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
@@ -1,60 +0,0 @@
|
|
1
|
-
# coding: utf-8
|
2
|
-
# /*##########################################################################
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
|
5
|
-
#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
-
# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
|
26
|
-
__authors__ = ["H. Payno"]
|
27
|
-
__license__ = "MIT"
|
28
|
-
__date__ = "24/11/2021"
|
29
|
-
|
30
|
-
|
31
|
-
from tomwer.core.process.reconstruction.darkref.darkrefs import (
|
32
|
-
requires_reduced_dark_and_flat,
|
33
|
-
)
|
34
|
-
from tomwer.core.utils.scanutils import MockEDF, MockNXtomo
|
35
|
-
|
36
|
-
|
37
|
-
def test_quick_run_necessary_edf(tmpdir):
|
38
|
-
"""test the `quick_run_necessary` function for EDFTomoScan"""
|
39
|
-
scan = MockEDF.mockScan(scanID=str(tmpdir), start_dark=True, start_flat=True)
|
40
|
-
assert scan.reduced_darks in (None, {})
|
41
|
-
assert scan.reduced_flats in (None, {})
|
42
|
-
requires_reduced_dark_and_flat(scan=scan)
|
43
|
-
assert len(scan.reduced_darks) == 1
|
44
|
-
assert len(scan.reduced_flats) == 1
|
45
|
-
|
46
|
-
|
47
|
-
def test_quick_run_necessary_hdf5(tmpdir):
|
48
|
-
"""test the `quick_run_necessary` function for NXtomoScan"""
|
49
|
-
scan = MockNXtomo(
|
50
|
-
scan_path=tmpdir,
|
51
|
-
n_proj=20,
|
52
|
-
n_ini_proj=20,
|
53
|
-
dim=10,
|
54
|
-
).scan
|
55
|
-
assert scan.reduced_darks in (None, {})
|
56
|
-
assert scan.reduced_flats in (None, {})
|
57
|
-
computed = requires_reduced_dark_and_flat(scan=scan)
|
58
|
-
assert len(computed) == 2
|
59
|
-
assert len(scan.reduced_darks) == 1
|
60
|
-
assert len(scan.reduced_flats) == 1
|
@@ -1,74 +0,0 @@
|
|
1
|
-
# coding: utf-8
|
2
|
-
# /*##########################################################################
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
|
5
|
-
#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
-
# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
|
26
|
-
__authors__ = ["H. Payno"]
|
27
|
-
__license__ = "MIT"
|
28
|
-
__date__ = "27/02/2021"
|
29
|
-
|
30
|
-
|
31
|
-
import os
|
32
|
-
import shutil
|
33
|
-
import tempfile
|
34
|
-
import unittest
|
35
|
-
|
36
|
-
from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
|
37
|
-
SADeltaBetaParams,
|
38
|
-
SADeltaBetaTask,
|
39
|
-
)
|
40
|
-
from tomwer.core.utils.scanutils import MockNXtomo
|
41
|
-
|
42
|
-
|
43
|
-
class TestSADeltaBetaProcess(unittest.TestCase):
|
44
|
-
"""Test the SAAxisProcess class"""
|
45
|
-
|
46
|
-
def setUp(self) -> None:
|
47
|
-
super().setUp()
|
48
|
-
self.tempdir = tempfile.mkdtemp()
|
49
|
-
dim = 10
|
50
|
-
mock = MockNXtomo(
|
51
|
-
scan_path=self.tempdir, n_proj=10, n_ini_proj=10, scan_range=180, dim=dim
|
52
|
-
)
|
53
|
-
self.scan = mock.scan
|
54
|
-
|
55
|
-
def tearDown(self) -> None:
|
56
|
-
shutil.rmtree(self.tempdir)
|
57
|
-
super().tearDown()
|
58
|
-
|
59
|
-
def test(self):
|
60
|
-
process = SADeltaBetaTask(
|
61
|
-
inputs={
