faser 0.3.2__tar.gz → 0.3.4__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 (78) hide show
  1. faser-0.3.4/PKG-INFO +156 -0
  2. faser-0.3.4/README.md +132 -0
  3. faser-0.3.4/psf.tif +0 -0
  4. faser-0.3.4/psf_config.json +55 -0
  5. {faser-0.3.2 → faser-0.3.4}/pyproject.toml +3 -1
  6. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/export.py +5 -5
  7. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/fields.py +10 -10
  8. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/helper_widget.py +14 -14
  9. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/main_widget.py +1 -2
  10. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/mpl_canvas.py +4 -4
  11. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/tob_bar.py +5 -8
  12. {faser-0.3.2 → faser-0.3.4}/uv.lock +9 -5
  13. faser-0.3.4/website/.gitignore +21 -0
  14. faser-0.3.4/website/.vscode/extensions.json +4 -0
  15. faser-0.3.4/website/.vscode/launch.json +11 -0
  16. faser-0.3.4/website/README.md +54 -0
  17. faser-0.3.4/website/astro.config.mjs +36 -0
  18. faser-0.3.4/website/package-lock.json +9012 -0
  19. faser-0.3.4/website/package.json +20 -0
  20. faser-0.3.4/website/public/favicon.svg +1 -0
  21. faser-0.3.4/website/src/assets/houston.webp +0 -0
  22. faser-0.3.4/website/src/content/docs/guides/introduction.md +14 -0
  23. faser-0.3.4/website/src/content/docs/index.mdx +36 -0
  24. faser-0.3.4/website/src/content/docs/reference/example.md +11 -0
  25. faser-0.3.4/website/src/content.config.ts +7 -0
  26. faser-0.3.4/website/src/tailwind.css +3 -0
  27. faser-0.3.4/website/tailwind.config.mjs +11 -0
  28. faser-0.3.4/website/tsconfig.json +5 -0
  29. faser-0.3.2/PKG-INFO +0 -25
  30. faser-0.3.2/README.md +0 -3
  31. {faser-0.3.2 → faser-0.3.4}/.github/workflows/publish.yml +0 -0
  32. {faser-0.3.2 → faser-0.3.4}/.github/workflows/test.yml +0 -0
  33. {faser-0.3.2 → faser-0.3.4}/.gitignore +0 -0
  34. {faser-0.3.2 → faser-0.3.4}/.vscode/launch.json +0 -0
  35. {faser-0.3.2 → faser-0.3.4}/.vscode/settings.json +0 -0
  36. {faser-0.3.2 → faser-0.3.4}/.vscode/tasks.json +0 -0
  37. {faser-0.3.2 → faser-0.3.4}/nap.py +0 -0
  38. {faser-0.3.2 → faser-0.3.4}/src/faser/__init__.py +0 -0
  39. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/Figure_ab.png +0 -0
  40. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/Figure_beam.png +0 -0
  41. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/Figure_geom.png +0 -0
  42. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/Figure_simu.png +0 -0
  43. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/batch.png +0 -0
  44. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/load.png +0 -0
  45. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/placeholder.png +0 -0
  46. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/refresh.png +0 -0
  47. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/save.png +0 -0
  48. {faser-0.3.2 → faser-0.3.4}/src/faser/assets/single.png +0 -0
  49. {faser-0.3.2 → faser-0.3.4}/src/faser/cli/__init__.py +0 -0
  50. {faser-0.3.2 → faser-0.3.4}/src/faser/cli/main.py +0 -0
  51. {faser-0.3.2 → faser-0.3.4}/src/faser/cli/qtmain.py +0 -0
  52. {faser-0.3.2 → faser-0.3.4}/src/faser/env.py +0 -0
  53. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/__init__.py +0 -0
  54. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/base.py +0 -0
  55. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/scalar/__init__.py +0 -0
  56. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/scalar/gibson_lanny/PSFGenerator.jar +0 -0
  57. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/scalar/gibson_lanny/__init__.py +0 -0
  58. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/scalar/gibson_lanny/config.txt +0 -0
  59. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/scalar/gibson_lanny/gen.py +0 -0
  60. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/scalar/phasenet/__init__.py +0 -0
  61. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/scalar/phasenet/generator.py +0 -0
