simba-uw-tf-dev 2.5.5__py3-none-any.whl

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Files changed (969) hide show
  1. simba/.DS_Store +0 -0
  2. simba/SimBA.py +1090 -0
  3. simba/SimBA_logo.ico +0 -0
  4. simba/__init__.py +0 -0
  5. simba/assets/.DS_Store +0 -0
  6. simba/assets/TheGoldenLab.PNG +0 -0
  7. simba/assets/UbuntuMono-Regular.ttf +0 -0
  8. simba/assets/__init__.py +0 -0
  9. simba/assets/dash_simba_base.css +460 -0
  10. simba/assets/fonts/.DS_Store +0 -0
  11. simba/assets/fonts/Playwrite ES Deco.ttf +0 -0
  12. simba/assets/fonts/Poppins Bold.ttf +0 -0
  13. simba/assets/fonts/Poppins Regular.ttf +0 -0
  14. simba/assets/icons/.DS_Store +0 -0
  15. simba/assets/icons/SimBA_logo.icns +0 -0
  16. simba/assets/icons/SimBA_logo.ico +0 -0
  17. simba/assets/icons/SimBA_logo.png +0 -0
  18. simba/assets/icons/SimBA_logo_3.ico +0 -0
  19. simba/assets/icons/SimBA_logo_3.png +0 -0
  20. simba/assets/icons/__init__.py +0 -0
  21. simba/assets/icons/about.png +0 -0
  22. simba/assets/icons/add.png +0 -0
  23. simba/assets/icons/add_on.png +0 -0
  24. simba/assets/icons/analyze_blue.png +0 -0
  25. simba/assets/icons/analyze_green.png +0 -0
  26. simba/assets/icons/api.png +0 -0
  27. simba/assets/icons/archive.png +0 -0
  28. simba/assets/icons/arrow_down_green.png +0 -0
  29. simba/assets/icons/average.png +0 -0
  30. simba/assets/icons/avi.png +0 -0
  31. simba/assets/icons/bar_graph_blue.png +0 -0
  32. simba/assets/icons/bar_graph_green.png +0 -0
  33. simba/assets/icons/blur.png +0 -0
  34. simba/assets/icons/bmp.png +0 -0
  35. simba/assets/icons/boris.png +0 -0
  36. simba/assets/icons/brightness.png +0 -0
  37. simba/assets/icons/browse.png +0 -0
  38. simba/assets/icons/bw.png +0 -0
  39. simba/assets/icons/calipher.png +0 -0
  40. simba/assets/icons/change.png +0 -0
  41. simba/assets/icons/check_blue.png +0 -0
  42. simba/assets/icons/circle.png +0 -0
  43. simba/assets/icons/circle_2.png +0 -0
  44. simba/assets/icons/clahe.png +0 -0
  45. simba/assets/icons/clean.png +0 -0
  46. simba/assets/icons/clean_red.png +0 -0
  47. simba/assets/icons/clf.png +0 -0
  48. simba/assets/icons/clf_2.png +0 -0
  49. simba/assets/icons/clip.png +0 -0
  50. simba/assets/icons/close.png +0 -0
  51. simba/assets/icons/cluster.png +0 -0
  52. simba/assets/icons/concat.png +0 -0
  53. simba/assets/icons/concat_icons/__init__.py +0 -0
  54. simba/assets/icons/concat_icons/horizontal.png +0 -0
  55. simba/assets/icons/concat_icons/mixed_mosaic.png +0 -0
  56. simba/assets/icons/concat_icons/mosaic.png +0 -0
  57. simba/assets/icons/concat_icons/vertical.png +0 -0
  58. simba/assets/icons/concat_videos.png +0 -0
  59. simba/assets/icons/convert.png +0 -0
  60. simba/assets/icons/counter.png +0 -0
  61. simba/assets/icons/create.png +0 -0
  62. simba/assets/icons/crop.png +0 -0
  63. simba/assets/icons/crossfade.png +0 -0
  64. simba/assets/icons/csv_grey.png +0 -0
  65. simba/assets/icons/curve_black.png +0 -0
  66. simba/assets/icons/dash_simba.css +454 -0
  67. simba/assets/icons/decision_tree_blue.png +0 -0
