pyTEMlib 0.2024.2.2__py2.py3-none-any.whl → 0.2024.6.0__py2.py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of pyTEMlib might be problematic. Click here for more details.

Files changed (15) hide show
  1. pyTEMlib/core_loss_widget.py +658 -0
  2. pyTEMlib/eels_dialog.py +13 -12
  3. pyTEMlib/eels_dialog_utilities.py +2 -3
  4. pyTEMlib/eels_tools.py +56 -71
  5. pyTEMlib/file_tools.py +7 -1
  6. pyTEMlib/image_tools.py +95 -23
  7. pyTEMlib/info_widget.py +301 -365
  8. pyTEMlib/low_loss_widget.py +176 -0
  9. pyTEMlib/version.py +2 -2
  10. {pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/METADATA +4 -4
  11. {pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/RECORD +15 -13
  12. {pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/WHEEL +1 -1
  13. {pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/LICENSE +0 -0
  14. {pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/entry_points.txt +0 -0
  15. {pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/top_level.txt +0 -0
pyTEMlib/low_loss_widget.py ADDED
@@ -0,0 +1,176 @@
1
+ from typing import Any
2
+
3
+ import numpy as np
4
+ import os
5
+ import ipywidgets
6
+ import matplotlib.pylab as plt
7
+ import matplotlib
8
+ from IPython.display import display
9
+
10
+ import sidpy
11
+ # from pyTEMlib.microscope import microscope
12
+ from pyTEMlib import file_tools
13
+ from pyTEMlib import eels_tools
14
+
15
+
16
+ def get_low_loss_sidebar() -> Any:
17
+ side_bar = ipywidgets.GridspecLayout(9, 3, width='auto', grid_gap="0px")
18
+
19
+ side_bar[0, :2] = ipywidgets.Dropdown(
20
+ options=[('None', 0)],
21
+ value=0,
22
+ description='Main Dataset:',
23
+ disabled=False)
24
+
25
+ row = 1
26
+
27
+ side_bar[row, :3] = ipywidgets.Button(description='Resolution Function',
28
+ layout=ipywidgets.Layout(width='auto', grid_area='header'),
29
+ style=ipywidgets.ButtonStyle(button_color='lightblue'))
30
+ row += 1
31
+ side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='fit width:', disabled=False, color='black',
32
+ layout=ipywidgets.Layout(width='200px'))
33
+ side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
34
+ row +=1
35
+ side_bar[row, 0] = ipywidgets.widgets.Label(value="thickness", layout=ipywidgets.Layout(width='100px'))
36
+ side_bar[row, 1] = ipywidgets.widgets.Label(value="", layout=ipywidgets.Layout(width='100px'))
37
+ side_bar[row, 2] = ipywidgets.widgets.Label(value="* iMFP", layout=ipywidgets.Layout(width='100px'))
38
+ row +=1
39
+ side_bar[row, 0] = ipywidgets.ToggleButton(description='Plot Res.Fct.',
40
+ disabled=False,
41
+ button_style='', # 'success', 'info', 'warning', 'danger' or ''
42
+ tooltip='Plots resolution function on right',
43
+ layout=ipywidgets.Layout(width='100px'))
44
+
45
+ side_bar[row, 2] = ipywidgets.ToggleButton(description='Probability',
46
