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
- tomwer/gui/reconstruction/normalization/intensity.py +5 -32
- tomwer/gui/reconstruction/normalization/test/test_intensity.py +89 -0
- tomwer/gui/reconstruction/saaxis/corrangeselector.py +32 -56
- tomwer/gui/reconstruction/saaxis/dimensionwidget.py +56 -96
- tomwer/gui/reconstruction/saaxis/saaxis.py +17 -38
- tomwer/gui/reconstruction/saaxis/sliceselector.py +8 -39
- tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py +19 -37
- tomwer/gui/reconstruction/scores/control.py +2 -30
- tomwer/gui/reconstruction/scores/scoreplot.py +23 -49
- tomwer/gui/reconstruction/tests/__init__.py +0 -0
- tomwer/gui/reconstruction/{test → tests}/test_axis.py +23 -49
- tomwer/gui/reconstruction/{test → tests}/test_nabu.py +16 -31
- tomwer/gui/reconstruction/{test → tests}/test_saaxis.py +10 -37
- tomwer/gui/reconstruction/{test → tests}/test_sadeltabeta.py +1 -26
- tomwer/gui/samplemoved/__init__.py +2 -30
- tomwer/gui/samplemoved/selectiontable.py +3 -33
- tomwer/gui/settings.py +7 -0
- tomwer/gui/stackplot.py +33 -661
- tomwer/gui/stacks.py +261 -135
- tomwer/gui/stitching/SingleAxisStitchingWidget.py +326 -0
- tomwer/gui/stitching/StitchingOptionsWidget.py +438 -0
- tomwer/gui/stitching/StitchingWindow.py +586 -0
- tomwer/gui/stitching/__init__.py +2 -0
- tomwer/gui/stitching/alignment.py +90 -0
- tomwer/gui/stitching/axisorderedlist.py +44 -34
- tomwer/gui/stitching/config/axisparams.py +25 -11
- tomwer/gui/stitching/config/output.py +6 -5
- tomwer/gui/stitching/config/positionoveraxis.py +313 -51
- tomwer/gui/stitching/config/stitchingstrategies.py +22 -16
- tomwer/gui/stitching/config/tests/test_axisparams.py +25 -0
- tomwer/gui/stitching/config/tomoobjdetails.py +3 -5
- tomwer/gui/stitching/normalization.py +1 -0
- tomwer/gui/stitching/preview.py +59 -0
- tomwer/gui/stitching/singleaxis.py +57 -0
- tomwer/gui/stitching/stitchandbackground.py +3 -2
- tomwer/gui/stitching/stitching_preview.py +44 -36
- tomwer/gui/stitching/stitching_raw.py +5 -3
- tomwer/gui/stitching/tests/test_ZStitchingWindow.py +88 -0
- tomwer/gui/stitching/tests/test_axis_ordered_list.py +21 -0
- tomwer/gui/stitching/tests/test_normalization.py +27 -0
- tomwer/gui/stitching/tests/test_preview.py +68 -0
- tomwer/gui/stitching/tests/test_stitching_raw.py +110 -0
- tomwer/gui/stitching/tests/utils.py +92 -0
- tomwer/gui/stitching/utils.py +14 -0
- tomwer/gui/stitching/z_stitching/fineestimation.py +5 -33
- tomwer/gui/stitching/z_stitching/tests/test_fine_estimation.py +35 -0
- tomwer/gui/stitching/z_stitching/tests/test_raw_estimation.py +215 -0
- tomwer/gui/stitching/z_stitching/tests/test_stitching_window.py +51 -0
- tomwer/gui/tests/__init__.py +0 -0
- tomwer/gui/tests/test_axis_gui.py +43 -0
- tomwer/gui/{test → tests}/test_qfolder_dialog.py +1 -1
- tomwer/gui/utils/RangeWidget.py +44 -0
- tomwer/gui/utils/buttons.py +4 -3
- tomwer/gui/utils/completer.py +2 -33
- tomwer/gui/utils/flow.py +11 -40
- tomwer/gui/utils/gpu.py +60 -0
- tomwer/gui/utils/illustrations.py +1 -26
- tomwer/gui/utils/inputwidget.py +35 -73
- tomwer/gui/utils/lineselector/lineselector.py +9 -46
- tomwer/gui/utils/loadingmode.py +81 -0
- tomwer/gui/utils/qt_utils.py +9 -0
- tomwer/gui/utils/sandboxes.py +1 -26
- tomwer/gui/utils/scandescription.py +2 -31
- tomwer/gui/utils/scrollarea.py +6 -55
- tomwer/gui/utils/slider.py +4 -28
- tomwer/gui/utils/splashscreen.py +0 -28
- tomwer/gui/utils/step.py +14 -13
- tomwer/gui/utils/tests/test_completer.py +41 -0
- tomwer/gui/utils/tests/test_line_selector.py +21 -0
- tomwer/gui/utils/tests/test_splashscreen.py +8 -0
- tomwer/gui/utils/tests/test_vignettes.py +68 -0
- tomwer/gui/utils/unitsystem.py +15 -69
- tomwer/gui/utils/utils.py +4 -5
- tomwer/gui/utils/vignettes.py +10 -41
- tomwer/gui/utils/waiterthread.py +0 -26
- tomwer/gui/visualization/__init__.py +2 -0
- tomwer/gui/visualization/dataviewer.py +68 -421
- tomwer/gui/visualization/diffviewer/diffviewer.py +2 -30
- tomwer/gui/visualization/diffviewer/shiftwidget.py +4 -29
- tomwer/gui/visualization/fullscreenplot.py +5 -5
- tomwer/gui/visualization/imagestack.py +403 -0
- tomwer/gui/visualization/nxtomometadata.py +0 -4
- tomwer/gui/visualization/reconstructionparameters.py +14 -32
- tomwer/gui/visualization/scanoverview.py +33 -66
- tomwer/gui/visualization/sinogramviewer.py +2 -28
- tomwer/gui/visualization/test/__init__.py +0 -28
- tomwer/gui/visualization/test/test_dataviewer.py +1 -28
- tomwer/gui/visualization/test/test_diffviewer.py +1 -28
- tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py +0 -5
- tomwer/gui/visualization/test/test_reconstruction_parameters.py +1 -27
- tomwer/gui/visualization/test/test_sinogramviewer.py +1 -28
- tomwer/gui/visualization/test/test_stacks.py +184 -115
- tomwer/gui/visualization/test/test_volumeviewer.py +3 -2
- tomwer/gui/visualization/tomoobjoverview.py +2 -2
- tomwer/gui/visualization/volumeoverview.py +3 -2
- tomwer/gui/visualization/volumeviewer.py +47 -43
- tomwer/io/__init__.py +2 -0
- tomwer/io/utils/h5pyutils.py +1 -27
- tomwer/io/utils/test/test_raw_and_processed_data.py +10 -0
- tomwer/io/utils/test/test_utils.py +67 -0
- tomwer/io/utils/utils.py +2 -31
- tomwer/resources/__init__.py +13 -33
- tomwer/resources/gui/icons/edit_downstream.svg +114 -0
- tomwer/resources/gui/icons/edit_upstream.svg +112 -0
- tomwer/resources/gui/icons/free_edition.svg +23 -0
- 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
- tomwer/synctools/{test → tests}/test_foldertransfer.py +2 -33
- tomwer/synctools/utils/scanstages.py +2 -31
- tomwer/tests/__init__.py +1 -0
- tomwer/tests/app/test_stitching.py +95 -0
- tomwer/tests/datasets.py +1 -5
- tomwer/tests/orangecontrib/tomwer/widgets/cluster/tests/test_future_supervisorow.py +48 -0
- tomwer/tests/orangecontrib/tomwer/widgets/cluster/tests/test_slurm_clusterow.py +40 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_advancement.py +8 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_data_validator.py +55 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datadiscovery.py +129 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datalistener.py +111 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_dataselector.py +69 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_datawatcher.py +411 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_emailow.py +29 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_notifier.py +24 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_nxtomo_concatenate_ow.py +64 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_nxtomomill.py +133 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_reduce_dark_flat_selector.py +40 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_singletomoobj.py +40 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_timerow.py +25 -0
- tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_tomoobj_series.py +96 -0
- 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
- tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py +138 -0
- tomwer/tests/orangecontrib/tomwer/widgets/other/tests/test_pythonscript.py +31 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_axis.py +199 -0
- tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_cast_volumeow.py +58 -0
- 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
- tomwer/tests/orangecontrib/tomwer/widgets/tests/test_darkref.py +225 -0
- 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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import numpy
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from nxtomo.application.nxtomo import NXtomo
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* 256.0
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)
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if x_positions_m is None:
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x_positions_m = [None] * len(z_positions_m)
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if shifts is None:
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shifts = [None] * len(z_positions_m)
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z_rois = [None] * len(z_positions_m)
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scans = []
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for i_frame, (z_pos, x_pos, z_roi, shift) in enumerate(
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zip(z_positions_m, x_positions_m, z_rois, shifts)
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nx_tomo = NXtomo()
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if isinstance(pixel_size, (tuple, list)):
|
56
|
+
y_pix_size, x_pix_size = pixel_size
|
57
|
+
else:
|
58
|
+
y_pix_size, x_pix_size = pixel_size, pixel_size
|
59
|
+
nx_tomo.instrument.detector.x_pixel_size = x_pix_size
|
60
|
+
nx_tomo.instrument.detector.y_pixel_size = y_pix_size
|
61
|
+
nx_tomo.instrument.detector.distance = 2.3
|
62
|
+
nx_tomo.energy = 19.2
|
63
|
+
nx_tomo.instrument.detector.transformations.add_transformation(
|
64
|
+
DetYFlipTransformation(flip=flip_ud)
|
65
|
+
)
|
66
|
+
nx_tomo.instrument.detector.transformations.add_transformation(
|
67
|
+
DetZFlipTransformation(flip=flip_lr)
|
68
|
+
)
|
69
|
+
|
70
|
+
if shift is not None:
|
71
|
+
sub_frame = shift_scipy(
|
72
|
+
input=frame.copy(), shift=shift, order=1, mode="constant"
|
73
|
+
)[:final_frame_width]
|
74
|
+
else:
|
75
|
+
sub_frame = frame
|
76
|
+
if z_roi is not None:
|
77
|
+
roi_start, roi_end = z_roi
|
78
|
+
sub_frame = sub_frame[roi_start:roi_end]
|
79
|
+
else:
|
80
|
+
sub_frame = sub_frame
|
81
|
+
if flip_lr:
|
82
|
+
sub_frame = numpy.fliplr(sub_frame)
|
83
|
+
if flip_ud:
|
84
|
+
sub_frame = numpy.flipud(sub_frame)
|
85
|
+
nx_tomo.instrument.detector.data = numpy.asarray([sub_frame] * n_proj)
|
86
|
+
|
87
|
+
file_path = os.path.join(output_dir, f"nxtomo_{i_frame}.nx")
|
88
|
+
entry = f"entry000{i_frame}"
|
89
|
+
nx_tomo.save(file_path=file_path, data_path=entry)
|
90
|
+
scans.append(NXtomoScan(scan=file_path, entry=entry))
|
91
|
+
|
92
|
+
return scans
|
@@ -0,0 +1,14 @@
|
|
1
|
+
def concatenate_dict(dict_1, dict_2) -> dict:
|
2
|
+
"""update dict which has dict as values. And we want concatenate those values to"""
|
3
|
+
res = dict_1.copy()
|
4
|
+
for key in dict_2:
|
5
|
+
if key in dict_1:
|
6
|
+
if key in [f"axis_{axis}_params" for axis in (0, 1, 2)]:
|
7
|
+
res[key] = ";".join((dict_1[key], dict_2[key]))
|
8
|
+
elif isinstance(dict_1[key], dict):
|
9
|
+
res[key] = concatenate_dict(dict_1=dict_1[key], dict_2=dict_2[key])
|
10
|
+
else:
|
11
|
+
res[key].update(dict_2[key])
|
12
|
+
else:
|
13
|
+
res[key] = dict_2[key]
|
14
|
+
return res
|
@@ -1,21 +1,15 @@
|
|
1
1
|
"""widgets to perform a z-sttiching in pre processing (from projections) or post processing (from reconstructed volumes)"""
|
2
2
|
|
3
|
-
|
4
|
-
|
5
|
-
__date__ = "20/01/2023"
|
3
|
+
from __future__ import annotations
|
4
|
+
|
6
5
|
|
7
6
|
import logging
|
8
|
-
from typing import Union
|
9
7
|
|
10
8
|
from nabu.stitching import config as _nabu_stitching_config
|
11
9
|
from nabu.stitching.config import StitchingType
|
12
10
|
from nabu.stitching.overlap import OverlapStitchingStrategy
|
13
11
|
from nabu.stitching.utils import ShiftAlgorithm as _NabuShiftAlgorithm
|
14
12
|
from silx.gui import qt
|
15
|
-
from tomoscan.serie import Serie
|
16
|
-
|
17
|
-
from tomwer.core.tomwer_object import TomwerObject
|
18
|
-
from tomwer.gui.stitching.stitching_preview import PreviewStitchingPlot
|
19
13
|
|
20
14
|
_logger = logging.getLogger(__name__)
|
21
15
|
|
@@ -79,7 +73,7 @@ class Axis_N_Params(qt.QGroupBox):
|
|
79
73
|
|
80
74
|
class AutoRefineWidget(qt.QWidget):
|
81
75
|
"""
|
82
|
-
widget grouping information not specific to objects (output file,
|
76
|
+
widget grouping information not specific to objects (output file, stitching strategy...)
|
83
77
|
"""
|
84
78
|
|
85
79
|
def __init__(self, parent=None):
|
@@ -145,7 +139,7 @@ class AutoRefineWidget(qt.QWidget):
|
|
145
139
|
self._preProcGroup.setVisible(mode is StitchingType.Z_PREPROC)
|
146
140
|
self._postProcGroup.setVisible(mode is StitchingType.Z_POSTPROC)
|
147
141
|
|
148
|
-
def getSliceForPreview(self) ->
|
142
|
+
def getSliceForPreview(self) -> int | str:
|
149
143
|
slice = self._sliceForPreview.text()
|
150
144
|
try:
|
151
145
|
return int(slice)
|
@@ -197,6 +191,7 @@ class _SliceGetter(qt.QLineEdit):
|
|
197
191
|
|
198
192
|
class RefineEstimationCtrlWidget(qt.QWidget):
|
199
193
|
sigSlicePreviewChanged = qt.Signal(str)
|
194
|
+
"""emit when the slice preview has changed"""
|
200
195
|
|
201
196
|
def __init__(self, parent=None) -> None:
|
202
197
|
super().__init__(parent)
|
@@ -222,26 +217,3 @@ class RefineEstimationCtrlWidget(qt.QWidget):
|
|
222
217
|
|
223
218
|
def setSliceForPreview(self, slice: str):
|
224
219
|
self._previewedSliceQLE.setText(str(slice))
|
225
|
-
|
226
|
-
|
227
|
-
class RefineEstimationWidget(qt.QMainWindow):
|
228
|
-
def __init__(self, parent=None) -> None:
|
229
|
-
super().__init__(parent)
|
230
|
-
# central window
|
231
|
-
self._preview = PreviewStitchingPlot(parent=self)
|
232
|
-
self.setCentralWidget(self._preview)
|
233
|
-
# controls
|
234
|
-
self._controlWidget = RefineEstimationCtrlWidget(parent=self)
|
235
|
-
self._controlDockWidget = qt.QDockWidget(self)
|
236
|
-
self._controlDockWidget.setWidget(self._controlWidget)
|
237
|
-
self._controlDockWidget.setFeatures(qt.QDockWidget.DockWidgetMovable)
|
238
|
-
self.addDockWidget(qt.Qt.RightDockWidgetArea, self._controlDockWidget)
|
239
|
-
|
240
|
-
def addTomoObj(self, tomo_obj: TomwerObject):
|
241
|
-
pass
|
242
|
-
|
243
|
-
def setSerie(self, serie: Serie):
|
244
|
-
pass
|
245
|
-
|
246
|
-
def setStitchingType(self, stitching_type: StitchingType):
|
247
|
-
pass
|
@@ -0,0 +1,35 @@
|
|
1
|
+
from nabu.stitching.utils import ShiftAlgorithm as _NabuShiftAlgorithm
|
2
|
+
from silx.gui import qt
|
3
|
+
from silx.gui.utils.testutils import TestCaseQt
|
4
|
+
|
5
|
+
from tomwer.gui.stitching.z_stitching.fineestimation import Axis_N_Params
|
6
|
+
|
7
|
+
|
8
|
+
class TestAxis_N_Params(TestCaseQt):
|
9
|
+
"""
|
10
|
+
Test definition of an axis shift research parameters
|
11
|
+
"""
|
12
|
+
|
13
|
+
def setUp(self):
|
14
|
+
super().setUp()
|
15
|
+
self._widget = Axis_N_Params("axis n", None)
|
16
|
+
|
17
|
+
def tearDown(self):
|
18
|
+
self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
|
19
|
+
self._widget.close()
|
20
|
+
self._widget = None
|
21
|
+
while self.qapp.hasPendingEvents():
|
22
|
+
self.qapp.processEvents()
|
23
|
+
|
24
|
+
def test(self):
|
25
|
+
self._widget.show()
|
26
|
+
assert self._widget.getCurrentMethod() == _NabuShiftAlgorithm.NONE
|
27
|
+
opts1 = self._widget.getOptsLine()
|
28
|
+
assert opts1 == "img_reg_method=None"
|
29
|
+
self._widget.setCurrentMethod(_NabuShiftAlgorithm.NABU_FFT)
|
30
|
+
opts2 = self._widget.getOptsLine()
|
31
|
+
assert opts2 == "img_reg_method=nabu-fft"
|
32
|
+
self._widget.setOptsLine(opts1)
|
33
|
+
assert self._widget.getOptsLine() == opts1
|
34
|
+
self._widget.setOptsLine(opts2)
|
35
|
+
assert self._widget.getOptsLine() == opts2
|
@@ -0,0 +1,215 @@
|
|
1
|
+
import os
|
2
|
+
import shutil
|
3
|
+
import tempfile
|
4
|
+
|
5
|
+
from silx.gui import qt
|
6
|
+
from silx.gui.utils.testutils import TestCaseQt
|
7
|
+
|
8
|
+
from tomwer.core.process.stitching.metadataholder import StitchingMetadata
|
9
|
+
from tomwer.gui.stitching.metadataholder import QStitchingMetadata
|
10
|
+
from tomwer.gui.stitching.tests.utils import create_scans_z_series
|
11
|
+
from tomwer.gui.stitching.config.tomoobjdetails import TomoObjectPositionInfos
|
12
|
+
from tomwer.gui.stitching.axisorderedlist import AxisOrderedTomoObjsModel
|
13
|
+
|
14
|
+
|
15
|
+
class TestTomoObjectPositionInfos(TestCaseQt):
|
16
|
+
"""
|
17
|
+
Test edition of the tomo object position information
|
18
|
+
"""
|
19
|
+
|
20
|
+
def setUp(self):
|
21
|
+
super().setUp()
|
22
|
+
self._tmp_path = tempfile.mkdtemp()
|
23
|
+
self._y_pixel_size = 0.002
|
24
|
+
self._x_pixel_size = 0.001
|
25
|
+
self.scans = create_scans_z_series(
|
26
|
+
self._tmp_path,
|
27
|
+
z_positions_m=(0.200, 0.205, 0.210),
|
28
|
+
x_positions_m=(0.0, 0.0, None),
|
29
|
+
pixel_size=(self._y_pixel_size, self._x_pixel_size),
|
30
|
+
raw_frame_width=100,
|
31
|
+
)
|
32
|
+
self.scan_0_metadata = QStitchingMetadata(tomo_obj=self.scans[0])
|
33
|
+
assert self.scan_0_metadata.get_raw_position_m(axis=0) == 0.20
|
34
|
+
assert self.scan_0_metadata.get_raw_position_m(axis=2) == 0.0
|
35
|
+
self.scan_2_metadata = QStitchingMetadata(tomo_obj=self.scans[2])
|
36
|
+
assert self.scan_2_metadata.get_raw_position_m(axis=0) == 0.21
|
37
|
+
self._widget = TomoObjectPositionInfos()
|
38
|
+
|
39
|
+
def tearDown(self):
|
40
|
+
self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
|
41
|
+
self._widget.close()
|
42
|
+
self._widget = None
|
43
|
+
while self.qapp.hasPendingEvents():
|
44
|
+
self.qapp.processEvents()
|
45
|
+
shutil.rmtree(self._tmp_path)
|
46
|
+
|
47
|
+
def testEdition(self):
|
48
|
+
# test QStitchingMetadata are correctly read
|
49
|
+
self._widget.show()
|
50
|
+
self._widget.setStitchingMetadata(self.scan_0_metadata)
|
51
|
+
self.qapp.processEvents()
|
52
|
+
assert self._widget._axis_0_pos.get_final_px_position() == int(0.20 / 0.002)
|
53
|
+
assert self._widget._axis_2_pos.get_final_px_position() == 0
|
54
|
+
self._widget.setStitchingMetadata(self.scan_2_metadata)
|
55
|
+
while self.qapp.hasPendingEvents():
|
56
|
+
self.qapp.processEvents()
|
57
|
+
assert self._widget._axis_0_pos.get_final_px_position() == int(0.21 / 0.002)
|
58
|
+
assert self._widget._axis_2_pos.get_final_px_position() is None
|
59
|
+
# test editing some parameters from the GUI. Make sure GUI is updated as the underlying metadata object
|
60
|
+
self._widget._axis_0_pos._overrideMetricPositionCB.setChecked(True)
|
61
|
+
self._widget._axis_0_pos.setRawMetricPosition(
|
62
|
+
position_m=0.4, displayed_unit="nm"
|
63
|
+
)
|
64
|
+
while self.qapp.hasPendingEvents():
|
65
|
+
self.qapp.processEvents()
|
66
|
+
assert self._widget._axis_0_pos.get_final_px_position() == int(
|
67
|
+
0.4 * 10e-6 / 0.002
|
68
|
+
)
|
69
|
+
self._widget._axis_0_pos._overridePixelPositionCB.setChecked(True)
|
70
|
+
self._widget._axis_0_pos.setOverrridePxPosition(position_px=120)
|
71
|
+
while self.qapp.hasPendingEvents():
|
72
|
+
self.qapp.processEvents()
|
73
|
+
assert self._widget._axis_0_pos.get_final_px_position() == int(120)
|
74
|
+
assert self.scan_2_metadata.get_abs_position_px(axis=0) == int(120)
|
75
|
+
|
76
|
+
|
77
|
+
class TestAxisOrderedTomoObjsModel(TestCaseQt):
|
78
|
+
"""
|
79
|
+
test the behavior of the z ordered model used for stitching
|
80
|
+
"""
|
81
|
+
|
82
|
+
def setUp(self):
|
83
|
+
super().setUp()
|
84
|
+
self._tmp_path = tempfile.mkdtemp()
|
85
|
+
self.scans_with_pos_and_pixel_size = create_scans_z_series(
|
86
|
+
os.path.join(self._tmp_path, "case1"),
|
87
|
+
z_positions_m=(0.200, 0.205, 0.210),
|
88
|
+
pixel_size=0.001,
|
89
|
+
raw_frame_width=100,
|
90
|
+
)
|
91
|
+
self.scans_with_pixel_size = create_scans_z_series(
|
92
|
+
os.path.join(self._tmp_path, "case2"),
|
93
|
+
z_positions_m=(None, None, None),
|
94
|
+
pixel_size=0.001,
|
95
|
+
raw_frame_width=100,
|
96
|
+
)
|
97
|
+
self.scans_without_metadata = create_scans_z_series(
|
98
|
+
os.path.join(self._tmp_path, "case3"),
|
99
|
+
z_positions_m=(None, None, None),
|
100
|
+
pixel_size=None,
|
101
|
+
