ePDFsuite 0.1.4__tar.gz

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.
Files changed (24) hide show
  1. epdfsuite-0.1.4/PKG-INFO +166 -0
  2. epdfsuite-0.1.4/README.md +127 -0
  3. epdfsuite-0.1.4/pyproject.toml +60 -0
  4. epdfsuite-0.1.4/setup.cfg +4 -0
  5. epdfsuite-0.1.4/setup.py +2 -0
  6. epdfsuite-0.1.4/src/ePDFsuite.egg-info/PKG-INFO +166 -0
  7. epdfsuite-0.1.4/src/ePDFsuite.egg-info/SOURCES.txt +22 -0
  8. epdfsuite-0.1.4/src/ePDFsuite.egg-info/dependency_links.txt +1 -0
  9. epdfsuite-0.1.4/src/ePDFsuite.egg-info/entry_points.txt +2 -0
  10. epdfsuite-0.1.4/src/ePDFsuite.egg-info/requires.txt +16 -0
  11. epdfsuite-0.1.4/src/ePDFsuite.egg-info/top_level.txt +1 -0
  12. epdfsuite-0.1.4/src/epdfsuite/PDF_BatchAnalysis.py +2616 -0
  13. epdfsuite-0.1.4/src/epdfsuite/__init__.py +23 -0
  14. epdfsuite-0.1.4/src/epdfsuite/_launcher.py +9 -0
  15. epdfsuite-0.1.4/src/epdfsuite/app_epdfsuite.py +813 -0
  16. epdfsuite-0.1.4/src/epdfsuite/calibration.py +180 -0
  17. epdfsuite-0.1.4/src/epdfsuite/camera_library.py +153 -0
  18. epdfsuite-0.1.4/src/epdfsuite/ePDFsuite.py +1078 -0
  19. epdfsuite-0.1.4/src/epdfsuite/filereader.py +444 -0
  20. epdfsuite-0.1.4/src/epdfsuite/lobato_scattering.py +184 -0
  21. epdfsuite-0.1.4/src/epdfsuite/pdf_extraction.py +510 -0
  22. epdfsuite-0.1.4/src/epdfsuite/recalibration.py +352 -0
  23. epdfsuite-0.1.4/src/epdfsuite/snr.py +52 -0
  24. epdfsuite-0.1.4/src/epdfsuite/utilities.py +1415 -0
epdfsuite-0.1.4/PKG-INFO ADDED
@@ -0,0 +1,166 @@
1
+ Metadata-Version: 2.4
2
+ Name: ePDFsuite
3
+ Version: 0.1.4
4
+ Summary: Python toolkit for electron pair distribution function (ePDF) analysis from SAED data
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+ Author: Nicolas Ratel-Ramond
6
+ License: MIT
7
+ Project-URL: Homepage, https://github.com/nicoratel/ePDFsuite
8
+ Project-URL: Documentation, https://epdfsuite.readthedocs.io
9
+ Project-URL: Repository, https://github.com/nicoratel/ePDFsuite
10
+ Project-URL: Issues, https://github.com/nicoratel/ePDFsuite/issues
11
+ Keywords: SAED,electron diffraction,PDF,RDF,distribution function,crystallography
12
+ Classifier: Programming Language :: Python :: 3
13
+ Classifier: Programming Language :: Python :: 3.8
14
+ Classifier: Programming Language :: Python :: 3.9
15
+ Classifier: Programming Language :: Python :: 3.10
16
+ Classifier: Programming Language :: Python :: 3.11
17
+ Classifier: License :: OSI Approved :: MIT License
18
+ Classifier: Operating System :: OS Independent
19
+ Classifier: Intended Audience :: Science/Research
20
+ Classifier: Topic :: Scientific/Engineering :: Physics
21
+ Classifier: Topic :: Scientific/Engineering :: Chemistry
22
+ Requires-Python: >=3.8
23
+ Description-Content-Type: text/markdown
24
+ Requires-Dist: numpy<2.0.0,>=1.26.0
25
+ Requires-Dist: scipy<2.0.0,>=1.11.0
26
+ Requires-Dist: matplotlib<4.0.0,>=3.8.0
27