+ disabled=False,
47
+ button_style='', # 'success', 'info', 'warning', 'danger' or ''
48
+ tooltip='Changes y-axis to probability if flux is given',
49
+ layout=ipywidgets.Layout(width='100px'))
50
+
51
+
52
+ row += 1
53
+ side_bar[row, :3] = ipywidgets.Button(description='Drude',
54
+ layout=ipywidgets.Layout(width='auto', grid_area='header'),
55
+ style=ipywidgets.ButtonStyle(button_color='lightblue'))
56
+ row += 1
57
+ side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Start Fit:', disabled=False, color='black',
58
+ layout=ipywidgets.Layout(width='200px'))
59
+ side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
60
+ row += 1
61
+ side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='End Fit:', disabled=False, color='black',
62
+ layout=ipywidgets.Layout(width='200px'))
63
+ side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='50px'))
64
+ row +=1
65
+ side_bar[row, 0] = ipywidgets.ToggleButton(description='Plot Drude',
66
+ disabled=False,
67
+ button_style='', # 'success', 'info', 'warning', 'danger' or ''
68
+ tooltip='Plots resolution function on right',
69
+ layout=ipywidgets.Layout(width='100px'))
70
+
71
+ side_bar[row, 2] = ipywidgets.ToggleButton(description='Plot Diel.Fct.',
72
+ disabled=False,
73
+ button_style='', # 'success', 'info', 'warning', 'danger' or ''
74
+ tooltip='Changes y-axis to probability if flux is given',
75
+ layout=ipywidgets.Layout(width='100px'))
76
+
77
+
78
+ return side_bar
79
+
80
+ class LowLoss(object):
81
+ def __init__(self, sidebar=None, parent=None):
82
+ self.parent = parent
83
+ self.dataset = parent.dataset
84
+ self.low_loss_tab = sidebar
85
+ self.set_ll_action()
86
+ self.update_ll_sidebar()
87
+
88
+ def update_ll_sidebar(self):
89
+ spectrum_list = ['None']
90
+ for index, key in enumerate(self.parent.datasets.keys()):
91
+ if isinstance(self.parent.datasets[key], sidpy.Dataset):
92
+ if 'SPECTR' in self.parent.datasets[key].data_type.name:
93
+ energy_offset = self.parent.datasets[key].get_spectral_dims(return_axis=True)[0][0]
94
+ if energy_offset < 0:
95
+ spectrum_list.append(f'{key}: {self.parent.datasets[key].title}')
96
+
97
+ self.low_loss_tab[0, 0].options = spectrum_list
98
+
99
+ def get_resolution_function(self, value):
100
+ self.low_loss_tab[4, 0].value = False
101
+ zero_loss_fit_width=self.low_loss_tab[2, 0].value
102
+ self.parent.datasets['resolution_functions'] = eels_tools.get_resolution_functions(self.parent.dataset,
103
+ startFitEnergy=-zero_loss_fit_width,
104
+ endFitEnergy=zero_loss_fit_width)
105
+ if 'low_loss' not in self.dataset.metadata:
106
+ self.dataset.metadata['zero_loss'] = {}
107
+ self.dataset.metadata['zero_loss'].update(self.parent.datasets['resolution_functions'].metadata['zero_loss'])
108
+ self.low_loss_tab[4, 0].value = True
109