  62. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/scalar/phasenet/wavefront.py +0 -0
  63. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/utils.py +0 -0
  64. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/vectorial/__init__.py +0 -0
  65. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/vectorial/stephane/__init__.py +0 -0
  66. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/vectorial/stephane/april_version.py +0 -0
  67. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/vectorial/stephane/tilted_compiled.py +0 -0
  68. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/vectorial/stephane/tilted_coverslip.py +0 -0
  69. {faser-0.3.2 → faser-0.3.4}/src/faser/generators/vectorial/utils.py +0 -0
  70. {faser-0.3.2 → faser-0.3.4}/src/faser/io.py +0 -0
  71. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/__init__.py +0 -0
  72. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/gui.py +0 -0
  73. {faser-0.3.2 → faser-0.3.4}/src/faser/napari/main.py +0 -0
  74. {faser-0.3.2 → faser-0.3.4}/src/faser/napari.yaml +0 -0
  75. {faser-0.3.2 → faser-0.3.4}/src/tests/psf/config.txt +0 -0
  76. {faser-0.3.2 → faser-0.3.4}/src/tests/psf/psf.tif +0 -0
  77. {faser-0.3.2 → faser-0.3.4}/src/tests/test_cli.py +0 -0
  78. {faser-0.3.2 → faser-0.3.4}/src/tests/test_random.py +0 -0
faser-0.3.4/PKG-INFO ADDED
@@ -0,0 +1,156 @@
1
+ Metadata-Version: 2.4
2
+ Name: faser
3
+ Version: 0.3.4
4
+ Summary: Faser is a tool for vectorial psf simulation
5
+ Author-email: Johannes Roos <jhnnsrs@gmail.com>
6
+ Classifier: Framework :: napari
7
+ Requires-Python: <3.13,>=3.9
8
+ Requires-Dist: matplotlib>=3.9.2
9
+ Requires-Dist: numpy<2
10
+ Requires-Dist: psygnal>=0.11.1
11
+ Requires-Dist: pydantic>2
12
+ Requires-Dist: python-slugify>=8.0.4
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+ Requires-Dist: qtpy>=2.4.2
14
+ Requires-Dist: superqt>=0.6.7
15
+ Requires-Dist: tifffile>=2024.8.30
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+ Provides-Extra: cli
17
+ Requires-Dist: rich-click>=1.8.3; extra == 'cli'
18
+ Provides-Extra: full
19
+ Requires-Dist: pyqt5>=5.15.11; extra == 'full'
20
+ Requires-Dist: rich-click>=1.8.3; extra == 'full'
21
+ Provides-Extra: numba
22
+ Requires-Dist: numba>=0.60.0; extra == 'numba'
23
+ Description-Content-Type: text/markdown
24
+
25
+ # faser
26
+
27
+ faser is a Python-based software package designed to simulate the excitation
28
+ point spread function (PSF) of optical microscopes. Faser calculates PSFs for high NA
29
+ focusing by using a vectorial model of the electromagnetic field, enabling exploration of the impact
30
+ of geometrical and optical parameters on imaging performance in advanced applications. The
31
+ software supports various beam profiles, including those used in STED microscopy, and allows for
32
+ the simulation of common experimental conditions such as a cranial window and a coverslip tilt.
33
+
34
+ We provide to prefered ways to use faser:
35
+
36
+ ## Faser as a Napari Plugin
37
+
38
+ The recommended way to install faser is as a Napari plugin, which provides a user-friendly GUI for interactively exploring the PSF simulation. This can be done via:
39
+
40
+ ```bash
41
+ pip install faser napari[pyqt5]
42
+ ```
43
+
44
+ #### Usage
45
+
46
+ You can run the GUI application via (or just as a Napari plugin)
47
+
48
+ ```bash
49
+ qtfaser
50
+ ```
51
+
52
+ For more information on how to use the GUI, please refer to the [preprint](https://faser.readthedocs.io/en/latest/).
53
+
54
+ ## Faser as a standalone application
55
+
56
+ Alternatively, you can install the package as a standalone application only, that you can run in enironments without Napari or GUI support:
57
+
58
+ ```bash
59
+ pip install faser[cli]
60
+ ```
61
+ This will install the package as a standalone application that can be run from the command line via:
62
+
63
+ ```bash
64
+ faser
65
+ ```
66
+ We generally recommend the GUI application for most users, as it provides a more user-friendly interface.
67
