tomwer 1.3.16__tar.gz → 1.4.6__tar.gz

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 (1347) hide show
  1. tomwer-1.4.6/LICENSE +29 -0
  2. tomwer-1.4.6/PKG-INFO +336 -0
  3. tomwer-1.4.6/README.rst +103 -0
  4. tomwer-1.4.6/pyproject.toml +10 -0
  5. tomwer-1.4.6/setup.cfg +174 -0
  6. tomwer-1.4.6/setup.py +4 -0
  7. tomwer-1.4.6/src/orangecontrib/tomwer/__init__.py +10 -0
  8. tomwer-1.4.6/src/orangecontrib/tomwer/orange/managedprocess.py +93 -0
  9. tomwer-1.4.6/src/orangecontrib/tomwer/orange/settings.py +26 -0
  10. tomwer-1.4.6/src/orangecontrib/tomwer/tests/TestAcquisition.py +220 -0
  11. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/append_raw_darks_and_flats_frames_to_NXtomos.ows +44 -0
  12. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/copy_reduced_darks_and_flats_meth1.ows +55 -0
  13. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/drac_publication.ows +44 -0
  14. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/id16b/ID16b_full_volume.ows +22 -0
  15. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows +302 -0
  16. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows +218 -0
  17. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows +64 -0
  18. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/test_cor.ows +19 -0
  19. tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/volume_casting_on_slurm.ows +54 -0
  20. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/__init__.py +41 -0
  21. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py +224 -0
  22. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py +71 -0
  23. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/cluster/__init__.py +19 -0
  24. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/AdvancementOW.py +37 -0
  25. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py +231 -0
  26. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataListenerOW.py +381 -0
  27. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataSelectorOW.py +126 -0
  28. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataTransfertOW.py +196 -0
  29. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataValidatorOW.py +167 -0
  30. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataWatcherOW.py +178 -0
  31. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py +249 -0
  32. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/EmailOW.py +92 -0
  33. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/FilterOW.py +101 -0
  34. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/NXTomomillOW.py +337 -0
  35. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/NXtomoConcatenate.py +202 -0
  36. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/NotifierOW.py +108 -0
  37. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/ReduceDarkFlatSelectorOW.py +94 -0
  38. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py +142 -0
  39. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/TimerOW.py +110 -0
  40. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/TomoObjSeriesOW.py +58 -0
  41. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/VolumeSelector.py +120 -0
  42. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/__init__.py +18 -0
  43. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/icons/nxtomomill.svg +222 -0
  44. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.png +344 -0
  45. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.svg +59 -0
  46. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/icons/tomoobjseries.svg +138 -0
  47. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/dataportal/PublishProcessedDataOW.py +172 -0
  48. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/dataportal/__init__.py +18 -0
  49. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py +149 -0
  50. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/debugtools/ObjectInspectorOW.py +37 -0
  51. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/debugtools/__init__.py +17 -0
  52. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py +157 -0
  53. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/ImageKeyEditorOW.py +106 -0
  54. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/ImageKeyUpgraderOW.py +109 -0
  55. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py +127 -0
  56. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/__init__.py +17 -0
  57. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/other/PythonScriptOW.py +827 -0
  58. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/other/__init__.py +17 -0
  59. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/AxisOW.py +530 -0
  60. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py +203 -0
  61. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py +243 -0
  62. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py +186 -0
  63. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/NabuOW.py +272 -0
  64. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py +456 -0
  65. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py +471 -0
  66. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py +386 -0
  67. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py +262 -0
  68. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/__init__.py +19 -0
  69. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/stitching/ZStitchingConfigOW.py +118 -0
  70. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/stitching/__init__.py +17 -0
