tomwer 1.3.26__py3-none-any.whl → 1.4.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- orangecontrib/tomwer/orange/managedprocess.py +1 -29
- orangecontrib/tomwer/orange/settings.py +2 -28
- orangecontrib/tomwer/tests/TestAcquisition.py +220 -0
- orangecontrib/tomwer/tutorials/append_raw_darks_and_flats_frames_to_NXtomos.ows +2 -2
- orangecontrib/tomwer/tutorials/copy_reduced_darks_and_flats_meth1.ows +1 -1
- orangecontrib/tomwer/tutorials/{icat_publication.ows → drac_publication.ows} +7 -21
- orangecontrib/tomwer/tutorials/id16b/ID16b_full_volume.ows +22 -0
- orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows +302 -0
- orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows +218 -0
- orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows +29 -24
- orangecontrib/tomwer/tutorials/test_cor.ows +19 -0
- orangecontrib/tomwer/tutorials/volume_casting_on_slurm.ows +54 -0
- orangecontrib/tomwer/widgets/__init__.py +3 -5
- orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py +35 -54
- orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py +1 -31
- orangecontrib/tomwer/widgets/control/AdvancementOW.py +1 -29
- orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py +5 -4
- orangecontrib/tomwer/widgets/control/DataListenerOW.py +1 -29
- orangecontrib/tomwer/widgets/control/DataSelectorOW.py +11 -30
- orangecontrib/tomwer/widgets/control/DataTransfertOW.py +2 -28
- orangecontrib/tomwer/widgets/control/DataValidatorOW.py +1 -28
- orangecontrib/tomwer/widgets/control/DataWatcherOW.py +1 -28
- orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py +48 -51
- orangecontrib/tomwer/widgets/control/EmailOW.py +12 -2
- orangecontrib/tomwer/widgets/control/FilterOW.py +1 -28
- orangecontrib/tomwer/widgets/control/NXTomomillOW.py +37 -53
- orangecontrib/tomwer/widgets/control/NXtomoConcatenate.py +21 -20
- orangecontrib/tomwer/widgets/control/NotifierOW.py +9 -28
- orangecontrib/tomwer/widgets/control/ReduceDarkFlatSelectorOW.py +3 -2
- orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py +1 -27
- orangecontrib/tomwer/widgets/control/TimerOW.py +9 -28
- orangecontrib/tomwer/widgets/control/TomoObjSeriesOW.py +58 -0
- orangecontrib/tomwer/widgets/control/VolumeSelector.py +8 -30
- orangecontrib/tomwer/widgets/control/icons/nxtomomill.svg +173 -119
- orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.png +0 -0
- orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.svg +55 -195
- orangecontrib/tomwer/widgets/control/icons/{tomoobjserie.svg → tomoobjseries.svg} +2 -2
- orangecontrib/tomwer/widgets/dataportal/PublishProcessedDataOW.py +172 -0
- orangecontrib/tomwer/widgets/{icat → dataportal}/__init__.py +2 -2
- orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py +2 -29
- orangecontrib/tomwer/widgets/debugtools/ObjectInspectorOW.py +1 -29
- orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py +48 -73
- orangecontrib/tomwer/widgets/edit/ImageKeyEditorOW.py +48 -75
- orangecontrib/tomwer/widgets/edit/ImageKeyUpgraderOW.py +5 -30
- orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py +51 -52
- orangecontrib/tomwer/widgets/other/PythonScriptOW.py +22 -10
- orangecontrib/tomwer/widgets/reconstruction/AxisOW.py +51 -60
- orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py +22 -68
- orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py +3 -30
- orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py +21 -19
- orangecontrib/tomwer/widgets/reconstruction/NabuOW.py +7 -70
- orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py +41 -84
- orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py +15 -40
- orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py +13 -35
- orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py +2 -30
- orangecontrib/tomwer/widgets/stitching/ZStitchingConfigOW.py +11 -11
- orangecontrib/tomwer/widgets/utils.py +2 -29
- orangecontrib/tomwer/widgets/visualization/DataViewerOW.py +1 -27
- orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py +1 -27
- orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py +1 -1
- orangecontrib/tomwer/widgets/visualization/RadioStackOW.py +2 -28
- orangecontrib/tomwer/widgets/visualization/SampleMovedOW.py +1 -27
- orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py +1 -27
- orangecontrib/tomwer/widgets/visualization/SliceStackOW.py +2 -28
- tomwer/__init__.py +3 -28
- tomwer/__main__.py +8 -4
- tomwer/app/__init__.py +2 -0
- tomwer/app/axis.py +8 -10
- tomwer/app/canvas.py +23 -29
- tomwer/app/canvas_launcher/config.py +14 -102
- tomwer/app/canvas_launcher/environ.py +5 -8
- tomwer/app/canvas_launcher/mainwindow.py +175 -69
- tomwer/app/canvas_launcher/splash.py +1 -3
- tomwer/app/canvas_launcher/utils.py +47 -0
- tomwer/app/canvas_launcher/widgetsscheme.py +3 -10
- tomwer/app/diffframe.py +2 -0
- tomwer/app/imagekeyeditor.py +2 -1
- tomwer/app/imagekeyupgrader.py +2 -0
- tomwer/app/multicor.py +5 -2
- tomwer/app/multipag.py +16 -5
- tomwer/app/nabuapp.py +2 -1
- tomwer/app/nxtomoeditor.py +17 -12
- tomwer/app/patchrawdarkflat.py +2 -0
- tomwer/app/radiostack.py +3 -2
- tomwer/app/reducedarkflat.py +3 -0
- tomwer/app/samplemoved.py +2 -0
- tomwer/app/scanviewer.py +2 -0
- tomwer/app/sinogramviewer.py +2 -0
- tomwer/app/slicestack.py +11 -13
- tomwer/app/stitching/common.py +431 -0
- tomwer/app/stopdatalistener.py +3 -0
- tomwer/app/ystitching.py +26 -0
- tomwer/app/zstitching.py +8 -363
- tomwer/core/__init__.py +2 -28
- tomwer/core/cluster/__init__.py +3 -0
- tomwer/core/cluster/cluster.py +10 -26
- tomwer/core/futureobject.py +17 -43
- tomwer/core/log/__init__.py +2 -0
- tomwer/core/log/processlog.py +0 -28
- tomwer/core/process/cluster/supervisor.py +52 -34
- tomwer/core/process/conditions/filters.py +3 -28
- tomwer/core/process/control/datalistener/datalistener.py +7 -75
- tomwer/core/process/control/datalistener/rpcserver.py +8 -38
- tomwer/core/process/control/datawatcher/datawatcher.py +11 -40
- tomwer/core/process/control/datawatcher/datawatcherobserver.py +30 -64
- tomwer/core/process/control/datawatcher/datawatcherprocess.py +11 -32