+ self.low_loss_tab[3, 1].value = f"{np.log(self.parent.dataset.sum()/self.parent.datasets['resolution_functions'].sum())}"
110
+
111
+
112
+
113
+ def set_ll_action(self):
114
+ self.low_loss_tab[0, 0].observe(self.update_ll_dataset)
115
+ #self.low_loss_tab[1, 0].on_click(self.fix_energy_scale)
116
+ #self.low_loss_tab[2, 0].observe(self.set_energy_scale, names='value')
117
+ #self.low_loss_tab[3, 0].observe(self.set_energy_scale, names='value')
118
+ self.low_loss_tab[1, 0].on_click(self.get_resolution_function)
119
+ self.low_loss_tab[4, 2].observe(self.parent.info.set_y_scale, names='value')
120
+ self.low_loss_tab[4, 0].observe(self._update, names='value')
121
+
122
+ def _update(self, ev=0):
123
+ self.parent._update(ev)
124
+
125
+ if self.low_loss_tab[4, 0].value:
126
+ if 'resolution_functions' in self.parent.datasets:
127
+ resolution_function = self.get_additional_spectrum('resolution_functions')
128
+ self.parent.axis.plot(self.parent.energy_scale, resolution_function, label='resolution_function')
129
+ self.parent.axis.plot(self.parent.energy_scale,
130
+ self.parent.spectrum -resolution_function, label='difference')
131
+
132
+ self.parent.axis.legend()
133
+
134
+ def get_additional_spectrum(self, key):
135
+ if key not in self.parent.datasets.keys():
136
+ return
137
+
138
+ if self.parent.datasets[key].data_type == sidpy.DataType.SPECTRUM:
139
+ self.spectrum = self.parent.datasets[key].copy()
140
+ else:
141
+ image_dims = self.parent.datasets[key].get_dimensions_by_type(sidpy.DimensionType.SPATIAL)
142
+ selection = []
143
+ for dim, axis in self.parent.datasets[key]._axes.items():
144
+ # print(dim, axis.dimension_type)
145
+ if axis.dimension_type == sidpy.DimensionType.SPATIAL:
146
+ if dim == image_dims[0]:
147
+ selection.append(slice(self.x, self.x + self.bin_x))
148
+ else:
149
+ selection.append(slice(self.y, self.y + self.bin_y))
150
+
151
+ elif axis.dimension_type == sidpy.DimensionType.SPECTRAL:
152
+ selection.append(slice(None))
153
+ elif axis.dimension_type == sidpy.DimensionType.CHANNEL:
154
+ selection.append(slice(None))
155
+ else:
156
+ selection.append(slice(0, 1))
157
+
158
+ self.spectrum = self.parent.datasets[key][tuple(selection)].mean(axis=tuple(image_dims))
159
+
160
+ self.spectrum *= self.parent.y_scale
161
+
162
+ return self.spectrum.squeeze()
163
+
164
+ def update_ll_dataset(self, value=0):
165
+ self.ll_key = self.low_loss_tab[0, 0].value.split(':')[0]
166
+ self.parent.set_dataset(self.ll_key)
167
+ self.dataset = self.parent.dataset
168
+
169
+
170
+ def set_binning(self, value):
171
+ if 'SPECTRAL' in self.dataset.data_type.name:
172
+ bin_x = self.info_tab[15, 0].value
173
+ bin_y = self.info_tab[16, 0].value
174
+ self.dataset.view.set_bin([bin_x, bin_y])
175
+ self.datasets[self.key].metadata['experiment']['SI_bin_x'] = bin_x
176
