scitex 2.5.0__py3-none-any.whl → 2.7.3__py3-none-any.whl

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 (1179) hide show
  1. scitex/__init__.py +25 -10
  2. scitex/__main__.py +2 -1
  3. scitex/__version__.py +1 -1
  4. scitex/_optional_deps.py +13 -20
  5. scitex/ai/__init__.py +5 -0
  6. scitex/ai/_gen_ai/_Anthropic.py +3 -1
  7. scitex/ai/_gen_ai/_BaseGenAI.py +3 -2
  8. scitex/ai/_gen_ai/_DeepSeek.py +1 -1
  9. scitex/ai/_gen_ai/_Google.py +3 -2
  10. scitex/ai/_gen_ai/_Llama.py +4 -2
  11. scitex/ai/_gen_ai/_OpenAI.py +3 -1
  12. scitex/ai/_gen_ai/_PARAMS.py +1 -0
  13. scitex/ai/_gen_ai/_Perplexity.py +3 -1
  14. scitex/ai/_gen_ai/__init__.py +1 -0
  15. scitex/ai/_gen_ai/_format_output_func.py +3 -1
  16. scitex/ai/classification/CrossValidationExperiment.py +8 -14
  17. scitex/ai/classification/examples/timeseries_cv_demo.py +128 -112
  18. scitex/ai/classification/reporters/_BaseClassificationReporter.py +2 -0
  19. scitex/ai/classification/reporters/_ClassificationReporter.py +30 -45
  20. scitex/ai/classification/reporters/_MultiClassificationReporter.py +8 -11
  21. scitex/ai/classification/reporters/_SingleClassificationReporter.py +126 -182
  22. scitex/ai/classification/reporters/__init__.py +1 -1
  23. scitex/ai/classification/reporters/reporter_utils/_Plotter.py +213 -119
  24. scitex/ai/classification/reporters/reporter_utils/__init__.py +28 -36
  25. scitex/ai/classification/reporters/reporter_utils/aggregation.py +125 -143
  26. scitex/ai/classification/reporters/reporter_utils/data_models.py +128 -120
  27. scitex/ai/classification/reporters/reporter_utils/reporting.py +507 -340
  28. scitex/ai/classification/reporters/reporter_utils/storage.py +4 -1
  29. scitex/ai/classification/reporters/reporter_utils/validation.py +141 -154
  30. scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +204 -129
  31. scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +215 -171
  32. scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +17 -17
  33. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +67 -143
  34. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +67 -143
  35. scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +12 -13
  36. scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +231 -144
  37. scitex/ai/classification/timeseries/__init__.py +2 -4
  38. scitex/ai/classification/timeseries/_normalize_timestamp.py +3 -0
  39. scitex/ai/clustering/_pca.py +0 -1
  40. scitex/ai/clustering/_umap.py +1 -2
  41. scitex/ai/feature_extraction/__init__.py +10 -8
  42. scitex/ai/feature_extraction/vit.py +0 -1
  43. scitex/ai/feature_selection/feature_selection.py +3 -8
  44. scitex/ai/metrics/_calc_conf_mat.py +2 -0
  45. scitex/ai/metrics/_calc_feature_importance.py +3 -7
  46. scitex/ai/metrics/_calc_pre_rec_auc.py +5 -5
  47. scitex/ai/metrics/_calc_roc_auc.py +4 -2
  48. scitex/ai/metrics/_calc_seizure_prediction_metrics.py +35 -20
  49. scitex/ai/metrics/_calc_silhouette_score.py +1 -3
  50. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +0 -3
  51. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +0 -3
  52. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +0 -3
  53. scitex/ai/optim/_optimizers.py +1 -1
  54. scitex/ai/plt/__init__.py +6 -1
  55. scitex/ai/plt/_plot_feature_importance.py +1 -3
  56. scitex/ai/plt/_plot_learning_curve.py +9 -24
  57. scitex/ai/plt/_plot_optuna_study.py +4 -3
  58. scitex/ai/plt/_plot_pre_rec_curve.py +9 -15
  59. scitex/ai/plt/_plot_roc_curve.py +6 -8
  60. scitex/ai/plt/_stx_conf_mat.py +121 -122
  61. scitex/ai/sampling/undersample.py +3 -2
  62. scitex/ai/sklearn/__init__.py +2 -2
  63. scitex/ai/training/_LearningCurveLogger.py +23 -10
  64. scitex/ai/utils/_check_params.py +0 -1
  65. scitex/audio/README.md +52 -0
  66. scitex/audio/__init__.py +384 -0
  67. scitex/audio/__main__.py +129 -0
  68. scitex/audio/_tts.py +334 -0
  69. scitex/audio/engines/__init__.py +44 -0
  70. scitex/audio/engines/base.py +275 -0
  71. scitex/audio/engines/elevenlabs_engine.py +143 -0
  72. scitex/audio/engines/gtts_engine.py +162 -0
  73. scitex/audio/engines/pyttsx3_engine.py +131 -0
  74. scitex/audio/mcp_server.py +757 -0
  75. scitex/benchmark/__init__.py +15 -25
  76. scitex/benchmark/benchmark.py +124 -117
  77. scitex/benchmark/monitor.py +117 -107
  78. scitex/benchmark/profiler.py +61 -58
  79. scitex/bridge/__init__.py +110 -0
  80. scitex/bridge/_helpers.py +149 -0
  81. scitex/bridge/_plt_vis.py +529 -0
  82. scitex/bridge/_protocol.py +283 -0
  83. scitex/bridge/_stats_plt.py +261 -0
  84. scitex/bridge/_stats_vis.py +265 -0
  85. scitex/browser/__init__.py +0 -2
  86. scitex/browser/auth/__init__.py +0 -0
  87. scitex/browser/auth/google.py +16 -11
  88. scitex/browser/automation/CookieHandler.py +2 -3
  89. scitex/browser/collaboration/__init__.py +3 -0
  90. scitex/browser/collaboration/auth_helpers.py +3 -1
  91. scitex/browser/collaboration/collaborative_agent.py +2 -0
  92. scitex/browser/collaboration/interactive_panel.py +2 -2
  93. scitex/browser/collaboration/shared_session.py +20 -11
  94. scitex/browser/collaboration/standard_interactions.py +1 -0
  95. scitex/browser/core/BrowserMixin.py +12 -30
  96. scitex/browser/core/ChromeProfileManager.py +9 -24
  97. scitex/browser/debugging/_browser_logger.py +15 -25
  98. scitex/browser/debugging/_failure_capture.py +9 -2
  99. scitex/browser/debugging/_highlight_element.py +15 -6
  100. scitex/browser/debugging/_show_grid.py +5 -6
  101. scitex/browser/debugging/_sync_session.py +4 -3
  102. scitex/browser/debugging/_test_monitor.py +14 -5
  103. scitex/browser/debugging/_visual_cursor.py +46 -35
  104. scitex/browser/interaction/click_center.py +4 -3
  105. scitex/browser/interaction/click_with_fallbacks.py +7 -10
  106. scitex/browser/interaction/close_popups.py +79 -66
  107. scitex/browser/interaction/fill_with_fallbacks.py +8 -8
  108. scitex/browser/pdf/__init__.py +3 -1
  109. scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
  110. scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
  111. scitex/browser/remote/CaptchaHandler.py +109 -96
  112. scitex/browser/remote/ZenRowsAPIClient.py +91 -97
  113. scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
  114. scitex/browser/stealth/HumanBehavior.py +4 -9
  115. scitex/browser/stealth/StealthManager.py +11 -26
  116. scitex/capture/__init__.py +17 -17
  117. scitex/capture/__main__.py +2 -3
  118. scitex/capture/capture.py +23 -51
  119. scitex/capture/cli.py +14 -39
  120. scitex/capture/gif.py +5 -9
  121. scitex/capture/mcp_server.py +7 -20
  122. scitex/capture/session.py +4 -3
  123. scitex/capture/utils.py +18 -53
  124. scitex/cli/__init__.py +1 -1
  125. scitex/cli/cloud.py +158 -116
  126. scitex/cli/config.py +224 -0
  127. scitex/cli/main.py +41 -40
  128. scitex/cli/scholar.py +60 -27
  129. scitex/cli/security.py +14 -20
  130. scitex/cli/web.py +87 -90
  131. scitex/cli/writer.py +51 -45
  132. scitex/cloud/__init__.py +14 -11
  133. scitex/cloud/_matplotlib_hook.py +6 -6
