tomwer 1.3.27__py3-none-any.whl → 1.4.0rc0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (632) hide show
  1. orangecontrib/tomwer/orange/managedprocess.py +1 -29
  2. orangecontrib/tomwer/orange/settings.py +2 -28
  3. orangecontrib/tomwer/tests/TestAcquisition.py +220 -0
  4. orangecontrib/tomwer/tutorials/append_raw_darks_and_flats_frames_to_NXtomos.ows +2 -2
  5. orangecontrib/tomwer/tutorials/copy_reduced_darks_and_flats_meth1.ows +1 -1
  6. orangecontrib/tomwer/tutorials/{icat_publication.ows → drac_publication.ows} +7 -21
  7. orangecontrib/tomwer/tutorials/id16b/ID16b_full_volume.ows +22 -0
  8. orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows +302 -0
  9. orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows +218 -0
  10. orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows +29 -24
  11. orangecontrib/tomwer/tutorials/test_cor.ows +19 -0
  12. orangecontrib/tomwer/tutorials/volume_casting_on_slurm.ows +54 -0
  13. orangecontrib/tomwer/widgets/__init__.py +3 -5
  14. orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py +35 -54
  15. orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py +1 -31
  16. orangecontrib/tomwer/widgets/control/AdvancementOW.py +1 -29
  17. orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py +5 -4
  18. orangecontrib/tomwer/widgets/control/DataListenerOW.py +1 -29
  19. orangecontrib/tomwer/widgets/control/DataSelectorOW.py +11 -30
  20. orangecontrib/tomwer/widgets/control/DataTransfertOW.py +2 -28
  21. orangecontrib/tomwer/widgets/control/DataValidatorOW.py +1 -28
  22. orangecontrib/tomwer/widgets/control/DataWatcherOW.py +1 -28
  23. orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py +48 -51
  24. orangecontrib/tomwer/widgets/control/EmailOW.py +12 -2
  25. orangecontrib/tomwer/widgets/control/FilterOW.py +1 -28
  26. orangecontrib/tomwer/widgets/control/NXTomomillOW.py +37 -53
  27. orangecontrib/tomwer/widgets/control/NXtomoConcatenate.py +21 -20
  28. orangecontrib/tomwer/widgets/control/NotifierOW.py +9 -28
  29. orangecontrib/tomwer/widgets/control/ReduceDarkFlatSelectorOW.py +3 -2
  30. orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py +1 -27
  31. orangecontrib/tomwer/widgets/control/TimerOW.py +9 -28
  32. orangecontrib/tomwer/widgets/control/TomoObjSeriesOW.py +58 -0
  33. orangecontrib/tomwer/widgets/control/VolumeSelector.py +8 -30
  34. orangecontrib/tomwer/widgets/control/icons/nxtomomill.svg +173 -119
  35. orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.png +0 -0
  36. orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.svg +55 -195
  37. orangecontrib/tomwer/widgets/control/icons/{tomoobjserie.svg → tomoobjseries.svg} +2 -2
  38. orangecontrib/tomwer/widgets/dataportal/PublishProcessedDataOW.py +172 -0
  39. orangecontrib/tomwer/widgets/{icat → dataportal}/__init__.py +2 -2
  40. orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py +2 -29
  41. orangecontrib/tomwer/widgets/debugtools/ObjectInspectorOW.py +1 -29
  42. orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py +48 -73
  43. orangecontrib/tomwer/widgets/edit/ImageKeyEditorOW.py +48 -75
  44. orangecontrib/tomwer/widgets/edit/ImageKeyUpgraderOW.py +5 -30
  45. orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py +51 -52
  46. orangecontrib/tomwer/widgets/other/PythonScriptOW.py +22 -10
  47. orangecontrib/tomwer/widgets/reconstruction/AxisOW.py +48 -49
  48. orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py +22 -68
  49. orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py +3 -30
  50. orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py +21 -19
  51. orangecontrib/tomwer/widgets/reconstruction/NabuOW.py +7 -70
  52. orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py +40 -85
  53. orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py +15 -40
  54. orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py +13 -35
  55. orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py +2 -30
  56. orangecontrib/tomwer/widgets/stitching/ZStitchingConfigOW.py +11 -11
  57. orangecontrib/tomwer/widgets/utils.py +2 -29
  58. orangecontrib/tomwer/widgets/visualization/DataViewerOW.py +1 -27
  59. orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py +1 -27
  60. orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py +1 -1
  61. orangecontrib/tomwer/widgets/visualization/RadioStackOW.py +2 -28
  62. orangecontrib/tomwer/widgets/visualization/SampleMovedOW.py +1 -27
  63. orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py +1 -27
  64. orangecontrib/tomwer/widgets/visualization/SliceStackOW.py +2 -28
  65. tomwer/__init__.py +3 -28
  66. tomwer/__main__.py +8 -4
  67. tomwer/app/__init__.py +2 -0
  68. tomwer/app/axis.py +8 -7
  69. tomwer/app/canvas.py +23 -29
  70. tomwer/app/canvas_launcher/config.py +14 -102
  71. tomwer/app/canvas_launcher/environ.py +5 -8
  72. tomwer/app/canvas_launcher/mainwindow.py +175 -69
  73. tomwer/app/canvas_launcher/splash.py +1 -3
  74. tomwer/app/canvas_launcher/utils.py +47 -0
  75. tomwer/app/canvas_launcher/widgetsscheme.py +3 -10
  76. tomwer/app/diffframe.py +2 -0
  77. tomwer/app/imagekeyeditor.py +2 -1
  78. tomwer/app/imagekeyupgrader.py +2 -0
  79. tomwer/app/multicor.py +5 -2
  80. tomwer/app/multipag.py +7 -4
  81. tomwer/app/nabuapp.py +2 -1
  82. tomwer/app/nxtomoeditor.py +17 -12
  83. tomwer/app/patchrawdarkflat.py +2 -0
  84. tomwer/app/radiostack.py +3 -2
  85. tomwer/app/reducedarkflat.py +3 -0
  86. tomwer/app/samplemoved.py +2 -0
  87. tomwer/app/scanviewer.py +2 -0
  88. tomwer/app/sinogramviewer.py +2 -0
  89. tomwer/app/slicestack.py +11 -13
  90. tomwer/app/stitching/common.py +431 -0
  91. tomwer/app/stopdatalistener.py +3 -0
  92. tomwer/app/ystitching.py +26 -0
  93. tomwer/app/zstitching.py +8 -363
  94. tomwer/core/__init__.py +2 -28
  95. tomwer/core/cluster/__init__.py +3 -0
  96. tomwer/core/cluster/cluster.py +10 -26
  97. tomwer/core/futureobject.py +17 -43
  98. tomwer/core/log/__init__.py +2 -0
  99. tomwer/core/log/processlog.py +0 -28
  100. tomwer/core/process/cluster/supervisor.py +52 -34
  101. tomwer/core/process/conditions/filters.py +3 -28
  102. tomwer/core/process/control/datalistener/datalistener.py +7 -75
  103. tomwer/core/process/control/datalistener/rpcserver.py +8 -38
  104. tomwer/core/process/control/datawatcher/datawatcher.py +11 -40
  105. tomwer/core/process/control/datawatcher/datawatcherobserver.py +30 -64
  106. tomwer/core/process/control/datawatcher/datawatcherprocess.py +11 -32
  107. tomwer/core/process/control/datawatcher/edfdwprocess.py +2 -27
  108. tomwer/core/process/control/datawatcher/hdf5dwprocess.py +1 -26
  109. tomwer/core/process/control/datawatcher/status.py +1 -26
  110. tomwer/core/process/control/emailnotifier.py +11 -23
  111. tomwer/core/process/control/nxtomoconcatenate.py +20 -18
  112. tomwer/core/process/control/nxtomomill.py +9 -44
  113. tomwer/core/process/control/scanlist.py +0 -27
  114. tomwer/core/process/control/scantransfer.py +15 -13
  115. tomwer/core/process/control/scanvalidator.py +4 -30