+ self.datasets[self.key].metadata['experiment']['SI_bin_y'] = bin_y
pyTEMlib/version.py CHANGED
@@ -1,6 +1,6 @@
1
1
  """
2
2
  version
3
3
  """
4
- _version = '0.2024.02.2'
4
+ _version = '0.2024.06.0'
5
5
  __version__ = _version
6
- _time = '2024-02-26 19:58:26'
6
+ _time = '2024-06-10 19:58:26'
{pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: pyTEMlib
3
- Version: 0.2024.2.2
3
+ Version: 0.2024.6.0
4
4
  Summary: pyTEM: TEM Data Quantification library through a model-based approach
5
5
  Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
6
6
  Author: Gerd Duscher
@@ -38,9 +38,9 @@ Requires-Dist: ipympl
38
38
  Requires-Dist: spglib
39
39
  Requires-Dist: scikit-image
40
40
  Requires-Dist: scikit-learn
41
- Requires-Dist: pyNSID >=0.0.7
42
- Requires-Dist: sidpy >=0.12.1
43
- Requires-Dist: SciFiReaders >=0.0.8
41
+ Requires-Dist: pyNSID>=0.0.7
42
+ Requires-Dist: sidpy>=0.12.1
43
+ Requires-Dist: SciFiReaders>=0.0.8
44
44
 
45
45
  pyTEMlib
46
46
  ========
{pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/RECORD RENAMED
@@ -2,34 +2,36 @@ pyTEMlib/__init__.py,sha256=nEN93amIEoZxO7rJgN71ABeCoXrnmaywBbE97l5lPio,178
2
2
  pyTEMlib/animation.py,sha256=oPxbTuy8LfdH2mOOgm9Q40ArFAJmXM_58UV97ptcNAY,25187
3
3
  pyTEMlib/atom_tools.py,sha256=ViO4ZZZoCZ_Cp2KijiqKKOiQhGOWnye45T0rsiPhf4I,7314
4
4
  pyTEMlib/config_dir.py,sha256=4evlo9P2Yht-AnqaLI-WweLjDQcislbAP3I7P7EZsPU,2085
5
+ pyTEMlib/core_loss_widget.py,sha256=BPGGNcYkdiX3pIfe600ERVAJjUHw5C2BA7idroP1pgU,29746
5
6
  pyTEMlib/crystal_tools.py,sha256=g4OXyvd5NLw7vaXhjDP3P6VZpVV6eiyuPn8MdgR2amI,61652
6
7
  pyTEMlib/diffraction_plot.py,sha256=pM5d3bdBGa8LlPZ5lw8sLT94mlYTXELxPLv-jUP2FWY,27959
7
8
  pyTEMlib/dynamic_scattering.py,sha256=O9MxnxfndWJ2VhQRjksKNQ4yY7y-gN_hitRQ4Qox4ns,9472
8
9
  pyTEMlib/eds_tools.py,sha256=34YYoix9rhq0aYnZrHVi0A8gQeu9XZ9fGGT0VxPQo8Y,24882
9
- pyTEMlib/eels_dialog.py,sha256=x5AOe2SjL4R8aR6X92HOWdC9mL0M-jKtSiNfR-SHQr8,32327
10
- pyTEMlib/eels_dialog_utilities.py,sha256=srkRvRDUWIzN38EWNGRWimsJLK4YXSnGEfL6Dd1V3IY,51778
11
- pyTEMlib/eels_tools.py,sha256=pzsiMY-1ZXth5ZIrPaRNOs6R3gMAyZr8TVYf-Lxnn5Y,77781
12
- pyTEMlib/file_tools.py,sha256=XbtKLWEK-zam4A4u5iS4lFhNw51Vcm8Syoa_133hFyo,46495
10
+ pyTEMlib/eels_dialog.py,sha256=oWLivCQ96Fq0tj52wbfs-5qKccUSWk2k1iP2TVneXZA,32379
11
+ pyTEMlib/eels_dialog_utilities.py,sha256=73W9jFbPx-eeLEiSaBptTgGLr40bIYYfSyzLnZbhfvo,51761
12
+ pyTEMlib/eels_tools.py,sha256=O22WENQ04fCfVvI4ktJdx6GfE8ZSNb-E6dAu4ZbfHqw,76041
13
+ pyTEMlib/file_tools.py,sha256=UScJenVk73MZUW-laoKymnO27eCUC0vlRxxlQ4Kq2Hg,46923
13
14
  pyTEMlib/file_tools_qt.py,sha256=tLZACS4JyGH_AOzNR_SGAhjA01y4VJB261opPhGMlm8,7223
14
15
  pyTEMlib/graph_tools.py,sha256=iu0Y2hIPU6CkQHQEh-dI1vKnUHnSNXx4-CXs2M-1Sr8,44097
15
16
  pyTEMlib/graph_viz.py,sha256=m5PwSn6l2r0bsaLWBDSHc9IGR3_PneG2BrZgnEdi07I,13644
16
17