+ Requires-Dist: pymatgen>=2024.1.1
28
+ Requires-Dist: hyperspy<3.0.0,>=2.0.0
29
+ Requires-Dist: pyFAI>=2024.0.0
30
+ Requires-Dist: scikit-image<1.0.0,>=0.22.0
31
+ Requires-Dist: ipywidgets>=8.0.0
32
+ Requires-Dist: ipykernel>=6.0.0
33
+ Requires-Dist: plotly>=5.0.0
34
+ Requires-Dist: h5py>=3.0.0
35
+ Requires-Dist: tqdm>=4.60.0
36
+ Requires-Dist: streamlit>=1.30.0
37
+ Provides-Extra: pdfanalysis
38
+ Requires-Dist: pdfanalysis>=0.13.0; extra == "pdfanalysis"
39
+
40
+ # ePDFsuite
41
+
42
+ **ePDFsuite** is a Python toolkit for extracting the electron Pair Distribution Function (ePDF) from Selected Area Electron Diffraction (SAED) images acquired in a transmission electron microscope (TEM).
43
+
44
+ It provides both a Python API for scripted workflows and an interactive graphical interface built with Streamlit.
45
+
46
+ > See [Documentation](https://epdfsuite.readthedocs.io/en/latest/)
47
+
48
+ ---
49
+
50
+ ## What is ePDF?
51
+
52
+ The electron Pair Distribution Function (ePDF) is a real-space representation of atomic pair correlations, derived from the Fourier transform of the reduced structure factor $F(q)$ extracted from electron diffraction data. It is particularly useful for characterizing the local atomic structure of amorphous, nanocrystalline, and disordered materials.
53
+
54
+ $$G(r) = \frac{2}{\pi} \int_{q_{\min}}^{q_{\max}} F(q) \sin(qr)\, dq$$
55
+
56
+ ---
57
+
58
+ ## Features
59
+
60
+ - **Camera geometric calibration** using a known crystalline standard (e.g. Au) via [pyFAI](https://pyfai.readthedocs.io/)
61
+ - **MTF determination** from a beamstop image using the slanted edge method
62
+ - **MTF deconvolution** of diffraction images (Wiener filter)
63
+ - **Automatic beam center recalibration** before each integration
64
+ - **Azimuthal integration** of 2D SAED patterns to 1D profiles
65
+ - **ePDF extraction**: background subtraction, scattering factor normalization using Lobato parameterization, and Fourier transform
66
+ - **Interactive GUI** (Streamlit) for interactive parameter tuning
67
+ - Support for **DM4, DM3, TIFF** input formats (via [HyperSpy](https://hyperspy.org/))
68
+ - Works with or without a `.poni` calibration file
69
+
70
+ ---
71
+
72
+ ## Installation
73
+
74
+ **Requirements:** Python ≥ 3.8, conda recommended.
75
+
76
+ ```bash
77
+ # Clone the repository
78
+ git clone https://github.com/nicoratel/ePDFsuite.git
79
+ cd ePDFsuite
80
+
81
+ # Create and activate a conda environment
82
+ conda create -n epdfsuite python=3.10
83
+ conda activate epdfsuite
84
+
85
+ # Install in editable mode
86
+ pip install -e .
87
+ ```
88
+
89
+ ---
90
+
91
+ ## Launching the GUI
92
+
93
+ Once installed, launch the interactive Streamlit application from anywhere:
94
+
95
+ ```bash
96
+ conda activate epdfsuite
97
+ epdfsuite-app
98
+ ```
99
+
100
+ The app opens at `http://localhost:8501` in your browser.
