tomwer 1.3.27__py3-none-any.whl → 1.4.0rc0__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 (632) hide show
  1. orangecontrib/tomwer/orange/managedprocess.py +1 -29
  2. orangecontrib/tomwer/orange/settings.py +2 -28
  3. orangecontrib/tomwer/tests/TestAcquisition.py +220 -0
  4. orangecontrib/tomwer/tutorials/append_raw_darks_and_flats_frames_to_NXtomos.ows +2 -2
  5. orangecontrib/tomwer/tutorials/copy_reduced_darks_and_flats_meth1.ows +1 -1
  6. orangecontrib/tomwer/tutorials/{icat_publication.ows → drac_publication.ows} +7 -21
  7. orangecontrib/tomwer/tutorials/id16b/ID16b_full_volume.ows +22 -0
  8. orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows +302 -0
  9. orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows +218 -0
  10. orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows +29 -24
  11. orangecontrib/tomwer/tutorials/test_cor.ows +19 -0
  12. orangecontrib/tomwer/tutorials/volume_casting_on_slurm.ows +54 -0
  13. orangecontrib/tomwer/widgets/__init__.py +3 -5
  14. orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py +35 -54
  15. orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py +1 -31
  16. orangecontrib/tomwer/widgets/control/AdvancementOW.py +1 -29
  17. orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py +5 -4
  18. orangecontrib/tomwer/widgets/control/DataListenerOW.py +1 -29
  19. orangecontrib/tomwer/widgets/control/DataSelectorOW.py +11 -30
  20. orangecontrib/tomwer/widgets/control/DataTransfertOW.py +2 -28
  21. orangecontrib/tomwer/widgets/control/DataValidatorOW.py +1 -28
  22. orangecontrib/tomwer/widgets/control/DataWatcherOW.py +1 -28
  23. orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py +48 -51
  24. orangecontrib/tomwer/widgets/control/EmailOW.py +12 -2
  25. orangecontrib/tomwer/widgets/control/FilterOW.py +1 -28
  26. orangecontrib/tomwer/widgets/control/NXTomomillOW.py +37 -53
  27. orangecontrib/tomwer/widgets/control/NXtomoConcatenate.py +21 -20
  28. orangecontrib/tomwer/widgets/control/NotifierOW.py +9 -28
  29. orangecontrib/tomwer/widgets/control/ReduceDarkFlatSelectorOW.py +3 -2
  30. orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py +1 -27
  31. orangecontrib/tomwer/widgets/control/TimerOW.py +9 -28
  32. orangecontrib/tomwer/widgets/control/TomoObjSeriesOW.py +58 -0
  33. orangecontrib/tomwer/widgets/control/VolumeSelector.py +8 -30
  34. orangecontrib/tomwer/widgets/control/icons/nxtomomill.svg +173 -119
  35. orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.png +0 -0
  36. orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.svg +55 -195
  37. orangecontrib/tomwer/widgets/control/icons/{tomoobjserie.svg → tomoobjseries.svg} +2 -2
  38. orangecontrib/tomwer/widgets/dataportal/PublishProcessedDataOW.py +172 -0
  39. orangecontrib/tomwer/widgets/{icat → dataportal}/__init__.py +2 -2
  40. orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py +2 -29
  41. orangecontrib/tomwer/widgets/debugtools/ObjectInspectorOW.py +1 -29
  42. orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py +48 -73
  43. orangecontrib/tomwer/widgets/edit/ImageKeyEditorOW.py +48 -75
  44. orangecontrib/tomwer/widgets/edit/ImageKeyUpgraderOW.py +5 -30
  45. orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py +51 -52
  46. orangecontrib/tomwer/widgets/other/PythonScriptOW.py +22 -10
  47. orangecontrib/tomwer/widgets/reconstruction/AxisOW.py +48 -49
  48. orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py +22 -68
  49. orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py +3 -30
  50. orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py +21 -19
  51. orangecontrib/tomwer/widgets/reconstruction/NabuOW.py +7 -70
  52. orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py +40 -85
  53. orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py +15 -40
  54. orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py +13 -35
  55. orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py +2 -30
  56. orangecontrib/tomwer/widgets/stitching/ZStitchingConfigOW.py +11 -11
  57. orangecontrib/tomwer/widgets/utils.py +2 -29
  58. orangecontrib/tomwer/widgets/visualization/DataViewerOW.py +1 -27
  59. orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py +1 -27
  60. orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py +1 -1
  61. orangecontrib/tomwer/widgets/visualization/RadioStackOW.py +2 -28
  62. orangecontrib/tomwer/widgets/visualization/SampleMovedOW.py +1 -27
  63. orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py +1 -27
  64. orangecontrib/tomwer/widgets/visualization/SliceStackOW.py +2 -28
  65. tomwer/__init__.py +3 -28
  66. tomwer/__main__.py +8 -4
  67. tomwer/app/__init__.py +2 -0
  68. tomwer/app/axis.py +8 -7
  69. tomwer/app/canvas.py +23 -29
  70. tomwer/app/canvas_launcher/config.py +14 -102
  71. tomwer/app/canvas_launcher/environ.py +5 -8
  72. tomwer/app/canvas_launcher/mainwindow.py +175 -69
  73. tomwer/app/canvas_launcher/splash.py +1 -3
  74. tomwer/app/canvas_launcher/utils.py +47 -0
  75. tomwer/app/canvas_launcher/widgetsscheme.py +3 -10
  76. tomwer/app/diffframe.py +2 -0
  77. tomwer/app/imagekeyeditor.py +2 -1
  78. tomwer/app/imagekeyupgrader.py +2 -0
  79. tomwer/app/multicor.py +5 -2
  80. tomwer/app/multipag.py +7 -4
  81. tomwer/app/nabuapp.py +2 -1
  82. tomwer/app/nxtomoeditor.py +17 -12
  83. tomwer/app/patchrawdarkflat.py +2 -0
  84. tomwer/app/radiostack.py +3 -2
  85. tomwer/app/reducedarkflat.py +3 -0
  86. tomwer/app/samplemoved.py +2 -0
  87. tomwer/app/scanviewer.py +2 -0
  88. tomwer/app/sinogramviewer.py +2 -0
  89. tomwer/app/slicestack.py +11 -13
  90. tomwer/app/stitching/common.py +431 -0
  91. tomwer/app/stopdatalistener.py +3 -0
  92. tomwer/app/ystitching.py +26 -0
  93. tomwer/app/zstitching.py +8 -363
  94. tomwer/core/__init__.py +2 -28
  95. tomwer/core/cluster/__init__.py +3 -0
  96. tomwer/core/cluster/cluster.py +10 -26
  97. tomwer/core/futureobject.py +17 -43
  98. tomwer/core/log/__init__.py +2 -0
  99. tomwer/core/log/processlog.py +0 -28
  100. tomwer/core/process/cluster/supervisor.py +52 -34
  101. tomwer/core/process/conditions/filters.py +3 -28
  102. tomwer/core/process/control/datalistener/datalistener.py +7 -75
  103. tomwer/core/process/control/datalistener/rpcserver.py +8 -38
  104. tomwer/core/process/control/datawatcher/datawatcher.py +11 -40
  105. tomwer/core/process/control/datawatcher/datawatcherobserver.py +30 -64
  106. tomwer/core/process/control/datawatcher/datawatcherprocess.py +11 -32
  107. tomwer/core/process/control/datawatcher/edfdwprocess.py +2 -27
  108. tomwer/core/process/control/datawatcher/hdf5dwprocess.py +1 -26
  109. tomwer/core/process/control/datawatcher/status.py +1 -26
  110. tomwer/core/process/control/emailnotifier.py +11 -23
  111. tomwer/core/process/control/nxtomoconcatenate.py +20 -18
  112. tomwer/core/process/control/nxtomomill.py +9 -44
  113. tomwer/core/process/control/scanlist.py +0 -27
  114. tomwer/core/process/control/scantransfer.py +15 -13
  115. tomwer/core/process/control/scanvalidator.py +4 -30
  116. tomwer/core/process/control/{test → tests}/test_concatenate_nxtomos.py +5 -5
  117. tomwer/core/process/control/timer.py +1 -27
  118. tomwer/core/process/control/tomoobjseries.py +12 -0
  119. tomwer/core/process/drac/binning.py +37 -0
  120. tomwer/core/process/drac/dracbase.py +170 -0
  121. tomwer/core/process/drac/gallery.py +109 -0
  122. tomwer/core/process/drac/output.py +12 -0
  123. tomwer/core/process/drac/processeddataset.py +147 -0
  124. tomwer/core/process/drac/publish.py +118 -0
  125. tomwer/core/process/drac/rawdataset.py +142 -0
  126. tomwer/core/process/drac/tests/test_gallery.py +71 -0
  127. tomwer/core/process/drac/tests/test_icat_processed_dataset.py +80 -0
  128. tomwer/core/process/drac/tests/test_icat_raw_dataset.py +90 -0
  129. tomwer/core/process/edit/darkflatpatch.py +1 -28
