pyTEMlib 0.2025.4.1__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

pyTEMlib/__init__.py

@@ -1,11 +1,33 @@
 # -*- coding: utf-8 -*-
 """
+PyTEMlib
+--------
+A Python package for analyzing and processing transmission electron microscopy (TEM) data.
+This package provides tools for data quantification through a model-based approach, 
+including functionalities for imaging, spectra analysis, and data visualization.
+
+The package is part of the pycrosccopy ecosystem and the dataformat is based on sidpy, 
+the fileformat is based on pyNSDI.
 Created on Sat Jan 19 10:07:35 2019
+Update on Sun Jul 20 2025
 
 @author: gduscher
 """
-from .version import _version as __version__
+from .version import  __version__
 
-__all__ = ['__version__']
+from . import file_tools
+from . import  image_tools
+from .image import image_atoms as atom_tools
+from . import graph_tools
+from . import probe_tools
+from . import eels_tools
+from . import eds_tools
+from . import crystal_tools
+from . import kinematic_scattering
+from . import dynamic_scattering
+from .config_dir import config_path
 
-name = "pyTEMlib"
+__all__ = ['__version__', 'file_tools', 'image_tools', 'atom_tools',
+           'graph_tools', 'probe_tools', 'eels_tools', 'eds_tools',
+           'crystal_tools', 'kinematic_scattering', 'dynamic_scattering', 'config_path']
+__author__ = 'Gerd Duscher'

pyTEMlib/animation.py

@@ -8,7 +8,7 @@ revision: 01/11/2021
 
 import numpy as np
 import matplotlib.pyplot as plt
-import matplotlib.patches as patches
+from matplotlib import patches
 
 from ipywidgets import widgets
 from IPython.display import display
@@ -50,8 +50,8 @@ def geometric_ray_diagram(focal_length=1., magnification=False):
     ax.add_patch(ellipse)
     ax.plot([1.5, -1.5], [0, 0], '--', color='black')
     ax.plot([0, 0], [u, -v], '--', color='black')
-    single_prop = dict(arrowstyle="->", shrinkA=0, shrinkB=0)
-    double_prop = dict(arrowstyle="<->", shrinkA=0, shrinkB=0)
+    single_prop = {"arrowstyle": '->', "shrinkA": 0, "shrinkB": 0}
+    double_prop = {"arrowstyle": "<->", "shrinkA": 0, "shrinkB": 0}
 
     if magnification:
         ax.annotate("", xy=(-x, u), xytext=(x, u), arrowprops=single_prop)
@@ -120,14 +120,16 @@ def add_lens(z, f, diam, lens_labels):
 def add_aperture(z, diam, radius, lens_labels):
     """add aperture to propagate beam plot"""
 
-    ww, tw, rad = diam / 10.0, diam / 3.0, diam / 2.0
+    # ww, tw, rad = diam / 10.0, diam / 3.0, diam / 2.0
+    rad = diam / 2
     radius = radius / 2
     plt.plot([z, z], [-rad, -radius], 'k', linewidth=2)
     plt.plot([z, z], [rad, radius], 'k', linewidth=2)
     plt.text(z, -rad - 2.0, lens_labels, fontsize=12)
 
 
-def propagate_beam(source_position, numerical_aperture, number_of_rays, lens_positions, focal_lengths,
+def propagate_beam(source_position, numerical_aperture, number_of_rays, 
+                   lens_positions, focal_lengths,
                    lens_labels='', color='b'):
     """geometrical propagation of light rays from given source
 
@@ -242,33 +244,35 @@ def deficient_holz_line(exact_bragg=False, shift=False, laue_zone=1, color='blac
     k_0[1] += shift_y
 
     # Ewald Sphere
-    ewald_sphere = patches.Circle((k_0[0], k_0[1]), radius=np.linalg.norm(k_0), clip_on=False, zorder=10, linewidth=1,
+    ewald_sphere = patches.Circle((k_0[0], k_0[1]), radius=np.linalg.norm(k_0), 
+                                  clip_on=False, zorder=10, linewidth=1,
                                   edgecolor=color, fill=False)
     plt.gca().add_artist(ewald_sphere)
 