101
+
102
+ > See [LAUNCH_APP.md](LAUNCH_APP.md) for alternative launch methods.
103
+
104
+ ---
105
+
106
+ ## Usage
107
+
108
+ > See [Documentation](https://epdfsuite.readthedocs.io/en/latest/)
109
+
110
+ ## Notebooks
111
+
112
+ | Notebook | Description |
113
+ |---|---|
114
+ | [`camera_calibration.ipynb`](notebooks/camera_calibration.ipynb) | Geometric calibration with pyFAI + MTF measurement |
115
+ | [`ePDF_Workflow.ipynb`](notebooks/ePDF_Workflow.ipynb) | Complete ePDF extraction workflow (basic) |
116
+ | [`MTF_determination.ipynb`](notebooks/MTF_determination.ipynb) | MTF computation from a beamstop image |
117
+
118
+
119
+ ---
120
+
121
+ ## Project structure
122
+
123
+ ```
124
+ ePDFsuite/
125
+ ├── src/epdfsuite/
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+ │ ├── ePDFsuite.py # SAEDProcessor class and extract_epdf function
127
+ │ ├── calibration.py # Geometric calibration from CIF
128
+ │ ├── recalibration.py # Automatic beam center refinement
129
+ │ ├── pdf_extraction.py # Structure factor and PDF computation
130
+ │ ├── lobato_scattering.py # Lobato electron scattering factors
131
+ │ ├── filereader.py # DM4/DM3/TIFF reader
132
+ │ ├── utilities.py # MTF tools, mask drawing
133
+ │ ├── camera_library.py # Known detector configurations
134
+ │ └── app_epdfsuite.py # Streamlit GUI
135
+ ├── notebooks/ # Example Jupyter notebooks
136
+ ├── pyproject.toml
137
+ ├── LAUNCH_APP.md # GUI launch instructions
138
+ └── README.md
139
+ ```
140
+
141
+ ---
142
+
143
+ ## Dependencies
144
+
145
+ | Package | Role |
146
+ |---|---|
147
+ | [pyFAI](https://pyfai.readthedocs.io/) | Geometric calibration and azimuthal integration |
148
+ | [HyperSpy](https://hyperspy.org/) | Reading DM4/DM3 files and pixel scale metadata |
149
+ | [diffpy-CMI / numpy](https://numpy.org/) | PDF computation and signal processing |
150
+ | [scikit-image](https://scikit-image.org/) | Image processing (MTF, beam center) |
151
+ | [Streamlit](https://streamlit.io/) | Interactive GUI |
152
+ | [plotly](https://plotly.com/python/) | Interactive plots in the GUI |
153
+ | [pymatgen](https://pymatgen.org/) | CIF reading for calibration |
154
+
155
+ ---
156
+
157
+ ## License
158
+
159
+ MIT License — see [LICENSE](LICENSE) for details.
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+
161
+ ---
162
+
163
+ ## Author
164
+
165
+ Nicolas Ratel-Ramond
166
+ [github.com/nicoratel/ePDFsuite](https://github.com/nicoratel/ePDFsuite)
epdfsuite-0.1.4/README.md ADDED
@@ -0,0 +1,127 @@
1
+ # ePDFsuite
2
+
3
+ **ePDFsuite** is a Python toolkit for extracting the electron Pair Distribution Function (ePDF) from Selected Area Electron Diffraction (SAED) images acquired in a transmission electron microscope (TEM).
4
+
5
+ It provides both a Python API for scripted workflows and an interactive graphical interface built with Streamlit.
6
+
7
+ > See [Documentation](https://epdfsuite.readthedocs.io/en/latest/)
8
+
9
+ ---
10
+
11
+ ## What is ePDF?
12
+
13
+ The electron Pair Distribution Function (ePDF) is a real-space representation of atomic pair correlations, derived from the Fourier transform of the reduced structure factor $F(q)$ extracted from electron diffraction data. It is particularly useful for characterizing the local atomic structure of amorphous, nanocrystalline, and disordered materials.