- tomwer/core/process/control/datawatcher/edfdwprocess.py +2 -27
- tomwer/core/process/control/datawatcher/hdf5dwprocess.py +1 -26
- tomwer/core/process/control/datawatcher/status.py +1 -26
- tomwer/core/process/control/emailnotifier.py +11 -23
- tomwer/core/process/control/nxtomoconcatenate.py +20 -18
- tomwer/core/process/control/nxtomomill.py +9 -44
- tomwer/core/process/control/scanlist.py +0 -27
- tomwer/core/process/control/scantransfer.py +15 -13
- tomwer/core/process/control/scanvalidator.py +4 -30
- tomwer/core/process/control/{test → tests}/test_concatenate_nxtomos.py +5 -5
- tomwer/core/process/control/timer.py +1 -27
- tomwer/core/process/control/tomoobjseries.py +12 -0
- tomwer/core/process/drac/binning.py +37 -0
- tomwer/core/process/drac/dracbase.py +170 -0
- tomwer/core/process/drac/gallery.py +109 -0
- tomwer/core/process/drac/output.py +12 -0
- tomwer/core/process/drac/processeddataset.py +147 -0
- tomwer/core/process/drac/publish.py +118 -0
- tomwer/core/process/drac/rawdataset.py +142 -0
- tomwer/core/process/drac/tests/test_gallery.py +71 -0
- tomwer/core/process/drac/tests/test_icat_processed_dataset.py +80 -0
- tomwer/core/process/drac/tests/test_icat_raw_dataset.py +90 -0
- tomwer/core/process/edit/darkflatpatch.py +1 -28
- tomwer/core/process/edit/imagekeyeditor.py +4 -32
- tomwer/core/process/edit/nxtomoeditor.py +307 -0
- tomwer/core/process/edit/tests/test_darkflatpatch.py +243 -0
- tomwer/core/process/edit/tests/test_imagekey_editor.py +99 -0
- tomwer/core/process/output.py +9 -2
- tomwer/core/process/reconstruction/__init__.py +0 -26
- tomwer/core/process/reconstruction/axis/anglemode.py +1 -29
- tomwer/core/process/reconstruction/axis/axis.py +47 -804
- tomwer/core/process/reconstruction/axis/mode.py +89 -25
- tomwer/core/process/reconstruction/axis/params.py +131 -283
- tomwer/core/process/reconstruction/axis/projectiontype.py +0 -28
- tomwer/core/process/reconstruction/axis/side.py +8 -0
- tomwer/core/process/reconstruction/darkref/darkrefs.py +14 -39
- tomwer/core/process/reconstruction/darkref/darkrefscopy.py +7 -39
- tomwer/core/process/reconstruction/darkref/params.py +1 -28
- tomwer/core/process/reconstruction/nabu/castvolume.py +19 -34
- tomwer/core/process/reconstruction/nabu/nabucommon.py +18 -43
- tomwer/core/process/reconstruction/nabu/nabuscores.py +64 -68
- tomwer/core/process/reconstruction/nabu/nabuslices.py +63 -105
- tomwer/core/process/reconstruction/nabu/nabuvolume.py +44 -70
- tomwer/core/process/reconstruction/nabu/plane.py +10 -0
- tomwer/core/process/reconstruction/nabu/settings.py +1 -28
- tomwer/core/process/reconstruction/nabu/target.py +0 -28
- tomwer/core/process/reconstruction/nabu/test/test_castvolume.py +116 -0
- tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py +277 -0
- tomwer/core/process/reconstruction/nabu/test/test_nabunormalization.py +199 -0
- tomwer/core/process/reconstruction/nabu/utils.py +11 -60
- tomwer/core/process/reconstruction/normalization/normalization.py +2 -32
- tomwer/core/process/reconstruction/normalization/params.py +3 -35
- tomwer/core/process/reconstruction/output.py +14 -19
- tomwer/core/process/reconstruction/paramsbase.py +4 -33
- tomwer/core/process/reconstruction/saaxis/params.py +5 -33
- tomwer/core/process/reconstruction/saaxis/saaxis.py +22 -51
- tomwer/core/process/reconstruction/sadeltabeta/params.py +2 -31
- tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +18 -46
- tomwer/core/process/reconstruction/scores/params.py +9 -39
- tomwer/core/process/reconstruction/scores/scores.py +10 -42
- tomwer/core/process/reconstruction/tests/__init__.py +0 -0
- tomwer/core/process/reconstruction/tests/test_axis.py +46 -0
- tomwer/core/process/reconstruction/tests/test_darkref.py +33 -0
- tomwer/core/process/reconstruction/{test → tests}/test_saaxis.py +1 -27
- tomwer/core/process/reconstruction/tests/test_sadeltabeta.py +48 -0
- tomwer/core/process/reconstruction/{test → tests}/test_utils.py +4 -4
- tomwer/core/process/reconstruction/utils/cor.py +8 -4
- tomwer/core/process/script/python.py +1 -27
- tomwer/core/process/script/tests/test_script.py +41 -0
- tomwer/core/process/stitching/metadataholder.py +5 -4
- tomwer/core/process/stitching/nabustitcher.py +35 -5
- tomwer/core/process/stitching/tests/test_metadataholder.py +17 -0
- tomwer/core/process/task.py +20 -63
- tomwer/core/process/tests/__init__.py +0 -0
- tomwer/core/process/{test → tests}/test_conditions.py +1 -28
- tomwer/core/process/{test → tests}/test_dark_and_flat.py +1 -27
- tomwer/core/process/{test → tests}/test_data_listener.py +1 -27
- tomwer/core/process/{test → tests}/test_data_transfer.py +2 -28
- tomwer/core/process/{test → tests}/test_data_watcher.py +1 -27
- tomwer/core/process/{test → tests}/test_nabu.py +2 -33
- tomwer/core/process/{test → tests}/test_normalization.py +1 -26
- tomwer/core/process/{test → tests}/test_timer.py +1 -27
- tomwer/core/process/utils.py +2 -31
- tomwer/core/process/visualization/dataviewer.py +1 -26
- tomwer/core/process/visualization/diffviewer.py +1 -26
- tomwer/core/process/visualization/imagestackviewer.py +0 -26
- tomwer/core/process/visualization/radiostack.py +0 -26
- tomwer/core/process/visualization/samplemoved.py +0 -28
- tomwer/core/process/visualization/sinogramviewer.py +0 -27
- tomwer/core/process/visualization/slicestack.py +0 -28
- tomwer/core/process/visualization/tests/test_data_viewer.py +12 -0
- tomwer/core/process/visualization/tests/test_diff_viewer.py +12 -0
- tomwer/core/process/visualization/tests/test_image_stack_viewer.py +14 -0
- tomwer/core/process/visualization/tests/test_radio_stack.py +12 -0
- tomwer/core/process/visualization/tests/test_sample_moved.py +14 -0
- tomwer/core/process/visualization/tests/test_sinogram_viewer.py +13 -0
- tomwer/core/process/visualization/tests/test_slice_stack.py +13 -0
- tomwer/core/process/visualization/tests/test_volume_viewer.py +12 -0
- tomwer/core/process/visualization/volumeviewer.py +0 -29
- tomwer/core/scan/__init__.py +3 -27
- tomwer/core/scan/blissscan.py +5 -34
- tomwer/core/scan/edfscan.py +19 -53
- tomwer/core/scan/hdf5scan.py +2 -2