  116. tomwer/core/process/control/{test → tests}/test_concatenate_nxtomos.py +5 -5
  117. tomwer/core/process/control/timer.py +1 -27
  118. tomwer/core/process/control/tomoobjseries.py +12 -0
  119. tomwer/core/process/drac/binning.py +37 -0
  120. tomwer/core/process/drac/dracbase.py +170 -0
  121. tomwer/core/process/drac/gallery.py +109 -0
  122. tomwer/core/process/drac/output.py +12 -0
  123. tomwer/core/process/drac/processeddataset.py +147 -0
  124. tomwer/core/process/drac/publish.py +118 -0
  125. tomwer/core/process/drac/rawdataset.py +142 -0
  126. tomwer/core/process/drac/tests/test_gallery.py +71 -0
  127. tomwer/core/process/drac/tests/test_icat_processed_dataset.py +80 -0
  128. tomwer/core/process/drac/tests/test_icat_raw_dataset.py +90 -0
  129. tomwer/core/process/edit/darkflatpatch.py +1 -28
  130. tomwer/core/process/edit/imagekeyeditor.py +4 -32
  131. tomwer/core/process/edit/nxtomoeditor.py +307 -0
  132. tomwer/core/process/edit/tests/test_darkflatpatch.py +243 -0
  133. tomwer/core/process/edit/tests/test_imagekey_editor.py +99 -0
  134. tomwer/core/process/output.py +9 -2
  135. tomwer/core/process/reconstruction/__init__.py +0 -26
  136. tomwer/core/process/reconstruction/axis/anglemode.py +1 -29
  137. tomwer/core/process/reconstruction/axis/axis.py +63 -111
  138. tomwer/core/process/reconstruction/axis/mode.py +5 -3
  139. tomwer/core/process/reconstruction/axis/params.py +5 -146
  140. tomwer/core/process/reconstruction/axis/projectiontype.py +0 -28
  141. tomwer/core/process/reconstruction/darkref/darkrefs.py +14 -39
  142. tomwer/core/process/reconstruction/darkref/darkrefscopy.py +7 -39
  143. tomwer/core/process/reconstruction/darkref/params.py +1 -28
  144. tomwer/core/process/reconstruction/nabu/castvolume.py +19 -34
  145. tomwer/core/process/reconstruction/nabu/nabucommon.py +18 -43
  146. tomwer/core/process/reconstruction/nabu/nabuscores.py +47 -48
  147. tomwer/core/process/reconstruction/nabu/nabuslices.py +59 -105
  148. tomwer/core/process/reconstruction/nabu/nabuvolume.py +44 -70
  149. tomwer/core/process/reconstruction/nabu/plane.py +10 -0
  150. tomwer/core/process/reconstruction/nabu/settings.py +1 -28
  151. tomwer/core/process/reconstruction/nabu/target.py +0 -28
  152. tomwer/core/process/reconstruction/nabu/test/test_castvolume.py +116 -0
  153. tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py +277 -0
  154. tomwer/core/process/reconstruction/nabu/test/test_nabunormalization.py +199 -0
  155. tomwer/core/process/reconstruction/nabu/utils.py +11 -60
  156. tomwer/core/process/reconstruction/normalization/normalization.py +2 -32
  157. tomwer/core/process/reconstruction/normalization/params.py +3 -35
  158. tomwer/core/process/reconstruction/output.py +14 -19
  159. tomwer/core/process/reconstruction/paramsbase.py +4 -33
  160. tomwer/core/process/reconstruction/saaxis/params.py +5 -33
  161. tomwer/core/process/reconstruction/saaxis/saaxis.py +18 -47
  162. tomwer/core/process/reconstruction/sadeltabeta/params.py +2 -31
  163. tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +16 -44
  164. tomwer/core/process/reconstruction/scores/params.py +9 -39
  165. tomwer/core/process/reconstruction/scores/scores.py +10 -42
  166. tomwer/core/process/reconstruction/tests/__init__.py +0 -0
  167. tomwer/core/process/reconstruction/tests/test_axis.py +46 -0
  168. tomwer/core/process/reconstruction/tests/test_darkref.py +33 -0
  169. tomwer/core/process/reconstruction/{test → tests}/test_saaxis.py +1 -27
  170. tomwer/core/process/reconstruction/tests/test_sadeltabeta.py +48 -0
  171. tomwer/core/process/script/python.py +1 -27
  172. tomwer/core/process/script/tests/test_script.py +41 -0
  173. tomwer/core/process/stitching/metadataholder.py +5 -4
  174. tomwer/core/process/stitching/nabustitcher.py +35 -5
  175. tomwer/core/process/stitching/tests/test_metadataholder.py +17 -0
  176. tomwer/core/process/task.py +20 -63
  177. tomwer/core/process/tests/__init__.py +0 -0
  178. tomwer/core/process/{test → tests}/test_axis.py +1 -79
  179. tomwer/core/process/{test → tests}/test_conditions.py +1 -28
  180. tomwer/core/process/{test → tests}/test_dark_and_flat.py +1 -27
  181. tomwer/core/process/{test → tests}/test_data_listener.py +1 -27
  182. tomwer/core/process/{test → tests}/test_data_transfer.py +2 -28
  183. tomwer/core/process/{test → tests}/test_data_watcher.py +1 -27
  184. tomwer/core/process/{test → tests}/test_nabu.py +4 -33
  185. tomwer/core/process/{test → tests}/test_normalization.py +1 -26
  186. tomwer/core/process/{test → tests}/test_timer.py +1 -27
  187. tomwer/core/process/utils.py +2 -31
  188. tomwer/core/process/visualization/dataviewer.py +1 -26
  189. tomwer/core/process/visualization/diffviewer.py +1 -26
  190. tomwer/core/process/visualization/imagestackviewer.py +0 -26
  191. tomwer/core/process/visualization/radiostack.py +0 -26
  192. tomwer/core/process/visualization/samplemoved.py +0 -28
  193. tomwer/core/process/visualization/sinogramviewer.py +0 -27
  194. tomwer/core/process/visualization/slicestack.py +0 -28
  195. tomwer/core/process/visualization/tests/test_data_viewer.py +12 -0
  196. tomwer/core/process/visualization/tests/test_diff_viewer.py +12 -0
  197. tomwer/core/process/visualization/tests/test_image_stack_viewer.py +14 -0
  198. tomwer/core/process/visualization/tests/test_radio_stack.py +12 -0
  199. tomwer/core/process/visualization/tests/test_sample_moved.py +14 -0
  200. tomwer/core/process/visualization/tests/test_sinogram_viewer.py +13 -0
  201. tomwer/core/process/visualization/tests/test_slice_stack.py +13 -0
  202. tomwer/core/process/visualization/tests/test_volume_viewer.py +12 -0
  203. tomwer/core/process/visualization/volumeviewer.py +0 -29
  204. tomwer/core/scan/__init__.py +3 -27
  205. tomwer/core/scan/blissscan.py +5 -34
  206. tomwer/core/scan/edfscan.py +19 -53
  207. tomwer/core/scan/hdf5scan.py +2 -2
  208. tomwer/core/scan/nxtomoscan.py +46 -54
  209. tomwer/core/scan/scanbase.py +104 -200
  210. tomwer/core/scan/scanfactory.py +11 -41
  211. tomwer/core/scan/tests/__init__.py +0 -0
  212. tomwer/core/scan/tests/test_edf.py +25 -0
  213. tomwer/core/scan/tests/test_future_scan.py +35 -0
  214. tomwer/core/scan/tests/test_nxtomoscan.py +143 -0
  215. tomwer/core/scan/{test → tests}/test_process_registration.py +1 -28
  216. tomwer/core/settings.py +18 -40
  217. tomwer/core/tests/__init__.py +0 -0
  218. tomwer/core/tests/test_scanutils.py +26 -0
  219. tomwer/core/{test → tests}/test_utils.py +1 -28
  220. tomwer/core/tomwer_object.py +4 -0
  221. tomwer/core/utils/__init__.py +2 -0
  222. tomwer/core/utils/char.py +0 -28
  223. tomwer/core/utils/deprecation.py +12 -38
  224. tomwer/core/utils/dictutils.py +1 -3
  225. tomwer/core/utils/ftseriesutils.py +1 -27
  226. tomwer/core/utils/gpu.py +0 -28
  227. tomwer/core/utils/image.py +8 -39
  228. tomwer/core/utils/locker.py +1 -28
  229. tomwer/core/utils/logconfig.py +0 -27
  230. tomwer/core/utils/normalization.py +4 -31
  231. tomwer/core/utils/nxtomoutils.py +8 -38
  232. tomwer/core/utils/resource.py +0 -26
  233. tomwer/core/utils/scanutils.py +23 -52
  234. tomwer/core/utils/slurm.py +7 -30
  235. tomwer/core/utils/spec.py +6 -6
  236. tomwer/core/utils/tests/__init__.py +0 -0
  237. tomwer/core/utils/tests/test_image.py +30 -0
  238. tomwer/core/utils/tests/test_nxtomo.py +38 -0
  239. tomwer/core/utils/tests/test_scan_utils.py +46 -0
  240. tomwer/core/utils/tests/test_time.py +6 -0
  241. tomwer/core/utils/threads.py +0 -26
  242. tomwer/core/utils/time.py +0 -27
  243. tomwer/core/volume/__init__.py +4 -0
  244. tomwer/core/volume/edfvolume.py +1 -28
  245. tomwer/core/volume/hdf5volume.py +1 -28
  246. tomwer/core/volume/jp2kvolume.py +1 -27
  247. tomwer/core/volume/rawvolume.py +1 -28
  248. tomwer/core/volume/tests/test_volumes.py +21 -0
  249. tomwer/core/volume/tiffvolume.py +1 -28
  250. tomwer/core/volume/volumebase.py +5 -0
  251. tomwer/core/volume/volumefactory.py +7 -33
  252. tomwer/gui/__init__.py +0 -28
  253. tomwer/gui/cluster/__init__.py +2 -0
  254. tomwer/gui/cluster/slurm.py +297 -95
  255. tomwer/gui/cluster/supervisor.py +1 -27
  256. tomwer/gui/cluster/tests/__init__.py +0 -0
  257. tomwer/gui/cluster/{test → tests}/test_cluster.py +21 -26
  258. tomwer/gui/cluster/{test → tests}/test_supervisor.py +1 -27
  259. tomwer/gui/conditions/__init__.py +2 -0
  260. tomwer/gui/conditions/filter.py +1 -26
  261. tomwer/gui/configuration/__init__.py +2 -0
  262. tomwer/gui/control/__init__.py +2 -0
  263. tomwer/gui/control/actions.py +2 -28
  264. tomwer/gui/control/datadiscovery.py +4 -3
  265. tomwer/gui/control/datalist.py +64 -69
  266. tomwer/gui/control/datalistener.py +1 -39
  267. tomwer/gui/control/datareacheractions.py +1 -28
  268. tomwer/gui/control/datatransfert.py +2 -29
  269. tomwer/gui/control/datavalidator.py +3 -37
  270. tomwer/gui/control/datawatcher/__init__.py +0 -28
  271. tomwer/gui/control/datawatcher/configuration.py +1 -28
  272. tomwer/gui/control/datawatcher/datawatcher.py +3 -32
  273. tomwer/gui/control/datawatcher/datawatcherobserver.py +2 -28
  274. tomwer/gui/control/history.py +5 -35
  275. tomwer/gui/control/nxtomomill.py +3 -30
  276. tomwer/gui/control/observations.py +61 -55
  277. tomwer/gui/control/reducedarkflatselector.py +24 -20
  278. tomwer/gui/control/scanselectorwidget.py +2 -28
  279. tomwer/gui/control/selectorwidgetbase.py +17 -17
  280. tomwer/gui/control/series/__init__.py +0 -0
  281. tomwer/gui/control/{serie/seriecreator.py → series/seriescreator.py} +214 -235
  282. tomwer/gui/control/series/serieswaiter.py +0 -0
  283. tomwer/gui/control/series/test/test_creator.py +424 -0
  284. tomwer/gui/control/series/test/test_nxtomo_concatenate.py +21 -0
  285. tomwer/gui/control/singletomoobj.py +1 -1
  286. tomwer/gui/control/tests/__init__.py +0 -0
  287. tomwer/gui/control/tests/test_datalist.py +47 -0
  288. tomwer/gui/control/{test → tests}/test_datalistener.py +1 -28
  289. tomwer/gui/control/tests/test_datavalidator.py +27 -0
  290. tomwer/gui/control/{test → tests}/test_inputwidget.py +1 -27
  291. tomwer/gui/control/tests/test_process_manager.py +38 -0
  292. tomwer/gui/control/tests/test_scan_observations.py +23 -0
  293. tomwer/gui/control/tests/test_scanselector.py +42 -0
  294. tomwer/gui/control/{test → tests}/test_scanvalidator.py +1 -27
  295. tomwer/gui/control/{test → tests}/test_volume_dialog.py +2 -30
  296. tomwer/gui/control/{test → tests}/test_volumeselector.py +1 -27
  297. tomwer/gui/control/volumeselectorwidget.py +2 -30
  298. tomwer/gui/dataportal/__init__.py +2 -0
  299. tomwer/gui/{icat → dataportal}/createscreenshots.py +3 -2
  300. tomwer/gui/dataportal/gallery.py +133 -0
  301. tomwer/gui/dataportal/outputformat.py +0 -0
  302. tomwer/gui/dataportal/publish.py +96 -0
  303. tomwer/gui/dataportal/tests/test_create_screenshots_gui.py +23 -0
  304. tomwer/gui/dataportal/tests/test_gallery_gui.py +21 -0
  305. tomwer/gui/debugtools/__init__.py +2 -0
  306. tomwer/gui/debugtools/datasetgenerator.py +1 -30
  307. tomwer/gui/debugtools/objectinspector.py +1 -29
  308. tomwer/gui/dialog/QDataDialog.py +89 -0
  309. tomwer/gui/{qfolderdialog.py → dialog/QVolumeDialog.py} +8 -107
  310. tomwer/gui/dialog/__init__.py +1 -0
  311. tomwer/gui/edit/__init__.py +2 -0
  312. tomwer/gui/edit/dkrfpatch.py +52 -87
  313. tomwer/gui/edit/imagekeyeditor.py +18 -54
  314. tomwer/gui/edit/nxtomoeditor.py +113 -300
  315. tomwer/gui/edit/nxtomowarmer.py +3 -2
  316. tomwer/gui/edit/tests/__init__.py +0 -0
  317. tomwer/gui/edit/{test → tests}/test_dkrf_patch.py +3 -29
  318. tomwer/gui/edit/{test → tests}/test_image_key_editor.py +1 -27
  319. tomwer/gui/edit/{test → tests}/test_nx_editor.py +45 -23
  320. tomwer/gui/icons.py +28 -66
  321. tomwer/gui/illustrations.py +4 -34
  322. tomwer/gui/imagefromfile.py +5 -30
  323. tomwer/gui/metadataloader.py +36 -0
  324. tomwer/gui/qconfigfile.py +3 -0
  325. tomwer/gui/qlefilesystem.py +3 -0
  326. tomwer/gui/reconstruction/__init__.py +2 -0
  327. tomwer/gui/reconstruction/axis/AxisMainWindow.py +264 -0
  328. tomwer/gui/reconstruction/axis/AxisOptionsWidget.py +153 -0
  329. tomwer/gui/reconstruction/axis/AxisSettingsWidget.py +776 -0
  330. tomwer/gui/reconstruction/axis/AxisWidget.py +526 -0
  331. tomwer/gui/reconstruction/axis/CalculationWidget.py +374 -0
  332. tomwer/gui/reconstruction/axis/CompareImages.py +11 -44
  333. tomwer/gui/reconstruction/axis/ControlWidget.py +277 -0
  334. tomwer/gui/reconstruction/axis/InputWidget.py +491 -0
  335. tomwer/gui/reconstruction/axis/ManualFramesSelection.py +168 -0
  336. tomwer/gui/reconstruction/axis/__init__.py +2 -2
  337. tomwer/gui/reconstruction/darkref/__init__.py +0 -27
  338. tomwer/gui/reconstruction/darkref/darkrefcopywidget.py +5 -34
  339. tomwer/gui/reconstruction/darkref/darkrefwidget.py +1 -27
  340. tomwer/gui/reconstruction/nabu/castvolume.py +40 -59
  341. tomwer/gui/reconstruction/nabu/check.py +7 -33
  342. tomwer/gui/reconstruction/nabu/nabuconfig/base.py +7 -34
  343. tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py +6 -5
  344. tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py +10 -69
  345. tomwer/gui/reconstruction/nabu/nabuconfig/output.py +3 -47
  346. tomwer/gui/reconstruction/nabu/nabuconfig/phase.py +54 -36
  347. tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py +103 -54
  348. tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py +116 -65
  349. tomwer/gui/reconstruction/nabu/nabuflow.py +31 -61
  350. tomwer/gui/reconstruction/nabu/platform.py +94 -0
  351. tomwer/gui/reconstruction/nabu/slices.py +81 -45
  352. tomwer/gui/reconstruction/nabu/slurm.py +1 -27
  353. tomwer/gui/reconstruction/nabu/test/test_cast_volume.py +82 -0
  354. tomwer/gui/reconstruction/nabu/test/test_check.py +66 -0
  355. tomwer/gui/reconstruction/nabu/test/test_ctf.py +46 -0
  356. tomwer/gui/reconstruction/nabu/test/test_helical.py +21 -0
  357. tomwer/gui/reconstruction/nabu/test/test_nabu_preprocessing.py +81 -0
  358. tomwer/gui/reconstruction/nabu/volume.py +62 -90
