tomwer 1.3.26__py3-none-any.whl → 1.4.0__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 (638) 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 +51 -60
  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 +41 -84
  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 -10
  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 +16 -5
  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 +47 -804
  138. tomwer/core/process/reconstruction/axis/mode.py +89 -25
  139. tomwer/core/process/reconstruction/axis/params.py +131 -283
  140. tomwer/core/process/reconstruction/axis/projectiontype.py +0 -28
  141. tomwer/core/process/reconstruction/axis/side.py +8 -0
  142. tomwer/core/process/reconstruction/darkref/darkrefs.py +14 -39
  143. tomwer/core/process/reconstruction/darkref/darkrefscopy.py +7 -39
  144. tomwer/core/process/reconstruction/darkref/params.py +1 -28
  145. tomwer/core/process/reconstruction/nabu/castvolume.py +19 -34
  146. tomwer/core/process/reconstruction/nabu/nabucommon.py +18 -43
  147. tomwer/core/process/reconstruction/nabu/nabuscores.py +64 -68
  148. tomwer/core/process/reconstruction/nabu/nabuslices.py +63 -105
  149. tomwer/core/process/reconstruction/nabu/nabuvolume.py +44 -70
  150. tomwer/core/process/reconstruction/nabu/plane.py +10 -0
  151. tomwer/core/process/reconstruction/nabu/settings.py +1 -28
  152. tomwer/core/process/reconstruction/nabu/target.py +0 -28
  153. tomwer/core/process/reconstruction/nabu/test/test_castvolume.py +116 -0
  154. tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py +277 -0
  155. tomwer/core/process/reconstruction/nabu/test/test_nabunormalization.py +199 -0
  156. tomwer/core/process/reconstruction/nabu/utils.py +11 -60
  157. tomwer/core/process/reconstruction/normalization/normalization.py +2 -32
  158. tomwer/core/process/reconstruction/normalization/params.py +3 -35
  159. tomwer/core/process/reconstruction/output.py +14 -19
  160. tomwer/core/process/reconstruction/paramsbase.py +4 -33
  161. tomwer/core/process/reconstruction/saaxis/params.py +5 -33
  162. tomwer/core/process/reconstruction/saaxis/saaxis.py +22 -51
  163. tomwer/core/process/reconstruction/sadeltabeta/params.py +2 -31
  164. tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +18 -46
  165. tomwer/core/process/reconstruction/scores/params.py +9 -39
  166. tomwer/core/process/reconstruction/scores/scores.py +10 -42
  167. tomwer/core/process/reconstruction/tests/__init__.py +0 -0
  168. tomwer/core/process/reconstruction/tests/test_axis.py +46 -0
  169. tomwer/core/process/reconstruction/tests/test_darkref.py +33 -0
  170. tomwer/core/process/reconstruction/{test → tests}/test_saaxis.py +1 -27
  171. tomwer/core/process/reconstruction/tests/test_sadeltabeta.py +48 -0
  172. tomwer/core/process/reconstruction/{test → tests}/test_utils.py +4 -4
  173. tomwer/core/process/reconstruction/utils/cor.py +8 -4
  174. tomwer/core/process/script/python.py +1 -27
  175. tomwer/core/process/script/tests/test_script.py +41 -0
  176. tomwer/core/process/stitching/metadataholder.py +5 -4
  177. tomwer/core/process/stitching/nabustitcher.py +35 -5
  178. tomwer/core/process/stitching/tests/test_metadataholder.py +17 -0
  179. tomwer/core/process/task.py +20 -63
  180. tomwer/core/process/tests/__init__.py +0 -0
  181. tomwer/core/process/{test → tests}/test_conditions.py +1 -28
  182. tomwer/core/process/{test → tests}/test_dark_and_flat.py +1 -27
  183. tomwer/core/process/{test → tests}/test_data_listener.py +1 -27
  184. tomwer/core/process/{test → tests}/test_data_transfer.py +2 -28
  185. tomwer/core/process/{test → tests}/test_data_watcher.py +1 -27
  186. tomwer/core/process/{test → tests}/test_nabu.py +2 -33
  187. tomwer/core/process/{test → tests}/test_normalization.py +1 -26
  188. tomwer/core/process/{test → tests}/test_timer.py +1 -27
  189. tomwer/core/process/utils.py +2 -31
  190. tomwer/core/process/visualization/dataviewer.py +1 -26
  191. tomwer/core/process/visualization/diffviewer.py +1 -26
  192. tomwer/core/process/visualization/imagestackviewer.py +0 -26
  193. tomwer/core/process/visualization/radiostack.py +0 -26
  194. tomwer/core/process/visualization/samplemoved.py +0 -28
  195. tomwer/core/process/visualization/sinogramviewer.py +0 -27
  196. tomwer/core/process/visualization/slicestack.py +0 -28
  197. tomwer/core/process/visualization/tests/test_data_viewer.py +12 -0
  198. tomwer/core/process/visualization/tests/test_diff_viewer.py +12 -0
  199. tomwer/core/process/visualization/tests/test_image_stack_viewer.py +14 -0
  200. tomwer/core/process/visualization/tests/test_radio_stack.py +12 -0
  201. tomwer/core/process/visualization/tests/test_sample_moved.py +14 -0
  202. tomwer/core/process/visualization/tests/test_sinogram_viewer.py +13 -0
  203. tomwer/core/process/visualization/tests/test_slice_stack.py +13 -0
  204. tomwer/core/process/visualization/tests/test_volume_viewer.py +12 -0
  205. tomwer/core/process/visualization/volumeviewer.py +0 -29
  206. tomwer/core/scan/__init__.py +3 -27
  207. tomwer/core/scan/blissscan.py +5 -34
  208. tomwer/core/scan/edfscan.py +19 -53
  209. tomwer/core/scan/hdf5scan.py +2 -2
  210. tomwer/core/scan/nxtomoscan.py +48 -54
  211. tomwer/core/scan/scanbase.py +107 -203
  212. tomwer/core/scan/scanfactory.py +11 -41
  213. tomwer/core/scan/tests/__init__.py +0 -0
  214. tomwer/core/scan/tests/test_edf.py +25 -0
  215. tomwer/core/scan/tests/test_future_scan.py +35 -0
  216. tomwer/core/scan/tests/test_nxtomoscan.py +143 -0
  217. tomwer/core/scan/tests/test_process_registration.py +64 -0
  218. tomwer/core/settings.py +18 -40
  219. tomwer/core/tests/__init__.py +0 -0
  220. tomwer/core/tests/test_scanutils.py +26 -0
  221. tomwer/core/{test → tests}/test_utils.py +1 -28
  222. tomwer/core/tomwer_object.py +4 -0
  223. tomwer/core/utils/__init__.py +2 -0
  224. tomwer/core/utils/char.py +0 -28
  225. tomwer/core/utils/deprecation.py +12 -38
  226. tomwer/core/utils/dictutils.py +1 -3
  227. tomwer/core/utils/ftseriesutils.py +1 -27
  228. tomwer/core/utils/gpu.py +0 -28
  229. tomwer/core/utils/image.py +8 -39
  230. tomwer/core/utils/locker.py +1 -28
  231. tomwer/core/utils/logconfig.py +0 -27
  232. tomwer/core/utils/normalization.py +4 -31