14
+
15
+ $$G(r) = \frac{2}{\pi} \int_{q_{\min}}^{q_{\max}} F(q) \sin(qr)\, dq$$
16
+
17
+ ---
18
+
19
+ ## Features
20
+
21
+ - **Camera geometric calibration** using a known crystalline standard (e.g. Au) via [pyFAI](https://pyfai.readthedocs.io/)
22
+ - **MTF determination** from a beamstop image using the slanted edge method
23
+ - **MTF deconvolution** of diffraction images (Wiener filter)
24
+ - **Automatic beam center recalibration** before each integration
25
+ - **Azimuthal integration** of 2D SAED patterns to 1D profiles
26
+ - **ePDF extraction**: background subtraction, scattering factor normalization using Lobato parameterization, and Fourier transform
27
+ - **Interactive GUI** (Streamlit) for interactive parameter tuning
28
+ - Support for **DM4, DM3, TIFF** input formats (via [HyperSpy](https://hyperspy.org/))
29
+ - Works with or without a `.poni` calibration file
30
+
31
+ ---
32
+
33
+ ## Installation
34
+
35
+ **Requirements:** Python ≥ 3.8, conda recommended.
36
+
37
+ ```bash
38
+ # Clone the repository
39
+ git clone https://github.com/nicoratel/ePDFsuite.git
40
+ cd ePDFsuite
41
+
42
+ # Create and activate a conda environment
43
+ conda create -n epdfsuite python=3.10
44
+ conda activate epdfsuite
45
+
46
+ # Install in editable mode
47
+ pip install -e .
48
+ ```
49
+
50
+ ---
51
+
52
+ ## Launching the GUI
53
+
54
+ Once installed, launch the interactive Streamlit application from anywhere:
55
+
56
+ ```bash
57
+ conda activate epdfsuite
58
+ epdfsuite-app
59
+ ```
60
+
61
+ The app opens at `http://localhost:8501` in your browser.
62
+
63
+ > See [LAUNCH_APP.md](LAUNCH_APP.md) for alternative launch methods.
64
+
65
+ ---
66
+
67
+ ## Usage
68
+
69
+ > See [Documentation](https://epdfsuite.readthedocs.io/en/latest/)
70
+
71
+ ## Notebooks
72
+
73
+ | Notebook | Description |
74
+ |---|---|
75
+ | [`camera_calibration.ipynb`](notebooks/camera_calibration.ipynb) | Geometric calibration with pyFAI + MTF measurement |
76
+ | [`ePDF_Workflow.ipynb`](notebooks/ePDF_Workflow.ipynb) | Complete ePDF extraction workflow (basic) |
77
+ | [`MTF_determination.ipynb`](notebooks/MTF_determination.ipynb) | MTF computation from a beamstop image |
78
+
79
+
80
+ ---
81
+
82
+ ## Project structure
83
+
84
+ ```
85
+ ePDFsuite/
86
+ ├── src/epdfsuite/
87
+ │ ├── ePDFsuite.py # SAEDProcessor class and extract_epdf function
88
+ │ ├── calibration.py # Geometric calibration from CIF
89
+ │ ├── recalibration.py # Automatic beam center refinement
90
+ │ ├── pdf_extraction.py # Structure factor and PDF computation
91
+ │ ├── lobato_scattering.py # Lobato electron scattering factors
92
+ │ ├── filereader.py # DM4/DM3/TIFF reader
93
+ │ ├── utilities.py # MTF tools, mask drawing
94
+ │ ├── camera_library.py # Known detector configurations
95
+ │ └── app_epdfsuite.py # Streamlit GUI
96
+ ├── notebooks/ # Example Jupyter notebooks
97
+ ├── pyproject.toml
98
+ ├── LAUNCH_APP.md # GUI launch instructions
99
+ └── README.md
100
+ ```
101
+
102
+ ---
103
+
104
+ ## Dependencies
105
+
106
+ | Package | Role |
107
+ |---|---|
108
+ | [pyFAI](https://pyfai.readthedocs.io/) | Geometric calibration and azimuthal integration |
109
+ | [HyperSpy](https://hyperspy.org/) | Reading DM4/DM3 files and pixel scale metadata |
110
+ | [diffpy-CMI / numpy](https://numpy.org/) | PDF computation and signal processing |
111
+ | [scikit-image](https://scikit-image.org/) | Image processing (MTF, beam center) |
112
+ | [Streamlit](https://streamlit.io/) | Interactive GUI |
113
+ | [plotly](https://plotly.com/python/) | Interactive plots in the GUI |
114
+ | [pymatgen](https://pymatgen.org/) | CIF reading for calibration |
115
+
116
+ ---
117
+
118
+ ## License
119
+
120
+ MIT License — see [LICENSE](LICENSE) for details.
