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
@@ -0,0 +1,92 @@
1
+ import os
2
+
3
+ import numpy
4
+ from nxtomo.application.nxtomo import NXtomo
5
+ from scipy.ndimage import shift as shift_scipy
6
+ from silx.image.phantomgenerator import PhantomGenerator
7
+ from nxtomo.nxobject.nxdetector import ImageKey
8
+
9
+ from tomwer.core.scan.nxtomoscan import NXtomoScan
10
+ from nxtomo.utils.transformation import DetYFlipTransformation, DetZFlipTransformation
11
+
12
+
13
+ def create_scans_z_series(
14
+ output_dir,
15
+ z_positions_m,
16
+ x_positions_m=None,
17
+ pixel_size=10e-6,
18
+ n_proj=20,
19
+ raw_frame_width=100,
20
+ final_frame_width=100,
21
+ shifts=None,
22
+ z_rois=None,
23
+ flip_lr: bool = False,
24
+ flip_ud: bool = False,
25
+ ):
26
+ """
27
+ :param Optional tuple: shift to be applied on the 2D frame
28
+ """
29
+ if not os.path.exists(output_dir):
30
+ os.makedirs(output_dir)
31
+ frame = (
32
+ PhantomGenerator.get2DPhantomSheppLogan(n=raw_frame_width).astype(numpy.float32)
33
+ * 256.0
34
+ )
35
+ if x_positions_m is None:
36
+ x_positions_m = [None] * len(z_positions_m)
37
+ if shifts is None:
38
+ shifts = [None] * len(z_positions_m)
39
+ if z_rois is None:
40
+ z_rois = [None] * len(z_positions_m)
41
+ scans = []
42
+ for i_frame, (z_pos, x_pos, z_roi, shift) in enumerate(
43
+ zip(z_positions_m, x_positions_m, z_rois, shifts)
44
+ ):
45
+ nx_tomo = NXtomo()
46
+ if z_pos is not None:
47
+ nx_tomo.sample.z_translation = [z_pos] * n_proj
48
+ if x_pos is not None:
49
+ nx_tomo.sample.x_translation = [x_pos] * n_proj
50
+ nx_tomo.sample.rotation_angle = numpy.linspace(
51
+ 0, 180, num=n_proj, endpoint=False
52
+ )
53
+ nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_proj
54
+ if pixel_size is not None:
55
+ if isinstance(pixel_size, (tuple, list)):
56
+ y_pix_size, x_pix_size = pixel_size
57
+ else:
58
+ y_pix_size, x_pix_size = pixel_size, pixel_size
59
+ nx_tomo.instrument.detector.x_pixel_size = x_pix_size
60
+ nx_tomo.instrument.detector.y_pixel_size = y_pix_size
61
+ nx_tomo.instrument.detector.distance = 2.3
62
+ nx_tomo.energy = 19.2
63
+ nx_tomo.instrument.detector.transformations.add_transformation(
64
+ DetYFlipTransformation(flip=flip_ud)
65
+ )
66
+ nx_tomo.instrument.detector.transformations.add_transformation(
67
+ DetZFlipTransformation(flip=flip_lr)
68
+ )
69
+
70
+ if shift is not None:
71
+ sub_frame = shift_scipy(
72
+ input=frame.copy(), shift=shift, order=1, mode="constant"
73
+ )[:final_frame_width]
74
+ else:
75
+ sub_frame = frame
76
+ if z_roi is not None:
77
+ roi_start, roi_end = z_roi
78
+ sub_frame = sub_frame[roi_start:roi_end]
79
+ else:
80
+ sub_frame = sub_frame
81
+ if flip_lr:
82
+ sub_frame = numpy.fliplr(sub_frame)
83
+ if flip_ud:
84
+ sub_frame = numpy.flipud(sub_frame)
85
+ nx_tomo.instrument.detector.data = numpy.asarray([sub_frame] * n_proj)
86
+
87
+ file_path = os.path.join(output_dir, f"nxtomo_{i_frame}.nx")
88
+ entry = f"entry000{i_frame}"
89
+ nx_tomo.save(file_path=file_path, data_path=entry)
90
+ scans.append(NXtomoScan(scan=file_path, entry=entry))
91
+
92
+ return scans
@@ -0,0 +1,14 @@
1
+ def concatenate_dict(dict_1, dict_2) -> dict:
2
+ """update dict which has dict as values. And we want concatenate those values to"""
3
+ res = dict_1.copy()
4
+ for key in dict_2:
5
+ if key in dict_1:
6
+ if key in [f"axis_{axis}_params" for axis in (0, 1, 2)]:
7
+ res[key] = ";".join((dict_1[key], dict_2[key]))
8
+ elif isinstance(dict_1[key], dict):
9
+ res[key] = concatenate_dict(dict_1=dict_1[key], dict_2=dict_2[key])
10
+ else:
11
+ res[key].update(dict_2[key])
12
+ else:
13
+ res[key] = dict_2[key]
14
+ return res
@@ -1,21 +1,15 @@
1
1
  """widgets to perform a z-sttiching in pre processing (from projections) or post processing (from reconstructed volumes)"""
2
2
 
3
- __author__ = ["H. Payno"]
4
- __license__ = "MIT"
5
- __date__ = "20/01/2023"
3
+ from __future__ import annotations
4
+
6
5
 
7
6
  import logging
8
- from typing import Union
9
7
 
10
8
  from nabu.stitching import config as _nabu_stitching_config
11
9
  from nabu.stitching.config import StitchingType
12
10
  from nabu.stitching.overlap import OverlapStitchingStrategy
13
11
  from nabu.stitching.utils import ShiftAlgorithm as _NabuShiftAlgorithm
14
12
  from silx.gui import qt
15
- from tomoscan.serie import Serie
16
-
17
- from tomwer.core.tomwer_object import TomwerObject
18
- from tomwer.gui.stitching.stitching_preview import PreviewStitchingPlot
19
13
 
20
14
  _logger = logging.getLogger(__name__)
21
15
 
@@ -79,7 +73,7 @@ class Axis_N_Params(qt.QGroupBox):
79
73
 
80
74
  class AutoRefineWidget(qt.QWidget):
81
75
  """
82
- widget grouping information not specific to objects (output file, stithcing strategy...)
76
+ widget grouping information not specific to objects (output file, stitching strategy...)
83
77
  """
84
78
 
85
79
  def __init__(self, parent=None):
@@ -145,7 +139,7 @@ class AutoRefineWidget(qt.QWidget):
145
139
  self._preProcGroup.setVisible(mode is StitchingType.Z_PREPROC)
146
140
  self._postProcGroup.setVisible(mode is StitchingType.Z_POSTPROC)
147
141
 
148
- def getSliceForPreview(self) -> Union[int, str]:
142
+ def getSliceForPreview(self) -> int | str:
149
143
  slice = self._sliceForPreview.text()
150
144
  try:
151
145
  return int(slice)
@@ -197,6 +191,7 @@ class _SliceGetter(qt.QLineEdit):
197
191
 
198
192
  class RefineEstimationCtrlWidget(qt.QWidget):
199
193
  sigSlicePreviewChanged = qt.Signal(str)
194
+ """emit when the slice preview has changed"""
200
195
 
201
196
  def __init__(self, parent=None) -> None:
202
197
  super().__init__(parent)
@@ -222,26 +217,3 @@ class RefineEstimationCtrlWidget(qt.QWidget):
222
217
 
223
218
  def setSliceForPreview(self, slice: str):
224
219
  self._previewedSliceQLE.setText(str(slice))
225
-
226
-
227
- class RefineEstimationWidget(qt.QMainWindow):
228
- def __init__(self, parent=None) -> None:
229
- super().__init__(parent)
230
- # central window
231
- self._preview = PreviewStitchingPlot(parent=self)
232
- self.setCentralWidget(self._preview)
233
- # controls
234
- self._controlWidget = RefineEstimationCtrlWidget(parent=self)
235
- self._controlDockWidget = qt.QDockWidget(self)
236
- self._controlDockWidget.setWidget(self._controlWidget)
237
- self._controlDockWidget.setFeatures(qt.QDockWidget.DockWidgetMovable)
238
- self.addDockWidget(qt.Qt.RightDockWidgetArea, self._controlDockWidget)
239
-
240
- def addTomoObj(self, tomo_obj: TomwerObject):
241
- pass
242
-
243
- def setSerie(self, serie: Serie):
244
- pass
245
-
246
- def setStitchingType(self, stitching_type: StitchingType):
247
- pass
@@ -0,0 +1,35 @@
1
+ from nabu.stitching.utils import ShiftAlgorithm as _NabuShiftAlgorithm
2
+ from silx.gui import qt
3
+ from silx.gui.utils.testutils import TestCaseQt
4
+
5
+ from tomwer.gui.stitching.z_stitching.fineestimation import Axis_N_Params
6
+
7
+
8
+ class TestAxis_N_Params(TestCaseQt):
9
+ """
10
+ Test definition of an axis shift research parameters
11
+ """
12
+
13
+ def setUp(self):
14
+ super().setUp()
15
+ self._widget = Axis_N_Params("axis n", None)
16
+
17
+ def tearDown(self):
18
+ self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
19
+ self._widget.close()
20
+ self._widget = None
21
+ while self.qapp.hasPendingEvents():
22
+ self.qapp.processEvents()
23
+
24
+ def test(self):
25
+ self._widget.show()
26
+ assert self._widget.getCurrentMethod() == _NabuShiftAlgorithm.NONE
27
+ opts1 = self._widget.getOptsLine()
28
+ assert opts1 == "img_reg_method=None"
29
+ self._widget.setCurrentMethod(_NabuShiftAlgorithm.NABU_FFT)
30
+ opts2 = self._widget.getOptsLine()
31
+ assert opts2 == "img_reg_method=nabu-fft"
32
+ self._widget.setOptsLine(opts1)
33
+ assert self._widget.getOptsLine() == opts1
34
+ self._widget.setOptsLine(opts2)
35
+ assert self._widget.getOptsLine() == opts2
@@ -0,0 +1,215 @@
1
+ import os
2
+ import shutil
3
+ import tempfile
4
+
5
+ from silx.gui import qt
6
+ from silx.gui.utils.testutils import TestCaseQt
7
+
8
+ from tomwer.core.process.stitching.metadataholder import StitchingMetadata
9
+ from tomwer.gui.stitching.metadataholder import QStitchingMetadata
10
+ from tomwer.gui.stitching.tests.utils import create_scans_z_series
11
+ from tomwer.gui.stitching.config.tomoobjdetails import TomoObjectPositionInfos
12
+ from tomwer.gui.stitching.axisorderedlist import AxisOrderedTomoObjsModel
13
+
14
+
15
+ class TestTomoObjectPositionInfos(TestCaseQt):
16
+ """
17
+ Test edition of the tomo object position information
18
+ """
19
+
20
+ def setUp(self):
21
+ super().setUp()
22
+ self._tmp_path = tempfile.mkdtemp()
23
+ self._y_pixel_size = 0.002
24
+ self._x_pixel_size = 0.001
25
+ self.scans = create_scans_z_series(
26
+ self._tmp_path,
27
+ z_positions_m=(0.200, 0.205, 0.210),
28
+ x_positions_m=(0.0, 0.0, None),
29
+ pixel_size=(self._y_pixel_size, self._x_pixel_size),
30
+ raw_frame_width=100,
31
+ )
32
+ self.scan_0_metadata = QStitchingMetadata(tomo_obj=self.scans[0])
33
+ assert self.scan_0_metadata.get_raw_position_m(axis=0) == 0.20
34
+ assert self.scan_0_metadata.get_raw_position_m(axis=2) == 0.0
35
+ self.scan_2_metadata = QStitchingMetadata(tomo_obj=self.scans[2])
36
+ assert self.scan_2_metadata.get_raw_position_m(axis=0) == 0.21
37
+ self._widget = TomoObjectPositionInfos()
38
+
39
+ def tearDown(self):
40
+ self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
41
+ self._widget.close()
42
+ self._widget = None
43
+ while self.qapp.hasPendingEvents():
44
+ self.qapp.processEvents()
45
+ shutil.rmtree(self._tmp_path)
46
+
47
+ def testEdition(self):
48
+ # test QStitchingMetadata are correctly read
49
+ self._widget.show()
50
+ self._widget.setStitchingMetadata(self.scan_0_metadata)
51
+ self.qapp.processEvents()
52
+ assert self._widget._axis_0_pos.get_final_px_position() == int(0.20 / 0.002)
53
+ assert self._widget._axis_2_pos.get_final_px_position() == 0
54
+ self._widget.setStitchingMetadata(self.scan_2_metadata)
55
+ while self.qapp.hasPendingEvents():
56
+ self.qapp.processEvents()
57
+ assert self._widget._axis_0_pos.get_final_px_position() == int(0.21 / 0.002)
58
+ assert self._widget._axis_2_pos.get_final_px_position() is None
59
+ # test editing some parameters from the GUI. Make sure GUI is updated as the underlying metadata object
60
+ self._widget._axis_0_pos._overrideMetricPositionCB.setChecked(True)
61
+ self._widget._axis_0_pos.setRawMetricPosition(
62
+ position_m=0.4, displayed_unit="nm"
63
+ )
64
+ while self.qapp.hasPendingEvents():
65
+ self.qapp.processEvents()
66
+ assert self._widget._axis_0_pos.get_final_px_position() == int(
67
+ 0.4 * 10e-6 / 0.002
68
+ )
69
+ self._widget._axis_0_pos._overridePixelPositionCB.setChecked(True)
70
+ self._widget._axis_0_pos.setOverrridePxPosition(position_px=120)
71
+ while self.qapp.hasPendingEvents():
72
+ self.qapp.processEvents()
73
+ assert self._widget._axis_0_pos.get_final_px_position() == int(120)
74
+ assert self.scan_2_metadata.get_abs_position_px(axis=0) == int(120)
75
+
76
+
77
+ class TestAxisOrderedTomoObjsModel(TestCaseQt):
78
+ """
79
+ test the behavior of the z ordered model used for stitching
80
+ """
81
+
82
+ def setUp(self):
83
+ super().setUp()
84
+ self._tmp_path = tempfile.mkdtemp()
85
+ self.scans_with_pos_and_pixel_size = create_scans_z_series(
86
+ os.path.join(self._tmp_path, "case1"),
87
+ z_positions_m=(0.200, 0.205, 0.210),
88
+ pixel_size=0.001,
89
+ raw_frame_width=100,
90
+ )
91
+ self.scans_with_pixel_size = create_scans_z_series(
92
+ os.path.join(self._tmp_path, "case2"),
93
+ z_positions_m=(None, None, None),
94
+ pixel_size=0.001,
95
+ raw_frame_width=100,
96
+ )
97
+ self.scans_without_metadata = create_scans_z_series(
98
+ os.path.join(self._tmp_path, "case3"),
99
+ z_positions_m=(None, None, None),
100
+ pixel_size=None,
101
+ raw_frame_width=100,
102
+ )
103
+ self._widget = qt.QTableView()
104
+ self._widget.setModel(AxisOrderedTomoObjsModel(parent=self._widget, axis=0))
105
+
106
+ def tearDown(self):
107
+ self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
108
+ self._widget.close()
109
+ self._widget = None
110
+ while self.qapp.hasPendingEvents():
111
+ self.qapp.processEvents()
112
+ shutil.rmtree(self._tmp_path)
113
+
114
+ def testWithMetadata(self):
115
+ """
116
+ make sure z ordering works in the best case scenario
117
+ """
118
+ first_expected_scan = (
119
+ self.scans_with_pos_and_pixel_size[2].get_identifier().short_description()
120
+ )
121
+ # try giving it ordered
122
+ for scan in self.scans_with_pos_and_pixel_size[::-1]:
123
+ self._widget.model().addTomoObj(scan)
124
+ assert (
125
+ self._widget.model().data(
126
+ self._widget.model().index(0, 1), qt.Qt.DisplayRole
127
+ )
128
+ == first_expected_scan
129
+ )
130
+ self._widget.model().clearTomoObjs()
131
+ # try giving it ordered (but inverted)
132
+ for scan in self.scans_with_pos_and_pixel_size:
133
+ self._widget.model().addTomoObj(scan)
134
+ assert (
135
+ self._widget.model().data(
136
+ self._widget.model().index(0, 1), qt.Qt.DisplayRole
137
+ )
138
+ == first_expected_scan
139
+ )
140
+
141
+ def testWithPixelSizeOnly(self):
142
+ """
143
+ make sure z ordering works when we are only aware about pixel size
144
+ """
145
+ for scan in self.scans_with_pixel_size[::-1]:
146
+ self._widget.model().addTomoObj(scan)
147
+
148
+ # try adding some metadata to object
149
+ scans = self._widget.model()._objs
150
+ scans = self._widget.model()._objs
151
+ scans[0].stitching_metadata = StitchingMetadata(tomo_obj=scans[0])
152
+ scans[1].stitching_metadata = QStitchingMetadata(tomo_obj=scans[1])
153
+
154
+ scans[0].stitching_metadata._pos_as_m = (0.1, 1, 2)
155
+ scans[1].stitching_metadata._pos_as_m = (-0.03, 1, 2)
156
+ scans[2].stitching_metadata._pos_as_m = (0.23, 1, 2)
157
+
158
+ self._widget.model().reorder_objs()
159
+ self._widget.model().layoutChanged.emit()
160
+
161
+ assert (
162
+ self._widget.model().data(
163
+ self._widget.model().index(0, 1), qt.Qt.DisplayRole
164
+ )
165
+ == scans[2].get_identifier().short_description()
166
+ )
167
+ assert (
168
+ self._widget.model().data(
169
+ self._widget.model().index(1, 1), qt.Qt.DisplayRole
170
+ )
171
+ == scans[0].get_identifier().short_description()
172
+ )
173
+ assert (
174
+ self._widget.model().data(
175
+ self._widget.model().index(2, 1), qt.Qt.DisplayRole
176
+ )
177
+ == scans[1].get_identifier().short_description()
178
+ )
179
+
180
+ def testWithoutMetadata(self):
181
+ """
182
+ make sure tomo obj are still displayed even if there is no metadata at all
183
+ """
184
+ for scan in self.scans_without_metadata[::-1]:
185
+ self._widget.model().addTomoObj(scan)
186
+ # try adding some metadata to object
187
+ scans = self._widget.model()._objs
188
+ scans[0].stitching_metadata = StitchingMetadata(tomo_obj=scans[0])
189
+ scans[1].stitching_metadata = QStitchingMetadata(tomo_obj=scans[1])
190
+
191
+ scans[0].stitching_metadata._pos_as_px = (12, None, 2)
192
+ scans[1].stitching_metadata._pos_as_px = (-12, None, None)
193
+ scans[2].stitching_metadata._pos_as_px = (9999, None, None)
194
+
195
+ self._widget.model().reorder_objs()
196
+ self._widget.model().layoutChanged.emit()
197
+
198
+ assert (
199
+ self._widget.model().data(
200
+ self._widget.model().index(0, 1), qt.Qt.DisplayRole
201
+ )
202
+ == scans[2].get_identifier().short_description()
203
+ )
204
+ assert (
205
+ self._widget.model().data(
206
+ self._widget.model().index(1, 1), qt.Qt.DisplayRole
207
+ )
208
+ == scans[0].get_identifier().short_description()
209
+ )
210
+ assert (
211
+ self._widget.model().data(
212
+ self._widget.model().index(2, 1), qt.Qt.DisplayRole
213
+ )
214
+ == scans[1].get_identifier().short_description()
215
+ )
@@ -0,0 +1,51 @@
1
+ import os
2
+ import shutil
3
+ import tempfile
4
+
5
+ from silx.gui import qt
6
+ from silx.gui.utils.testutils import TestCaseQt
7
+
8
+ from tomwer.gui.stitching.tests.utils import create_scans_z_series
9
+ from tomwer.gui.stitching.StitchingWindow import ZStitchingWindow
10
+
11
+
12
+ class TestZStichingWindow(TestCaseQt):
13
+ """
14
+ Test high level z stitching definition
15
+ """
16
+
17
+ def setUp(self):
18
+ super().setUp()
19
+ self._tmp_path = tempfile.mkdtemp()
20
+ self.scans = create_scans_z_series(
21
+ os.path.join(self._tmp_path, "case1"),
22
+ z_positions_m=(0.200, 0.205, 0.210),
23
+ pixel_size=0.001,
24
+ raw_frame_width=100,
25
+ )
26
+
27
+ self._widget = ZStitchingWindow()
28
+
29
+ def tearDown(self):
30
+ self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
31
+ self._widget.close()
32
+ self._widget = None
33
+ while self.qapp.hasPendingEvents():
34
+ self.qapp.processEvents()
35
+ shutil.rmtree(self._tmp_path)
36
+
37
+ @staticmethod
38
+ def checkNbReceivers(scan, nb_receivers):
39
+ return (
40
+ scan.stitching_metadata.receivers(scan.stitching_metadata.sigChanged)
41
+ == nb_receivers
42
+ )
43
+
44
+ def test(self):
45
+ self._widget.show()
46
+ # fill the widget with scans
47
+
48
+ scan_0, scan_1, scan_2 = self.scans
49
+ for scan in self.scans:
50
+ self._widget.addTomoObj(scan)
51
+ # note: add the sigChanged to the z ordered list 'update z' slot
File without changes
@@ -0,0 +1,43 @@
1
+ import pytest
2
+ import numpy
3
+
4
+ from tomwer.gui.reconstruction.axis.AxisSettingsWidget import AxisSettingsTabWidget
5
+ from tomwer.synctools.axis import QAxisRP
6
+ from tomwer.tests.utils import skip_gui_test
7
+ from tomwer.tests.conftest import qtapp # noqa F401
8
+
9
+
10
+ @pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
11
+ def test_get_nabu_cor_opts(qtapp): # noqa F811
12
+ axis_params = QAxisRP()
13
+ widget = AxisSettingsTabWidget(recons_params=axis_params)
14
+ assert axis_params.get_nabu_cor_options_as_dict() == {
15
+ "side": "right",
16
+ "radio_angles": (0.0, numpy.pi),
17
+ "slice_idx": "middle",
18
+ }
19
+ widget._optionsWidget._corOpts.setText("low_pass=2.0")
20
+ widget._optionsWidget._corOpts.editingFinished.emit()
21
+ assert axis_params.get_nabu_cor_options_as_dict() == {
22
+ "side": "right",
23
+ "radio_angles": (0.0, numpy.pi),
24
+ "slice_idx": "middle",
25
+ "low_pass": 2.0,
26
+ }
27
+ widget._optionsWidget._corOpts.setText("low_pass=2 ; high_pass=10")
28
+ widget._optionsWidget._corOpts.editingFinished.emit()
29
+ assert axis_params.get_nabu_cor_options_as_dict() == {
30
+ "side": "right",
31
+ "radio_angles": (0.0, numpy.pi),
32
+ "slice_idx": "middle",
33
+ "low_pass": 2.0,
34
+ "high_pass": 10.0,
35
+ }
36
+ widget._calculationWidget.setEstimatedCorValue("left")
37
+ assert axis_params.get_nabu_cor_options_as_dict() == {
38
+ "side": "left",
39
+ "radio_angles": (0.0, numpy.pi),
40
+ "slice_idx": "middle",
41
+ "low_pass": 2.0,
42
+ "high_pass": 10.0,
43
+ }
@@ -1,6 +1,6 @@
1
1
  import pytest
2
2
 
3
- from tomwer.gui.qfolderdialog import QDataDialog
3
+ from tomwer.gui.dialog.QDataDialog import QDataDialog
4
4
  from tomwer.tests.conftest import qtapp # noqa F401
5
5
 
6
6
 
@@ -0,0 +1,44 @@
1
+ from __future__ import annotations
2
+
3
+ import sys
4
+ from silx.gui import qt
5
+
6
+
7
+ class RangeWidget(qt.QWidget):
8
+ """widget to select a range of float"""
9
+
10
+ sigChanged = qt.Signal()
11
+
12
+ def __init__(self, parent=None):
13
+ super().__init__(parent)
14
+ self.setLayout(qt.QHBoxLayout())
15
+
16
+ # start
17
+ self.layout().addWidget(qt.QLabel("from"))
18
+ self._startQLE = qt.QDoubleSpinBox(self)
19
+ self.layout().addWidget(self._startQLE)
20
+ self._startQLE.setRange(sys.float_info.min, sys.float_info.max)
21
+
22
+ # stop
23
+ self.layout().addWidget(qt.QLabel("to"))
24
+ self._stopQLE = qt.QDoubleSpinBox(self)
25
+ self.layout().addWidget(self._stopQLE)
26
+ self._stopQLE.setRange(sys.float_info.min, sys.float_info.max)
27
+
28
+ # connect signal / slot
29
+ self._startQLE.editingFinished.connect(self.sigChanged)
30
+ self._stopQLE.editingFinished.connect(self.sigChanged)
31
+
32
+ def getRange(self) -> tuple[float]:
33
+ return (
34
+ self._startQLE.value(),
35
+ self._stopQLE.value(),
36
+ )
37
+
38
+ def setRange(self, start: float, stop: float) -> None:
39
+ self._startQLE.setValue(float(start))
40
+ self._stopQLE.setValue(float(stop))
41
+
42
+ def setSuffix(self, suffix: str):
43
+ self._startQLE.setSuffix(suffix)
44
+ self._stopQLE.setSuffix(suffix)
@@ -2,9 +2,10 @@
2
2
  Button of general usage.
3
3
  """
4
4
 
5
+ from __future__ import annotations
6
+
5
7
  import numpy
6
8
  import logging
7
- from typing import Optional, Union
8
9
  from silx.gui import qt
9
10
  from silx.gui.plot.tools.roi import RegionOfInterestManager
10
11
  from silx.gui.plot.items.roi import LineROI
@@ -102,7 +103,7 @@ class TapeMeasureToolButton(PlotToolButton):
102
103
  value, unit = MetricSystem.cast_metric_to_best_unit(distance_m)
103
104
  self._updateText(f"{distance_px :.1f}px ({value:.2f}{unit})")
104
105
 
105
- def setPixelSize(self, pixel_size_m: Optional[Union[tuple, float]]):
106
+ def setPixelSize(self, pixel_size_m: tuple | float | None):
106
107
  if isinstance(pixel_size_m, (tuple, list)):
107
108
  assert (
108
109
  len(pixel_size_m) == 2
@@ -128,7 +129,7 @@ class TapeMeasureToolButton(PlotToolButton):
128
129
  def setPlot(self, plot):
129
130
  return super().setPlot(plot)
130
131
 
131
- def setPixelSize(self, pixel_size_m: Optional[Union[tuple, float]]):
132
+ def setPixelSize(self, pixel_size_m: tuple | float | None):
132
133
  self._pixel_sixel_m = pixel_size_m
133
134
 
134
135
  def _callback(self, toggled):
@@ -1,37 +1,6 @@
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
1
  """module defining dedicated completer"""
27
2
 
28
-
29
- __authors__ = ["H. Payno"]
30
- __license__ = "MIT"
31
- __date__ = "23/03/2022"
32
-
33
-
34
- from typing import Optional
3
+ from __future__ import annotations
35
4
 
36
5
  from silx.gui import qt
37
6
 
@@ -103,7 +72,7 @@ class _TextCompleterWidget(qt.QWidget):
103
72
 
104
73
  class UrlCompleterDialog(qt.QDialog):
105
74
  def __init__(
106
- self, urls: tuple, parent=None, current_url: Optional[str] = None
75
+ self, urls: tuple, parent=None, current_url: str | None = None
107
76
  ) -> None:
108
77
  super().__init__(parent)
109
78
  self._urls = urls