-    plt.gca().arrow(g[-1] + .1 / d / 4, 1 / d / 2, 0, 1 / d / 2, head_width=0.03, head_length=0.04, fc='k', ec='k',
-                    length_includes_head=True)
-    plt.gca().arrow(g[-1] + .1 / d / 4, 1 / d / 2, 0, -1 / d / 2, head_width=0.03, head_length=0.04, fc='k', ec='k',
-                    length_includes_head=True)
-    plt.gca().annotate("$|g_{HOLZ}|$", xytext=(g[-1] + .1 / d / 3, 1 / d / 3), xy=(g[-1] + 1 / d / 3, 1 / d / 3))
-
-    # k_0
+    plt.gca().arrow(g[-1] + .1 / d / 4, 1 / d / 2, 0, 1 / d / 2, head_width=0.03, 
+                    head_length=0.04, fc='k', ec='k', length_includes_head=True)
+    plt.gca().arrow(g[-1] + .1 / d / 4, 1 / d / 2, 0, -1 / d / 2, head_width=0.03, 
+                    head_length=0.04, fc='k', ec='k', length_includes_head=True)
+    plt.gca().annotate("$|g_{HOLZ}|$", xytext=(g[-1] + .1 / d / 3, 1 / d / 3), 
+                       xy=(g[-1] + 1 / d / 3, 1 / d / 3))
     plt.scatter(k_0[0], k_0[1])
-    plt.gca().arrow(k_0[0], k_0[1], -k_0[0] + shift_x, -k_0[1] + shift_y, head_width=0.03, head_length=0.04, fc=color,
-                    ec=color, length_includes_head=True)
+    plt.gca().arrow(k_0[0], k_0[1], -k_0[0] + shift_x, -k_0[1] + shift_y, head_width=0.03, 
+                    head_length=0.04, fc=color, ec=color, length_includes_head=True)
     plt.gca().annotate("K$_0$", xytext=(k_0[0] / 2, k_0[1] / 3), xy=(k_0[0] / 2, k_0[1] / 2))
 
     # K_d Bragg of HOLZ reflection
-    plt.gca().arrow(k_0[0], k_0[1], -k_0[0] + g_d[0] + shift_x, -k_0[1] + g_d[1] + s_g + shift_y, head_width=0.03,
-                    head_length=0.04, fc=color,
-                    ec=color, length_includes_head=True)
-    plt.gca().annotate("K$_d$", xytext=(k_0[0] + (g_d[0] - k_0[0]) / 2, k_0[1] / 2), xy=(6.5 / d / 2, k_0[1] / 2))
+    plt.gca().arrow(k_0[0], k_0[1], -k_0[0] + g_d[0] + shift_x, -k_0[1] + g_d[1] + s_g + shift_y, 
+                    head_width=0.03, head_length=0.04, fc=color, ec=color, 
+                    length_includes_head=True)
+    plt.gca().annotate("K$_d$", xytext=(k_0[0] + (g_d[0] - k_0[0]) / 2, k_0[1] / 2), 
+                       xy=(6.5 / d / 2, k_0[1] / 2))
 
     # s_g excitation Error of HOLZ reflection
     if s_g > 0:
         plt.gca().arrow(g_d[0], g_d[1], 0, s_g, head_width=0.03, head_length=0.04, fc='k',
                         ec='k', length_includes_head=True)
-        plt.gca().annotate("s$_g$", xytext=(g_d[0] * 1.01, g_d[1] + s_g / 3), xy=(g_d[0] * 1.01, g_d[1] + s_g / 3))
+        plt.gca().annotate("s$_g$", xytext=(g_d[0] * 1.01, g_d[1] + s_g / 3), 
+                           xy=(g_d[0] * 1.01, g_d[1] + s_g / 3))
 
     # Bragg angle
     g_sg = g_d
@@ -311,6 +315,7 @@ def deficient_holz_line(exact_bragg=False, shift=False, laue_zone=1, color='blac
 
 
 def deficient_kikuchi_line(s_g=0., color_b='black'):
+    """Draw the deficient Kikuchi line in the plot."""
     k_len = 1 / ks.get_wavelength(20)
     d = 2  # lattice parameter in nm
 
@@ -391,7 +396,7 @@ def deficient_kikuchi_line(s_g=0., color_b='black'):
     plt.gca().set_xlim(-.2, 1.03)
 
 
-class InteractiveAberration(object):
+class InteractiveAberration():
     """
     ### Interactive explanation of aberrations
 
@@ -423,6 +428,7 @@ class InteractiveAberration(object):
         # self.cid = self.figure.canvas.mpl_connect('button_press_event', self.onclick)
 
     def on_button_clicked(self, b):
+        """Handle button click events to update the analysis options"""
         # print(b['owner'].description)
         selection = b['owner'].description
         if selection in self.analysis:
@@ -432,6 +438,7 @@ class InteractiveAberration(object):
         self.update()
 
     def update(self):
+        """Update the plot based on the selected analysis options"""
         ax = self.ax
         ax.clear()
         selection = self.analysis
@@ -519,7 +526,7 @@ class InteractiveAberration(object):
             plt.gca().add_patch(aberration2)
 
 
-class InteractiveRonchigramMagnification(object):
+class InteractiveRonchigramMagnification():
     """    
     ### Interactive explanation of magnification 
 