  71. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/utils.py +34 -0
  72. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/DataViewerOW.py +121 -0
  73. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py +53 -0
  74. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py +69 -0
  75. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/RadioStackOW.py +70 -0
  76. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/SampleMovedOW.py +89 -0
  77. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py +65 -0
  78. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/SliceStackOW.py +85 -0
  79. tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/__init__.py +19 -0
  80. tomwer-1.4.6/src/tomwer/__init__.py +19 -0
  81. tomwer-1.4.6/src/tomwer/__main__.py +259 -0
  82. tomwer-1.4.6/src/tomwer/app/__init__.py +2 -0
  83. tomwer-1.4.6/src/tomwer/app/axis.py +196 -0
  84. tomwer-1.4.6/src/tomwer/app/canvas.py +57 -0
  85. tomwer-1.4.6/src/tomwer/app/canvas_launcher/config.py +120 -0
  86. tomwer-1.4.6/src/tomwer/app/canvas_launcher/environ.py +90 -0
  87. tomwer-1.4.6/src/tomwer/app/canvas_launcher/mainwindow.py +677 -0
  88. tomwer-1.4.6/src/tomwer/app/canvas_launcher/splash.py +24 -0
  89. tomwer-1.4.6/src/tomwer/app/canvas_launcher/utils.py +47 -0
  90. tomwer-1.4.6/src/tomwer/app/canvas_launcher/widgetsscheme.py +89 -0
  91. tomwer-1.4.6/src/tomwer/app/diffframe.py +107 -0
  92. tomwer-1.4.6/src/tomwer/app/imagekeyeditor.py +99 -0
  93. tomwer-1.4.6/src/tomwer/app/imagekeyupgrader.py +110 -0
  94. tomwer-1.4.6/src/tomwer/app/intensitynormalization.py +195 -0
  95. tomwer-1.4.6/src/tomwer/app/multicor.py +276 -0
  96. tomwer-1.4.6/src/tomwer/app/multipag.py +350 -0
  97. tomwer-1.4.6/src/tomwer/app/nabuapp.py +246 -0
  98. tomwer-1.4.6/src/tomwer/app/nxtomoeditor.py +111 -0
  99. tomwer-1.4.6/src/tomwer/app/patchrawdarkflat.py +130 -0
  100. tomwer-1.4.6/src/tomwer/app/radiostack.py +96 -0
  101. tomwer-1.4.6/src/tomwer/app/reducedarkflat.py +207 -0
  102. tomwer-1.4.6/src/tomwer/app/samplemoved.py +94 -0
  103. tomwer-1.4.6/src/tomwer/app/scanviewer.py +101 -0
  104. tomwer-1.4.6/src/tomwer/app/sinogramviewer.py +126 -0
  105. tomwer-1.4.6/src/tomwer/app/slicestack.py +90 -0
  106. tomwer-1.4.6/src/tomwer/app/stitching/common.py +418 -0
  107. tomwer-1.4.6/src/tomwer/app/stopdatalistener.py +42 -0
  108. tomwer-1.4.6/src/tomwer/app/ystitching.py +26 -0
  109. tomwer-1.4.6/src/tomwer/app/zstitching.py +26 -0
  110. tomwer-1.4.6/src/tomwer/core/__init__.py +2 -0
  111. tomwer-1.4.6/src/tomwer/core/cluster/__init__.py +4 -0
  112. tomwer-1.4.6/src/tomwer/core/cluster/cluster.py +148 -0
  113. tomwer-1.4.6/src/tomwer/core/futureobject.py +159 -0
  114. tomwer-1.4.6/src/tomwer/core/log/__init__.py +2 -0
  115. tomwer-1.4.6/src/tomwer/core/log/processlog.py +78 -0
  116. tomwer-1.4.6/src/tomwer/core/process/cluster/supervisor.py +61 -0
  117. tomwer-1.4.6/src/tomwer/core/process/conditions/filters.py +214 -0
  118. tomwer-1.4.6/src/tomwer/core/process/control/datalistener/datalistener.py +295 -0
  119. tomwer-1.4.6/src/tomwer/core/process/control/datalistener/rpcserver.py +276 -0
  120. tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/datawatcher.py +432 -0
  121. tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/datawatcherobserver.py +648 -0
  122. tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/datawatcherprocess.py +228 -0
  123. tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/edfdwprocess.py +174 -0
  124. tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/hdf5dwprocess.py +58 -0
  125. tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/status.py +52 -0
  126. tomwer-1.4.6/src/tomwer/core/process/control/emailnotifier.py +136 -0
  127. tomwer-1.4.6/src/tomwer/core/process/control/nxtomoconcatenate.py +129 -0
  128. tomwer-1.4.6/src/tomwer/core/process/control/nxtomomill.py +202 -0
  129. tomwer-1.4.6/src/tomwer/core/process/control/scanlist.py +24 -0
  130. tomwer-1.4.6/src/tomwer/core/process/control/scantransfer.py +641 -0
  131. tomwer-1.4.6/src/tomwer/core/process/control/scanvalidator.py +260 -0
  132. tomwer-1.4.6/src/tomwer/core/process/control/tests/test_concatenate_nxtomos.py +81 -0
  133. tomwer-1.4.6/src/tomwer/core/process/control/timer.py +79 -0
  134. tomwer-1.4.6/src/tomwer/core/process/control/tomoobjseries.py +12 -0
  135. tomwer-1.4.6/src/tomwer/core/process/drac/binning.py +37 -0
  136. tomwer-1.4.6/src/tomwer/core/process/drac/dracbase.py +170 -0
  137. tomwer-1.4.6/src/tomwer/core/process/drac/gallery.py +109 -0
  138. tomwer-1.4.6/src/tomwer/core/process/drac/output.py +12 -0
  139. tomwer-1.4.6/src/tomwer/core/process/drac/processeddataset.py +147 -0
  140. tomwer-1.4.6/src/tomwer/core/process/drac/publish.py +118 -0
  141. tomwer-1.4.6/src/tomwer/core/process/drac/rawdataset.py +142 -0
  142. tomwer-1.4.6/src/tomwer/core/process/drac/tests/test_gallery.py +71 -0
  143. tomwer-1.4.6/src/tomwer/core/process/drac/tests/test_icat_processed_dataset.py +80 -0
  144. tomwer-1.4.6/src/tomwer/core/process/drac/tests/test_icat_raw_dataset.py +90 -0
  145. tomwer-1.4.6/src/tomwer/core/process/edit/darkflatpatch.py +121 -0
  146. tomwer-1.4.6/src/tomwer/core/process/edit/imagekeyeditor.py +238 -0
  147. tomwer-1.4.6/src/tomwer/core/process/edit/nxtomoeditor.py +307 -0
  148. tomwer-1.4.6/src/tomwer/core/process/edit/tests/test_darkflatpatch.py +243 -0
  149. tomwer-1.4.6/src/tomwer/core/process/edit/tests/test_imagekey_editor.py +99 -0