+ However faser can also be used as a library, and the CLI application is useful for scripting and batch processing.
68
+
69
+ #### Usage
70
+
71
+ To simulate the PSF, with a specific numerical aperture (NA) and a beam profile, you can run the following command:
72
+
73
+ ```bash
74
+ faser --na 1.4 --window=NO
75
+ ```
76
+
77
+ For more information and options you can run:
78
+
79
+ ```bash
80
+ faser --help
81
+ ```
82
+
83
+ To display the GUI interface and the available options:
84
+
85
+ ```
86
+ __
87
+ / _| __ _ ___ ___ _ __
88
+ | |_ / _` / __|/ _ \ '__|
89
+ | _| (_| \__ \ __/ |
90
+ |_| \__,_|___/\___|_|
91
+
92
+ Generating PSF with config
93
+ faser➜ faser git:(master) ✗ uv run faser --help
94
+
95
+ Usage: faser [OPTIONS]
96
+
97
+ ╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
98
+ │ --config FILENAME Path to a JSON file │
99
+ │ --detector_gaussian_noise FLOAT Detector Gaussian noise │
100
+ │ --gaussian_beam_noise FLOAT Gaussian_beam noise │
101
+ │ --add_noise NOISE │
102
+ │ --loaded_phase_mask OPTIONAL Loaded Phasemak │
103
+ │ --p FLOAT Ratio between Donut (p) and Bottle (1-p) intensity │
104
+ │ --mask_offset_y FLOAT Y offset of the phase mask in regard to pupil center │
105
+ │ --mask_offset_x FLOAT X offset of the phase mask in regard to pupil center │
106
+ │ --ring_radius FLOAT Radius of the ring phase mask (on unit pupil) │
107
+ │ --rc FLOAT Ring charge (should be odd to produce bottle) │
108
+ │ --vc FLOAT Vortex charge (should be integer to produce donut) │
109
+ │ --epsilon FLOAT Ellipticity of the polarization (in °) │
110
+ │ --psi FLOAT Direction of the polarization (in °) │
111
+ │ --ampl_offset_y FLOAT Y offset of the amplitude profile in regard to pupil center │
112
+ │ --ampl_offset_x FLOAT X offset of the amplitude profile in regard to pupil center │
113
+ │ --waist FLOAT Diameter of the input beam on the objective pupil (in µm) │
114
+ │ --wavelength FLOAT Wavelength of light (in µm) │
115
+ │ --polarization POLARIZATION │
116
+ │ --mode MODE │
117
+ │ --aberration_offset_y FLOAT Y offset of the aberration function in regard to pupil center │
118
+ │ --aberration_offset_x FLOAT X offset of the aberration function in regard to pupil center │
119
+ │ --a24 ABERRATIONFLOAT Secondary spherical │
120
+ │ --a12 ABERRATIONFLOAT Primary spherical │
121
+ │ --a9 ABERRATIONFLOAT Oblique Trefoil │
122
+ │ --a8 ABERRATIONFLOAT Horizontal Coma │
123
+ │ --a7 ABERRATIONFLOAT Vertical Coma │
124
+ │ --a6 ABERRATIONFLOAT Vertical Trefoil │
125
+ │ --a5 ABERRATIONFLOAT Vertical Astigmatism │
126
+ │ --a4 ABERRATIONFLOAT Defocus │
127
+ │ --a3 ABERRATIONFLOAT Oblique Astigmatism │
128
+ │ --a2 ABERRATIONFLOAT Horizontal Tilt │
129
+ │ --a1 ABERRATIONFLOAT Vertical Tilt │
130
+ │ --a0 ABERRATIONFLOAT Piston │
131
+ │ --wind_offset_y FLOAT Y offset of the cranial window in regard to pupil center │
132
+ │ --wind_offset_x FLOAT X offset of the cranial window in regard to pupil center │
133
+ │ --wind_depth FLOAT Depth of the cranial window (in mm) │
134
+ │ --wind_radius FLOAT Diameter of the cranial window (in mm) │
135
+ │ --window WINDOW │
136
+ │ --tilt FLOAT Tilt angle of the coverslip (in °) │
137
+ │ --depth FLOAT Imaging depth in the sample (in µm) │
138
+ │ --collar FLOAT Correction collar setting to compensate coverslip thickness │
139
+ │ --thickness FLOAT Thickness of the coverslip (in µm) │
140
+ │ --n3 FLOAT Refractive index of the sample │
141
+ │ --n2 FLOAT Refractive index of the coverslip │
142
+ │ --n1 FLOAT Refractive index of the immersion medium │
143
+ │ --wd FLOAT Working Distance of the objective lens (in µm) │
144
+ │ --na FLOAT Numerical Aperture of Objective Lens │
145
+ │ --normalize NORMALIZE │
146
+ │ --nphi INTEGER Integration sted of the aximutal angle on the pupil │
147
+ │ --ntheta INTEGER Integration sted of the focalization angle │
148
+ │ --nz INTEGER Discretization of Z axis - better be odd number for perfect 0 │
149
+ │ --nxy INTEGER Discretization of image plane - better be odd number for perfect 0 │
150