|
62
|
-
"data": self.scan,
|
63
|
-
"sa_delta_beta_params": SADeltaBetaParams().to_dict(),
|
64
|
-
"serialize_output_data": False,
|
65
|
-
}
|
66
|
-
)
|
67
|
-
|
68
|
-
default_sadelta_beta_params = SADeltaBetaParams()
|
69
|
-
default_sadelta_beta_params.output_dir = os.path.join(
|
70
|
-
self.tempdir, "output_dir"
|
71
|
-
)
|
72
|
-
default_sadelta_beta_params.dry_run = True
|
73
|
-
|
74
|
-
process.run()
|
@@ -1,309 +0,0 @@
|
|
1
|
-
# coding: utf-8
|
2
|
-
# /*##########################################################################
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
|
5
|
-
#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
-
# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
|
26
|
-
__authors__ = ["H. Payno"]
|
27
|
-
__license__ = "MIT"
|
28
|
-
__date__ = "05/04/2019"
|
29
|
-
|
30
|
-
|
31
|
-
import os
|
32
|
-
import shutil
|
33
|
-
import tempfile
|
34
|
-
import unittest
|
35
|
-
|
36
|
-
import h5py
|
37
|
-
from tomoscan.io import get_swmr_mode
|
38
|
-
import numpy
|
39
|
-
from silx.io.utils import h5py_read_dataset
|
40
|
-
|
41
|
-
from tomwer.core.process.reconstruction.axis.mode import AxisMode
|
42
|
-
from tomwer.core.process.reconstruction.axis.params import AxisRP
|
43
|
-
from tomwer.core.process.task import Task
|
44
|
-
from tomwer.core.scan.edfscan import EDFTomoScan
|
45
|
-
from tomwer.core.scan.scanbase import TomwerScanBase
|
46
|
-
from tomwer.core.utils.scanutils import MockEDF, MockNXtomo
|
47
|
-
from tomwer.tests.datasets import TomwerCIDatasets
|
48
|
-
|
49
|
-
from ..reconstruction.axis.axis import AxisTask
|
50
|
-
|
51
|
-
|
52
|
-
class TestAxisIO(unittest.TestCase):
|
53
|
-
"""Test inputs and outputs types of the handler functions"""
|
54
|
-
|
55
|
-
@staticmethod
|
56
|
-
def _random_calc(scan):
|
57
|
-
return numpy.random.random()
|
58
|
-
|
59
|
-
def setUp(self):
|
60
|
-
self.scan_folder = tempfile.mkdtemp()
|
61
|
-
|
62
|
-
self.scan = MockEDF.mockScan(
|
63
|
-
scanID=self.scan_folder, nRadio=10, nRecons=1, nPagRecons=4, dim=10
|
64
|
-
)
|
65
|
-
self.recons_params = AxisRP()
|
66
|
-
|
67
|
-
# set the axis url to be used
|
68
|
-
projections = self.scan.projections
|
69
|
-
urls = list(projections.values())
|
70
|
-
self.scan.axis_params = AxisRP()
|
71
|
-
self.scan.axis_params.axis_url_1 = urls[0]
|
72
|
-
self.scan.axis_params.axis_url_2 = urls[1]
|
73
|
-
|
74
|
-
def tearDown(self):
|
75
|
-
shutil.rmtree(self.scan_folder)
|
76
|
-
|
77
|
-
def testInputOutput(self):
|
78
|
-
"""Test that io using TomoBase instance work"""
|
79
|
-
for input_type in (dict, TomwerScanBase):
|
80
|
-
for serialize_output_data in (True, False):
|
81
|
-
with self.subTest(
|
82
|
-
serialize_output_data=serialize_output_data,
|
83
|
-
input_type=input_type,
|
84
|
-
):
|
85
|
-
input_obj = self.scan
|
86
|
-
if input_obj is dict:
|
87
|
-
input_obj = input_obj.to_dict()
|
88
|
-
axis_process = AxisTask(
|
89
|
-
inputs={
|
90
|
-
"axis_params": self.recons_params,
|
91
|
-
"data": input_obj,
|
92
|
-
"serialize_output_data": serialize_output_data,
|
93
|
-
}
|
94
|
-
)
|
95
|
-
|
96
|
-
# patch the axis process
|
97
|
-
axis_process._CALCULATIONS_METHODS[AxisMode.centered] = (
|
98
|
-
TestAxisIO._random_calc
|
99
|
-
)
|
100
|
-
|
101
|
-
axis_process.run()
|
102
|
-
out = axis_process.outputs.data
|
103
|
-
if serialize_output_data:
|
104
|
-
self.assertTrue(isinstance(out, dict))
|
105
|
-
else:
|
106
|
-
self.assertTrue(isinstance(out, TomwerScanBase))
|
107
|
-
|
108
|
-
|
109
|
-
class TestAxis(unittest.TestCase):
|
110
|
-
"""Test the axis process"""
|
111
|
-
|
112
|
-
def setUp(self):
|
113
|
-
self.recons_params = AxisRP()
|
114
|
-
self.recons_params.mode = "centered"
|
115
|
-
|
116
|
-
def test_process_saved_edf(self):
|
117
|
-
"""Test that if process is called, the tomwer.h5 file is created
|
118
|
-
and is correctly saving information regarding the center of position
|
119
|
-
"""
|
120
|
-
self.tempdir = tempfile.mkdtemp()
|
121
|
-
mock = MockEDF(scan_path=self.tempdir, n_radio=10, n_ini_radio=10)
|
122
|
-
scan = EDFTomoScan(mock.scan_path)
|
123
|
-
self.recons_params.mode = "centered"
|
124
|
-
axis_process = AxisTask(
|
125
|
-
inputs={
|
126
|
-
"data": scan,
|
127
|
-
"axis_params": self.recons_params,
|
128
|
-
"serialize_output_data": False,
|
129
|
-
}
|
130
|
-
)
|
131
|
-
|
132
|
-
axis_process.run()
|
133
|
-
self.assertTrue(os.path.exists(scan.process_file))
|
134
|
-
|
135
|
-
with h5py.File(scan.process_file, "r", swmr=get_swmr_mode()) as h5f:
|
136
|
-
self.assertTrue("entry" in h5f)
|
137
|
-
self.assertTrue("tomwer_process_0" in h5f["entry"])
|
138
|
-
group_axis = h5f["entry"]["tomwer_process_0"]
|
139
|
-
self.assertTrue("configuration" in group_axis)
|
140
|
-
self.assertTrue("program" in group_axis)
|
141
|
-
self.assertTrue("results" in group_axis)
|
142
|
-
self.assertTrue("center_of_rotation" in group_axis["results"])
|
143
|
-
axis_value = h5py_read_dataset(group_axis["results"]["center_of_rotation"])
|
144
|
-
|
145
|
-
processes = Task.get_processes_frm_type(
|
146
|
-
process_file=scan.process_file, process_type=AxisTask, entry="entry"
|
147
|
-
)
|
148
|
-
self.assertEqual(len(processes), 1)
|
149
|
-
self.assertEqual(processes[0].results["center_of_rotation"], axis_value)
|
150
|
-
|
151
|
-
# make sure the process file can be loaded by an instance of AxisRP
|
152
|
-
new_axis_params = AxisRP()
|
153
|
-
new_axis_params.set_relative_value(-10000)
|
154
|
-
new_axis_params.set_position_frm_par_file(
|
155
|
-
file_path=scan.process_file, entry=None
|
156
|
-
)
|
157
|
-
self.assertEqual(
|
158
|
-
new_axis_params.relative_cor_value, scan.axis_params.relative_cor_value
|
159
|
-
)
|
160
|
-
|
161
|
-
def test_process_saved_hdf5(self):
|
162
|
-
"""Test that if process is called, the tomwer.h5 file is created
|
163
|
-
and is correctly saving information regarding the center of position
|
164
|
-
"""
|
165
|
-
self.tempdir = tempfile.mkdtemp()
|
166
|
-
dim = 10
|
167
|
-