  233. tomwer/core/utils/nxtomoutils.py +8 -38
  234. tomwer/core/utils/resource.py +0 -26
  235. tomwer/core/utils/scanutils.py +23 -52
  236. tomwer/core/utils/slurm.py +7 -30
  237. tomwer/core/utils/spec.py +6 -6
  238. tomwer/core/utils/tests/__init__.py +0 -0
  239. tomwer/core/utils/tests/test_image.py +30 -0
  240. tomwer/core/utils/tests/test_nxtomo.py +38 -0
  241. tomwer/core/utils/tests/test_scan_utils.py +46 -0
  242. tomwer/core/utils/tests/test_time.py +6 -0
  243. tomwer/core/utils/threads.py +0 -26
  244. tomwer/core/utils/time.py +0 -27
  245. tomwer/core/volume/__init__.py +4 -0
  246. tomwer/core/volume/edfvolume.py +1 -28
  247. tomwer/core/volume/hdf5volume.py +1 -28
  248. tomwer/core/volume/jp2kvolume.py +1 -27
  249. tomwer/core/volume/rawvolume.py +1 -28
  250. tomwer/core/volume/tests/test_volumes.py +21 -0
  251. tomwer/core/volume/tiffvolume.py +1 -28
  252. tomwer/core/volume/volumebase.py +5 -0
  253. tomwer/core/volume/volumefactory.py +7 -33
  254. tomwer/gui/__init__.py +0 -28
  255. tomwer/gui/cluster/__init__.py +2 -0
  256. tomwer/gui/cluster/slurm.py +297 -95
  257. tomwer/gui/cluster/supervisor.py +1 -27
  258. tomwer/gui/cluster/tests/__init__.py +0 -0
  259. tomwer/gui/cluster/{test → tests}/test_cluster.py +21 -26
  260. tomwer/gui/cluster/{test → tests}/test_supervisor.py +1 -27
  261. tomwer/gui/conditions/__init__.py +2 -0
  262. tomwer/gui/conditions/filter.py +1 -26
  263. tomwer/gui/configuration/__init__.py +2 -0
  264. tomwer/gui/control/__init__.py +2 -0
  265. tomwer/gui/control/actions.py +2 -28
  266. tomwer/gui/control/datadiscovery.py +4 -3
  267. tomwer/gui/control/datalist.py +64 -69
  268. tomwer/gui/control/datalistener.py +1 -39
  269. tomwer/gui/control/datareacheractions.py +1 -28
  270. tomwer/gui/control/datatransfert.py +2 -29
  271. tomwer/gui/control/datavalidator.py +3 -37
  272. tomwer/gui/control/datawatcher/__init__.py +0 -28
  273. tomwer/gui/control/datawatcher/configuration.py +1 -28
  274. tomwer/gui/control/datawatcher/datawatcher.py +3 -32
  275. tomwer/gui/control/datawatcher/datawatcherobserver.py +2 -28
  276. tomwer/gui/control/history.py +5 -35
  277. tomwer/gui/control/nxtomomill.py +3 -30
  278. tomwer/gui/control/observations.py +61 -55
  279. tomwer/gui/control/reducedarkflatselector.py +24 -20
  280. tomwer/gui/control/scanselectorwidget.py +2 -28
  281. tomwer/gui/control/selectorwidgetbase.py +17 -17
  282. tomwer/gui/control/series/__init__.py +0 -0
  283. tomwer/gui/control/{serie/seriecreator.py → series/seriescreator.py} +214 -235
  284. tomwer/gui/control/series/serieswaiter.py +0 -0
  285. tomwer/gui/control/series/test/test_creator.py +424 -0
  286. tomwer/gui/control/series/test/test_nxtomo_concatenate.py +21 -0
  287. tomwer/gui/control/singletomoobj.py +1 -1
  288. tomwer/gui/control/tests/__init__.py +0 -0
  289. tomwer/gui/control/tests/test_datalist.py +47 -0
  290. tomwer/gui/control/{test → tests}/test_datalistener.py +1 -28
  291. tomwer/gui/control/tests/test_datavalidator.py +27 -0
  292. tomwer/gui/control/{test → tests}/test_inputwidget.py +1 -27
  293. tomwer/gui/control/tests/test_process_manager.py +38 -0
  294. tomwer/gui/control/tests/test_scan_observations.py +23 -0
  295. tomwer/gui/control/tests/test_scanselector.py +42 -0
  296. tomwer/gui/control/{test → tests}/test_scanvalidator.py +1 -27
  297. tomwer/gui/control/{test → tests}/test_volume_dialog.py +2 -30
  298. tomwer/gui/control/{test → tests}/test_volumeselector.py +1 -27
  299. tomwer/gui/control/volumeselectorwidget.py +2 -30
  300. tomwer/gui/dataportal/__init__.py +2 -0
  301. tomwer/gui/{icat → dataportal}/createscreenshots.py +3 -2
  302. tomwer/gui/dataportal/gallery.py +133 -0
  303. tomwer/gui/dataportal/outputformat.py +0 -0
  304. tomwer/gui/dataportal/publish.py +96 -0
  305. tomwer/gui/dataportal/tests/test_create_screenshots_gui.py +23 -0
  306. tomwer/gui/dataportal/tests/test_gallery_gui.py +21 -0
  307. tomwer/gui/debugtools/__init__.py +2 -0
  308. tomwer/gui/debugtools/datasetgenerator.py +1 -30
  309. tomwer/gui/debugtools/objectinspector.py +1 -29
  310. tomwer/gui/dialog/QDataDialog.py +89 -0
  311. tomwer/gui/{qfolderdialog.py → dialog/QVolumeDialog.py} +8 -107
  312. tomwer/gui/dialog/__init__.py +1 -0
  313. tomwer/gui/edit/__init__.py +2 -0
  314. tomwer/gui/edit/dkrfpatch.py +52 -87
  315. tomwer/gui/edit/imagekeyeditor.py +18 -54
  316. tomwer/gui/edit/nxtomoeditor.py +113 -300
  317. tomwer/gui/edit/nxtomowarmer.py +3 -2
  318. tomwer/gui/edit/tests/__init__.py +0 -0
  319. tomwer/gui/edit/{test → tests}/test_dkrf_patch.py +3 -29
  320. tomwer/gui/edit/{test → tests}/test_image_key_editor.py +1 -27
  321. tomwer/gui/edit/{test → tests}/test_nx_editor.py +45 -23
  322. tomwer/gui/fonts.py +5 -0
  323. tomwer/gui/icons.py +28 -66
  324. tomwer/gui/illustrations.py +4 -34
  325. tomwer/gui/imagefromfile.py +5 -30
  326. tomwer/gui/metadataloader.py +36 -0
  327. tomwer/gui/qconfigfile.py +3 -0
  328. tomwer/gui/qlefilesystem.py +3 -0
  329. tomwer/gui/reconstruction/__init__.py +2 -0
  330. tomwer/gui/reconstruction/axis/AxisMainWindow.py +275 -0
  331. tomwer/gui/reconstruction/axis/AxisOptionsWidget.py +313 -0
  332. tomwer/gui/reconstruction/axis/AxisSettingsWidget.py +797 -0
  333. tomwer/gui/reconstruction/axis/AxisWidget.py +534 -0
  334. tomwer/gui/reconstruction/axis/CalculationWidget.py +218 -0
  335. tomwer/gui/reconstruction/axis/CompareImages.py +11 -44
  336. tomwer/gui/reconstruction/axis/ControlWidget.py +285 -0
  337. tomwer/gui/reconstruction/axis/EstimatedCORWidget.py +394 -0
  338. tomwer/gui/reconstruction/axis/EstimatedCorComboBox.py +118 -0
  339. tomwer/gui/reconstruction/axis/InputWidget.py +347 -0
  340. tomwer/gui/reconstruction/axis/ManualFramesSelection.py +168 -0
  341. tomwer/gui/reconstruction/axis/__init__.py +2 -2
  342. tomwer/gui/reconstruction/darkref/__init__.py +0 -27
  343. tomwer/gui/reconstruction/darkref/darkrefcopywidget.py +5 -34
  344. tomwer/gui/reconstruction/darkref/darkrefwidget.py +1 -27
  345. tomwer/gui/reconstruction/nabu/castvolume.py +40 -59
  346. tomwer/gui/reconstruction/nabu/check.py +7 -33
  347. tomwer/gui/reconstruction/nabu/nabuconfig/base.py +7 -34
  348. tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py +6 -5