+ │ --l_obs_z FLOAT Observation scale in Z (in µm) │
151
+ │ --l_obs_xy FLOAT Observation scale in XY (in µm) │
152
+ │ --help Show this message and exit. │
153
+ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
154
+ ```
155
+
156
+
faser-0.3.4/README.md ADDED
@@ -0,0 +1,132 @@
1
+ # faser
2
+
3
+ faser is a Python-based software package designed to simulate the excitation
4
+ point spread function (PSF) of optical microscopes. Faser calculates PSFs for high NA
5
+ focusing by using a vectorial model of the electromagnetic field, enabling exploration of the impact
6
+ of geometrical and optical parameters on imaging performance in advanced applications. The
7
+ software supports various beam profiles, including those used in STED microscopy, and allows for
8
+ the simulation of common experimental conditions such as a cranial window and a coverslip tilt.
9
+
10
+ We provide to prefered ways to use faser:
11
+
12
+ ## Faser as a Napari Plugin
13
+
14
+ The recommended way to install faser is as a Napari plugin, which provides a user-friendly GUI for interactively exploring the PSF simulation. This can be done via:
15
+
16
+ ```bash
17
+ pip install faser napari[pyqt5]
18
+ ```
19
+
20
+ #### Usage
21
+
22
+ You can run the GUI application via (or just as a Napari plugin)
23
+
24
+ ```bash
25
+ qtfaser
26
+ ```
27
+
28
+ For more information on how to use the GUI, please refer to the [preprint](https://faser.readthedocs.io/en/latest/).
29
+
30
+ ## Faser as a standalone application
31
+
32
+ Alternatively, you can install the package as a standalone application only, that you can run in enironments without Napari or GUI support:
33
+
34
+ ```bash
35
+ pip install faser[cli]
36
+ ```
37
+ This will install the package as a standalone application that can be run from the command line via:
38
+
39
+ ```bash
40
+ faser
41
+ ```
42
+ We generally recommend the GUI application for most users, as it provides a more user-friendly interface.
43
+ However faser can also be used as a library, and the CLI application is useful for scripting and batch processing.
44
+
45
+ #### Usage
46
+
47
+ To simulate the PSF, with a specific numerical aperture (NA) and a beam profile, you can run the following command:
48
+
49
+ ```bash
50
+ faser --na 1.4 --window=NO
51
+ ```
52
+
53
+ For more information and options you can run:
54
+
55
+ ```bash
56
+ faser --help
57
+ ```
58
+
59
+ To display the GUI interface and the available options:
60
+
61
+ ```
62
+ __
63
+ / _| __ _ ___ ___ _ __
64
+ | |_ / _` / __|/ _ \ '__|
65
+ | _| (_| \__ \ __/ |
66
+ |_| \__,_|___/\___|_|
67
+
68
+ Generating PSF with config
69
+ faser➜ faser git:(master) ✗ uv run faser --help
70
+
71
+ Usage: faser [OPTIONS]
72
+
73
+ ╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
74
+ │ --config FILENAME Path to a JSON file │
75
+ │ --detector_gaussian_noise FLOAT Detector Gaussian noise │
76
+ │ --gaussian_beam_noise FLOAT Gaussian_beam noise │
77
+ │ --add_noise NOISE │
78
+ │ --loaded_phase_mask OPTIONAL Loaded Phasemak │
79
+ │ --p FLOAT Ratio between Donut (p) and Bottle (1-p) intensity │
80
+ │ --mask_offset_y FLOAT Y offset of the phase mask in regard to pupil center │
81
+ │ --mask_offset_x FLOAT X offset of the phase mask in regard to pupil center │
82
+ │ --ring_radius FLOAT Radius of the ring phase mask (on unit pupil) │
83
+ │ --rc FLOAT Ring charge (should be odd to produce bottle) │
84
+ │ --vc FLOAT Vortex charge (should be integer to produce donut) │
85
+ │ --epsilon FLOAT Ellipticity of the polarization (in °) │
86
+ │ --psi FLOAT Direction of the polarization (in °) │
87
+ │ --ampl_offset_y FLOAT Y offset of the amplitude profile in regard to pupil center │
88
+ │ --ampl_offset_x FLOAT X offset of the amplitude profile in regard to pupil center │
89
+ │ --waist FLOAT Diameter of the input beam on the objective pupil (in µm) │
90
+ │ --wavelength FLOAT Wavelength of light (in µm) │
91
+ │ --polarization POLARIZATION │
92
+ │ --mode MODE │
93
+ │ --aberration_offset_y FLOAT Y offset of the aberration function in regard to pupil center │