  359. tomwer/gui/reconstruction/normalization/intensity.py +5 -32
  360. tomwer/gui/reconstruction/normalization/test/test_intensity.py +89 -0
  361. tomwer/gui/reconstruction/saaxis/corrangeselector.py +16 -49
  362. tomwer/gui/reconstruction/saaxis/dimensionwidget.py +56 -96
  363. tomwer/gui/reconstruction/saaxis/saaxis.py +17 -38
  364. tomwer/gui/reconstruction/saaxis/sliceselector.py +8 -39
  365. tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py +19 -37
  366. tomwer/gui/reconstruction/scores/control.py +2 -30
  367. tomwer/gui/reconstruction/scores/scoreplot.py +19 -48
  368. tomwer/gui/reconstruction/tests/__init__.py +0 -0
  369. tomwer/gui/reconstruction/{test → tests}/test_axis.py +23 -49
  370. tomwer/gui/reconstruction/{test → tests}/test_nabu.py +8 -31
  371. tomwer/gui/reconstruction/{test → tests}/test_saaxis.py +10 -37
  372. tomwer/gui/reconstruction/{test → tests}/test_sadeltabeta.py +1 -26
  373. tomwer/gui/samplemoved/__init__.py +2 -30
  374. tomwer/gui/samplemoved/selectiontable.py +3 -33
  375. tomwer/gui/settings.py +7 -0
  376. tomwer/gui/stackplot.py +33 -661
  377. tomwer/gui/stacks.py +261 -135
  378. tomwer/gui/stitching/SingleAxisStitchingWidget.py +326 -0
  379. tomwer/gui/stitching/StitchingOptionsWidget.py +438 -0
  380. tomwer/gui/stitching/StitchingWindow.py +586 -0
  381. tomwer/gui/stitching/__init__.py +2 -0
  382. tomwer/gui/stitching/alignment.py +90 -0
  383. tomwer/gui/stitching/axisorderedlist.py +44 -34
  384. tomwer/gui/stitching/config/axisparams.py +23 -11
  385. tomwer/gui/stitching/config/output.py +6 -5
  386. tomwer/gui/stitching/config/positionoveraxis.py +313 -51
  387. tomwer/gui/stitching/config/stitchingstrategies.py +22 -16
  388. tomwer/gui/stitching/config/tests/test_axisparams.py +25 -0
  389. tomwer/gui/stitching/config/tomoobjdetails.py +3 -5
  390. tomwer/gui/stitching/normalization.py +1 -0
  391. tomwer/gui/stitching/preview.py +59 -0
  392. tomwer/gui/stitching/singleaxis.py +57 -0
  393. tomwer/gui/stitching/stitchandbackground.py +3 -2
  394. tomwer/gui/stitching/stitching_preview.py +44 -36
  395. tomwer/gui/stitching/stitching_raw.py +5 -3
  396. tomwer/gui/stitching/tests/test_ZStitchingWindow.py +88 -0
  397. tomwer/gui/stitching/tests/test_axis_ordered_list.py +21 -0
  398. tomwer/gui/stitching/tests/test_normalization.py +27 -0
  399. tomwer/gui/stitching/tests/test_preview.py +68 -0
  400. tomwer/gui/stitching/tests/test_stitching_raw.py +110 -0
  401. tomwer/gui/stitching/tests/utils.py +92 -0
  402. tomwer/gui/stitching/utils.py +14 -0
  403. tomwer/gui/stitching/z_stitching/fineestimation.py +4 -32
  404. tomwer/gui/stitching/z_stitching/tests/test_fine_estimation.py +35 -0
  405. tomwer/gui/stitching/z_stitching/tests/test_raw_estimation.py +215 -0
  406. tomwer/gui/stitching/z_stitching/tests/test_stitching_window.py +51 -0
  407. tomwer/gui/tests/__init__.py +0 -0
  408. tomwer/gui/tests/test_axis_gui.py +27 -0
  409. tomwer/gui/{test → tests}/test_qfolder_dialog.py +1 -1
  410. tomwer/gui/utils/RangeWidget.py +44 -0
  411. tomwer/gui/utils/buttons.py +4 -3
  412. tomwer/gui/utils/completer.py +2 -33
  413. tomwer/gui/utils/flow.py +11 -40
  414. tomwer/gui/utils/gpu.py +60 -0
  415. tomwer/gui/utils/illustrations.py +1 -26
  416. tomwer/gui/utils/inputwidget.py +35 -73
  417. tomwer/gui/utils/lineselector/lineselector.py +9 -46
  418. tomwer/gui/utils/loadingmode.py +81 -0
  419. tomwer/gui/utils/qt_utils.py +9 -0
  420. tomwer/gui/utils/sandboxes.py +1 -26
  421. tomwer/gui/utils/scandescription.py +2 -31
  422. tomwer/gui/utils/scrollarea.py +6 -55
  423. tomwer/gui/utils/slider.py +4 -28
  424. tomwer/gui/utils/splashscreen.py +0 -28
  425. tomwer/gui/utils/step.py +14 -13
  426. tomwer/gui/utils/tests/test_completer.py +41 -0
  427. tomwer/gui/utils/tests/test_line_selector.py +21 -0
  428. tomwer/gui/utils/tests/test_splashscreen.py +8 -0
  429. tomwer/gui/utils/tests/test_vignettes.py +68 -0
  430. tomwer/gui/utils/unitsystem.py +15 -69
  431. tomwer/gui/utils/utils.py +4 -5
  432. tomwer/gui/utils/vignettes.py +10 -41
  433. tomwer/gui/utils/waiterthread.py +0 -26
  434. tomwer/gui/visualization/__init__.py +2 -0
  435. tomwer/gui/visualization/dataviewer.py +68 -421
  436. tomwer/gui/visualization/diffviewer/diffviewer.py +2 -30
  437. tomwer/gui/visualization/diffviewer/shiftwidget.py +4 -29
  438. tomwer/gui/visualization/fullscreenplot.py +5 -5
  439. tomwer/gui/visualization/imagestack.py +403 -0
  440. tomwer/gui/visualization/nxtomometadata.py +0 -4
  441. tomwer/gui/visualization/reconstructionparameters.py +14 -32
  442. tomwer/gui/visualization/scanoverview.py +33 -66
  443. tomwer/gui/visualization/sinogramviewer.py +2 -28
  444. tomwer/gui/visualization/test/__init__.py +0 -28
  445. tomwer/gui/visualization/test/test_dataviewer.py +1 -28
  446. tomwer/gui/visualization/test/test_diffviewer.py +1 -28
  447. tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py +0 -5
  448. tomwer/gui/visualization/test/test_reconstruction_parameters.py +1 -27
  449. tomwer/gui/visualization/test/test_sinogramviewer.py +1 -28
  450. tomwer/gui/visualization/test/test_stacks.py +184 -115
  451. tomwer/gui/visualization/test/test_volumeviewer.py +3 -2
  452. tomwer/gui/visualization/tomoobjoverview.py +2 -2
  453. tomwer/gui/visualization/volumeoverview.py +3 -2
  454. tomwer/gui/visualization/volumeviewer.py +47 -43
  455. tomwer/io/__init__.py +2 -0
  456. tomwer/io/utils/h5pyutils.py +1 -27
  457. tomwer/io/utils/test/test_raw_and_processed_data.py +10 -0
  458. tomwer/io/utils/test/test_utils.py +67 -0
  459. tomwer/io/utils/utils.py +2 -31
  460. tomwer/resources/__init__.py +13 -33
  461. tomwer/resources/gui/icons/edit_downstream.svg +114 -0
  462. tomwer/resources/gui/icons/edit_upstream.svg +112 -0
  463. tomwer/resources/gui/icons/free_edition.svg +23 -0
  464. tomwer/resources/gui/icons/icat_gallery_opts.png +0 -0
  465. tomwer/resources/gui/icons/icat_gallery_opts.svg +80 -0
  466. tomwer/resources/gui/icons/search.png +0 -0
  467. tomwer/resources/gui/icons/search.svg +23 -0
  468. tomwer/resources/gui/icons/warning.png +0 -0
  469. tomwer/synctools/__init__.py +2 -0
  470. tomwer/synctools/axis.py +1 -27
  471. tomwer/synctools/darkref.py +1 -26
  472. tomwer/synctools/datalistener.py +1 -27
  473. tomwer/synctools/datatransfert.py +2 -27
  474. tomwer/synctools/imageloaderthread.py +1 -28
  475. tomwer/synctools/rsyncmanager.py +1 -25
  476. tomwer/synctools/saaxis.py +1 -26
  477. tomwer/synctools/sadeltabeta.py +1 -26
  478. tomwer/synctools/stacks/control/datalistener.py +1 -26
  479. tomwer/synctools/stacks/processingstack.py +4 -33
  480. tomwer/synctools/stacks/reconstruction/axis.py +2 -31
  481. tomwer/synctools/stacks/reconstruction/castvolume.py +12 -43
  482. tomwer/synctools/stacks/reconstruction/dkrefcopy.py +3 -26
  483. tomwer/synctools/stacks/reconstruction/nabu.py +1 -26
  484. tomwer/synctools/stacks/reconstruction/normalization.py +1 -26
  485. tomwer/synctools/stacks/reconstruction/saaxis.py +1 -26
