tomwer 1.0.4__py3-none-any.whl → 1.1.0__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 (256) hide show
  1. orangecontrib/tomwer/tutorials/EBS_tomo_listener.ows +39 -0
  2. orangecontrib/tomwer/tutorials/cast_volume.ows +34 -0
  3. orangecontrib/tomwer/tutorials/simple_slice_reconstruction.ows +39 -0
  4. orangecontrib/tomwer/tutorials/simple_volume_local_reconstruction.ows +49 -0
  5. orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows +59 -0
  6. orangecontrib/tomwer/tutorials/using_saaxis_to_find_cor.ows +44 -0
  7. orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py +1 -1
  8. orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py +14 -4
  9. orangecontrib/tomwer/widgets/cluster/__init__.py +1 -1
  10. orangecontrib/tomwer/widgets/control/DataListOW.py +12 -5
  11. orangecontrib/tomwer/widgets/control/DataListenerOW.py +18 -9
  12. orangecontrib/tomwer/widgets/control/DataSelectorOW.py +13 -6
  13. orangecontrib/tomwer/widgets/control/DataTransfertOW.py +4 -5
  14. orangecontrib/tomwer/widgets/control/DataValidatorOW.py +8 -4
  15. orangecontrib/tomwer/widgets/control/DataWatcherOW.py +4 -6
  16. orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py +49 -62
  17. orangecontrib/tomwer/widgets/control/FilterOW.py +2 -4
  18. orangecontrib/tomwer/widgets/control/NXTomomillMixIn.py +93 -0
  19. orangecontrib/tomwer/widgets/control/NXTomomillOW.py +135 -128
  20. orangecontrib/tomwer/widgets/control/NotifierOW.py +31 -7
  21. orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py +3 -5
  22. orangecontrib/tomwer/widgets/control/TomoObjSerieOW.py +85 -0
  23. orangecontrib/tomwer/widgets/control/VolumeSelector.py +12 -4
  24. orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py +11 -7
  25. orangecontrib/tomwer/widgets/control/icons/notification.svg +4 -4
  26. orangecontrib/tomwer/widgets/control/icons/nxtomomill.png +0 -0
  27. orangecontrib/tomwer/widgets/control/icons/nxtomomill.svg +8 -5
  28. orangecontrib/tomwer/widgets/control/icons/tomoobjserie.png +0 -0
  29. orangecontrib/tomwer/widgets/control/icons/tomoobjserie.svg +138 -0
  30. orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py +16 -4
  31. orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py +100 -0
  32. orangecontrib/tomwer/widgets/edit/icons/image_key_editor.png +0 -0
  33. orangecontrib/tomwer/widgets/edit/icons/image_key_upgrader.png +0 -0
  34. orangecontrib/tomwer/widgets/edit/icons/nx_tomo_editor.png +0 -0
  35. orangecontrib/tomwer/widgets/edit/icons/nx_tomo_editor.svg +123 -0
  36. orangecontrib/tomwer/widgets/edit/test/test_dark_flat_patch.py +21 -1
  37. orangecontrib/tomwer/widgets/edit/test/test_image_key_editor.py +1 -1
  38. orangecontrib/tomwer/widgets/edit/test/test_image_key_upgrader.py +1 -1
  39. orangecontrib/tomwer/widgets/edit/test/test_nxtomo_editor.py +25 -0
  40. orangecontrib/tomwer/widgets/other/PythonScriptOW.py +19 -10
  41. orangecontrib/tomwer/widgets/reconstruction/AxisOW.py +20 -14
  42. orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py +24 -10
  43. orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py +26 -21
  44. orangecontrib/tomwer/widgets/reconstruction/NabuOW.py +29 -12
  45. orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py +44 -17
  46. orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py +28 -18
  47. orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py +24 -17
  48. orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py +6 -6
  49. orangecontrib/tomwer/widgets/reconstruction/TofuOW.py +4 -2
  50. orangecontrib/tomwer/widgets/reconstruction/icons/nabu_2d.png +0 -0
  51. orangecontrib/tomwer/widgets/reconstruction/icons/nabu_2d.svg +11 -8
  52. orangecontrib/tomwer/widgets/visualization/DataViewerOW.py +10 -4
  53. orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py +1 -1
  54. orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py +69 -0
  55. orangecontrib/tomwer/widgets/visualization/SampleMovedOW.py +2 -4
  56. orangecontrib/tomwer/widgets/visualization/icons/nx_tomo_metadata_viewer.png +0 -0
  57. orangecontrib/tomwer/widgets/visualization/icons/nx_tomo_metadata_viewer.svg +105 -0
  58. tomwer/__main__.py +10 -5
  59. tomwer/app/canvas_launcher/config.py +10 -10
  60. tomwer/app/canvas_launcher/mainwindow.py +68 -6
  61. tomwer/app/canvas_launcher/widgetsscheme.py +1 -3
  62. tomwer/app/darkref.py +16 -12
  63. tomwer/app/imagekeyeditor.py +2 -2
  64. tomwer/app/imagekeyupgrader.py +104 -0
  65. tomwer/app/nxtomoeditor.py +103 -0
  66. tomwer/app/rsync.py +1 -1
  67. tomwer/core/cluster/cluster.py +1 -1
  68. tomwer/core/futureobject.py +1 -0
  69. tomwer/core/process/control/datalistener/datalistener.py +7 -1
  70. tomwer/core/process/control/datalistener/rpcserver.py +3 -3
  71. tomwer/core/process/control/datawatcher/datawatcher.py +18 -18
  72. tomwer/core/process/control/datawatcher/datawatcherobserver.py +5 -8
  73. tomwer/core/process/control/datawatcher/datawatcherprocess.py +2 -3
  74. tomwer/core/process/control/datawatcher/edfdwprocess.py +2 -2
  75. tomwer/core/process/control/nxtomomill.py +33 -58
  76. tomwer/core/process/control/scanlist.py +2 -1
  77. tomwer/core/process/control/scanselector.py +7 -0
  78. tomwer/core/process/control/scantransfer.py +9 -18
  79. tomwer/core/process/control/scanvalidator.py +6 -5
  80. tomwer/core/process/control/singletomoobj.py +2 -1
  81. tomwer/core/process/control/timer.py +2 -1
  82. tomwer/core/process/control/tomoobjserie.py +8 -0
  83. tomwer/core/process/control/volumeselector.py +2 -1
  84. tomwer/core/process/control/volumesymlink.py +2 -1
  85. tomwer/core/process/edit/darkflatpatch.py +2 -1
  86. tomwer/core/process/edit/imagekeyeditor.py +4 -3
  87. tomwer/core/process/reconstruction/axis/axis.py +29 -32
  88. tomwer/core/process/reconstruction/axis/mode.py +3 -2
  89. tomwer/core/process/reconstruction/axis/params.py +35 -16
  90. tomwer/core/process/reconstruction/darkref/darkrefs.py +90 -707
  91. tomwer/core/process/reconstruction/darkref/darkrefscopy.py +44 -16
  92. tomwer/core/process/reconstruction/darkref/params.py +62 -67
  93. tomwer/core/process/reconstruction/lamino/tofu.py +1 -1