raw_frame_width=100,
|
102
|
+
)
|
103
|
+
self._widget = qt.QTableView()
|
104
|
+
self._widget.setModel(AxisOrderedTomoObjsModel(parent=self._widget, axis=0))
|
105
|
+
|
106
|
+
def tearDown(self):
|
107
|
+
self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
|
108
|
+
self._widget.close()
|
109
|
+
self._widget = None
|
110
|
+
while self.qapp.hasPendingEvents():
|
111
|
+
self.qapp.processEvents()
|
112
|
+
shutil.rmtree(self._tmp_path)
|
113
|
+
|
114
|
+
def testWithMetadata(self):
|
115
|
+
"""
|
116
|
+
make sure z ordering works in the best case scenario
|
117
|
+
"""
|
118
|
+
first_expected_scan = (
|
119
|
+
self.scans_with_pos_and_pixel_size[2].get_identifier().short_description()
|
120
|
+
)
|
121
|
+
# try giving it ordered
|
122
|
+
for scan in self.scans_with_pos_and_pixel_size[::-1]:
|
123
|
+
self._widget.model().addTomoObj(scan)
|
124
|
+
assert (
|
125
|
+
self._widget.model().data(
|
126
|
+
self._widget.model().index(0, 1), qt.Qt.DisplayRole
|
127
|
+
)
|
128
|
+
== first_expected_scan
|
129
|
+
)
|
130
|
+
self._widget.model().clearTomoObjs()
|
131
|
+
# try giving it ordered (but inverted)
|
132
|
+
for scan in self.scans_with_pos_and_pixel_size:
|
133
|
+
self._widget.model().addTomoObj(scan)
|
134
|
+
assert (
|
135
|
+
self._widget.model().data(
|
136
|
+
self._widget.model().index(0, 1), qt.Qt.DisplayRole
|
137
|
+
)
|
138
|
+
== first_expected_scan
|
139
|
+
)
|
140
|
+
|
141
|
+
def testWithPixelSizeOnly(self):
|
142
|
+
"""
|
143
|
+
make sure z ordering works when we are only aware about pixel size
|
144
|
+
"""
|
145
|
+
for scan in self.scans_with_pixel_size[::-1]:
|
146
|
+
self._widget.model().addTomoObj(scan)
|
147
|
+
|
148
|
+
# try adding some metadata to object
|
149
|
+
scans = self._widget.model()._objs
|
150
|
+
scans = self._widget.model()._objs
|
151
|
+
scans[0].stitching_metadata = StitchingMetadata(tomo_obj=scans[0])
|
152
|
+
scans[1].stitching_metadata = QStitchingMetadata(tomo_obj=scans[1])
|
153
|
+
|
154
|
+
scans[0].stitching_metadata._pos_as_m = (0.1, 1, 2)
|
155
|
+
scans[1].stitching_metadata._pos_as_m = (-0.03, 1, 2)
|
156
|
+
scans[2].stitching_metadata._pos_as_m = (0.23, 1, 2)
|
157
|
+
|
158
|
+
self._widget.model().reorder_objs()
|
159
|
+
self._widget.model().layoutChanged.emit()
|
160
|
+
|
161
|
+
assert (
|
162
|
+
self._widget.model().data(
|
163
|
+
self._widget.model().index(0, 1), qt.Qt.DisplayRole
|
164
|
+
)
|
165
|
+
== scans[2].get_identifier().short_description()
|
166
|
+
)
|
167
|
+
assert (
|
168
|
+
self._widget.model().data(
|
169
|
+
self._widget.model().index(1, 1), qt.Qt.DisplayRole
|
170
|
+
)
|
171
|
+
== scans[0].get_identifier().short_description()
|
172
|
+
)
|
173
|
+
assert (
|
174
|
+
self._widget.model().data(
|
175
|
+
self._widget.model().index(2, 1), qt.Qt.DisplayRole
|
176
|
+
)
|
177
|
+
== scans[1].get_identifier().short_description()
|
178
|
+
)
|
179
|
+
|
180
|
+
def testWithoutMetadata(self):
|
181
|
+
"""
|
182
|
+
make sure tomo obj are still displayed even if there is no metadata at all
|
183
|
+
"""
|
184
|
+
for scan in self.scans_without_metadata[::-1]:
|
185
|
+
self._widget.model().addTomoObj(scan)
|
186
|
+
# try adding some metadata to object
|
187
|
+
scans = self._widget.model()._objs
|
188
|
+
scans[0].stitching_metadata = StitchingMetadata(tomo_obj=scans[0])
|
189
|
+
scans[1].stitching_metadata = QStitchingMetadata(tomo_obj=scans[1])
|
190
|
+
|
191
|
+
scans[0].stitching_metadata._pos_as_px = (12, None, 2)
|
192
|
+
scans[1].stitching_metadata._pos_as_px = (-12, None, None)
|
193
|
+
scans[2].stitching_metadata._pos_as_px = (9999, None, None)
|
194
|
+
|
195
|
+
self._widget.model().reorder_objs()
|
196
|
+
self._widget.model().layoutChanged.emit()
|
197
|
+
|
198
|
+
assert (
|
199
|
+
self._widget.model().data(
|
200
|
+
self._widget.model().index(0, 1), qt.Qt.DisplayRole