  349. tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py +10 -69
  350. tomwer/gui/reconstruction/nabu/nabuconfig/output.py +3 -47
  351. tomwer/gui/reconstruction/nabu/nabuconfig/phase.py +54 -36
  352. tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py +103 -54
  353. tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py +116 -65
  354. tomwer/gui/reconstruction/nabu/nabuflow.py +31 -61
  355. tomwer/gui/reconstruction/nabu/platform.py +94 -0
  356. tomwer/gui/reconstruction/nabu/slices.py +81 -45
  357. tomwer/gui/reconstruction/nabu/slurm.py +1 -27
  358. tomwer/gui/reconstruction/nabu/test/test_cast_volume.py +82 -0
  359. tomwer/gui/reconstruction/nabu/test/test_check.py +66 -0
  360. tomwer/gui/reconstruction/nabu/test/test_ctf.py +46 -0
  361. tomwer/gui/reconstruction/nabu/test/test_helical.py +21 -0
  362. tomwer/gui/reconstruction/nabu/test/test_nabu_preprocessing.py +81 -0
  363. tomwer/gui/reconstruction/nabu/volume.py +62 -90
  364. tomwer/gui/reconstruction/normalization/intensity.py +5 -32
  365. tomwer/gui/reconstruction/normalization/test/test_intensity.py +89 -0
  366. tomwer/gui/reconstruction/saaxis/corrangeselector.py +32 -56
  367. tomwer/gui/reconstruction/saaxis/dimensionwidget.py +56 -96
  368. tomwer/gui/reconstruction/saaxis/saaxis.py +17 -38
  369. tomwer/gui/reconstruction/saaxis/sliceselector.py +8 -39
  370. tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py +19 -37
  371. tomwer/gui/reconstruction/scores/control.py +2 -30
  372. tomwer/gui/reconstruction/scores/scoreplot.py +23 -49
  373. tomwer/gui/reconstruction/tests/__init__.py +0 -0
  374. tomwer/gui/reconstruction/{test → tests}/test_axis.py +23 -49
  375. tomwer/gui/reconstruction/{test → tests}/test_nabu.py +16 -31
  376. tomwer/gui/reconstruction/{test → tests}/test_saaxis.py +10 -37
  377. tomwer/gui/reconstruction/{test → tests}/test_sadeltabeta.py +1 -26
  378. tomwer/gui/samplemoved/__init__.py +2 -30
  379. tomwer/gui/samplemoved/selectiontable.py +3 -33
  380. tomwer/gui/settings.py +7 -0
  381. tomwer/gui/stackplot.py +33 -661
  382. tomwer/gui/stacks.py +261 -135
  383. tomwer/gui/stitching/SingleAxisStitchingWidget.py +326 -0
  384. tomwer/gui/stitching/StitchingOptionsWidget.py +438 -0
  385. tomwer/gui/stitching/StitchingWindow.py +586 -0
  386. tomwer/gui/stitching/__init__.py +2 -0
  387. tomwer/gui/stitching/alignment.py +90 -0
  388. tomwer/gui/stitching/axisorderedlist.py +44 -34
  389. tomwer/gui/stitching/config/axisparams.py +25 -11
  390. tomwer/gui/stitching/config/output.py +6 -5
  391. tomwer/gui/stitching/config/positionoveraxis.py +313 -51
  392. tomwer/gui/stitching/config/stitchingstrategies.py +22 -16
  393. tomwer/gui/stitching/config/tests/test_axisparams.py +25 -0
  394. tomwer/gui/stitching/config/tomoobjdetails.py +3 -5
  395. tomwer/gui/stitching/normalization.py +1 -0
  396. tomwer/gui/stitching/preview.py +59 -0
  397. tomwer/gui/stitching/singleaxis.py +57 -0
  398. tomwer/gui/stitching/stitchandbackground.py +3 -2
  399. tomwer/gui/stitching/stitching_preview.py +44 -36
  400. tomwer/gui/stitching/stitching_raw.py +5 -3
  401. tomwer/gui/stitching/tests/test_ZStitchingWindow.py +88 -0
  402. tomwer/gui/stitching/tests/test_axis_ordered_list.py +21 -0
  403. tomwer/gui/stitching/tests/test_normalization.py +27 -0
  404. tomwer/gui/stitching/tests/test_preview.py +68 -0
  405. tomwer/gui/stitching/tests/test_stitching_raw.py +110 -0
  406. tomwer/gui/stitching/tests/utils.py +92 -0
  407. tomwer/gui/stitching/utils.py +14 -0
  408. tomwer/gui/stitching/z_stitching/fineestimation.py +5 -33
  409. tomwer/gui/stitching/z_stitching/tests/test_fine_estimation.py +35 -0
  410. tomwer/gui/stitching/z_stitching/tests/test_raw_estimation.py +215 -0
  411. tomwer/gui/stitching/z_stitching/tests/test_stitching_window.py +51 -0
  412. tomwer/gui/tests/__init__.py +0 -0
  413. tomwer/gui/tests/test_axis_gui.py +43 -0
  414. tomwer/gui/{test → tests}/test_qfolder_dialog.py +1 -1
  415. tomwer/gui/utils/RangeWidget.py +44 -0
  416. tomwer/gui/utils/buttons.py +4 -3
  417. tomwer/gui/utils/completer.py +2 -33
  418. tomwer/gui/utils/flow.py +11 -40
  419. tomwer/gui/utils/gpu.py +60 -0
  420. tomwer/gui/utils/illustrations.py +1 -26
  421. tomwer/gui/utils/inputwidget.py +35 -73
  422. tomwer/gui/utils/lineselector/lineselector.py +9 -46
  423. tomwer/gui/utils/loadingmode.py +81 -0
  424. tomwer/gui/utils/qt_utils.py +9 -0
  425. tomwer/gui/utils/sandboxes.py +1 -26
  426. tomwer/gui/utils/scandescription.py +2 -31
  427. tomwer/gui/utils/scrollarea.py +6 -55
  428. tomwer/gui/utils/slider.py +4 -28
  429. tomwer/gui/utils/splashscreen.py +0 -28
  430. tomwer/gui/utils/step.py +14 -13
  431. tomwer/gui/utils/tests/test_completer.py +41 -0
  432. tomwer/gui/utils/tests/test_line_selector.py +21 -0
  433. tomwer/gui/utils/tests/test_splashscreen.py +8 -0
  434. tomwer/gui/utils/tests/test_vignettes.py +68 -0
  435. tomwer/gui/utils/unitsystem.py +15 -69
  436. tomwer/gui/utils/utils.py +4 -5
  437. tomwer/gui/utils/vignettes.py +10 -41
  438. tomwer/gui/utils/waiterthread.py +0 -26
  439. tomwer/gui/visualization/__init__.py +2 -0
  440. tomwer/gui/visualization/dataviewer.py +68 -421
  441. tomwer/gui/visualization/diffviewer/diffviewer.py +2 -30
  442. tomwer/gui/visualization/diffviewer/shiftwidget.py +4 -29
  443. tomwer/gui/visualization/fullscreenplot.py +5 -5
  444. tomwer/gui/visualization/imagestack.py +403 -0
  445. tomwer/gui/visualization/nxtomometadata.py +0 -4
  446. tomwer/gui/visualization/reconstructionparameters.py +14 -32
  447. tomwer/gui/visualization/scanoverview.py +33 -66
  448. tomwer/gui/visualization/sinogramviewer.py +2 -28
  449. tomwer/gui/visualization/test/__init__.py +0 -28
  450. tomwer/gui/visualization/test/test_dataviewer.py +1 -28
  451. tomwer/gui/visualization/test/test_diffviewer.py +1 -28
  452. tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py +0 -5
  453. tomwer/gui/visualization/test/test_reconstruction_parameters.py +1 -27
  454. tomwer/gui/visualization/test/test_sinogramviewer.py +1 -28
  455. tomwer/gui/visualization/test/test_stacks.py +184 -115
  456. tomwer/gui/visualization/test/test_volumeviewer.py +3 -2
  457. tomwer/gui/visualization/tomoobjoverview.py +2 -2
  458. tomwer/gui/visualization/volumeoverview.py +3 -2