121
+
122
+ ---
123
+
124
+ ## Author
125
+
126
+ Nicolas Ratel-Ramond
127
+ [github.com/nicoratel/ePDFsuite](https://github.com/nicoratel/ePDFsuite)
epdfsuite-0.1.4/pyproject.toml ADDED
@@ -0,0 +1,60 @@
1
+ [build-system]
2
+ requires = ["setuptools"]
3
+ build-backend = "setuptools.build_meta"
4
+
5
+ [project]
6
+ name = "ePDFsuite"
7
+ version = "0.1.4"
8
+ description = "Python toolkit for electron pair distribution function (ePDF) analysis from SAED data"
9
+ authors = [{name = "Nicolas Ratel-Ramond"}]
10
+ readme = "README.md"
11
+ requires-python = ">=3.8"
12
+ license = {text = "MIT"}
13
+ keywords = ["SAED", "electron diffraction", "PDF", "RDF", "distribution function", "crystallography"]
14
+ classifiers = [
15
+ "Programming Language :: Python :: 3",
16
+ "Programming Language :: Python :: 3.8",
17
+ "Programming Language :: Python :: 3.9",
18
+ "Programming Language :: Python :: 3.10",
19
+ "Programming Language :: Python :: 3.11",
20
+ "License :: OSI Approved :: MIT License",
21
+ "Operating System :: OS Independent",
22
+ "Intended Audience :: Science/Research",
23
+ "Topic :: Scientific/Engineering :: Physics",
24
+ "Topic :: Scientific/Engineering :: Chemistry",
25
+ ]
26
+ dependencies = [
27
+ "numpy>=1.26.0,<2.0.0",
28
+ "scipy>=1.11.0,<2.0.0",
29
+ "matplotlib>=3.8.0,<4.0.0",
30
+ #"diffpy-cmi>=3.1.0,<4.0.0",
31
+ #"ase>=3.22.0,<4.0.0",
32
+ "pymatgen>=2024.1.1",
33
+ #"abtem>=1.0.0,<2.0.0",
34
+ "hyperspy>=2.0.0,<3.0.0",
35
+ "pyFAI>=2024.0.0",
36
+ "scikit-image>=0.22.0,<1.0.0",
37
+ "ipywidgets>=8.0.0",
38
+ "ipykernel>=6.0.0",
39
+ "plotly>=5.0.0",
40
+ "h5py>=3.0.0",
41
+ "tqdm>=4.60.0",
42
+ "streamlit>=1.30.0",
43
+ ]
44
+
45
+ [project.optional-dependencies]
46
+ pdfanalysis = [
47
+ "pdfanalysis>=0.13.0",
48
+ ]
49
+
50
+ [project.urls]
51
+ Homepage = "https://github.com/nicoratel/ePDFsuite"
52
+ Documentation = "https://epdfsuite.readthedocs.io"
53
+ Repository = "https://github.com/nicoratel/ePDFsuite"
54
+ Issues = "https://github.com/nicoratel/ePDFsuite/issues"
55
+
56
+ [project.scripts]
57
+ epdfsuite-app = "epdfsuite._launcher:main"
58
+
59
+ [tool.setuptools.packages.find]
60
+ where = ["src"]
epdfsuite-0.1.4/setup.cfg ADDED
@@ -0,0 +1,4 @@
1
+ [egg_info]
2
+ tag_build =
3
+ tag_date = 0
4
+
epdfsuite-0.1.4/setup.py ADDED
@@ -0,0 +1,2 @@
1
+ from setuptools import setup
2
+ setup()