  130. tomwer/core/process/edit/imagekeyeditor.py +4 -32
  131. tomwer/core/process/edit/nxtomoeditor.py +307 -0
  132. tomwer/core/process/edit/tests/test_darkflatpatch.py +243 -0
  133. tomwer/core/process/edit/tests/test_imagekey_editor.py +99 -0
  134. tomwer/core/process/output.py +9 -2
  135. tomwer/core/process/reconstruction/__init__.py +0 -26
  136. tomwer/core/process/reconstruction/axis/anglemode.py +1 -29
  137. tomwer/core/process/reconstruction/axis/axis.py +63 -111
  138. tomwer/core/process/reconstruction/axis/mode.py +5 -3
  139. tomwer/core/process/reconstruction/axis/params.py +5 -146
  140. tomwer/core/process/reconstruction/axis/projectiontype.py +0 -28
  141. tomwer/core/process/reconstruction/darkref/darkrefs.py +14 -39
  142. tomwer/core/process/reconstruction/darkref/darkrefscopy.py +7 -39
  143. tomwer/core/process/reconstruction/darkref/params.py +1 -28
  144. tomwer/core/process/reconstruction/nabu/castvolume.py +19 -34
  145. tomwer/core/process/reconstruction/nabu/nabucommon.py +18 -43
  146. tomwer/core/process/reconstruction/nabu/nabuscores.py +47 -48
  147. tomwer/core/process/reconstruction/nabu/nabuslices.py +59 -105
  148. tomwer/core/process/reconstruction/nabu/nabuvolume.py +44 -70
  149. tomwer/core/process/reconstruction/nabu/plane.py +10 -0
  150. tomwer/core/process/reconstruction/nabu/settings.py +1 -28
  151. tomwer/core/process/reconstruction/nabu/target.py +0 -28
  152. tomwer/core/process/reconstruction/nabu/test/test_castvolume.py +116 -0
  153. tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py +277 -0
  154. tomwer/core/process/reconstruction/nabu/test/test_nabunormalization.py +199 -0
  155. tomwer/core/process/reconstruction/nabu/utils.py +11 -60
  156. tomwer/core/process/reconstruction/normalization/normalization.py +2 -32
  157. tomwer/core/process/reconstruction/normalization/params.py +3 -35
  158. tomwer/core/process/reconstruction/output.py +14 -19
  159. tomwer/core/process/reconstruction/paramsbase.py +4 -33
  160. tomwer/core/process/reconstruction/saaxis/params.py +5 -33
  161. tomwer/core/process/reconstruction/saaxis/saaxis.py +18 -47
  162. tomwer/core/process/reconstruction/sadeltabeta/params.py +2 -31
  163. tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +16 -44
  164. tomwer/core/process/reconstruction/scores/params.py +9 -39
  165. tomwer/core/process/reconstruction/scores/scores.py +10 -42
  166. tomwer/core/process/reconstruction/tests/__init__.py +0 -0
  167. tomwer/core/process/reconstruction/tests/test_axis.py +46 -0
  168. tomwer/core/process/reconstruction/tests/test_darkref.py +33 -0
  169. tomwer/core/process/reconstruction/{test → tests}/test_saaxis.py +1 -27
  170. tomwer/core/process/reconstruction/tests/test_sadeltabeta.py +48 -0
  171. tomwer/core/process/script/python.py +1 -27
  172. tomwer/core/process/script/tests/test_script.py +41 -0
  173. tomwer/core/process/stitching/metadataholder.py +5 -4
  174. tomwer/core/process/stitching/nabustitcher.py +35 -5
  175. tomwer/core/process/stitching/tests/test_metadataholder.py +17 -0
  176. tomwer/core/process/task.py +20 -63
  177. tomwer/core/process/tests/__init__.py +0 -0
  178. tomwer/core/process/{test → tests}/test_axis.py +1 -79
  179. tomwer/core/process/{test → tests}/test_conditions.py +1 -28
  180. tomwer/core/process/{test → tests}/test_dark_and_flat.py +1 -27
  181. tomwer/core/process/{test → tests}/test_data_listener.py +1 -27
  182. tomwer/core/process/{test → tests}/test_data_transfer.py +2 -28
  183. tomwer/core/process/{test → tests}/test_data_watcher.py +1 -27
  184. tomwer/core/process/{test → tests}/test_nabu.py +4 -33
  185. tomwer/core/process/{test → tests}/test_normalization.py +1 -26
  186. tomwer/core/process/{test → tests}/test_timer.py +1 -27
  187. tomwer/core/process/utils.py +2 -31
  188. tomwer/core/process/visualization/dataviewer.py +1 -26
  189. tomwer/core/process/visualization/diffviewer.py +1 -26
  190. tomwer/core/process/visualization/imagestackviewer.py +0 -26
  191. tomwer/core/process/visualization/radiostack.py +0 -26
  192. tomwer/core/process/visualization/samplemoved.py +0 -28
  193. tomwer/core/process/visualization/sinogramviewer.py +0 -27
  194. tomwer/core/process/visualization/slicestack.py +0 -28
  195. tomwer/core/process/visualization/tests/test_data_viewer.py +12 -0
  196. tomwer/core/process/visualization/tests/test_diff_viewer.py +12 -0
  197. tomwer/core/process/visualization/tests/test_image_stack_viewer.py +14 -0
  198. tomwer/core/process/visualization/tests/test_radio_stack.py +12 -0
  199. tomwer/core/process/visualization/tests/test_sample_moved.py +14 -0
  200. tomwer/core/process/visualization/tests/test_sinogram_viewer.py +13 -0
  201. tomwer/core/process/visualization/tests/test_slice_stack.py +13 -0
  202. tomwer/core/process/visualization/tests/test_volume_viewer.py +12 -0
  203. tomwer/core/process/visualization/volumeviewer.py +0 -29
  204. tomwer/core/scan/__init__.py +3 -27
  205. tomwer/core/scan/blissscan.py +5 -34
  206. tomwer/core/scan/edfscan.py +19 -53
  207. tomwer/core/scan/hdf5scan.py +2 -2
  208. tomwer/core/scan/nxtomoscan.py +46 -54
  209. tomwer/core/scan/scanbase.py +104 -200
  210. tomwer/core/scan/scanfactory.py +11 -41
  211. tomwer/core/scan/tests/__init__.py +0 -0
  212. tomwer/core/scan/tests/test_edf.py +25 -0
  213. tomwer/core/scan/tests/test_future_scan.py +35 -0
  214. tomwer/core/scan/tests/test_nxtomoscan.py +143 -0
  215. tomwer/core/scan/{test → tests}/test_process_registration.py +1 -28
  216. tomwer/core/settings.py +18 -40
  217. tomwer/core/tests/__init__.py +0 -0
  218. tomwer/core/tests/test_scanutils.py +26 -0
  219. tomwer/core/{test → tests}/test_utils.py +1 -28
  220. tomwer/core/tomwer_object.py +4 -0
  221. tomwer/core/utils/__init__.py +2 -0
  222. tomwer/core/utils/char.py +0 -28
  223. tomwer/core/utils/deprecation.py +12 -38
  224. tomwer/core/utils/dictutils.py +1 -3
  225. tomwer/core/utils/ftseriesutils.py +1 -27
  226. tomwer/core/utils/gpu.py +0 -28
  227. tomwer/core/utils/image.py +8 -39
  228. tomwer/core/utils/locker.py +1 -28
  229. tomwer/core/utils/logconfig.py +0 -27
  230. tomwer/core/utils/normalization.py +4 -31
  231. tomwer/core/utils/nxtomoutils.py +8 -38
  232. tomwer/core/utils/resource.py +0 -26
  233. tomwer/core/utils/scanutils.py +23 -52
  234. tomwer/core/utils/slurm.py +7 -30
  235. tomwer/core/utils/spec.py +6 -6
  236. tomwer/core/utils/tests/__init__.py +0 -0
  237. tomwer/core/utils/tests/test_image.py +30 -0
  238. tomwer/core/utils/tests/test_nxtomo.py +38 -0
  239. tomwer/core/utils/tests/test_scan_utils.py +46 -0
  240. tomwer/core/utils/tests/test_time.py +6 -0
  241. tomwer/core/utils/threads.py +0 -26
  242. tomwer/core/utils/time.py +0 -27
  243. tomwer/core/volume/__init__.py +4 -0
  244. tomwer/core/volume/edfvolume.py +1 -28
  245. tomwer/core/volume/hdf5volume.py +1 -28
  246. tomwer/core/volume/jp2kvolume.py +1 -27
  247. tomwer/core/volume/rawvolume.py +1 -28
  248. tomwer/core/volume/tests/test_volumes.py +21 -0
  249. tomwer/core/volume/tiffvolume.py +1 -28
  250. tomwer/core/volume/volumebase.py +5 -0
  251. tomwer/core/volume/volumefactory.py +7 -33
  252. tomwer/gui/__init__.py +0 -28
  253. tomwer/gui/cluster/__init__.py +2 -0
  254. tomwer/gui/cluster/slurm.py +297 -95
  255. tomwer/gui/cluster/supervisor.py +1 -27
  256. tomwer/gui/cluster/tests/__init__.py +0 -0
  257. tomwer/gui/cluster/{test → tests}/test_cluster.py +21 -26
  258. tomwer/gui/cluster/{test → tests}/test_supervisor.py +1 -27
  259. tomwer/gui/conditions/__init__.py +2 -0
  260. tomwer/gui/conditions/filter.py +1 -26
  261. tomwer/gui/configuration/__init__.py +2 -0
  262. tomwer/gui/control/__init__.py +2 -0
  263. tomwer/gui/control/actions.py +2 -28
  264. tomwer/gui/control/datadiscovery.py +4 -3
  265. tomwer/gui/control/datalist.py +64 -69