  459. tomwer/gui/visualization/volumeviewer.py +47 -43
  460. tomwer/io/__init__.py +2 -0
  461. tomwer/io/utils/h5pyutils.py +1 -27
  462. tomwer/io/utils/test/test_raw_and_processed_data.py +10 -0
  463. tomwer/io/utils/test/test_utils.py +67 -0
  464. tomwer/io/utils/utils.py +2 -31
  465. tomwer/resources/__init__.py +13 -33
  466. tomwer/resources/gui/icons/edit_downstream.svg +114 -0
  467. tomwer/resources/gui/icons/edit_upstream.svg +112 -0
  468. tomwer/resources/gui/icons/free_edition.svg +23 -0
  469. tomwer/resources/gui/icons/icat_gallery_opts.png +0 -0
  470. tomwer/resources/gui/icons/icat_gallery_opts.svg +80 -0
  471. tomwer/resources/gui/icons/search.png +0 -0
  472. tomwer/resources/gui/icons/search.svg +23 -0
  473. tomwer/resources/gui/icons/warning.png +0 -0
  474. tomwer/synctools/__init__.py +2 -0
  475. tomwer/synctools/axis.py +1 -27
  476. tomwer/synctools/darkref.py +1 -26
  477. tomwer/synctools/datalistener.py +1 -27
  478. tomwer/synctools/datatransfert.py +2 -27
  479. tomwer/synctools/imageloaderthread.py +1 -28
  480. tomwer/synctools/rsyncmanager.py +1 -25
  481. tomwer/synctools/saaxis.py +1 -26
  482. tomwer/synctools/sadeltabeta.py +1 -26
  483. tomwer/synctools/stacks/control/datalistener.py +1 -26
  484. tomwer/synctools/stacks/processingstack.py +4 -33
  485. tomwer/synctools/stacks/reconstruction/axis.py +6 -53
  486. tomwer/synctools/stacks/reconstruction/castvolume.py +12 -43
  487. tomwer/synctools/stacks/reconstruction/dkrefcopy.py +4 -27
  488. tomwer/synctools/stacks/reconstruction/nabu.py +3 -28
  489. tomwer/synctools/stacks/reconstruction/normalization.py +2 -27
  490. tomwer/synctools/stacks/reconstruction/saaxis.py +2 -27
  491. tomwer/synctools/stacks/reconstruction/sadeltabeta.py +2 -27
  492. tomwer/synctools/tests/__init__.py +0 -0
  493. tomwer/synctools/{test → tests}/test_darkRefs.py +16 -40
  494. tomwer/synctools/{test → tests}/test_foldertransfer.py +2 -33
  495. tomwer/synctools/utils/scanstages.py +2 -31
  496. tomwer/tests/__init__.py +1 -0
  497. tomwer/tests/app/test_stitching.py +95 -0
  498. tomwer/tests/datasets.py +1 -5
  499. tomwer/tests/orangecontrib/tomwer/widgets/cluster/tests/test_future_supervisorow.py +48 -0
  500. tomwer/tests/orangecontrib/tomwer/widgets/cluster/tests/test_slurm_clusterow.py +40 -0
  501. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_advancement.py +8 -0
  502. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_data_validator.py +55 -0
  503. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datadiscovery.py +129 -0
  504. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datalistener.py +111 -0
  505. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_dataselector.py +69 -0
  506. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datawatcher.py +411 -0
  507. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_emailow.py +29 -0
  508. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_notifier.py +24 -0
  509. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_nxtomo_concatenate_ow.py +64 -0
  510. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_nxtomomill.py +133 -0
  511. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_reduce_dark_flat_selector.py +40 -0
  512. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_singletomoobj.py +40 -0
  513. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_timerow.py +25 -0
  514. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_tomoobj_series.py +96 -0
  515. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_volume_selector.py +69 -0
  516. orangecontrib/tomwer/widgets/edit/test/test_image_key_editor.py → tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_dataset_generator.py +17 -16
  517. tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_object_inspector.py +36 -0
  518. {orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_dark_flat_patch.py +1 -27
  519. tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_image_key_editor.py +30 -0
  520. tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py +138 -0
  521. tomwer/tests/orangecontrib/tomwer/widgets/other/tests/test_pythonscript.py +31 -0
  522. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_axis.py +199 -0
  523. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_cast_volumeow.py +58 -0
  524. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_dark_refs_widget.py +136 -0
  525. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_delta_beta_selector.py +15 -0
  526. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_i_norm.py +200 -0
  527. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_helical_prepare_weights_double.py +20 -0
  528. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_volume.py +74 -0
  529. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_widget.py +107 -0
  530. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_sa_delta_beta.py +194 -0
  531. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_saaxis.py +194 -0
  532. tomwer/tests/orangecontrib/tomwer/widgets/stitching/tests/test_zstitching.py +313 -0
  533. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_conditions.py +85 -0
  534. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_darkref.py +225 -0
  535. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_foldertransfert.py +105 -0
  536. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_dataviewerow.py +57 -0
  537. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_diffviewerow.py +39 -0
  538. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_nxtomo_metadata_viewer.py +29 -0
  539. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_radio_stackow.py +31 -0
  540. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_sample_movedow.py +46 -0
  541. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_sinogram_viewerow.py +31 -0
  542. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_slice_stackow.py +31 -0
  543. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_volume_viewerow.py +32 -0
  544. tomwer/tests/test_ewoks/test_conversion.py +104 -0
  545. tomwer/tests/test_ewoks/test_single_node_execution.py +87 -0
  546. tomwer/tests/test_ewoks/test_workflows.py +138 -0
  547. tomwer/utils.py +11 -39
  548. tomwer/version.py +2 -2