  94. tomwer/core/process/reconstruction/nabu/castvolume.py +21 -26
  95. tomwer/core/process/reconstruction/nabu/nabucommon.py +36 -38
  96. tomwer/core/process/reconstruction/nabu/nabuscores.py +28 -13
  97. tomwer/core/process/reconstruction/nabu/nabuslices.py +41 -14
  98. tomwer/core/process/reconstruction/nabu/nabuvolume.py +21 -12
  99. tomwer/core/process/reconstruction/nabu/utils.py +12 -1
  100. tomwer/core/process/reconstruction/normalization/normalization.py +9 -8
  101. tomwer/core/process/reconstruction/saaxis/saaxis.py +46 -20
  102. tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +38 -12
  103. tomwer/core/process/reconstruction/test/__init__.py +0 -39
  104. tomwer/core/process/reconstruction/test/test_axis_params.py +25 -3
  105. tomwer/core/process/reconstruction/test/test_darkref_copy.py +117 -1
  106. tomwer/core/process/script/python.py +16 -12
  107. tomwer/core/process/task.py +3 -7
  108. tomwer/core/process/test/test_axis.py +1 -1
  109. tomwer/core/process/test/test_dark_and_flat.py +41 -111
  110. tomwer/core/process/test/test_data_listener.py +0 -29
  111. tomwer/core/process/test/test_data_transfer.py +10 -14
  112. tomwer/core/process/test/test_nabu.py +1 -1
  113. tomwer/core/process/test/test_normalization.py +1 -1
  114. tomwer/core/process/visualization/liveslice.py +6 -0
  115. tomwer/core/scan/blissscan.py +37 -2
  116. tomwer/core/scan/edfscan.py +14 -4
  117. tomwer/core/scan/hdf5scan.py +10 -4
  118. tomwer/core/scan/scanbase.py +35 -29
  119. tomwer/core/scan/scanfactory.py +3 -17
  120. tomwer/core/scan/test/test_h5.py +1 -1
  121. tomwer/core/scan/test/test_process_registration.py +0 -11
  122. tomwer/core/scan/test/test_scan.py +32 -30
  123. tomwer/core/settings.py +2 -2
  124. tomwer/core/test/test_utils.py +1 -1
  125. tomwer/core/tomwer_object.py +19 -0
  126. tomwer/core/utils/__init__.py +0 -45
  127. tomwer/core/utils/char.py +2 -0
  128. tomwer/core/utils/gpu.py +5 -5
  129. tomwer/core/utils/nxtomoutils.py +2 -2
  130. tomwer/core/utils/scanutils.py +50 -0
  131. tomwer/core/utils/volumeutils.py +13 -0
  132. tomwer/core/volume/edfvolume.py +4 -0
  133. tomwer/core/volume/hdf5volume.py +4 -0
  134. tomwer/core/volume/jp2kvolume.py +4 -0
  135. tomwer/core/volume/rawvolume.py +4 -0
  136. tomwer/core/volume/tiffvolume.py +4 -0
  137. tomwer/core/volume/volumebase.py +19 -12
  138. tomwer/core/volume/volumefactory.py +20 -1
  139. tomwer/gui/cluster/slurm.py +1 -1
  140. tomwer/gui/cluster/test/test_cluster.py +2 -2
  141. tomwer/gui/control/datalist.py +109 -34
  142. tomwer/gui/control/datatransfert.py +1 -1
  143. tomwer/gui/control/datawatcher/datawatcher.py +23 -13
  144. tomwer/gui/control/datawatcher/datawatcherobserver.py +1 -1
  145. tomwer/gui/control/observations.py +0 -3
  146. tomwer/gui/control/selectorwidgetbase.py +42 -11
  147. tomwer/gui/control/serie/seriecreator.py +967 -0
  148. tomwer/{web/__init__.py → gui/control/serie/seriewaiter.py} +5 -7
  149. tomwer/gui/control/singletomoobj.py +15 -3
  150. tomwer/gui/control/test/test_datalist.py +1 -1