mock = MockNXtomo(
|
168
|
-
scan_path=self.tempdir, n_proj=10, n_ini_proj=10, scan_range=180, dim=dim
|
169
|
-
)
|
170
|
-
mock.add_alignment_radio(index=10, angle=90)
|
171
|
-
mock.add_alignment_radio(index=10, angle=0)
|
172
|
-
scan = mock.scan
|
173
|
-
self.recons_params.mode = "centered"
|
174
|
-
|
175
|
-
# check data url take
|
176
|
-
axis_process = AxisTask(
|
177
|
-
inputs={
|
178
|
-
"data": scan,
|
179
|
-
"axis_params": self.recons_params,
|
180
|
-
"serialize_output_data": False,
|
181
|
-
}
|
182
|
-
)
|
183
|
-
axis_process.run()
|
184
|
-
# make sure center of position has been computed
|
185
|
-
self.assertTrue(os.path.exists(scan.process_file))
|
186
|
-
|
187
|
-
with h5py.File(scan.process_file, "r", swmr=get_swmr_mode()) as h5f:
|
188
|
-
self.assertTrue("entry" in h5f)
|
189
|
-
self.assertTrue("tomwer_process_0" in h5f["entry"])
|
190
|
-
group_axis = h5f["entry"]["tomwer_process_0"]
|
191
|
-
self.assertTrue("configuration" in group_axis)
|
192
|
-
self.assertTrue("program" in group_axis)
|
193
|
-
self.assertTrue("results" in group_axis)
|
194
|
-
self.assertTrue("center_of_rotation" in group_axis["results"])
|
195
|
-
axis_value = h5py_read_dataset(group_axis["results"]["center_of_rotation"])
|
196
|
-
self.assertTrue(-dim / 2 <= axis_value <= dim / 2)
|
197
|
-
processes = Task.get_processes_frm_type(
|
198
|
-
process_file=scan.process_file, process_type=AxisTask
|
199
|
-
)
|
200
|
-
self.assertEqual(len(processes), 1)
|
201
|
-
self.assertEqual(processes[0].results["center_of_rotation"], axis_value)
|
202
|
-
|
203
|
-
# make sure the process file can be loaded by an instance of AxisRP
|
204
|
-
new_axis_params = AxisRP()
|
205
|
-
new_axis_params.set_relative_value(-10000)
|
206
|
-
new_axis_params.set_position_frm_par_file(file_path=scan.process_file)
|
207
|
-
self.assertEqual(
|
208
|
-
new_axis_params.relative_cor_value, scan.axis_params.relative_cor_value
|
209
|
-
)
|
210
|
-
|
211
|
-
|
212
|
-
class TestAxisRP(unittest.TestCase):
|
213
|
-
"""Test the class used for AxisProcess configuration"""
|
214
|
-
|
215
|
-
def setUp(self):
|
216
|
-
self.axis_rp = AxisRP()
|
217
|
-
self.tmp_folder = tempfile.mkdtemp()
|
218
|
-
|
219
|
-
def tearDown(self):
|
220
|
-
shutil.rmtree(self.tmp_folder)
|
221
|
-
|
222
|
-
def testSetPositionFromParFile(self):
|
223
|
-
"""Test that the position can be managed from a par file"""
|
224
|
-
old_value = self.axis_rp.value_ref_tomwer
|
225
|
-
|
226
|
-
with self.assertRaises(ValueError):
|
227
|
-
self.axis_rp.set_position_frm_par_file("ghost_file.par", force=False)
|
228
|
-
self.assertEqual(self.axis_rp.value_ref_tomwer, old_value)
|
229
|
-
|
230
|
-
existing_empty_file = os.path.join(self.tmp_folder, "par_file.par")
|
231
|
-
with open(existing_empty_file, "w") as _file:
|
232
|
-
_file.write("toto")
|
233
|
-
|
234
|
-
with self.assertRaises(KeyError):
|
235
|
-
self.axis_rp.set_position_frm_par_file(existing_empty_file, force=False)
|
236
|
-
self.assertEqual(self.axis_rp.value_ref_tomwer, old_value)