  486. tomwer/synctools/stacks/reconstruction/sadeltabeta.py +1 -26
  487. tomwer/synctools/tests/__init__.py +0 -0
  488. tomwer/synctools/{test → tests}/test_darkRefs.py +16 -40
  489. tomwer/synctools/{test → tests}/test_foldertransfer.py +2 -33
  490. tomwer/synctools/utils/scanstages.py +2 -31
  491. tomwer/tests/__init__.py +1 -0
  492. tomwer/tests/app/test_stitching.py +95 -0
  493. tomwer/tests/datasets.py +1 -5
  494. tomwer/tests/orangecontrib/tomwer/widgets/cluster/tests/test_future_supervisorow.py +48 -0
  495. tomwer/tests/orangecontrib/tomwer/widgets/cluster/tests/test_slurm_clusterow.py +40 -0
  496. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_advancement.py +8 -0
  497. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_data_validator.py +55 -0
  498. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datadiscovery.py +129 -0
  499. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datalistener.py +111 -0
  500. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_dataselector.py +69 -0
  501. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datawatcher.py +411 -0
  502. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_emailow.py +29 -0
  503. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_notifier.py +24 -0
  504. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_nxtomo_concatenate_ow.py +64 -0
  505. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_nxtomomill.py +133 -0
  506. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_reduce_dark_flat_selector.py +40 -0
  507. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_singletomoobj.py +40 -0
  508. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_timerow.py +25 -0
  509. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_tomoobj_series.py +96 -0
  510. tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_volume_selector.py +69 -0
  511. orangecontrib/tomwer/widgets/edit/test/test_image_key_editor.py → tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_dataset_generator.py +17 -16
  512. tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_object_inspector.py +36 -0
  513. {orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_dark_flat_patch.py +1 -27
  514. tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_image_key_editor.py +30 -0
  515. tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py +138 -0
  516. tomwer/tests/orangecontrib/tomwer/widgets/other/tests/test_pythonscript.py +31 -0
  517. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_axis.py +215 -0
  518. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_cast_volumeow.py +58 -0
  519. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_dark_refs_widget.py +136 -0
  520. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_delta_beta_selector.py +15 -0
  521. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_i_norm.py +200 -0
  522. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_helical_prepare_weights_double.py +20 -0
  523. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_volume.py +74 -0
  524. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_widget.py +107 -0
  525. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_sa_delta_beta.py +194 -0
  526. tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_saaxis.py +194 -0
  527. tomwer/tests/orangecontrib/tomwer/widgets/stitching/tests/test_zstitching.py +313 -0
  528. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_conditions.py +85 -0
  529. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_darkref.py +225 -0
  530. tomwer/tests/orangecontrib/tomwer/widgets/tests/test_foldertransfert.py +105 -0
  531. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_dataviewerow.py +57 -0
  532. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_diffviewerow.py +39 -0
  533. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_nxtomo_metadata_viewer.py +29 -0
  534. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_radio_stackow.py +31 -0
  535. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_sample_movedow.py +46 -0
  536. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_sinogram_viewerow.py +31 -0
  537. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_slice_stackow.py +31 -0
  538. tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_volume_viewerow.py +32 -0
  539. tomwer/tests/test_ewoks/test_conversion.py +104 -0
  540. tomwer/tests/test_ewoks/test_single_node_execution.py +87 -0
  541. tomwer/tests/test_ewoks/test_workflows.py +138 -0
  542. tomwer/utils.py +11 -39
  543. tomwer/version.py +3 -3
  544. {tomwer-1.3.27.dist-info → tomwer-1.4.0rc0.dist-info}/LICENSE +3 -3
  545. tomwer-1.4.0rc0.dist-info/METADATA +337 -0
  546. tomwer-1.4.0rc0.dist-info/RECORD +909 -0
  547. {tomwer-1.3.27.dist-info → tomwer-1.4.0rc0.dist-info}/WHEEL +1 -1
  548. {tomwer-1.3.27.dist-info → tomwer-1.4.0rc0.dist-info}/entry_points.txt +1 -0
  549. orangecontrib/tomwer/widgets/control/DataListOW.py +0 -129
  550. orangecontrib/tomwer/widgets/control/TomoObjSerieOW.py +0 -86
  551. orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py +0 -182
  552. orangecontrib/tomwer/widgets/edit/test/test_nxtomo_editor.py +0 -141
  553. orangecontrib/tomwer/widgets/icat/PublishProcessedDataOW.py +0 -115
  554. orangecontrib/tomwer/widgets/icat/RawDataScreenshotCreatorOW.py +0 -98
  555. orangecontrib/tomwer/widgets/icat/SaveToGalleryAndPublishOW.py +0 -129
  556. orangecontrib/tomwer/widgets/icat/icons/add_gallery.png +0 -0
  557. orangecontrib/tomwer/widgets/icat/icons/add_gallery.svg +0 -82
  558. orangecontrib/tomwer/widgets/icat/icons/raw_screenshots.png +0 -0
  559. orangecontrib/tomwer/widgets/icat/icons/raw_screenshots.svg +0 -143
  560. orangecontrib/tomwer/widgets/visualization/LivesliceOW.py +0 -87
  561. orangecontrib/tomwer/widgets/visualization/icons/liveslice.png +0 -0
  562. orangecontrib/tomwer/widgets/visualization/icons/liveslice.svg +0 -110
  563. tomwer/core/log/logger.py +0 -130
  564. tomwer/core/process/control/test/test_volume_link.py +0 -74
  565. tomwer/core/process/control/tomoobjserie.py +0 -12
  566. tomwer/core/process/control/volumesymlink.py +0 -200
  567. tomwer/core/process/icat/createscreenshots.py +0 -100
  568. tomwer/core/process/icat/gallery.py +0 -377
  569. tomwer/core/process/icat/icatbase.py +0 -36
  570. tomwer/core/process/icat/publish.py +0 -228
  571. tomwer/core/process/icat/screenshots.py +0 -27
  572. tomwer/core/process/reconstruction/test/test_darkref.py +0 -60
  573. tomwer/core/process/reconstruction/test/test_sadeltabeta.py +0 -74
  574. tomwer/core/process/visualization/liveslice.py +0 -6
  575. tomwer/core/progress.py +0 -100
  576. tomwer/core/scan/test/test_edf.py +0 -53
  577. tomwer/core/scan/test/test_future_scan.py +0 -61
  578. tomwer/core/scan/test/test_h5.py +0 -96
  579. tomwer/core/test/test_scanutils.py +0 -53
  580. tomwer/gui/control/emailnotifier.py +0 -174
  581. tomwer/gui/control/serie/seriewaiter.py +0 -28
  582. tomwer/gui/control/test/__init__.py +0 -28
  583. tomwer/gui/control/test/test_datalist.py +0 -96