  134. scitex/config/README.md +313 -0
  135. scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
  136. scitex/config/_ScitexConfig.py +319 -0
  137. scitex/config/__init__.py +41 -9
  138. scitex/config/_paths.py +325 -0
  139. scitex/config/default.yaml +81 -0
  140. scitex/context/_suppress_output.py +2 -3
  141. scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
  142. scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
  143. scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
  144. scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
  145. scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
  146. scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
  147. scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
  148. scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
  149. scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
  150. scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
  151. scitex/db/_BaseMixins/__init__.py +1 -1
  152. scitex/db/__init__.py +9 -1
  153. scitex/db/__main__.py +8 -21
  154. scitex/db/_check_health.py +15 -31
  155. scitex/db/_delete_duplicates.py +7 -4
  156. scitex/db/_inspect.py +22 -38
  157. scitex/db/_inspect_optimized.py +89 -85
  158. scitex/db/_postgresql/_PostgreSQL.py +0 -1
  159. scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
  160. scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
  161. scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
  162. scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
  163. scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
  164. scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
  165. scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
  166. scitex/db/_postgresql/__init__.py +1 -1
  167. scitex/db/_sqlite3/_SQLite3.py +2 -4
  168. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
  169. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
  170. scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
  171. scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
  172. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
  173. scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
  174. scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
  175. scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
  176. scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
  177. scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
  178. scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
  179. scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
  180. scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
  181. scitex/db/_sqlite3/__init__.py +1 -1
  182. scitex/db/_sqlite3/_delete_duplicates.py +13 -11
  183. scitex/decorators/__init__.py +29 -4
  184. scitex/decorators/_auto_order.py +43 -43
  185. scitex/decorators/_batch_fn.py +12 -6
  186. scitex/decorators/_cache_disk.py +8 -9
  187. scitex/decorators/_cache_disk_async.py +8 -7
  188. scitex/decorators/_combined.py +19 -13
  189. scitex/decorators/_converters.py +16 -3
  190. scitex/decorators/_deprecated.py +32 -22
  191. scitex/decorators/_numpy_fn.py +18 -4
  192. scitex/decorators/_pandas_fn.py +17 -5
  193. scitex/decorators/_signal_fn.py +17 -3
  194. scitex/decorators/_torch_fn.py +32 -15
  195. scitex/decorators/_xarray_fn.py +23 -9
  196. scitex/dev/_analyze_code_flow.py +0 -2
  197. scitex/dev/plt/__init__.py +272 -0
  198. scitex/dev/plt/plot_mpl_axhline.py +28 -0
  199. scitex/dev/plt/plot_mpl_axhspan.py +28 -0
  200. scitex/dev/plt/plot_mpl_axvline.py +28 -0
  201. scitex/dev/plt/plot_mpl_axvspan.py +28 -0
  202. scitex/dev/plt/plot_mpl_bar.py +29 -0
  203. scitex/dev/plt/plot_mpl_barh.py +29 -0
  204. scitex/dev/plt/plot_mpl_boxplot.py +28 -0
  205. scitex/dev/plt/plot_mpl_contour.py +31 -0
  206. scitex/dev/plt/plot_mpl_contourf.py +31 -0
  207. scitex/dev/plt/plot_mpl_errorbar.py +30 -0
  208. scitex/dev/plt/plot_mpl_eventplot.py +28 -0
  209. scitex/dev/plt/plot_mpl_fill.py +30 -0
  210. scitex/dev/plt/plot_mpl_fill_between.py +31 -0
  211. scitex/dev/plt/plot_mpl_hexbin.py +28 -0
  212. scitex/dev/plt/plot_mpl_hist.py +28 -0
  213. scitex/dev/plt/plot_mpl_hist2d.py +28 -0
  214. scitex/dev/plt/plot_mpl_imshow.py +29 -0
  215. scitex/dev/plt/plot_mpl_pcolormesh.py +31 -0
  216. scitex/dev/plt/plot_mpl_pie.py +29 -0
  217. scitex/dev/plt/plot_mpl_plot.py +29 -0
  218. scitex/dev/plt/plot_mpl_quiver.py +31 -0
  219. scitex/dev/plt/plot_mpl_scatter.py +28 -0
  220. scitex/dev/plt/plot_mpl_stackplot.py +31 -0
  221. scitex/dev/plt/plot_mpl_stem.py +29 -0
  222. scitex/dev/plt/plot_mpl_step.py +29 -0
  223. scitex/dev/plt/plot_mpl_violinplot.py +28 -0
  224. scitex/dev/plt/plot_sns_barplot.py +29 -0
  225. scitex/dev/plt/plot_sns_boxplot.py +29 -0
  226. scitex/dev/plt/plot_sns_heatmap.py +28 -0
  227. scitex/dev/plt/plot_sns_histplot.py +29 -0
  228. scitex/dev/plt/plot_sns_kdeplot.py +29 -0
  229. scitex/dev/plt/plot_sns_lineplot.py +31 -0
  230. scitex/dev/plt/plot_sns_scatterplot.py +29 -0
  231. scitex/dev/plt/plot_sns_stripplot.py +29 -0
  232. scitex/dev/plt/plot_sns_swarmplot.py +29 -0
  233. scitex/dev/plt/plot_sns_violinplot.py +29 -0
  234. scitex/dev/plt/plot_stx_bar.py +29 -0
  235. scitex/dev/plt/plot_stx_barh.py +29 -0
  236. scitex/dev/plt/plot_stx_box.py +28 -0
  237. scitex/dev/plt/plot_stx_boxplot.py +28 -0
  238. scitex/dev/plt/plot_stx_conf_mat.py +28 -0
  239. scitex/dev/plt/plot_stx_contour.py +31 -0
  240. scitex/dev/plt/plot_stx_ecdf.py +28 -0
  241. scitex/dev/plt/plot_stx_errorbar.py +30 -0
  242. scitex/dev/plt/plot_stx_fill_between.py +31 -0
  243. scitex/dev/plt/plot_stx_fillv.py +28 -0
  244. scitex/dev/plt/plot_stx_heatmap.py +28 -0
  245. scitex/dev/plt/plot_stx_image.py +28 -0
  246. scitex/dev/plt/plot_stx_imshow.py +28 -0
  247. scitex/dev/plt/plot_stx_joyplot.py +28 -0
  248. scitex/dev/plt/plot_stx_kde.py +28 -0
  249. scitex/dev/plt/plot_stx_line.py +28 -0
  250. scitex/dev/plt/plot_stx_mean_ci.py +28 -0
  251. scitex/dev/plt/plot_stx_mean_std.py +28 -0
  252. scitex/dev/plt/plot_stx_median_iqr.py +28 -0
  253. scitex/dev/plt/plot_stx_raster.py +28 -0
  254. scitex/dev/plt/plot_stx_rectangle.py +28 -0
  255. scitex/dev/plt/plot_stx_scatter.py +29 -0
  256. scitex/dev/plt/plot_stx_shaded_line.py +29 -0
  257. scitex/dev/plt/plot_stx_violin.py +28 -0
  258. scitex/dev/plt/plot_stx_violinplot.py +28 -0
  259. scitex/dict/_DotDict.py +15 -19
  260. scitex/dict/_flatten.py +1 -0
  261. scitex/dict/_listed_dict.py +1 -0
  262. scitex/dict/_pop_keys.py +1 -0
  263. scitex/dict/_replace.py +1 -0
  264. scitex/dict/_safe_merge.py +1 -0
  265. scitex/dict/_to_str.py +2 -3
  266. scitex/dsp/__init__.py +13 -4
  267. scitex/dsp/_crop.py +3 -1
  268. scitex/dsp/_detect_ripples.py +3 -1
  269. scitex/dsp/_modulation_index.py +3 -1
  270. scitex/dsp/_time.py +3 -1
  271. scitex/dsp/_wavelet.py +0 -1
  272. scitex/dsp/example.py +0 -5
  273. scitex/dsp/filt.py +4 -0
  274. scitex/dsp/utils/__init__.py +4 -1
  275. scitex/dsp/utils/pac.py +3 -3
  276. scitex/dt/_normalize_timestamp.py +4 -1
  277. scitex/errors.py +3 -6
  278. scitex/etc/__init__.py +1 -1
  279. scitex/fig/__init__.py +352 -0
  280. scitex/{vis → fig}/backend/__init__.py +3 -3
  281. scitex/{vis/backend/export.py → fig/backend/_export.py} +1 -1
  282. scitex/{vis/backend/parser.py → fig/backend/_parser.py} +2 -4
  283. scitex/{vis/backend/render.py → fig/backend/_render.py} +1 -1
  284. scitex/{vis → fig}/canvas.py +16 -4
  285. scitex/{vis → fig}/editor/__init__.py +0 -0
  286. scitex/{vis → fig}/editor/_dearpygui_editor.py +450 -304
  287. scitex/fig/editor/_defaults.py +300 -0
  288. scitex/fig/editor/_edit.py +751 -0
  289. scitex/{vis → fig}/editor/_flask_editor.py +8 -8
  290. scitex/{vis → fig}/editor/_mpl_editor.py +63 -48
  291. scitex/{vis → fig}/editor/_qt_editor.py +391 -160
  292. scitex/{vis → fig}/editor/_tkinter_editor.py +146 -89
  293. scitex/fig/editor/flask_editor/__init__.py +21 -0
  294. scitex/fig/editor/flask_editor/_bbox.py +1276 -0
  295. scitex/fig/editor/flask_editor/_core.py +624 -0
  296. scitex/fig/editor/flask_editor/_plotter.py +601 -0
  297. scitex/fig/editor/flask_editor/_renderer.py +739 -0
  298. scitex/{vis/editor/flask_editor/utils.py → fig/editor/flask_editor/_utils.py} +13 -14
  299. scitex/{vis → fig}/editor/flask_editor/templates/__init__.py +6 -6
  300. scitex/fig/editor/flask_editor/templates/_html.py +834 -0
  301. scitex/fig/editor/flask_editor/templates/_scripts.py +3136 -0
  302. scitex/fig/editor/flask_editor/templates/_styles.py +1346 -0
  303. scitex/{vis → fig}/io/__init__.py +18 -6
  304. scitex/fig/io/_bundle.py +973 -0
  305. scitex/{vis/io/canvas.py → fig/io/_canvas.py} +9 -5
  306. scitex/{vis/io/data.py → fig/io/_data.py} +14 -10
  307. scitex/{vis/io/directory.py → fig/io/_directory.py} +7 -4
  308. scitex/{vis/io/export.py → fig/io/_export.py} +16 -13
  309. scitex/{vis/io/load.py → fig/io/_load.py} +2 -2
  310. scitex/{vis/io/panel.py → fig/io/_panel.py} +22 -14
  311. scitex/{vis/io/save.py → fig/io/_save.py} +1 -1
  312. scitex/{vis → fig}/model/__init__.py +8 -8
  313. scitex/{vis/model/annotations.py → fig/model/_annotations.py} +3 -5
  314. scitex/{vis/model/axes.py → fig/model/_axes.py} +2 -2
  315. scitex/{vis/model/figure.py → fig/model/_figure.py} +1 -1
  316. scitex/{vis/model/guides.py → fig/model/_guides.py} +2 -2
  317. scitex/{vis/model/plot.py → fig/model/_plot.py} +3 -5
  318. scitex/{vis/model/plot_types.py → fig/model/_plot_types.py} +0 -0
  319. scitex/{vis/model/styles.py → fig/model/_styles.py} +1 -1
  320. scitex/{vis → fig}/utils/__init__.py +3 -3
  321. scitex/{vis/utils/defaults.py → fig/utils/_defaults.py} +1 -2
  322. scitex/{vis/utils/validate.py → fig/utils/_validate.py} +3 -9
  323. scitex/gen/_DimHandler.py +6 -6
  324. scitex/gen/__init__.py +5 -1
  325. scitex/gen/_deprecated_close.py +1 -0
  326. scitex/gen/_deprecated_start.py +5 -3
  327. scitex/gen/_detect_environment.py +44 -41
  328. scitex/gen/_detect_notebook_path.py +51 -47
  329. scitex/gen/_embed.py +1 -1
  330. scitex/gen/_get_notebook_path.py +81 -62
  331. scitex/gen/_inspect_module.py +0 -1
  332. scitex/gen/_norm.py +16 -7
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  334. scitex/gen/_print_config.py +0 -3
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  928. scitex/scholar/url_finder/translators/individual/caod.py +50 -46
  929. scitex/scholar/url_finder/translators/individual/cbc.py +91 -67
  930. scitex/scholar/url_finder/translators/individual/ccfr_bnf.py +49 -53
  931. scitex/scholar/url_finder/translators/individual/cia_world_factbook.py +43 -33
  932. scitex/scholar/url_finder/translators/individual/crossref_rest.py +208 -174
  933. scitex/scholar/url_finder/translators/individual/current_affairs.py +29 -35
  934. scitex/scholar/url_finder/translators/individual/dabi.py +70 -66
  935. scitex/scholar/url_finder/translators/individual/dagens_nyheter.py +3 -1
  936. scitex/scholar/url_finder/translators/individual/dagstuhl.py +10 -15
  937. scitex/scholar/url_finder/translators/individual/dar_almandumah.py +13 -9
  938. scitex/scholar/url_finder/translators/individual/dart_europe.py +19 -22
  939. scitex/scholar/url_finder/translators/individual/data_gov.py +2 -2
  940. scitex/scholar/url_finder/translators/individual/databrary.py +27 -28
  941. scitex/scholar/url_finder/translators/individual/datacite_json.py +152 -137
  942. scitex/scholar/url_finder/translators/individual/dataverse.py +68 -64
  943. scitex/scholar/url_finder/translators/individual/daum_news.py +38 -38
  944. scitex/scholar/url_finder/translators/individual/dblp.py +4 -8
  945. scitex/scholar/url_finder/translators/individual/dblp_computer_science_bibliography.py +8 -3
  946. scitex/scholar/url_finder/translators/individual/dbpia.py +5 -3
  947. scitex/scholar/url_finder/translators/individual/defense_technical_information_center.py +30 -28
  948. scitex/scholar/url_finder/translators/individual/delpher.py +102 -79
  949. scitex/scholar/url_finder/translators/individual/demographic_research.py +35 -31
  950. scitex/scholar/url_finder/translators/individual/denik_cz.py +58 -54
  951. scitex/scholar/url_finder/translators/individual/depatisnet.py +7 -10
  952. scitex/scholar/url_finder/translators/individual/der_freitag.py +81 -66
  953. scitex/scholar/url_finder/translators/individual/der_spiegel.py +56 -54
  954. scitex/scholar/url_finder/translators/individual/digibib_net.py +3 -1
  955. scitex/scholar/url_finder/translators/individual/digizeitschriften.py +3 -1
  956. scitex/scholar/url_finder/translators/individual/dpla.py +13 -14
  957. scitex/scholar/url_finder/translators/individual/dspace.py +2 -2
  958. scitex/scholar/url_finder/translators/individual/ebrary.py +3 -1
  959. scitex/scholar/url_finder/translators/individual/ebscohost.py +3 -1
  960. scitex/scholar/url_finder/translators/individual/electronic_colloquium_on_computational_complexity.py +3 -1
  961. scitex/scholar/url_finder/translators/individual/elife.py +3 -1
  962. scitex/scholar/url_finder/translators/individual/elsevier_health_journals.py +3 -1
  963. scitex/scholar/url_finder/translators/individual/emerald.py +3 -1
  964. scitex/scholar/url_finder/translators/individual/emerald_insight.py +3 -1
  965. scitex/scholar/url_finder/translators/individual/epicurious.py +3 -1
  966. scitex/scholar/url_finder/translators/individual/eurogamerusgamer.py +3 -1
  967. scitex/scholar/url_finder/translators/individual/fachportal_padagogik.py +3 -1
  968. scitex/scholar/url_finder/translators/individual/frontiers.py +1 -1
  969. scitex/scholar/url_finder/translators/individual/gale_databases.py +3 -1
  970. scitex/scholar/url_finder/translators/individual/gms_german_medical_science.py +6 -2
  971. scitex/scholar/url_finder/translators/individual/ieee_computer_society.py +6 -2
  972. scitex/scholar/url_finder/translators/individual/ieee_xplore.py +41 -35
  973. scitex/scholar/url_finder/translators/individual/inter_research_science_center.py +6 -2