  266. tomwer/gui/control/datalistener.py +1 -39
  267. tomwer/gui/control/datareacheractions.py +1 -28
  268. tomwer/gui/control/datatransfert.py +2 -29
  269. tomwer/gui/control/datavalidator.py +3 -37
  270. tomwer/gui/control/datawatcher/__init__.py +0 -28
  271. tomwer/gui/control/datawatcher/configuration.py +1 -28
  272. tomwer/gui/control/datawatcher/datawatcher.py +3 -32
  273. tomwer/gui/control/datawatcher/datawatcherobserver.py +2 -28
  274. tomwer/gui/control/history.py +5 -35
  275. tomwer/gui/control/nxtomomill.py +3 -30
  276. tomwer/gui/control/observations.py +61 -55
  277. tomwer/gui/control/reducedarkflatselector.py +24 -20
  278. tomwer/gui/control/scanselectorwidget.py +2 -28
  279. tomwer/gui/control/selectorwidgetbase.py +17 -17
  280. tomwer/gui/control/series/__init__.py +0 -0
  281. tomwer/gui/control/{serie/seriecreator.py → series/seriescreator.py} +214 -235
  282. tomwer/gui/control/series/serieswaiter.py +0 -0
  283. tomwer/gui/control/series/test/test_creator.py +424 -0
  284. tomwer/gui/control/series/test/test_nxtomo_concatenate.py +21 -0
  285. tomwer/gui/control/singletomoobj.py +1 -1
  286. tomwer/gui/control/tests/__init__.py +0 -0
  287. tomwer/gui/control/tests/test_datalist.py +47 -0
  288. tomwer/gui/control/{test → tests}/test_datalistener.py +1 -28
  289. tomwer/gui/control/tests/test_datavalidator.py +27 -0
  290. tomwer/gui/control/{test → tests}/test_inputwidget.py +1 -27
  291. tomwer/gui/control/tests/test_process_manager.py +38 -0
  292. tomwer/gui/control/tests/test_scan_observations.py +23 -0
  293. tomwer/gui/control/tests/test_scanselector.py +42 -0
  294. tomwer/gui/control/{test → tests}/test_scanvalidator.py +1 -27
  295. tomwer/gui/control/{test → tests}/test_volume_dialog.py +2 -30
  296. tomwer/gui/control/{test → tests}/test_volumeselector.py +1 -27
  297. tomwer/gui/control/volumeselectorwidget.py +2 -30
  298. tomwer/gui/dataportal/__init__.py +2 -0
  299. tomwer/gui/{icat → dataportal}/createscreenshots.py +3 -2
  300. tomwer/gui/dataportal/gallery.py +133 -0
  301. tomwer/gui/dataportal/outputformat.py +0 -0
  302. tomwer/gui/dataportal/publish.py +96 -0
  303. tomwer/gui/dataportal/tests/test_create_screenshots_gui.py +23 -0
  304. tomwer/gui/dataportal/tests/test_gallery_gui.py +21 -0
  305. tomwer/gui/debugtools/__init__.py +2 -0
  306. tomwer/gui/debugtools/datasetgenerator.py +1 -30
  307. tomwer/gui/debugtools/objectinspector.py +1 -29
  308. tomwer/gui/dialog/QDataDialog.py +89 -0
  309. tomwer/gui/{qfolderdialog.py → dialog/QVolumeDialog.py} +8 -107
  310. tomwer/gui/dialog/__init__.py +1 -0
  311. tomwer/gui/edit/__init__.py +2 -0
  312. tomwer/gui/edit/dkrfpatch.py +52 -87
  313. tomwer/gui/edit/imagekeyeditor.py +18 -54
  314. tomwer/gui/edit/nxtomoeditor.py +113 -300
  315. tomwer/gui/edit/nxtomowarmer.py +3 -2
  316. tomwer/gui/edit/tests/__init__.py +0 -0
  317. tomwer/gui/edit/{test → tests}/test_dkrf_patch.py +3 -29
  318. tomwer/gui/edit/{test → tests}/test_image_key_editor.py +1 -27
  319. tomwer/gui/edit/{test → tests}/test_nx_editor.py +45 -23
  320. tomwer/gui/icons.py +28 -66
  321. tomwer/gui/illustrations.py +4 -34
  322. tomwer/gui/imagefromfile.py +5 -30
  323. tomwer/gui/metadataloader.py +36 -0
  324. tomwer/gui/qconfigfile.py +3 -0
  325. tomwer/gui/qlefilesystem.py +3 -0
  326. tomwer/gui/reconstruction/__init__.py +2 -0
  327. tomwer/gui/reconstruction/axis/AxisMainWindow.py +264 -0
  328. tomwer/gui/reconstruction/axis/AxisOptionsWidget.py +153 -0
  329. tomwer/gui/reconstruction/axis/AxisSettingsWidget.py +776 -0
  330. tomwer/gui/reconstruction/axis/AxisWidget.py +526 -0
  331. tomwer/gui/reconstruction/axis/CalculationWidget.py +374 -0
  332. tomwer/gui/reconstruction/axis/CompareImages.py +11 -44
  333. tomwer/gui/reconstruction/axis/ControlWidget.py +277 -0
  334. tomwer/gui/reconstruction/axis/InputWidget.py +491 -0
  335. tomwer/gui/reconstruction/axis/ManualFramesSelection.py +168 -0
  336. tomwer/gui/reconstruction/axis/__init__.py +2 -2
  337. tomwer/gui/reconstruction/darkref/__init__.py +0 -27
  338. tomwer/gui/reconstruction/darkref/darkrefcopywidget.py +5 -34
  339. tomwer/gui/reconstruction/darkref/darkrefwidget.py +1 -27
  340. tomwer/gui/reconstruction/nabu/castvolume.py +40 -59
  341. tomwer/gui/reconstruction/nabu/check.py +7 -33
  342. tomwer/gui/reconstruction/nabu/nabuconfig/base.py +7 -34
  343. tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py +6 -5
  344. tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py +10 -69
  345. tomwer/gui/reconstruction/nabu/nabuconfig/output.py +3 -47
  346. tomwer/gui/reconstruction/nabu/nabuconfig/phase.py +54 -36
  347. tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py +103 -54
  348. tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py +116 -65
  349. tomwer/gui/reconstruction/nabu/nabuflow.py +31 -61
  350. tomwer/gui/reconstruction/nabu/platform.py +94 -0
  351. tomwer/gui/reconstruction/nabu/slices.py +81 -45
  352. tomwer/gui/reconstruction/nabu/slurm.py +1 -27
  353. tomwer/gui/reconstruction/nabu/test/test_cast_volume.py +82 -0
  354. tomwer/gui/reconstruction/nabu/test/test_check.py +66 -0
  355. tomwer/gui/reconstruction/nabu/test/test_ctf.py +46 -0
  356. tomwer/gui/reconstruction/nabu/test/test_helical.py +21 -0
  357. tomwer/gui/reconstruction/nabu/test/test_nabu_preprocessing.py +81 -0
  358. tomwer/gui/reconstruction/nabu/volume.py +62 -90
  359. tomwer/gui/reconstruction/normalization/intensity.py +5 -32
  360. tomwer/gui/reconstruction/normalization/test/test_intensity.py +89 -0
  361. tomwer/gui/reconstruction/saaxis/corrangeselector.py +16 -49
  362. tomwer/gui/reconstruction/saaxis/dimensionwidget.py +56 -96
  363. tomwer/gui/reconstruction/saaxis/saaxis.py +17 -38
  364. tomwer/gui/reconstruction/saaxis/sliceselector.py +8 -39
  365. tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py +19 -37
  366. tomwer/gui/reconstruction/scores/control.py +2 -30
  367. tomwer/gui/reconstruction/scores/scoreplot.py +19 -48
  368. tomwer/gui/reconstruction/tests/__init__.py +0 -0
  369. tomwer/gui/reconstruction/{test → tests}/test_axis.py +23 -49
  370. tomwer/gui/reconstruction/{test → tests}/test_nabu.py +8 -31
  371. tomwer/gui/reconstruction/{test → tests}/test_saaxis.py +10 -37
  372. tomwer/gui/reconstruction/{test → tests}/test_sadeltabeta.py +1 -26
  373. tomwer/gui/samplemoved/__init__.py +2 -30
  374. tomwer/gui/samplemoved/selectiontable.py +3 -33
  375. tomwer/gui/settings.py +7 -0
  376. tomwer/gui/stackplot.py +33 -661
  377. tomwer/gui/stacks.py +261 -135
  378. tomwer/gui/stitching/SingleAxisStitchingWidget.py +326 -0
  379. tomwer/gui/stitching/StitchingOptionsWidget.py +438 -0
  380. tomwer/gui/stitching/StitchingWindow.py +586 -0
  381. tomwer/gui/stitching/__init__.py +2 -0
  382. tomwer/gui/stitching/alignment.py +90 -0
  383. tomwer/gui/stitching/axisorderedlist.py +44 -34
  384. tomwer/gui/stitching/config/axisparams.py +23 -11
  385. tomwer/gui/stitching/config/output.py +6 -5
  386. tomwer/gui/stitching/config/positionoveraxis.py +313 -51
  387. tomwer/gui/stitching/config/stitchingstrategies.py +22 -16
  388. tomwer/gui/stitching/config/tests/test_axisparams.py +25 -0
  389. tomwer/gui/stitching/config/tomoobjdetails.py +3 -5
  390. tomwer/gui/stitching/normalization.py +1 -0
  391. tomwer/gui/stitching/preview.py +59 -0
  392. tomwer/gui/stitching/singleaxis.py +57 -0
  393. tomwer/gui/stitching/stitchandbackground.py +3 -2
  394. tomwer/gui/stitching/stitching_preview.py +44 -36
  395. tomwer/gui/stitching/stitching_raw.py +5 -3
  396. tomwer/gui/stitching/tests/test_ZStitchingWindow.py +88 -0
  397. tomwer/gui/stitching/tests/test_axis_ordered_list.py +21 -0
  398. tomwer/gui/stitching/tests/test_normalization.py +27 -0
  399. tomwer/gui/stitching/tests/test_preview.py +68 -0
  400. tomwer/gui/stitching/tests/test_stitching_raw.py +110 -0