|
237
|
-
|
238
|
-
valid_par_file = TomwerCIDatasets.get_dataset(
|
239
|
-
"edf_datasets/scan_3_/scan_3_slice.par"
|
240
|
-
)
|
241
|
-
assert os.path.isfile(valid_par_file)
|
242
|
-
self.axis_rp.set_position_frm_par_file(valid_par_file, force=False)
|
243
|
-
self.assertEqual(self.axis_rp.value_ref_tomwer, 1024.742042)
|
244
|
-
|
245
|
-
self.axis_rp.set_position_frm_par_file(existing_empty_file, force=True)
|
246
|
-
self.assertEqual(self.axis_rp.value_ref_tomwer, None)
|
247
|
-
|
248
|
-
self.axis_rp.set_position_frm_par_file("ghost_file.par", force=True)
|
249
|
-
self.assertEqual(self.axis_rp.value_ref_tomwer, None)
|
250
|
-
|
251
|
-
self.axis_rp.set_position_frm_par_file(valid_par_file, force=True)
|
252
|
-
self.assertEqual(self.axis_rp.value_ref_tomwer, 1024.742042)
|
253
|
-
|
254
|
-
|
255
|
-
class TestSinogramAlgorithm(unittest.TestCase):
|
256
|
-
def setUp(self) -> None:
|
257
|
-
self.tmp_folder = tempfile.mkdtemp()
|
258
|
-
dim = 512
|
259
|
-
self.scan = MockNXtomo(
|
260
|
-
scan_path=self.tmp_folder,
|
261
|
-
n_proj=10,
|
262
|
-
n_ini_proj=10,
|
263
|
-
create_ini_dark=True,
|
264
|
-
create_final_flat=True,
|
265
|
-
scan_range=360,
|
266
|
-
dim=dim,
|
267
|
-
).scan
|
268
|
-
|
269
|
-
def tearDown(self):
|
270
|
-
shutil.rmtree(self.tmp_folder)
|
271
|
-
|
272
|
-
def test_growing_window_sinogram(self):
|
273
|
-
recons_params = AxisRP()
|
274
|
-
axis_process = AxisTask(
|
275
|
-
inputs={"axis_params": recons_params, "data": self.scan}
|
276
|
-
)
|
277
|
-
recons_params.mode = AxisMode.growing_window_sinogram
|
278
|
-
recons_params.use_sinogram = True
|
279
|
-
recons_params.sinogram_subsampling = 1
|
280
|
-
axis_process.run()
|
281
|
-
|
282
|
-
def test_sliding_window(self):
|
283
|
-
recons_params = AxisRP()
|
284
|
-
axis_process = AxisTask(
|
285
|
-
inputs={
|
286
|
-
"axis_params": recons_params,
|
287
|
-
"data": self.scan,
|
288
|
-
"serialize_output_data": False,
|
289
|
-
}
|
290
|
-
)
|
291
|
-
recons_params.mode = AxisMode.sliding_window_sinogram
|
292
|
-
recons_params.side = "left"
|
293
|
-
recons_params.sinogram_subsampling = 1
|
294
|
-
recons_params.use_sinogram = True
|
295
|
-
axis_process.run()
|
296
|
-
|
297
|
-
def test_sino_coarse_to_fine(self):
|
298
|
-
recons_params = AxisRP()
|
299
|
-
axis_process = AxisTask(
|
300
|
-
inputs={
|
301
|
-
"axis_params": recons_params,
|
302
|
-
"data": self.scan,
|
303
|
-
"serialize_output_data": False,
|
304
|
-
}
|
305
|
-
)
|
306
|
-
recons_params.mode = AxisMode.sino_coarse_to_fine
|
307
|
-
recons_params.sinogram_subsampling = 1
|
308
|
-
recons_params.sinogram_line = 2
|
309
|
-
axis_process.run()
|
tomwer/core/progress.py
DELETED
@@ -1,100 +0,0 @@
|
|
1
|
-
# coding: utf-8
|
2
|
-
# /*##########################################################################
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
|
5
|
-
#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
-
# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