- tomwer/core/scan/nxtomoscan.py +48 -54
- tomwer/core/scan/scanbase.py +107 -203
- tomwer/core/scan/scanfactory.py +11 -41
- tomwer/core/scan/tests/__init__.py +0 -0
- tomwer/core/scan/tests/test_edf.py +25 -0
- tomwer/core/scan/tests/test_future_scan.py +35 -0
- tomwer/core/scan/tests/test_nxtomoscan.py +143 -0
- tomwer/core/scan/tests/test_process_registration.py +64 -0
- tomwer/core/settings.py +18 -40
- tomwer/core/tests/__init__.py +0 -0
- tomwer/core/tests/test_scanutils.py +26 -0
- tomwer/core/{test → tests}/test_utils.py +1 -28
- tomwer/core/tomwer_object.py +4 -0
- tomwer/core/utils/__init__.py +2 -0
- tomwer/core/utils/char.py +0 -28
- tomwer/core/utils/deprecation.py +12 -38
- tomwer/core/utils/dictutils.py +1 -3
- tomwer/core/utils/ftseriesutils.py +1 -27
- tomwer/core/utils/gpu.py +0 -28
- tomwer/core/utils/image.py +8 -39
- tomwer/core/utils/locker.py +1 -28
- tomwer/core/utils/logconfig.py +0 -27
- tomwer/core/utils/normalization.py +4 -31
- tomwer/core/utils/nxtomoutils.py +8 -38
- tomwer/core/utils/resource.py +0 -26
- tomwer/core/utils/scanutils.py +23 -52
- tomwer/core/utils/slurm.py +7 -30
- tomwer/core/utils/spec.py +6 -6
- tomwer/core/utils/tests/__init__.py +0 -0
- tomwer/core/utils/tests/test_image.py +30 -0
- tomwer/core/utils/tests/test_nxtomo.py +38 -0
- tomwer/core/utils/tests/test_scan_utils.py +46 -0
- tomwer/core/utils/tests/test_time.py +6 -0
- tomwer/core/utils/threads.py +0 -26
- tomwer/core/utils/time.py +0 -27
- tomwer/core/volume/__init__.py +4 -0
- tomwer/core/volume/edfvolume.py +1 -28
- tomwer/core/volume/hdf5volume.py +1 -28
- tomwer/core/volume/jp2kvolume.py +1 -27
- tomwer/core/volume/rawvolume.py +1 -28
- tomwer/core/volume/tests/test_volumes.py +21 -0
- tomwer/core/volume/tiffvolume.py +1 -28
- tomwer/core/volume/volumebase.py +5 -0
- tomwer/core/volume/volumefactory.py +7 -33
- tomwer/gui/__init__.py +0 -28
- tomwer/gui/cluster/__init__.py +2 -0
- tomwer/gui/cluster/slurm.py +297 -95
- tomwer/gui/cluster/supervisor.py +1 -27
- tomwer/gui/cluster/tests/__init__.py +0 -0
- tomwer/gui/cluster/{test → tests}/test_cluster.py +21 -26
- tomwer/gui/cluster/{test → tests}/test_supervisor.py +1 -27
- tomwer/gui/conditions/__init__.py +2 -0
- tomwer/gui/conditions/filter.py +1 -26
- tomwer/gui/configuration/__init__.py +2 -0
- tomwer/gui/control/__init__.py +2 -0
- tomwer/gui/control/actions.py +2 -28
- tomwer/gui/control/datadiscovery.py +4 -3
- tomwer/gui/control/datalist.py +64 -69
- tomwer/gui/control/datalistener.py +1 -39
- tomwer/gui/control/datareacheractions.py +1 -28
- tomwer/gui/control/datatransfert.py +2 -29
- tomwer/gui/control/datavalidator.py +3 -37
- tomwer/gui/control/datawatcher/__init__.py +0 -28
- tomwer/gui/control/datawatcher/configuration.py +1 -28
- tomwer/gui/control/datawatcher/datawatcher.py +3 -32
- tomwer/gui/control/datawatcher/datawatcherobserver.py +2 -28
- tomwer/gui/control/history.py +5 -35
- tomwer/gui/control/nxtomomill.py +3 -30
- tomwer/gui/control/observations.py +61 -55
- tomwer/gui/control/reducedarkflatselector.py +24 -20
- tomwer/gui/control/scanselectorwidget.py +2 -28
- tomwer/gui/control/selectorwidgetbase.py +17 -17
- tomwer/gui/control/series/__init__.py +0 -0
- tomwer/gui/control/{serie/seriecreator.py → series/seriescreator.py} +214 -235
- tomwer/gui/control/series/serieswaiter.py +0 -0
- tomwer/gui/control/series/test/test_creator.py +424 -0
- tomwer/gui/control/series/test/test_nxtomo_concatenate.py +21 -0
- tomwer/gui/control/singletomoobj.py +1 -1
- tomwer/gui/control/tests/__init__.py +0 -0
- tomwer/gui/control/tests/test_datalist.py +47 -0
- tomwer/gui/control/{test → tests}/test_datalistener.py +1 -28
- tomwer/gui/control/tests/test_datavalidator.py +27 -0
- tomwer/gui/control/{test → tests}/test_inputwidget.py +1 -27
- tomwer/gui/control/tests/test_process_manager.py +38 -0
- tomwer/gui/control/tests/test_scan_observations.py +23 -0
- tomwer/gui/control/tests/test_scanselector.py +42 -0
- tomwer/gui/control/{test → tests}/test_scanvalidator.py +1 -27
- tomwer/gui/control/{test → tests}/test_volume_dialog.py +2 -30
- tomwer/gui/control/{test → tests}/test_volumeselector.py +1 -27
- tomwer/gui/control/volumeselectorwidget.py +2 -30
- tomwer/gui/dataportal/__init__.py +2 -0
- tomwer/gui/{icat → dataportal}/createscreenshots.py +3 -2
- tomwer/gui/dataportal/gallery.py +133 -0
- tomwer/gui/dataportal/outputformat.py +0 -0
- tomwer/gui/dataportal/publish.py +96 -0
- tomwer/gui/dataportal/tests/test_create_screenshots_gui.py +23 -0
- tomwer/gui/dataportal/tests/test_gallery_gui.py +21 -0
- tomwer/gui/debugtools/__init__.py +2 -0
- tomwer/gui/debugtools/datasetgenerator.py +1 -30
- tomwer/gui/debugtools/objectinspector.py +1 -29
- tomwer/gui/dialog/QDataDialog.py +89 -0
- tomwer/gui/{qfolderdialog.py → dialog/QVolumeDialog.py} +8 -107
- tomwer/gui/dialog/__init__.py +1 -0
- tomwer/gui/edit/__init__.py +2 -0
- tomwer/gui/edit/dkrfpatch.py +52 -87
- tomwer/gui/edit/imagekeyeditor.py +18 -54
- tomwer/gui/edit/nxtomoeditor.py +113 -300
- tomwer/gui/edit/nxtomowarmer.py +3 -2
- tomwer/gui/edit/tests/__init__.py +0 -0
- tomwer/gui/edit/{test → tests}/test_dkrf_patch.py +3 -29
- tomwer/gui/edit/{test → tests}/test_image_key_editor.py +1 -27
- tomwer/gui/edit/{test → tests}/test_nx_editor.py +45 -23
- tomwer/gui/fonts.py +5 -0
- tomwer/gui/icons.py +28 -66
- tomwer/gui/illustrations.py +4 -34
- tomwer/gui/imagefromfile.py +5 -30
- tomwer/gui/metadataloader.py +36 -0
- tomwer/gui/qconfigfile.py +3 -0
- tomwer/gui/qlefilesystem.py +3 -0
- tomwer/gui/reconstruction/__init__.py +2 -0
- tomwer/gui/reconstruction/axis/AxisMainWindow.py +275 -0
- tomwer/gui/reconstruction/axis/AxisOptionsWidget.py +313 -0
- tomwer/gui/reconstruction/axis/AxisSettingsWidget.py +797 -0
- tomwer/gui/reconstruction/axis/AxisWidget.py +534 -0
- tomwer/gui/reconstruction/axis/CalculationWidget.py +218 -0
- tomwer/gui/reconstruction/axis/CompareImages.py +11 -44
- tomwer/gui/reconstruction/axis/ControlWidget.py +285 -0
- tomwer/gui/reconstruction/axis/EstimatedCORWidget.py +394 -0
- tomwer/gui/reconstruction/axis/EstimatedCorComboBox.py +118 -0
- tomwer/gui/reconstruction/axis/InputWidget.py +347 -0
- tomwer/gui/reconstruction/axis/ManualFramesSelection.py +168 -0
- tomwer/gui/reconstruction/axis/__init__.py +2 -2
- tomwer/gui/reconstruction/darkref/__init__.py +0 -27
- tomwer/gui/reconstruction/darkref/darkrefcopywidget.py +5 -34
- tomwer/gui/reconstruction/darkref/darkrefwidget.py +1 -27
- tomwer/gui/reconstruction/nabu/castvolume.py +40 -59
- tomwer/gui/reconstruction/nabu/check.py +7 -33
- tomwer/gui/reconstruction/nabu/nabuconfig/base.py +7 -34
- tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py +6 -5
- tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py +10 -69
- tomwer/gui/reconstruction/nabu/nabuconfig/output.py +3 -47
- tomwer/gui/reconstruction/nabu/nabuconfig/phase.py +54 -36
- tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py +103 -54
- tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py +116 -65
- tomwer/gui/reconstruction/nabu/nabuflow.py +31 -61
- tomwer/gui/reconstruction/nabu/platform.py +94 -0
- tomwer/gui/reconstruction/nabu/slices.py +81 -45
- tomwer/gui/reconstruction/nabu/slurm.py +1 -27
- tomwer/gui/reconstruction/nabu/test/test_cast_volume.py +82 -0
- tomwer/gui/reconstruction/nabu/test/test_check.py +66 -0
- tomwer/gui/reconstruction/nabu/test/test_ctf.py +46 -0
- tomwer/gui/reconstruction/nabu/test/test_helical.py +21 -0
- tomwer/gui/reconstruction/nabu/test/test_nabu_preprocessing.py +81 -0
- tomwer/gui/reconstruction/nabu/volume.py +62 -90
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- tomwer/gui/reconstruction/{test → tests}/test_saaxis.py +10 -37
- tomwer/gui/reconstruction/{test → tests}/test_sadeltabeta.py +1 -26
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- tomwer/gui/tests/__init__.py +0 -0
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- tomwer/gui/{test → tests}/test_qfolder_dialog.py +1 -1
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- tomwer/gui/visualization/test/test_stacks.py +184 -115
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- tomwer/gui/visualization/volumeviewer.py +47 -43
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- tomwer/io/utils/test/test_utils.py +67 -0
- tomwer/io/utils/utils.py +2 -31
- tomwer/resources/__init__.py +13 -33
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- tomwer/resources/gui/icons/icat_gallery_opts.png +0 -0
- tomwer/resources/gui/icons/icat_gallery_opts.svg +80 -0
- tomwer/resources/gui/icons/search.png +0 -0
- tomwer/resources/gui/icons/search.svg +23 -0
- tomwer/resources/gui/icons/warning.png +0 -0
- tomwer/synctools/__init__.py +2 -0
- tomwer/synctools/axis.py +1 -27
- tomwer/synctools/darkref.py +1 -26
- tomwer/synctools/datalistener.py +1 -27
- tomwer/synctools/datatransfert.py +2 -27
- tomwer/synctools/imageloaderthread.py +1 -28
- tomwer/synctools/rsyncmanager.py +1 -25
- tomwer/synctools/saaxis.py +1 -26
- tomwer/synctools/sadeltabeta.py +1 -26
- tomwer/synctools/stacks/control/datalistener.py +1 -26
- tomwer/synctools/stacks/processingstack.py +4 -33
- tomwer/synctools/stacks/reconstruction/axis.py +6 -53
- tomwer/synctools/stacks/reconstruction/castvolume.py +12 -43
- tomwer/synctools/stacks/reconstruction/dkrefcopy.py +4 -27
- tomwer/synctools/stacks/reconstruction/nabu.py +3 -28
- tomwer/synctools/stacks/reconstruction/normalization.py +2 -27
- tomwer/synctools/stacks/reconstruction/saaxis.py +2 -27
- tomwer/synctools/stacks/reconstruction/sadeltabeta.py +2 -27
- tomwer/synctools/tests/__init__.py +0 -0
- tomwer/synctools/{test → tests}/test_darkRefs.py +16 -40
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- tomwer/synctools/utils/scanstages.py +2 -31
- tomwer/tests/__init__.py +1 -0
- tomwer/tests/app/test_stitching.py +95 -0
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- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_reduce_dark_flat_selector.py +40 -0
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- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_volume_selector.py +69 -0
- orangecontrib/tomwer/widgets/edit/test/test_image_key_editor.py → tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_dataset_generator.py +17 -16
- tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_object_inspector.py +36 -0
- {orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_dark_flat_patch.py +1 -27
- tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_image_key_editor.py +30 -0
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- tomwer/tests/orangecontrib/tomwer/widgets/other/tests/test_pythonscript.py +31 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_axis.py +199 -0
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- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_dark_refs_widget.py +136 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_delta_beta_selector.py +15 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_i_norm.py +200 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_helical_prepare_weights_double.py +20 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_volume.py +74 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_nabu_widget.py +107 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_sa_delta_beta.py +194 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_saaxis.py +194 -0
- tomwer/tests/orangecontrib/tomwer/widgets/stitching/tests/test_zstitching.py +313 -0
- tomwer/tests/orangecontrib/tomwer/widgets/tests/test_conditions.py +85 -0
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- tomwer/tests/orangecontrib/tomwer/widgets/tests/test_foldertransfert.py +105 -0
- tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_dataviewerow.py +57 -0
- tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_diffviewerow.py +39 -0
- tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_nxtomo_metadata_viewer.py +29 -0
- tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_radio_stackow.py +31 -0
- tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_sample_movedow.py +46 -0
- tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_sinogram_viewerow.py +31 -0
- tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_slice_stackow.py +31 -0
- tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_volume_viewerow.py +32 -0
- tomwer/tests/test_ewoks/test_conversion.py +104 -0
- tomwer/tests/test_ewoks/test_single_node_execution.py +87 -0
- tomwer/tests/test_ewoks/test_workflows.py +138 -0
- tomwer/utils.py +11 -39
- tomwer/version.py +2 -2
- {tomwer-1.3.26.dist-info → tomwer-1.4.0.dist-info}/LICENSE +3 -3
- tomwer-1.4.0.dist-info/METADATA +337 -0
- tomwer-1.4.0.dist-info/RECORD +912 -0
- {tomwer-1.3.26.dist-info → tomwer-1.4.0.dist-info}/WHEEL +1 -1
- {tomwer-1.3.26.dist-info → tomwer-1.4.0.dist-info}/entry_points.txt +1 -0
- orangecontrib/tomwer/widgets/control/DataListOW.py +0 -129
- orangecontrib/tomwer/widgets/control/TomoObjSerieOW.py +0 -86
- orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py +0 -182
- orangecontrib/tomwer/widgets/edit/test/test_nxtomo_editor.py +0 -141
- orangecontrib/tomwer/widgets/icat/PublishProcessedDataOW.py +0 -115
- orangecontrib/tomwer/widgets/icat/RawDataScreenshotCreatorOW.py +0 -98
- orangecontrib/tomwer/widgets/icat/SaveToGalleryAndPublishOW.py +0 -129
- orangecontrib/tomwer/widgets/icat/icons/add_gallery.png +0 -0
- orangecontrib/tomwer/widgets/icat/icons/add_gallery.svg +0 -82
- orangecontrib/tomwer/widgets/icat/icons/raw_screenshots.png +0 -0
- orangecontrib/tomwer/widgets/icat/icons/raw_screenshots.svg +0 -143
- orangecontrib/tomwer/widgets/visualization/LivesliceOW.py +0 -87
- orangecontrib/tomwer/widgets/visualization/icons/liveslice.png +0 -0
- orangecontrib/tomwer/widgets/visualization/icons/liveslice.svg +0 -110
- tomwer/core/log/logger.py +0 -130
- tomwer/core/process/control/test/test_volume_link.py +0 -74
- tomwer/core/process/control/tomoobjserie.py +0 -12
- tomwer/core/process/control/volumesymlink.py +0 -200
- tomwer/core/process/icat/createscreenshots.py +0 -100
- tomwer/core/process/icat/gallery.py +0 -377
- tomwer/core/process/icat/icatbase.py +0 -36
- tomwer/core/process/icat/publish.py +0 -228
- tomwer/core/process/icat/screenshots.py +0 -27
- tomwer/core/process/reconstruction/test/test_darkref.py +0 -60
- tomwer/core/process/reconstruction/test/test_sadeltabeta.py +0 -74
- tomwer/core/process/test/test_axis.py +0 -309
- tomwer/core/process/visualization/liveslice.py +0 -6
- tomwer/core/progress.py +0 -100
- tomwer/core/scan/test/test_edf.py +0 -53
- tomwer/core/scan/test/test_future_scan.py +0 -61
- tomwer/core/scan/test/test_h5.py +0 -96
- tomwer/core/scan/test/test_process_registration.py +0 -109
- tomwer/core/test/test_scanutils.py +0 -53
- tomwer/gui/control/emailnotifier.py +0 -174
- tomwer/gui/control/serie/seriewaiter.py +0 -28
- tomwer/gui/control/test/__init__.py +0 -28
- tomwer/gui/control/test/test_datalist.py +0 -96
- tomwer/gui/control/test/test_datavalidator.py +0 -54
- tomwer/gui/control/test/test_email.py +0 -35
- tomwer/gui/control/test/test_process_manager.py +0 -65
- tomwer/gui/control/test/test_scanselector.py +0 -67
- tomwer/gui/edit/test/__init__.py +0 -28
- tomwer/gui/icat/gallery.py +0 -214
- tomwer/gui/icat/publish.py +0 -187
- tomwer/gui/reconstruction/axis/axis.py +0 -733
- tomwer/gui/reconstruction/axis/radioaxis.py +0 -2467
- tomwer/gui/stitching/stitching.py +0 -1392
- tomwer/gui/test/__init__.py +0 -28
- tomwer/gui/test/test_axis_gui.py +0 -34
- tomwer/synctools/stacks/edit/darkflatpatch.py +0 -169
- tomwer/synctools/stacks/edit/imagekeyeditor.py +0 -135
- tomwer/third_part/WaitingOverlay.py +0 -110
- tomwer-1.3.26-py3.11-nspkg.pth +0 -1
- tomwer-1.3.26.dist-info/METADATA +0 -292
- tomwer-1.3.26.dist-info/RECORD +0 -785
- tomwer-1.3.26.dist-info/namespace_packages.txt +0 -1
- /orangecontrib/tomwer/{widgets/edit/test → tests}/__init__.py +0 -0
- {tomwer/core/process/control/test → orangecontrib/tomwer/tutorials/id16b}/__init__.py +0 -0
- {tomwer/core/process/icat → orangecontrib/tomwer/widgets/cluster/tests}/__init__.py +0 -0
- /orangecontrib/tomwer/widgets/control/icons/{tomoobjserie.png → tomoobjseries.png} +0 -0
- {tomwer/core/process/reconstruction/test → orangecontrib/tomwer/widgets/control/tests}/__init__.py +0 -0
- /orangecontrib/tomwer/widgets/{icat → dataportal}/icons/publish_processed_data.png +0 -0
- /orangecontrib/tomwer/widgets/{icat → dataportal}/icons/publish_processed_data.svg +0 -0
- {tomwer/core/process/test → orangecontrib/tomwer/widgets/debugtools/tests}/__init__.py +0 -0
- {tomwer/core/scan/test → orangecontrib/tomwer/widgets/edit/tests}/__init__.py +0 -0
- {tomwer/core/test → orangecontrib/tomwer/widgets/other/tests}/__init__.py +0 -0
- {tomwer/gui/cluster/test → orangecontrib/tomwer/widgets/reconstruction/tests}/__init__.py +0 -0
- {tomwer/gui/control/serie → orangecontrib/tomwer/widgets/stitching/tests}/__init__.py +0 -0
- {tomwer/gui/icat → orangecontrib/tomwer/widgets/tests}/__init__.py +0 -0
- {tomwer/gui/reconstruction/test → orangecontrib/tomwer/widgets/visualization/tests}/__init__.py +0 -0
- /tomwer/{synctools/stacks/edit → app/stitching}/__init__.py +0 -0
- /tomwer/{synctools/test → core/process/control/tests}/__init__.py +0 -0
- /tomwer/core/process/control/{test → tests}/test_email.py +0 -0
- /tomwer/core/process/control/{test → tests}/test_h52nx_process.py +0 -0
- /tomwer/{third_part → core/process/drac}/__init__.py +0 -0
- /tomwer/core/process/reconstruction/{test → tests}/test_axis_params.py +0 -0
- /tomwer/core/process/reconstruction/{test → tests}/test_darkref_copy.py +0 -0
- /tomwer/core/process/reconstruction/{test → tests}/test_paramsbase.py +0 -0
- /tomwer/core/scan/{test → tests}/test_scan.py +0 -0
- /tomwer/gui/control/{serie → series}/nxtomoconcatenate.py +0 -0
- /tomwer/gui/control/{test → tests}/test_datadiscovery.py +0 -0
- /tomwer/gui/control/{test → tests}/test_reducedarkflat_selector.py +0 -0
- /tomwer/gui/control/{test → tests}/test_single_tomo_obj.py +0 -0
- {orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_image_key_upgrader.py +0 -0
- {tomwer-1.3.26.dist-info → tomwer-1.4.0.dist-info}/top_level.txt +0 -0
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# THE SOFTWARE.