  401. tomwer/gui/stitching/tests/utils.py +92 -0
  402. tomwer/gui/stitching/utils.py +14 -0
  403. tomwer/gui/stitching/z_stitching/fineestimation.py +4 -32
  404. tomwer/gui/stitching/z_stitching/tests/test_fine_estimation.py +35 -0
  405. tomwer/gui/stitching/z_stitching/tests/test_raw_estimation.py +215 -0
  406. tomwer/gui/stitching/z_stitching/tests/test_stitching_window.py +51 -0
  407. tomwer/gui/tests/__init__.py +0 -0
  408. tomwer/gui/tests/test_axis_gui.py +27 -0
  409. tomwer/gui/{test → tests}/test_qfolder_dialog.py +1 -1
  410. tomwer/gui/utils/RangeWidget.py +44 -0
  411. tomwer/gui/utils/buttons.py +4 -3
  412. tomwer/gui/utils/completer.py +2 -33
  413. tomwer/gui/utils/flow.py +11 -40
  414. tomwer/gui/utils/gpu.py +60 -0
  415. tomwer/gui/utils/illustrations.py +1 -26
  416. tomwer/gui/utils/inputwidget.py +35 -73
  417. tomwer/gui/utils/lineselector/lineselector.py +9 -46
  418. tomwer/gui/utils/loadingmode.py +81 -0
  419. tomwer/gui/utils/qt_utils.py +9 -0
  420. tomwer/gui/utils/sandboxes.py +1 -26
  421. tomwer/gui/utils/scandescription.py +2 -31
  422. tomwer/gui/utils/scrollarea.py +6 -55
  423. tomwer/gui/utils/slider.py +4 -28
  424. tomwer/gui/utils/splashscreen.py +0 -28
  425. tomwer/gui/utils/step.py +14 -13
  426. tomwer/gui/utils/tests/test_completer.py +41 -0
  427. tomwer/gui/utils/tests/test_line_selector.py +21 -0
  428. tomwer/gui/utils/tests/test_splashscreen.py +8 -0
  429. tomwer/gui/utils/tests/test_vignettes.py +68 -0
  430. tomwer/gui/utils/unitsystem.py +15 -69
  431. tomwer/gui/utils/utils.py +4 -5
  432. tomwer/gui/utils/vignettes.py +10 -41
  433. tomwer/gui/utils/waiterthread.py +0 -26
  434. tomwer/gui/visualization/__init__.py +2 -0
  435. tomwer/gui/visualization/dataviewer.py +68 -421
  436. tomwer/gui/visualization/diffviewer/diffviewer.py +2 -30
  437. tomwer/gui/visualization/diffviewer/shiftwidget.py +4 -29
  438. tomwer/gui/visualization/fullscreenplot.py +5 -5
  439. tomwer/gui/visualization/imagestack.py +403 -0
  440. tomwer/gui/visualization/nxtomometadata.py +0 -4
  441. tomwer/gui/visualization/reconstructionparameters.py +14 -32
  442. tomwer/gui/visualization/scanoverview.py +33 -66
  443. tomwer/gui/visualization/sinogramviewer.py +2 -28
  444. tomwer/gui/visualization/test/__init__.py +0 -28
  445. tomwer/gui/visualization/test/test_dataviewer.py +1 -28
  446. tomwer/gui/visualization/test/test_diffviewer.py +1 -28
  447. tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py +0 -5
  448. tomwer/gui/visualization/test/test_reconstruction_parameters.py +1 -27
  449. tomwer/gui/visualization/test/test_sinogramviewer.py +1 -28
  450. tomwer/gui/visualization/test/test_stacks.py +184 -115
  451. tomwer/gui/visualization/test/test_volumeviewer.py +3 -2
  452. tomwer/gui/visualization/tomoobjoverview.py +2 -2
  453. tomwer/gui/visualization/volumeoverview.py +3 -2
  454. tomwer/gui/visualization/volumeviewer.py +47 -43
  455. tomwer/io/__init__.py +2 -0
  456. tomwer/io/utils/h5pyutils.py +1 -27
  457. tomwer/io/utils/test/test_raw_and_processed_data.py +10 -0
  458. tomwer/io/utils/test/test_utils.py +67 -0
  459. tomwer/io/utils/utils.py +2 -31
  460. tomwer/resources/__init__.py +13 -33
  461. tomwer/resources/gui/icons/edit_downstream.svg +114 -0
  462. tomwer/resources/gui/icons/edit_upstream.svg +112 -0
  463. tomwer/resources/gui/icons/free_edition.svg +23 -0
  464. tomwer/resources/gui/icons/icat_gallery_opts.png +0 -0
  465. tomwer/resources/gui/icons/icat_gallery_opts.svg +80 -0
  466. tomwer/resources/gui/icons/search.png +0 -0
  467. tomwer/resources/gui/icons/search.svg +23 -0
  468. tomwer/resources/gui/icons/warning.png +0 -0
  469. tomwer/synctools/__init__.py +2 -0
  470. tomwer/synctools/axis.py +1 -27
  471. tomwer/synctools/darkref.py +1 -26
  472. tomwer/synctools/datalistener.py +1 -27
  473. tomwer/synctools/datatransfert.py +2 -27
  474. tomwer/synctools/imageloaderthread.py +1 -28
  475. tomwer/synctools/rsyncmanager.py +1 -25
  476. tomwer/synctools/saaxis.py +1 -26
  477. tomwer/synctools/sadeltabeta.py +1 -26
  478. tomwer/synctools/stacks/control/datalistener.py +1 -26
  479. tomwer/synctools/stacks/processingstack.py +4 -33
  480. tomwer/synctools/stacks/reconstruction/axis.py +2 -31
  481. tomwer/synctools/stacks/reconstruction/castvolume.py +12 -43
  482. tomwer/synctools/stacks/reconstruction/dkrefcopy.py +3 -26
  483. tomwer/synctools/stacks/reconstruction/nabu.py +1 -26
  484. tomwer/synctools/stacks/reconstruction/normalization.py +1 -26
  485. tomwer/synctools/stacks/reconstruction/saaxis.py +1 -26
  486. tomwer/synctools/stacks/reconstruction/sadeltabeta.py +1 -26
  487. tomwer/synctools/tests/__init__.py +0 -0
  488. tomwer/synctools/{test → tests}/test_darkRefs.py +16 -40
  489. tomwer/synctools/{test → tests}/test_foldertransfer.py +2 -33
  490. tomwer/synctools/utils/scanstages.py +2 -31
  491. tomwer/tests/__init__.py +1 -0
  492. tomwer/tests/app/test_stitching.py +95 -0
  493. tomwer/tests/datasets.py +1 -5
  494. tomwer/tests/orangecontrib/tomwer/widgets/cluster/tests/test_future_supervisorow.py +48 -0
  495. tomwer/tests/orangecontrib/tomwer/widgets/cluster/tests/test_slurm_clusterow.py +40 -0
  496. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_advancement.py +8 -0
  497. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_data_validator.py +55 -0
  498. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datadiscovery.py +129 -0
  499. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datalistener.py +111 -0
  500. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_dataselector.py +69 -0
  501. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datawatcher.py +411 -0
  502. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_emailow.py +29 -0
  503. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_notifier.py +24 -0
  504. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_nxtomo_concatenate_ow.py +64 -0
  505. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_nxtomomill.py +133 -0
  506. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_reduce_dark_flat_selector.py +40 -0
  507. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_singletomoobj.py +40 -0
  508. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_timerow.py +25 -0
  509. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_tomoobj_series.py +96 -0
  510. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_volume_selector.py +69 -0
  511. orangecontrib/tomwer/widgets/edit/test/test_image_key_editor.py → tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_dataset_generator.py +17 -16
  512. tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_object_inspector.py +36 -0
  513. {orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_dark_flat_patch.py +1 -27
  514. tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_image_key_editor.py +30 -0
  515. tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py +138 -0
  516. tomwer/tests/orangecontrib/tomwer/widgets/other/tests/test_pythonscript.py +31 -0
  517. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_axis.py +215 -0
  518. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_cast_volumeow.py +58 -0
  519. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_dark_refs_widget.py +136 -0
  520. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_delta_beta_selector.py +15 -0
  521. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_i_norm.py +200 -0
  522. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_helical_prepare_weights_double.py +20 -0
  523. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_volume.py +74 -0
  524. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_widget.py +107 -0
  525. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_sa_delta_beta.py +194 -0
  526. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_saaxis.py +194 -0