  549. {tomwer-1.3.26.dist-info → tomwer-1.4.0.dist-info}/LICENSE +3 -3
  550. tomwer-1.4.0.dist-info/METADATA +337 -0
  551. tomwer-1.4.0.dist-info/RECORD +912 -0
  552. {tomwer-1.3.26.dist-info → tomwer-1.4.0.dist-info}/WHEEL +1 -1
  553. {tomwer-1.3.26.dist-info → tomwer-1.4.0.dist-info}/entry_points.txt +1 -0
  554. orangecontrib/tomwer/widgets/control/DataListOW.py +0 -129
  555. orangecontrib/tomwer/widgets/control/TomoObjSerieOW.py +0 -86
  556. orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py +0 -182
  557. orangecontrib/tomwer/widgets/edit/test/test_nxtomo_editor.py +0 -141
  558. orangecontrib/tomwer/widgets/icat/PublishProcessedDataOW.py +0 -115
  559. orangecontrib/tomwer/widgets/icat/RawDataScreenshotCreatorOW.py +0 -98
  560. orangecontrib/tomwer/widgets/icat/SaveToGalleryAndPublishOW.py +0 -129
  561. orangecontrib/tomwer/widgets/icat/icons/add_gallery.png +0 -0
  562. orangecontrib/tomwer/widgets/icat/icons/add_gallery.svg +0 -82
  563. orangecontrib/tomwer/widgets/icat/icons/raw_screenshots.png +0 -0
  564. orangecontrib/tomwer/widgets/icat/icons/raw_screenshots.svg +0 -143
  565. orangecontrib/tomwer/widgets/visualization/LivesliceOW.py +0 -87
  566. orangecontrib/tomwer/widgets/visualization/icons/liveslice.png +0 -0
  567. orangecontrib/tomwer/widgets/visualization/icons/liveslice.svg +0 -110
  568. tomwer/core/log/logger.py +0 -130
  569. tomwer/core/process/control/test/test_volume_link.py +0 -74
  570. tomwer/core/process/control/tomoobjserie.py +0 -12
  571. tomwer/core/process/control/volumesymlink.py +0 -200
  572. tomwer/core/process/icat/createscreenshots.py +0 -100
  573. tomwer/core/process/icat/gallery.py +0 -377
  574. tomwer/core/process/icat/icatbase.py +0 -36
  575. tomwer/core/process/icat/publish.py +0 -228
  576. tomwer/core/process/icat/screenshots.py +0 -27
  577. tomwer/core/process/reconstruction/test/test_darkref.py +0 -60
  578. tomwer/core/process/reconstruction/test/test_sadeltabeta.py +0 -74
  579. tomwer/core/process/test/test_axis.py +0 -309
  580. tomwer/core/process/visualization/liveslice.py +0 -6
  581. tomwer/core/progress.py +0 -100
  582. tomwer/core/scan/test/test_edf.py +0 -53
  583. tomwer/core/scan/test/test_future_scan.py +0 -61
  584. tomwer/core/scan/test/test_h5.py +0 -96
  585. tomwer/core/scan/test/test_process_registration.py +0 -109
  586. tomwer/core/test/test_scanutils.py +0 -53
  587. tomwer/gui/control/emailnotifier.py +0 -174
  588. tomwer/gui/control/serie/seriewaiter.py +0 -28
  589. tomwer/gui/control/test/__init__.py +0 -28
  590. tomwer/gui/control/test/test_datalist.py +0 -96
  591. tomwer/gui/control/test/test_datavalidator.py +0 -54
  592. tomwer/gui/control/test/test_email.py +0 -35
  593. tomwer/gui/control/test/test_process_manager.py +0 -65
  594. tomwer/gui/control/test/test_scanselector.py +0 -67
  595. tomwer/gui/edit/test/__init__.py +0 -28
  596. tomwer/gui/icat/gallery.py +0 -214
  597. tomwer/gui/icat/publish.py +0 -187
  598. tomwer/gui/reconstruction/axis/axis.py +0 -733
  599. tomwer/gui/reconstruction/axis/radioaxis.py +0 -2467
  600. tomwer/gui/stitching/stitching.py +0 -1392
  601. tomwer/gui/test/__init__.py +0 -28
  602. tomwer/gui/test/test_axis_gui.py +0 -34
  603. tomwer/synctools/stacks/edit/darkflatpatch.py +0 -169
  604. tomwer/synctools/stacks/edit/imagekeyeditor.py +0 -135
  605. tomwer/third_part/WaitingOverlay.py +0 -110
  606. tomwer-1.3.26-py3.11-nspkg.pth +0 -1
  607. tomwer-1.3.26.dist-info/METADATA +0 -292
  608. tomwer-1.3.26.dist-info/RECORD +0 -785
  609. tomwer-1.3.26.dist-info/namespace_packages.txt +0 -1
  610. /orangecontrib/tomwer/{widgets/edit/test → tests}/__init__.py +0 -0
  611. {tomwer/core/process/control/test → orangecontrib/tomwer/tutorials/id16b}/__init__.py +0 -0
  612. {tomwer/core/process/icat → orangecontrib/tomwer/widgets/cluster/tests}/__init__.py +0 -0
  613. /orangecontrib/tomwer/widgets/control/icons/{tomoobjserie.png → tomoobjseries.png} +0 -0
  614. {tomwer/core/process/reconstruction/test → orangecontrib/tomwer/widgets/control/tests}/__init__.py +0 -0
  615. /orangecontrib/tomwer/widgets/{icat → dataportal}/icons/publish_processed_data.png +0 -0
  616. /orangecontrib/tomwer/widgets/{icat → dataportal}/icons/publish_processed_data.svg +0 -0
  617. {tomwer/core/process/test → orangecontrib/tomwer/widgets/debugtools/tests}/__init__.py +0 -0
  618. {tomwer/core/scan/test → orangecontrib/tomwer/widgets/edit/tests}/__init__.py +0 -0
  619. {tomwer/core/test → orangecontrib/tomwer/widgets/other/tests}/__init__.py +0 -0
  620. {tomwer/gui/cluster/test → orangecontrib/tomwer/widgets/reconstruction/tests}/__init__.py +0 -0
  621. {tomwer/gui/control/serie → orangecontrib/tomwer/widgets/stitching/tests}/__init__.py +0 -0
  622. {tomwer/gui/icat → orangecontrib/tomwer/widgets/tests}/__init__.py +0 -0
  623. {tomwer/gui/reconstruction/test → orangecontrib/tomwer/widgets/visualization/tests}/__init__.py +0 -0
  624. /tomwer/{synctools/stacks/edit → app/stitching}/__init__.py +0 -0
  625. /tomwer/{synctools/test → core/process/control/tests}/__init__.py +0 -0
  626. /tomwer/core/process/control/{test → tests}/test_email.py +0 -0
  627. /tomwer/core/process/control/{test → tests}/test_h52nx_process.py +0 -0
  628. /tomwer/{third_part → core/process/drac}/__init__.py +0 -0
  629. /tomwer/core/process/reconstruction/{test → tests}/test_axis_params.py +0 -0
  630. /tomwer/core/process/reconstruction/{test → tests}/test_darkref_copy.py +0 -0
  631. /tomwer/core/process/reconstruction/{test → tests}/test_paramsbase.py +0 -0
  632. /tomwer/core/scan/{test → tests}/test_scan.py +0 -0
  633. /tomwer/gui/control/{serie → series}/nxtomoconcatenate.py +0 -0
  634. /tomwer/gui/control/{test → tests}/test_datadiscovery.py +0 -0
  635. /tomwer/gui/control/{test → tests}/test_reducedarkflat_selector.py +0 -0
  636. /tomwer/gui/control/{test → tests}/test_single_tomo_obj.py +0 -0
  637. {orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_image_key_upgrader.py +0 -0
  638. {tomwer-1.3.26.dist-info → tomwer-1.4.0.dist-info}/top_level.txt +0 -0
@@ -1,30 +1,5 @@
1
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
- __authors__ = ["H. Payno"]
26
- __license__ = "MIT"
27
- __date__ = "19/10/2021"
2
+ from __future__ import annotations
28
3
 