  584. tomwer/gui/control/test/test_datavalidator.py +0 -54
  585. tomwer/gui/control/test/test_email.py +0 -35
  586. tomwer/gui/control/test/test_process_manager.py +0 -65
  587. tomwer/gui/control/test/test_scanselector.py +0 -67
  588. tomwer/gui/edit/test/__init__.py +0 -28
  589. tomwer/gui/icat/gallery.py +0 -214
  590. tomwer/gui/icat/publish.py +0 -187
  591. tomwer/gui/reconstruction/axis/axis.py +0 -733
  592. tomwer/gui/reconstruction/axis/radioaxis.py +0 -2467
  593. tomwer/gui/stitching/stitching.py +0 -1388
  594. tomwer/gui/test/__init__.py +0 -28
  595. tomwer/gui/test/test_axis_gui.py +0 -34
  596. tomwer/synctools/stacks/edit/darkflatpatch.py +0 -169
  597. tomwer/synctools/stacks/edit/imagekeyeditor.py +0 -135
  598. tomwer/third_part/WaitingOverlay.py +0 -110
  599. tomwer-1.3.27-py3.11-nspkg.pth +0 -1
  600. tomwer-1.3.27.dist-info/METADATA +0 -292
  601. tomwer-1.3.27.dist-info/RECORD +0 -785
  602. tomwer-1.3.27.dist-info/namespace_packages.txt +0 -1
  603. /orangecontrib/tomwer/{widgets/edit/test → tests}/__init__.py +0 -0
  604. {tomwer/core/process/control/test → orangecontrib/tomwer/tutorials/id16b}/__init__.py +0 -0
  605. {tomwer/core/process/icat → orangecontrib/tomwer/widgets/cluster/tests}/__init__.py +0 -0
  606. /orangecontrib/tomwer/widgets/control/icons/{tomoobjserie.png → tomoobjseries.png} +0 -0
  607. {tomwer/core/process/reconstruction/test → orangecontrib/tomwer/widgets/control/tests}/__init__.py +0 -0
  608. /orangecontrib/tomwer/widgets/{icat → dataportal}/icons/publish_processed_data.png +0 -0
  609. /orangecontrib/tomwer/widgets/{icat → dataportal}/icons/publish_processed_data.svg +0 -0
  610. {tomwer/core/process/test → orangecontrib/tomwer/widgets/debugtools/tests}/__init__.py +0 -0
  611. {tomwer/core/scan/test → orangecontrib/tomwer/widgets/edit/tests}/__init__.py +0 -0
  612. {tomwer/core/test → orangecontrib/tomwer/widgets/other/tests}/__init__.py +0 -0
  613. {tomwer/gui/cluster/test → orangecontrib/tomwer/widgets/reconstruction/tests}/__init__.py +0 -0
  614. {tomwer/gui/control/serie → orangecontrib/tomwer/widgets/stitching/tests}/__init__.py +0 -0
  615. {tomwer/gui/icat → orangecontrib/tomwer/widgets/tests}/__init__.py +0 -0
  616. {tomwer/gui/reconstruction/test → orangecontrib/tomwer/widgets/visualization/tests}/__init__.py +0 -0
  617. /tomwer/{synctools/stacks/edit → app/stitching}/__init__.py +0 -0
  618. /tomwer/{synctools/test → core/process/control/tests}/__init__.py +0 -0
  619. /tomwer/core/process/control/{test → tests}/test_email.py +0 -0
  620. /tomwer/core/process/control/{test → tests}/test_h52nx_process.py +0 -0
  621. /tomwer/{third_part → core/process/drac}/__init__.py +0 -0
  622. /tomwer/core/process/reconstruction/{test → tests}/test_axis_params.py +0 -0
  623. /tomwer/core/process/reconstruction/{test → tests}/test_darkref_copy.py +0 -0
  624. /tomwer/core/process/reconstruction/{test → tests}/test_paramsbase.py +0 -0
  625. /tomwer/core/process/reconstruction/{test → tests}/test_utils.py +0 -0
  626. /tomwer/core/scan/{test → tests}/test_scan.py +0 -0
  627. /tomwer/gui/control/{serie → series}/nxtomoconcatenate.py +0 -0
  628. /tomwer/gui/control/{test → tests}/test_datadiscovery.py +0 -0
  629. /tomwer/gui/control/{test → tests}/test_reducedarkflat_selector.py +0 -0
  630. /tomwer/gui/control/{test → tests}/test_single_tomo_obj.py +0 -0
  631. {orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_image_key_upgrader.py +0 -0
  632. {tomwer-1.3.27.dist-info → tomwer-1.4.0rc0.dist-info}/top_level.txt +0 -0
@@ -1,60 +0,0 @@
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- # coding: utf-8
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- # /*##########################################################################
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- #
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- # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
-
26
- __authors__ = ["H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "24/11/2021"
29
-
30
-
31
- from tomwer.core.process.reconstruction.darkref.darkrefs import (
32
- requires_reduced_dark_and_flat,
33
- )
34
- from tomwer.core.utils.scanutils import MockEDF, MockNXtomo
35
-
36
-
37
- def test_quick_run_necessary_edf(tmpdir):
38
- """test the `quick_run_necessary` function for EDFTomoScan"""
39
- scan = MockEDF.mockScan(scanID=str(tmpdir), start_dark=True, start_flat=True)
40
- assert scan.reduced_darks in (None, {})
41
- assert scan.reduced_flats in (None, {})
42
- requires_reduced_dark_and_flat(scan=scan)
43
- assert len(scan.reduced_darks) == 1
44
- assert len(scan.reduced_flats) == 1
45
-
46
-
47
- def test_quick_run_necessary_hdf5(tmpdir):
48
- """test the `quick_run_necessary` function for NXtomoScan"""
49
- scan = MockNXtomo(
50
- scan_path=tmpdir,
51
- n_proj=20,
52
- n_ini_proj=20,
53
- dim=10,
54
- ).scan
55
- assert scan.reduced_darks in (None, {})
56
- assert scan.reduced_flats in (None, {})
57
- computed = requires_reduced_dark_and_flat(scan=scan)
58
- assert len(computed) == 2
59
- assert len(scan.reduced_darks) == 1
60
- assert len(scan.reduced_flats) == 1
@@ -1,74 +0,0 @@
1
- # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
-
26
- __authors__ = ["H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "27/02/2021"
29
-
30
-
31
- import os
32
- import shutil
33
- import tempfile
34
- import unittest
35
-
36
- from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
37
- SADeltaBetaParams,
38
- SADeltaBetaTask,
39
- )
40
- from tomwer.core.utils.scanutils import MockNXtomo
41
-
42
-
43
- class TestSADeltaBetaProcess(unittest.TestCase):
44
- """Test the SAAxisProcess class"""
45
-
46
- def setUp(self) -> None:
47
- super().setUp()
48
- self.tempdir = tempfile.mkdtemp()
49
- dim = 10
50
- mock = MockNXtomo(
51
- scan_path=self.tempdir, n_proj=10, n_ini_proj=10, scan_range=180, dim=dim
52
- )
53
- self.scan = mock.scan
54
-
55
- def tearDown(self) -> None:
56
- shutil.rmtree(self.tempdir)
57
- super().tearDown()
58
-
59
- def test(self):
60
- process = SADeltaBetaTask(
61
- inputs={
62
- "data": self.scan,
63
- "sa_delta_beta_params": SADeltaBetaParams().to_dict(),
64
- "serialize_output_data": False,
65
- }
66
- )
67
-
68
- default_sadelta_beta_params = SADeltaBetaParams()
69
- default_sadelta_beta_params.output_dir = os.path.join(
70
- self.tempdir, "output_dir"
71
- )
72
- default_sadelta_beta_params.dry_run = True
73
-
74
- process.run()
@@ -1,6 +0,0 @@
1
- from ewokscore.task import Task as EwoksTask
2
-
3
-
4
- class _LiveSlicePlaceHolder(EwoksTask, input_names=("data",), output_names=("data",)):
5
- def run(self):
6
- self.outputs.data = self.inputs.data
tomwer/core/progress.py DELETED
@@ -1,100 +0,0 @@
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
- """module for giving information on process progress"""
26
-
27
- __authors__ = ["H. Payno"]
28
- __license__ = "MIT"
29
- __date__ = "07/08/2019"
30
-
31
-
32
- import logging
33
- import sys
34
- from enum import Enum
35
-
36
- _logger = logging.getLogger(__name__)
