spacr 0.4.15__tar.gz → 0.5.0__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 (468) hide show
  1. {spacr-0.4.15 → spacr-0.5.0}/MANIFEST.in +10 -0
  2. {spacr-0.4.15/spacr.egg-info → spacr-0.5.0}/PKG-INFO +5 -2
  3. {spacr-0.4.15 → spacr-0.5.0}/README.rst +1 -1
  4. spacr-0.5.0/docs/.doctrees/environment.pickle +0 -0
  5. spacr-0.5.0/docs/_modules/SetupDict.html +256 -0
  6. spacr-0.5.0/docs/_modules/core/BasePredictor.html +355 -0
  7. spacr-0.5.0/docs/_modules/core/BaseTrainer.html +505 -0
  8. spacr-0.5.0/docs/_modules/core/Baseline/Predictor.html +270 -0
  9. spacr-0.5.0/docs/_modules/core/Baseline/Trainer.html +327 -0
  10. spacr-0.5.0/docs/_modules/core/Baseline/utils.html +294 -0
  11. spacr-0.5.0/docs/_modules/core/MEDIAR/EnsemblePredictor.html +319 -0
  12. spacr-0.5.0/docs/_modules/core/MEDIAR/Predictor.html +451 -0
  13. spacr-0.5.0/docs/_modules/core/MEDIAR/Trainer.html +392 -0
  14. spacr-0.5.0/docs/_modules/core/MEDIAR/utils.html +673 -0
  15. spacr-0.5.0/docs/_modules/core/utils.html +254 -0
  16. spacr-0.5.0/docs/_modules/evaluate.html +282 -0
  17. spacr-0.5.0/docs/_modules/generate_mapping.html +344 -0
  18. spacr-0.5.0/docs/_modules/index.html +261 -0
  19. spacr-0.5.0/docs/_modules/main.html +345 -0
  20. spacr-0.5.0/docs/_modules/predict.html +290 -0
  21. spacr-0.5.0/docs/_modules/spacr/app_annotate.html +277 -0
  22. spacr-0.5.0/docs/_modules/spacr/app_classify.html +219 -0
  23. spacr-0.5.0/docs/_modules/spacr/app_make_masks.html +258 -0
  24. spacr-0.5.0/docs/_modules/spacr/app_mask.html +219 -0
  25. spacr-0.5.0/docs/_modules/spacr/app_measure.html +219 -0
  26. spacr-0.5.0/docs/_modules/spacr/app_sequencing.html +219 -0
  27. spacr-0.5.0/docs/_modules/spacr/app_umap.html +219 -0
  28. spacr-0.5.0/docs/_modules/spacr/chat_bot.html +245 -0
  29. spacr-0.5.0/docs/_modules/spacr/core.html +1242 -0
  30. spacr-0.5.0/docs/_modules/spacr/deep_spacr.html +1483 -0
  31. spacr-0.5.0/docs/_modules/spacr/gui.html +418 -0
  32. spacr-0.5.0/docs/_modules/spacr/gui_core.html +1639 -0
  33. spacr-0.5.0/docs/_modules/spacr/gui_elements.html +4548 -0
  34. spacr-0.5.0/docs/_modules/spacr/gui_utils.html +1265 -0
  35. spacr-0.5.0/docs/_modules/spacr/io.html +3980 -0
  36. spacr-0.5.0/docs/_modules/spacr/logger.html +256 -0
  37. spacr-0.5.0/docs/_modules/spacr/measure.html +1371 -0
  38. spacr-0.5.0/docs/_modules/spacr/mediar.html +623 -0
  39. spacr-0.5.0/docs/_modules/spacr/ml.html +2323 -0
  40. spacr-0.5.0/docs/_modules/spacr/plot.html +4379 -0
  41. spacr-0.5.0/docs/_modules/spacr/sequencing.html +896 -0
  42. spacr-0.5.0/docs/_modules/spacr/settings.html +1897 -0
  43. spacr-0.5.0/docs/_modules/spacr/sim.html +2041 -0
  44. spacr-0.5.0/docs/_modules/spacr/sp_stats.html +447 -0
  45. spacr-0.5.0/docs/_modules/spacr/spacr_cellpose.html +527 -0
  46. spacr-0.5.0/docs/_modules/spacr/submodules.html +2086 -0
  47. spacr-0.5.0/docs/_modules/spacr/timelapse.html +1096 -0
  48. spacr-0.5.0/docs/_modules/spacr/toxo.html +878 -0
  49. spacr-0.5.0/docs/_modules/spacr/utils.html +6305 -0
  50. spacr-0.5.0/docs/_modules/spacr/version.html +233 -0
  51. spacr-0.5.0/docs/_modules/train_tools/data_utils/custom/CellAware.html +308 -0
  52. spacr-0.5.0/docs/_modules/train_tools/data_utils/custom/LoadImage.html +387 -0
  53. spacr-0.5.0/docs/_modules/train_tools/data_utils/custom/NormalizeImage.html +297 -0
  54. spacr-0.5.0/docs/_modules/train_tools/data_utils/datasetter.html +425 -0
  55. spacr-0.5.0/docs/_modules/train_tools/data_utils/transforms.html +371 -0
  56. spacr-0.5.0/docs/_modules/train_tools/data_utils/utils.html +298 -0
  57. spacr-0.5.0/docs/_modules/train_tools/measures.html +414 -0
  58. spacr-0.5.0/docs/_modules/train_tools/models/MEDIARFormer.html +325 -0