  527. tomwer/tests/orangecontrib/tomwer/widgets/stitching/tests/test_zstitching.py +313 -0
  528. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_conditions.py +85 -0
  529. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_darkref.py +225 -0
  530. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_foldertransfert.py +105 -0
  531. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_dataviewerow.py +57 -0
  532. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_diffviewerow.py +39 -0
  533. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_nxtomo_metadata_viewer.py +29 -0
  534. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_radio_stackow.py +31 -0
  535. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_sample_movedow.py +46 -0
  536. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_sinogram_viewerow.py +31 -0
  537. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_slice_stackow.py +31 -0
  538. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_volume_viewerow.py +32 -0
  539. tomwer/tests/test_ewoks/test_conversion.py +104 -0
  540. tomwer/tests/test_ewoks/test_single_node_execution.py +87 -0
  541. tomwer/tests/test_ewoks/test_workflows.py +138 -0
  542. tomwer/utils.py +11 -39
  543. tomwer/version.py +3 -3
  544. {tomwer-1.3.27.dist-info → tomwer-1.4.0rc0.dist-info}/LICENSE +3 -3
  545. tomwer-1.4.0rc0.dist-info/METADATA +337 -0
  546. tomwer-1.4.0rc0.dist-info/RECORD +909 -0
  547. {tomwer-1.3.27.dist-info → tomwer-1.4.0rc0.dist-info}/WHEEL +1 -1
  548. {tomwer-1.3.27.dist-info → tomwer-1.4.0rc0.dist-info}/entry_points.txt +1 -0
  549. orangecontrib/tomwer/widgets/control/DataListOW.py +0 -129
  550. orangecontrib/tomwer/widgets/control/TomoObjSerieOW.py +0 -86
  551. orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py +0 -182
  552. orangecontrib/tomwer/widgets/edit/test/test_nxtomo_editor.py +0 -141
  553. orangecontrib/tomwer/widgets/icat/PublishProcessedDataOW.py +0 -115
  554. orangecontrib/tomwer/widgets/icat/RawDataScreenshotCreatorOW.py +0 -98
  555. orangecontrib/tomwer/widgets/icat/SaveToGalleryAndPublishOW.py +0 -129
  556. orangecontrib/tomwer/widgets/icat/icons/add_gallery.png +0 -0
  557. orangecontrib/tomwer/widgets/icat/icons/add_gallery.svg +0 -82
  558. orangecontrib/tomwer/widgets/icat/icons/raw_screenshots.png +0 -0
  559. orangecontrib/tomwer/widgets/icat/icons/raw_screenshots.svg +0 -143
  560. orangecontrib/tomwer/widgets/visualization/LivesliceOW.py +0 -87
  561. orangecontrib/tomwer/widgets/visualization/icons/liveslice.png +0 -0
  562. orangecontrib/tomwer/widgets/visualization/icons/liveslice.svg +0 -110
  563. tomwer/core/log/logger.py +0 -130
  564. tomwer/core/process/control/test/test_volume_link.py +0 -74
  565. tomwer/core/process/control/tomoobjserie.py +0 -12
  566. tomwer/core/process/control/volumesymlink.py +0 -200
  567. tomwer/core/process/icat/createscreenshots.py +0 -100
  568. tomwer/core/process/icat/gallery.py +0 -377
  569. tomwer/core/process/icat/icatbase.py +0 -36
  570. tomwer/core/process/icat/publish.py +0 -228
  571. tomwer/core/process/icat/screenshots.py +0 -27
  572. tomwer/core/process/reconstruction/test/test_darkref.py +0 -60
  573. tomwer/core/process/reconstruction/test/test_sadeltabeta.py +0 -74
  574. tomwer/core/process/visualization/liveslice.py +0 -6
  575. tomwer/core/progress.py +0 -100
  576. tomwer/core/scan/test/test_edf.py +0 -53
  577. tomwer/core/scan/test/test_future_scan.py +0 -61
  578. tomwer/core/scan/test/test_h5.py +0 -96
  579. tomwer/core/test/test_scanutils.py +0 -53
  580. tomwer/gui/control/emailnotifier.py +0 -174
  581. tomwer/gui/control/serie/seriewaiter.py +0 -28
  582. tomwer/gui/control/test/__init__.py +0 -28
  583. tomwer/gui/control/test/test_datalist.py +0 -96
  584. tomwer/gui/control/test/test_datavalidator.py +0 -54
  585. tomwer/gui/control/test/test_email.py +0 -35
  586. tomwer/gui/control/test/test_process_manager.py +0 -65
  587. tomwer/gui/control/test/test_scanselector.py +0 -67
  588. tomwer/gui/edit/test/__init__.py +0 -28
  589. tomwer/gui/icat/gallery.py +0 -214
  590. tomwer/gui/icat/publish.py +0 -187
  591. tomwer/gui/reconstruction/axis/axis.py +0 -733
  592. tomwer/gui/reconstruction/axis/radioaxis.py +0 -2467
  593. tomwer/gui/stitching/stitching.py +0 -1388
  594. tomwer/gui/test/__init__.py +0 -28
  595. tomwer/gui/test/test_axis_gui.py +0 -34
  596. tomwer/synctools/stacks/edit/darkflatpatch.py +0 -169
  597. tomwer/synctools/stacks/edit/imagekeyeditor.py +0 -135
  598. tomwer/third_part/WaitingOverlay.py +0 -110
  599. tomwer-1.3.27-py3.11-nspkg.pth +0 -1
  600. tomwer-1.3.27.dist-info/METADATA +0 -292
  601. tomwer-1.3.27.dist-info/RECORD +0 -785
  602. tomwer-1.3.27.dist-info/namespace_packages.txt +0 -1
  603. /orangecontrib/tomwer/{widgets/edit/test → tests}/__init__.py +0 -0
  604. {tomwer/core/process/control/test → orangecontrib/tomwer/tutorials/id16b}/__init__.py +0 -0
  605. {tomwer/core/process/icat → orangecontrib/tomwer/widgets/cluster/tests}/__init__.py +0 -0
  606. /orangecontrib/tomwer/widgets/control/icons/{tomoobjserie.png → tomoobjseries.png} +0 -0
  607. {tomwer/core/process/reconstruction/test → orangecontrib/tomwer/widgets/control/tests}/__init__.py +0 -0
  608. /orangecontrib/tomwer/widgets/{icat → dataportal}/icons/publish_processed_data.png +0 -0
  609. /orangecontrib/tomwer/widgets/{icat → dataportal}/icons/publish_processed_data.svg +0 -0
  610. {tomwer/core/process/test → orangecontrib/tomwer/widgets/debugtools/tests}/__init__.py +0 -0
  611. {tomwer/core/scan/test → orangecontrib/tomwer/widgets/edit/tests}/__init__.py +0 -0
  612. {tomwer/core/test → orangecontrib/tomwer/widgets/other/tests}/__init__.py +0 -0
  613. {tomwer/gui/cluster/test → orangecontrib/tomwer/widgets/reconstruction/tests}/__init__.py +0 -0
  614. {tomwer/gui/control/serie → orangecontrib/tomwer/widgets/stitching/tests}/__init__.py +0 -0
  615. {tomwer/gui/icat → orangecontrib/tomwer/widgets/tests}/__init__.py +0 -0
  616. {tomwer/gui/reconstruction/test → orangecontrib/tomwer/widgets/visualization/tests}/__init__.py +0 -0
  617. /tomwer/{synctools/stacks/edit → app/stitching}/__init__.py +0 -0
  618. /tomwer/{synctools/test → core/process/control/tests}/__init__.py +0 -0
  619. /tomwer/core/process/control/{test → tests}/test_email.py +0 -0
  620. /tomwer/core/process/control/{test → tests}/test_h52nx_process.py +0 -0
  621. /tomwer/{third_part → core/process/drac}/__init__.py +0 -0
  622. /tomwer/core/process/reconstruction/{test → tests}/test_axis_params.py +0 -0
  623. /tomwer/core/process/reconstruction/{test → tests}/test_darkref_copy.py +0 -0
  624. /tomwer/core/process/reconstruction/{test → tests}/test_paramsbase.py +0 -0
  625. /tomwer/core/process/reconstruction/{test → tests}/test_utils.py +0 -0
  626. /tomwer/core/scan/{test → tests}/test_scan.py +0 -0
  627. /tomwer/gui/control/{serie → series}/nxtomoconcatenate.py +0 -0
  628. /tomwer/gui/control/{test → tests}/test_datadiscovery.py +0 -0
  629. /tomwer/gui/control/{test → tests}/test_reducedarkflat_selector.py +0 -0
  630. /tomwer/gui/control/{test → tests}/test_single_tomo_obj.py +0 -0
  631. {orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_image_key_upgrader.py +0 -0
  632. {tomwer-1.3.27.dist-info → tomwer-1.4.0rc0.dist-info}/top_level.txt +0 -0
@@ -1,37 +1,9 @@
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  # coding: utf-8
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- # /*##########################################################################
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- #
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- # Copyright (c) 2016-2020 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
-
26
- __authors__ = ["H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "06/08/2020"
29
-
2
+ from __future__ import annotations
30
3
 
31
4
  import datetime
32
5
  import logging
33
6
  import os
34
- import typing
35
7
  from contextlib import AbstractContextManager
36
8
 
37
9
  from nabu.pipeline.config import generate_nabu_configfile, parse_nabu_config_file
@@ -78,7 +50,7 @@ def retrieve_lst_of_value_from_str(my_string: str, type_) -> tuple:
78
50
  Return a list of value from a string like '12,23' or '(12, 23)',
79
51
  '[12;23]', '12;23' or with the pattern from:to:step like '0:10:1'
80
52
 
81
- :param str mystring:
53
+ :param mystring:
82
54
  :return: list of single value
83
55
  """
84
56
  if not isinstance(my_string, str):
@@ -113,31 +85,10 @@ def retrieve_lst_of_value_from_str(my_string: str, type_) -> tuple:
113
85
  return tuple(res)
114
86
 
115
87
 
116
- def get_nabu_resources_desc(scan: TomwerScanBase, method, workers=1) -> dict:
117
- """
118
- Create the descriptor of nabu's resources
119
-
120
- :param TomwerScanBase scan:
121
- :param str method:
122
- :return: nabu's description of resources to be used
123
- """
124
- assert isinstance(scan, TomwerScanBase)
125
- res = {
126
- "method": method,
127
- "cpu_workers": workers,
128
- "partition": "gpu",
129
- "memory_per_node": "90%",
130
- "threads_per_node": "100%",
131
- }
132
- return res
133
-
134
-
135
- def get_nabu_about_desc(overwrite) -> dict:
88
+ def get_nabu_about_desc(overwrite: bool) -> dict:
136
89
  """
137
- Create the description for nabu's about
90
+ Create the description for nabu's 'about'
138
91
 
139
- :param self:
140
- :return:
141
92
  """
142
93
  return {"overwrite_results": str(bool(overwrite))}
143
94
 
@@ -147,7 +98,7 @@ def get_recons_volume_identifier(
147
98
  location: str,
148
99
  file_format: str,
149
100
  scan: TomwerScanBase,
150
- slice_index: typing.Union[int, None],
101
+ slice_index: int | None,
151
102
  axis: NabuPlane,
152
103
  ) -> tuple:
153
104
  """
@@ -240,11 +191,11 @@ def get_multi_cor_recons_volume_identifiers(
240
191
  """
241
192
  util to retrieve Volumes (identifier) reconstructed by nabu-multicor
242
193
 
243
- :param TomwerScanBase scan: scam processed by the nabu-multicor
244
- :param str location: location of the files
245
- :param tuple cors: cors for which we want the reconstructed slices. As this extension is created by nabu
194
+ :param scan: scam processed by the nabu-multicor
195
+ :param location: location of the files
196
+ :param cors: cors for which we want the reconstructed slices. As this extension is created by nabu
246
197
  the cor reference is in absolute.
247
- :param str file_format: file format of the reconstruction
198
+ :param file_format: file format of the reconstruction
248
199
 