  68. simba/assets/icons/decision_tree_purple.png +0 -0
  69. simba/assets/icons/details.png +0 -0
  70. simba/assets/icons/dice_green.png +0 -0
  71. simba/assets/icons/dimensionality_reduction.png +0 -0
  72. simba/assets/icons/direction.png +0 -0
  73. simba/assets/icons/direction_2.png +0 -0
  74. simba/assets/icons/distance_red.png +0 -0
  75. simba/assets/icons/documentation.png +0 -0
  76. simba/assets/icons/dumbbell.png +0 -0
  77. simba/assets/icons/duplicate.png +0 -0
  78. simba/assets/icons/edit.png +0 -0
  79. simba/assets/icons/ethovision.png +0 -0
  80. simba/assets/icons/exit.png +0 -0
  81. simba/assets/icons/factory.png +0 -0
  82. simba/assets/icons/fast_forward.png +0 -0
  83. simba/assets/icons/feather_green.png +0 -0
  84. simba/assets/icons/features.png +0 -0
  85. simba/assets/icons/ffmpeg.png +0 -0
  86. simba/assets/icons/finish.png +0 -0
  87. simba/assets/icons/flip_black.png +0 -0
  88. simba/assets/icons/flip_green.png +0 -0
  89. simba/assets/icons/flip_red.png +0 -0
  90. simba/assets/icons/fps.png +0 -0
  91. simba/assets/icons/frames.png +0 -0
  92. simba/assets/icons/gif.png +0 -0
  93. simba/assets/icons/github.png +0 -0
  94. simba/assets/icons/gitter.png +0 -0
  95. simba/assets/icons/gpu.png +0 -0
  96. simba/assets/icons/gpu_2.png +0 -0
  97. simba/assets/icons/green_check.png +0 -0
  98. simba/assets/icons/grey.png +0 -0
  99. simba/assets/icons/greyscale.png +0 -0
  100. simba/assets/icons/half_circle.png +0 -0
  101. simba/assets/icons/heatmap.png +0 -0
  102. simba/assets/icons/hexagon.png +0 -0
  103. simba/assets/icons/hierarchy.png +0 -0
  104. simba/assets/icons/home.png +0 -0
  105. simba/assets/icons/id_card.png +0 -0
  106. simba/assets/icons/image.png +0 -0
  107. simba/assets/icons/import.png +0 -0
  108. simba/assets/icons/info.png +0 -0
  109. simba/assets/icons/interactive_blue.png +0 -0
  110. simba/assets/icons/join_purple.png +0 -0
  111. simba/assets/icons/join_red.png +0 -0
  112. simba/assets/icons/join_yellow.png +0 -0
  113. simba/assets/icons/jpeg.png +0 -0
  114. simba/assets/icons/label.png +0 -0
  115. simba/assets/icons/label_blue.png +0 -0
  116. simba/assets/icons/label_yellow.png +0 -0
  117. simba/assets/icons/line_chart_blue.png +0 -0
  118. simba/assets/icons/link.png +0 -0
  119. simba/assets/icons/load.png +0 -0
  120. simba/assets/icons/load_black.png +0 -0
  121. simba/assets/icons/load_blue.png +0 -0
  122. simba/assets/icons/mars.png +0 -0
  123. simba/assets/icons/merge.png +0 -0
  124. simba/assets/icons/metrics.png +0 -0
  125. simba/assets/icons/metrics_blue.png +0 -0
  126. simba/assets/icons/metrics_green.png +0 -0
  127. simba/assets/icons/minus.png +0 -0
  128. simba/assets/icons/mov.png +0 -0
  129. simba/assets/icons/move.png +0 -0
  130. simba/assets/icons/mp4.png +0 -0
  131. simba/assets/icons/multiple_blue.png +0 -0
  132. simba/assets/icons/multiple_green.png +0 -0
  133. simba/assets/icons/multiple_yellow.png +0 -0
  134. simba/assets/icons/number_black.png +0 -0
  135. simba/assets/icons/one.png +0 -0
  136. simba/assets/icons/one_blue.png +0 -0
  137. simba/assets/icons/osf.png +0 -0
  138. simba/assets/icons/outlier.png +0 -0
  139. simba/assets/icons/paint.png +0 -0
  140. simba/assets/icons/parquet.png +0 -0
  141. simba/assets/icons/path.png +0 -0
  142. simba/assets/icons/permutation_blue.png +0 -0
  143. simba/assets/icons/plot.png +0 -0
  144. simba/assets/icons/plus.png +0 -0
  145. simba/assets/icons/png.png +0 -0
  146. simba/assets/icons/polygon.png +0 -0
  147. simba/assets/icons/polygon_2.png +0 -0
  148. simba/assets/icons/pose.png +0 -0
  149. simba/assets/icons/print.png +0 -0
  150. simba/assets/icons/progressbar_black.png +0 -0
  151. simba/assets/icons/readthedocs_logo.png +0 -0
  152. simba/assets/icons/rectangle.png +0 -0
  153. simba/assets/icons/remove_bg.png +0 -0
  154. simba/assets/icons/reorganize.png +0 -0
  155. simba/assets/icons/restart.png +0 -0
  156. simba/assets/icons/reverse.png +0 -0
  157. simba/assets/icons/reverse_blue.png +0 -0
  158. simba/assets/icons/rocket.png +0 -0
  159. simba/assets/icons/roi.png +0 -0
  160. simba/assets/icons/roi_green.png +0 -0
  161. simba/assets/icons/rotate.png +0 -0
  162. simba/assets/icons/sample.png +0 -0
  163. simba/assets/icons/save.png +0 -0
  164. simba/assets/icons/save_blue.png +0 -0
  165. simba/assets/icons/save_green.png +0 -0
  166. simba/assets/icons/search.png +0 -0
  167. simba/assets/icons/segment.png +0 -0
  168. simba/assets/icons/seperate_green.png +0 -0
  169. simba/assets/icons/settings.png +0 -0
  170. simba/assets/icons/shap.png +0 -0
  171. simba/assets/icons/simba_logo_2.png +0 -0
  172. simba/assets/icons/single_black.png +0 -0
  173. simba/assets/icons/single_blue.png +0 -0
  174. simba/assets/icons/single_green.png +0 -0
  175. simba/assets/icons/size_black.png +0 -0
  176. simba/assets/icons/skip.png +0 -0
  177. simba/assets/icons/skip_2.png +0 -0
  178. simba/assets/icons/split.png +0 -0
  179. simba/assets/icons/square_black.png +0 -0
  180. simba/assets/icons/stopwatch.png +0 -0
  181. simba/assets/icons/subset_blue.png +0 -0
  182. simba/assets/icons/superimpose.png +0 -0
  183. simba/assets/icons/system.png +0 -0
  184. simba/assets/icons/t.png +0 -0
  185. simba/assets/icons/table.png +0 -0
  186. simba/assets/icons/text_black.png +0 -0
  187. simba/assets/icons/tick.png +0 -0
  188. simba/assets/icons/tiff.png +0 -0
  189. simba/assets/icons/tile_green.png +0 -0
  190. simba/assets/icons/timer.png +0 -0
  191. simba/assets/icons/trash.png +0 -0
  192. simba/assets/icons/trash_red.png +0 -0
  193. simba/assets/icons/triangle_black.png +0 -0
  194. simba/assets/icons/video.png +0 -0
  195. simba/assets/icons/video_2.png +0 -0
  196. simba/assets/icons/visualize.png +0 -0
  197. simba/assets/icons/visualize_blue.png +0 -0
  198. simba/assets/icons/visualize_green.png +0 -0
  199. simba/assets/icons/wand_blue.png +0 -0
  200. simba/assets/icons/watermark_green.png +0 -0
  201. simba/assets/icons/webm.png +0 -0
  202. simba/assets/icons/webp.png +0 -0
  203. simba/assets/icons/zero.png +0 -0
  204. simba/assets/icons/zoom_in.png +0 -0
  205. simba/assets/icons/zoom_out.png +0 -0
  206. simba/assets/img/__init__.py +0 -0
  207. simba/assets/img/about_me.png +0 -0
  208. simba/assets/img/bg.png +0 -0
  209. simba/assets/img/bg_2.png +0 -0
  210. simba/assets/img/bg_2024.png +0 -0
  211. simba/assets/img/splash.mp4 +0 -0
  212. simba/assets/img/splash.pptx +0 -0
  213. simba/assets/img/splash_2024.mp4 +0 -0
  214. simba/assets/img/~$splash.pptx +0 -0
  215. simba/assets/lookups/__init__.py +0 -0
  216. simba/assets/lookups/critical_values_05.pickle +0 -0
  217. simba/assets/lookups/feature_extraction_headers.csv +49 -0
  218. simba/assets/lookups/features.csv +414 -0
  219. simba/assets/lookups/model_names.parquet +0 -0
  220. simba/assets/lookups/unsupervised_example_x.csv +414 -0
  221. simba/assets/lookups/yolo.yaml +7 -0
  222. simba/assets/shap/UbuntuMono-Regular.ttf +0 -0
  223. simba/assets/shap/__init__.py +0 -0
  224. simba/assets/shap/animal_distances.jpg +0 -0
  225. simba/assets/shap/baseline_scale.jpg +0 -0
  226. simba/assets/shap/color_bar.jpg +0 -0
  227. simba/assets/shap/down_arrow.jpg +0 -0
  228. simba/assets/shap/feature_categories/__init__.py +0 -0
  229. simba/assets/shap/feature_categories/shap_feature_categories.csv +20 -0
  230. simba/assets/shap/intruder_movement.jpg +0 -0
  231. simba/assets/shap/intruder_shape.jpg +0 -0
  232. simba/assets/shap/resident_intruder_movement.jpg +0 -0
  233. simba/assets/shap/resident_intruder_shape.jpg +0 -0
  234. simba/assets/shap/resident_movement.jpg +0 -0
  235. simba/assets/shap/resident_shape.jpg +0 -0
  236. simba/assets/shap/side_scale.jpg +0 -0
  237. simba/assets/shap/side_scale_5.jpg +0 -0
  238. simba/assets/shap/ubuntu.regular.ttf +0 -0
  239. simba/assets/stl/__init__.py +0 -0
  240. simba/assets/stl/grid_floor.stl +0 -0
  241. simba/assets/stl/operant_lever.stl +1570 -0
  242. simba/assets/stl/operant_tray.stl +12567 -0
  243. simba/assets/stl/operant_walls.stl +2186 -0
  244. simba/assets/unsupervised/__init__.py +0 -0
  245. simba/assets/unsupervised/features.csv +414 -0
  246. simba/assets/unsupervised/model_names.parquet +0 -0
  247. simba/bounding_box_tools/__init__.py +0 -0
  248. simba/bounding_box_tools/agg_boundary_stats.py +204 -0
  249. simba/bounding_box_tools/boundary_menus.py +643 -0
  250. simba/bounding_box_tools/boundary_statistics.py +218 -0
  251. simba/bounding_box_tools/find_boundaries.py +151 -0
  252. simba/bounding_box_tools/visualize_boundaries.py +260 -0
  253. simba/bounding_box_tools/yolo/__init__.py +0 -0
  254. simba/bounding_box_tools/yolo/geometries_to_annotations.py +195 -0
  255. simba/bounding_box_tools/yolo/model.py +194 -0
  256. simba/bounding_box_tools/yolo/visualize.py +93 -0
  257. simba/cue_light_tools/__init__.py +0 -0
  258. simba/cue_light_tools/cue_light_analyzer.py +325 -0
  259. simba/cue_light_tools/cue_light_clf_statistics.py +211 -0
  260. simba/cue_light_tools/cue_light_menues.py +436 -0
  261. simba/cue_light_tools/cue_light_movement_statistics.py +332 -0