94
+ │ --aberration_offset_x FLOAT X offset of the aberration function in regard to pupil center │
95
+ │ --a24 ABERRATIONFLOAT Secondary spherical │
96
+ │ --a12 ABERRATIONFLOAT Primary spherical │
97
+ │ --a9 ABERRATIONFLOAT Oblique Trefoil │
98
+ │ --a8 ABERRATIONFLOAT Horizontal Coma │
99
+ │ --a7 ABERRATIONFLOAT Vertical Coma │
100
+ │ --a6 ABERRATIONFLOAT Vertical Trefoil │
101
+ │ --a5 ABERRATIONFLOAT Vertical Astigmatism │
102
+ │ --a4 ABERRATIONFLOAT Defocus │
103
+ │ --a3 ABERRATIONFLOAT Oblique Astigmatism │
104
+ │ --a2 ABERRATIONFLOAT Horizontal Tilt │
105
+ │ --a1 ABERRATIONFLOAT Vertical Tilt │
106
+ │ --a0 ABERRATIONFLOAT Piston │
107
+ │ --wind_offset_y FLOAT Y offset of the cranial window in regard to pupil center │
108
+ │ --wind_offset_x FLOAT X offset of the cranial window in regard to pupil center │
109
+ │ --wind_depth FLOAT Depth of the cranial window (in mm) │
110
+ │ --wind_radius FLOAT Diameter of the cranial window (in mm) │
111
+ │ --window WINDOW │
112
+ │ --tilt FLOAT Tilt angle of the coverslip (in °) │
113
+ │ --depth FLOAT Imaging depth in the sample (in µm) │
114
+ │ --collar FLOAT Correction collar setting to compensate coverslip thickness │
115
+ │ --thickness FLOAT Thickness of the coverslip (in µm) │
116
+ │ --n3 FLOAT Refractive index of the sample │
117
+ │ --n2 FLOAT Refractive index of the coverslip │
118
+ │ --n1 FLOAT Refractive index of the immersion medium │
119
+ │ --wd FLOAT Working Distance of the objective lens (in µm) │
120
+ │ --na FLOAT Numerical Aperture of Objective Lens │
121
+ │ --normalize NORMALIZE │
122
+ │ --nphi INTEGER Integration sted of the aximutal angle on the pupil │
123
+ │ --ntheta INTEGER Integration sted of the focalization angle │
124
+ │ --nz INTEGER Discretization of Z axis - better be odd number for perfect 0 │
125
+ │ --nxy INTEGER Discretization of image plane - better be odd number for perfect 0 │
126
+ │ --l_obs_z FLOAT Observation scale in Z (in µm) │
127
+ │ --l_obs_xy FLOAT Observation scale in XY (in µm) │
128
+ │ --help Show this message and exit. │
129
+ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
130
+ ```
131
+
132
+
faser-0.3.4/psf.tif ADDED
Binary file
faser-0.3.4/psf_config.json ADDED
@@ -0,0 +1,55 @@
1
+ {
2
+ "L_obs_XY": 2.0,
3
+ "L_obs_Z": 2.0,
4
+ "Nxy": 31,
5
+ "Nz": 31,
6
+ "Ntheta": 31,
7
+ "Nphi": 31,
8
+ "Normalize": "NO",
9
+ "NA": 1.0,
10
+ "WD": 2800.0,
11
+ "n1": 1.33,
12
+ "n2": 1.52,
13
+ "n3": 1.38,
14
+ "Thickness": 170.0,
15
+ "Collar": 170.0,
16
+ "Depth": 0.0,
17
+ "Tilt": 0.0,
18
+ "Window": "NO",
19
+ "Wind_Radius": 2.3,
20
+ "Wind_Depth": 2.23,
21
+ "Wind_Offset_x": 0.0,
22
+ "Wind_Offset_y": 0.0,
23
+ "a0": 0.0,
24
+ "a1": 0.0,
25
+ "a2": 0.0,
26
+ "a3": 0.0,
27
+ "a4": 0.0,
28
+ "a5": 0.0,
29
+ "a6": 0.0,
30
+ "a7": 0.0,
31
+ "a8": 0.0,
32
+ "a9": 0.0,
33
+ "a12": 0.0,
34
+ "a24": 0.0,
35
+ "Aberration_offset_x": 0.0,
36
+ "Aberration_offset_y": 0.0,
37
+ "Mode": "GAUSSIAN",
38
+ "Polarization": 1,
39
+ "Wavelength": 0.592,
40
+ "Waist": 8000.0,
41
+ "Ampl_offset_x": 0.0,
42
+ "Ampl_offset_y": 0.0,
43
+ "Psi": 0.0,
44
+ "Epsilon": 45.0,
45
+ "VC": 1.0,
46
+ "RC": 1.0,
47
+ "Ring_Radius": 0.707,
48
+ "Mask_offset_x": 0.0,
49
+ "Mask_offset_y": 0.0,
50
+ "p": 0.5,
51
+ "loaded_phase_mask": null,
52
+ "Add_noise": "YES",
53
+ "Gaussian_beam_noise": 0.0,
54
+ "Detector_gaussian_noise": 0.0
55
+ }
{faser-0.3.2 → faser-0.3.4}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "faser"
3
- version = "0.3.2"
3
+ version = "0.3.4"
4
4
  description = "Faser is a tool for vectorial psf simulation"
5
5
  authors = [
6
6
  { name = "Johannes Roos", email = "jhnnsrs@gmail.com" }
@@ -12,6 +12,8 @@ dependencies = [
12
12
  "python-slugify>=8.0.4",
13
13
  "tifffile>=2024.8.30",
14
14
  "psygnal>=0.11.1",
15
+ "qtpy>=2.4.2",
16
+ "superqt>=0.6.7",
15
17
  ]
16
18
  classifiers = [
17
19
  "Framework :: napari",
{faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/export.py RENAMED
@@ -1,16 +1,16 @@
1
1
  import sys
2
+
2
3
  import matplotlib
3
4
 