37
-
38
-
39
- class _Advancement(Enum):
40
- step_1 = "\\"
41
- step_2 = "-"
42
- step_3 = "/"
43
- step_4 = "|"
44
-
45
- @staticmethod
46
- def getNextStep(step):
47
- if step is _Advancement.step_1:
48
- return _Advancement.step_2
49
- elif step is _Advancement.step_2:
50
- return _Advancement.step_3
51
- elif step is _Advancement.step_3:
52
- return _Advancement.step_4
53
- else:
54
- return _Advancement.step_1
55
-
56
- @staticmethod
57
- def getStep(value):
58
- if value % 4 == 0:
59
- return _Advancement.step_4
60
- elif value % 3 == 0:
61
- return _Advancement.step_3
62
- elif value % 2 == 0:
63
- return _Advancement.step_2
64
- else:
65
- return _Advancement.step_1
66
-
67
-
68
- class Progress(object):
69
- """Simple interface for defining advancement on a 100 percentage base"""
70
-
71
- def __init__(self, name):
72
- self._name = name
73
- self.reset()
74
-
75
- def reset(self, max_=None):
76
- self._nProcessed = 0
77
- self._maxProcessed = max_
78
-
79
- def startProcess(self):
80
- self.setAdvancement(0)
81
-
82
- def setAdvancement(self, value):
83
- length = 20 # modify this to change the length
84
- block = int(round(length * value / 100))
85
- blocks_str = "#" * block + "-" * (length - block)
86
- msg = f"\r{self._name}: [{blocks_str}] {round(value, 2)}%"
87
- if value >= 100:
88
- msg += " DONE\r\n"
89
- sys.stdout.write(msg)
90
- sys.stdout.flush()
91
-
92
- def endProcess(self):
93
- self.setAdvancement(100)
94
-
95
- def setMaxAdvancement(self, n):
96
- self._maxProcessed = n
97
-
98
- def increaseAdvancement(self, i=1):
99
- self._nProcessed += i
100
- self.setAdvancement((self._nProcessed / self._maxProcessed) * 100)
@@ -1,53 +0,0 @@
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
- """Unit test for the scan defined at the hdf5 format"""
26
-
27
- __authors__ = ["H. Payno"]
28
- __license__ = "MIT"
29
- __date__ = "23/11/2021"
30
-
31
-
32
- import os
33
-
34
- from tomwer.core.scan.edfscan import EDFTomoScan
35
- from tomwer.core.utils.scanutils import MockEDF
36
-
37
-
38
- def test_scan_dir(tmpdir):
39
- full_path = os.path.join(tmpdir, "my", "aquisition", "folder")
40
- MockEDF.fastMockAcquisition(full_path)
41
- scan = EDFTomoScan(full_path)
42
- assert scan.scan_dir_name() == "folder"
43
- assert scan.scan_basename() == full_path
44
-
45
-
46
- def test_working_directory():
47
- """test behavior of the working directory function"""
48
- scan = EDFTomoScan(scan=None)
49
- assert scan.working_directory is None
50
- scan = EDFTomoScan(scan="my_folder")
51
- assert scan.working_directory == os.path.abspath("my_folder")
52
- scan = EDFTomoScan(scan="/full/path/to/my/folder")
53
- assert scan.working_directory == os.path.abspath("/full/path/to/my/folder")
@@ -1,61 +0,0 @@
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
- """Unit test for the scan defined at the hdf5 format"""
26
-
27
- __authors__ = ["H. Payno"]
28
- __license__ = "MIT"
29
- __date__ = "04/11/2021"
30
-
31
-
32
- import asyncio
33
- import os
34
-
35
- from tomwer.core.futureobject import FutureTomwerObject
36
- from tomwer.core.utils.scanutils import MockNXtomo
37
-
38
-
39
- def test_simple_future_tomo_obj(tmpdir):
40
- """Simple test of the FutureTomwerScan API"""
41
- scan = MockNXtomo(
42
- scan_path=os.path.join(tmpdir, "scan_test"),
43
- n_proj=10,
44
- n_ini_proj=10,
45
- create_ini_dark=False,
46
- create_ini_flat=False,
47
- dim=10,
48
- ).scan
49
- future = asyncio.Future()
50
- future.set_result(None)
51
-
52
- future_tomo_obj = FutureTomwerObject(
53
- tomo_obj=scan,
54
- futures=[
55
- future,
56
- ],
57
- )
58
-
59
- future_tomo_obj.results()
60
- assert future_tomo_obj.exceptions() is None
61
- assert future_tomo_obj.cancelled() is False
@@ -1,96 +0,0 @@
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
- """Unit test for the scan defined at the hdf5 format"""
26
-
27
- __authors__ = ["H. Payno"]
28
- __license__ = "MIT"
29
- __date__ = "16/09/2019"
30
-
31
- import os
32
- import shutil
33
- import tempfile
34
- import unittest
35
-
36
- from tomwer.core.scan.nxtomoscan import NXtomoScan
37
- from tomwer.core.utils.scanutils import MockNXtomo
38
- from tomwer.tests.datasets import TomwerCIDatasets
39
-
40
-
41
- class TestHDF5Scan(unittest.TestCase):
42
- """Basic test for the hdf5 scan"""
43
-
44
- def setUp(self) -> None:
45
- super(TestHDF5Scan, self).setUp()
46
- self._tmp_dir = tempfile.mkdtemp()
47
- self.dataset_file = os.path.join(self._tmp_dir, "frm_edftomomill_twoentries.nx")
48
- shutil.copyfile(
49
- TomwerCIDatasets.get_dataset(
50
- "h5_datasets/frm_edftomomill_twoentries.nx",
51
- ),
52
- self.dataset_file,
53
- )
54
- assert os.path.isfile(self.dataset_file)
55
- self.scan = NXtomoScan(scan=self.dataset_file, entry="entry0000")
56
-
57
- def test_scan_dir(self):
58
- assert self.scan.scan_dir_name() == self._tmp_dir.split(os.sep)[-1]
59
-
60
- def testFFInterval(self):
61
- """test the call to ff_interval"""
62
- scan_path = os.path.join(self._tmp_dir, "my_scan_1")
63
- scan_1 = MockNXtomo(
64
- scan_path=scan_path,
65
- n_ini_proj=20,
66
- n_proj=20,
67
- n_alignement_proj=2,
68
- create_final_flat=True,
69
- create_ini_dark=True,
70
- create_ini_flat=True,
71
- n_refs=5,
72
- ).scan
73
- self.assertEqual(scan_1.ff_interval, 20)
74
-
75
- scan_path2 = os.path.join(self._tmp_dir, "my_scan_2")
76
- scan_2 = MockNXtomo(
77
- scan_path=scan_path2,
78
- n_ini_proj=10,
79
- n_proj=10,
80
- n_alignement_proj=2,
81
- create_final_flat=False,
82
- create_ini_dark=True,
83
- create_ini_flat=True,
84
- n_refs=1,
85
- ).scan
86
- self.assertEqual(scan_2.ff_interval, 0)
87
-
88
-
89
- def test_working_directory():
90
- """test behavior of the working directory function"""
91
- scan = NXtomoScan(scan=None, entry="my_entry")
92
- assert scan.working_directory is None
93
- scan = NXtomoScan(scan="/full/path/my_file.sh", entry="my_entry")
94
- assert scan.working_directory == os.path.abspath("/full/path")
95
- scan = NXtomoScan(scan="my_file.sh", entry="my_entry")
96
- assert scan.working_directory == os.path.abspath(".")
@@ -1,53 +0,0 @@
1
- # coding: utf-8
2
- # /*##########################################################################
3
- #
4
- # Copyright (c) 2017 European Synchrotron Radiation Facility
5
- #
6
- # Permission is hereby granted, free of charge, to any person obtaining a copy
7
- # of this software and associated documentation files (the "Software"), to deal
8
- # in the Software without restriction, including without limitation the rights
9
- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10
- # copies of the Software, and to permit persons to whom the Software is
11
- # furnished to do so, subject to the following conditions:
12
- #
13
- # The above copyright notice and this permission notice shall be included in
14
- # all copies or substantial portions of the Software.
15
- #
16
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19
- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21
- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22
- # THE SOFTWARE.