  974. scitex/scholar/url_finder/translators/individual/jisc_historical_texts.py +3 -1
  975. scitex/scholar/url_finder/translators/individual/jstor.py +14 -12
  976. scitex/scholar/url_finder/translators/individual/korean_national_library.py +3 -1
  977. scitex/scholar/url_finder/translators/individual/la_times.py +3 -1
  978. scitex/scholar/url_finder/translators/individual/landesbibliographie_baden_wurttemberg.py +3 -1
  979. scitex/scholar/url_finder/translators/individual/legislative_insight.py +3 -1
  980. scitex/scholar/url_finder/translators/individual/libraries_tasmania.py +3 -1
  981. scitex/scholar/url_finder/translators/individual/library_catalog__koha_.py +3 -1
  982. scitex/scholar/url_finder/translators/individual/lingbuzz.py +2 -2
  983. scitex/scholar/url_finder/translators/individual/max_planck_institute_for_the_history_of_science_virtual_laboratory_library.py +3 -1
  984. scitex/scholar/url_finder/translators/individual/mdpi.py +12 -6
  985. scitex/scholar/url_finder/translators/individual/microbiology_society_journals.py +3 -1
  986. scitex/scholar/url_finder/translators/individual/midas_journals.py +3 -1
  987. scitex/scholar/url_finder/translators/individual/nagoya_university_opac.py +3 -1
  988. scitex/scholar/url_finder/translators/individual/nature_publishing_group.py +32 -19
  989. scitex/scholar/url_finder/translators/individual/ntsb_accident_reports.py +3 -1
  990. scitex/scholar/url_finder/translators/individual/openedition_journals.py +8 -4
  991. scitex/scholar/url_finder/translators/individual/orcid.py +16 -15
  992. scitex/scholar/url_finder/translators/individual/oxford.py +25 -19
  993. scitex/scholar/url_finder/translators/individual/oxford_dictionaries_premium.py +3 -1
  994. scitex/scholar/url_finder/translators/individual/ozon_ru.py +3 -1
  995. scitex/scholar/url_finder/translators/individual/plos.py +9 -12
  996. scitex/scholar/url_finder/translators/individual/polygon.py +3 -1
  997. scitex/scholar/url_finder/translators/individual/primo.py +3 -1
  998. scitex/scholar/url_finder/translators/individual/project_muse.py +3 -1
  999. scitex/scholar/url_finder/translators/individual/pubfactory_journals.py +3 -1
  1000. scitex/scholar/url_finder/translators/individual/pubmed.py +71 -65
  1001. scitex/scholar/url_finder/translators/individual/pubmed_central.py +8 -6
  1002. scitex/scholar/url_finder/translators/individual/rechtspraak_nl.py +3 -1
  1003. scitex/scholar/url_finder/translators/individual/sage_journals.py +25 -17
  1004. scitex/scholar/url_finder/translators/individual/sciencedirect.py +36 -17
  1005. scitex/scholar/url_finder/translators/individual/semantics_visual_library.py +3 -1
  1006. scitex/scholar/url_finder/translators/individual/silverchair.py +70 -52
  1007. scitex/scholar/url_finder/translators/individual/sora.py +3 -1
  1008. scitex/scholar/url_finder/translators/individual/springer.py +15 -11
  1009. scitex/scholar/url_finder/translators/individual/ssrn.py +3 -3
  1010. scitex/scholar/url_finder/translators/individual/stanford_encyclopedia_of_philosophy.py +3 -1
  1011. scitex/scholar/url_finder/translators/individual/superlib.py +3 -1
  1012. scitex/scholar/url_finder/translators/individual/treesearch.py +3 -1
  1013. scitex/scholar/url_finder/translators/individual/university_of_chicago_press_books.py +3 -1
  1014. scitex/scholar/url_finder/translators/individual/vlex.py +3 -1
  1015. scitex/scholar/url_finder/translators/individual/web_of_science.py +3 -1
  1016. scitex/scholar/url_finder/translators/individual/web_of_science_nextgen.py +3 -1
  1017. scitex/scholar/url_finder/translators/individual/wiley.py +31 -25
  1018. scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +3 -1
  1019. scitex/scholar/utils/bibtex/_parse_bibtex.py +3 -3
  1020. scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +5 -9
  1021. scitex/scholar/utils/text/_TextNormalizer.py +249 -176
  1022. scitex/scholar/utils/validation/DOIValidator.py +31 -28
  1023. scitex/scholar/utils/validation/__init__.py +0 -0
  1024. scitex/scholar/utils/validation/validate_library_dois.py +61 -57
  1025. scitex/scholar/zotero/__init__.py +1 -1
  1026. scitex/security/cli.py +7 -20
  1027. scitex/security/github.py +45 -32
  1028. scitex/session/__init__.py +8 -9
  1029. scitex/session/_decorator.py +49 -42
  1030. scitex/session/_lifecycle.py +39 -39
  1031. scitex/session/_manager.py +24 -20
  1032. scitex/sh/__init__.py +4 -3
  1033. scitex/sh/_execute.py +10 -7
  1034. scitex/sh/_security.py +3 -3
  1035. scitex/sh/_types.py +2 -3
  1036. scitex/stats/__init__.py +174 -6
  1037. scitex/stats/_schema.py +42 -569
  1038. scitex/stats/auto/__init__.py +188 -0
  1039. scitex/stats/auto/_context.py +331 -0
  1040. scitex/stats/auto/_formatting.py +679 -0
  1041. scitex/stats/auto/_rules.py +901 -0
  1042. scitex/stats/auto/_selector.py +554 -0
  1043. scitex/stats/auto/_styles.py +721 -0
  1044. scitex/stats/correct/__init__.py +4 -4
  1045. scitex/stats/correct/_correct_bonferroni.py +43 -34
  1046. scitex/stats/correct/_correct_fdr.py +14 -40
  1047. scitex/stats/correct/_correct_fdr_.py +39 -46
  1048. scitex/stats/correct/_correct_holm.py +14 -32
  1049. scitex/stats/correct/_correct_sidak.py +36 -21
  1050. scitex/stats/descriptive/_circular.py +20 -21
  1051. scitex/stats/descriptive/_describe.py +19 -5
  1052. scitex/stats/descriptive/_nan.py +5 -7
  1053. scitex/stats/descriptive/_real.py +4 -3
  1054. scitex/stats/effect_sizes/__init__.py +10 -11
  1055. scitex/stats/effect_sizes/_cliffs_delta.py +35 -32
  1056. scitex/stats/effect_sizes/_cohens_d.py +30 -31
  1057. scitex/stats/effect_sizes/_epsilon_squared.py +19 -22
  1058. scitex/stats/effect_sizes/_eta_squared.py +23 -27
  1059. scitex/stats/effect_sizes/_prob_superiority.py +18 -21
  1060. scitex/stats/io/__init__.py +29 -0
  1061. scitex/stats/io/_bundle.py +156 -0
  1062. scitex/stats/posthoc/__init__.py +3 -3
  1063. scitex/stats/posthoc/_dunnett.py +75 -55
  1064. scitex/stats/posthoc/_games_howell.py +61 -43
  1065. scitex/stats/posthoc/_tukey_hsd.py +42 -34
  1066. scitex/stats/power/__init__.py +2 -2
  1067. scitex/stats/power/_power.py +56 -56
  1068. scitex/stats/tests/__init__.py +1 -1
  1069. scitex/stats/tests/correlation/__init__.py +1 -1
  1070. scitex/stats/tests/correlation/_test_pearson.py +28 -38
  1071. scitex/stats/utils/__init__.py +14 -17
  1072. scitex/stats/utils/_effect_size.py +85 -78
  1073. scitex/stats/utils/_formatters.py +49 -43
  1074. scitex/stats/utils/_normalizers.py +7 -14
  1075. scitex/stats/utils/_power.py +56 -56
  1076. scitex/str/__init__.py +1 -0
  1077. scitex/str/_clean_path.py +3 -3
  1078. scitex/str/_factor_out_digits.py +86 -58
  1079. scitex/str/_format_plot_text.py +180 -111
  1080. scitex/str/_latex.py +19 -19
  1081. scitex/str/_latex_fallback.py +9 -10
  1082. scitex/str/_parse.py +3 -6
  1083. scitex/str/_print_debug.py +13 -13
  1084. scitex/str/_printc.py +2 -0
  1085. scitex/str/_search.py +3 -3
  1086. scitex/template/.legacy/_clone_project.py +9 -13