249
200
  :return: a dict with absolute cor value as key and the Volume identifier as value
250
201
  """
@@ -442,7 +393,7 @@ class RingCorrectionMethod(_Enum):
442
393
  MEAN_DIVISION = "mean-division"
443
394
 
444
395
 
445
- def nabu_std_err_has_error(errs: typing.Optional[bytes]):
396
+ def nabu_std_err_has_error(errs: bytes | None):
446
397
  """
447
398
  small util to parse stderr where some warning can exists.
448
399
  But I don't think we want to catch all warnings from nabu so this is a (bad) concession
@@ -513,7 +464,7 @@ def update_cfg_file_after_transfer(config_file_path, old_path, new_path):
513
464
 
514
465
 
515
466
  def slice_index_to_int(
516
- slice_index: typing.Union[int, str],
467
+ slice_index: int | str,
517
468
  scan: TomwerScanBase,
518
469
  axis=NabuPlane.XY,
519
470
  ) -> int:
@@ -1,38 +1,9 @@
1
1
  # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
2
+
25
3
  """
26
4
  material for radio and sinogram normalization
27
5
  """
28
-
29
-
30
- __authors__ = [
31
- "H. Payno",
32
- ]
33
- __license__ = "MIT"
34
- __date__ = "25/06/2021"
35
-
6
+ from __future__ import annotations
36
7
 
37
8
  import functools
38
9
  import logging
@@ -208,7 +179,6 @@ class SinoNormalizationTask(
208
179
  :param end_y:
209
180
  :param calc_area:
210
181
  :return:
211
- :rtype: dict
212
182
  """
213
183
  if start_x is None or end_x is None or start_y is None or end_y is None:
214
184
  raise ValueError("min_x, max_x, min_y and max_y should all be provided.")
@@ -1,40 +1,8 @@
1
1
  # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
2
  """
26
3
  material for radio and sinogram normalization
27
4
  """
28
-
29
-
30
- __authors__ = [
31
- "H. Payno",
32
- ]
33
- __license__ = "MIT"
34
- __date__ = "25/06/2021"
35
-
36
-
37
- import typing
5
+ from __future__ import annotations
38
6
 
39
7
  from silx.utils.enum import Enum as _Enum
40
8
  from tomoscan.normalization import Method
@@ -70,7 +38,7 @@ class _DatasetInfos:
70
38
  return self._scope
71
39
 
72
40
  @scope.setter
73
- def scope(self, scope: typing.Union[str, _DatasetScope]):
41
+ def scope(self, scope: str | _DatasetScope):
74
42
  self._scope = _DatasetScope.from_value(scope)
75
43
 
76
44
  @property
@@ -115,7 +83,7 @@ class SinoNormalizationParams:
115
83
  return self._method
116
84
 
117
85
  @method.setter
118
- def method(self, method: typing.Union[str, Method, None]):
86
+ def method(self, method: str | Method | None):
119
87
  if method is None:
120
88
  method = Method.NONE
121
89
  self._method = Method.from_value(method)
@@ -4,22 +4,17 @@ import logging
4
4
  from silx.utils.enum import Enum as _Enum
5
5
  from tomwer.io.utils.raw_and_processed_data import (
6
6
  to_processed_data_path,
7
- to_raw_data_path,
8
7
  )
9
8
  from tomwer.core.scan.scanbase import TomwerScanBase
9
+ from tomwer.core.process.output import ProcessDataOutputDirMode
10
10
  from tomwer.core.utils.scanutils import format_output_location
11
11
 
12
12
  _logger = logging.getLogger(__name__)
13
13
 
14
14
 
15
- PROCESS_FOLDER_NAME = "reconstructed_volumes"
15
+ PROCESS_FOLDER_RECONSTRUCTED_VOLUMES = "reconstructed_volumes"
16
16
 
17
-
18
- class ProcessDataOutputDirMode(_Enum):
19
- IN_SCAN_FOLDER = "same folder as scan"
20
- PROCESSED_DATA_FOLDER = "PROCESSED_DATA folder"
21
- RAW_DATA_FOLDER = "RAW_DATA folder"
22
- OTHER = "other"
17
+ PROCESS_FOLDER_RECONSTRUCTED_SLICES = "reconstructed_slices"
23
18
 
24
19
 
25
20
  class NabuOutputFileFormat(_Enum):
@@ -59,8 +54,16 @@ def get_output_folder_from_scan(
59
54
  nabu_location: str | None,
60
55
  file_basename: str,
61
56
  file_format: NabuOutputFileFormat,
57
+ processed_data_folder_name: str | None,
62
58
  ) -> tuple[str, str]:
63
59
  """
60
+
61
+ :param mode: output mode, should save this to raw data, processed data...
62
+ :param scan: scan for which we want to get the output folder
63
+ :param nabu_location: output location provided by user (in case mode is 'other')
64
+ :param file_basename: file basename to take in order to create output files
65
+ :param file_format: output volume format (edf...)
66
+ :param processed_data_folder_name: name of the processed data folder. Like 'reconstructed_volumes' or 'reconstructed_slices'...
64
67
  :return: (location, location_cfg_files). Location is the nabu configuration field 'output/location' 'location_cfg_files' is the information on where to save the nabu configuration file
65
68
 
66
69
  """
@@ -68,27 +71,22 @@ def get_output_folder_from_scan(
68
71
  file_format = NabuOutputFileFormat.from_value(file_format)
69
72
 
70
73
  if output_mode is ProcessDataOutputDirMode.OTHER and nabu_location in ("", None):
71
- _logger.info(
72
- "output dir requested is other bit no path provided. Fall back on the output dir to the scan folder"
74
+ _logger.error(
75
+ "'other' output dir requested but no path provided. Fall back on the output dir to the scan folder"
73
76
  )
74
77
  # note: this is only an info because we expect to pass by this one for all .ows configuration (before 1.3 version)
75
78
  # as there was no different option by the time
76
79
  output_mode = ProcessDataOutputDirMode.IN_SCAN_FOLDER
77
80
 
78
81
  if output_mode is ProcessDataOutputDirMode.OTHER:
79
- assert nabu_location not in (
80
- "",
81
- None,
82
- ), "nabu_location not provided when expected"
83
82
  location = format_output_location(nabu_location, scan=scan)
84
83
  location_cfg_files = location
85
84
  elif output_mode in (
86
85
  ProcessDataOutputDirMode.IN_SCAN_FOLDER,
87
86
  ProcessDataOutputDirMode.PROCESSED_DATA_FOLDER,
88
- ProcessDataOutputDirMode.RAW_DATA_FOLDER,
89
87
  ):
90
88
  # otherwise default location will be the data root level
91
- location = os.path.join(scan.path, PROCESS_FOLDER_NAME)
89
+ location = os.path.join(scan.path, processed_data_folder_name)
92
90
  location_cfg_files = location
93
91
  if file_format in (
94
92
  NabuOutputFileFormat.EDF.value,
@@ -99,9 +97,6 @@ def get_output_folder_from_scan(
99
97
  if output_mode is ProcessDataOutputDirMode.PROCESSED_DATA_FOLDER:
100
98
  location = to_processed_data_path(location)
101
99
  location_cfg_files = to_processed_data_path(location_cfg_files)
102
- if output_mode is ProcessDataOutputDirMode.RAW_DATA_FOLDER:
103
- location = to_raw_data_path(location)
104
- location_cfg_files = to_raw_data_path(location_cfg_files)
105
100
  else:
106
101
  raise NotImplementedError(f"mode {output_mode.value} is not implemented yet")
107
102
 
@@ -1,32 +1,5 @@
1
1
  # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
-
26
- __authors__ = ["H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "05/03/2019"
29
-
2
+ from __future__ import annotations
30
3
 
31
4
  import copy
32
5
  import itertools
@@ -109,16 +82,14 @@ class _ReconsParam(object):
109
82
  self.__unmanaged_params[parameter] = value
110
83
  self.changed()
111
84
 
112
- def to_unique_recons_set(self, as_to_dict=False) -> tuple:
85
+ def to_unique_recons_set(self, as_to_dict: bool = False) -> tuple:
113
86
  """
114
87
 
