AMS-BP 0.0.231__tar.gz → 0.0.251__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 (108) hide show
  1. {ams_bp-0.0.231 → ams_bp-0.0.251}/PKG-INFO +3 -1
  2. {ams_bp-0.0.231 → ams_bp-0.0.251}/README.md +2 -0
  3. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_base_[[0. 0.]].txt +10 -0
  4. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_base_[[0.04 0.04]].txt +10 -0
  5. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_base_[[0.1 0.1]].txt +10 -0
  6. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_base_[[0.4 0.4]].txt +10 -0
  7. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_data_[[0. 0.]].txt +10 -0
  8. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_data_[[0.04 0.04]].txt +10 -0
  9. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_data_[[0.1 0.1]].txt +10 -0
  10. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_data_[[0.4 0.4]].txt +10 -0
  11. ams_bp-0.0.251/examples/QuantitativeExperiments/FRAP_methods.ipynb +1025 -0
  12. ams_bp-0.0.251/examples/VisualizingIndividualModules/laser_modulation.ipynb +1094 -0
  13. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/__init__.py +1 -1
  14. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/lasers/laser_profiles.py +5 -168
  15. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/photophysics/state_kinetics.py +4 -1
  16. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/sim_microscopy.py +3 -1
  17. {ams_bp-0.0.231 → ams_bp-0.0.251}/.github/workflows/lint.yml +0 -0
  18. {ams_bp-0.0.231 → ams_bp-0.0.251}/.github/workflows/pages.yml +0 -0
  19. {ams_bp-0.0.231 → ams_bp-0.0.251}/.github/workflows/publish_pypi.yml +0 -0
  20. {ams_bp-0.0.231 → ams_bp-0.0.251}/.gitignore +0 -0
  21. {ams_bp-0.0.231 → ams_bp-0.0.251}/LICENSE +0 -0
  22. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/cells/base_cell.md +0 -0
  23. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/cells/rectangular_cell.md +0 -0
  24. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/cells/rod_cell.md +0 -0
  25. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/cells/spherical_cell.md +0 -0
  26. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/configio/configmodels.md +0 -0
  27. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/configio/convertconfig.md +0 -0
  28. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/configio/experiments.md +0 -0
  29. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/configio/saving.md +0 -0
  30. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/metadata/metadata.md +0 -0
  31. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/motion/condensate_movement.md +0 -0
  32. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/motion/movement/boundary_conditions.md +0 -0
  33. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/motion/movement/fbm_BP.md +0 -0
  34. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/motion/track_gen.md +0 -0
  35. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/optics/camera/detectors.md +0 -0
  36. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/optics/camera/quantum_eff.md +0 -0
  37. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/optics/filters/channels/channelschema.md +0 -0
  38. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/optics/filters/filters.md +0 -0
  39. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/optics/lasers/laser_profiles.md +0 -0
  40. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/optics/psf/psf_engine.md +0 -0
  41. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/photophysics/photon_physics.md +0 -0
  42. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/photophysics/state_kinetics.md +0 -0
  43. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/probabilityfuncs/markov_chain.md +0 -0
  44. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/probabilityfuncs/probability_functions.md +0 -0
  45. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/run_cell_simulation.md +0 -0
  46. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/sample/flurophore/flurophore_schema.md +0 -0
  47. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/sample/sim_sampleplane.md +0 -0
  48. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/sim_config.md +0 -0
  49. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/sim_microscopy.md +0 -0
  50. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/utils/constants.md +0 -0
  51. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/utils/errors.md +0 -0
  52. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/API_Documentation/utils/util_functions.md +0 -0
  53. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/assets/icons/Cells-actin-like-a-tree-Jamie-Whitelaw-1.png +0 -0
  54. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/assets/icons/drawing.pdf +0 -0
  55. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/assets/icons/drawing.png +0 -0
  56. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/assets/icons/drawing.svg +0 -0
  57. {ams_bp-0.0.231 → ams_bp-0.0.251}/docs/index.md +0 -0
  58. {ams_bp-0.0.231 → ams_bp-0.0.251}/examples/VisualizingIndividualModules/modules_explained.ipynb +0 -0
  59. {ams_bp-0.0.231 → ams_bp-0.0.251}/mkdocs.yml +0 -0
  60. {ams_bp-0.0.231 → ams_bp-0.0.251}/pyproject.toml +0 -0
  61. {ams_bp-0.0.231 → ams_bp-0.0.251}/pytest.ini +0 -0
  62. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/cells/__init__.py +0 -0
  63. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/cells/base_cell.py +0 -0
  64. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/cells/rectangular_cell.py +0 -0
  65. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/cells/rod_cell.py +0 -0
  66. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/cells/spherical_cell.py +0 -0
  67. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/configio/__init__.py +0 -0
  68. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/configio/configmodels.py +0 -0
  69. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/configio/convertconfig.py +0 -0
  70. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/configio/experiments.py +0 -0
  71. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/configio/saving.py +0 -0
  72. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/metadata/__init__.py +0 -0
  73. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/metadata/metadata.py +0 -0