@@ -551,6 +558,7 @@ class InteractiveRonchigramMagnification(object):
         # self.cid = self.figure.canvas.mpl_connect('button_press_event', self.onclick)
 
     def on_button_clicked(self, b):
+        """Handle button click events"""
         # print(b['owner'].description)
         selection = b['owner'].description
         if selection in self.analysis:
@@ -560,6 +568,7 @@ class InteractiveRonchigramMagnification(object):
         self.update()
 
     def update(self):
+        """Update the plot based on the selected analysis options"""
         ax = self.ax
         ax.clear()
         selection = self.analysis

pyTEMlib/atom_tools.py

@@ -12,20 +12,16 @@ a pycroscopy package
 """
 
 import numpy as np
-import sys
 
-# from skimage.feature import peak_local_max
-from skimage.feature import blob_log
+import skimage.feature
+import sklearn.cluster
+import scipy.spatial
+import scipy.optimize
 
-from sklearn.cluster import KMeans
-from scipy.spatial import cKDTree
-import scipy.optimize as optimization
-
-import pyTEMlib.probe_tools as probe_tools
-import pyTEMlib.file_tools as ft
-import sidpy
 from tqdm.auto import trange
 
+import sidpy
+import pyTEMlib
 
 def find_atoms(image, atom_size=0.1, threshold=0.):
     """ Find atoms is a simple wrapper for blob_log in skimage.feature
@@ -37,7 +33,8 @@ def find_atoms(image, atom_size=0.1, threshold=0.):
     atom_size: float
         visible size of atom blob diameter in nm gives minimal distance between found blobs
     threshold: float
-        threshold for blob finder; (usually between 0.001 and 1.0) for threshold <= 0 we use the RMS contrast
+        threshold for blob finder; (usually between 0.001 and 1.0) 
+        for threshold <= 0 we use the RMS contrast
 
     Returns
     -------
@@ -59,10 +56,7 @@ def find_atoms(image, atom_size=0.1, threshold=0.):
     im = im/im.max()
     if threshold <= 0.:
         threshold = np.std(im)
-    atoms = blob_log(im, max_sigma=atom_size/scale_x, threshold=threshold)
-
-    
-
+    atoms = skimage.feature.blob_log(im, max_sigma=atom_size/scale_x, threshold=threshold)
     return atoms
 
 
@@ -86,12 +80,12 @@ def atoms_clustering(atoms, mid_atoms, number_of_clusters=3, nearest_neighbours=
     """
 
     # get distances
-    nn_tree = cKDTree(np.array(atoms)[:, 0:2])
+    nn_tree = scipy.spatial.KDTree(np.array(atoms)[:, 0:2])
 
     distances, indices = nn_tree.query(np.array(mid_atoms)[:, 0:2], nearest_neighbours)
 
-    # Clustering
-    k_means = KMeans(n_clusters=number_of_clusters, random_state=0)  # Fixing the RNG in kmeans
+    # Clustering with fixed RNG in kmeans
+    k_means = sklearn.cluster.KMeans(n_clusters=number_of_clusters, random_state=0)
     k_means.fit(distances)
     clusters = k_means.predict(distances)
 
@@ -115,8 +109,9 @@ def gauss_difference(params, area):
     numpy array: flattened array of difference
 
     """
-    gauss = probe_tools.make_gauss(area.shape[0], area.shape[1], width=params[0], x0=params[1], y0=params[2],
-                                   intensity=params[3])
+    gauss = pyTEMlib.probe_tools.make_gauss(area.shape[0], area.shape[1],
+                                             width=params[0], x0=params[1],
+                                             y0=params[2], intensity=params[3])
     return (area - gauss).flatten()
 
 
@@ -131,19 +126,20 @@ def atom_refine(image, atoms, radius, max_int=0, min_int=0, max_dist=4):
     radius: float
         radius of circular mask to define fitting of Gaussian
     max_int: float
-        optional - maximum intensity to be considered for fitting (to exclude contaminated areas for example)
+        optional - maximum intensity to be considered for fitting 
+        (to exclude contaminated areas for example)
     min_int: float
-        optional - minimum intensity to be considered for fitting (to exclude contaminated holes for example)
+        optional - minimum intensity to be considered for fitting
+        (to exclude contaminated holes for example)
     max_dist: float
         optional - maximum distance of movement of Gaussian during fitting
 
     Returns
     -------
     sym: dict
-        dictionary containing new atom positions and other output such as intensity of the fitted Gaussian
+        dictionary containing new atom positions and other output
     """
     rr = int(radius + 0.5)  # atom radius
-    print('using radius ', rr, 'pixels')
 
     pixels = np.linspace(0, 2 * rr, 2 * rr + 1) - rr
     x, y = np.meshgrid(pixels, pixels)
@@ -162,7 +158,7 @@ def atom_refine(image, atoms, radius, max_int=0, min_int=0, max_dist=4):
     gauss_amplitude = []
     gauss_intensity = []
 