  59. spacr-0.5.0/docs/_modules/train_tools/utils.html +299 -0
  60. spacr-0.5.0/docs/_sources/api/SetupDict/index.rst.txt +17 -0
  61. spacr-0.5.0/docs/_sources/api/core/BasePredictor/index.rst.txt +41 -0
  62. spacr-0.5.0/docs/_sources/api/core/BaseTrainer/index.rst.txt +93 -0
  63. spacr-0.5.0/docs/_sources/api/core/Baseline/Predictor/index.rst.txt +16 -0
  64. spacr-0.5.0/docs/_sources/api/core/Baseline/Trainer/index.rst.txt +22 -0
  65. spacr-0.5.0/docs/_sources/api/core/Baseline/index.rst.txt +17 -0
  66. spacr-0.5.0/docs/_sources/api/core/Baseline/utils/index.rst.txt +31 -0
  67. spacr-0.5.0/docs/_sources/api/core/MEDIAR/EnsemblePredictor/index.rst.txt +19 -0
  68. spacr-0.5.0/docs/_sources/api/core/MEDIAR/Predictor/index.rst.txt +22 -0
  69. spacr-0.5.0/docs/_sources/api/core/MEDIAR/Trainer/index.rst.txt +31 -0
  70. spacr-0.5.0/docs/_sources/api/core/MEDIAR/index.rst.txt +18 -0
  71. spacr-0.5.0/docs/_sources/api/core/MEDIAR/utils/index.rst.txt +83 -0
  72. spacr-0.5.0/docs/_sources/api/core/index.rst.txt +19 -0
  73. spacr-0.5.0/docs/_sources/api/core/utils/index.rst.txt +26 -0
  74. spacr-0.5.0/docs/_sources/api/evaluate/index.rst.txt +13 -0
  75. spacr-0.5.0/docs/_sources/api/generate_mapping/index.rst.txt +35 -0
  76. spacr-0.5.0/docs/_sources/api/index.rst.txt +18 -0
  77. spacr-0.5.0/docs/_sources/api/main/index.rst.txt +26 -0
  78. spacr-0.5.0/docs/_sources/api/predict/index.rst.txt +26 -0
  79. spacr-0.5.0/docs/_sources/api/spacr/app_annotate/index.rst.txt +17 -0
  80. spacr-0.5.0/docs/_sources/api/spacr/app_classify/index.rst.txt +13 -0
  81. spacr-0.5.0/docs/_sources/api/spacr/app_make_masks/index.rst.txt +15 -0
  82. spacr-0.5.0/docs/_sources/api/spacr/app_mask/index.rst.txt +13 -0
  83. spacr-0.5.0/docs/_sources/api/spacr/app_measure/index.rst.txt +13 -0
  84. spacr-0.5.0/docs/_sources/api/spacr/app_sequencing/index.rst.txt +13 -0
  85. spacr-0.5.0/docs/_sources/api/spacr/app_umap/index.rst.txt +13 -0
  86. spacr-0.5.0/docs/_sources/api/spacr/chat_bot/index.rst.txt +18 -0
  87. spacr-0.5.0/docs/_sources/api/spacr/core/index.rst.txt +109 -0
  88. spacr-0.5.0/docs/_sources/api/spacr/deep_spacr/index.rst.txt +141 -0
  89. spacr-0.5.0/docs/_sources/api/spacr/gui/index.rst.txt +63 -0
  90. spacr-0.5.0/docs/_sources/api/spacr/gui_core/index.rst.txt +134 -0
  91. spacr-0.5.0/docs/_sources/api/spacr/gui_elements/index.rst.txt +1389 -0
  92. spacr-0.5.0/docs/_sources/api/spacr/gui_utils/index.rst.txt +196 -0
  93. spacr-0.5.0/docs/_sources/api/spacr/index.rst.txt +45 -0
  94. spacr-0.5.0/docs/_sources/api/spacr/io/index.rst.txt +534 -0
  95. spacr-0.5.0/docs/_sources/api/spacr/logger/index.rst.txt +19 -0
  96. spacr-0.5.0/docs/_sources/api/spacr/measure/index.rst.txt +86 -0
  97. spacr-0.5.0/docs/_sources/api/spacr/mediar/index.rst.txt +100 -0
  98. spacr-0.5.0/docs/_sources/api/spacr/ml/index.rst.txt +176 -0
  99. spacr-0.5.0/docs/_sources/api/spacr/openai/index.rst.txt +6 -0
  100. spacr-0.5.0/docs/_sources/api/spacr/plot/index.rst.txt +461 -0
  101. spacr-0.5.0/docs/_sources/api/spacr/sequencing/index.rst.txt +41 -0
  102. spacr-0.5.0/docs/_sources/api/spacr/settings/index.rst.txt +89 -0
  103. spacr-0.5.0/docs/_sources/api/spacr/sim/index.rst.txt +673 -0
  104. spacr-0.5.0/docs/_sources/api/spacr/sp_stats/index.rst.txt +56 -0
  105. spacr-0.5.0/docs/_sources/api/spacr/spacr_cellpose/index.rst.txt +23 -0
  106. spacr-0.5.0/docs/_sources/api/spacr/submodules/index.rst.txt +90 -0
  107. spacr-0.5.0/docs/_sources/api/spacr/timelapse/index.rst.txt +29 -0
  108. spacr-0.5.0/docs/_sources/api/spacr/toxo/index.rst.txt +57 -0
  109. spacr-0.5.0/docs/_sources/api/spacr/utils/index.rst.txt +1395 -0
  110. spacr-0.5.0/docs/_sources/api/spacr/version/index.rst.txt +46 -0