4
5
  matplotlib.use("Qt5Agg")
5
6
 
6
- from PyQt5 import QtCore, QtWidgets
7
-
8
- from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
9
- from matplotlib.figure import Figure
10
7
  import napari
8
+ from matplotlib.backends.backend_qt import FigureCanvasQT
9
+ from matplotlib.figure import Figure
10
+ from qtpy import QtCore, QtWidgets
11
11
 
12
12
 
13
- class MplCanvas(FigureCanvasQTAgg):
13
+ class MplCanvas(FigureCanvasQT):
14
14
  def __init__(self, parent=None, width=5, height=4, dpi=100):
15
15
  fig = Figure(figsize=(width, height), dpi=dpi)
16
16
  self.axes = fig.add_subplot(111)
{faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/fields.py RENAMED
@@ -15,9 +15,9 @@ from annotated_types import Ge, Gt, Le, Lt
15
15
  # from faser.generators.vectorial.stephane.tilted_coverslip import generate_psf
16
16
  from pydantic import BaseModel, Field
17
17
  from pydantic.fields import FieldInfo
18
- from PyQt5 import QtCore
19
- from PyQt5.QtWidgets import QWidget
20
- from qtpy import QtGui, QtWidgets
18
+ from qtpy import QtCore, QtGui, QtWidgets
19
+ from qtpy.QtCore import Signal
20
+ from qtpy.QtWidgets import QWidget
21
21
  from superqt import QEnumComboBox # QDoubleRangeSlider,
22
22
  from superqt import QLabeledDoubleRangeSlider, QLabeledDoubleSlider
23
23
 