29
4
 
30
5
  import pytest
@@ -33,9 +8,11 @@ from silx.gui.utils.testutils import TestCaseQt
33
8
 
34
9
  from tomwer.core.settings import SlurmSettings
35
10
  from tomwer.gui.cluster.slurm import (
11
+ is_op_account,
36
12
  SlurmSettingsMode,
37
13
  SlurmSettingsWidget,
38
14
  SlurmSettingsWindow,
15
+ _WallTime,
39
16
  )
40
17
  from tomwer.tests.utils import skip_gui_test
41
18
  from tomwer.tests.conftest import qtapp # noqa F401
@@ -63,6 +40,7 @@ class TestSlurmWidget(TestCaseQt):
63
40
  "job_name": "tomwer_{scan}_-_{process}_-_{info}",
64
41
  "n_jobs": 1,
65
42
  "modules": ("tomotools/stable",),
43
+ "walltime": "01:00:00",
66
44
  "sbatch_extra_params": {
67
45
  "export": "NONE",
68
46
  "gpu_card": None,
@@ -104,3 +82,20 @@ def test_SlurmSettingsWindow(qtapp): # noqa F811
104
82
  for mode in SlurmSettingsMode:
105
83
  widget.setCurrentSettingsMode(mode)
106
84
  widget.getConfiguration()
85
+
86
+
87
+ def test_is_op_account():
88
+ assert is_op_account("opid19")
89
+ assert not is_op_account("opid0")
90
+ assert not is_op_account("dopid05")
91
+ assert not is_op_account("opid")
92
+ assert is_op_account("opd12")
93
+
94
+
95
+ def test__WallTime():
96
+ assert _WallTime("11:00:02") > _WallTime("10:25:45")
97
+ assert _WallTime("1-00:00:00") > _WallTime("10:25:45")
98
+ assert _WallTime("01:00:0") < _WallTime("01:00:01")
99
+ assert _WallTime("1-00:00:00") == _WallTime(
100
+ "24:00:0"
101
+ ), f"{_WallTime('1-00:00:00').value} != {_WallTime('24:00:0').value} "
@@ -1,31 +1,5 @@
1
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
- __authors__ = ["H. Payno"]
26
- __license__ = "MIT"
27
- __date__ = "08/11/2021"
28
-
2
+ from __future__ import annotations
29
3
 
30
4
  import asyncio
31
5
  import os
@@ -0,0 +1,2 @@
1
+ """Widgets for conditions (filters to let a scan continue processing or not)
2
+ """
@@ -1,35 +1,10 @@
1
1
  # coding: utf-8
2
- # /*##########################################################################
3
- # Copyright (C) 2017 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
2
 
25
3
  """
26
4
  This module is used to define the process of the reference creator.
27
5
  This is related to the issue #184
28
6
  """
29
-
30
- __authors__ = ["H.Payno"]
31
- __license__ = "MIT"
32
- __date__ = "19/07/2018"
7
+ from __future__ import annotations
33
8
 
34
9
 
35
10
  from silx.gui import qt
@@ -0,0 +1,2 @@
1
+ """Widgets to define the configuration level we want to display (display only basic configuration/settings, advance...)
2
+ """
@@ -0,0 +1,2 @@
1
+ """Widgets related to 'control' tasks (select a scan, convert a scan with nxtomomill...)
2
+ """
@@ -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__ = ["C. Nemoz", "H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "23/03/2021"
29
-
2
+ from __future__ import annotations
30
3
 
31
4
  from silx.gui import qt
32
5
  from functools import partial
@@ -79,6 +52,7 @@ class TomoObjDisplayModeToolButton(qt.QToolButton):
79
52
  """
80
53
 
81
54
  sigDisplayModeChanged = qt.Signal(str)
55
+ """signal emit when the display mode change"""
82
56
 
83
57
  _SHORT_DESC_TOOLTIP = "Use a short description of the tomo object. Two different scans can have the same short desciption"
84
58
  _URL_TOOLTIP = (
@@ -1,4 +1,4 @@
1
- from typing import Optional
1
+ from __future__ import annotations
2
2
 
3
3
  from silx.gui import qt
4
4
 
@@ -9,6 +9,7 @@ from tomwer.gui.control.datawatcher.controlwidget import ControlWidget
9
9
 
10
10
  class ScanDiscoveryConfigWidget(qt.QGroupBox):
11
11
  sigScanTypeChanged = qt.Signal()
12
+ """emit when scan typo change"""
12
13
 
13
14
  def __init__(self, *args, **kwargs):
14
15
  super().__init__(*args, **kwargs)
@@ -86,14 +87,14 @@ class _MainWidget(qt.QWidget):
86
87
  def setFolderObserved(self, dir_):
87
88
  return self.controlWidget._qteFolderSelected.setText(dir_)
88
89
 
89
- def getLinuxFilePattern(self) -> Optional[str]:
90
+ def getLinuxFilePattern(self) -> str | None:
90
91
  text = self.controlWidget._filterQLE.text()
91
92
  if text.replace(" ", "") == "":
92
93
  return None
93
94
  else:
94
95
  return text
95
96
 
96
- def setLinuxFilePattern(self, pattern: Optional[str]):
97
+ def setLinuxFilePattern(self, pattern: str | None):
97
98
  if pattern is None:
98
99
  pattern = ""
99
100
  self.controlWidget._filterQLE.setText(pattern)
@@ -1,36 +1,9 @@
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__ = ["C. Nemoz", "H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "12/07/2022"
1
+ from __future__ import annotations
29
2
 
30
3
  import logging
31
4
  import os
32
5
  from collections import OrderedDict
33
- from typing import Any, Optional, Union
6
+ from typing import Any
34
7
  from nxtomomill import converter as nxtomomill_converter
35
8
  from nxtomomill.io import generate_default_edf_config, generate_default_h5_config
36
9
  from nxtomomill.io.config import TomoEDFConfig as EDFConfig
@@ -49,7 +22,8 @@ from tomwer.core.tomwer_object import TomwerObject
49
22
  from tomwer.core.volume.volumefactory import VolumeFactory
50
23
  from tomwer.io.utils.tomoobj import DEFAULT_SCHEME_TO_VOL
51
24
  from tomwer.gui.control.actions import CFGFileActiveLabel, NXTomomillParamsAction
52
- from tomwer.gui.qfolderdialog import QDataDialog, QVolumeDialog
25
+ from tomwer.gui.dialog.QDataDialog import QDataDialog
26
+ from tomwer.gui.dialog.QVolumeDialog import QVolumeDialog
53
27
  from tomwer.gui.utils.inputwidget import (
54
28
  EDFConfigFileSelector,
55
29
  HDF5ConfigFileSelector,
@@ -89,8 +63,10 @@ class _DataListDialog(qt.QDialog):
89
63
  self._rmAllButton = qt.QPushButton("Remove all", parent=self)
90
64
  self._buttons.addButton(self._rmAllButton, qt.QDialogButtonBox.ActionRole)
91
65
 
92
- self._sendButton = qt.QPushButton("Send", parent=self)
93
- self._buttons.addButton(self._sendButton, qt.QDialogButtonBox.AcceptRole)
66
+ self._sendSelectedButton = qt.QPushButton("Send selected", parent=self)
67
+ self._buttons.addButton(
68
+ self._sendSelectedButton, qt.QDialogButtonBox.AcceptRole
69
+ )
94
70
  self.layout().addWidget(self._buttons)
95
71
 
96
72
  # connect signal / slot
@@ -104,9 +80,6 @@ class _DataListDialog(qt.QDialog):
104
80
  def clear(self):
105
81
  self.datalist.clear()
106
82
 
107
- def _sendList(self):
108
- return self.datalist._sendList()
109
-
110
83
  def add(self, scan) -> tuple:
111
84
  added_objs = self.datalist.add(scan)
112
85
  self.datalist.setMySelection(added_objs)
@@ -219,25 +192,29 @@ class _NXtomomillConfigFileDialog(qt.QDialog):
219
192
 
220
193
 
221
194
  class BlissHDF5DataListDialog(_DataListDialog):
222
- """Dialog used to load .h5 only (used when for nxtomomillOW when we need)
223
- to do a conversion from bliss.h5 to NXtomo"""
195
+ """Dialog used to load .h5 files only (used for nxtomomillOW when we need to do a conversion from bliss.h5 to NXtomo)"""
224
196
 
225
197
  def __init__(self, parent):
226
198
  assert isinstance(parent, _RawDataListMainWindow)
227
199
  _DataListDialog.__init__(self, parent)
228
- self._sendButton.setText("Send all")
229
- self._sendSelectedButton = qt.QPushButton("Send selected", self)
230
- self._buttons.addButton(
231
- self._sendSelectedButton, qt.QDialogButtonBox.AcceptRole
232
- )
200
+ self._sendSelectedButton.setText("Send selected")
233
201
 
234
202
  def createDataList(self):
235
203
  return BlissScanList(self)
236
204
 
237
205
  def _callbackAddPath(self): # pragma: no cover
238
- """ """
206
+ """Open file dialog to select HDF5 files or directories, allowing multi-selection"""
239
207
  dialog = qt.QFileDialog(self)
240
- dialog.setNameFilters(["HDF5 file *.h5 *.hdf5 *.nx *.nexus", "nxs"])
208
+ dialog.setFileMode(qt.QFileDialog.ExistingFiles)
209
+ dialog.setNameFilters(
210
+ [
211
+ "HDF5 files (*.h5 *.hdf5)",
212
+ "Nexus files (*.h5 *.hdf5 *.nx *.nxs *.nexus)",
213
+ "Any files (*)",
214
+ ]
215
+ )
216
+
217
+ # Set default directory if available
241
218
  if os.environ.get("TOMWER_DEFAULT_INPUT_DIR", None) and os.path.exists(
242
219
  os.environ["TOMWER_DEFAULT_INPUT_DIR"]
243
220
  ):
@@ -266,26 +243,29 @@ class BlissHDF5DataListDialog(_DataListDialog):
266
243
 
267
244
 
268
245
  class EDFDataListDialog(_DataListDialog):
269
- """Dialog used to load .h5 only (used when for nxtomomillOW when we need)
270
- to do a conversion from bliss.h5 to NXtomo"""
246
+ """Dialog used to load EDF directories and files for conversion"""
271
247
 
272
248
  def __init__(self, parent):
273
249
  assert isinstance(parent, EDFDataListMainWindow)
274
250
  _DataListDialog.__init__(self, parent)
275
- self._sendButton.setText("Convert and send all")
276
- self._sendSelectedButton = qt.QPushButton("Convert and send selected", self)
277
- self._buttons.addButton(
278
- self._sendSelectedButton, qt.QDialogButtonBox.AcceptRole
279
- )
251
+ self._sendSelectedButton.setText("Convert and send selected")
280
252
 
281
253
  def createDataList(self):
282
254
  return EDFDataList(self)
283
255
 
284
256
  def _callbackAddPath(self): # pragma: no cover
285
- """ """
257
+ """Open file dialog to select EDF directories or files"""
286
258
  dialog = qt.QFileDialog(self)
287
259
  dialog.setFileMode(qt.QFileDialog.DirectoryOnly)
288
260
 
261
+ # Set default directory if available
262
+ if os.environ.get("TOMWER_DEFAULT_INPUT_DIR", None) and os.path.exists(
263
+ os.environ["TOMWER_DEFAULT_INPUT_DIR"]
264
+ ):
265
+ dialog.setDirectory(os.environ["TOMWER_DEFAULT_INPUT_DIR"])
266
+ elif os.path.isdir("/data"):
267
+ dialog.setDirectory("/data")
268
+
289
269
  if not dialog.exec_():
290
270
  dialog.close()
291
271
  return
@@ -355,7 +335,6 @@ class _RawDataListMainWindow(qt.QMainWindow):
355
335
  # expose API
356
336
  self.getCFGFilePath = self._dialog.getCFGFilePath
357
337
  self.setCFGFilePath = self._dialog.setCFGFilePath
358
- self._sendButton = self._widget._sendButton
359
338
  self._sendSelectedButton = self._widget._sendSelectedButton
360
339
  self.add = self._widget.add
361
340
  self.n_scan = self._widget.n_scan
@@ -454,7 +433,16 @@ class BlissHDF5DataListMainWindow(_RawDataListMainWindow):
454
433
  files_selected = file_dialog.selectedFiles()
455
434
  if len(files_selected) > 0:
456
435
  file_path = files_selected[0]
457
- configuration = generate_default_h5_config(config_3dxrd=False)
436
+ try:
437
+ # nxtomomill 1.1.0a5 or higher
438
+ configuration = (
439
+ generate_default_h5_config() # pylint: disable=E1123
440
+ )
441
+
442
+ except TypeError:
443
+ configuration = generate_default_h5_config( # pylint: disable=E1123
444
+ config_3dxrd=False
445
+ )
458
446
  HDF5Config.dict_to_cfg(file_path=file_path, dict_=configuration)
459
447
  # if we create a configuration file then let consider we want to use it
460
448
  self.setCFGFilePath(file_path)
@@ -499,7 +487,7 @@ class EDFDataListMainWindow(_RawDataListMainWindow):
499
487
 
500
488
 
501
489
  class GenericScanListDialog(_DataListDialog):
502
- """Dialog used to load EDFScan or HEDF5 scans"""
490
+ """Dialog used to load EDFScan or HDF5 scans"""
503
491
 
504
492
  def createDataList(self):
505
493
  return GenericScanList(self)
@@ -564,7 +552,7 @@ class GenericScanListWindow(qt.QMainWindow):
564
552
  return self._widget.n_scan()
565
553
 
566
554
  def add(self, *args, **kwargs):
567
- self._widget.add(*args, **kwargs)
555
+ return self._widget.add(*args, **kwargs)
568
556
 
569
557
 
570
558
  class VolumeListDialog(_DataListDialog):
@@ -644,12 +632,13 @@ class _TomwerObjectList(qt.QTableWidget):
644
632
  pass
645
633
  self._update()
646
634
 
647
- def _sendList(self):
635
+ def _sendSelected(self):
636
+ raise NotImplementedError
648
637
  for _, item in self._myitems.items():
649
638
  data = item.data(qt.Qt.UserRole)
650
639
  self.dataReady.emit(data)
651
640
 
652
- def remove(self, data: Union[None, TomwerObject, str]):
641
+ def remove(self, data: TomwerObject | str | None):
653
642
  if data is None:
654
643
  return
655
644
  if isinstance(data, str):
@@ -688,20 +677,18 @@ class _TomwerObjectList(qt.QTableWidget):
688
677
  """
689
678
  some rules to return a TomwerObject from an object (probably a path) from children class
690
679
 
691
- :param bool allow_several: allow returning several objects for one input. This can be the case for example if 'obj' is a file path.
680
+ :param allow_several: allow returning several objects for one input. This can be the case for example if 'obj' is a file path.
692
681
  """
693
682
  raise NotImplementedError("Base class")
694
683
 
695
- def add(
696
- self, obj: Union[None, TomwerObject, str, BaseIdentifier]
697
- ) -> Optional[tuple]:
684
+ def add(self, obj: TomwerObject | BaseIdentifier | str | None) -> tuple | None:
698
685
  """add a data"""
699
686
  if obj is None:
700
687
  return
701
688
  if isinstance(obj, TomwerObject):
702
689
  # remove heavy cache obj. This could bring troubles if some processing is done.
703
690
  # but I guess this is better than keeping in memory volumes...
704
- # nethertheless processing using volume.data should keep a reference on the data.
691
+ # nevertheless processing using volume.data should keep a reference on the data.
705
692
  obj._clear_heavy_cache()
706
693
  elif isinstance(obj, str):
707
694
  obj = self._getTomoObject(obj, allow_several=True)
@@ -709,9 +696,10 @@ class _TomwerObjectList(qt.QTableWidget):
709
696
  return
710
697
  elif isinstance(obj, (tuple, list)):
711
698
  # in the case it contains in fact several objects. Related to allow_several=True
699
+ new_objs = []
712
700
  for o in obj:
713
- self.add(o)
714
- return
701
+ new_objs.extend(list(self.add(o)))
702
+ return new_objs
715
703
  elif not isinstance(obj, TomwerObject):
716
704
  raise TypeError(
717
705
  f"return object from _getTomoObject is not a {TomwerObject} but {type(obj)}"
@@ -760,9 +748,17 @@ class _TomwerObjectList(qt.QTableWidget):
760
748
  f"Requested display mode {self._displayMode} is not handled"
761
749
  )
762
750
 
763
- def setMySelection(self, datasets: tuple):
751
+ def setMySelection(self, datasets: tuple[str | TomwerObject]):
764
752
  if datasets is None:
765
753
  datasets = tuple()
754
+
755
+ def convert_dataset(dataset: str | TomwerObject):
756
+ if isinstance(dataset, TomwerObject):
757
+ return dataset.get_identifier().to_str()
758
+ else:
759
+ return dataset
760
+
761
+ datasets = tuple([convert_dataset(dataset) for dataset in datasets])
766
762
  for row in range(self.rowCount()):
767
763
  item = self.item(row, 0)
768
764
  select_it = (
@@ -856,7 +852,7 @@ class _TomwerObjectList(qt.QTableWidget):
856
852
  try:
857
853
  self.add(identifier)
858
854
  except Exception as e:
859
- logger.error(f"Failed to add {identifier}. Error is {e}")
855
+ logger.error(f"Failed to add '{identifier}'. Error is {e}")
860
856
 
861
857
 
862
858
  class GenericScanList(_TomwerObjectList):
@@ -925,8 +921,7 @@ class BlissScanList(_TomwerObjectList):
925
921
  def add(self, data) -> tuple:
926
922
  """Add the path folder d in the scan list
927
923
 
928
- :param d: the path of the directory to add
929
- :type d: Union[str, TomoBase]
924
+ :param data: the path of the directory to add
930
925
  """
931
926
  possible_entries = []
932
927
  if os.path.exists(data):
@@ -1,36 +1,9 @@
1
1
  # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016 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__ = "16/03/2020"
2
+ from __future__ import annotations
29
3
 
30
4
 
31
5
  import os
32
6
  import socket
33
- import weakref
34
7
 
35
8
  from silx.gui import qt
36
9
 
@@ -160,17 +133,6 @@ class DataListenerWidget(qt.QMainWindow):
160
133
  def setOutputFolder(self, output_dir):
161
134
  self._configWindow.setOutputFolder(output_dir)
162
135
 
163
- def setListener(self, listener):
164
- self._listener = weakref.ref(listener, self._cleanConnection)
165
- self._listener().sigAcquisitionStarted.connect(self._acquisitionStarted)
166
- self._listener().sigScanAdded.connect(self._acquisitionUpdated)
167
- self._listener().sigAcquisitionEnded.connect(self._acquisitionEnded)
168
-
169
- def _cleanConnection(self):
170
- self._listener().sigAcquisitionStarted.disconnect(self._acquisitionStarted)
171
- self._listener().sigScanAdded.disconnect(self._acquisitionUpdated)
172
- self._listener().sigAcquisitionEnded.disconnect(self._acquisitionEnded)
173
-
174
136
  def _updateCentralWidget(self, action_triggered):
175
137
  action_to_widget = {
176
138
  self._controlAction: self._controlWidget,
@@ -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__ = ["C. Nemoz", "H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "18/02/2018"
29
-
2
+ from __future__ import annotations
30
3
 
31
4
  from silx.gui import qt
32
5
 
@@ -1,32 +1,5 @@
1
1
  # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016 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__ = "08/02/2019"
29
-
2
+ from __future__ import annotations
30
3
 
31
4
  import logging
32
5
  import os
@@ -132,7 +105,7 @@ class DataTransfertSelector(qt.QWidget):
132
105
  """
133
106
  Define the root folder to move scan
134
107
 
135
- :param Union[None, str] folder_path: root folder for received scan
108
+ :param folder_path: root folder for received scan
136
109
  """
137
110
  assert type(folder_path) is str or folder_path is None
138
111
  if folder_path is None: