pyTEMlib 0.2025.4.2__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

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Files changed (94) hide show
  1. build/lib/pyTEMlib/__init__.py +33 -0
  2. build/lib/pyTEMlib/animation.py +640 -0
  3. build/lib/pyTEMlib/atom_tools.py +238 -0
  4. build/lib/pyTEMlib/config_dir.py +31 -0
  5. build/lib/pyTEMlib/crystal_tools.py +1219 -0
  6. build/lib/pyTEMlib/diffraction_plot.py +756 -0
  7. build/lib/pyTEMlib/dynamic_scattering.py +293 -0
  8. build/lib/pyTEMlib/eds_tools.py +826 -0
  9. build/lib/pyTEMlib/eds_xsections.py +432 -0
  10. build/lib/pyTEMlib/eels_tools/__init__.py +44 -0
  11. build/lib/pyTEMlib/eels_tools/core_loss_tools.py +751 -0
  12. build/lib/pyTEMlib/eels_tools/eels_database.py +134 -0
  13. build/lib/pyTEMlib/eels_tools/low_loss_tools.py +655 -0
  14. build/lib/pyTEMlib/eels_tools/peak_fit_tools.py +175 -0
  15. build/lib/pyTEMlib/eels_tools/zero_loss_tools.py +264 -0
  16. build/lib/pyTEMlib/file_reader.py +274 -0
  17. build/lib/pyTEMlib/file_tools.py +811 -0
  18. build/lib/pyTEMlib/get_bote_salvat.py +69 -0
  19. build/lib/pyTEMlib/graph_tools.py +1153 -0
  20. build/lib/pyTEMlib/graph_viz.py +599 -0
  21. build/lib/pyTEMlib/image/__init__.py +37 -0
  22. build/lib/pyTEMlib/image/image_atoms.py +270 -0
  23. build/lib/pyTEMlib/image/image_clean.py +197 -0
  24. build/lib/pyTEMlib/image/image_distortion.py +299 -0
  25. build/lib/pyTEMlib/image/image_fft.py +277 -0
  26. build/lib/pyTEMlib/image/image_graph.py +926 -0
  27. build/lib/pyTEMlib/image/image_registration.py +316 -0
  28. build/lib/pyTEMlib/image/image_utilities.py +309 -0
  29. build/lib/pyTEMlib/image/image_window.py +421 -0
  30. build/lib/pyTEMlib/image_tools.py +699 -0
  31. build/lib/pyTEMlib/interactive_image.py +1 -0
  32. build/lib/pyTEMlib/kinematic_scattering.py +1196 -0
  33. build/lib/pyTEMlib/microscope.py +61 -0
  34. build/lib/pyTEMlib/probe_tools.py +906 -0
  35. build/lib/pyTEMlib/sidpy_tools.py +153 -0
  36. build/lib/pyTEMlib/simulation_tools.py +104 -0
  37. build/lib/pyTEMlib/test.py +437 -0
  38. build/lib/pyTEMlib/utilities.py +314 -0
  39. build/lib/pyTEMlib/version.py +5 -0
  40. build/lib/pyTEMlib/xrpa_x_sections.py +20976 -0
  41. pyTEMlib/__init__.py +25 -3
  42. pyTEMlib/animation.py +31 -22
  43. pyTEMlib/atom_tools.py +29 -34
  44. pyTEMlib/config_dir.py +2 -28
  45. pyTEMlib/crystal_tools.py +129 -165
  46. pyTEMlib/eds_tools.py +559 -342
  47. pyTEMlib/eds_xsections.py +432 -0
  48. pyTEMlib/eels_tools/__init__.py +44 -0
  49. pyTEMlib/eels_tools/core_loss_tools.py +751 -0
  50. pyTEMlib/eels_tools/eels_database.py +134 -0
  51. pyTEMlib/eels_tools/low_loss_tools.py +655 -0
  52. pyTEMlib/eels_tools/peak_fit_tools.py +175 -0
  53. pyTEMlib/eels_tools/zero_loss_tools.py +264 -0
  54. pyTEMlib/file_reader.py +274 -0
  55. pyTEMlib/file_tools.py +260 -1130
  56. pyTEMlib/get_bote_salvat.py +69 -0
  57. pyTEMlib/graph_tools.py +101 -174
  58. pyTEMlib/graph_viz.py +150 -0
  59. pyTEMlib/image/__init__.py +37 -0
  60. pyTEMlib/image/image_atoms.py +270 -0
  61. pyTEMlib/image/image_clean.py +197 -0
  62. pyTEMlib/image/image_distortion.py +299 -0
  63. pyTEMlib/image/image_fft.py +277 -0
  64. pyTEMlib/image/image_graph.py +926 -0
  65. pyTEMlib/image/image_registration.py +316 -0
  66. pyTEMlib/image/image_utilities.py +309 -0
  67. pyTEMlib/image/image_window.py +421 -0
  68. pyTEMlib/image_tools.py +154 -928
  69. pyTEMlib/kinematic_scattering.py +1 -1
  70. pyTEMlib/probe_tools.py +1 -1
  71. pyTEMlib/test.py +437 -0
  72. pyTEMlib/utilities.py +314 -0
  73. pyTEMlib/version.py +2 -3
  74. pyTEMlib/xrpa_x_sections.py +14 -10
  75. {pytemlib-0.2025.4.2.dist-info → pytemlib-0.2025.9.1.dist-info}/METADATA +13 -16
  76. pytemlib-0.2025.9.1.dist-info/RECORD +86 -0
  77. {pytemlib-0.2025.4.2.dist-info → pytemlib-0.2025.9.1.dist-info}/WHEEL +1 -1
  78. pytemlib-0.2025.9.1.dist-info/top_level.txt +6 -0
  79. pyTEMlib/core_loss_widget.py +0 -721
  80. pyTEMlib/eels_dialog.py +0 -754
  81. pyTEMlib/eels_dialog_utilities.py +0 -1199
  82. pyTEMlib/eels_tools.py +0 -2359
  83. pyTEMlib/file_tools_qt.py +0 -193
  84. pyTEMlib/image_dialog.py +0 -158
  85. pyTEMlib/image_dlg.py +0 -146
  86. pyTEMlib/info_widget.py +0 -1086
  87. pyTEMlib/info_widget3.py +0 -1120
  88. pyTEMlib/low_loss_widget.py +0 -479
  89. pyTEMlib/peak_dialog.py +0 -1129
  90. pyTEMlib/peak_dlg.py +0 -286
  91. pytemlib-0.2025.4.2.dist-info/RECORD +0 -38
  92. pytemlib-0.2025.4.2.dist-info/top_level.txt +0 -1
  93. {pytemlib-0.2025.4.2.dist-info → pytemlib-0.2025.9.1.dist-info}/entry_points.txt +0 -0
  94. {pytemlib-0.2025.4.2.dist-info → pytemlib-0.2025.9.1.dist-info}/licenses/LICENSE +0 -0
build/lib/pyTEMlib/probe_tools.py ADDED
@@ -0,0 +1,906 @@
1
+ """Functions to calculate electron probe"""
2
+ import numpy as np
3
+ import pyTEMlib.image_tools
4
+ import scipy.ndimage as ndimage
5
+ import skimage
6
+
7
+ get_wavelength = pyTEMlib.image_tools.get_wavelength
8
+
9
+
10
+
11
+ def make_gauss(size_x, size_y, width=1.0, x0=0.0, y0=0.0, intensity=1.0):
12
+ """Make a Gaussian shaped probe """
13
+ size_x = size_x / 2
14
+ size_y = size_y / 2
15
+ x, y = np.mgrid[-size_x:size_x, -size_y:size_y]
16
+ g = np.exp(-((x - x0) ** 2 + (y - y0) ** 2) / 2.0 / width ** 2)
17
+ probe = g / (g.sum()+ 0.00001) * intensity
18
+
19
+ return probe
20
+
21
+
22
+ def make_lorentz(size_x, size_y, gamma=1.0, x0=0., y0=0., intensity=1.):
23
+ """Make a Lorentzian shaped probe """
24
+
25
+ size_x = np.floor(size_x / 2)
26
+ size_y = np.floor(size_y / 2)
27
+ x, y = np.mgrid[-size_x:size_x, -size_y:size_y]
28
+ g = gamma / (2 * np.pi) / np.power(((x - x0) ** 2 + (y - y0) ** 2 + gamma ** 2), 1.5)
29
+ probe = g / g.sum() * intensity
30
+
31
+ return probe
32
+
33
+
34
+ def zero_loss_peak_weight():
35
+ # US100 zero_loss peak for Cc of aberrations
36
+ x = np.linspace(-0.5, 0.9, 29)
37
+ y = [0.0143, 0.0193, 0.0281, 0.0440, 0.0768, 0.1447, 0.2785, 0.4955, 0.7442, 0.9380, 1.0000, 0.9483, 0.8596,
38
+ 0.7620, 0.6539, 0.5515, 0.4478, 0.3500, 0.2683, 0.1979, 0.1410, 0.1021, 0.0752, 0.0545, 0.0401, 0.0300,
39
+ 0.0229, 0.0176, 0.0139]
40
+
41
+ return x, y
42
+
43
+
44
+ def make_chi(phi, theta, aberrations):
45
+ maximum_aberration_order = 5
46
+ chi = np.zeros(theta.shape)
47
+ for n in range(maximum_aberration_order + 1): # First Sum up to fifth order
48
+ term_first_sum = np.power(theta, n + 1) / (n + 1) # term in first sum
49
+
50
+ second_sum = np.zeros(theta.shape) # second Sum initialized with zeros
51
+ for m in range((n + 1) % 2, n + 2, 2):
52
+ if m > 0:
53
+ if f'C{n}{m}a' not in aberrations: # Set non existent aberrations coefficient to zero
54
+ aberrations[f'C{n}{m}a'] = 0.
55
+ if f'C{n}{m}b' not in aberrations:
56
+ aberrations[f'C{n}{m}b'] = 0.
57
+
58
+ # term in second sum
59
+ second_sum = second_sum + aberrations[f'C{n}{m}a'] * np.cos(m * phi) + aberrations[
60
+ f'C{n}{m}b'] * np.sin(m * phi)
61
+ else:
62
+ if f'C{n}{m}' not in aberrations: # Set non existent aberrations coefficient to zero
63
+ aberrations[f'C{n}{m}'] = 0.
64
+
65
+ # term in second sum
66
+ second_sum = second_sum + aberrations[f'C{n}{m}']
67
+ chi = chi + term_first_sum * second_sum * 2 * np.pi / aberrations['wavelength']
68
+
69
+ return chi
70
+
71
+
72
+ def get_chi(ab, size_x, size_y, verbose=False):
73
+ """ Get aberration function chi without defocus spread
74
+
75
+ # Internally reciprocal lattice vectors in 1/nm or rad.
76
+ # All calculations of chi in angles.
77
+ # All aberration coefficients in nm
78
+ """
79
+ aperture_angle = ab['convergence_angle'] / 1000.0 # in rad
80
+
81
+ wavelength = pyTEMlib.image_tools.get_wavelength(ab['acceleration_voltage'])
82
+ if verbose:
83
+ print(f"Acceleration voltage {ab['acceleration_voltage'] / 1000:}kV => wavelength {wavelength * 1000.:.2f}pm")
84
+
85
+ ab['wavelength'] = wavelength
86
+
87
+ # Reciprocal plane in 1/nm
88
+ dk = 1 / ab['FOV']
89
+ k_x = np.array(dk * (-size_x / 2. + np.arange(size_x)))
90
+ k_y = np.array(dk * (-size_y / 2. + np.arange(size_y)))
91
+ t_x_v, t_y_v = np.meshgrid(k_x, k_y)
92
+
93
+ # define reciprocal plane in angles
94
+ phi = np.arctan2(t_x_v, t_y_v)
95
+ theta = np.arctan2(np.sqrt(t_x_v ** 2 + t_y_v ** 2), 1 / wavelength)
96
+
97
+ # calculate chi
98
+ chi = make_chi(phi, theta, ab)
99
+
100
+ # Aperture function
101
+ print(aperture_angle)
102
+ mask = theta >= aperture_angle
103
+
104
+ aperture = np.ones((size_x, size_y), dtype=float)
105
+ aperture[mask] = 0.
106
+
107
+ return chi, aperture
108
+
109
+
110
+
111
+ def print_aberrations(ab):
112
+ from IPython.display import HTML, display
113
+ output = '<html><body>'
114
+ output += f"Aberrations [nm] for acceleration voltage: {ab['acceleration_voltage'] / 1e3:.0f} kV"
115
+ output += '<table>'
116
+ output += f"<tr><td> C10 </td><td> {ab['C10']:.1f} </tr>"
117
+ output += f"<tr><td> C12a (A1) </td><td> {ab['C12a']:20.1f} <td> C12b (A1) </td><td> {ab['C12b']:20.1f} </tr>"
118
+ output += f"<tr><td> C21a (B2) </td><td> {ab['C21a']:.1f} <td> C21b (B2)</td><td> {ab['C21b']:.1f} "
119
+ output += f" <td> C23a (A2) </td><td> {ab['C23a']:.1f} <td> C23b (A2) </td><td> {ab['C23b']:.1f} </tr>"
120
+ output += f"<tr><td> C30 </td><td> {ab['C30']:.1f} </tr>"
121
+ output += f"<tr><td> C32a (S3) </td><td> {ab['C32a']:20.1f} <td> C32b (S3)</td><td> {ab['C32b']:20.1f} "
122
+ output += f"<td> C34a (A3) </td><td> {ab['C34a']:20.1f} <td> C34b (A3) </td><td> {ab['C34b']:20.1f} </tr>"
123
+ output += f"<tr><td> C41a (B4) </td><td> {ab['C41a']:.3g} <td> C41b (B4) </td><td> {ab['C41b']:.3g} "
124
+ output += f" <td> C43a (D4) </td><td> {ab['C43a']:.3g} <td> C43b (D4) </td><td> {ab['C41b']:.3g} "
125
+ output += f" <td> C45a (A4) </td><td> {ab['C45a']:.3g} <td> C45b (A4)</td><td> {ab['C45b']:.3g} </tr>"
126
+ output += f"<tr><td> C50 </td><td> {ab['C50']:.3g} </tr>"
127
+ output += f"<tr><td> C52a </td><td> {ab['C52a']:20.1f} <td> C52b </td><td> {ab['C52b']:20.1f} "
128
+ output += f"<td> C54a </td><td> {ab['C54a']:20.1f} <td> C54b </td><td> {ab['C54b']:20.1f} "
129
+ output += f"<td> C56a </td><td> {ab['C56a']:20.1f} <td> C56b </td><td> {ab['C56b']:20.1f} </tr>"
130
+ output += f"<tr><td> Cc </td><td> {ab['Cc']:.3g} </tr>"
131
+
132
+ output += '</table></body></html>'
133
+
134
+ display(HTML(output))
135
+
136
+
137
+
138
+ def print_aberrations_polar(ab):
139
+ from IPython.display import HTML, display
140
+
141
+ ab['C12_r'], ab['C12_phi'] = cart2pol(ab['C12a'], ab['C12b'])
142
+ ab['C21_r'], ab['C21_phi'] = cart2pol(ab['C21a'], ab['C21b'])
143
+ ab['C23_r'], ab['C23_phi'] = cart2pol(ab['C23a'], ab['C23b'])
144
+ ab['C32_r'], ab['C32_phi'] = cart2pol(ab['C32a'], ab['C32b'])
145
+ ab['C34_r'], ab['C34_phi'] = cart2pol(ab['C34a'], ab['C34b'])
146
+ ab['C41_r'], ab['C41_phi'] = cart2pol(ab['C41a'], ab['C41b'])
147
+ ab['C43_r'], ab['C43_phi'] = cart2pol(ab['C43a'], ab['C43b'])
148
+ ab['C45_r'], ab['C45_phi'] = cart2pol(ab['C45a'], ab['C45b'])
149
+ ab['C52_r'], ab['C52_phi'] = cart2pol(ab['C52a'], ab['C52b'])
150
+ ab['C54_r'], ab['C54_phi'] = cart2pol(ab['C54a'], ab['C54b'])
151
+ ab['C56_r'], ab['C56_phi'] = cart2pol(ab['C56a'], ab['C56b'])
152
+
153
+ output = '<html><body>'
154
+ output += f"Aberrations [nm] for acceleration voltage: {ab['acceleration_voltage'] / 1e3:.0f} kV"
155
+ output += '<table>'
156
+ output += f"<tr><td> C10 </td><td> {ab['C10']:.1f} </tr>"
157
+ output += f"<tr><td> C12(A1): r </td><td> {ab['C12_r']:20.1f} <td> φ </td><td> {ab['C12_phi']:20.1f} </tr>"
158
+ output += f"<tr><td> C21a (B2): r</td><td> {ab['C21_r']:20.1f} <td> φ </td><td> {ab['C21_phi']:20.1f} "
159
+ output += f" <td> C23a (A2) </td><td> {ab['C23_r']:20.1f} <td> φ </td><td> {ab['C23_phi']:20.1f} </tr>"
160
+ output += f"<tr><td> C30 </td><td> {ab['C30']:.1f} </tr>"
161
+ output += f"<tr><td> C32 (S3) </td><td> {ab['C32_r']:20.1f} <td> φ </td><td> {ab['C32_phi']:20.1f} "
162
+ output += f"<td> C34a (A3) </td><td> {ab['C34a']:20.1f} <td> φ </td><td> {ab['C34_phi']:20.1f} </tr>"
163
+ output += f"<tr><td> C41 (B4) </td><td> {ab['C41_r']:.3g} <td> φ </td><td> {ab['C41_phi']:20.1f} "
164
+ output += f" <td> C43 (D4) </td><td> {ab['C43_r']:.3g} <td> φ (D4) </td><td> {ab['C43_phi']:20.1f} "
165
+ output += f" <td> C45 (A4) </td><td> {ab['C45_r']:.3g} <td> φ (A4)</td><td> {ab['C45_phi']:20.1f} </tr>"
166
+ output += f"<tr><td> C50 </td><td> {ab['C50']:.3g} </tr>"
167
+ output += f"<tr><td> C52 </td><td> {ab['C52a']:.3g} <td> φ </td><td> {ab['C52_phi']:20.1f} "
168
+ output += f"<td> C54 </td><td> {ab['C54_r']:.3g} <td> C54 φ </td><td> {ab['C54_phi']:.1f} "
169
+ output += f"<td> C56 </td><td> {ab['C56_r']:.3g} <td> C56 </td><td> {ab['C56_phi']:.1f} </tr>"
170
+ output += f"<tr><td> Cc </td><td> {ab['Cc']:.3g} </tr>"
171
+
172
+ output += '</table></body></html>'
173
+
174
+ display(HTML(output))
175
+
176
+
177
+ def pol2cart(rho, theta):
178
+ x = rho * np.cos(theta)
179
+ y = rho * np.sin(theta)
180
+ return x, y
181
+
182
+ def ceos_to_nion(ab):
183
+ aberrations = {'C10': 0, 'C12a': 0, 'C12b': 0, 'C21a': 0, 'C21b': 0, 'C23a': 0, 'C23b': 0, 'C30': 0.,
184
+ 'C32a': 0., 'C32b': -0., 'C34a': 0., 'C34b': 0., 'C41a': 0., 'C41b': -0., 'C43a': 0.,
185
+ 'C43b': -0., 'C45a': -0., 'C45b': -0., 'C50': 0., 'C52a': -0., 'C52b': 0.,
186
+ 'C54a': -0., 'C54b': -0., 'C56a': -0., 'C56b': 0., 'C70': 0.}
187
+ aberrations['acceleration_voltage'] = 200000
188
+ for key in ab.keys():
189
+ if key == 'C1':
190
+ aberrations['C10'] = ab['C10']
191
+ elif key == 'A1-a':
192
+ x, y = pol2cart(ab['A1-a'], ab['A1-p'])
193
+ aberrations['C12a'] = x
194
+ aberrations['C12b'] = y
195
+ elif key == 'B2-a':
196
+ x, y = pol2cart(ab['B2-a'], ab['B2-p'])
197
+ aberrations['C21a'] = 3 * x
198
+ aberrations['C21b'] = 3 * y
199
+ elif key == 'A2-a':
200
+ x, y = pol2cart(ab['A2-a'], ab['A2-p'])
201
+ aberrations['C23a'] = x
202
+ aberrations['C23b'] = y
203
+ elif key == 'C3':
204
+ aberrations['C30'] = ab['C3']
205
+ elif key == 'S3-a':
206
+ x, y = pol2cart(ab['S3-a'], ab['S3-p'])
207
+ aberrations['C32a'] = 4 * x
208
+ aberrations['C32b'] = 4 * y
209
+ elif key == 'A3-a':
210
+ x, y = pol2cart(ab['A3-a'], ab['A3-p'])
211
+ aberrations['C34a'] = x
212
+ aberrations['C34b'] = y
213
+ elif key == 'B4-a':
214
+ x, y = pol2cart(ab['B4-a'], ab['B4-p'])
215
+ aberrations['C41a'] = 4 * x
216
+ aberrations['C41b'] = 4 * y
217
+ elif key == 'D4-a':
218
+ x, y = pol2cart(ab['D4-a'], ab['D4-p'])
219
+ aberrations['C43a'] = 4 * x
220
+ aberrations['C43b'] = 4 * y
221
+ elif key == 'A4-a':
222
+ x, y = pol2cart(ab['A4-a'], ab['A4-p'])
223
+ aberrations['C45a'] = x
224
+ aberrations['C45b'] = y
225
+ elif key == 'C5':
226
+ aberrations['C50'] = ab['C5']
227
+ elif key == 'A5-a':
228
+ x, y = pol2cart(ab['A5-a'], ab['A5-p'])
229
+ aberrations['C56a'] = x
230
+ aberrations['C56b'] = y
231
+ return aberrations
232
+
233
+ def ceos_carth_to_nion(ab):
234
+ aberrations = {'C10': 0, 'C12a': 0, 'C12b': 0, 'C21a': 0, 'C21b': 0, 'C23a': 0, 'C23b': 0, 'C30': 0.,
235
+ 'C32a': 0., 'C32b': -0., 'C34a': 0., 'C34b': 0., 'C41a': 0., 'C41b': -0., 'C43a': 0.,
236
+ 'C43b': -0., 'C45a': -0., 'C45b': -0., 'C50': 0., 'C52a': -0., 'C52b': 0.,
237
+ 'C54a': -0., 'C54b': -0., 'C56a': -0., 'C56b': 0., 'C70': 0.}
238
+ aberrations['acceleration_voltage'] = 200000
239
+ for key in ab.keys():
240
+ if key == 'C1':
241
+ aberrations['C10'] = ab['C1'][0]*1e9
242
+ elif key == 'A1':
243
+ aberrations['C12a'] = ab['A1'][0]*1e9
244
+ aberrations['C12b'] = ab['A1'][1]*1e9
245
+ elif key == 'B2':
246
+ print('B2', ab['B2'])
247
+ aberrations['C21a'] = 3 * ab['B2'][0]*1e9
248
+ aberrations['C21b'] = 3 * ab['B2'][1]*1e9
249
+ elif key == 'A2':
250
+ aberrations['C23a'] = ab['A2'][0]*1e9
251
+ aberrations['C23b'] = ab['A2'][1]*1e9
252
+ elif key == 'C3':
253
+ aberrations['C30'] = ab['C3'][0]*1e9
254
+ elif key == 'S3':
255
+ aberrations['C32a'] = 4 * ab['S3'][0]*1e9
256
+ aberrations['C32b'] = 4 * ab['S3'][1]*1e9
257
+ elif key == 'A3':
258
+ aberrations['C34a'] = ab['A3'][0]*1e9
259
+ aberrations['C34b'] = ab['A3'][1]*1e9
260
+ elif key == 'B4':
261
+ aberrations['C41a'] = 4 * ab['B4'][0]*1e9
262
+ aberrations['C41b'] = 4 * ab['B4'][1]*1e9
263
+ elif key == 'D4':
264
+ aberrations['C43a'] = 4 * ab['D4'][0]*1e9
265
+ aberrations['C43b'] = 4 * ab['D4'][1]*1e9
266
+ elif key == 'A4':
267
+ aberrations['C45a'] = ab['A4'][0]*1e9
268
+ aberrations['C45b'] = ab['A4'][1]*1e9
269
+ elif key == 'C5':
270
+ aberrations['C50'] = ab['C5'][0]*1e9
271
+ elif key == 'A5':
272
+ aberrations['C56a'] = ab['A5'][0]*1e9
273
+ aberrations['C56b'] = ab['A5'][1]*1e9
274
+
275
+
276
+ return aberrations
277
+
278
+ def cart2pol(x, y):
279
+ theta = np.arctan2(y, x)
280
+ rho = np.hypot(x, y)
281
+ return theta, rho
282
+
283
+ def nion_to_ceos(ab):
284
+ aberrations = {'C1': 0, 'A1-a': 0, 'A1-b': 0, 'B2-a': 0, 'B2-p': 0, 'A2-a': 0, 'A2-p': 0, 'C3': 0.,
285
+ 'S3-a': 0., 'S3-p': -0., 'A3-a': 0., 'A3-p': 0., 'B4-a': 0., 'B4-p': -0., 'D4-a': 0.,
286
+ 'D4-p': -0., 'A4-s': -0., 'A4-p': -0., 'C5': 0., 'A5-a': -0., 'A5-p': 0.}
287
+ aberrations['acceleration_voltage'] = 200000
288
+ for key in ab.keys():
289
+ if key == 'C10':
290
+ aberrations['C1'] = ab['C10']
291
+ elif key == 'C12a':
292
+ r, p = cart2pol(ab['C12a'], ab['C12b'])
293
+ aberrations['A1-a'] = r
294
+ aberrations['A1-p'] = p
295
+ elif key == 'C21a':
296
+ r, p = cart2pol(ab['C21a'], ab['C21b'])
297
+ aberrations['B2-a'] = r/3
298
+ aberrations['B2-p'] = p
299
+ elif key == 'C23a':
300
+ r, p = cart2pol(ab['C23a'], ab['C23b'])
301
+ aberrations['A2-a'] = r
302
+ aberrations['A2-p'] = p
303
+ elif key == 'C30':
304
+ aberrations['C3'] = ab['C30']
305
+ elif key == 'C32a':
306
+ r, p = cart2pol(ab['C32a'], ab['C32b'])
307
+ aberrations['S3-a'] = r/4
308
+ aberrations['S3-p'] = p
309
+ elif key == 'C34a':
310
+ r, p = cart2pol(ab['C34a'], ab['C34b'])
311
+ aberrations['A3-a'] = r
312
+ aberrations['A3-p'] = p
313
+ elif key == 'C41a':
314
+ r, p = cart2pol(ab['C41a'], ab['C41b'])
315
+ aberrations['B4-a'] = r/4
316
+ aberrations['B4-p'] = p
317
+ elif key == 'C43a':
318
+ r, p = cart2pol(ab['C43a'], ab['C43b'])
319
+ aberrations['D4-a'] = r/4
320
+ aberrations['D4-p'] = p
321
+ elif key == 'C31a':
322
+ r, p = cart2pol(ab['C41a'], ab['C41b'])
323
+ aberrations['A4-a'] = r
324
+ aberrations['A4-p'] = p
325
+ elif key == 'C50':
326
+ aberrations['C5'] = ab['C50']
327
+ elif key == 'C56a':
328
+ r, p = cart2pol(ab['C56a'], ab['C56b'])
329
+ aberrations['A5-a'] = r
330
+ aberrations['A5-p'] = p
331
+
332
+ return aberrations
333
+
334
+ def get_ronchigram(size, ab, scale='mrad'):
335
+ """ Get Ronchigram
336
+
337
+ """
338
+ size_x = size_y = size
339
+ chi, A_k = get_chi(ab, size_x, size_y)
340
+
341
+ v_noise = np.random.rand(size_x, size_y)
342
+ smoothing = 5
343
+ phi_r = ndimage.gaussian_filter(v_noise, sigma=(smoothing, smoothing), order=0)
344
+
345
+ sigma = 6 # 6 for carbon and thin
346
+
347
+ q_r = np.exp(-1j * sigma * phi_r)
348
+ # q_r = 1-phi_r * sigma
349
+
350
+ T_k = A_k * (np.exp(-1j * chi))
351
+ t_r = (np.fft.ifft2(np.fft.fftshift(T_k)))
352
+
353
+ psi_k = np.fft.fftshift(np.fft.fft2(q_r * t_r))
354
+
355
+ ronchigram = np.absolute(psi_k * np.conjugate(psi_k))
356
+
357
+ fov_reciprocal = 1 / ab['FOV'] * size_x / 2
358
+ if scale == '1/nm':
359
+ extent = [-fov_reciprocal, fov_reciprocal, -fov_reciprocal, fov_reciprocal]
360
+ ylabel = 'reciprocal distance [1/nm]'
361
+ else:
362
+ fov_mrad = fov_reciprocal * ab['wavelength'] * 1000
363
+ extent = [-fov_mrad, fov_mrad, -fov_mrad, fov_mrad]
364
+ ylabel = 'reciprocal distance [mrad]'
365
+
366
+ ab['chi'] = chi
367
+ ab['ronchi_extent'] = extent
368
+ ab['ronchi_label'] = ylabel
369
+ return ronchigram
370
+
371
+
372
+ def make_probe (chi, aperture):
373
+ chi2 = np.fft.ifftshift(chi)
374
+ chiT = np.fft.ifftshift (np.vectorize(complex)(np.cos(chi2), -np.sin(chi2)) )
375
+ ## Aply aperture function
376
+ chiT = chiT*aperture
377
+ ## inverse fft of aberration function
378
+ i2 = np.fft.fftshift(np.fft.ifft2(np.fft.ifftshift (chiT)))
379
+ ## intensity
380
+ probe = np.real(i2 * np.conjugate(i2))
381
+
382
+ return probe
383
+
384
+
385
+ def get_probe( ab, sizeX, sizeY, scale = 'mrad', verbose= True):
386
+
387
+ chi, A_k = get_chi( ab, sizeX, sizeY, verbose= False)
388
+ probe = make_probe (chi, A_k)
389
+
390
+ return probe, A_k, chi
391
+
392
+
393
+ def get_probe_large(ab):
394
+ ab['FOV'] = 20
395
+ sizeX = 512*2
396
+ probe, A_k, chi = pyTEMlib.probe_tools.get_probe( ab, sizeX, sizeX, scale = 'mrad', verbose= True)
397
+
398
+ res = np.zeros((512, 512))
399
+ res[256-32:256+32, 256-32:256+32 ] = skimage.transform.resize(probe, (64, 64))
400
+
401
+ return res
402
+
403
+
404
+ def get_chi_2(ab, u, v):
405
+ chi1 = ab['C10'] * (u ** 2 + v ** 2) / 2 \
406
+ + ab['C12a'] * (u ** 2 - v ** 2) / 2 \
407
+ - ab['C12b'] * u * v
408
+
409
+ chi2 = ab['C21a'] * (u ** 3 + u * v ** 2) / 3 \
410
+ - ab['C21b'] * (u ** 2 * v + v ** 3) / 3 \
411
+ + ab['C23a'] * (u ** 3 - 3 * u * v ** 2) / 3 \
412
+ - ab['C23b'] * (3 * u ** 2 * v - v ** 3) / 3
413
+
414
+ chi3 = ab['C30'] * (u ** 4 + 2 * u ** 2 * v ** 2 + v ** 4) / 4 \
415
+ + ab['C32a'] * (u ** 4 - v ** 4) / 4 \
416
+ - ab['C32b'] * (u ** 3 * v + u * v ** 3) / 2 \
417
+ + ab['C34a'] * (u ** 4 - 6 * u ** 2 * v ** 2 + v ** 4) / 4 \
418
+ - ab['C34b'] * (4 * u ** 3 * v - 4 * u * v ** 3) / 4
419
+
420
+ chi4 = ab['C41a'] * (u ** 5 + 2 * u ** 3 * v ** 2 + u * v ** 4) / 5 \
421
+ - ab['C41b'] * (u ** 4 * v + 2 * u ** 2 * v ** 3 + v ** 5) / 5 \
422
+ + ab['C43a'] * (u ** 5 - 2 * u ** 3 * v ** 2 - 3 * u * v ** 4) / 5 \
423
+ - ab['C43b'] * (3 * u ** 4 * v + 2 * u ** 2 * v ** 3 - v ** 5) / 5 \
424
+ + ab['C45a'] * (u ** 5 - 10 * u ** 3 * v ** 2 + 5 * u * v ** 4) / 5 \
425
+ - ab['C45b'] * (5 * u ** 4 * v - 10 * u ** 2 * v ** 3 + v ** 5) / 5
426
+
427
+ chi5 = ab['C50'] * (u ** 6 + 3 * u ** 4 * v ** 2 + 3 * u ** 2 * v ** 4 + v ** 6) / 6 \
428
+ + ab['C52a'] * (u ** 6 + u ** 4 * v ** 2 - u ** 2 * v ** 4 - v ** 6) / 6 \
429
+ - ab['C52b'] * (2 * u ** 5 * v + 4 * u ** 3 * v ** 3 + 2 * u * v ** 5) / 6 \
430
+ + ab['C54a'] * (u ** 6 - 5 * u ** 4 * v ** 2 - 5 * u ** 2 * v ** 4 + v ** 6) / 6 \
431
+ - ab['C54b'] * (4 * u ** 5 * v - 4 * u * v ** 5) / 6 \
432
+ + ab['C56a'] * (u ** 6 - 15 * u ** 4 * v ** 2 + 15 * u ** 2 * v ** 4 - v ** 6) / 6 \
433
+ - ab['C56b'] * (6 * u ** 5 * v - 20 * u ** 3 * v ** 3 + 6 * u * v ** 5) / 6
434
+
435
+ chi = chi1 + chi2 + chi3 + chi4 + chi5
436
+ return chi * 2 * np.pi / ab['wavelength']
437
+
438
+
439
+ def get_d2chidu2(ab, u, v):
440
+ d2chi1du2 = ab['C10'] + ab['C12a']
441
+
442
+ d2chi2du2 = ab['C21a'] * 2 * u \
443
+ - ab['C21b'] * 2 / 3 * v \
444
+ + ab['C23a'] * 2 * u \
445
+ - ab['C23b'] * 2 * v
446
+
447
+ d2chi3du2 = ab['C30'] * (3 * u ** 2 + v ** 2) \
448
+ + ab['C32a'] * 3 * u ** 2 \
449
+ - ab['C32b'] * 3 * u * v \
450
+ + ab['C34a'] * (3 * u ** 2 - 3 * v ** 2) \
451
+ - ab['C34b'] * 6 * u * v
452
+
453
+ d2chi4du2 = ab['C41a'] * 4 / 5 * (5 * u ** 3 + 3 * u * v ** 2) \
454
+ - ab['C41b'] * 4 / 5 * (3 * u ** 2 * v + v ** 3) \
455
+ + ab['C43a'] * 4 / 5 * (5 * u ** 3 - 3 * u * v ** 2) \
456
+ - ab['C43b'] * 4 / 5 * (9 * u ** 2 * v + v ** 3) \
457
+ + ab['C45a'] * 4 * (u ** 3 - 3 * u * v ** 2) \
458
+ - ab['C45b'] * 4 * (3 * u ** 2 * v - v ** 3)
459
+
460
+ d2chi5du2 = ab['C50'] * (5 * u ** 4 + 6 * u ** 2 * v ** 2 + v ** 4) \
461
+ + ab['C52a'] * (15 * u ** 4 + 6 * u ** 2 * v ** 2 - v ** 4) / 3 \
462
+ - ab['C52b'] * (20 * u ** 3 * v + 12 * u * v ** 3) / 3 \
463
+ + ab['C54a'] * 5 / 3 * (3 * u ** 4 - 6 * u ** 2 * v ** 2 - v ** 4) \
464
+ - ab['C54b'] * 5 / 3 * (8 * u ** 3 * v) \
465
+ + ab['C56a'] * 5 * (u ** 4 - 6 * u ** 2 * v ** 2 + v ** 4) \
466
+ - ab['C56b'] * 20 * (u ** 3 * v - u * v ** 3)
467
+
468
+ d2chidu2 = d2chi1du2 + d2chi2du2 + d2chi3du2 + d2chi4du2 + d2chi5du2
469
+ return d2chidu2
470
+
471
+
472
+ def get_d2chidudv(ab, u, v):
473
+ d2chi1dudv = -ab['C12b']
474
+
475
+ d2chi2dudv = ab['C21a'] * 2 / 3 * v \
476
+ - ab['C21b'] * 2 / 3 * u \
477
+ - ab['C23a'] * 2 * v \
478
+ - ab['C23b'] * 2 * u
479
+
480
+ d2chi3dudv = ab['C30'] * 2 * u * v \
481
+ + ab['C32a'] * 0 \
482
+ - ab['C32b'] * 3 / 2 * (u ** 2 + v ** 2) \
483
+ - ab['C34a'] * 6 * u * v \
484
+ - ab['C34b'] * 3 * (u ** 2 - v ** 2)
485
+
486
+ d2chi4dudv = ab['C41a'] * 4 / 5 * (3 * u ** 2 * v + v ** 3) \
487
+ - ab['C41b'] * 4 / 5 * (u ** 3 + 3 * u * v ** 2) \
488
+ - ab['C43a'] * 12 / 5 * (u ** 2 * v + v ** 3) \
489
+ - ab['C43b'] * 12 / 5 * (u ** 3 + u * v ** 2) \
490
+ - ab['C45a'] * 4 * (3 * u ** 2 * v - v ** 3) \
491
+ - ab['C45b'] * 4 * (u ** 3 - 3 * u * v ** 2)
492
+
493
+ d2chi5dudv = ab['C50'] * 4 * u * v * (u ** 2 + v ** 2) \
494
+ + ab['C52a'] * 4 / 3 * (u ** 3 * v - u * v ** 3) \
495
+ - ab['C52b'] * (5 * u ** 4 + 18 * u ** 2 * v ** 2 + 5 * v ** 4) / 3 \
496
+ - ab['C54a'] * 20 / 3 * (u ** 3 * v + u * v ** 3) \
497
+ - ab['C54b'] * 10 / 3 * (u ** 4 - v ** 4) \
498
+ - ab['C56a'] * 20 * (u ** 3 * v - u * v ** 3) \
499
+ - ab['C56b'] * 5 * (u ** 4 - 6 * u ** 2 * v ** 2 + v ** 4)
500
+
501
+ d2chidudv = d2chi1dudv + d2chi2dudv + d2chi3dudv + d2chi4dudv + d2chi5dudv
502
+ return d2chidudv
503
+
504
+
505
+ def get_d2chidv2(ab, u, v):
506
+ d2chi1dv2 = ab['C10'] - ab['C12a']
507
+
508
+ d2chi2dv2 = ab['C21a'] * 2 / 3 * u \
509
+ - ab['C21b'] * 2 * v \
510
+ - ab['C23a'] * 2 * u \
511
+ + ab['C23b'] * 2 * v
512
+
513
+ d2chi3dv2 = ab['C30'] * (u ** 2 + 3 * v ** 2) \
514
+ - ab['C32a'] * 3 * v ** 2 \
515
+ - ab['C32b'] * 3 * v * u \
516
+ - ab['C34a'] * 3 * (u ** 2 - v ** 2) \
517
+ + ab['C34b'] * 6 * u * v
518
+
519
+ d2chi4dv2 = ab['C41a'] * 4 / 5 * (u ** 3 + 3 * u * v ** 2) \
520
+ - ab['C41b'] * 4 / 5 * (3 * u ** 2 * v + 5 * v ** 3) \
521
+ - ab['C43a'] * 4 / 5 * (u ** 3 + 9 * u * v ** 2) \
522
+ - ab['C43b'] * 4 / 5 * (3 * u ** 2 * v - 5 * v ** 3) \
523
+ - ab['C45a'] * 4 * (u ** 3 - 3 * u * v ** 2) \
524
+ + ab['C45b'] * 4 * (3 * u ** 2 * v - v ** 3)
525
+
526
+ d2chi5dv2 = ab['C50'] * (u ** 4 + 6 * u ** 2 * v ** 2 + 5 * v ** 4) \
527
+ + ab['C52a'] * (u ** 4 - 6 * u ** 2 * v ** 2 - 15 * v ** 4) / 3 \
528
+ - ab['C52b'] * (12 * u ** 3 * v + 20 * u * v ** 3) / 3 \
529
+ - ab['C54a'] * 5 / 3 * (u ** 4 + 6 * u ** 2 * v ** 2 - 3 * v ** 4) \
530
+ + ab['C54b'] * 40 / 3 * u * v ** 3 \
531
+ - ab['C56a'] * 5 * (u ** 4 - 6 * u ** 2 * v ** 2 + v ** 4) \
532
+ + ab['C56b'] * 20 * (u ** 3 * v - u * v ** 3)
533
+
534
+ d2chidv2 = d2chi1dv2 + d2chi2dv2 + d2chi3dv2 + d2chi4dv2 + d2chi5dv2
535
+ return d2chidv2
536
+
537
+
538
+ def get_source_energy_spread():
539
+ x = np.linspace(-0.5, .9, 29)
540
+ y = [0.0143, 0.0193, 0.0281, 0.0440, 0.0768, 0.1447, 0.2785, 0.4955, 0.7442, 0.9380, 1.0000, 0.9483, 0.8596, 0.7620,
541
+ 0.6539, 0.5515, 0.4478, 0.3500, 0.2683, 0.1979, 0.1410, 0.1021, 0.0752, 0.0545, 0.0401, 0.0300, 0.0229, 0.0176,
542
+ 0.0139]
543
+
544
+ return x, y
545
+
546
+
547
+ def get_target_aberrations(TEM_name, acceleration_voltage):
548
+ ab = {}
549
+ if TEM_name == 'NionUS200':
550
+ if int(acceleration_voltage) == 200000:
551
+ print(f' **** Using Target Values at {acceleration_voltage / 1000}kV for Aberrations of {TEM_name}****')
552
+ ab = {'C10': 0, 'C12a': 0, 'C12b': 0, 'C21a': -335., 'C21b': 283., 'C23a': -34., 'C23b': 220.,
553
+ 'C30': -8080.,
554
+ 'C32a': 18800., 'C32b': -2260., 'C34a': 949., 'C34b': 949., 'C41a': 54883., 'C41b': -464102.,
555
+ 'C43a': 77240.5,
556
+ 'C43b': -540842., 'C45a': -79844.4, 'C45b': -76980.8, 'C50': 9546970., 'C52a': -2494290.,
557
+ 'C52b': 2999910.,
558
+ 'C54a': -2020140., 'C54b': -2019630., 'C56a': -535079., 'C56b': 1851850.}
559
+ ab['source_size'] = 0.051
560
+ ab['acceleration_voltage'] = acceleration_voltage
561
+ ab['convergence_angle'] = 30
562
+
563
+ ab['Cc'] = 1.3e6 # // Cc in nm
564
+
565
+ if int(acceleration_voltage) == 100000:
566
+ print(f' **** Using Target Values at {acceleration_voltage / 1000}kV for Aberrations of {TEM_name}****')
567
+
568
+ ab = {'C10': 0, 'C12a': 0, 'C12b': 0, 'C21a': 157., 'C21b': 169, 'C23a': -173., 'C23b': 48.7, 'C30': 201.,
569
+ 'C32a': 1090., 'C32b': 6840., 'C34a': 1010., 'C34b': 79.9, 'C41a': -210696., 'C41b': -262313.,
570
+ 'C43a': 348450., 'C43b': -9.7888e4, 'C45a': 6.80247e4, 'C45b': -3.14637e1, 'C50': -193896.,
571
+ 'C52a': -1178950, 'C52b': -7414340, 'C54a': -1753890, 'C54b': -1753890, 'C56a': -631786,
572
+ 'C56b': -165705}
573
+ ab['source_size'] = 0.051
574
+ ab['acceleration_voltage'] = acceleration_voltage
575
+ ab['convergence_angle'] = 30
576
+ ab['Cc'] = 1.3e6
577
+
578
+ if int(acceleration_voltage) == 60000:
579
+ print(f' **** Using Target Values at {acceleration_voltage / 1000}kV for Aberrations of {TEM_name}****')
580
+
581
+ ab = {'C10': 0, 'C12a': 0, 'C12b': 0, 'C21a': 11.5, 'C21b': 113, 'C23a': -136., 'C23b': 18.2, 'C30': 134.,
582
+ 'C32a': 1080., 'C32b': 773., 'C34a': 1190., 'C34b': -593., 'C41a': -179174., 'C41b': -350378.,
583
+ 'C43a': 528598, 'C43b': -257349., 'C45a': 63853.4, 'C45b': 1367.98, 'C50': 239021., 'C52a': 1569280.,
584
+ 'C52b': -6229310., 'C54a': -3167620., 'C54b': -449198., 'C56a': -907315., 'C56b': -16281.9}
585
+ ab['source_size'] = 0.081
586
+ ab['acceleration_voltage'] = acceleration_voltage
587
+ ab['convergence_angle'] = 30
588
+ ab['Cc'] = 1.3e6 # // Cc in nm
589
+
590
+ ab['origin'] = 'target aberrations'
591
+ ab['TEM_name'] = TEM_name
592
+ ab['wavelength'] = pyTEMlib.image_tools.get_wavelength(ab['acceleration_voltage'])
593
+
594
+ if TEM_name == 'NionUS100':
595
+ if int(acceleration_voltage) == 100000:
596
+ print(f' **** Using Target Values at {acceleration_voltage / 1000}kV for Aberrations of {TEM_name}****')
597
+
598
+ ab = {'C10': 0, 'C12a': 0, 'C12b': 0, 'C21a': 157., 'C21b': 169, 'C23a': -173., 'C23b': 48.7, 'C30': 201.,
599
+ 'C32a': 1090., 'C32b': 6840., 'C34a': 1010., 'C34b': 79.9, 'C41a': -210696., 'C41b': -262313.,
600
+ 'C43a': 348450., 'C43b': -9.7888e4, 'C45a': 6.80247e4, 'C45b': -3.14637e1, 'C50': -193896.,
601
+ 'C52a': -1178950, 'C52b': -7414340, 'C54a': -1753890, 'C54b': -1753890, 'C56a': -631786,
602
+ 'C56b': -165705}
603
+ ab['source_size'] = 0.051
604
+ ab['acceleration_voltage'] = acceleration_voltage
605
+ ab['convergence_angle'] = 30
606
+ ab['Cc'] = 1.3e6 # // Cc in nm
607
+
608
+ if int(acceleration_voltage) == 60000:
609
+ print(f' **** Using Target Values at {acceleration_voltage / 1000}kV for Aberrations of {TEM_name}****')
610
+
611
+ ab = {'C10': 0, 'C12a': 0, 'C12b': 0, 'C21a': 11.5, 'C21b': 113, 'C23a': -136., 'C23b': 18.2, 'C30': 134.,
612
+ 'C32a': 1080., 'C32b': 773., 'C34a': 1190., 'C34b': -593., 'C41a': -179174., 'C41b': -350378.,
613
+ 'C43a': 528598, 'C43b': -257349., 'C45a': 63853.4, 'C45b': 1367.98, 'C50': 239021., 'C52a': 1569280.,
614
+ 'C52b': -6229310., 'C54a': -3167620., 'C54b': -449198., 'C56a': -907315., 'C56b': -16281.9}
615
+ ab['source_size'] = 0.081
616
+ ab['acceleration_voltage'] = acceleration_voltage
617
+ ab['convergence_angle'] = 30
618
+ ab['Cc'] = 1.3e6 # // Cc in nm
619
+
620
+ ab['origin'] = 'target aberrations'
621
+ ab['TEM_name'] = TEM_name
622
+ ab['wavelength'] = pyTEMlib.image_tools.get_wavelength(ab['acceleration_voltage'])
623
+
624
+ if TEM_name == 'ZeissMC200':
625
+ ab = {'C10': 0, 'C12a': 0, 'C12b': 0, 'C21a': 0, 'C21b': 0, 'C23a': 0, 'C23b': 0, 'C30': 0.,
