spacr 0.3.80__tar.gz → 0.4.12__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 (340) hide show
  1. {spacr-0.3.80 → spacr-0.4.12}/.readthedocs.yaml +1 -1
  2. {spacr-0.3.80 → spacr-0.4.12}/MANIFEST.in +5 -2
  3. {spacr-0.3.80/spacr.egg-info → spacr-0.4.12}/PKG-INFO +2 -1
  4. spacr-0.4.12/docs/source/_build/doctrees/environment.pickle +0 -0
  5. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_sources/index.rst.txt +1 -1
  6. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/badge_only.css +1 -1
  7. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/theme.css +1 -1
  8. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/documentation_options.js +1 -1
  9. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-bold.eot +0 -0
  10. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-bold.ttf +0 -0
  11. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-bold.woff +0 -0
  12. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-bold.woff2 +0 -0
  13. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-bolditalic.eot +0 -0
  14. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-bolditalic.ttf +0 -0
  15. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-bolditalic.woff +0 -0
  16. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-bolditalic.woff2 +0 -0
  17. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-italic.eot +0 -0
  18. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-italic.ttf +0 -0
  19. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-italic.woff +0 -0
  20. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-italic.woff2 +0 -0
  21. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-regular.eot +0 -0
  22. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-regular.ttf +0 -0
  23. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-regular.woff +0 -0
  24. spacr-0.4.12/docs/source/_build/html/_static/fonts/Lato/lato-regular.woff2 +0 -0
  25. spacr-0.4.12/docs/source/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot +0 -0
  26. spacr-0.4.12/docs/source/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf +0 -0
  27. spacr-0.4.12/docs/source/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff +0 -0
  28. spacr-0.4.12/docs/source/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 +0 -0
  29. spacr-0.4.12/docs/source/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot +0 -0
  30. spacr-0.4.12/docs/source/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf +0 -0
  31. spacr-0.4.12/docs/source/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff +0 -0
  32. spacr-0.4.12/docs/source/_build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 +0 -0
  33. spacr-0.4.12/docs/source/_build/html/_static/js/versions.js +228 -0
  34. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/searchtools.js +4 -3
  35. spacr-0.4.12/docs/source/_build/html/genindex.html +103 -0
  36. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/index.html +18 -31
  37. spacr-0.4.12/docs/source/_build/html/objects.inv +0 -0
  38. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/search.html +13 -20
  39. spacr-0.4.12/docs/source/_build/html/searchindex.js +1 -0
  40. {spacr-0.3.80 → spacr-0.4.12}/docs/source/conf.py +4 -4
  41. {spacr-0.3.80 → spacr-0.4.12}/docs/source/index.rst +1 -1
  42. {spacr-0.3.80 → spacr-0.4.12}/setup.py +2 -1
  43. {spacr-0.3.80 → spacr-0.4.12}/setup_docs.sh +2 -2
  44. spacr-0.4.12/source/conf.py +39 -0
  45. {spacr-0.3.80 → spacr-0.4.12}/source/index.rst +4 -4
  46. spacr-0.4.12/source/modules.rst +9 -0
  47. spacr-0.4.12/source/setup.rst +33 -0
  48. {spacr-0.3.80/docs → spacr-0.4.12}/source/spacr.rst +72 -56
  49. {spacr-0.3.80 → spacr-0.4.12}/spacr/__init__.py +2 -6
  50. {spacr-0.3.80 → spacr-0.4.12}/spacr/core.py +27 -13
  51. {spacr-0.3.80 → spacr-0.4.12}/spacr/deep_spacr.py +285 -5