  1087. scitex/template/__init__.py +10 -2
  1088. scitex/template/_clone_project.py +7 -2
  1089. scitex/template/_copy.py +1 -0
  1090. scitex/template/_customize.py +3 -6
  1091. scitex/template/_git_strategy.py +2 -3
  1092. scitex/template/_rename.py +1 -0
  1093. scitex/template/clone_pip_project.py +6 -7
  1094. scitex/template/clone_research.py +7 -10
  1095. scitex/template/clone_singularity.py +6 -7
  1096. scitex/template/clone_writer_directory.py +6 -7
  1097. scitex/tex/__init__.py +4 -0
  1098. scitex/tex/_export.py +890 -0
  1099. scitex/tex/_preview.py +26 -11
  1100. scitex/tex/_to_vec.py +10 -7
  1101. scitex/torch/__init__.py +11 -1
  1102. scitex/types/_ArrayLike.py +2 -0
  1103. scitex/types/_is_listed_X.py +3 -3
  1104. scitex/units.py +110 -77
  1105. scitex/utils/_compress_hdf5.py +3 -3
  1106. scitex/utils/_email.py +8 -4
  1107. scitex/utils/_notify.py +14 -8
  1108. scitex/utils/_search.py +6 -6
  1109. scitex/utils/_verify_scitex_format.py +17 -42
  1110. scitex/utils/_verify_scitex_format_v01.py +12 -34
  1111. scitex/utils/template.py +4 -3
  1112. scitex/web/__init__.py +7 -1
  1113. scitex/web/_scraping.py +54 -38
  1114. scitex/web/_search_pubmed.py +30 -14
  1115. scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
  1116. scitex/writer/.legacy/_compile.py +18 -28
  1117. scitex/writer/Writer.py +8 -21
  1118. scitex/writer/__init__.py +11 -11
  1119. scitex/writer/_clone_writer_project.py +2 -6
  1120. scitex/writer/_compile/__init__.py +1 -0
  1121. scitex/writer/_compile/_parser.py +1 -0
  1122. scitex/writer/_compile/_runner.py +35 -38
  1123. scitex/writer/_compile/_validator.py +1 -0
  1124. scitex/writer/_compile/manuscript.py +1 -0
  1125. scitex/writer/_compile/revision.py +1 -0
  1126. scitex/writer/_compile/supplementary.py +1 -0
  1127. scitex/writer/_compile_async.py +5 -12
  1128. scitex/writer/_project/__init__.py +1 -0
  1129. scitex/writer/_project/_create.py +10 -25
  1130. scitex/writer/_project/_trees.py +4 -9
  1131. scitex/writer/_project/_validate.py +2 -3
  1132. scitex/writer/_validate_tree_structures.py +7 -18
  1133. scitex/writer/dataclasses/__init__.py +8 -10
  1134. scitex/writer/dataclasses/config/_CONSTANTS.py +2 -3
  1135. scitex/writer/dataclasses/config/_WriterConfig.py +4 -9
  1136. scitex/writer/dataclasses/contents/_ManuscriptContents.py +14 -25
  1137. scitex/writer/dataclasses/contents/_RevisionContents.py +21 -16
  1138. scitex/writer/dataclasses/contents/_SupplementaryContents.py +21 -24
  1139. scitex/writer/dataclasses/core/_Document.py +2 -3
  1140. scitex/writer/dataclasses/core/_DocumentSection.py +8 -23
  1141. scitex/writer/dataclasses/results/_CompilationResult.py +2 -3
  1142. scitex/writer/dataclasses/results/_LaTeXIssue.py +3 -6
  1143. scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
  1144. scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
  1145. scitex/writer/dataclasses/tree/_ConfigTree.py +7 -4
  1146. scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
  1147. scitex/writer/dataclasses/tree/_RevisionTree.py +16 -17
  1148. scitex/writer/dataclasses/tree/_ScriptsTree.py +10 -5
  1149. scitex/writer/dataclasses/tree/_SharedTree.py +10 -13
  1150. scitex/writer/dataclasses/tree/_SupplementaryTree.py +15 -14
  1151. scitex/writer/utils/.legacy_git_retry.py +3 -8
  1152. scitex/writer/utils/_parse_latex_logs.py +2 -3
  1153. scitex/writer/utils/_parse_script_args.py +20 -23
  1154. scitex/writer/utils/_watch.py +5 -5
  1155. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/METADATA +14 -10
  1156. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/RECORD +1149 -985
  1157. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
  1158. scitex/io/memo.md +0 -2827
  1159. scitex/plt/_subplots/TODO.md +0 -53
  1160. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +0 -537
  1161. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +0 -1499
  1162. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +0 -431
  1163. scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
  1164. scitex/vis/__init__.py +0 -177
  1165. scitex/vis/editor/_defaults.py +0 -244
  1166. scitex/vis/editor/_edit.py +0 -378
  1167. scitex/vis/editor/flask_editor/__init__.py +0 -21
  1168. scitex/vis/editor/flask_editor/bbox.py +0 -216
  1169. scitex/vis/editor/flask_editor/core.py +0 -152
  1170. scitex/vis/editor/flask_editor/plotter.py +0 -130
  1171. scitex/vis/editor/flask_editor/renderer.py +0 -184
  1172. scitex/vis/editor/flask_editor/templates/html.py +0 -295
  1173. scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
  1174. scitex/vis/editor/flask_editor/templates/styles.py +0 -549
  1175. /scitex/{vis → fig}/README.md +0 -0
  1176. /scitex/{vis → fig}/docs/CANVAS_ARCHITECTURE.md +0 -0
  1177. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/WHEEL +0 -0
  1178. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/entry_points.txt +0 -0
  1179. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/licenses/LICENSE +0 -0
@@ -6,37 +6,50 @@
6
6
  import os
7
7
  import pandas as pd
8
8
 
9
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
10
+ from ._format_plot import _parse_tracking_id
11
+
9
12
  __FILE__ = __file__
10
13
  __DIR__ = os.path.dirname(__FILE__)
11
14
  # ----------------------------------------
12
15
 
16
+
13
17
  def _format_plot_ecdf(id, tracked_dict, kwargs):
14
18
  """Format data from a stx_ecdf call.
15
-
19
+
16
20
  Args:
17
21
  id (str): Identifier for the plot
18
22
  tracked_dict (dict): Dictionary containing 'ecdf_df' key with ECDF data
19
23
  kwargs (dict): Keyword arguments passed to stx_ecdf
20
-
24
+
21
25
  Returns:
22
26
  pd.DataFrame: Formatted ECDF data
23
27
  """
24
28
  # Check if tracked_dict is empty or not a dictionary
25
29
  if not tracked_dict or not isinstance(tracked_dict, dict):
26
30
  return pd.DataFrame()
27
-
31
+
28
32
  # Get the ecdf_df from tracked_dict
29
- ecdf_df = tracked_dict.get('ecdf_df')
30
-
33
+ ecdf_df = tracked_dict.get("ecdf_df")
34
+
31
35
  if ecdf_df is None or not isinstance(ecdf_df, pd.DataFrame):
32
36
  return pd.DataFrame()
33
-
37
+
34
38
  # Create a copy to avoid modifying the original
35
39
  result = ecdf_df.copy()
36
-
40
+
37
41
  # Add prefix to column names if ID is provided
38
42
  if id is not None:
39
- # Rename columns with ID prefix
40
- result.columns = [f"{id}_ecdf_{col}" for col in result.columns]
41
-
42
- return result
43
+ # Parse the tracking ID to get axes position and trace ID
44
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
45
+
46
+ # Rename columns using single source of truth
47
+ renamed = {}
48
+ for col in result.columns:
49
+ # Use the original column name as the variable (e.g., "ecdf_value", "ecdf_prob")
50
+ renamed[col] = get_csv_column_name(
51
+ f"ecdf_{col}", ax_row, ax_col, trace_id=trace_id
52
+ )
53
+ result = result.rename(columns=renamed)
54
+
55
+ return result
@@ -0,0 +1,120 @@
1
+ #!/usr/bin/env python3
2
+ # -*- coding: utf-8 -*-
3
+ """CSV formatter for stx_errorbar() calls."""
4
+
5
+ import pandas as pd
6
+ import numpy as np
7
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
8
+ from ._format_plot import _parse_tracking_id
9
+
10
+
11
+ def _format_stx_errorbar(id, tracked_dict, kwargs):
12
+ """Format data from stx_errorbar call for CSV export.
13
+
14
+ Parameters
15
+ ----------
16
+ id : str
17
+ Tracking identifier
18
+ tracked_dict : dict
19
+ Dictionary containing tracked data with 'errorbar_df' key
20
+ kwargs : dict
21
+ Additional keyword arguments (may contain yerr, xerr)
22
+
23
+ Returns
24
+ -------
25
+ pd.DataFrame
26
+ Formatted errorbar data with standardized column names
27
+ """
28
+ if not tracked_dict or not isinstance(tracked_dict, dict):
29
+ return pd.DataFrame()
30
+
31
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
32
+
33
+ # Get errorbar_df from tracked data
34
+ errorbar_df = tracked_dict.get("errorbar_df")
35
+ if errorbar_df is not None and isinstance(errorbar_df, pd.DataFrame):
36
+ result = errorbar_df.copy()
37
+ renamed = {}
38
+
39
+ # Map columns to standardized names
40
+ for col in result.columns:
41
+ if col == "x":
42
+ renamed[col] = get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id)
43
+ elif col == "y":
44
+ renamed[col] = get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id)
45
+ elif col == "yerr":
46
+ # Check if yerr is asymmetric (tuple/list of 2)
47
+ yerr_value = result[col].iloc[0] if len(result) > 0 else None
48
+ if isinstance(yerr_value, (list, tuple)) and len(yerr_value) == 2:
49
+ # Handle asymmetric yerr separately below
50
+ continue
51
+ else:
52
+ renamed[col] = get_csv_column_name("yerr", ax_row, ax_col, trace_id=trace_id)
53
+ elif col == "xerr":
54
+ # Check if xerr is asymmetric (tuple/list of 2)
55
+ xerr_value = result[col].iloc[0] if len(result) > 0 else None
56
+ if isinstance(xerr_value, (list, tuple)) and len(xerr_value) == 2:
57
+ # Handle asymmetric xerr separately below
58
+ continue
59
+ else:
60
+ renamed[col] = get_csv_column_name("xerr", ax_row, ax_col, trace_id=trace_id)
61
+ else:
62
+ renamed[col] = get_csv_column_name(col, ax_row, ax_col, trace_id=trace_id)
63
+
64
+ result = result.rename(columns=renamed)
65
+
66
+ # Handle asymmetric error bars if needed from kwargs
67
+ yerr = kwargs.get("yerr") if kwargs else None
68
+ xerr = kwargs.get("xerr") if kwargs else None
69
+
70
+ if yerr is not None and isinstance(yerr, (list, tuple)) and len(yerr) == 2:
71
+ col_yerr_neg = get_csv_column_name("yerr-neg", ax_row, ax_col, trace_id=trace_id)
72
+ col_yerr_pos = get_csv_column_name("yerr-pos", ax_row, ax_col, trace_id=trace_id)
73
+ result[col_yerr_neg] = yerr[0]
74
+ result[col_yerr_pos] = yerr[1]
75
+
76
+ if xerr is not None and isinstance(xerr, (list, tuple)) and len(xerr) == 2:
77
+ col_xerr_neg = get_csv_column_name("xerr-neg", ax_row, ax_col, trace_id=trace_id)
78
+ col_xerr_pos = get_csv_column_name("xerr-pos", ax_row, ax_col, trace_id=trace_id)
79
+ result[col_xerr_neg] = xerr[0]
80
+ result[col_xerr_pos] = xerr[1]
81
+
82
+ return result
83
+
84
+ # Fallback to args if errorbar_df not found
85
+ args = tracked_dict.get("args", [])
86
+ if len(args) >= 2:
87
+ col_x = get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id)
88
+ col_y = get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id)
89
+ data = {col_x: args[0], col_y: args[1]}
90
+
91
+ # Add error bars if present
92
+ yerr = kwargs.get("yerr") if kwargs else None
93
+ xerr = kwargs.get("xerr") if kwargs else None
94
+
95
+ if yerr is not None:
96
+ if isinstance(yerr, (list, tuple)) and len(yerr) == 2:
97
+ col_yerr_neg = get_csv_column_name("yerr-neg", ax_row, ax_col, trace_id=trace_id)
98
+ col_yerr_pos = get_csv_column_name("yerr-pos", ax_row, ax_col, trace_id=trace_id)
99
+ data[col_yerr_neg] = yerr[0]
100
+ data[col_yerr_pos] = yerr[1]
101
+ else:
102
+ col_yerr = get_csv_column_name("yerr", ax_row, ax_col, trace_id=trace_id)
103
+ data[col_yerr] = yerr
104
+
105
+ if xerr is not None:
106
+ if isinstance(xerr, (list, tuple)) and len(xerr) == 2:
107
+ col_xerr_neg = get_csv_column_name("xerr-neg", ax_row, ax_col, trace_id=trace_id)
108
+ col_xerr_pos = get_csv_column_name("xerr-pos", ax_row, ax_col, trace_id=trace_id)
109
+ data[col_xerr_neg] = xerr[0]
110
+ data[col_xerr_pos] = xerr[1]
111
+ else:
112
+ col_xerr = get_csv_column_name("xerr", ax_row, ax_col, trace_id=trace_id)
113
+ data[col_xerr] = xerr
114
+
115
+ return pd.DataFrame(data)
116
+
117
+ return pd.DataFrame()
118
+
119
+
120
+ # EOF
@@ -1,45 +1,52 @@
1
1
  #!/usr/bin/env python3
2
2
  # -*- coding: utf-8 -*-
3
- # Timestamp: "2025-05-18 18:14:26 (ywatanabe)"
4
- # File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_fillv.py
5
- # ----------------------------------------
6
- import os
7
- __FILE__ = __file__
8
- __DIR__ = os.path.dirname(__FILE__)
9
- # ----------------------------------------
3
+ # Timestamp: "2025-12-10 12:00:00 (ywatanabe)"
4
+ # File: ./src/scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_fillv.py
5
+
6
+ """CSV formatter for stx_fillv() calls - uses standard column naming."""
10
7
 
11
8
  import numpy as np
12
9
  import pandas as pd
13
10
 
11
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
12
+
13
+ from ._format_plot import _parse_tracking_id
14
+
15
+
14
16
  def _format_plot_fillv(id, tracked_dict, kwargs):
15
17
  """Format data from a stx_fillv call.
16
-
18
+
17
19
  Formats data similar to line plot format for better compatibility.
18
-
20
+ Uses standard column naming convention:
21
+ (ax-row-{r}-col-{c}_trace-id-{id}_variable-{var}).
22
+
19
23
  Args:
20
24
  id (str): Identifier for the plot
21
25
  tracked_dict (dict): Dictionary containing tracked data
22
26
  kwargs (dict): Keyword arguments passed to stx_fillv
23
-
27
+
24
28
  Returns:
25
29
  pd.DataFrame: Formatted fillv data in a long-format dataframe
26
30
  """
27
31
  # Check if tracked_dict is empty or not a dictionary
28
32
  if not tracked_dict or not isinstance(tracked_dict, dict):
29
33
  return pd.DataFrame()
30
-
34
+
35
+ # Parse tracking ID to get axes position
36
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
37
+
31
38
  # Try to get starts/ends directly from tracked_dict first
32
- starts = tracked_dict.get('starts')
33
- ends = tracked_dict.get('ends')
34
-
39
+ starts = tracked_dict.get("starts")
40
+ ends = tracked_dict.get("ends")
41
+
35
42
  # If not found, get from args
36
43
  if starts is None or ends is None:
37
- args = tracked_dict.get('args', [])
38
-
44
+ args = tracked_dict.get("args", [])
45
+
39
46
  # Extract data if available from args
40
47
  if len(args) >= 2:
41
48
  starts, ends = args[0], args[1]
42
-
49
+
43
50
  # If we have valid starts and ends, create a DataFrame in a format similar to line plot
44
51
  if starts is not None and ends is not None:
45
52
  # Convert to numpy arrays if they're lists for better handling
@@ -47,22 +54,19 @@ def _format_plot_fillv(id, tracked_dict, kwargs):
47
54
  starts = np.array(starts)
48
55
  if isinstance(ends, list):
49
56
  ends = np.array(ends)
50
-
57
+
58
+ # Get standard column names
59
+ x_col = get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id)
60
+ y_col = get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id)
61
+ type_col = get_csv_column_name("type", ax_row, ax_col, trace_id=trace_id)
62
+
51
63
  # Create a DataFrame with x, y pairs for each fill span
52
64
  rows = []
53
65
  for start, end in zip(starts, ends):
54
- rows.append({
55
- f"{id}_x": start,
56
- f"{id}_y": 0,
57
- f"{id}_type": "start"
58
- })
59
- rows.append({
60
- f"{id}_x": end,
61
- f"{id}_y": 0,
62
- f"{id}_type": "end"
63
- })
64
-
66
+ rows.append({x_col: start, y_col: 0, type_col: "start"})
67
+ rows.append({x_col: end, y_col: 0, type_col: "end"})
68
+
65
69
  if rows:
66
70
  return pd.DataFrame(rows)
67
-
68
- return pd.DataFrame()
71
+
72
+ return pd.DataFrame()
@@ -4,6 +4,7 @@
4
4
  # File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_heatmap.py
5
5
  # ----------------------------------------
6
6
  import os
7
+
7
8
  __FILE__ = __file__
8
9
  __DIR__ = os.path.dirname(__FILE__)
9
10
  # ----------------------------------------
@@ -11,54 +12,63 @@ __DIR__ = os.path.dirname(__FILE__)
11
12
  import numpy as np
12
13
  import pandas as pd
13
14
 
15
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
16
+ from ._format_plot import _parse_tracking_id
17
+
18
+
14
19
  def _format_plot_heatmap(id, tracked_dict, kwargs):
15
20
  """Format data from a stx_heatmap call.