23
- #
24
- # ###########################################################################*/
25
-
26
- __authors__ = ["H. Payno"]
27
- __license__ = "MIT"
28
- __date__ = "30/09/2019"
29
-
30
- import os
31
- import tempfile
32
- import unittest
33
-
34
- from nxtomo.application.nxtomo import NXtomo
35
- from tomwer.core.scan.nxtomoscan import NXtomoScan
36
- from tomwer.core.utils.scanutils import MockNXtomo
37
-
38
-
39
- class TestMockNXtomo(unittest.TestCase):
40
- """Test the MockNXtomo file"""
41
-
42
- def test_creation(self):
43
- folder = tempfile.mkdtemp()
44
- mock = MockNXtomo(scan_path=folder, n_proj=10, n_ini_proj=10)
45
- self.assertEqual(
46
- mock.scan_master_file,
47
- os.path.join(folder, os.path.basename(folder) + ".h5"),
48
- )
49
- tomoScan = NXtomoScan(mock.scan_path, entry=mock.scan_entry)
50
- self.assertEqual(len(NXtomo.get_valid_entries(mock.scan_master_file)), 1)
51
- tomoScan.update()
52
- self.assertEqual(tomoScan.scan_range, 360)
53
- self.assertEqual(len(tomoScan.projections), 10)
@@ -1,174 +0,0 @@
1
- from typing import Optional
2
- from silx.gui import qt
3
- from tomwer.gui import icons as tomwericons
4
- from tomwer.core.utils.dictutils import concatenate_dict
5
-
6
-
7
- class EmailComposition(qt.QWidget):
8
- """
9
- Widget used to compose an email
10
-
11
- Please see https://confluence.esrf.fr/display/SCKB/Rules+about+email for email rules at esrf
12
- """
13
-
14
- sigChanged = qt.Signal()
15
- """emit when the composition changed"""
16
-
17
- def __init__(self, parent: Optional[qt.QWidget]) -> None:
18
- super().__init__(parent)
19
- self.setLayout(qt.QFormLayout())
20
- # from
21
- self._fromAddressesQLE = qt.QLineEdit(self)
22
- singleEmailValidator = qt.QRegularExpressionValidator(
23
- qt.QRegularExpression(
24
- r"(^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$)"
25
- ),
26
- self._fromAddressesQLE,
27
- )
28
- self._fromAddressesQLE.setValidator(singleEmailValidator)
29
- self.layout().addRow("from", self._fromAddressesQLE)
30
- # to
31
- self._toAdressesQLE = qt.QLineEdit(self)
32
- severalEmailValidator = qt.QRegularExpressionValidator(
33
- qt.QRegularExpression(
34
- r"(([a-zA-Z0-9_\-\.]+)@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.)|(([a-zA-Z0-9\-]+\.)+))([a-zA-Z]{2,4}|[0-9]{1,3})(\]?)(\s*;\s*|\s*$))*"
35
- ),
36
- self,
37
- )
38
- self._toAdressesQLE.setValidator(severalEmailValidator)
39
- self.layout().addRow("to", self._toAdressesQLE)
40
- # subject
41
- self._subjectQLE = qt.QLineEdit("tomwer: {tomo_obj_short_id} received", self)
42
- tooltip = """
43
- this section can contain some predefine `keywords` and will be formatting before sending the email.\n
44
- Reserve keywords are: \n
45
- - {tomo_obj_short_id}: tomo_obj short identifier
46
- - {tomo_obj_id}: tomo_obj id
47
- - {ls_tomo_obj}: ls of the scan folder
48
- - {timestamp}: current time
49
- - {footnote}: some footnote defined by tomwer
50
- - {dataset_processing_states}: list dataset state regarding met processes
51
- """
52
- self._subjectQLE.setToolTip(tooltip)
53
- self.layout().addRow("subject", self._subjectQLE)
54
- # text
55
- self._textQLE = qt.QPlainTextEdit(
56
- "{tomo_obj_id} received at {timestamp} \n\nprocesses:\n{dataset_processing_states}\n\nfile listening:\n{ls_tomo_obj}\n\nInfo: {footnote}"
57
- )
58
- self._textQLE.setToolTip(tooltip)
59
- self.layout().addRow(self._textQLE)
60
-
61
- # connect signal / slot
62
- self._fromAddressesQLE.editingFinished.connect(self.sigChanged)
63
- self._toAdressesQLE.editingFinished.connect(self.sigChanged)
64
- self._subjectQLE.editingFinished.connect(self.sigChanged)
65
- self._textQLE.textChanged.connect(self.sigChanged)
66
-
67
- def getToAddrs(self) -> tuple:
68
- adresses = self._toAdressesQLE.text().replace(" ", "")
69
- adresses.replace(",", ";")
70
- return tuple(set(adresses.split(";")))
71
-
72
- def getConfiguration(self) -> dict:
73
- return {
74
- "subject": self._subjectQLE.text(),
75
- "from_addr": self._fromAddressesQLE.text(),
76
- "to_addrs": self.getToAddrs(),
77
- "text": self._textQLE.toPlainText(),
78
- }
79
-
80
- def setConfiguration(self, config: dict):
81
- assert isinstance(config, dict)
82
- subject = config.get("subject", None)
83
- if subject is not None:
84
- self._subjectQLE.setText(str(subject))
85
- from_addr = config.get("from_addr", None)
86
- if from_addr is not None:
87
- self._fromAddressesQLE.setText(str(from_addr))
88
- to_addrs = config.get("to_addrs", None)
89
- if to_addrs is not None:
90
- if not isinstance(to_addrs, str):
91
- to_addrs = ";".join(to_addrs)
92
- self._toAdressesQLE.setText(str(to_addrs))
93
- text = config.get("text", None)
94
- if text is not None:
95
- self._textQLE.setPlainText(str(text))
96
-
97
-
98
- class EmailSettings(qt.QWidget):
99
- """
100
- Widget to set up mail server
101
- """
102
-
103
- sigChanged = qt.Signal()
104
- """emit when the settings changed"""
105
-
106
- def __init__(self, parent: Optional[qt.QWidget]) -> None:
107
- super().__init__(parent)
108
- self.setLayout(qt.QFormLayout(self))
109
- # server
110
- self._hostQLE = qt.QLineEdit("smtps.esrf.fr", self)
111
- self.layout().addRow("host", self._hostQLE)
112
- # port
113
- self._portQLE = qt.QLineEdit("0", self)
114
- self._portQLE.setValidator(qt.QIntValidator(self._portQLE))
115
- self.layout().addRow("port", self._portQLE)
116
-
117
- # connect signal / slot
118
- self._hostQLE.editingFinished.connect(self.sigChanged)
119
- self._portQLE.editingFinished.connect(self.sigChanged)
120
-
121
- def getConfiguration(self) -> dict:
122
- return {"host": self._hostQLE.text(), "port": int(self._portQLE.text())}
123
-
124
- def setConfiguration(self, config: dict):
125
- server = config.get("host", None)
126
- if server is not None:
127
- self._hostQLE.setText(str(server))
128
- port = config.get("port", None)
129
- if port is not None:
130
- self._portQLE.setText(str(port))
131
-
132
-
133
- class Emailwidget(qt.QTabWidget):
134
- """
135
- Main widget to send email
136
- """
137
-
138
- sigChanged = qt.Signal()
139
- """emit when the email settings or composition changed"""
140
-
141
- def __init__(self, parent: Optional[qt.QWidget] = None) -> None:
142
- super().__init__(parent)
143
-
144
- self.setTabPosition(qt.QTabWidget.East)
145
-
146
- self._compositionWidget = EmailComposition(self)
147
- composeIcon = tomwericons.getQIcon("compose")
148
- self.addTab(
149
- self._compositionWidget,
150
- composeIcon,
151
- "",
152
- )
153
-
154
- self._serverSettingsWidget = EmailSettings(self)
155
- settingsIcon = tomwericons.getQIcon("parameters")
156
- self.addTab(
157
- self._serverSettingsWidget,
158
- settingsIcon,
159
- "",
160
- )
161
-
162
- # connect signal / slot
163
- self._compositionWidget.sigChanged.connect(self.sigChanged)
164
- self._serverSettingsWidget.sigChanged.connect(self.sigChanged)
165
-
166
- def getConfiguration(self) -> dict:
167
- return concatenate_dict(
168
- self._serverSettingsWidget.getConfiguration(),
169
- self._compositionWidget.getConfiguration(),
170
- )
171
-
172
- def setConfiguration(self, config: dict):
173
- self._serverSettingsWidget.setConfiguration(config)
174
- self._compositionWidget.setConfiguration(config)