  52. {spacr-0.3.80 → spacr-0.4.12}/spacr/gui_core.py +82 -20
  53. {spacr-0.3.80 → spacr-0.4.12}/spacr/gui_elements.py +192 -3
  54. {spacr-0.3.80 → spacr-0.4.12}/spacr/gui_utils.py +1 -1
  55. {spacr-0.3.80 → spacr-0.4.12}/spacr/io.py +5 -176
  56. {spacr-0.3.80 → spacr-0.4.12}/spacr/measure.py +10 -6
  57. {spacr-0.3.80 → spacr-0.4.12}/spacr/ml.py +369 -46
  58. {spacr-0.3.80 → spacr-0.4.12}/spacr/plot.py +203 -92
  59. {spacr-0.3.80 → spacr-0.4.12}/spacr/settings.py +81 -22
  60. {spacr-0.3.80 → spacr-0.4.12}/spacr/submodules.py +283 -2
  61. {spacr-0.3.80 → spacr-0.4.12}/spacr/toxo.py +98 -75
  62. {spacr-0.3.80 → spacr-0.4.12}/spacr/utils.py +138 -43
  63. {spacr-0.3.80 → spacr-0.4.12/spacr.egg-info}/PKG-INFO +2 -1
  64. {spacr-0.3.80 → spacr-0.4.12}/spacr.egg-info/SOURCES.txt +26 -67
  65. {spacr-0.3.80 → spacr-0.4.12}/spacr.egg-info/requires.txt +1 -0
  66. spacr-0.3.80/docs/source/_build/doctrees/environment.pickle +0 -0
  67. spacr-0.3.80/docs/source/_build/html/_modules/index.html +0 -128
  68. spacr-0.3.80/docs/source/_build/html/_modules/spacr/app_annotate.html +0 -164
  69. spacr-0.3.80/docs/source/_build/html/_modules/spacr/app_classify.html +0 -117
  70. spacr-0.3.80/docs/source/_build/html/_modules/spacr/app_make_masks.html +0 -156
  71. spacr-0.3.80/docs/source/_build/html/_modules/spacr/app_mask.html +0 -117
  72. spacr-0.3.80/docs/source/_build/html/_modules/spacr/app_measure.html +0 -117
  73. spacr-0.3.80/docs/source/_build/html/_modules/spacr/app_sequencing.html +0 -117
  74. spacr-0.3.80/docs/source/_build/html/_modules/spacr/app_umap.html +0 -117
  75. spacr-0.3.80/docs/source/_build/html/_modules/spacr/core.html +0 -3319
  76. spacr-0.3.80/docs/source/_build/html/_modules/spacr/deep_spacr.html +0 -909
  77. spacr-0.3.80/docs/source/_build/html/_modules/spacr/graph_learning.html +0 -503
  78. spacr-0.3.80/docs/source/_build/html/_modules/spacr/gui.html +0 -271
  79. spacr-0.3.80/docs/source/_build/html/_modules/spacr/gui_core.html +0 -1065
  80. spacr-0.3.80/docs/source/_build/html/_modules/spacr/gui_elements.html +0 -3217
  81. spacr-0.3.80/docs/source/_build/html/_modules/spacr/gui_utils.html +0 -873
  82. spacr-0.3.80/docs/source/_build/html/_modules/spacr/io.html +0 -2866
  83. spacr-0.3.80/docs/source/_build/html/_modules/spacr/logger.html +0 -129
  84. spacr-0.3.80/docs/source/_build/html/_modules/spacr/measure.html +0 -1292
  85. spacr-0.3.80/docs/source/_build/html/_modules/spacr/plot.html +0 -1904
  86. spacr-0.3.80/docs/source/_build/html/_modules/spacr/sequencing.html +0 -1976
  87. spacr-0.3.80/docs/source/_build/html/_modules/spacr/settings.html +0 -1390
  88. spacr-0.3.80/docs/source/_build/html/_modules/spacr/sim.html +0 -1941
  89. spacr-0.3.80/docs/source/_build/html/_modules/spacr/timelapse.html +0 -996
  90. spacr-0.3.80/docs/source/_build/html/_modules/spacr/utils.html +0 -4955
  91. spacr-0.3.80/docs/source/_build/html/_sources/modules.rst.txt +0 -7
  92. spacr-0.3.80/docs/source/_build/html/_sources/spacr.rst.txt +0 -213
  93. spacr-0.3.80/docs/source/_build/html/_static/js/html5shiv-printshiv.min.js +0 -4
  94. spacr-0.3.80/docs/source/_build/html/_static/js/html5shiv.min.js +0 -4
  95. spacr-0.3.80/docs/source/_build/html/genindex.html +0 -1784
  96. spacr-0.3.80/docs/source/_build/html/modules.html +0 -861
  97. spacr-0.3.80/docs/source/_build/html/objects.inv +0 -0
  98. spacr-0.3.80/docs/source/_build/html/py-modindex.html +0 -250
  99. spacr-0.3.80/docs/source/_build/html/searchindex.js +0 -1
  100. spacr-0.3.80/docs/source/_build/html/spacr.html +0 -5170
  101. spacr-0.3.80/docs/source/modules.rst +0 -7
  102. spacr-0.3.80/notebooks/.ipynb_checkpoints/3b_spacr_computer_vision-checkpoint.ipynb +0 -462
  103. spacr-0.3.80/notebooks/.ipynb_checkpoints/3b_spacr_computer_vision_sophia-checkpoint.ipynb +0 -190