16
-
21
+
17
22
  Exports heatmap data in xyz format (x, y, value) for better compatibility.
18
-
23
+
19
24
  Args:
20
25
  id (str): Identifier for the plot
21
26
  tracked_dict (dict): Dictionary containing tracked data
22
27
  kwargs (dict): Keyword arguments passed to stx_heatmap
23
-
28
+
24
29
  Returns:
25
30
  pd.DataFrame: Formatted heatmap data in xyz format
26
31
  """
27
32
  # Check if tracked_dict is empty or not a dictionary
28
33
  if not tracked_dict or not isinstance(tracked_dict, dict):
29
34
  return pd.DataFrame()
30
-
35
+
31
36
  # Extract data from tracked_dict
32
- data = tracked_dict.get('data')
33
- x_labels = tracked_dict.get('x_labels')
34
- y_labels = tracked_dict.get('y_labels')
35
-
37
+ data = tracked_dict.get("data")
38
+ x_labels = tracked_dict.get("x_labels")
39
+ y_labels = tracked_dict.get("y_labels")
40
+
36
41
  if data is not None and hasattr(data, "shape") and len(data.shape) == 2:
37
42
  rows, cols = data.shape
38
- row_indices, col_indices = np.meshgrid(
39
- range(rows), range(cols), indexing="ij"
40
- )
41
-
42
- # Format data in xyz format (x, y, value)
43
+ row_indices, col_indices = np.meshgrid(range(rows), range(cols), indexing="ij")
44
+
45
+ # Parse the tracking ID to get axes position and trace ID
46
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
47
+
48
+ # Format data in xyz format (x, y, value) using single source of truth
43
49
  df = pd.DataFrame(
44
50
  {
45
- f"{id}_x": col_indices.flatten(), # x is column
46
- f"{id}_y": row_indices.flatten(), # y is row
47
- f"{id}_value": data.flatten(), # z is intensity/value
51
+ get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id): col_indices.flatten(), # x is column
52
+ get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id): row_indices.flatten(), # y is row
53
+ get_csv_column_name("value", ax_row, ax_col, trace_id=trace_id): data.flatten(), # z is intensity/value
48
54
  }
49
55
  )
50
-
56
+
51
57
  # Add label information if available
52
58
  if x_labels is not None and len(x_labels) == cols:
53
59
  # Map column indices to x labels (columns are x)
54
60
  x_label_map = {i: label for i, label in enumerate(x_labels)}
55
- df[f"{id}_x_label"] = df[f"{id}_x"].map(x_label_map)
56
-
61
+ x_col_name = get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id)
62
+ x_label_col_name = get_csv_column_name("x_label", ax_row, ax_col, trace_id=trace_id)
63
+ df[x_label_col_name] = df[x_col_name].map(x_label_map)
64
+
57
65
  if y_labels is not None and len(y_labels) == rows:
58
66
  # Map row indices to y labels (rows are y)
59
67
  y_label_map = {i: label for i, label in enumerate(y_labels)}
60
- df[f"{id}_y_label"] = df[f"{id}_y"].map(y_label_map)
61
-
68
+ y_col_name = get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id)
69
+ y_label_col_name = get_csv_column_name("y_label", ax_row, ax_col, trace_id=trace_id)
70
+ df[y_label_col_name] = df[y_col_name].map(y_label_map)
71
+
62
72
  return df
63
-
64
- return pd.DataFrame()
73
+
74
+ return pd.DataFrame()
@@ -7,28 +7,35 @@ import os
7
7
  import numpy as np
8
8
  import pandas as pd
9
9
 
10
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
11
+ from ._format_plot import _parse_tracking_id
12
+
10
13
  __FILE__ = __file__
11
14
  __DIR__ = os.path.dirname(__FILE__)
12
15
  # ----------------------------------------
13
16
 
17
+
14
18
  def _format_plot_image(id, tracked_dict, kwargs):
15
19
  """Format data from a stx_image call.
16
-
20
+
17
21
  Exports image data in long-format xyz format for better compatibility.
18
22
  Also saves channel data for RGB/RGBA images.
19
-
23
+
20
24
  Args:
21
25
  id (str or int): Identifier for the plot
22
26
  tracked_dict (dict): Dictionary containing tracked data
23
27
  kwargs (dict): Keyword arguments passed to stx_image
24
-
28
+
25
29
  Returns:
26
30
  pd.DataFrame: Formatted image data in xyz format
27
31
  """
28
32
  # Check if tracked_dict is not a dictionary or is empty
29
33
  if not tracked_dict or not isinstance(tracked_dict, dict):
30
34
  return pd.DataFrame()
31
-
35
+
36
+ # Parse the tracking ID to get axes position and trace ID
37
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
38
+
32
39
  # Check if image_df is available and use it if present
33
40
  if "image_df" in tracked_dict:
34
41
  image_df = tracked_dict.get("image_df")
@@ -36,17 +43,21 @@ def _format_plot_image(id, tracked_dict, kwargs):
36
43
  # Add prefix if ID is provided
37
44
  if id is not None:
38
45
  image_df = image_df.copy()
39
- id_str = str(id)
40
- # Convert columns to strings first to handle integer column names
41
- image_df.columns = [str(col) for col in image_df.columns]
42
- image_df.columns = [f"{id_str}_{col}" if not col.startswith(f"{id_str}_") else col for col in image_df.columns]
46
+ # Rename columns using single source of truth
47
+ renamed = {}
48
+ for col in image_df.columns:
49
+ # Convert to string to handle integer column names
50
+ col_str = str(col)
51
+ renamed[col] = get_csv_column_name(
52
+ col_str, ax_row, ax_col, trace_id=trace_id
53
+ )
54
+ image_df = image_df.rename(columns=renamed)
43
55
  return image_df
44
-
56
+
45
57
  # If we have image data
46
58
  if "image" in tracked_dict:
47
59
  img = tracked_dict["image"]
48
- id_str = str(id) if id is not None else "image"
49
-
60
+
50
61
  # Handle 2D grayscale images - create xyz format (x, y, value)
51
62
  if isinstance(img, np.ndarray) and img.ndim == 2:
52
63
  rows, cols = img.shape
@@ -54,12 +65,12 @@ def _format_plot_image(id, tracked_dict, kwargs):
54
65
  range(rows), range(cols), indexing="ij"
55
66
  )
56
67
 
57
- # Create xyz format
68
+ # Create xyz format using single source of truth
58
69
  df = pd.DataFrame(
59
70
  {
60
- f"{id_str}_x": col_indices.flatten(), # x is column
61
- f"{id_str}_y": row_indices.flatten(), # y is row
62
- f"{id_str}_value": img.flatten(), # z is intensity
71
+ get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id): col_indices.flatten(), # x is column
72
+ get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id): row_indices.flatten(), # y is row
73
+ get_csv_column_name("value", ax_row, ax_col, trace_id=trace_id): img.flatten(), # z is intensity
63
74
  }
64
75
  )
65
76
  return df
@@ -67,27 +78,32 @@ def _format_plot_image(id, tracked_dict, kwargs):
67
78
  # Handle RGB/RGBA images - create xyz format with additional channel information
68
79
  elif isinstance(img, np.ndarray) and img.ndim == 3:
69
80
  rows, cols, channels = img.shape
70
- row_indices, col_indices = np.meshgrid(
71
- range(rows), range(cols), indexing="ij"
72
- )
73
81
 
74
82
  # Create a list to hold rows for a long-format DataFrame
75
83
  data_rows = []
76
84
  channel_names = ["r", "g", "b", "a"]
77
-
85
+
86
+ # Get column names using single source of truth
87
+ x_col = get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id)
88
+ y_col = get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id)
89
+ channel_col = get_csv_column_name("channel", ax_row, ax_col, trace_id=trace_id)
90
+ value_col = get_csv_column_name("value", ax_row, ax_col, trace_id=trace_id)
91
+
78
92
  # Create long-format data (x, y, channel, value)
79
93
  for r in range(rows):
80
94
  for c in range(cols):
81
95
  for ch in range(min(channels, len(channel_names))):
82
- data_rows.append({
83
- f"{id_str}_x": c, # x is column
84
- f"{id_str}_y": r, # y is row
85
- f"{id_str}_channel": channel_names[ch], # channel name
86
- f"{id_str}_value": img[r, c, ch] # channel value
87
- })
88
-
96
+ data_rows.append(
97
+ {
98
+ x_col: c, # x is column
99
+ y_col: r, # y is row
100
+ channel_col: channel_names[ch], # channel name
101
+ value_col: img[r, c, ch], # channel value
102
+ }
103
+ )
104
+
89
105
  # Return long-format DataFrame
90
106
  return pd.DataFrame(data_rows)
91
-
107
+
92
108
  # Skip CSV export if no suitable data format found
93
- return pd.DataFrame()
109
+ return pd.DataFrame()
@@ -0,0 +1,63 @@
1
+ #!/usr/bin/env python3
2
+ # -*- coding: utf-8 -*-
3
+ """CSV formatter for stx_imshow() calls."""