  151. tomwer/gui/control/test/test_datalistener.py +1 -1
  152. tomwer/gui/control/test/test_inputwidget.py +1 -1
  153. tomwer/gui/control/test/test_process_manager.py +1 -13
  154. tomwer/gui/control/test/test_scanselector.py +1 -1
  155. tomwer/gui/control/test/test_scanvalidator.py +1 -1
  156. tomwer/gui/control/test/test_single_tomo_obj.py +1 -1
  157. tomwer/gui/control/test/test_volume_dialog.py +19 -7
  158. tomwer/gui/control/test/test_volumeselector.py +4 -4
  159. tomwer/gui/debugtools/datasetgenerator.py +1 -8
  160. tomwer/gui/edit/dkrfpatch.py +2 -2
  161. tomwer/gui/edit/imagekeyeditor.py +12 -9
  162. tomwer/gui/edit/nxtomoeditor.py +475 -0
  163. tomwer/gui/edit/test/test_dkrf_patch.py +2 -14
  164. tomwer/gui/edit/test/test_image_key_editor.py +2 -2
  165. tomwer/gui/edit/test/test_nx_editor.py +155 -0
  166. tomwer/gui/qfolderdialog.py +11 -0
  167. tomwer/gui/reconstruction/axis/CompareImages.py +27 -29
  168. tomwer/gui/reconstruction/axis/axis.py +2 -0
  169. tomwer/gui/reconstruction/axis/radioaxis.py +67 -11
  170. tomwer/gui/reconstruction/darkref/darkrefcopywidget.py +7 -9
  171. tomwer/gui/reconstruction/darkref/darkrefwidget.py +22 -24
  172. tomwer/gui/reconstruction/lamino/tofu/projections.py +1 -1
  173. tomwer/gui/reconstruction/lamino/tofu/tofu.py +3 -3
  174. tomwer/gui/reconstruction/lamino/tofu/tofuexpert.py +4 -4
  175. tomwer/gui/reconstruction/lamino/tofu/tofuoutput.py +10 -4
  176. tomwer/gui/reconstruction/nabu/castvolume.py +80 -11
  177. tomwer/gui/reconstruction/nabu/check.py +1 -1
  178. tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py +352 -0
  179. tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py +0 -9
  180. tomwer/gui/reconstruction/nabu/nabuconfig/output.py +1 -1
  181. tomwer/gui/reconstruction/nabu/nabuconfig/phase.py +18 -19
  182. tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py +30 -7
  183. tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py +26 -13
  184. tomwer/gui/reconstruction/nabu/slices.py +10 -2
  185. tomwer/gui/reconstruction/nabu/slurm.py +1 -1
  186. tomwer/gui/reconstruction/nabu/volume.py +13 -7
  187. tomwer/gui/reconstruction/normalization/intensity.py +1 -1
  188. tomwer/gui/reconstruction/saaxis/corrangeselector.py +10 -34
  189. tomwer/gui/reconstruction/saaxis/saaxis.py +11 -6
  190. tomwer/gui/reconstruction/saaxis/sliceselector.py +11 -26
  191. tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py +13 -8
  192. tomwer/gui/reconstruction/scores/scoreplot.py +67 -61
  193. tomwer/gui/reconstruction/test/test_axis.py +2 -2
  194. tomwer/gui/reconstruction/test/test_lamino.py +2 -2
  195. tomwer/gui/reconstruction/test/test_nabu.py +14 -1
  196. tomwer/gui/reconstruction/test/test_saaxis.py +8 -17
  197. tomwer/gui/reconstruction/test/test_sadeltabeta.py +7 -13
  198. tomwer/gui/stackplot.py +11 -28
  199. tomwer/gui/test/test_axis_gui.py +4 -4
  200. tomwer/gui/test/test_qfolder_dialog.py +12 -0
  201. tomwer/gui/utils/inputwidget.py +42 -21
  202. tomwer/gui/utils/lineselector/lineselector.py +13 -21