  104. spacr-0.3.80/notebooks/.ipynb_checkpoints/3b_spacr_computer_vision_yifan-checkpoint.ipynb +0 -767
  105. spacr-0.3.80/notebooks/.ipynb_checkpoints/4_spacr_annotate-checkpoint.ipynb +0 -48
  106. spacr-0.3.80/notebooks/1_spacr_generate_masks.ipynb +0 -72
  107. spacr-0.3.80/notebooks/2_spacr_generate_mesurments_crop_images.ipynb +0 -61
  108. spacr-0.3.80/notebooks/3a_spacr_machine_learning.ipynb +0 -110
  109. spacr-0.3.80/notebooks/3b_spacr_computer_vision.ipynb +0 -209
  110. spacr-0.3.80/notebooks/3b_spacr_computer_vision_sophia.ipynb +0 -190
  111. spacr-0.3.80/notebooks/3b_spacr_computer_vision_yifan.ipynb +0 -767
  112. spacr-0.3.80/notebooks/4_spacr_annotate.ipynb +0 -48
  113. spacr-0.3.80/notebooks/old/.ipynb_checkpoints/Untitled-checkpoint.ipynb +0 -337
  114. spacr-0.3.80/notebooks/old/.ipynb_checkpoints/Untitled1-checkpoint.ipynb +0 -6
  115. spacr-0.3.80/notebooks/old/.ipynb_checkpoints/figure_2-checkpoint.ipynb +0 -2623
  116. spacr-0.3.80/notebooks/old/.ipynb_checkpoints/interperate_vision_classes-checkpoint.ipynb +0 -816
  117. spacr-0.3.80/notebooks/old/.ipynb_checkpoints/machine_learning_spacr_nb-checkpoint.ipynb +0 -101
  118. spacr-0.3.80/notebooks/old/.ipynb_checkpoints/spacr_image_umap-checkpoint.ipynb +0 -96
  119. spacr-0.3.80/notebooks/old/.ipynb_checkpoints/submodule_1_frequency_analysis-checkpoint.ipynb +0 -92
  120. spacr-0.3.80/notebooks/old/.ipynb_checkpoints/trade_2025-checkpoint.ipynb +0 -6
  121. spacr-0.3.80/notebooks/old/Untitled.ipynb +0 -1029
  122. spacr-0.3.80/notebooks/old/Untitled1.ipynb +0 -230
  123. spacr-0.3.80/notebooks/old/cv_scoring_nb.ipynb +0 -171
  124. spacr-0.3.80/notebooks/old/deep_learning_spacr.ipynb +0 -141
  125. spacr-0.3.80/notebooks/old/figure_2.ipynb +0 -2623
  126. spacr-0.3.80/notebooks/old/figure_3-Copy1.ipynb +0 -2952
  127. spacr-0.3.80/notebooks/old/figure_3.ipynb +0 -9183
  128. spacr-0.3.80/notebooks/old/interperate_vision_classes.ipynb +0 -1353
  129. spacr-0.3.80/notebooks/old/machine_learning_spacr_nb.ipynb +0 -535
  130. spacr-0.3.80/notebooks/old/spacr_0.1_all_settings_git.ipynb +0 -864
  131. spacr-0.3.80/notebooks/old/spacr_0.1_minimal.ipynb +0 -731
  132. spacr-0.3.80/notebooks/old/spacr_image_umap.ipynb +0 -878
  133. spacr-0.3.80/notebooks/old/trade_2025.ipynb +0 -692
  134. spacr-0.3.80/notebooks/submodules/submodule_1_frequency_analysis.ipynb +0 -92
  135. spacr-0.3.80/source/conf.py +0 -22
  136. spacr-0.3.80/source/modules.rst +0 -8
  137. spacr-0.3.80/source/setup.rst +0 -7
  138. spacr-0.3.80/source/spacr.rst +0 -189
  139. {spacr-0.3.80 → spacr-0.4.12}/LICENSE +0 -0
  140. {spacr-0.3.80 → spacr-0.4.12}/README.rst +0 -0
  141. {spacr-0.3.80 → spacr-0.4.12}/deploy_docs.sh +0 -0
  142. {spacr-0.3.80 → spacr-0.4.12}/docs/requirements.txt +0 -0
  143. {spacr-0.3.80 → spacr-0.4.12}/docs/source/Makefile +0 -0
  144. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js +0 -0
  145. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/basic.css +0 -0
  146. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
  147. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
  148. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
  149. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
  150. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.eot +0 -0
  151. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.svg +0 -0
  152. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.ttf +0 -0
  153. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.woff +0 -0
  154. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
  155. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/lato-bold-italic.woff +0 -0
  156. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/lato-bold-italic.woff2 +0 -0
  157. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/lato-bold.woff +0 -0
  158. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/lato-bold.woff2 +0 -0
  159. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/lato-normal-italic.woff +0 -0
  160. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/lato-normal-italic.woff2 +0 -0
  161. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/lato-normal.woff +0 -0
  162. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/css/fonts/lato-normal.woff2 +0 -0
  163. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/doctools.js +0 -0
  164. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/file.png +0 -0
  165. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/jquery.js +0 -0
  166. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/js/badge_only.js +0 -0
  167. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/js/theme.js +0 -0
  168. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/language_data.js +0 -0
  169. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/minus.png +0 -0
  170. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/plus.png +0 -0
  171. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/pygments.css +0 -0
  172. {spacr-0.3.80 → spacr-0.4.12}/docs/source/_build/html/_static/sphinx_highlight.js +0 -0
  173. {spacr-0.3.80 → spacr-0.4.12}/docs/source/make.bat +0 -0
  174. {spacr-0.3.80 → spacr-0.4.12}/environment.yaml +0 -0
  175. {spacr-0.3.80 → spacr-0.4.12}/fonts/OpenSans-Regular.ttf +0 -0
  176. {spacr-0.3.80 → spacr-0.4.12}/path/home/carruthers/datasets/plate1/measurements/measurements.db +0 -0
  177. {spacr-0.3.80 → spacr-0.4.12}/path/home/carruthers/datasets/plate1/settings/measure_crop_settings.csv +0 -0
  178. {spacr-0.3.80 → spacr-0.4.12}/path/settings/preprocess_generate_masks_settings.csv +0 -0
  179. {spacr-0.3.80 → spacr-0.4.12}/requirements.txt +0 -0
  180. {spacr-0.3.80 → spacr-0.4.12}/settings/measure_crop_settings.csv +0 -0
  181. {spacr-0.3.80 → spacr-0.4.12}/setup.cfg +0 -0
  182. {spacr-0.3.80 → spacr-0.4.12}/spacr/__main__.py +0 -0
  183. {spacr-0.3.80 → spacr-0.4.12}/spacr/app_annotate.py +0 -0
  184. {spacr-0.3.80 → spacr-0.4.12}/spacr/app_classify.py +0 -0
  185. {spacr-0.3.80 → spacr-0.4.12}/spacr/app_make_masks.py +0 -0
  186. {spacr-0.3.80 → spacr-0.4.12}/spacr/app_mask.py +0 -0
  187. {spacr-0.3.80 → spacr-0.4.12}/spacr/app_measure.py +0 -0
  188. {spacr-0.3.80 → spacr-0.4.12}/spacr/app_sequencing.py +0 -0
  189. {spacr-0.3.80 → spacr-0.4.12}/spacr/app_umap.py +0 -0
  190. {spacr-0.3.80 → spacr-0.4.12}/spacr/cellpose.py +0 -0
  191. {spacr-0.3.80 → spacr-0.4.12}/spacr/chat_bot.py +0 -0
  192. {spacr-0.3.80 → spacr-0.4.12}/spacr/gui.py +0 -0
  193. {spacr-0.3.80 → spacr-0.4.12}/spacr/logger.py +0 -0
  194. {spacr-0.3.80 → spacr-0.4.12}/spacr/mediar.py +0 -0
  195. {spacr-0.3.80 → spacr-0.4.12}/spacr/openai.py +0 -0
  196. {spacr-0.3.80 → spacr-0.4.12}/spacr/resources/MEDIAR/.gitignore +0 -0
  197. {spacr-0.3.80 → spacr-0.4.12}/spacr/resources/MEDIAR/LICENSE +0 -0
  198. {spacr-0.3.80 → spacr-0.4.12}/spacr/resources/MEDIAR/README.md +0 -0
  199. {spacr-0.3.80 → spacr-0.4.12}/spacr/resources/MEDIAR/SetupDict.py +0 -0
  200. {spacr-0.3.80 → spacr-0.4.12}/spacr/resources/MEDIAR/config/baseline.json +0 -0
  201. {spacr-0.3.80 → spacr-0.4.12}/spacr/resources/MEDIAR/config/mediar_example.json +0 -0
  202. {spacr-0.3.80 → spacr-0.4.12}/spacr/resources/MEDIAR/config/pred/pred_mediar.json +0 -0
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  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
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  Author: Einar Birnir Olafsson
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  .. spacr documentation master file, created by
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  =================================
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