  150. tomwer-1.4.6/src/tomwer/core/process/output.py +59 -0
  151. tomwer-1.4.6/src/tomwer/core/process/reconstruction/__init__.py +4 -0
  152. tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/anglemode.py +21 -0
  153. tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/axis.py +461 -0
  154. tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/mode.py +274 -0
  155. tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/params.py +798 -0
  156. tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/projectiontype.py +10 -0
  157. tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/side.py +8 -0
  158. tomwer-1.4.6/src/tomwer/core/process/reconstruction/darkref/darkrefs.py +476 -0
  159. tomwer-1.4.6/src/tomwer/core/process/reconstruction/darkref/darkrefscopy.py +361 -0
  160. tomwer-1.4.6/src/tomwer/core/process/reconstruction/darkref/params.py +273 -0
  161. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/castvolume.py +239 -0
  162. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/nabucommon.py +688 -0
  163. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/nabuscores.py +714 -0
  164. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/nabuslices.py +887 -0
  165. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/nabuvolume.py +575 -0
  166. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/plane.py +19 -0
  167. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/settings.py +35 -0
  168. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/target.py +8 -0
  169. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/test/test_castvolume.py +116 -0
  170. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py +277 -0
  171. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/test/test_nabunormalization.py +199 -0
  172. tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/utils.py +516 -0
  173. tomwer-1.4.6/src/tomwer/core/process/reconstruction/normalization/normalization.py +334 -0
  174. tomwer-1.4.6/src/tomwer/core/process/reconstruction/normalization/params.py +134 -0
  175. tomwer-1.4.6/src/tomwer/core/process/reconstruction/output.py +103 -0
  176. tomwer-1.4.6/src/tomwer/core/process/reconstruction/params_cache.py +36 -0
  177. tomwer-1.4.6/src/tomwer/core/process/reconstruction/paramsbase.py +183 -0
  178. tomwer-1.4.6/src/tomwer/core/process/reconstruction/saaxis/params.py +134 -0
  179. tomwer-1.4.6/src/tomwer/core/process/reconstruction/saaxis/saaxis.py +828 -0
  180. tomwer-1.4.6/src/tomwer/core/process/reconstruction/sadeltabeta/params.py +78 -0
  181. tomwer-1.4.6/src/tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +836 -0
  182. tomwer-1.4.6/src/tomwer/core/process/reconstruction/scores/params.py +184 -0
  183. tomwer-1.4.6/src/tomwer/core/process/reconstruction/scores/scores.py +198 -0
  184. tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_axis.py +46 -0
  185. tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_darkref.py +33 -0
  186. tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_params_cache.py +37 -0
  187. tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_saaxis.py +91 -0
  188. tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_sadeltabeta.py +48 -0
  189. tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_utils.py +29 -0
  190. tomwer-1.4.6/src/tomwer/core/process/reconstruction/utils/cor.py +16 -0
  191. tomwer-1.4.6/src/tomwer/core/process/script/python.py +61 -0
  192. tomwer-1.4.6/src/tomwer/core/process/script/tests/test_script.py +41 -0
  193. tomwer-1.4.6/src/tomwer/core/process/stitching/metadataholder.py +186 -0
  194. tomwer-1.4.6/src/tomwer/core/process/stitching/nabustitcher.py +188 -0
  195. tomwer-1.4.6/src/tomwer/core/process/stitching/tests/test_metadataholder.py +17 -0
  196. tomwer-1.4.6/src/tomwer/core/process/task.py +130 -0
  197. tomwer-1.4.6/src/tomwer/core/process/tests/test_conditions.py +65 -0
  198. tomwer-1.4.6/src/tomwer/core/process/tests/test_dark_and_flat.py +359 -0
  199. tomwer-1.4.6/src/tomwer/core/process/tests/test_data_listener.py +88 -0
  200. tomwer-1.4.6/src/tomwer/core/process/tests/test_data_transfer.py +354 -0
  201. tomwer-1.4.6/src/tomwer/core/process/tests/test_data_watcher.py +39 -0
  202. tomwer-1.4.6/src/tomwer/core/process/tests/test_nabu.py +460 -0
  203. tomwer-1.4.6/src/tomwer/core/process/tests/test_normalization.py +79 -0
  204. tomwer-1.4.6/src/tomwer/core/process/tests/test_timer.py +51 -0
  205. tomwer-1.4.6/src/tomwer/core/process/utils.py +85 -0
  206. tomwer-1.4.6/src/tomwer/core/process/visualization/dataviewer.py +14 -0
  207. tomwer-1.4.6/src/tomwer/core/process/visualization/diffviewer.py +14 -0
  208. tomwer-1.4.6/src/tomwer/core/process/visualization/imagestackviewer.py +13 -0
  209. tomwer-1.4.6/src/tomwer/core/process/visualization/radiostack.py +13 -0
  210. tomwer-1.4.6/src/tomwer/core/process/visualization/samplemoved.py +12 -0
  211. tomwer-1.4.6/src/tomwer/core/process/visualization/sinogramviewer.py +12 -0
  212. tomwer-1.4.6/src/tomwer/core/process/visualization/slicestack.py +12 -0
  213. tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_data_viewer.py +12 -0
  214. tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_diff_viewer.py +12 -0
  215. tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_image_stack_viewer.py +14 -0
  216. tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_radio_stack.py +12 -0
  217. tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_sample_moved.py +14 -0