4
+
5
+ import numpy as np
6
+ import pandas as pd
7
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
8
+ from ._format_plot import _parse_tracking_id
9
+
10
+
11
+ def _format_stx_imshow(id, tracked_dict, kwargs):
12
+ """Format data from stx_imshow call for CSV export.
13
+
14
+ Parameters
15
+ ----------
16
+ id : str
17
+ Identifier for the plot
18
+ tracked_dict : dict
19
+ Dictionary containing tracked data with 'imshow_df'
20
+ kwargs : dict
21
+ Keyword arguments passed to stx_imshow
22
+
23
+ Returns
24
+ -------
25
+ pd.DataFrame
26
+ Formatted imshow data in row, col, value format (or row, col, R, G, B for RGB)
27
+ """
28
+ if not tracked_dict or not isinstance(tracked_dict, dict):
29
+ return pd.DataFrame()
30
+
31
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
32
+
33
+ # Get imshow_df from tracked_dict
34
+ imshow_df = tracked_dict.get("imshow_df")
35
+ if imshow_df is not None and isinstance(imshow_df, pd.DataFrame):
36
+ # Convert from 2D DataFrame format (with col_0, col_1, ... columns)
37
+ # to row, col, value format for easier analysis
38
+ n_rows, n_cols = imshow_df.shape
39
+
40
+ # Create row and column indices
41
+ row_indices = np.repeat(np.arange(n_rows), n_cols)
42
+ col_indices = np.tile(np.arange(n_cols), n_rows)
43
+
44
+ # Get column names from single source of truth
45
+ col_row = get_csv_column_name("row", ax_row, ax_col, trace_id=trace_id)
46
+ col_col = get_csv_column_name("col", ax_row, ax_col, trace_id=trace_id)
47
+ col_value = get_csv_column_name("value", ax_row, ax_col, trace_id=trace_id)
48
+
49
+ # Flatten the DataFrame values
50
+ values = imshow_df.values.flatten()
51
+
52
+ result = pd.DataFrame({
53
+ col_row: row_indices,
54
+ col_col: col_indices,
55
+ col_value: values
56
+ })
57
+
58
+ return result
59
+
60
+ return pd.DataFrame()
61
+
62
+
63
+ # EOF
@@ -4,6 +4,7 @@
4
4
  # File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_joyplot.py
5
5
  # ----------------------------------------
6
6
  import os
7
+
7
8
  __FILE__ = __file__
8
9
  __DIR__ = os.path.dirname(__FILE__)
9
10
  # ----------------------------------------
@@ -11,25 +12,31 @@ __DIR__ = os.path.dirname(__FILE__)
11
12
  import numpy as np
12
13
  import pandas as pd
13
14
  from scitex.pd import force_df
15
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
16
+ from ._format_plot import _parse_tracking_id
17
+
14
18
 
15
19
  def _format_plot_joyplot(id, tracked_dict, kwargs):
16
20
  """Format data from a stx_joyplot call.
17
-
21
+
18
22
  Args:
19
23
  id (str): Identifier for the plot
20
24
  tracked_dict (dict): Dictionary containing 'joyplot_data' key with joyplot data
21
25
  kwargs (dict): Keyword arguments passed to stx_joyplot
22
-
26
+
23
27
  Returns:
24
28
  pd.DataFrame: Formatted joyplot data
25
29
  """
26
30
  # Check if tracked_dict is empty or not a dictionary
27
31
  if not tracked_dict or not isinstance(tracked_dict, dict):
28
32
  return pd.DataFrame()
29
-
33
+
34
+ # Parse tracking ID to get axes position and trace ID
35
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
36
+
30
37
  # Get joyplot_data from tracked_dict
31
- data = tracked_dict.get('joyplot_data')
32
-
38
+ data = tracked_dict.get("joyplot_data")
39
+
33
40
  if data is None:
34
41
  return pd.DataFrame()
35
42
 
@@ -37,16 +44,22 @@ def _format_plot_joyplot(id, tracked_dict, kwargs):
37
44
  if isinstance(data, pd.DataFrame):
38
45
  # Make a copy to avoid modifying original
39
46
  result = data.copy()
40
- # Add prefix to column names if ID is provided
47
+ # Add prefix to column names using single source of truth
41
48
  if id is not None:
42
- result.columns = [f"{id}_joyplot_{col}" for col in result.columns]
49
+ result.columns = [
50
+ get_csv_column_name(f"joyplot-{col}", ax_row, ax_col, trace_id=trace_id)
51
+ for col in result.columns
52
+ ]
43
53
  return result
44
54
 
45
55
  elif isinstance(data, dict):
46
56
  # Convert dictionary to DataFrame
47
57
  result = pd.DataFrame()
48
58
  for group, values in data.items():
49
- result[f"{id}_joyplot_{group}"] = pd.Series(values)
59
+ col_name = get_csv_column_name(
60
+ f"joyplot-{group}", ax_row, ax_col, trace_id=trace_id
61
+ )
62
+ result[col_name] = pd.Series(values)
50
63
  return result
51
64
 
52
65
  elif isinstance(data, (list, tuple)) and all(
@@ -55,11 +68,17 @@ def _format_plot_joyplot(id, tracked_dict, kwargs):
55
68
  # Convert list of arrays to DataFrame
56
69
  result = pd.DataFrame()
57
70
  for i, values in enumerate(data):
58
- result[f"{id}_joyplot_group{i:02d}"] = pd.Series(values)
71
+ col_name = get_csv_column_name(
72
+ f"joyplot-group{i:02d}", ax_row, ax_col, trace_id=trace_id
73
+ )
74
+ result[col_name] = pd.Series(values)
59
75
  return result
60
-
76
+
61
77
  # Try to force to DataFrame as a last resort
62
78
  try:
63
- return force_df({f"{id}_joyplot_data": data})
79
+ col_name = get_csv_column_name(
80
+ "joyplot-data", ax_row, ax_col, trace_id=trace_id
81
+ )
82
+ return force_df({col_name: data})
64
83
  except:
65
- return pd.DataFrame()
84
+ return pd.DataFrame()