@@ -44,8 +44,8 @@ def get_field_lt(field: FieldInfo) -> float:
44
44
 
45
45
 
46
46
  class FormField(QtWidgets.QWidget):
47
- on_child_value_changed = QtCore.pyqtSignal(str, object)
48
- on_child_range_value_changed = QtCore.pyqtSignal(str, object)
47
+ on_child_value_changed = Signal(str, object)
48
+ on_child_range_value_changed = Signal(str, object)
49
49
 
50
50
  def __init__(
51
51
  self, key: str, field: FieldInfo, toggable: bool = True, *args, **kwargs
@@ -220,7 +220,7 @@ class IntList(pydantic.BaseModel):
220
220
 
221
221
 
222
222
  class FloatRangeStepSliderField(QtWidgets.QWidget):
223
- on_range_changed = QtCore.pyqtSignal(object)
223
+ on_range_changed = Signal(object)
224
224
 
225
225
  def __init__(self, *args, gt=None, lt=None, steps=None, **kwargs):
226
226
  super().__init__(*args, **kwargs)
@@ -279,7 +279,7 @@ class IntRange(pydantic.BaseModel):
279
279
 
280
280
 
281
281
  class FloatRangeArrayField(QtWidgets.QWidget):
282
- on_range_changed = QtCore.pyqtSignal(object)
282
+ on_range_changed = Signal(object)
283
283
 
284
284
  def __init__(self, default, *args, **kwargs):
285
285
  super().__init__(*args, **kwargs)
@@ -333,7 +333,7 @@ class FloatRangeArrayField(QtWidgets.QWidget):
333
333
 
334
334
 
335
335
  class IntRangeStepSliderField(QtWidgets.QWidget):
336
- on_range_changed = QtCore.pyqtSignal(object)
336
+ on_range_changed = Signal(object)
337
337
 
338
338
  def __init__(self, *args, gt=None, lt=None, steps=None, **kwargs):
339
339
  super().__init__(*args, **kwargs)
@@ -392,7 +392,7 @@ class FloatSliderField(FormField):
392
392
 
393
393
 
394
394
  class IntRangeArrayField(QtWidgets.QWidget):
395
- on_range_changed = QtCore.pyqtSignal(object)
395
+ on_range_changed = Signal(object)
396
396
 
397
397
  def __init__(self, default, *args, **kwargs):
398
398
  super().__init__(*args, **kwargs)
@@ -492,7 +492,7 @@ class OptionRange(pydantic.BaseModel):
492
492
 
493
493
 
494
494
  class MultiEnumField(QtWidgets.QWidget):
495
- on_range_changed = QtCore.pyqtSignal(object)
495
+ on_range_changed = Signal(object)
496
496
 
497
497
  def __init__(self, *args, enum: Enum, **kwargs):
498
498
  super().__init__(*args, **kwargs)
{faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/helper_widget.py RENAMED
@@ -6,16 +6,17 @@ from typing import Any, Callable, List, Type
6
6
 
7
7
  import dask
8
8
  import dask.array as da
9
- from matplotlib.figure import Figure
9
+ import matplotlib.pyplot as plt
10
10
  import napari
11
11
  import numpy as np
12
12
  import pydantic
13
+ import skimage.draw as draw
13
14
  import tifffile
14
- from PyQt5 import QtCore
15
- from PyQt5.QtWidgets import QWidget
16
- from qtpy import QtGui, QtWidgets
17
- from scipy import ndimage
18
- from scipy import signal
15
+ from matplotlib.figure import Figure
16
+ from qtpy import QtCore, QtGui, QtWidgets
17
+ from qtpy.QtCore import Signal
18
+ from qtpy.QtWidgets import QWidget
19
+ from scipy import ndimage, signal
19
20
  from slugify import slugify
20
21
  from superqt import (
21
22
  QDoubleRangeSlider,
@@ -24,8 +25,7 @@ from superqt import (
24
25
  QLabeledDoubleSlider,
25
26
  )
26
27
  from superqt.utils import thread_worker
27
- import matplotlib.pyplot as plt
28
- import skimage.draw as draw
28
+
29
29
  from faser.env import get_asset_file
30
30
  from faser.generators.base import AberrationFloat, PSFConfig
31
31
  from faser.generators.vectorial.stephane.tilted_coverslip import generate_psf
@@ -50,8 +50,8 @@ class HelperTab(QtWidgets.QWidget):
50
50
 