epdfsuite-0.1.4/src/ePDFsuite.egg-info/PKG-INFO ADDED
@@ -0,0 +1,166 @@
1
+ Metadata-Version: 2.4
2
+ Name: ePDFsuite
3
+ Version: 0.1.4
4
+ Summary: Python toolkit for electron pair distribution function (ePDF) analysis from SAED data
5
+ Author: Nicolas Ratel-Ramond
6
+ License: MIT
7
+ Project-URL: Homepage, https://github.com/nicoratel/ePDFsuite
8
+ Project-URL: Documentation, https://epdfsuite.readthedocs.io
9
+ Project-URL: Repository, https://github.com/nicoratel/ePDFsuite
10
+ Project-URL: Issues, https://github.com/nicoratel/ePDFsuite/issues
11
+ Keywords: SAED,electron diffraction,PDF,RDF,distribution function,crystallography
12
+ Classifier: Programming Language :: Python :: 3
13
+ Classifier: Programming Language :: Python :: 3.8
14
+ Classifier: Programming Language :: Python :: 3.9
15
+ Classifier: Programming Language :: Python :: 3.10
16
+ Classifier: Programming Language :: Python :: 3.11
17
+ Classifier: License :: OSI Approved :: MIT License
18
+ Classifier: Operating System :: OS Independent
19
+ Classifier: Intended Audience :: Science/Research
20
+ Classifier: Topic :: Scientific/Engineering :: Physics
21
+ Classifier: Topic :: Scientific/Engineering :: Chemistry
22
+ Requires-Python: >=3.8
23
+ Description-Content-Type: text/markdown
24
+ Requires-Dist: numpy<2.0.0,>=1.26.0
25
+ Requires-Dist: scipy<2.0.0,>=1.11.0
26
+ Requires-Dist: matplotlib<4.0.0,>=3.8.0
27
+ Requires-Dist: pymatgen>=2024.1.1
28
+ Requires-Dist: hyperspy<3.0.0,>=2.0.0
29
+ Requires-Dist: pyFAI>=2024.0.0
30
+ Requires-Dist: scikit-image<1.0.0,>=0.22.0
31
+ Requires-Dist: ipywidgets>=8.0.0
32
+ Requires-Dist: ipykernel>=6.0.0
33
+ Requires-Dist: plotly>=5.0.0
34
+ Requires-Dist: h5py>=3.0.0
35
+ Requires-Dist: tqdm>=4.60.0
36
+ Requires-Dist: streamlit>=1.30.0
37
+ Provides-Extra: pdfanalysis
38
+ Requires-Dist: pdfanalysis>=0.13.0; extra == "pdfanalysis"
39
+
40
+ # ePDFsuite
41
+
42
+ **ePDFsuite** is a Python toolkit for extracting the electron Pair Distribution Function (ePDF) from Selected Area Electron Diffraction (SAED) images acquired in a transmission electron microscope (TEM).
43
+
44
+ It provides both a Python API for scripted workflows and an interactive graphical interface built with Streamlit.
45
+
46
+ > See [Documentation](https://epdfsuite.readthedocs.io/en/latest/)
47
+
48
+ ---
49
+
50
+ ## What is ePDF?