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#
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# ###########################################################################*/
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__authors__ = ["H. Payno"]
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__license__ = "MIT"
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__date__ = "11/03/2020"
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from __future__ import annotations
|
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import logging
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from copy import copy
|
@@ -33,10 +6,12 @@ from copy import copy
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from nxtomomill.io.config import TomoEDFConfig as EDFConfig
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from orangewidget import gui
|
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from silx.gui import qt
|
9
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from silx.gui.utils import blockSignals
|
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10
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from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
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from orangecontrib.tomwer.widgets.control.NXTomomillMixIn import NXTomomillMixIn
|
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13
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from tomwer.core.process.control.nxtomomill import EDFToNxProcess
|
14
|
+
from tomwer.core.process.output import ProcessDataOutputDirMode
|
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15
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from tomwer.core.scan.edfscan import EDFTomoScan
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from tomwer.core.scan.nxtomoscan import NXtomoScan
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from tomwer.gui.control.datalist import EDFDataListMainWindow
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@@ -104,7 +79,6 @@ class EDF2NXOW(
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_layout.addWidget(self._convertAutoCB)
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# connect signal / slot
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self.widget._sendButton.clicked.connect(self._sendAll)
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self.widget._sendSelectedButton.clicked.connect(self._sendSelected)
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self.widget.sigNXTomoCFGFileChanged.connect(self._saveNXTomoCfgFile)
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self.widget.sigUpdated.connect(self._updateSettings)
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@@ -126,9 +100,19 @@ class EDF2NXOW(
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self._loadSettings()
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# keep auto conversion setting
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self._ewoks_default_inputs[ # pylint: disable=E1137
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"convert_auto_edfscan_channel"
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] = self.convertAutoEDFScanReceivedFromChannel()
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# store scans
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self._scans = []
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for scan in self.widget.datalist._myitems:
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self._scans.append(scan)
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# store output folder
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output_dir = self.widget.getOutputFolder()
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if isinstance(output_dir, ProcessDataOutputDirMode):
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output_dir = output_dir.value
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self._ewoks_default_inputs["output_dir"] = output_dir # pylint: disable=E1137
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def convertAutoEDFScanReceivedFromChannel(self) -> bool:
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self._convertAutoCB.setChecked(checked)
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def _loadSettings(self):
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self.
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"nxtomomill_cfg_file"
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"
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)
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with blockSignals(self.widget):
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for scan in self._scans: # pylint: disable=E1133
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self.widget.add(scan)
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if (
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"nxtomomill_cfg_file" in self._ewoks_default_inputs
|
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): # pylint: disable=E1135
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self._nxtomo_cfg_file = (
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self._ewoks_default_inputs[ # pylint: disable=E1136
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"nxtomomill_cfg_file"
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]
|
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+
)
|
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+
self.widget.setCFGFilePath(self._nxtomo_cfg_file)
|
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if "output_dir" in self._ewoks_default_inputs: # pylint: disable=E1135
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self.widget.setOutputFolder(
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self._ewoks_default_inputs["output_dir"] # pylint: disable=E1136
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)
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if (
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"convert_auto_edfscan_channel"
|
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+
in self._ewoks_default_inputs # pylint: disable=E1135
|
143
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+
):
|
144
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+
self.setConvertAutoEDFScanReceivedFromChannel(
|
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self._ewoks_default_inputs[ # pylint: disable=E1136
|
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"convert_auto_edfscan_channel"
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]
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)
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def _convertAndSend(self, edf_scan: EDFTomoScan):
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# cache updated for each folder in order to match `_execute_ewoks_task` design
|
@@ -193,7 +182,7 @@ class EDF2NXOW(
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log_missing_inputs=False,
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)
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except Exception:
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self._execute_ewoks_task(propagate=True) # pylint: disable=E1123
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self._execute_ewoks_task(propagate=True) # pylint: disable=E1123, E1120
|
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|
198
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def get_task_inputs(self):
|
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return {
|
@@ -230,7 +219,7 @@ class EDF2NXOW(
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else:
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self.notify_failed(scan=scan)
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except Exception as e:
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logger.error(f"failed to handle task finished callback.
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logger.error(f"failed to handle task finished callback. Reason is {e}")
|
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235
224
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def _saveNXTomoCfgFile(self, cfg_file):
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super()._saveNXTomoCfgFile(cfg_file, keyword="edf_to_nx_configuration")
|
@@ -250,3 +239,11 @@ class EDF2NXOW(
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tomo_obj = self.widget.datalist.getEDFTomoScan(scan_id, None)
|
251
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if tomo_obj:
|
252
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self._convertAndSend(tomo_obj)
|
242
|
+
|
243
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+
def keyPressEvent(self, event):
|
244
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# forward Ctrl+A to the list as the shift ease selection of all
|
245
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+
modifiers = event.modifiers()
|
246
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+
key = event.key()
|
247
|
+
if key == qt.Qt.Key_A and modifiers == qt.Qt.KeyboardModifier.ControlModifier:
|
248
|
+
self.widget._widget.datalist.keyPressEvent(event)
|
249
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super().keyPressEvent(event)
|
@@ -5,9 +5,15 @@ from silx.gui import qt
|
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5
5
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from ewoksorange.bindings.owwidgets import OWEwoksWidgetNoThread
|
6
6
|
|
7
7
|
import tomwer.core.process.control.emailnotifier
|
8
|
-
from tomwer.gui.control.emailnotifier import Emailwidget
|
9
8
|
from tomwer.core.utils.dictutils import concatenate_dict
|
10
9
|
|
10
|
+
try:
|
11
|
+
from ewoksnotify.gui.email import EmailWidget
|
12
|
+
except ImportError:
|
13
|
+
has_ewoksnotify = False
|
14
|
+
else:
|
15
|
+
has_ewoksnotify = True
|
16
|
+
|
11
17
|
|
12
18
|
class EmailOW(
|
13
19
|
OWEwoksWidgetNoThread,
|
@@ -42,7 +48,11 @@ class EmailOW(
|
|
42
48
|
|
43
49
|
def __init__(self, *args, **kwargs):
|
44
50
|
super().__init__(*args, **kwargs)
|
45
|
-
|
51
|
+
if not has_ewoksnotify:
|
52
|
+
raise ImportError(
|
53
|
+
"ewoksnotify not install but required. Please run 'pip install ewoksnotify[full]'"
|
54
|
+
)
|
55
|
+
self._widget = EmailWidget(parent=self)
|
46
56
|
|
47
57
|
self._box = gui.vBox(self.mainArea, self.name)
|
48
58
|
layout = self._box.layout()
|
@@ -1,31 +1,4 @@
|
|
1
|
-
|
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__ = "19/07/2018"
|
1
|
+
from __future__ import annotations
|
29
2
|
|
30
3
|
import logging
|
31
4
|
|
@@ -1,31 +1,4 @@
|
|
1
|
-
|
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__ = "11/03/2020"
|
1
|
+
from __future__ import annotations
|
29
2
|
|
30
3
|
import logging
|
31
4
|
import os
|
@@ -34,6 +7,7 @@ from copy import copy
|
|
34
7
|
from nxtomomill.io.config import TomoHDF5Config as HDF5Config
|
35
8
|
from orangewidget import gui
|
36
9
|
from silx.gui import qt
|
10
|
+
from silx.gui.utils import blockSignals
|
37
11
|
|
38
12
|
from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
|
39
13
|
from orangecontrib.tomwer.widgets.control.NXTomomillMixIn import NXTomomillMixIn
|
@@ -114,7 +88,6 @@ class NXTomomillOW(
|
|
114
88
|
self.start = self._sendAll
|
115
89
|
|
116
90
|
# connect signal / slot
|
117
|
-
self.widget._sendButton.clicked.connect(self._sendAll)
|
118
91
|
self.widget._sendSelectedButton.clicked.connect(self._sendSelected)
|
119
92
|
self.widget.sigNXTomoCFGFileChanged.connect(self._saveNXTomoCfgFile)
|
120
93
|
self.widget.sigUpdated.connect(self._updateSettings)
|
@@ -177,7 +150,7 @@ class NXTomomillOW(
|
|
177
150
|
def _convertAndSend(self, bliss_url: str):
|
178
151
|
"""
|
179
152
|
|
180
|
-
:param
|
153
|
+
:param bliss_url: string at entry@file format
|
181
154
|
"""
|
182
155
|
logger.processStarted(f"Start translate {bliss_url} to NXTomo")
|
183
156
|
self.__configuration_cache = HDF5Config.from_dict(
|
@@ -255,26 +228,29 @@ class NXTomomillOW(
|
|
255
228
|
log_missing_inputs=False,
|
256
229
|
)
|
257
230
|
except Exception:
|
258
|
-
self._execute_ewoks_task(propagate=True) # pylint: disable=E1123
|
231
|
+
self._execute_ewoks_task(propagate=True) # pylint: disable=E1123, E1120
|
259
232
|
|
260
233
|
def _loadSettings(self):
|
261
|
-
|
262
|
-
|
263
|
-
|
264
|
-
|
265
|
-
|
266
|
-
|
267
|
-
|
268
|
-
|
269
|
-
|
270
|
-
|
271
|
-
"nxtomomill_cfg_file"
|
272
|
-
|
273
|
-
|
274
|
-
|
275
|
-
|
276
|
-
self.
|
277
|
-
|
234
|
+
with blockSignals(self.widget):
|
235
|
+
for scan in self._scans:
|
236
|
+
assert isinstance(scan, str)
|
237
|
+
try:
|
238
|
+
self.widget.add(scan)
|
239
|
+
except Exception as e:
|
240
|
+
logger.error(f"Fail to add {scan}. Error is {e}")
|
241
|
+
else:
|
242
|
+
logger.warning(f"{scan} is an invalid link to a file")
|
243
|
+
if (
|
244
|
+
"nxtomomill_cfg_file" in self._ewoks_default_inputs
|
245
|
+
): # pylint: disable=E1135
|
246
|
+
nxtomo_cfg_file = self._ewoks_default_inputs[ # pylint: disable=E1136
|
247
|
+
"nxtomomill_cfg_file"
|
248
|
+
]
|
249
|
+
self.widget.setCFGFilePath(nxtomo_cfg_file)
|
250
|
+
if "output_dir" in self._ewoks_default_inputs: # pylint: disable=E1135
|
251
|
+
self.widget.setOutputFolder(
|
252
|
+
self._ewoks_default_inputs["output_dir"] # pylint: disable=E1136
|
253
|
+
)
|
278
254
|
|
279
255
|
def getHDF5Config(self):
|
280
256
|
configuration_file = self.widget.getCFGFilePath()
|
@@ -333,21 +309,29 @@ class NXTomomillOW(
|
|
333
309
|
else:
|
334
310
|
self.notify_failed(scan=scan)
|
335
311
|
except Exception as e:
|
336
|
-
logger.error(f"failed to handle task finished callback.
|
312
|
+
logger.error(f"failed to handle task finished callback. Reason is {e}")
|
337
313
|
|
338
314
|
def trigger_downstream(self) -> None:
|
339
315
|
for ewoksname, var in self.get_task_outputs().items():
|
340
316
|
# note: for now we want to trigger 'data' for each items of 'datas'
|
341
|
-
if ewoksname == "
|
317
|
+
if ewoksname == "series" and not (
|
342
318
|
invalid_data.is_invalid_data(var.value) or var.value is None
|
343
319
|
):
|
344
320
|
for data in var.value:
|
345
321
|
data_channel = self._get_output_signal("data")
|
346
322
|
data_channel.send(data)
|
347
|
-
serie_channel = self._get_output_signal("
|
348
|
-
# then send the list of value /
|
323
|
+
serie_channel = self._get_output_signal("series")
|
324
|
+
# then send the list of value / series (also know as datas)
|
349
325
|
serie_channel.send(var.value)
|
350
326
|
elif ewoksname == "data" and not (
|
351
327
|
invalid_data.is_invalid_data(var.value) or var.value is None
|
352
328
|
):
|
353
|
-
pass # handle by '
|
329
|
+
pass # handle by 'series' in this case
|
330
|
+
|
331
|
+
def keyPressEvent(self, event):
|
332
|
+
# forward Ctrl+A to the list as the shift ease selection of all
|
333
|
+
modifiers = event.modifiers()
|
334
|
+
key = event.key()
|
335
|
+
if key == qt.Qt.Key_A and modifiers == qt.Qt.KeyboardModifier.ControlModifier:
|
336
|
+
self.widget._widget.datalist.keyPressEvent(event)
|
337
|
+
super().keyPressEvent(event)
|
@@ -1,13 +1,14 @@
|
|
1
|
+
from __future__ import annotations
|
2
|
+
|
1
3
|
import logging
|
2
4
|
|
3
|
-
from tomoscan.
|
5
|
+
from tomoscan.series import Series
|
4
6
|
|
5
7
|
from orangewidget import gui
|
6
8
|
from orangewidget.settings import Setting
|
7
9
|
from orangewidget.widget import Input, Output
|
8
10
|
from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
|
9
11
|
from silx.gui import qt
|
10
|
-
from typing import Optional
|
11
12
|
|
12
13
|
from tomwer.core.scan.scanbase import TomwerScanBase
|
13
14
|
from tomwer.core.scan.nxtomoscan import NXtomoScan
|
@@ -16,7 +17,7 @@ from tomwer.core.process.control.nxtomoconcatenate import (
|
|
16
17
|
format_output_location,
|
17
18
|
)
|
18
19
|
|
19
|
-
from tomwer.gui.control.
|
20
|
+
from tomwer.gui.control.series.nxtomoconcatenate import NXtomoConcatenateWidget
|
20
21
|
|
21
22
|
_logger = logging.getLogger(__name__)
|
22
23
|
|
@@ -53,7 +54,7 @@ class NXtomoConcatenateOW(
|
|
53
54
|
|
54
55
|
_ewoks_default_inputs = Setting(
|
55
56
|
{
|
56
|
-
"
|
57
|
+
"series": None,
|
57
58
|
"output_file": "{common_path}/concatenate.nx",
|
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59
|
"output_entry": "entry0000",
|
59
60
|
"overwrite": False,
|
@@ -70,10 +71,10 @@ class NXtomoConcatenateOW(
|
|
70
71
|
TIMEOUT = 30
|
71
72
|
|
72
73
|
class Inputs:
|
73
|
-
|
74
|
-
name="
|
75
|
-
type=
|
76
|
-
doc="
|
74
|
+
series = Input(
|
75
|
+
name="series",
|
76
|
+
type=Series,
|
77
|
+
doc="series to concatenate",
|
77
78
|
default=True,
|
78
79
|
multiple=False,
|
79
80
|
)
|
@@ -85,7 +86,7 @@ class NXtomoConcatenateOW(
|
|
85
86
|
|
86
87
|
def __init__(self, parent=None):
|
87
88
|
super().__init__(parent)
|
88
|
-
self.
|
89
|
+
self.__series = None
|
89
90
|
|
90
91
|
# gui definition
|
91
92
|
_layout = gui.vBox(self.mainArea, self.name).layout()
|
@@ -120,9 +121,9 @@ class NXtomoConcatenateOW(
|
|
120
121
|
self.__request_input = request
|
121
122
|
|
122
123
|
def get_task_inputs(self):
|
123
|
-
assert self.
|
124
|
+
assert self.__series is not None
|
124
125
|
return {
|
125
|
-
"
|
126
|
+
"series": self.__series,
|
126
127
|
"output_file": self.widget.getConfiguration()["output_file"],
|
127
128
|
"output_entry": self.widget.getConfiguration()["output_entry"],
|
128
129
|
"overwrite": self.widget.getConfiguration()["overwrite"],
|
@@ -151,7 +152,7 @@ class NXtomoConcatenateOW(
|
|
151
152
|
scan_about_to_be_created = NXtomoScan(
|
152
153
|
scan=format_output_location(
|
153
154
|
file_path=task_executor.current_task.inputs.output_file_path,
|
154
|
-
|
155
|
+
series=task_executor.current_task.inputs.series,
|
155
156
|
),
|
156
157
|
entry=task_executor.current_task.inputs.output_entry,
|
157
158
|
)
|
@@ -169,21 +170,21 @@ class NXtomoConcatenateOW(
|
|
169
170
|
else:
|
170
171
|
self.notify_failed(scan=scan)
|
171
172
|
except Exception as e:
|
172
|
-
_logger.error(f"failed to handle task finished callback.
|
173
|
+
_logger.error(f"failed to handle task finished callback. Reason is {e}")
|
173
174
|
|
174
|
-
@Inputs.
|
175
|
-
def
|
176
|
-
self.
|
175
|
+
@Inputs.series
|
176
|
+
def process_series(self, series: Series | None):
|
177
|
+
self._process_series(series=series)
|
177
178
|
|
178
|
-
def
|
179
|
-
if
|
179
|
+
def _process_series(self, series: Series | None):
|
180
|
+
if series is None:
|
180
181
|
return
|
181
182
|
else:
|
182
|
-
self.
|
183
|
+
self.__series = series
|
183
184
|
scan_about_to_be_created = NXtomoScan(
|
184
185
|
scan=format_output_location(
|
185
186
|
file_path=self.getOutputFilePath(),
|
186
|
-
|
187
|
+
series=series,
|
187
188
|
),
|
188
189
|
entry=self.getOutputEntry(),
|
189
190
|
)
|
@@ -1,37 +1,11 @@
|
|
1
|
-
|
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__ = "19/07/2018"
|
1
|
+
from __future__ import annotations
|
29
2
|
|
30
3
|
from orangewidget import gui, settings, widget
|
31
4
|
from orangewidget.widget import Input, Output
|
32
5
|
from silx.gui import qt
|
33
6
|
|
34
7
|
from tomwer.core.tomwer_object import TomwerObject
|
8
|
+
from tomwer.core.utils.deprecation import deprecated_warning
|
35
9
|
|
36
10
|
|
37
11
|
class NotifierWidgetOW(widget.OWBaseWidget):
|
@@ -60,6 +34,13 @@ class NotifierWidgetOW(widget.OWBaseWidget):
|
|
60
34
|
|
61
35
|
def __init__(self, parent=None):
|
62
36
|
super().__init__(parent)
|
37
|
+
deprecated_warning(
|
38
|
+
type_="class",
|
39
|
+
name="orangecontrib.tomwer.widgets.control.NotifierOW",
|
40
|
+
replacement="orangecontrib.ewoksnotify.ToneNotifierOW",
|
41
|
+
reason="moved to ewoksnotify (pip install ewoksnotify[full] to get the orange widget)",
|
42
|
+
since_version="1.4",
|
43
|
+
)
|
63
44
|
self.pop_up = None
|
64
45
|
layout = gui.vBox(self.mainArea, self.name).layout()
|
65
46
|
self._soundButton = qt.QPushButton(parent=self)
|
@@ -1,5 +1,6 @@
|
|
1
|
+
from __future__ import annotations
|
2
|
+
|
1
3
|
import logging
|
2
|
-
from typing import Optional
|
3
4
|
|
4
5
|
from orangewidget import gui
|
5
6
|
from orangewidget.settings import Setting
|
@@ -79,7 +80,7 @@ class ReduceDarkFlatSelectorOW(OWBaseWidget, openclass=True):
|
|
79
80
|
self.Outputs.out_reduced_flats.send(flats)
|
80
81
|
|
81
82
|
@Inputs.in_reduced_frames
|
82
|
-
def addReduceFrames(self, reduce_frames:
|
83
|
+
def addReduceFrames(self, reduce_frames: dict | None, *args, **kwargs):
|
83
84
|
if reduce_frames is not None:
|
84
85
|
self._dialog.addReduceFrames(reduce_frames)
|
85
86
|
|
@@ -1,31 +1,5 @@
|
|
1
1
|
# coding: utf-8
|
2
|
-
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2021 European Synchrotron Radiation Facility
|
5
|
-
#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
-
# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
|
26
|
-
__authors__ = ["C. Nemoz", "H. Payno"]
|
27
|
-
__license__ = "MIT"
|
28
|
-
__date__ = "25/08/2022"
|
2
|
+
from __future__ import annotations
|
29
3
|
|
30
4
|
import logging
|
31
5
|
|
@@ -1,31 +1,4 @@
|
|
1
|
-
|
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__ = "19/07/2018"
|
1
|
+
from __future__ import annotations
|
29
2
|
|
30
3
|
import functools
|
31
4
|
import logging
|
@@ -40,6 +13,7 @@ import tomwer.core.process.control.timer
|
|
40
13
|
from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
|
41
14
|
from tomwer.core.scan.scanbase import TomwerScanBase
|
42
15
|
from tomwer.utils import docstring
|
16
|
+
from tomwer.core.utils.deprecation import deprecated_warning
|
43
17
|
|
44
18
|
_logger = logging.getLogger(__name__)
|
45
19
|
|
@@ -90,6 +64,13 @@ class TimerOW(SuperviseOW):
|
|
90
64
|
def __init__(self, parent=None):
|
91
65
|
""" """
|
92
66
|
SuperviseOW.__init__(self, parent)
|
67
|
+
deprecated_warning(
|
68
|
+
type_="class",
|
69
|
+
name="orangecontrib.tomwer.widgets.control.TimerOW",
|
70
|
+
replacement="orangecontrib.ewoksnotify.WaiterOW",
|
71
|
+
reason="moved to ewoksnotify (pip install ewoksnotify[full] to get the orange widget)",
|
72
|
+
since_version="1.4",
|
73
|
+
)
|
93
74
|
self._widget = _TimerWidget(parent=self, _time=self._waiting_time)
|
94
75
|
self._widget.setContentsMargins(0, 0, 0, 0)
|
95
76
|
|