"""module for giving information on process progress"""
|
26
|
-
|
27
|
-
__authors__ = ["H. Payno"]
|
28
|
-
__license__ = "MIT"
|
29
|
-
__date__ = "07/08/2019"
|
30
|
-
|
31
|
-
|
32
|
-
import logging
|
33
|
-
import sys
|
34
|
-
from enum import Enum
|
35
|
-
|
36
|
-
_logger = logging.getLogger(__name__)
|
37
|
-
|
38
|
-
|
39
|
-
class _Advancement(Enum):
|
40
|
-
step_1 = "\\"
|
41
|
-
step_2 = "-"
|
42
|
-
step_3 = "/"
|
43
|
-
step_4 = "|"
|
44
|
-
|
45
|
-
@staticmethod
|
46
|
-
def getNextStep(step):
|
47
|
-
if step is _Advancement.step_1:
|
48
|
-
return _Advancement.step_2
|
49
|
-
elif step is _Advancement.step_2:
|
50
|
-
return _Advancement.step_3
|
51
|
-
elif step is _Advancement.step_3:
|
52
|
-
return _Advancement.step_4
|
53
|
-
else:
|
54
|
-
return _Advancement.step_1
|
55
|
-
|
56
|
-
@staticmethod
|
57
|
-
def getStep(value):
|
58
|
-
if value % 4 == 0:
|
59
|
-
return _Advancement.step_4
|
60
|
-
elif value % 3 == 0:
|
61
|
-
return _Advancement.step_3
|
62
|
-
elif value % 2 == 0:
|
63
|
-
return _Advancement.step_2
|
64
|
-
else:
|
65
|
-
return _Advancement.step_1
|
66
|
-
|
67
|
-
|
68
|
-
class Progress(object):
|
69
|
-
"""Simple interface for defining advancement on a 100 percentage base"""
|
70
|
-
|
71
|
-
def __init__(self, name):
|
72
|
-
self._name = name
|
73
|
-
self.reset()
|
74
|
-
|
75
|
-
def reset(self, max_=None):
|
76
|
-
self._nProcessed = 0
|
77
|
-
self._maxProcessed = max_
|
78
|
-
|
79
|
-
def startProcess(self):
|
80
|
-
self.setAdvancement(0)
|
81
|
-
|
82
|
-
def setAdvancement(self, value):
|
83
|
-
length = 20 # modify this to change the length
|
84
|
-
block = int(round(length * value / 100))
|
85
|
-
blocks_str = "#" * block + "-" * (length - block)
|
86
|
-
msg = f"\r{self._name}: [{blocks_str}] {round(value, 2)}%"
|
87
|
-
if value >= 100:
|
88
|
-
msg += " DONE\r\n"
|
89
|
-
sys.stdout.write(msg)
|
90
|
-
sys.stdout.flush()
|
91
|
-
|
92
|
-
def endProcess(self):
|
93
|
-
self.setAdvancement(100)
|
94
|
-
|
95
|
-
def setMaxAdvancement(self, n):
|
96
|
-
self._maxProcessed = n
|
97
|
-
|
98
|
-
def increaseAdvancement(self, i=1):
|
99
|
-
self._nProcessed += i
|
100
|
-
self.setAdvancement((self._nProcessed / self._maxProcessed) * 100)
|
@@ -1,53 +0,0 @@
|
|
1
|
-
# coding: utf-8
|
2
|
-
# /*##########################################################################
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
|
5
|
-
#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
-
# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
"""Unit test for the scan defined at the hdf5 format"""
|
26
|
-
|
27
|
-
__authors__ = ["H. Payno"]
|
28
|
-
__license__ = "MIT"
|
29
|
-
__date__ = "23/11/2021"
|
30
|
-
|
31
|
-
|
32
|
-
import os
|
33
|
-
|
34
|
-
from tomwer.core.scan.edfscan import EDFTomoScan
|
35
|
-
from tomwer.core.utils.scanutils import MockEDF
|
36
|
-
|
37
|
-
|
38
|
-
def test_scan_dir(tmpdir):
|
39
|
-
full_path = os.path.join(tmpdir, "my", "aquisition", "folder")
|
40