51
+
52
+ The electron Pair Distribution Function (ePDF) is a real-space representation of atomic pair correlations, derived from the Fourier transform of the reduced structure factor $F(q)$ extracted from electron diffraction data. It is particularly useful for characterizing the local atomic structure of amorphous, nanocrystalline, and disordered materials.
53
+
54
+ $$G(r) = \frac{2}{\pi} \int_{q_{\min}}^{q_{\max}} F(q) \sin(qr)\, dq$$
55
+
56
+ ---
57
+
58
+ ## Features
59
+
60
+ - **Camera geometric calibration** using a known crystalline standard (e.g. Au) via [pyFAI](https://pyfai.readthedocs.io/)
61
+ - **MTF determination** from a beamstop image using the slanted edge method
62
+ - **MTF deconvolution** of diffraction images (Wiener filter)
63
+ - **Automatic beam center recalibration** before each integration
64
+ - **Azimuthal integration** of 2D SAED patterns to 1D profiles
65
+ - **ePDF extraction**: background subtraction, scattering factor normalization using Lobato parameterization, and Fourier transform
66
+ - **Interactive GUI** (Streamlit) for interactive parameter tuning
67
+ - Support for **DM4, DM3, TIFF** input formats (via [HyperSpy](https://hyperspy.org/))
68
+ - Works with or without a `.poni` calibration file
69
+
70
+ ---
71
+
72
+ ## Installation
73
+
74
+ **Requirements:** Python ≥ 3.8, conda recommended.
75
+
76
+ ```bash
77
+ # Clone the repository
78
+ git clone https://github.com/nicoratel/ePDFsuite.git
79
+ cd ePDFsuite
80
+
81
+ # Create and activate a conda environment
82
+ conda create -n epdfsuite python=3.10
83
+ conda activate epdfsuite
84
+
85
+ # Install in editable mode
86
+ pip install -e .
87
+ ```
88
+
89
+ ---
90
+
91
+ ## Launching the GUI
92
+
93
+ Once installed, launch the interactive Streamlit application from anywhere:
94
+
95
+ ```bash
96
+ conda activate epdfsuite
97
+ epdfsuite-app
98
+ ```
99
+
100
+ The app opens at `http://localhost:8501` in your browser.
101
+
102
+ > See [LAUNCH_APP.md](LAUNCH_APP.md) for alternative launch methods.
103
+
104
+ ---
105
+
106
+ ## Usage
107
+
108
+ > See [Documentation](https://epdfsuite.readthedocs.io/en/latest/)
109
+
110
+ ## Notebooks
111
+
112
+ | Notebook | Description |
113
+ |---|---|
114
+ | [`camera_calibration.ipynb`](notebooks/camera_calibration.ipynb) | Geometric calibration with pyFAI + MTF measurement |
115
+ | [`ePDF_Workflow.ipynb`](notebooks/ePDF_Workflow.ipynb) | Complete ePDF extraction workflow (basic) |
116
+ | [`MTF_determination.ipynb`](notebooks/MTF_determination.ipynb) | MTF computation from a beamstop image |
117
+
118
+
119
+ ---
120
+
121
+ ## Project structure
122
+
123
+ ```
124
+ ePDFsuite/
125
+ ├── src/epdfsuite/
126
+ │ ├── ePDFsuite.py # SAEDProcessor class and extract_epdf function
127
+ │ ├── calibration.py # Geometric calibration from CIF
128
+ │ ├── recalibration.py # Automatic beam center refinement
129
+ │ ├── pdf_extraction.py # Structure factor and PDF computation
130
+ │ ├── lobato_scattering.py # Lobato electron scattering factors
131
+ │ ├── filereader.py # DM4/DM3/TIFF reader
132
+ │ ├── utilities.py # MTF tools, mask drawing
133
+ │ ├── camera_library.py # Known detector configurations
134
+ │ └── app_epdfsuite.py # Streamlit GUI
135
+ ├── notebooks/ # Example Jupyter notebooks
136
+ ├── pyproject.toml
137
+ ├── LAUNCH_APP.md # GUI launch instructions
138
+ └── README.md
139
+ ```
140
+
141
+ ---
142
+
143
+ ## Dependencies
144
+
145
+ | Package | Role |
146
+ |---|---|
147
+ | [pyFAI](https://pyfai.readthedocs.io/) | Geometric calibration and azimuthal integration |
148
+ | [HyperSpy](https://hyperspy.org/) | Reading DM4/DM3 files and pixel scale metadata |
149
+ | [diffpy-CMI / numpy](https://numpy.org/) | PDF computation and signal processing |
150
+ | [scikit-image](https://scikit-image.org/) | Image processing (MTF, beam center) |
151
+ | [Streamlit](https://streamlit.io/) | Interactive GUI |
152
+ | [plotly](https://plotly.com/python/) | Interactive plots in the GUI |
153
+ | [pymatgen](https://pymatgen.org/) | CIF reading for calibration |
154
+
155
+ ---
156
+
157
+ ## License
158
+
159
+ MIT License — see [LICENSE](LICENSE) for details.