626
+ 'C32a': 0., 'C32b': -0., 'C34a': 0., 'C34b': 0., 'C41a': 0., 'C41b': -0., 'C43a': 0.,
627
+ 'C43b': -0., 'C45a': -0., 'C45b': -0., 'C50': 0., 'C52a': -0., 'C52b': 0.,
628
+ 'C54a': -0., 'C54b': -0., 'C56a': -0., 'C56b': 0.}
629
+ ab['C30'] = 2.2 * 1e6
630
+
631
+ ab['Cc'] = 2.0 * 1e6
632
+
633
+ ab['source_size'] = 0.2
634
+ ab['acceleration_voltage'] = acceleration_voltage
635
+ ab['convergence_angle'] = 10
636
+
637
+ ab['origin'] = 'target aberrations'
638
+ ab['TEM_name'] = TEM_name
639
+
640
+ ab['wavelength'] = pyTEMlib.image_tools.get_wavelength(ab['acceleration_voltage'])
641
+
642
+ if TEM_name == 'Spectra300':
643
+ ab = {'C10': 0, 'C12a': 0, 'C12b': 0.38448128113770325,
644
+ 'C21a': -68.45251255685642, 'C21b': 64.85359774641199, 'C23a': 11.667578600494137, 'C23b': -29.775627778458194,
645
+ 'C30': 123,
646
+ 'C32a': 95.3047364258614, 'C32b': -189.72105710231244, 'C34a': -47.45099594807912, 'C34b': -94.67424667529909,
647
+ 'C41a': -905.31842572806, 'C41b': 981.316128853203, 'C43a': 4021.8433526960034, 'C43b': 131.72716642732158,
648
+ 'C45a': -4702.390968272048, 'C45b': -208.25028574642903, 'C50': 552000., 'C52a': -0., 'C52b': 0.,
649
+ 'C54a': -0., 'C54b': -0., 'C56a': -36663.643489934424, 'C56b': 21356.079837905396,
650
+ 'acceleration_voltage': 200000,
651
+ 'FOV': 34.241659495148205,
652
+ 'Cc': 1* 1e6,
653
+ 'convergence_angle': 30,
654
+ 'wavelength': 0.0025079340450548005}
655
+ return ab
656
+
657
+
658
+ def get_ronchigram_2(size, ab, scale='mrad', threshold=3):
659
+ aperture_angle = ab['convergence_angle'] / 1000.0 # in rad
660
+
661
+ wavelength = pyTEMlib.image_tools.get_wavelength(ab['acceleration_voltage'])
662
+ # if verbose:
663
+ # print(f"Acceleration voltage {ab['acceleration_voltage']/1000:}kV => wavelength {wavelength*1000.:.2f}pm")
664
+
665
+ ab['wavelength'] = wavelength
666
+
667
+ size_x = size_y = size
668
+
669
+ # Reciprocal plane in 1/nm
670
+ dk = ab['reciprocal_FOV'] / size
671
+ k_x = np.array(dk * (-size_x / 2. + np.arange(size_x)))
672
+ k_y = np.array(dk * (-size_y / 2. + np.arange(size_y)))
673
+ t_x_v, t_y_v = np.meshgrid(k_x, k_y)
674
+
675
+ chi = get_chi_2(ab, t_x_v, t_y_v) # , verbose= True)
676
+ # define reciprocal plane in angles
677
+ phi = np.arctan2(t_x_v, t_y_v)
678
+ theta = np.arctan2(np.sqrt(t_x_v ** 2 + t_y_v ** 2), 1 / wavelength)
679
+
680
+ # Aperture function
681
+ mask = theta >= aperture_angle
682
+
683
+ aperture = np.ones((size_x, size_y), dtype=float)
684
+ aperture[mask] = 0.
685
+
686
+ v_noise = np.random.rand(size_x, size_y)
687
+ smoothing = 10
688
+ phi_r = ndimage.gaussian_filter(v_noise, sigma=(smoothing, smoothing), order=0)
689
+
690
+ sigma = 6 # 6 for carbon and thin
691
+
692
+ q_r = np.exp(-1j * sigma * phi_r)
693
+ # q_r = 1-phi_r * sigma
694
+
695
+ T_k = aperture * (np.exp(-1j * chi))
696
+ t_r = np.fft.ifft2(np.fft.fftshift(T_k))
697
+
698
+ Psi_k = np.fft.fftshift(np.fft.fft2(q_r * t_r))
699
+
700
+ ronchigram = I_k = np.absolute(Psi_k * np.conjugate(Psi_k))
701
+
702
+ fov_reciprocal = ab['reciprocal_FOV']
703
+ if scale == '1/nm':
704
+ extent = [-fov_reciprocal, fov_reciprocal, -fov_reciprocal, fov_reciprocal]
705
+ ylabel = 'reciprocal distance [1/nm]'
706
+ else:
707
+ fov_mrad = fov_reciprocal * ab['wavelength'] * 1000
708
+ extent = [-fov_mrad, fov_mrad, -fov_mrad, fov_mrad]
709
+ ylabel = 'reciprocal distance [mrad]'
710
+
711
+ ab['chi'] = chi
712
+ ab['ronchi_extent'] = extent
713
+ ab['ronchi_label'] = ylabel
714
+
715
+ h = np.zeros([chi.shape[0], chi.shape[1], 2, 2])
716
+ h[:, :, 0, 0] = get_d2chidu2(ab, t_x_v, t_y_v)
717
+ h[:, :, 0, 1] = get_d2chidudv(ab, t_x_v, t_y_v)
718
+ h[:, :, 1, 0] = get_d2chidudv(ab, t_x_v, t_y_v)
719
+ h[:, :, 1, 1] = get_d2chidv2(ab, t_x_v, t_y_v)
720
+
721
+ # get Eigenvalues
722
+ _, s, _ = np.linalg.svd(h)
723
+
724
+ # get smallest Eigenvalue per pixel
725
+ infinite_magnification = np.min(s, axis=2)
726
+
727
+ # set all values below a threshold value to one, otherwise 0
728
+ infinite_magnification[infinite_magnification <= threshold] = 1
729
+ infinite_magnification[infinite_magnification > threshold] = 0
730
+
731
+ return ronchigram, infinite_magnification
732
+
733
+
734
+ # ## Aberration Function for Probe calculations
735
+ def make_chi1(phi, theta, wavelength, ab, c1_include):
736
+ """
737
+ # ##
738
+ # Aberration function chi without defocus
739
+ # ##
740
+ """
741
+ t0 = np.power(theta, 1) / 1 * (float(ab['C01a']) * np.cos(1 * phi) + float(ab['C01b']) * np.sin(1 * phi))
742
+
743
+ if c1_include == 1: # First and second terms
744
+ t1 = np.power(theta, 2) / 2 * (ab['C10'] + ab['C12a'] * np.cos(2 * phi) + ab['C12b'] * np.sin(2 * phi))
745
+ elif c1_include == 2: # Second terms only
746
+ t1 = np.power(theta, 2) / 2 * (ab['C12a'] * np.cos(2 * phi) + ab['C12b'] * np.sin(2 * phi))
747
+ else: # none for zero
748
+ t1 = t0 * 0.