  218. tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_sinogram_viewer.py +13 -0
  219. tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_slice_stack.py +13 -0
  220. tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_volume_viewer.py +12 -0
  221. tomwer-1.4.6/src/tomwer/core/process/visualization/volumeviewer.py +11 -0
  222. tomwer-1.4.6/src/tomwer/core/resourcemanager.py +33 -0
  223. tomwer-1.4.6/src/tomwer/core/scan/__init__.py +6 -0
  224. tomwer-1.4.6/src/tomwer/core/scan/blissscan.py +233 -0
  225. tomwer-1.4.6/src/tomwer/core/scan/edfscan.py +582 -0
  226. tomwer-1.4.6/src/tomwer/core/scan/hdf5scan.py +26 -0
  227. tomwer-1.4.6/src/tomwer/core/scan/nxtomoscan.py +516 -0
  228. tomwer-1.4.6/src/tomwer/core/scan/scanbase.py +706 -0
  229. tomwer-1.4.6/src/tomwer/core/scan/scanfactory.py +226 -0
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  943. tomwer-1.3.16/tomwer/gui/visualization/test/test_stacks.py +0 -134
  944. tomwer-1.3.16/tomwer/gui/visualization/test/test_volumeviewer.py +0 -82
  945. tomwer-1.3.16/tomwer/gui/visualization/tomoobjoverview.py +0 -52
  946. tomwer-1.3.16/tomwer/gui/visualization/volumeoverview.py +0 -66
  947. tomwer-1.3.16/tomwer/gui/visualization/volumeviewer.py +0 -448
  948. tomwer-1.3.16/tomwer/io/utils/h5pyutils.py +0 -78
  949. tomwer-1.3.16/tomwer/io/utils/utils.py +0 -284
  950. tomwer-1.3.16/tomwer/resources/__init__.py +0 -156
  951. tomwer-1.3.16/tomwer/resources/gui/icons/warning.png +0 -0
  952. tomwer-1.3.16/tomwer/synctools/__init__.py +0 -4
  953. tomwer-1.3.16/tomwer/synctools/axis.py +0 -54
  954. tomwer-1.3.16/tomwer/synctools/darkref.py +0 -48
  955. tomwer-1.3.16/tomwer/synctools/datalistener.py +0 -270
  956. tomwer-1.3.16/tomwer/synctools/datatransfert.py +0 -44
  957. tomwer-1.3.16/tomwer/synctools/imageloaderthread.py +0 -79
  958. tomwer-1.3.16/tomwer/synctools/rsyncmanager.py +0 -193
  959. tomwer-1.3.16/tomwer/synctools/saaxis.py +0 -54
  960. tomwer-1.3.16/tomwer/synctools/sadeltabeta.py +0 -54
  961. tomwer-1.3.16/tomwer/synctools/stacks/control/datalistener.py +0 -136
  962. tomwer-1.3.16/tomwer/synctools/stacks/edit/darkflatpatch.py +0 -169
  963. tomwer-1.3.16/tomwer/synctools/stacks/edit/imagekeyeditor.py +0 -135
  964. tomwer-1.3.16/tomwer/synctools/stacks/processingstack.py +0 -197
  965. tomwer-1.3.16/tomwer/synctools/stacks/reconstruction/axis.py +0 -218
  966. tomwer-1.3.16/tomwer/synctools/stacks/reconstruction/castvolume.py +0 -212
  967. tomwer-1.3.16/tomwer/synctools/stacks/reconstruction/dkrefcopy.py +0 -192
  968. tomwer-1.3.16/tomwer/synctools/stacks/reconstruction/nabu.py +0 -205
  969. tomwer-1.3.16/tomwer/synctools/stacks/reconstruction/normalization.py +0 -136
  970. tomwer-1.3.16/tomwer/synctools/stacks/reconstruction/saaxis.py +0 -182
  971. tomwer-1.3.16/tomwer/synctools/stacks/reconstruction/sadeltabeta.py +0 -183
  972. tomwer-1.3.16/tomwer/synctools/test/test_darkRefs.py +0 -423
  973. tomwer-1.3.16/tomwer/synctools/test/test_foldertransfer.py +0 -407
  974. tomwer-1.3.16/tomwer/synctools/utils/scanstages.py +0 -207
  975. tomwer-1.3.16/tomwer/tests/datasets.py +0 -13
  976. tomwer-1.3.16/tomwer/third_part/WaitingOverlay.py +0 -110
  977. tomwer-1.3.16/tomwer/utils.py +0 -253
  978. tomwer-1.3.16/tomwer/version.py +0 -134
  979. tomwer-1.3.16/tomwer.egg-info/PKG-INFO +0 -306
  980. tomwer-1.3.16/tomwer.egg-info/SOURCES.txt +0 -790
  981. tomwer-1.3.16/tomwer.egg-info/entry_points.txt +0 -20
  982. tomwer-1.3.16/tomwer.egg-info/namespace_packages.txt +0 -1
  983. tomwer-1.3.16/tomwer.egg-info/requires.txt +0 -185
  984. {tomwer-1.3.16 → tomwer-1.4.6}/MANIFEST.in +0 -0
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  1127. {tomwer-1.3.16 → tomwer-1.4.6/src}/orangecontrib/tomwer/widgets/visualization/icons/tomwer.png +0 -0
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  1129. {tomwer-1.3.16 → tomwer-1.4.6/src}/orangecontrib/tomwer/widgets/visualization/icons/volumeviewer.svg +0 -0
  1130. {tomwer-1.3.16/tomwer/core/process/icat → tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/tests}/__init__.py +0 -0
  1131. {tomwer-1.3.16/tomwer/core/process/reconstruction/darkref → tomwer-1.4.6/src/tomwer/app/canvas_launcher}/__init__.py +0 -0
  1132. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/app/darkref.py +0 -0
  1133. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/app/darkrefpatch.py +0 -0
  1134. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/app/rsync.py +0 -0
  1135. {tomwer-1.3.16/tomwer/core/process/reconstruction/nabu → tomwer-1.4.6/src/tomwer/app/stitching}/__init__.py +0 -0
  1136. {tomwer-1.3.16/tomwer/core/process/reconstruction/test → tomwer-1.4.6/src/tomwer/core/process}/__init__.py +0 -0
  1137. {tomwer-1.3.16/tomwer/core/process/reconstruction/utils → tomwer-1.4.6/src/tomwer/core/process/cluster}/__init__.py +0 -0
  1138. {tomwer-1.3.16/tomwer/core/process/script → tomwer-1.4.6/src/tomwer/core/process/conditions}/__init__.py +0 -0
  1139. {tomwer-1.3.16/tomwer/core/process/stitching → tomwer-1.4.6/src/tomwer/core/process/control}/__init__.py +0 -0
  1140. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/control/datadiscovery.py +0 -0
  1141. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/control/datalistener/__init__.py +0 -0
  1142. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/control/datawatcher/__init__.py +0 -0
  1143. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/control/scanselector.py +0 -0