51
51
  # Step 1: Create a worker class
52
52
  class ExportWorker(QtCore.QObject):
53
- finished = QtCore.pyqtSignal()
54
- progress = QtCore.pyqtSignal(int)
53
+ finished = Signal()
54
+ progress = Signal(int)
55
55
 
56
56
  def __init__(self, layers, export_dir):
57
57
  super().__init__()
@@ -459,8 +459,8 @@ class ConvolveModel(pydantic.BaseModel):
459
459
 
460
460
  # Step 1: Create a worker class
461
461
  class ConvolveWorker(QtCore.QObject):
462
- finished = QtCore.pyqtSignal(object)
463
- progress = QtCore.pyqtSignal(int)
462
+ finished = Signal(object)
463
+ progress = Signal(int)
464
464
 
465
465
  def __init__(self, image_data, psf_data):
466
466
  super().__init__()
@@ -644,8 +644,8 @@ def calculate_config_labels(configs: PSFConfig):
644
644
 
645
645
  # Step 1: Create a worker class
646
646
  class MetricWorker(QtCore.QObject):
647
- finished = QtCore.pyqtSignal(object, object)
648
- progress = QtCore.pyqtSignal(int)
647
+ finished = QtCore.Signal(object, object)
648
+ progress = QtCore.Signal(int)
649
649
 
650
650
  def __init__(self, psf_data, configs):
651
651
  super().__init__()
{faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/main_widget.py RENAMED
@@ -15,10 +15,9 @@ import napari
15
15
 
16
16
  # from pydantic.types import ConstrainedFloat
17
17
  import numpy as np
18
- from PyQt5 import QtCore
19
18
 
20
19
  # from PyQt5.QtWidgets import QWidget
21
- from qtpy import QtGui, QtWidgets
20
+ from qtpy import QtCore, QtGui, QtWidgets
22
21
  from qtpy.QtWidgets import QStyle
23
22
 
24
23
  # from superqt import QDoubleRangeSlider, QLabeledDoubleRangeSlider, QLabeledDoubleSlider
{faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/mpl_canvas.py RENAMED
@@ -1,16 +1,16 @@
1
1
  import sys
2
2
  import typing
3
- from PyQt5.QtWidgets import QWidget
3
+
4
4
  import matplotlib
5
5
  import numpy as np
6
+ from qtpy.QtWidgets import QWidget
6
7
 
7
8
  matplotlib.use("Qt5Agg")
8
9
 
9
- from PyQt5 import QtCore, QtWidgets
10
-
11
10
  from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
11
+ from matplotlib.cm import coolwarm, turbo, viridis
12
12
  from matplotlib.figure import Figure
13
- from matplotlib.cm import coolwarm, viridis, turbo
13
+ from qtpy import QtCore, QtWidgets
14
14
 
15
15
 
16
16
  class MplCanvas(FigureCanvasQTAgg):
{faser-0.3.2 → faser-0.3.4}/src/faser/napari/widgets/tob_bar.py RENAMED
@@ -1,16 +1,13 @@
1
1
  import sys
2
- import matplotlib
3
-
4
- matplotlib.use("Qt5Agg")
5
-
6
- from PyQt5 import QtCore, QtWidgets
7
2
 
8
- from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
9
- from matplotlib.figure import Figure
3
+ import matplotlib
10
4
  import napari
5
+ from matplotlib.backends.backend_qt import FigureCanvasQT
6
+ from matplotlib.figure import Figure
7
+ from qtpy import QtCore, QtWidgets
11
8
 
12
9
 
13
- class MplCanvas(FigureCanvasQTAgg):
10
+ class MplCanvas(FigureCanvasQT):
14
11
  def __init__(self, parent=None, width=5, height=4, dpi=100):
15
12
  fig = Figure(figsize=(width, height), dpi=dpi)
16
13
  self.axes = fig.add_subplot(111)