  111. spacr-0.5.0/docs/_sources/api/train_tools/data_utils/custom/CellAware/index.rst.txt +35 -0
  112. spacr-0.5.0/docs/_sources/api/train_tools/data_utils/custom/LoadImage/index.rst.txt +53 -0
  113. spacr-0.5.0/docs/_sources/api/train_tools/data_utils/custom/NormalizeImage/index.rst.txt +35 -0
  114. spacr-0.5.0/docs/_sources/api/train_tools/data_utils/custom/index.rst.txt +17 -0
  115. spacr-0.5.0/docs/_sources/api/train_tools/data_utils/datasetter/index.rst.txt +56 -0
  116. spacr-0.5.0/docs/_sources/api/train_tools/data_utils/index.rst.txt +18 -0
  117. spacr-0.5.0/docs/_sources/api/train_tools/data_utils/transforms/index.rst.txt +21 -0
  118. spacr-0.5.0/docs/_sources/api/train_tools/data_utils/utils/index.rst.txt +31 -0
  119. spacr-0.5.0/docs/_sources/api/train_tools/index.rst.txt +18 -0
  120. spacr-0.5.0/docs/_sources/api/train_tools/measures/index.rst.txt +29 -0
  121. spacr-0.5.0/docs/_sources/api/train_tools/models/MEDIARFormer/index.rst.txt +36 -0
  122. spacr-0.5.0/docs/_sources/api/train_tools/models/index.rst.txt +15 -0
  123. spacr-0.5.0/docs/_sources/api/train_tools/utils/index.rst.txt +47 -0
  124. spacr-0.5.0/docs/_sources/index.rst.txt +13 -0
  125. {spacr-0.4.15/docs/source/_build/html → spacr-0.5.0/docs}/_static/documentation_options.js +1 -1
  126. spacr-0.5.0/docs/_static/graphviz.css +19 -0
  127. spacr-0.5.0/docs/_static/logo_spacr.png +0 -0
  128. spacr-0.5.0/docs/api/SetupDict/index.html +235 -0
  129. spacr-0.5.0/docs/api/core/BasePredictor/index.html +266 -0
  130. spacr-0.5.0/docs/api/core/BaseTrainer/index.html +318 -0
  131. spacr-0.5.0/docs/api/core/Baseline/Predictor/index.html +228 -0
  132. spacr-0.5.0/docs/api/core/Baseline/Trainer/index.html +234 -0
  133. spacr-0.5.0/docs/api/core/Baseline/index.html +228 -0
  134. spacr-0.5.0/docs/api/core/Baseline/utils/index.html +242 -0
  135. spacr-0.5.0/docs/api/core/MEDIAR/EnsemblePredictor/index.html +233 -0
  136. spacr-0.5.0/docs/api/core/MEDIAR/Predictor/index.html +238 -0
  137. spacr-0.5.0/docs/api/core/MEDIAR/Trainer/index.html +245 -0
  138. spacr-0.5.0/docs/api/core/MEDIAR/index.html +229 -0
  139. spacr-0.5.0/docs/api/core/MEDIAR/utils/index.html +313 -0
  140. spacr-0.5.0/docs/api/core/index.html +229 -0
  141. spacr-0.5.0/docs/api/core/utils/index.html +241 -0
  142. spacr-0.5.0/docs/api/evaluate/index.html +225 -0
  143. spacr-0.5.0/docs/api/generate_mapping/index.html +247 -0
  144. spacr-0.5.0/docs/api/index.html +306 -0
  145. spacr-0.5.0/docs/api/main/index.html +241 -0
  146. spacr-0.5.0/docs/api/predict/index.html +241 -0
  147. spacr-0.5.0/docs/api/spacr/app_annotate/index.html +236 -0
  148. spacr-0.5.0/docs/api/spacr/app_classify/index.html +226 -0
  149. spacr-0.5.0/docs/api/spacr/app_make_masks/index.html +231 -0
  150. spacr-0.5.0/docs/api/spacr/app_mask/index.html +226 -0
  151. spacr-0.5.0/docs/api/spacr/app_measure/index.html +226 -0
  152. spacr-0.5.0/docs/api/spacr/app_sequencing/index.html +226 -0
  153. spacr-0.5.0/docs/api/spacr/app_umap/index.html +226 -0
  154. spacr-0.5.0/docs/api/spacr/chat_bot/index.html +232 -0
  155. spacr-0.5.0/docs/api/spacr/core/index.html +330 -0
  156. spacr-0.5.0/docs/api/spacr/deep_spacr/index.html +389 -0
  157. spacr-0.5.0/docs/api/spacr/gui/index.html +299 -0
  158. spacr-0.5.0/docs/api/spacr/gui_core/index.html +425 -0
  159. spacr-0.5.0/docs/api/spacr/gui_elements/index.html +1997 -0
  160. spacr-0.5.0/docs/api/spacr/gui_utils/index.html +481 -0
  161. spacr-0.5.0/docs/api/spacr/index.html +255 -0
  162. spacr-0.5.0/docs/api/spacr/io/index.html +871 -0
  163. spacr-0.5.0/docs/api/spacr/logger/index.html +236 -0
  164. spacr-0.5.0/docs/api/spacr/measure/index.html +331 -0