|
-
MockEDF.fastMockAcquisition(full_path)
|
41
|
-
scan = EDFTomoScan(full_path)
|
42
|
-
assert scan.scan_dir_name() == "folder"
|
43
|
-
assert scan.scan_basename() == full_path
|
44
|
-
|
45
|
-
|
46
|
-
def test_working_directory():
|
47
|
-
"""test behavior of the working directory function"""
|
48
|
-
scan = EDFTomoScan(scan=None)
|
49
|
-
assert scan.working_directory is None
|
50
|
-
scan = EDFTomoScan(scan="my_folder")
|
51
|
-
assert scan.working_directory == os.path.abspath("my_folder")
|
52
|
-
scan = EDFTomoScan(scan="/full/path/to/my/folder")
|
53
|
-
assert scan.working_directory == os.path.abspath("/full/path/to/my/folder")
|
@@ -1,61 +0,0 @@
|
|
1
|
-
# coding: utf-8
|
2
|
-
# /*##########################################################################
|
3
|
-
#
|
4
|
-
# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
|
5
|
-
#
|
6
|
-
# Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
-
# of this software and associated documentation files (the "Software"), to deal
|
8
|
-
# in the Software without restriction, including without limitation the rights
|
9
|
-
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
-
# copies of the Software, and to permit persons to whom the Software is
|
11
|
-
# furnished to do so, subject to the following conditions:
|
12
|
-
#
|
13
|
-
# The above copyright notice and this permission notice shall be included in
|
14
|
-
# all copies or substantial portions of the Software.
|
15
|
-
#
|
16
|
-
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
-
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
-
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
-
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
-
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
-
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
22
|
-
# THE SOFTWARE.
|
23
|
-
#
|
24
|
-
# ###########################################################################*/
|
25
|
-
"""Unit test for the scan defined at the hdf5 format"""
|
26
|
-
|
27
|
-
__authors__ = ["H. Payno"]
|
28
|
-
__license__ = "MIT"
|
29
|
-
__date__ = "04/11/2021"
|
30
|
-
|
31
|
-
|
32
|
-
import asyncio
|
33
|
-
import os
|
34
|
-
|
35
|
-
from tomwer.core.futureobject import FutureTomwerObject
|
36
|
-
from tomwer.core.utils.scanutils import MockNXtomo
|
37
|
-
|
38
|
-
|
39
|
-
def test_simple_future_tomo_obj(tmpdir):
|
40
|
-
"""Simple test of the FutureTomwerScan API"""
|
41
|
-
scan = MockNXtomo(
|
42
|
-
scan_path=os.path.join(tmpdir, "scan_test"),
|
43
|
-
n_proj=10,
|
44
|
-
n_ini_proj=10,
|
45
|
-
create_ini_dark=False,
|
46
|
-
create_ini_flat=False,
|
47
|
-
dim=10,
|
48
|
-
).scan
|
49
|
-
future = asyncio.Future()
|
50
|
-
future.set_result(None)
|
51
|
-
|
52
|
-
future_tomo_obj = FutureTomwerObject(
|
53
|
-
tomo_obj=scan,
|
54
|
-
futures=[
|
55
|
-
future,
|
56
|
-
],
|
57
|
-
)
|
58
|
-
|
59
|
-
future_tomo_obj.results()
|
60
|
-
assert future_tomo_obj.exceptions() is None
|
61
|
-
assert future_tomo_obj.cancelled() is False
|