  262. simba/cue_light_tools/cue_light_tools.py +53 -0
  263. simba/cue_light_tools/cue_light_visualizer.py +462 -0
  264. simba/dash_app/SimBA_dash_app.py +1678 -0
  265. simba/dash_app/__init__.py +0 -0
  266. simba/dash_app/dash_app.py +754 -0
  267. simba/dash_app/run_dash_tkinter.py +168 -0
  268. simba/data_processors/.DS_Store +0 -0
  269. simba/data_processors/__init__.py +0 -0
  270. simba/data_processors/advanced_interpolator.py +213 -0
  271. simba/data_processors/advanced_smoothing.py +206 -0
  272. simba/data_processors/agg_clf_calculator.py +256 -0
  273. simba/data_processors/blob_location_computer.py +126 -0
  274. simba/data_processors/boolean_conditional_calculator.py +108 -0
  275. simba/data_processors/circling_detector.py +133 -0
  276. simba/data_processors/cuda/__init__.py +0 -0
  277. simba/data_processors/cuda/circular_statistics.py +733 -0
  278. simba/data_processors/cuda/create_shap_log.py +161 -0
  279. simba/data_processors/cuda/data.py +178 -0
  280. simba/data_processors/cuda/geometry.py +414 -0
  281. simba/data_processors/cuda/image.py +1202 -0
  282. simba/data_processors/cuda/statistics.py +753 -0
  283. simba/data_processors/cuda/timeseries.py +263 -0
  284. simba/data_processors/cuda/utils.py +235 -0
  285. simba/data_processors/directing_animal_to_bodypart.py +254 -0
  286. simba/data_processors/directing_other_animals_calculator.py +321 -0
  287. simba/data_processors/egocentric_aligner.py +175 -0
  288. simba/data_processors/freezing_detector.py +138 -0
  289. simba/data_processors/fsttc_calculator.py +449 -0
  290. simba/data_processors/gibbs_sampler.py +153 -0
  291. simba/data_processors/interpolate.py +119 -0
  292. simba/data_processors/interpolate_pose.py +167 -0
  293. simba/data_processors/interpolation_smoothing.py +819 -0
  294. simba/data_processors/kleinberg_calculator.py +179 -0
  295. simba/data_processors/movement_calculator.py +127 -0
  296. simba/data_processors/mutual_exclusivity_corrector.py +190 -0
  297. simba/data_processors/pup_retrieval_calculator.py +422 -0
  298. simba/data_processors/pybursts_calculator.py +113 -0
  299. simba/data_processors/severity_bout_based_calculator.py +295 -0
  300. simba/data_processors/severity_calculator.py +121 -0
  301. simba/data_processors/severity_frame_based_calculator.py +304 -0
  302. simba/data_processors/smoothing.py +126 -0
  303. simba/data_processors/spontaneous_alternation_calculator.py +184 -0
  304. simba/data_processors/timebins_clf_calculator.py +211 -0
  305. simba/data_processors/timebins_movement_calculator.py +164 -0
  306. simba/feature_extractors/.DS_Store +0 -0
  307. simba/feature_extractors/__init__.py +0 -0
  308. simba/feature_extractors/amber_feature_extractor.py +1637 -0
  309. simba/feature_extractors/feature_extractor_14bp.py +1211 -0
  310. simba/feature_extractors/feature_extractor_16bp.py +1294 -0
  311. simba/feature_extractors/feature_extractor_4bp.py +461 -0
  312. simba/feature_extractors/feature_extractor_7bp.py +607 -0
  313. simba/feature_extractors/feature_extractor_8bp.py +671 -0
  314. simba/feature_extractors/feature_extractor_8bps_2_animals.py +793 -0
  315. simba/feature_extractors/feature_extractor_9bp.py +800 -0
  316. simba/feature_extractors/feature_extractor_user_defined.py +196 -0
  317. simba/feature_extractors/feature_subsets.py +556 -0
  318. simba/feature_extractors/misc/add_probability_cnt_features.py +76 -0
  319. simba/feature_extractors/misc/convex_hull_3_scratch_3.py +69 -0
  320. simba/feature_extractors/misc/convex_hull_scratch_1.py +197 -0
  321. simba/feature_extractors/misc/convex_hull_scratch_2.py +71 -0
  322. simba/feature_extractors/misc/count_values_in_range.py +41 -0
  323. simba/feature_extractors/misc/doctests.py +55 -0
  324. simba/feature_extractors/misc/egocentrical_aligner.py +180 -0
  325. simba/feature_extractors/misc/fish_feature_extractor_2022.py +403 -0
  326. simba/feature_extractors/misc/fish_feature_extractor_2023_version_2.py +637 -0
  327. simba/feature_extractors/misc/fish_feature_extractor_2023_version_3.py +705 -0
  328. simba/feature_extractors/misc/fish_feature_extractor_2023_version_4.py +878 -0
  329. simba/feature_extractors/misc/fish_feature_extractor_2023_version_5.py +878 -0
  330. simba/feature_extractors/misc/graph_3d_plotter.py +60 -0
  331. simba/feature_extractors/misc/graph_creator.py +135 -0
  332. simba/feature_extractors/misc/make_splash.py +55 -0
  333. simba/feature_extractors/misc/mutual_exclusive.py +20 -0
  334. simba/feature_extractors/misc/peaks.py +70 -0
  335. simba/feature_extractors/misc/read_in_mp.py +76 -0
  336. simba/feature_extractors/misc/termite_rois.csv +50 -0
  337. simba/feature_extractors/misc/time_stamp_calculator.py +51 -0
  338. simba/feature_extractors/misc/video_color.py +77 -0
  339. simba/feature_extractors/misc/video_rotator.py +147 -0
  340. simba/feature_extractors/misc/video_rotator_mp.py +147 -0
  341. simba/feature_extractors/perimeter_jit.py +122 -0
  342. simba/labelling/__init__.py +0 -0
  343. simba/labelling/extract_labelled_frames.py +96 -0
  344. simba/labelling/extract_labelling_meta.py +98 -0
  345. simba/labelling/labelling_advanced_interface.py +564 -0
  346. simba/labelling/labelling_interface.py +394 -0
  347. simba/labelling/play_annotation_video.py +169 -0
  348. simba/labelling/targeted_annotations_clips.py +57 -0
  349. simba/mixins/.DS_Store +0 -0
  350. simba/mixins/__init__.py +8 -0
  351. simba/mixins/abstract_classes.py +20 -0
  352. simba/mixins/annotator_mixin.py +937 -0
  353. simba/mixins/circular_statistics.py +1449 -0
  354. simba/mixins/config_reader.py +965 -0
  355. simba/mixins/feature_extraction_mixin.py +1039 -0
  356. simba/mixins/feature_extraction_supplement_mixin.py +797 -0
  357. simba/mixins/geometry_mixin.py +4007 -0
  358. simba/mixins/image_mixin.py +1961 -0
  359. simba/mixins/network_mixin.py +863 -0
  360. simba/mixins/plotting_mixin.py +2035 -0
  361. simba/mixins/pop_up_mixin.py +470 -0
  362. simba/mixins/pose_importer_mixin.py +413 -0
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