  165. spacr-0.5.0/docs/api/spacr/mediar/index.html +345 -0
  166. spacr-0.5.0/docs/api/spacr/ml/index.html +431 -0
  167. spacr-0.5.0/docs/api/spacr/openai/index.html +218 -0
  168. spacr-0.5.0/docs/api/spacr/plot/index.html +740 -0
  169. spacr-0.5.0/docs/api/spacr/sequencing/index.html +296 -0
  170. spacr-0.5.0/docs/api/spacr/settings/index.html +401 -0
  171. spacr-0.5.0/docs/api/spacr/sim/index.html +928 -0
  172. spacr-0.5.0/docs/api/spacr/sp_stats/index.html +268 -0
  173. spacr-0.5.0/docs/api/spacr/spacr_cellpose/index.html +251 -0
  174. spacr-0.5.0/docs/api/spacr/submodules/index.html +343 -0
  175. spacr-0.5.0/docs/api/spacr/timelapse/index.html +266 -0
  176. spacr-0.5.0/docs/api/spacr/toxo/index.html +277 -0
  177. spacr-0.5.0/docs/api/spacr/utils/index.html +2114 -0
  178. spacr-0.5.0/docs/api/spacr/version/index.html +246 -0
  179. spacr-0.5.0/docs/api/train_tools/data_utils/custom/CellAware/index.html +247 -0
  180. spacr-0.5.0/docs/api/train_tools/data_utils/custom/LoadImage/index.html +269 -0
  181. spacr-0.5.0/docs/api/train_tools/data_utils/custom/NormalizeImage/index.html +247 -0
  182. spacr-0.5.0/docs/api/train_tools/data_utils/custom/index.html +229 -0
  183. spacr-0.5.0/docs/api/train_tools/data_utils/datasetter/index.html +275 -0
  184. spacr-0.5.0/docs/api/train_tools/data_utils/index.html +229 -0
  185. spacr-0.5.0/docs/api/train_tools/data_utils/transforms/index.html +247 -0
  186. spacr-0.5.0/docs/api/train_tools/data_utils/utils/index.html +249 -0
  187. spacr-0.5.0/docs/api/train_tools/index.html +228 -0
  188. spacr-0.5.0/docs/api/train_tools/measures/index.html +237 -0
  189. spacr-0.5.0/docs/api/train_tools/models/MEDIARFormer/index.html +250 -0
  190. spacr-0.5.0/docs/api/train_tools/models/index.html +226 -0
  191. spacr-0.5.0/docs/api/train_tools/utils/index.html +263 -0
  192. spacr-0.5.0/docs/genindex.html +3384 -0
  193. spacr-0.5.0/docs/index.html +221 -0
  194. spacr-0.5.0/docs/objects.inv +0 -0
  195. spacr-0.5.0/docs/py-modindex.html +563 -0
  196. spacr-0.5.0/docs/search.html +227 -0
  197. spacr-0.5.0/docs/searchindex.js +1 -0
  198. spacr-0.5.0/docs/source/_static/custom.css +14 -0
  199. spacr-0.5.0/docs/source/_static/logo_spacr.png +0 -0
  200. spacr-0.5.0/docs/source/conf.py +54 -0
  201. spacr-0.5.0/docs/source/index.rst +13 -0
  202. spacr-0.5.0/rtd_trigger.txt +0 -0
  203. {spacr-0.4.15 → spacr-0.5.0}/setup.py +6 -1
  204. spacr-0.5.0/setup_docs.sh +132 -0
  205. {spacr-0.4.15 → spacr-0.5.0}/spacr/__init__.py +2 -2
  206. {spacr-0.4.15 → spacr-0.5.0}/spacr/core.py +52 -10
  207. {spacr-0.4.15 → spacr-0.5.0}/spacr/deep_spacr.py +2 -3
  208. {spacr-0.4.15 → spacr-0.5.0}/spacr/gui.py +0 -1
  209. {spacr-0.4.15 → spacr-0.5.0}/spacr/gui_core.py +247 -41
  210. {spacr-0.4.15 → spacr-0.5.0}/spacr/gui_elements.py +133 -2
  211. {spacr-0.4.15 → spacr-0.5.0}/spacr/gui_utils.py +22 -17
  212. {spacr-0.4.15 → spacr-0.5.0}/spacr/io.py +624 -149
  213. {spacr-0.4.15 → spacr-0.5.0}/spacr/ml.py +141 -258
  214. {spacr-0.4.15 → spacr-0.5.0}/spacr/plot.py +76 -34
  215. spacr-0.5.0/spacr/resources/icons/logo_spacr.png +0 -0
  216. {spacr-0.4.15 → spacr-0.5.0}/spacr/sequencing.py +73 -38
  217. {spacr-0.4.15 → spacr-0.5.0}/spacr/settings.py +161 -135
  218. {spacr-0.4.15 → spacr-0.5.0}/spacr/submodules.py +618 -215
  219. {spacr-0.4.15 → spacr-0.5.0}/spacr/timelapse.py +197 -29
  220. {spacr-0.4.15 → spacr-0.5.0}/spacr/toxo.py +23 -23
  221. {spacr-0.4.15 → spacr-0.5.0}/spacr/utils.py +186 -128
  222. {spacr-0.4.15 → spacr-0.5.0/spacr.egg-info}/PKG-INFO +5 -2
  223. spacr-0.5.0/spacr.egg-info/SOURCES.txt +424 -0
  224. {spacr-0.4.15 → spacr-0.5.0}/spacr.egg-info/requires.txt +3 -0
  225. spacr-0.4.15/.readthedocs.yaml +0 -15