  203. tomwer/gui/utils/scandescription.py +2 -4
  204. tomwer/gui/utils/slider.py +1 -102
  205. tomwer/gui/utils/unitsystem.py +48 -11
  206. tomwer/gui/visualization/dataviewer.py +24 -17
  207. tomwer/gui/visualization/diffviewer/diffviewer.py +2 -11
  208. tomwer/gui/visualization/nxtomometadata.py +21 -0
  209. tomwer/gui/visualization/scanoverview.py +0 -1
  210. tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py +72 -0
  211. tomwer/gui/visualization/test/test_stacks.py +1 -1
  212. tomwer/gui/visualization/tomoobjoverview.py +49 -0
  213. tomwer/gui/visualization/volumeoverview.py +64 -0
  214. tomwer/gui/visualization/volumeviewer.py +1 -1
  215. tomwer/resources/gui/icons/multi-document-save.png +0 -0
  216. tomwer/resources/gui/icons/multi-document-save.svg +101 -0
  217. tomwer/resources/gui/illustrations/ctf_z1.png +0 -0
  218. tomwer/resources/gui/illustrations/ctf_z1.svg +471 -0
  219. tomwer/synctools/datalistener.py +5 -1
  220. tomwer/synctools/imageloaderthread.py +2 -2
  221. tomwer/synctools/stacks/edit/imagekeyeditor.py +1 -1
  222. tomwer/synctools/stacks/processingstack.py +2 -2
  223. tomwer/synctools/stacks/reconstruction/castvolume.py +1 -0
  224. tomwer/synctools/stacks/reconstruction/lamino.py +1 -3
  225. tomwer/synctools/stacks/reconstruction/sadeltabeta.py +0 -2
  226. tomwer/synctools/test/test_darkRefs.py +32 -149
  227. tomwer/synctools/test/test_foldertransfer.py +1 -1
  228. tomwer/synctools/test/test_scanstages.py +2 -2
  229. tomwer/tests/__init__.py +0 -0
  230. tomwer/tests/conftest.py +51 -0
  231. tomwer/{test → tests}/test_scripts.py +1 -1
  232. tomwer/tests/test_utils.py +10 -0
  233. tomwer/{test → tests}/utils/utilstest.py +0 -11
  234. tomwer/version.py +3 -3
  235. {tomwer-1.0.4.dist-info → tomwer-1.1.0.dist-info}/METADATA +14 -16
  236. {tomwer-1.0.4.dist-info → tomwer-1.1.0.dist-info}/RECORD +245 -217
  237. {tomwer-1.0.4.dist-info → tomwer-1.1.0.dist-info}/WHEEL +1 -1
  238. {tomwer-1.0.4.dist-info → tomwer-1.1.0.dist-info}/entry_points.txt +6 -0
  239. orangecontrib/tomwer/setup.py +0 -45
  240. orangecontrib/tomwer/widgets/setup.py +0 -49
  241. tomwer/app/process.py +0 -153
  242. tomwer/core/process/reconstruction/nabu/slurm.py +0 -36
  243. tomwer/core/process/reconstruction/utils/nabu_slice_exec.py +0 -10
  244. tomwer/core/utils/laminoutils.py +0 -80
  245. tomwer/gui/utils/lineselector/lineselection.py +0 -76
  246. tomwer/setup.py +0 -52
  247. tomwer/web/client.py +0 -43
  248. tomwer/web/config.py +0 -36
  249. tomwer/web/test/test_graylog_connection.py +0 -59
  250. {tomwer/test → orangecontrib/tomwer/tutorials}/__init__.py +0 -0
  251. /tomwer/{web/test → gui/control/serie}/__init__.py +0 -0
  252. /tomwer/{test → tests}/utils/__init__.py +0 -0
  253. /tomwer-1.0.4-py3.8-nspkg.pth → /tomwer-1.1.0-py3.9-nspkg.pth +0 -0
  254. {tomwer-1.0.4.dist-info → tomwer-1.1.0.dist-info}/LICENSE +0 -0
  255. {tomwer-1.0.4.dist-info → tomwer-1.1.0.dist-info}/namespace_packages.txt +0 -0
  256. {tomwer-1.0.4.dist-info → tomwer-1.1.0.dist-info}/top_level.txt +0 -0