  pyTEMlib/image_dialog.py,sha256=F-ZgKq7UnMtPPd1b9eqb7t8MXDfWN-8hVKwB2Il0x28,6235
17
18
  pyTEMlib/image_dlg.py,sha256=n5gradDiYOFGEQ3k_Wlk9RUYYzl4bl_hKLzNVcYteNE,5694
18
- pyTEMlib/image_tools.py,sha256=Z1ZClIl0nqqPbehJzpLeWd0C_-dMCgzegPFIiNjJDNM,45665
19
- pyTEMlib/info_widget.py,sha256=G8MArXYI_xdvRY3cD7-3UxUjczEUWPjlrGJOj2BKU2Y,49903
19
+ pyTEMlib/image_tools.py,sha256=PU13i2KgKVoAf_NyCRdCGTfb6c42UZqprmgJ9zthMCw,48970
20
+ pyTEMlib/info_widget.py,sha256=wd1F6UDcLMsWEg1DHHVPa1P7_MRGv8iLOUjRsYkZOQY,46453
20
21
  pyTEMlib/interactive_image.py,sha256=5PwypcA1OjLAD-fi8bmWWFHuOjdIPVY9Dh59V24WuDA,34
21
22
  pyTEMlib/kinematic_scattering.py,sha256=CUdJnclkok7d8qm_jDUF92MVHrmaTeMkKdvxxB6AqvA,43309
23
+ pyTEMlib/low_loss_widget.py,sha256=nSU6-pu7gP8ch61w2wpImNNIuo_3bBN1HAB3UVlEJoQ,9043
22
24
  pyTEMlib/microscope.py,sha256=iigUF1UImHEfmL2wqEBBj3aNRgEYouDbIln8VCo4_KM,1545
23
25
  pyTEMlib/peak_dialog.py,sha256=-HhgmoscfJMme9N495hDzfniYwuhn7iBzsDwZOOhTd4,48260
24
26
  pyTEMlib/peak_dlg.py,sha256=qcjcnhwpGa4jBCeXzwQz9sCyX-tHsLLQ67ToqfKOiQY,11550
25
27
  pyTEMlib/probe_tools.py,sha256=8tPQuANClLsGAKnZo6Vo4gNIGKfyDR6WUMO3dXcm_4k,27177
26
28
  pyTEMlib/sidpy_tools.py,sha256=0oIx-qMtEmcZmLazQKW19dd-KoxyY3B15aIeMcyHA8E,4878
27
29
  pyTEMlib/simulation_tools.py,sha256=RmegD5TpQMU68uASvzZWVplAqs7bM5KkF6bWDWLjyc0,2799
28
- pyTEMlib/version.py,sha256=_bRzJnpABIwsBmU7vcbAzkVQOcrs4FDhOj7NU--rmwI,94
30
+ pyTEMlib/version.py,sha256=eTxYL1VM1SZB6XwKQ7HgZ3bzXDIpG0PDiLYHW8AqAyw,94
29
31
  pyTEMlib/xrpa_x_sections.py,sha256=peb2pozcH0T-3zlWITx-5rdyeoP2YhOfBpwsWD1-4T4,1813751
30
- pyTEMlib-0.2024.2.2.dist-info/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
31
- pyTEMlib-0.2024.2.2.dist-info/METADATA,sha256=ysRSA7XOwpB9J7hwnDBzAHaD1GxOpCCyUQFqe0yGkFM,3306
32
- pyTEMlib-0.2024.2.2.dist-info/WHEEL,sha256=-G_t0oGuE7UD0DrSpVZnq1hHMBV9DD2XkS5v7XpmTnk,110
33
- pyTEMlib-0.2024.2.2.dist-info/entry_points.txt,sha256=qiIFPP3ffSz-gxj-TowzbA0Setq5Lo0RJTVtSrqD1IY,44
34
- pyTEMlib-0.2024.2.2.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
35
- pyTEMlib-0.2024.2.2.dist-info/RECORD,,
32
+ pyTEMlib-0.2024.6.0.dist-info/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
33
+ pyTEMlib-0.2024.6.0.dist-info/METADATA,sha256=5wU66BPQnYNIQK_7KmkB3N_dDgzahaDzk9L41GaB6CM,3303
34
+ pyTEMlib-0.2024.6.0.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
35
+ pyTEMlib-0.2024.6.0.dist-info/entry_points.txt,sha256=qiIFPP3ffSz-gxj-TowzbA0Setq5Lo0RJTVtSrqD1IY,44
36
+ pyTEMlib-0.2024.6.0.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
37
+ pyTEMlib-0.2024.6.0.dist-info/RECORD,,
{pyTEMlib-0.2024.2.2.dist-info → pyTEMlib-0.2024.6.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: bdist_wheel (0.42.0)
2
+ Generator: bdist_wheel (0.44.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py2-none-any
5
5
  Tag: py3-none-any