  226. spacr-0.4.15/docs/requirements.txt +0 -3
  227. spacr-0.4.15/docs/source/Makefile +0 -20
  228. spacr-0.4.15/docs/source/_build/doctrees/environment.pickle +0 -0
  229. spacr-0.4.15/docs/source/_build/html/_sources/index.rst.txt +0 -18
  230. spacr-0.4.15/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js +0 -123
  231. spacr-0.4.15/docs/source/_build/html/_static/jquery.js +0 -2
  232. spacr-0.4.15/docs/source/_build/html/genindex.html +0 -103
  233. spacr-0.4.15/docs/source/_build/html/index.html +0 -116
  234. spacr-0.4.15/docs/source/_build/html/objects.inv +0 -0
  235. spacr-0.4.15/docs/source/_build/html/search.html +0 -118
  236. spacr-0.4.15/docs/source/_build/html/searchindex.js +0 -1
  237. spacr-0.4.15/docs/source/conf.py +0 -58
  238. spacr-0.4.15/docs/source/index.rst +0 -18
  239. spacr-0.4.15/docs/source/make.bat +0 -35
  240. spacr-0.4.15/path/home/carruthers/datasets/plate1/measurements/measurements.db +0 -0
  241. spacr-0.4.15/path/home/carruthers/datasets/plate1/settings/measure_crop_settings.csv +0 -61
  242. spacr-0.4.15/path/settings/preprocess_generate_masks_settings.csv +0 -67
  243. spacr-0.4.15/settings/measure_crop_settings.csv +0 -48
  244. spacr-0.4.15/setup_docs.sh +0 -110
  245. spacr-0.4.15/source/conf.py +0 -39
  246. spacr-0.4.15/source/index.rst +0 -20
  247. spacr-0.4.15/source/modules.rst +0 -9
  248. spacr-0.4.15/source/setup.rst +0 -33
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{spacr-0.4.15 → spacr-0.5.0}/MANIFEST.in RENAMED
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+ # Exclude model files from distribution
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{spacr-0.4.15/spacr.egg-info → spacr-0.5.0}/PKG-INFO RENAMED
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  Metadata-Version: 2.1
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  Name: spacr
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- Version: 0.4.15
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  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
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  Home-page: https://github.com/EinarOlafsson/spacr
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  Author: Einar Birnir Olafsson
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{spacr-0.4.15 → spacr-0.5.0}/README.rst RENAMED
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+ <li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.public_paths_labeled"><code class="docutils literal notranslate"><span class="pre">public_paths_labeled()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.official_paths_labeled"><code class="docutils literal notranslate"><span class="pre">official_paths_labeled()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.official_paths_tuning"><code class="docutils literal notranslate"><span class="pre">official_paths_tuning()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.add_mapping_to_json"><code class="docutils literal notranslate"><span class="pre">add_mapping_to_json()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.parser"><code class="docutils literal notranslate"><span class="pre">parser</span></code></a></li>
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+ <li class="breadcrumb-item active">SetupDict</li>
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+
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+ <h1>Source code for SetupDict</h1><div class="highlight"><pre>
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+ <span></span><span class="kn">import</span> <span class="nn">torch.optim</span> <span class="k">as</span> <span class="nn">optim</span>
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+ <span class="kn">import</span> <span class="nn">torch.optim.lr_scheduler</span> <span class="k">as</span> <span class="nn">lr_scheduler</span>
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+ <span class="kn">import</span> <span class="nn">monai</span>
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+
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+ <span class="kn">import</span> <span class="nn">core</span>
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+ <span class="kn">from</span> <span class="nn">train_tools</span> <span class="kn">import</span> <span class="n">models</span>
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+ <span class="kn">from</span> <span class="nn">train_tools.models</span> <span class="kn">import</span> <span class="o">*</span>
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+
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+ <span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;TRAINER&quot;</span><span class="p">,</span> <span class="s2">&quot;OPTIMIZER&quot;</span><span class="p">,</span> <span class="s2">&quot;SCHEDULER&quot;</span><span class="p">]</span>
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+
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+ <div class="viewcode-block" id="TRAINER">
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+ <a class="viewcode-back" href="../api/SetupDict/index.html#SetupDict.TRAINER">[docs]</a>
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+ <span class="n">TRAINER</span> <span class="o">=</span> <span class="p">{</span>
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+ <span class="s2">&quot;baseline&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">Baseline</span><span class="o">.</span><span class="n">Trainer</span><span class="p">,</span>
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+ <span class="s2">&quot;mediar&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">MEDIAR</span><span class="o">.</span><span class="n">Trainer</span><span class="p">,</span>
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+ <span class="p">}</span></div>
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+
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+
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+ <span class="n">PREDICTOR</span> <span class="o">=</span> <span class="p">{</span>
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+ <span class="s2">&quot;baseline&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">Baseline</span><span class="o">.</span><span class="n">Predictor</span><span class="p">,</span>
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+ <span class="s2">&quot;mediar&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">MEDIAR</span><span class="o">.</span><span class="n">Predictor</span><span class="p">,</span>
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+ <span class="s2">&quot;ensemble_mediar&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">MEDIAR</span><span class="o">.</span><span class="n">EnsemblePredictor</span><span class="p">,</span>
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+ <span class="p">}</span>
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+
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+ <span class="n">MODELS</span> <span class="o">=</span> <span class="p">{</span>
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+ <span class="s2">&quot;unet&quot;</span><span class="p">:</span> <span class="n">monai</span><span class="o">.</span><span class="n">networks</span><span class="o">.</span><span class="n">nets</span><span class="o">.</span><span class="n">UNet</span><span class="p">,</span>
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+ <span class="s2">&quot;unetr&quot;</span><span class="p">:</span> <span class="n">monai</span><span class="o">.</span><span class="n">networks</span><span class="o">.</span><span class="n">nets</span><span class="o">.</span><span class="n">unetr</span><span class="o">.</span><span class="n">UNETR</span><span class="p">,</span>
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+ <span class="s2">&quot;swinunetr&quot;</span><span class="p">:</span> <span class="n">monai</span><span class="o">.</span><span class="n">networks</span><span class="o">.</span><span class="n">nets</span><span class="o">.</span><span class="n">SwinUNETR</span><span class="p">,</span>
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+ <span class="s2">&quot;mediar-former&quot;</span><span class="p">:</span> <span class="n">models</span><span class="o">.</span><span class="n">MEDIARFormer</span><span class="p">,</span>
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+ <span class="p">}</span>
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+
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+ <div class="viewcode-block" id="OPTIMIZER">
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+ <a class="viewcode-back" href="../api/SetupDict/index.html#SetupDict.OPTIMIZER">[docs]</a>
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+ <span class="n">OPTIMIZER</span> <span class="o">=</span> <span class="p">{</span>
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+ <span class="s2">&quot;sgd&quot;</span><span class="p">:</span> <span class="n">optim</span><span class="o">.</span><span class="n">SGD</span><span class="p">,</span>
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+ <span class="s2">&quot;adam&quot;</span><span class="p">:</span> <span class="n">optim</span><span class="o">.</span><span class="n">Adam</span><span class="p">,</span>
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+ <span class="s2">&quot;adamw&quot;</span><span class="p">:</span> <span class="n">optim</span><span class="o">.</span><span class="n">AdamW</span><span class="p">,</span>
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+ <span class="p">}</span></div>
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+
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+
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+ <div class="viewcode-block" id="SCHEDULER">
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+ <a class="viewcode-back" href="../api/SetupDict/index.html#SetupDict.SCHEDULER">[docs]</a>
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+ <span class="n">SCHEDULER</span> <span class="o">=</span> <span class="p">{</span>
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+ <span class="s2">&quot;step&quot;</span><span class="p">:</span> <span class="n">lr_scheduler</span><span class="o">.</span><span class="n">StepLR</span><span class="p">,</span>
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+ <span class="s2">&quot;multistep&quot;</span><span class="p">:</span> <span class="n">lr_scheduler</span><span class="o">.</span><span class="n">MultiStepLR</span><span class="p">,</span>
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+ <span class="s2">&quot;cosine&quot;</span><span class="p">:</span> <span class="n">lr_scheduler</span><span class="o">.</span><span class="n">CosineAnnealingLR</span><span class="p">,</span>
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+ <span class="p">}</span></div>
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+
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+ </pre></div>
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+
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