  1144. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/control/singletomoobj.py +0 -0
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  1147. {tomwer-1.3.16/tomwer/core/process/control/test → tomwer-1.4.6/src/tomwer/core/process/control/tests}/test_h52nx_process.py +0 -0
  1148. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/control/volumeselector.py +0 -0
  1149. {tomwer-1.3.16/tomwer/core/process/visualization → tomwer-1.4.6/src/tomwer/core/process/drac}/__init__.py +0 -0
  1150. {tomwer-1.3.16/tomwer/core/scan/test → tomwer-1.4.6/src/tomwer/core/process/edit}/__init__.py +0 -0
  1151. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/reconstruction/axis/__init__.py +0 -0
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  1153. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/reconstruction/darkref/settings.py +0 -0
  1154. {tomwer-1.3.16/tomwer/core/utils → tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu}/__init__.py +0 -0
  1155. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/reconstruction/nabu/helical.py +0 -0
  1156. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/reconstruction/normalization/__init__.py +0 -0
  1157. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/reconstruction/saaxis/__init__.py +0 -0
  1158. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/reconstruction/sadeltabeta/__init__.py +0 -0
  1159. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/process/reconstruction/scores/__init__.py +0 -0
  1160. {tomwer-1.3.16/tomwer/gui/cluster → tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests}/__init__.py +0 -0
  1161. {tomwer-1.3.16/tomwer/core/process/reconstruction/test → tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests}/test_axis_params.py +0 -0
  1162. {tomwer-1.3.16/tomwer/core/process/reconstruction/test → tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests}/test_darkref_copy.py +0 -0
  1163. {tomwer-1.3.16/tomwer/core/process/reconstruction/test → tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests}/test_paramsbase.py +0 -0
  1164. {tomwer-1.3.16/tomwer/gui/cluster/test → tomwer-1.4.6/src/tomwer/core/process/reconstruction/utils}/__init__.py +0 -0
  1165. {tomwer-1.3.16/tomwer/gui/conditions → tomwer-1.4.6/src/tomwer/core/process/script}/__init__.py +0 -0
  1166. {tomwer-1.3.16/tomwer/gui/configuration → tomwer-1.4.6/src/tomwer/core/process/stitching}/__init__.py +0 -0
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  1169. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/core/scan/futurescan.py +0 -0
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  1184. {tomwer-1.3.16/tomwer/gui/control/serie → tomwer-1.4.6/src/tomwer/gui/control/series}/nxtomoconcatenate.py +0 -0
  1185. /tomwer-1.3.16/tomwer/gui/reconstruction/saaxis/__init__.py → /tomwer-1.4.6/src/tomwer/gui/control/series/serieswaiter.py +0 -0
  1186. {tomwer-1.3.16/tomwer/gui/reconstruction/scores → tomwer-1.4.6/src/tomwer/gui/control/tests}/__init__.py +0 -0
  1187. {tomwer-1.3.16/tomwer/gui/control/test → tomwer-1.4.6/src/tomwer/gui/control/tests}/test_datadiscovery.py +0 -0
  1188. {tomwer-1.3.16/tomwer/gui/control/test → tomwer-1.4.6/src/tomwer/gui/control/tests}/test_reducedarkflat_selector.py +0 -0
  1189. {tomwer-1.3.16/tomwer/gui/control/test → tomwer-1.4.6/src/tomwer/gui/control/tests}/test_single_tomo_obj.py +0 -0
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  1192. {tomwer-1.3.16/tomwer/gui/stitching → tomwer-1.4.6/src/tomwer/gui/edit/tests}/__init__.py +0 -0
  1193. {tomwer-1.3.16/tomwer/gui/stitching/config → tomwer-1.4.6/src/tomwer/gui/reconstruction/darkref}/__init__.py +0 -0
  1194. {tomwer-1.3.16 → tomwer-1.4.6/src}/tomwer/gui/reconstruction/nabu/__init__.py +0 -0
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  1198. {tomwer-1.3.16/tomwer/gui/visualization → tomwer-1.4.6/src/tomwer/gui/reconstruction/saaxis}/__init__.py +0 -0
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  1200. {tomwer-1.3.16/tomwer/io → tomwer-1.4.6/src/tomwer/gui/reconstruction/scores}/__init__.py +0 -0
  1201. {tomwer-1.3.16/tomwer/synctools/stacks/control → tomwer-1.4.6/src/tomwer/gui/reconstruction/tests}/__init__.py +0 -0
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  1205. {tomwer-1.3.16/tomwer/synctools/stacks/reconstruction → tomwer-1.4.6/src/tomwer/gui/stitching/z_stitching}/__init__.py +0 -0
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tomwer-1.4.6/LICENSE ADDED
@@ -0,0 +1,29 @@
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+
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+ The Tomwer library goal is to provide some useful process for acquisition/reconstruction automation.
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+
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+ Tomwer is distributed under the MIT license.
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+
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+ Tomwer is using the Qt library. A word of caution is to be provided. If users develop and distribute software using modules accessing Qt by means of Riverbank Computing Qt bindings PyQt4 or PyQt5, those users will be conditioned by the license of their PyQt4/5 software (GPL or commercial). If the end user does not own a commercial license of PyQt4 or PyQt5 and wishes to be free of any distribution condition, (s)he should be able to use PySide because it uses the LGPL license.