|
201
|
+
)
|
202
|
+
== scans[2].get_identifier().short_description()
|
203
|
+
)
|
204
|
+
assert (
|
205
|
+
self._widget.model().data(
|
206
|
+
self._widget.model().index(1, 1), qt.Qt.DisplayRole
|
207
|
+
)
|
208
|
+
== scans[0].get_identifier().short_description()
|
209
|
+
)
|
210
|
+
assert (
|
211
|
+
self._widget.model().data(
|
212
|
+
self._widget.model().index(2, 1), qt.Qt.DisplayRole
|
213
|
+
)
|
214
|
+
== scans[1].get_identifier().short_description()
|
215
|
+
)
|
@@ -0,0 +1,51 @@
|
|
1
|
+
import os
|
2
|
+
import shutil
|
3
|
+
import tempfile
|
4
|
+
|
5
|
+
from silx.gui import qt
|
6
|
+
from silx.gui.utils.testutils import TestCaseQt
|
7
|
+
|
8
|
+
from tomwer.gui.stitching.tests.utils import create_scans_z_series
|
9
|
+
from tomwer.gui.stitching.StitchingWindow import ZStitchingWindow
|
10
|
+
|
11
|
+
|
12
|
+
class TestZStichingWindow(TestCaseQt):
|
13
|
+
"""
|
14
|
+
Test high level z stitching definition
|
15
|
+
"""
|
16
|
+
|
17
|
+
def setUp(self):
|
18
|
+
super().setUp()
|
19
|
+
self._tmp_path = tempfile.mkdtemp()
|
20
|
+
self.scans = create_scans_z_series(
|
21
|
+
os.path.join(self._tmp_path, "case1"),
|
22
|
+
z_positions_m=(0.200, 0.205, 0.210),
|
23
|
+
pixel_size=0.001,
|
24
|
+
raw_frame_width=100,
|
25
|
+
)
|
26
|
+
|
27
|
+
self._widget = ZStitchingWindow()
|
28
|
+
|
29
|
+
def tearDown(self):
|
30
|
+
self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
|
31
|
+
self._widget.close()
|
32
|
+
self._widget = None
|
33
|
+
while self.qapp.hasPendingEvents():
|
34
|
+
self.qapp.processEvents()
|
35
|
+
shutil.rmtree(self._tmp_path)
|
36
|
+
|
37
|
+
@staticmethod
|
38
|
+
def checkNbReceivers(scan, nb_receivers):
|
39
|
+
return (
|
40
|
+
scan.stitching_metadata.receivers(scan.stitching_metadata.sigChanged)
|
41
|
+
== nb_receivers
|
42
|
+
)
|
43
|
+
|
44
|
+
def test(self):
|
45
|
+
self._widget.show()
|
46
|
+
# fill the widget with scans
|
47
|
+
|
48
|
+
scan_0, scan_1, scan_2 = self.scans
|
49
|
+
for scan in self.scans:
|
50
|
+
self._widget.addTomoObj(scan)
|
51
|
+
# note: add the sigChanged to the z ordered list 'update z' slot
|
File without changes
|
@@ -0,0 +1,43 @@
|
|
1
|
+
import pytest
|
2
|
+
import numpy
|
3
|
+
|
4
|
+
from tomwer.gui.reconstruction.axis.AxisSettingsWidget import AxisSettingsTabWidget
|
5
|
+
from tomwer.synctools.axis import QAxisRP
|
6
|
+
from tomwer.tests.utils import skip_gui_test
|
7
|
+
from tomwer.tests.conftest import qtapp # noqa F401
|
8
|
+
|
9
|
+
|
10
|
+
@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
|
11
|
+
def test_get_nabu_cor_opts(qtapp): # noqa F811
|
12
|
+
axis_params = QAxisRP()
|
13
|
+
widget = AxisSettingsTabWidget(recons_params=axis_params)
|
14
|
+
assert axis_params.get_nabu_cor_options_as_dict() == {
|
15
|
+
"side": "right",
|
16
|
+
"radio_angles": (0.0, numpy.pi),
|
17
|
+
"slice_idx": "middle",
|
18
|
+
}
|
19
|
+
widget._optionsWidget._corOpts.setText("low_pass=2.0")
|
20
|
+
widget._optionsWidget._corOpts.editingFinished.emit()
|
21
|
+
assert axis_params.get_nabu_cor_options_as_dict() == {
|
22
|
+
"side": "right",
|
23
|
+
"radio_angles": (0.0, numpy.pi),
|
24
|
+
"slice_idx": "middle",
|
25
|
+
"low_pass": 2.0,
|
26
|
+
}
|
27
|
+
widget._optionsWidget._corOpts.setText("low_pass=2 ; high_pass=10")
|
28
|
+
widget._optionsWidget._corOpts.editingFinished.emit()
|
29
|
+
assert axis_params.get_nabu_cor_options_as_dict() == {
|
30
|
+
"side": "right",
|
31
|
+
"radio_angles": (0.0, numpy.pi),
|
32
|
+
"slice_idx": "middle",
|
33
|
+
"low_pass": 2.0,
|
34
|
+
"high_pass": 10.0,
|
35
|
+
}
|
36
|
+
widget._calculationWidget.setEstimatedCorValue("left")
|
37
|
+
assert axis_params.get_nabu_cor_options_as_dict() == {
|
38
|
+
"side": "left",
|
39
|
+
"radio_angles": (0.0, numpy.pi),
|
40
|
+
"slice_idx": "middle",
|
41
|
+
"low_pass": 2.0,
|
42
|
+
"high_pass": 10.0,
|
43
|
+
}
|
@@ -0,0 +1,44 @@
|
|
1
|
+
from __future__ import annotations
|
2
|
+
|
3
|
+
import sys
|
4
|
+
from silx.gui import qt
|
5
|
+
|
6
|
+
|
7
|
+
class RangeWidget(qt.QWidget):
|
8
|
+
"""widget to select a range of float"""
|
9
|
+
|
10
|
+
sigChanged = qt.Signal()
|
11
|
+
|
12
|
+
def __init__(self, parent=None):
|
13
|
+
super().__init__(parent)
|
14
|
+
self.setLayout(qt.QHBoxLayout())
|
15
|
+
|
16
|
+
# start
|
17
|
+
self.layout().addWidget(qt.QLabel("from"))
|
18
|
+
self._startQLE = qt.QDoubleSpinBox(self)
|
19
|
+
self.layout().addWidget(self._startQLE)
|
20
|
+
self._startQLE.setRange(sys.float_info.min, sys.float_info.max)
|
21
|
+
|
22
|
+
# stop
|
23
|
+
self.layout().addWidget(qt.QLabel("to"))
|
24
|
+
self._stopQLE = qt.QDoubleSpinBox(self)
|
25
|
+
self.layout().addWidget(self._stopQLE)
|
26
|
+
self._stopQLE.setRange(sys.float_info.min, sys.float_info.max)
|
27
|
+
|
28
|
+
# connect signal / slot
|
29
|
+
self._startQLE.editingFinished.connect(self.sigChanged)
|
30
|
+
self._stopQLE.editingFinished.connect(self.sigChanged)
|
31
|
+
|
32
|
+
def getRange(self) -> tuple[float]:
|
33
|
+
return (
|
34
|
+
self._startQLE.value(),
|
35
|
+
self._stopQLE.value(),
|
36
|
+
)
|
37
|
+
|
38
|
+
def setRange(self, start: float, stop: float) -> None:
|
39
|
+
self._startQLE.setValue(float(start))
|
40
|
+
self._stopQLE.setValue(float(stop))
|
41
|
+
|
42
|
+
def setSuffix(self, suffix: str):
|
43
|
+
self._startQLE.setSuffix(suffix)
|
44
|
+
self._stopQLE.setSuffix(suffix)
|
tomwer/gui/utils/buttons.py
CHANGED
@@ -2,9 +2,10 @@
|
|
2
2
|
Button of general usage.
|
3
3
|
"""
|
4
4
|
|
5
|
+
from __future__ import annotations
|
6
|
+
|
5
7
|
import numpy
|
6
8
|
import logging
|
7
|
-
from typing import Optional, Union
|
8
9
|
from silx.gui import qt
|
9
10
|
from silx.gui.plot.tools.roi import RegionOfInterestManager
|
10
11
|
from silx.gui.plot.items.roi import LineROI
|
@@ -102,7 +103,7 @@ class TapeMeasureToolButton(PlotToolButton):
|
|
102
103
|
value, unit = MetricSystem.cast_metric_to_best_unit(distance_m)
|
103
104
|
self._updateText(f"{distance_px :.1f}px ({value:.2f}{unit})")
|
104
105
|
|
105
|
-
def setPixelSize(self, pixel_size_m:
|
106
|
+
def setPixelSize(self, pixel_size_m: tuple | float | None):
|
106
107
|
if isinstance(pixel_size_m, (tuple, list)):
|
107
108
|
assert (
|
108
109
|
len(pixel_size_m) == 2
|
@@ -128,7 +129,7 @@ class TapeMeasureToolButton(PlotToolButton):
|
|
128
129
|
def setPlot(self, plot):
|
129
130
|
return super().setPlot(plot)
|
130
131
|
|
131
|
-
def setPixelSize(self, pixel_size_m:
|
132
|
+
def setPixelSize(self, pixel_size_m: tuple | float | None):
|
132
133
|
self._pixel_sixel_m = pixel_size_m
|
133
134
|
|
134
135
|
def _callback(self, toggled):
|
tomwer/gui/utils/completer.py
CHANGED
@@ -1,37 +1,6 @@
|
|
1
|
-
# coding: utf-8
|
2
|
-
# /*##########################################################################
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
|
5
|
-
#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
-
# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
|
26
1
|
"""module defining dedicated completer"""
|
27
2
|
|
28
|
-
|
29
|
-
__authors__ = ["H. Payno"]
|
30
|
-
__license__ = "MIT"
|
31
|
-
__date__ = "23/03/2022"
|
32
|
-
|
33
|
-
|
34
|
-
from typing import Optional
|
3
|
+
from __future__ import annotations
|
35
4
|
|
36
5
|
from silx.gui import qt
|
37
6
|
|
@@ -103,7 +72,7 @@ class _TextCompleterWidget(qt.QWidget):
|
|
103
72
|
|
104
73
|
class UrlCompleterDialog(qt.QDialog):
|
105
74
|
def __init__(
|
106
|
-
self, urls: tuple, parent=None, current_url:
|
75
|
+
self, urls: tuple, parent=None, current_url: str | None = None
|
107
76
|
) -> None:
|
108
77
|
super().__init__(parent)
|
109
78
|
self._urls = urls
|