-    for i in trange(len(atoms)):
+    for i in range(len(atoms)):
         x, y = atoms[i][0:2]
         x = int(x)
         y = int(y)
@@ -171,7 +167,7 @@ def atom_refine(image, atoms, radius, max_int=0, min_int=0, max_dist=4):
 
         append = False
 
-        if (x - rr) < 0 or y - rr < 0 or x + rr + 1 > image.shape[0] or y + rr + 1 > image.shape[1]:  # atom not found
+        if x-rr < 0 or y-rr < 0 or x+rr+1 > image.shape[0] or y+rr+1 > image.shape[1]:
             position.append(-1)
             intensities.append(-1.)
             maximum_area.append(-1.)
@@ -189,11 +185,10 @@ def atom_refine(image, atoms, radius, max_int=0, min_int=0, max_dist=4):
 
         pout = [0, 0, 0, 0]
         if append:
-            if (x - rr) < 0 or y - rr < 0 or x + rr + 1 > image.shape[0] or y + rr + 1 > image.shape[1]:
+            if x-rr < 0 or y-rr < 0 or x+rr+1 > image.shape[0] or y+rr+1 > image.shape[1]:
                 pass
             else:
-                [pout, _] = optimization.leastsq(gauss_difference, guess, args=area)
-
+                [pout, _] = scipy.optimize.leastsq(gauss_difference, guess, args=area)
             if (abs(pout[1]) > max_dist) or (abs(pout[2]) > max_dist):
                 pout = [0, 0, 0, 0]
 
@@ -203,8 +198,8 @@ def atom_refine(image, atoms, radius, max_int=0, min_int=0, max_dist=4):
         if all(v == 0 for v in pout):
             gauss_intensity.append(0.)
         else:
-            gauss = probe_tools.make_gauss(area.shape[0], area.shape[1], width=pout[0], x0=pout[1], y0=pout[2],
-                                           intensity=pout[3])
+            gauss = pyTEMlib.probe_tools.make_gauss(area.shape[0], area.shape[1], width=pout[0],
+                                                    x0=pout[1], y0=pout[2], intensity=pout[3])
             gauss_intensity.append((gauss * mask).sum())
         gauss_width.append(pout[0])
         gauss_amplitude.append(pout[3])
@@ -232,9 +227,9 @@ def intensity_area(image, atoms, radius):
     x, y = np.meshgrid(pixels, pixels)
     mask = np.array((x ** 2 + y ** 2) < rr ** 2)
     intensities = []
-    for i in range(len(atoms)):
-        x = int(atoms[i][1])
-        y = int(atoms[i][0])
+    for atom in atoms:
+        x = int(atom[1])
+        y = int(atom[0])
         area = image[x - rr:x + rr + 1, y - rr:y + rr + 1]
         if area.shape == mask.shape:
             intensities.append((area * mask).sum())

pyTEMlib/config_dir.py

@@ -9,12 +9,8 @@ config_dir: setup of directory ~/.pyTEMlib for custom sources and database
 import os
 
 # import wget
-if os.name == 'posix':
+if os.name in ['nt', 'dos', 'posix']:
     config_path = os.path.join(os.path.expanduser('~'), '.pyTEMlib')
-    os_name = 'posix'
-elif os.name in ['nt', 'dos']:
-    config_path = os.path.join(os.path.expanduser('~'), '.pyTEMlib')
-    os_name = 'windows'
 else:
     config_path = '.'
 
@@ -31,27 +27,5 @@ lines = ['Microscope,E0,alpha,beta,pppc,correlation_factor,VOA_conv,EELS_b1,EELS
 
 config_file = os.path.join(config_path, 'microscopes.csv')
 if os.path.isfile(config_file) is False:  # Do not overwrite users microscopy files
-    with open(config_file, 'w') as f:
+    with open(config_file, 'w', encoding='utf-8') as f:
         f.write('\n'.join(lines))
-
-""" 
-import pickle
-from pkg_resources import resource_filename
-
-data_path = resource_filename(__name__, 'data')
-pkl_file = open(data_path + '/old/edges_db.pkl', 'rb')
-x_sections = pickle.load(pkl_file)
-pkl_file.close()
-for key in range(80, 83):
-    print(f'\'{key}\': ', x_sections[str(key)], ',')
-
-# config_file = os.path.join(config_path, 'edges_db.pkl')
-ref = importlib_resources.files('pyTEMlib') / 'data/edges_db.pkl'
-with importlib_resources.as_file(ref) as templates_file:
-    if os.path.isfile(config_file) is False:
-        try:
-            shutil.copy(templates_file, config_file)
-        except FileNotFoundError:
-            pass
-            # wget('https://github.com/pycroscopy/pyTEMlib/tree/main/pyTEMlib/data/'+file)
-"""