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+
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+ It can also be used as an Orange3 add-on. If you wan't to distribute Orange you must stick to there license (GNU [GPL-3.0]+ license)
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+
10
+ The MIT license follows:
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+
12
+ Copyright (c) European Synchrotron Radiation Facility (ESRF)
13
+
14
+ Permission is hereby granted, free of charge, to any person obtaining a copy of
15
+ this software and associated documentation files (the "Software"), to deal in
16
+ the Software without restriction, including without limitation the rights to
17
+ use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
18
+ the Software, and to permit persons to whom the Software is furnished to do so,
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+ subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
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+ FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
27
+ COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
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+ IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
29
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
tomwer-1.4.6/PKG-INFO ADDED
@@ -0,0 +1,336 @@
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+ Metadata-Version: 2.2
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+ Name: tomwer
3
+ Version: 1.4.6
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+ Summary: "tomography workflow tools"
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+ Home-page: https://gitlab.esrf.fr/tomotools/tomwer
6
+ Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
7
+ Author-email: henri.payno@esrf.fr, pierre.paleo@esrf.fr, pierre-olivier.autran@esrf.fr, jerome.lesaint@esrf.fr, mirone@esrf.fr
8
+ License: MIT
9
+ Project-URL: Bug Tracker, https://gitlab.esrf.fr/tomotools/tomwer/-/issues
10
+ Keywords: orange3 add-on,ewoks
11
+ Classifier: Intended Audience :: Education
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Environment :: Console
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+ Classifier: Environment :: X11 Applications :: Qt
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+ Classifier: Operating System :: POSIX
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+ Classifier: Natural Language :: English
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+ Classifier: Topic :: Scientific/Engineering :: Physics
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+ Classifier: Topic :: Software Development :: Libraries :: Python Modules
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+ Requires-Dist: timeout-decorator; extra == "dev-no-cuda"
206
+ Requires-Dist: pyopencl; extra == "dev-no-cuda"
207
+ Provides-Extra: test
208
+ Requires-Dist: orange-canvas-core; extra == "test"
209
+ Requires-Dist: orange-widget-base; extra == "test"
210
+ Requires-Dist: ewoks[orange]>=0.1.1; extra == "test"
211
+ Requires-Dist: ewoksorange>=0.7.0rc0; extra == "test"
212
+ Requires-Dist: rsyncmanager; extra == "test"
213
+ Requires-Dist: fabio; extra == "test"
214
+ Requires-Dist: h5py>=3; extra == "test"
215
+ Requires-Dist: lxml; extra == "test"
216
+ Requires-Dist: werkzeug; extra == "test"
217
+ Requires-Dist: json-rpc; extra == "test"
218
+ Requires-Dist: scipy; extra == "test"
219
+ Requires-Dist: Pillow; extra == "test"
220
+ Requires-Dist: glymur; extra == "test"
221
+ Requires-Dist: resource; extra == "test"
222
+ Requires-Dist: tifffile; extra == "test"
223
+ Requires-Dist: hdf5plugin; extra == "test"
224
+ Requires-Dist: pyicat_plus; extra == "test"
225
+ Requires-Dist: ewoksnotify[full]; extra == "test"
226
+ Requires-Dist: pyicat_plus; extra == "test"
227
+ Requires-Dist: nabu>=2023.3.1dev; extra == "test"
228
+ Requires-Dist: pytest-asyncio; extra == "test"
229
+ Requires-Dist: tomoscan[test]>=2.1.0a18; extra == "test"
230
+ Provides-Extra: setup-requires
231
+ Requires-Dist: setuptools; extra == "setup-requires"
232
+ Requires-Dist: numpy>=1.12; extra == "setup-requires"
233
+
234
+ .. image:: doc/img/tomwer.png
235
+ :alt: Tomwer Logo
236
+ :align: left
237
+ :width: 400px
238
+
239
+ Introduction
240
+ ------------
241
+
242
+ **Tomwer** provides tools to automate acquisition and reconstruction processes for tomography. The package includes:
243
+
244
+ - A library to individually access each acquisition process.
245
+ - Graphical User Interface (GUI) applications to control key processes such as reconstruction and data transfer, which can be executed as standalone applications.
246
+ - An Orange add-on to help users define custom workflows (`Orange3 <http://orange.biolab.si>`_).
247
+
248
+ Tomwer relies on `Nabu <https://gitlab.esrf.fr/tomotools/nabu>`_ for tomographic reconstruction.
249
+
250
+ **Note**: Currently, the software is only compatible with Linux.
251
+
252
+ Documentation
253
+ -------------
254
+
255
+ The latest version of the documentation is available `here <https://tomotools.gitlab-pages.esrf.fr/tomwer/>`_.
256
+
257
+ Installation
258
+ ------------
259
+
260
+ Step 1: Installing Tomwer
261
+ '''''''''''''''''''''''''
262
+
263
+ To install Tomwer with all features:
264
+
265
+ .. code-block:: bash
266
+
267
+ pip install tomwer[full]
268
+
269
+ Alternatively, you can install the latest development branch from the repository:
270
+
271
+ .. code-block:: bash
272
+
273
+ pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]
274
+
275
+
276
+ Step 2: (Optional) Update Orange-CANVAS-CORE and Orange-WIDGET-BASE
277
+ ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
278
+
279
+ If you need access to additional 'processing' wheels and 'reprocess action,' you may want to update these Orange forks. This is optional, as the project works with the native Orange libraries.
280
+
281
+ .. code-block:: bash
282
+
283
+ pip install git+https://github.com/payno/orange-canvas-core --no-deps --upgrade
284
+ pip install git+https://github.com/payno/orange-widget-base --no-deps --upgrade
285
+
286
+
287
+ Launching Applications
288
+ -----------------------
289
+
290
+ After installation, Tomwer includes several applications. You can launch an application by running:
291
+
292
+ .. code-block:: bash
293
+
294
+ tomwer <appName> [options]
295
+
296
+ - If you run `tomwer` without arguments, a manual page will be displayed.
297
+ - For application-specific help, run:
298
+
299
+ .. code-block:: bash
300
+
301
+ tomwer <appName> --help
302
+
303
+
304
+ Tomwer Canvas - Orange Canvas
305
+ -----------------------------
306
+
307
+ You can launch the Orange canvas to create workflows using the available building blocks:
308
+
309
+ .. code-block:: bash
310
+
311
+ tomwer canvas
312
+
313
+ - Alternatively, you can use `orange-canvas`.