749
+
750
+ t2 = np.power(theta, 3) / 3 * (ab['C21a'] * np.cos(1 * phi) + ab['C21b'] * np.sin(1 * phi)
751
+ + ab['C23a'] * np.cos(3 * phi) + ab['C23b'] * np.sin(3 * phi))
752
+
753
+ t3 = np.power(theta, 4) / 4 * (ab['C30']
754
+ + ab['C32a'] * np.cos(2 * phi)
755
+ + ab['C32b'] * np.sin(2 * phi)
756
+ + ab['C34a'] * np.cos(4 * phi)
757
+ + ab['C34b'] * np.sin(4 * phi))
758
+
759
+ t4 = np.power(theta, 5) / 5 * (ab['C41a'] * np.cos(1 * phi)
760
+ + ab['C41b'] * np.sin(1 * phi)
761
+ + ab['C43a'] * np.cos(3 * phi)
762
+ + ab['C43b'] * np.sin(3 * phi)
763
+ + ab['C45a'] * np.cos(5 * phi)
764
+ + ab['C45b'] * np.sin(5 * phi))
765
+
766
+ t5 = np.power(theta, 6) / 6 * (ab['C50']
767
+ + ab['C52a'] * np.cos(2 * phi)
768
+ + ab['C52b'] * np.sin(2 * phi)
769
+ + ab['C54a'] * np.cos(4 * phi)
770
+ + ab['C54b'] * np.sin(4 * phi)
771
+ + ab['C56a'] * np.cos(6 * phi)
772
+ + ab['C56b'] * np.sin(6 * phi))
773
+
774
+ chi = t0 + t1 + t2 + t3 + t4 + t5
775
+ if 'C70' in ab:
776
+ chi += np.power(theta, 8) / 8 * (ab['C70'])
777
+
778
+ return chi * 2 * np.pi / wavelength # np.power(theta,6)/6*( ab['C50'] )
779
+
780
+
781
+ def probe2(ab, size_x, size_y, tags, verbose=False):
782
+ """
783
+
784
+ * This function creates an incident STEM probe
785
+ * at position (0,0)
786
+ * with parameters given in ab dictionary
787
+ *
788
+ * The following Aberration functions are being used:
789
+ * 1) ddf = Cc*de/E but not + Cc2*(de/E)^2,
790
+ * Cc, Cc2 = chrom. Aber. (1st, 2nd order) [1]
791
+ * 2) chi(qx,qy) = (2*pi/lambda)*{0.5*C1*(qx^2+qy^2)+
792
+ * 0.5*C12a*(qx^2-qy^2)+
793
+ * C12b*qx*qy+
794
+ * C21a/3*qx*(qx^2+qy^2)+
795
+ * ...
796
+ * +0.5*C3*(qx^2+qy^2)^2
797
+ * +0.125*C5*(qx^2+qy^2)^3
798
+ * ... (need to finish)
799
+ *
800
+ *
801
+ * qx = acos(k_x/K), qy = acos(k_y/K)
802
+ *
803
+ * References:
804
+ * [1] J. Zach, M. Haider,
805
+ * "Correction of spherical and Chromatic Aberration
806
+ * in a low Voltage SEM", Optik 98 (3), 112-118 (1995)
807
+ * [2] O.L. Krivanek, N. Delby, A.R. Lupini,
808
+ * "Towards sub-Angstrom Electron Beams",
809
+ * Ultramicroscopy 78, 1-11 (1999)
810
+ *
811
+
812
+
813
+ # Internally reciprocal lattice vectors in 1/nm or rad.
814
+ # All calculations of chi in angles.
815
+ # All aberration coefficients in nm
816
+ """
817
+
818
+ if 'fov' not in ab:
819
+ if 'fov' not in tags:
820
+ print(' need field of view in tags ')
821
+ else:
822
+ ab['fov'] = tags['fov']
823
+
824
+ if 'convAngle' not in ab:
825
+ ab['convAngle'] = 30 # in mrad
826
+
827
+ ap_angle = ab['convAngle'] / 1000.0 # in rad
828
+
829
+ e0 = ab['EHT'] = float(ab['EHT']) # acceleration voltage in ev
830
+
831
+ # defocus = ab['C10']
832
+
833
+ if 'C01a' not in ab:
834
+ ab['C01a'] = 0.
835
+ if 'C01b' not in ab:
836
+ ab['C01b'] = 0.
837
+
838
+ if 'C50' not in ab:
839
+ ab['C50'] = 0.
840
+ if 'C70' not in ab:
841
+ ab['C70'] = 0.
842
+
843
+ if 'Cc' not in ab:
844
+ ab['Cc'] = 1.3e6 # Cc in nm
845
+
846
+ def get_wl():
847
+ h = 6.626 * 10 ** -34
848
+ m0 = 9.109 * 10 ** -31
849
+ ev = 1.602 * 10 ** -19 * e0
850
+ c = 2.998 * 10 ** 8
851
+ return h / np.sqrt(2 * m0 * ev * (1 + ev / (2 * m0 * c ** 2))) * 10 ** 9
852
+
853
+ wavelength = get_wl()
854
+ if verbose:
855
+ print('Acceleration voltage {0:}kV => wavelength {1:.2f}pm'.format(int(e0 / 1000), wavelength * 1000))
856
+ ab['wavelength'] = wavelength
857
+
858
+ # Reciprocal plane in 1/nm
859
+ dk = 1 / ab['fov']
860
+ k_x = np.array(dk * (-size_x / 2. + np.arange(size_x)))
861
+ k_y = np.array(dk * (-size_y / 2. + np.arange(size_y)))
862
+ t_xv, t_yv = np.meshgrid(k_x, k_y)
863
+
864
+ # define reciprocal plane in angles
865
+ phi = np.arctan2(t_xv, t_yv)
866
+ theta = np.arctan2(np.sqrt(t_xv ** 2 + t_yv ** 2), 1 / wavelength)
867
+
868
+ # calculate chi but omit defocus
869
+ chi = np.fft.ifftshift(make_chi1(phi, theta, wavelength, ab, 2))
870
+ probe = np.zeros((size_x, size_y))
871
+
872
+ # Aperture function
873
+ mask = theta >= ap_angle
874
+
875
+ # Calculate probe with Cc
876
+
877
+ for i in range(len(ab['zeroLoss'])):
878
+ df = ab['C10'] + ab['Cc'] * ab['zeroEnergy'][i] / e0
879
+ if verbose:
880
+ print('defocus due to Cc: {0:.2f} nm with weight {1:.2f}'.format(df, ab['zeroLoss'][i]))
881
+ # Add defocus
882
+ chi2 = chi + np.power(theta, 2) / 2 * df
883
+ # Calculate exponent of - i * chi
884
+ chi_t = np.fft.ifftshift(np.vectorize(complex)(np.cos(chi2), -np.sin(chi2)))
885
+ # Apply aperture function
886
+ chi_t[mask] = 0.
887
+ # inverse fft of aberration function
888
+ i2 = np.fft.fftshift(np.fft.ifft2(np.fft.ifftshift(chi_t)))
889
+ # add intensities
890
+ probe = probe + np.real(i2 * np.conjugate(i2)).T * ab['zeroLoss'][i]
891
+
892
+ ab0 = {}
893
+ for key in ab:
894
+ ab0[key] = 0.
895
+ # chiIA = np.fft.fftshift(make_chi1(phi, theta, wavelength, ab0, 0)) # np.ones(chi2.shape)*2*np.pi/wavelength
896
+ chi_i = np.ones((size_y, size_x))
897
+ chi_i[mask] = 0.
898
+ i2 = np.fft.fftshift(np.fft.ifft2(np.fft.ifftshift(chi_i)))
899
+ ideal = np.real(i2 * np.conjugate(i2))
900
+
901
+ probe_f = np.fft.fft2(probe, probe.shape) + 1e-12
902
+ ideal_f = np.fft.fft2(ideal, probe.shape)
903
+ fourier_space_division = ideal_f / probe_f
904
+ probe_r = (np.fft.ifft2(fourier_space_division, probe.shape))
905
+
906
+ return probe / sum(ab['zeroLoss']), np.real(probe_r)