ -67,7 +67,6 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Cython
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10

{pyTEMlib-0.2023.4.0 → pyTEMlib-0.2023.8.0}/pyTEMlib/crystal_tools.py

@@ -26,7 +26,7 @@ import ase.build
 import ase.data.colors
 
 import matplotlib.pylab as plt  # basic plotting
-
+from scipy.spatial import cKDTree
 _spglib_present = True
 try:
     import spglib
@@ -119,6 +119,47 @@ def set_bond_radii(atoms):
     atoms.info['bond_radii'] = bond_radii
 
 
+def get_projection(crystal, layers=1):
+    zone_axis = crystal.info['experimental']['zone_axis']
+    angle = crystal.info['experimental']['angle']
+    projected_crystal = ase.build.surface(crystal, zone_axis, vacuum=.0, layers=layers)
+
+    element_tree = cKDTree(projected_crystal.positions[:, 0:2])
+    done = []
+    projected = []
+    for atom in projected_crystal:
+        if atom.index not in done:
+            near = element_tree.query_ball_point(atom.position[:2], 0.05)
+            projected.append(near)
+            done.extend(near)
+    print('projected atomic numbers')
+    atomic_numbers = []
+    for pro in projected:
+        atomic_numbers.append(projected_crystal.get_atomic_numbers()[pro].sum())
+        
+    projected_crystal.rotate(np.degrees(angle)%360, 'z', rotate_cell=True)
+    
+    near_base = np.array([projected_crystal.cell[0,:2], -projected_crystal.cell[0,:2],
+                          projected_crystal.cell[1,:2], -projected_crystal.cell[1,:2],
+                          projected_crystal.cell[0,:2] + projected_crystal.cell[1,:2],
+                          -(projected_crystal.cell[0,:2] + projected_crystal.cell[1,:2])])
+    lines = np.array( [[[0, near_base[0,0]],[0, near_base[0,1]]],
+                       [[0, near_base[2,0]],[0, near_base[2,1]]],
+                       [[near_base[0,0], near_base[4,0]],[near_base[0,1], near_base[4,1]]],
+                       [[near_base[2,0], near_base[4,0]],[near_base[2,1], near_base[4,1]]]])
+    projected_atoms = []
+    for index in projected:
+       projected_atoms.append(index[0])
+    
+    projected_crystal.info['projection']={'indices': projected, 
+                                          'projected': projected_atoms,
+                                          'projected_Z': atomic_numbers, 
+                                          'angle': np.degrees(angle)+180%360,
+                                          'near_base': near_base,
+                                          'lines': lines}    
+    return projected_crystal
+
+
 def jmol_viewer(atoms, size=2):
     """
     jmol viewer of ase .Atoms object
@@ -257,7 +298,7 @@ def ball_and_stick(atoms, extend=1, max_bond_length=0.):
     return super_cell
 
 
-def plot_unit_cell(atoms, extend=1, max_bond_length=1.0):
+def plot_unit_cell(atoms, extend=1, max_bond_length=1.0, ax = None):
     """
     Simple plot of unit cell
     """
@@ -267,8 +308,9 @@ def plot_unit_cell(atoms, extend=1, max_bond_length=1.0):
     corners = super_cell.info['plot_cell']['corner_vectors']
     positions = super_cell.positions - super_cell.cell.lengths()/2
 
-    fig = plt.figure()
-    ax = fig.add_subplot(111, projection='3d')
+    if ax is None:
+       fig = plt.figure()
+       ax = fig.add_subplot(111, projection='3d')
     # draw unit_cell
 
     for line in super_cell.info['plot_cell']['corner_matrix'].keys():
@@ -296,7 +338,7 @@ def plot_unit_cell(atoms, extend=1, max_bond_length=1.0):
     ax.set_xlabel('x [Å]')
     ax.set_ylabel('y [Å]')
     ax.set_zlabel('z [Å]')
-    return fig
+    return ax.get_figure()
 
 
 # Jmol colors.  See: http://jmol.sourceforge.net/jscolors/#color_U