160
+
161
+ ---
162
+
163
+ ## Author
164
+
165
+ Nicolas Ratel-Ramond
166
+ [github.com/nicoratel/ePDFsuite](https://github.com/nicoratel/ePDFsuite)
epdfsuite-0.1.4/src/ePDFsuite.egg-info/SOURCES.txt ADDED
@@ -0,0 +1,22 @@
1
+ README.md
2
+ pyproject.toml
3
+ setup.py
4
+ src/ePDFsuite.egg-info/PKG-INFO
5
+ src/ePDFsuite.egg-info/SOURCES.txt
6
+ src/ePDFsuite.egg-info/dependency_links.txt
7
+ src/ePDFsuite.egg-info/entry_points.txt
8
+ src/ePDFsuite.egg-info/requires.txt
9
+ src/ePDFsuite.egg-info/top_level.txt
10
+ src/epdfsuite/PDF_BatchAnalysis.py
11
+ src/epdfsuite/__init__.py
12
+ src/epdfsuite/_launcher.py
13
+ src/epdfsuite/app_epdfsuite.py
14
+ src/epdfsuite/calibration.py
15
+ src/epdfsuite/camera_library.py
16
+ src/epdfsuite/ePDFsuite.py
17
+ src/epdfsuite/filereader.py
18
+ src/epdfsuite/lobato_scattering.py
19
+ src/epdfsuite/pdf_extraction.py
20
+ src/epdfsuite/recalibration.py
21
+ src/epdfsuite/snr.py
22
+ src/epdfsuite/utilities.py
epdfsuite-0.1.4/src/ePDFsuite.egg-info/entry_points.txt ADDED
@@ -0,0 +1,2 @@
1
+ [console_scripts]
2
+ epdfsuite-app = epdfsuite._launcher:main
epdfsuite-0.1.4/src/ePDFsuite.egg-info/requires.txt ADDED
@@ -0,0 +1,16 @@
1
+ numpy<2.0.0,>=1.26.0
2
+ scipy<2.0.0,>=1.11.0
3
+ matplotlib<4.0.0,>=3.8.0
4
+ pymatgen>=2024.1.1
5
+ hyperspy<3.0.0,>=2.0.0
6
+ pyFAI>=2024.0.0
7
+ scikit-image<1.0.0,>=0.22.0
8
+ ipywidgets>=8.0.0
9
+ ipykernel>=6.0.0
10
+ plotly>=5.0.0
11
+ h5py>=3.0.0
12
+ tqdm>=4.60.0
13
+ streamlit>=1.30.0
14
+
15
+ [pdfanalysis]
16
+ pdfanalysis>=0.13.0
epdfsuite-0.1.4/src/ePDFsuite.egg-info/top_level.txt ADDED
@@ -0,0 +1 @@
1
+ epdfsuite