  74. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/motion/__init__.py +0 -0
  75. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/motion/condensate_movement.py +0 -0
  76. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/motion/movement/__init__.py +0 -0
  77. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/motion/movement/boundary_conditions.py +0 -0
  78. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/motion/movement/fbm_BP.py +0 -0
  79. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/motion/track_gen.py +0 -0
  80. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/__init__.py +0 -0
  81. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/camera/__init__.py +0 -0
  82. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/camera/detectors.py +0 -0
  83. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/camera/quantum_eff.py +0 -0
  84. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/filters/__init__.py +0 -0
  85. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/filters/channels/__init__.py +0 -0
  86. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/filters/channels/channelschema.py +0 -0
  87. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/filters/filters.py +0 -0
  88. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/lasers/__init__.py +0 -0
  89. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/psf/__init__.py +0 -0
  90. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/optics/psf/psf_engine.py +0 -0
  91. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/photophysics/__init__.py +0 -0
  92. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/photophysics/photon_physics.py +0 -0
  93. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/probabilityfuncs/__init__.py +0 -0
  94. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/probabilityfuncs/markov_chain.py +0 -0
  95. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/probabilityfuncs/probability_functions.py +0 -0
  96. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/run_cell_simulation.py +0 -0
  97. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/sample/__init__.py +0 -0
  98. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/sample/flurophores/__init__.py +0 -0
  99. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/sample/flurophores/flurophore_schema.py +0 -0
  100. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/sample/sim_sampleplane.py +0 -0
  101. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/sim_config.toml +0 -0
  102. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/utils/__init__.py +0 -0
  103. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/utils/constants.py +0 -0
  104. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/utils/decorators.py +0 -0
  105. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/utils/errors.py +0 -0
  106. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/utils/maskMaker.py +0 -0
  107. {ams_bp-0.0.231 → ams_bp-0.0.251}/src/AMS_BP/utils/util_functions.py +0 -0
  108. {ams_bp-0.0.231 → ams_bp-0.0.251}/uv.lock +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: AMS_BP
3
- Version: 0.0.231
3
+ Version: 0.0.251
4
4
  Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
5
5
  Project-URL: Documentation, https://joemans3.github.io/AMS_BP/
6
6
  Project-URL: Source code, https://github.com/joemans3/AMS_BP
@@ -171,3 +171,5 @@ frames, metadata = function_exp(microscope=microscope, config=config_exp)
171
171
  from AMS_BP.configio.saving import save_config_frames
172
172
  save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
173
173
  ```
174
+
175
+ > A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
@@ -151,3 +151,5 @@ frames, metadata = function_exp(microscope=microscope, config=config_exp)
151
151
  from AMS_BP.configio.saving import save_config_frames
152
152
  save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
153
153
  ```
154
+
155
+ > A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
@@ -0,0 +1,10 @@
1
+ 1.000000000000000000e+00
2
+ 9.919409645923475960e-01
3
+ 9.759078449584305259e-01
4
+ 9.525972407856285740e-01
5
+ 9.425163672609473409e-01
6
+ 9.301984459597217869e-01
7
+ 9.145617651722810493e-01
8
+ 8.904356296581564800e-01
9
+ 8.667682305235258067e-01
10
+ 8.406655641891126463e-01
@@ -0,0 +1,10 @@
1
+ 1.000000000000000000e+00
2
+ 9.837507842285604376e-01
3
+ 9.505911876839920893e-01
4
+ 9.410742724771969936e-01
5
+ 9.187442690989816585e-01
6
+ 9.319579170889435993e-01
7
+ 9.181313643163939719e-01
8
+ 9.040297282949664170e-01
9
+ 8.851358525167704050e-01
10
+ 8.656676801312678249e-01
@@ -0,0 +1,10 @@
1
+ 1.000000000000000000e+00
2
+ 1.005785307540083107e+00
3
+ 9.584225192843585095e-01
4
+ 9.479271838778724479e-01
5
+ 8.799170065829328147e-01
6
+ 8.644440854569686028e-01
7
+ 8.454525261499938882e-01
8
+ 8.081155849925285573e-01
9
+ 7.953939663180000785e-01
10
+ 8.103418682605710854e-01
@@ -0,0 +1,10 @@
1
+ 1.000000000000000000e+00
2
+ 9.523666648922527456e-01
3
+ 9.304591054050260768e-01
4
+ 8.483650388838613887e-01
5
+ 9.080676148489409405e-01
6
+ 9.141941821806901514e-01
7
+ 8.881538513654114730e-01
8
+ 9.016458495651878957e-01
9
+ 8.415900039198416227e-01
10
+ 8.004752203096191510e-01
@@ -0,0 +1,10 @@
1
+ 1.000000000000000000e+00
2
+ 5.967216318272994258e-01
3
+ 2.076453109104598460e-01
4
+ 2.068234198713711780e-01
5
+ 2.042945243664829325e-01
6
+ 2.023116403910591998e-01
7
+ 2.001448367425526786e-01
8
+ 1.982424176241026625e-01
9
+ 1.934605061239503543e-01
10
+ 1.917017742500962685e-01
@@ -0,0 +1,10 @@
1
+ 1.000000000000000000e+00
2
+ 6.123104231381659712e-01
3
+ 2.697851679761935628e-01
4
+ 3.143073429220287762e-01
5
+ 3.378892688402203026e-01
6
+ 3.607089717820877728e-01
7
+ 3.939230990106763475e-01
8
+ 3.994466052363674358e-01
9
+ 3.895429272494714268e-01
10
+ 4.050640841577697326e-01
@@ -0,0 +1,10 @@
1
+ 1.000000000000000000e+00
2
+ 5.810793586050424508e-01
3
+ 2.825859739465164111e-01
4
+ 3.334336044051291470e-01
5
+ 4.232594896372396387e-01
6
+ 4.553649272184974728e-01
7
+ 5.016697682718536111e-01
8
+ 5.625003186580671555e-01
9
+ 5.732174267723761929e-01
10
+ 5.734774517551686213e-01
@@ -0,0 +1,10 @@
1
+ 1.000000000000000000e+00
2
+ 6.466539977024081676e-01
3
+ 5.146927776167316004e-01
4
+ 5.921559785701249190e-01
5
+ 7.037072825071665205e-01
6
+ 7.620328319429682251e-01
7
+ 8.211904531838825072e-01
8
+ 8.104969884368860011e-01
9
+ 8.116457843484609080e-01
10
+ 7.618127355300029491e-01