314
+ - If you're using a virtual environment, remember to activate it:
315
+
316
+ .. code-block:: bash
317
+
318
+ source myvirtualenv/bin/activate
319
+
320
+
321
+ Building Documentation
322
+ -----------------------
323
+
324
+ To build the documentation:
325
+
326
+ .. code-block:: bash
327
+
328
+ sphinx-build doc build/html
329
+
330
+ The documentation will be generated in `doc/build/html`, and the entry point is `index.html`. To view the documentation in a browser:
331
+
332
+ .. code-block:: bash
333
+
334
+ firefox build/html/index.html
335
+
336
+ **Note**: Building the documentation requires `sphinx` to be installed, which is not a hard dependency of Tomwer. If needed, install it separately.
@@ -0,0 +1,103 @@
1
+ .. image:: doc/img/tomwer.png
2
+ :alt: Tomwer Logo
3
+ :align: left
4
+ :width: 400px
5
+
6
+ Introduction
7
+ ------------
8
+
9
+ **Tomwer** provides tools to automate acquisition and reconstruction processes for tomography. The package includes:
10
+
11
+ - A library to individually access each acquisition process.
12
+ - Graphical User Interface (GUI) applications to control key processes such as reconstruction and data transfer, which can be executed as standalone applications.
13
+ - An Orange add-on to help users define custom workflows (`Orange3 <http://orange.biolab.si>`_).
14
+
15
+ Tomwer relies on `Nabu <https://gitlab.esrf.fr/tomotools/nabu>`_ for tomographic reconstruction.
16
+
17
+ **Note**: Currently, the software is only compatible with Linux.
18
+
19
+ Documentation
20
+ -------------
21
+
22
+ The latest version of the documentation is available `here <https://tomotools.gitlab-pages.esrf.fr/tomwer/>`_.
23
+
24
+ Installation
25
+ ------------
26
+
27
+ Step 1: Installing Tomwer
28
+ '''''''''''''''''''''''''
29
+
30
+ To install Tomwer with all features:
31
+
32
+ .. code-block:: bash
33
+
34
+ pip install tomwer[full]
35
+
36
+ Alternatively, you can install the latest development branch from the repository:
37
+
38
+ .. code-block:: bash
39
+
40
+ pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]
41
+
42
+
43
+ Step 2: (Optional) Update Orange-CANVAS-CORE and Orange-WIDGET-BASE
44
+ ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
45
+
46
+ If you need access to additional 'processing' wheels and 'reprocess action,' you may want to update these Orange forks. This is optional, as the project works with the native Orange libraries.
47
+
48
+ .. code-block:: bash
49
+
50
+ pip install git+https://github.com/payno/orange-canvas-core --no-deps --upgrade
51
+ pip install git+https://github.com/payno/orange-widget-base --no-deps --upgrade
52
+
53
+
54
+ Launching Applications
55
+ -----------------------
56
+
57
+ After installation, Tomwer includes several applications. You can launch an application by running:
58
+
59
+ .. code-block:: bash
60
+
61
+ tomwer <appName> [options]
62
+
63
+ - If you run `tomwer` without arguments, a manual page will be displayed.
64
+ - For application-specific help, run:
65
+
66
+ .. code-block:: bash
67
+
68
+ tomwer <appName> --help
69
+
70
+
71
+ Tomwer Canvas - Orange Canvas
72
+ -----------------------------
73
+
74
+ You can launch the Orange canvas to create workflows using the available building blocks:
75
+
76
+ .. code-block:: bash
77
+
78
+ tomwer canvas
79
+
80
+ - Alternatively, you can use `orange-canvas`.
81
+ - If you're using a virtual environment, remember to activate it:
82
+
83
+ .. code-block:: bash
84
+
85
+ source myvirtualenv/bin/activate
86
+
87
+
88
+ Building Documentation
89
+ -----------------------
90
+
91
+ To build the documentation:
92
+
93
+ .. code-block:: bash
94
+
95
+ sphinx-build doc build/html
96
+
97
+ The documentation will be generated in `doc/build/html`, and the entry point is `index.html`. To view the documentation in a browser:
98
+
99
+ .. code-block:: bash
100
+
101
+ firefox build/html/index.html
102
+
103
+ **Note**: Building the documentation requires `sphinx` to be installed, which is not a hard dependency of Tomwer. If needed, install it separately.
@@ -0,0 +1,10 @@
1
+ [build-system]
2
+ requires = [
3
+ "setuptools>=46.4",
4
+ "wheel",
5
+ ]
6
+ build-backend = "setuptools.build_meta"
7
+
8
+ [tool.pytest.ini_options]
9
+ # consider_namespace_packages = true # for pytest>=8.1
10
+ addopts = "--import-mode=importlib" # for all pytest versions, pytest-cov needs `pip install -e .`
tomwer-1.4.6/setup.cfg ADDED
@@ -0,0 +1,174 @@
1
+ [metadata]
2
+ name = tomwer
3
+ version = attr: tomwer.__version__
4
+ author = Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
5
+ author_email = henri.payno@esrf.fr, pierre.paleo@esrf.fr, pierre-olivier.autran@esrf.fr, jerome.lesaint@esrf.fr, mirone@esrf.fr
6
+ description = "tomography workflow tools"
7
+ long_description = file: README.rst
8
+ long_description_content_type = text/x-rst
9
+ license = MIT
10
+ url = https://gitlab.esrf.fr/tomotools/tomwer
11
+ project_urls =
12
+ Bug Tracker = https://gitlab.esrf.fr/tomotools/tomwer/-/issues
13
+ classifiers =
14
+ Intended Audience :: Education
15
+ Intended Audience :: Science/Research
16
+ License :: OSI Approved :: MIT License
17
+ Programming Language :: Python :: 3
18
+ Environment :: Console
19
+ Environment :: X11 Applications :: Qt
20
+ Operating System :: POSIX
21
+ Natural Language :: English
22
+ Topic :: Scientific/Engineering :: Physics
23
+ Topic :: Software Development :: Libraries :: Python Modules
24
+ keywords =
25
+ orange3 add-on,ewoks
26
+
27
+ [options]
28
+ package_dir =
29
+ =src
30
+ packages = find_namespace:
31
+ python_requires = >=3.6
32
+ install_requires =
33
+ numpy
34
+ setuptools
35
+ psutil
36
+ silx[full] >= 2.0
37
+ tomoscan>=2.1.0a18
38
+ nxtomo>=1.3.0dev4
39
+ nxtomomill>=1.1.0a0
40
+ processview>=1.5.0
41
+ ewoks>=0.1.1
42
+ sluurp>=0.4.1
43
+ packaging
44
+ pyunitsystem>=2.0.0a
45
+ tqdm
46
+
47
+ [options.packages.find]
48
+ where = src
49
+
50
+ [options.entry_points]
51
+ console_scripts =
52
+ tomwer=tomwer.__main__:main
53
+ orange3.addon =
54
+ tomwer-add-on=orangecontrib.tomwer
55
+ orange.widgets =
56
+ tomwer=orangecontrib.tomwer.widgets
57
+ orangecanvas.examples =
58
+ tomo_examples=orangecontrib.tomwer.examples
59
+ orange.widgets.tutorials =
60
+ tomo_tutorials=orangecontrib.tomwer.tutorials
61
+ tomo_tutorials_id16b=orangecontrib.tomwer.tutorials.id16b
62
+ orange.canvas.help =
63
+ html-index=orangecontrib.tomwer.widgets:WIDGET_HELP_PATH
64
+ ewoks.tasks.class =
65
+ tomwer.core.process.*.*=tomwer
66
+
67
+ [options.package_data]
68
+ tomwer.resources =
69
+ gui/icons/*.png
70
+ gui/icons/*.svg
71
+ gui/icons/*.npy
72
+ gui/illustrations/*.svg
73
+ gui/illustrations/*.png
74
+ orangecontrib.tomwer =
75
+ tutorials/*.ows
76
+ tutorials/id16b/*.ows
77
+ widgets/icons/*.png
78
+ widgets/icons/*.svg
79
+ widgets/cluster/icons/*.png
80
+ widgets/cluster/icons/*.svg
81
+ widgets/control/icons/*.png
82
+ widgets/control/icons/*.svg
83
+ widgets/debugtools/icons/*.png
84
+ widgets/debugtools/icons/*.svg
85
+ widgets/edit/icons/*.png
86
+ widgets/edit/icons/*.svg
87
+ widgets/dataportal/icons/*.png
88
+ widgets/dataportal/icons/*.svg
89
+ widgets/reconstruction/icons/*.png
90
+ widgets/reconstruction/icons/*.svg
91
+ widgets/visualization/icons/*.png
92
+ widgets/visualization/icons/*.svg
93
+ widgets/other/icons/*.png
94
+ widgets/other/icons/*.svg
95
+
96
+ [options.extras_require]
97
+ full_base =
98
+ orange-canvas-core
99
+ orange-widget-base
100
+ ewoks[orange]>=0.1.1
101
+ ewoksorange >= 0.7.0rc0
102
+ rsyncmanager
103
+ fabio
104
+ h5py>=3
105
+ lxml
106
+ werkzeug
107
+ json-rpc
108
+ scipy
109
+ Pillow
110
+ glymur
111
+ resource
112
+ tifffile
113
+ hdf5plugin
114
+ pyicat_plus
115
+ ewoksnotify[full]
116
+ pyicat_plus
117
+ full_no_nabu =
118
+ %(full_base)s
119
+ full_no_cuda =
120
+ %(full_base)s
121
+ nabu>=2023.3.1dev
122
+ full =
123
+ %(full_base)s
124
+ nabu[full]>=2023.3.1dev
125
+ pycuda<2024.1.1
126
+ scikit-cuda
127
+ doc =
128
+ %(full_no_cuda)s
129
+ Sphinx>=4.0.0
130
+ nbsphinx
131
+ pandoc
132
+ jupyterlab
133
+ pydata_sphinx_theme
134
+ sphinx-design
135
+ sphinx-autodoc-typehints
136
+ sphinxcontrib-youtube
137
+ dev_spec =
138
+ black
139
+ flake8
140
+ timeout-decorator
141
+ pyopencl
142
+ dev =
143
+ %(full)s
144
+ %(dev_spec)s
145
+ dev_no_cuda =
146
+ %(full_no_cuda)s
147
+ %(dev_spec)s
148
+ test =
149
+ %(full_no_cuda)s
150
+ pytest-asyncio
151
+ tomoscan[test]>=2.1.0a18
152
+ setup_requires =
153
+ setuptools
154
+ numpy>=1.12
155
+
156
+ [build_sphinx]
157
+ source-dir = ./doc
158
+
159
+ [flake8]
160
+ ignore = E501,W503,E203,E265,E266,E712,E262
161
+ max-line-length = 88
162
+ exclude =
163
+ .eggs
164
+ doc/ext
165
+
166
+ [coverage:run]
167
+ omit =
168
+ setup.py
169
+ */test/*
170
+
171
+ [egg_info]
172
+ tag_build =
173
+ tag_date = 0
174
+
tomwer-1.4.6/setup.py ADDED
@@ -0,0 +1,4 @@
1
+ import setuptools
2
+
3
+ if __name__ == "__main__":
4
+ setuptools.setup()
@@ -0,0 +1,10 @@
1
+ """
2
+ Orange add-on for tomography
3
+ """
4
+
5
+ import logging
6
+
7
+ from . import state_summary # noqa F401
8
+
9
+ fabio_logger = logging.getLogger("fabio.edfimage")
10
+ fabio_logger.setLevel(logging.WARNING)