115
88
  :return: a tuple of unique reconstruction parameters in order to have
116
89
  each parameter as a single value (and no list)
117
- :param bool as_to_dict: True if we want to get the same value as if we
90
+ :param as_to_dict: True if we want to get the same value as if we
118
91
  where exporting it with to_dict function. There
119
92
  is some cast in the to_dict function.
120
- :type: Union[tuple, None]
121
- :rtype: tuple
122
93
  """
123
94
  params_list = OrderedDict()
124
95
  dict_values = self.to_dict()
@@ -174,7 +145,7 @@ class _ReconsParam(object):
174
145
  """
175
146
  copy parameters value from other_rp
176
147
 
177
- :param _ReconsParam: reconsparam to copy
148
+ :param other_rp: reconsparam to copy
178
149
  """
179
150
  if other_rp is None:
180
151
  return
@@ -1,35 +1,7 @@
1
- # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
-
26
- __authors__ = ["H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "18/02/2021"
29
-
30
-
31
- from collections.abc import Iterable
32
- from typing import Union
1
+ from __future__ import annotations
2
+
3
+
4
+ from typing import Iterable
33
5
 
34
6
  import numpy
35
7
  from silx.utils.enum import Enum as _Enum
@@ -88,7 +60,7 @@ class SAAxisParams(SABaseParams):
88
60
  self._mode = mode
89
61
 
90
62
  @property
91
- def image_width(self) -> Union[None, float]:
63
+ def image_width(self) -> float | None:
92
64
  return self._image_width
93
65
 
94
66
  @image_width.setter
@@ -1,40 +1,10 @@
1
- # coding: utf-8
2
- ###########################################################################
3
- # Copyright (C) 2016 European Synchrotron Radiation Facility
4
- #
5
- # Permission is hereby granted, free of charge, to any person obtaining a copy
6
- # of this software and associated documentation files (the "Software"), to deal
7
- # in the Software without restriction, including without limitation the rights
8
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
- # copies of the Software, and to permit persons to whom the Software is
10
- # furnished to do so, subject to the following conditions:
11
- #
12
- # The above copyright notice and this permission notice shall be included in
13
- # all copies or substantial portions of the Software.
14
- #
15
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
21
- # THE SOFTWARE.
22
- #
23
- #############################################################################
24
-
25
1
  """contain the SAAxisProcess. Half automatic center of rotation calculation
26
2
  """
27
3
 
28
- __authors__ = [
29
- "H.Payno",
30
- ]
31
- __license__ = "MIT"
32
- __date__ = "10/02/2021"
33
-
4
+ from __future__ import annotations
34
5
 
35
6
  import logging
36
7
  import os
37
- from typing import Optional
38
8
 
39
9
  import h5py
40
10
  import numpy
@@ -85,7 +55,6 @@ from tomwer.core.process.reconstruction.nabu.utils import (
85
55
  )
86
56
  from tomwer.core.process.reconstruction.nabu.nabuscores import _ReconstructorMultiCor
87
57
 
88
- from ..nabu import utils
89
58
  from .params import SAAxisParams
90
59
 
91
60
  _logger = logging.getLogger(__name__)
@@ -97,7 +66,7 @@ DEFAULT_RECONS_FOLDER = "multi_cor_results"
97
66
  def one_slice_several_cor(
98
67
  scan,
99
68
  configuration: dict,
100
- process_id: Optional[int] = None,
69
+ process_id: int | None = None,
101
70
  ) -> tuple:
102
71
  """
103
72
  Run a slice reconstruction using nabu per Center Of Rotation (cor) provided
@@ -106,13 +75,12 @@ def one_slice_several_cor(
106
75
  .. warning:: if target if the slurm cluster this will wait for the processing to be done to return the result.
107
76
  as this function is returning the result of the score process on reconstructed slices
108
77
 
109
- :param TomwerScanBase scan:
110
- :param dict configuration: nabu reconstruction parameters (can include 'slurm-cluster' key defining the slurm configuration)
111
- :param int process_id: process id
78
+ :param scan:
79
+ :param configuration: nabu reconstruction parameters (can include 'slurm-cluster' key defining the slurm configuration)
80
+ :param process_id: process id
112
81
  :return: cor_reconstructions, outs, errs
113
82
  cor_reconstructions is a dictionary of cor as key and a tuple
114
83
  (url, score) as value
115
- :rtype: tuple
116
84
  """
117
85
  task = SAAxisTask(
118
86
  process_id=process_id,
@@ -197,7 +165,7 @@ class SAAxisTask(
197
165
  self._dump_roi = dump
198
166
 
199
167
  @staticmethod
200
- def autofocus(scan) -> Optional[float]:
168
+ def autofocus(scan) -> float | None:
201
169
  scores = scan.saaxis_params.scores
202
170
  if scores is None:
203
171
  return
@@ -258,9 +226,9 @@ class SAAxisTask(
258
226
  nabu_configuration["output"]["location"] = output_dir
259
227
  nabu_configuration["output"]["file_format"] = file_format
260
228
  # handle resources section
261
- nabu_configuration["resources"] = utils.get_nabu_resources_desc(
262
- scan=scan, workers=1, method="local"
263
- )
229
+ nabu_configuration["resources"] = nabu_configuration.get("resources", {})
230
+ nabu_configuration["resources"]["method"] = "local"
231
+
264
232
  return nabu_configuration
265
233
 
266
234
  def _run_nabu_multicor(
@@ -270,7 +238,7 @@ class SAAxisTask(
270
238
  cors,
271
239
  slice_index,
272
240
  file_format,
273
- cluster_config: Optional[dict],
241
+ cluster_config: dict | None,
274
242
  dry_run=False,
275
243
  ):
276
244
  if not (cluster_config is None or isinstance(cluster_config, dict)):
@@ -286,7 +254,7 @@ class SAAxisTask(
286
254
  file_format=file_format,
287
255
  cluster_config=cluster_config if cluster_config is not None else None,
288
256
  process_id=self.process_id,
289
- instanciate_classes_only=True,
257
+ instantiate_classes_only=True,
290
258
  output_file_prefix_pattern="cor_{file_name}_{value}", # as the cor is evolving, create different files to make sure the name will be unique
291
259
  )
292
260
 
@@ -371,7 +339,7 @@ class SAAxisTask(
371
339
  """
372
340
  compute score along the different slices
373
341
 
374
- :param dict cor_reconstructions: key is expected to be a float with the cor value and the value is expected to be a volume identifier (volume with a single frame)
342
+ :param cor_reconstructions: key is expected to be a float with the cor value and the value is expected to be a volume identifier (volume with a single frame)
375
343
  """
376
344
  post_processing = _PostProcessing(
377
345
  slice_index=slice_index,
@@ -447,9 +415,12 @@ class SAAxisTask(
447
415
  _logger.info(
448
416
  f"{scan}: set estimated cor from previously computed cor ({params.estimated_cor})"
449
417
  )
450
- # from scan.estimated_cor_position
451
- if params.estimated_cor is None and scan.estimated_cor_frm_motor is not None:
452
- params.estimated_cor = scan.estimated_cor_frm_motor
418
+ # from scan.x_rotation_axis_pixel_position
419
+ if (
420
+ params.estimated_cor is None
421
+ and scan.x_rotation_axis_pixel_position is not None
422
+ ):
423
+ params.estimated_cor = scan.x_rotation_axis_pixel_position
453
424
  _logger.info(
454
425
  f"{scan}: set estimated cor from motor position ({params.estimated_cor})"
455
426
  )
@@ -1,34 +1,5 @@
1
1
  # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
-
26
- __authors__ = ["H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "04/05/2021"
29
-
30
-
31
- import typing
2
+ from __future__ import annotations
32
3
 
33
4
  from tomwer.core.process.reconstruction.nabu.utils import retrieve_lst_of_value_from_str
34
5
  from tomwer.core.process.reconstruction.scores.params import SABaseParams
@@ -59,7 +30,7 @@ class SADeltaBetaParams(SABaseParams):
59
30
  self._selected_db = value
60
31
 
61
32
  @property
62
- def selected_delta_beta_value(self) -> typing.Union[None, float]:
33
+ def selected_delta_beta_value(self) -> float | None:
63
34
  return self._selected_db
64
35
 
65
36
  def to_dict(self) -> dict: