tomwer 1.1.1__py3-none-any.whl → 1.2.0a0__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/__init__.py +1 -0
- orangecontrib/tomwer/orange/managedprocess.py +6 -4
- orangecontrib/tomwer/state_summary.py +3 -2
- orangecontrib/tomwer/widgets/__init__.py +2 -2
- orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py +9 -7
- orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py +6 -5
- orangecontrib/tomwer/widgets/control/AdvancementOW.py +2 -1
- orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py +235 -0
- orangecontrib/tomwer/widgets/control/DataListOW.py +7 -5
- orangecontrib/tomwer/widgets/control/DataListenerOW.py +13 -14
- orangecontrib/tomwer/widgets/control/DataSelectorOW.py +8 -6
- orangecontrib/tomwer/widgets/control/DataTransfertOW.py +9 -9
- orangecontrib/tomwer/widgets/control/DataValidatorOW.py +7 -8
- orangecontrib/tomwer/widgets/control/DataWatcherOW.py +25 -17
- orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py +8 -8
- orangecontrib/tomwer/widgets/control/FilterOW.py +9 -8
- orangecontrib/tomwer/widgets/control/NXTomomillMixIn.py +3 -4
- orangecontrib/tomwer/widgets/control/NXTomomillOW.py +13 -14
- orangecontrib/tomwer/widgets/control/NotifierOW.py +3 -4
- orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py +7 -5
- orangecontrib/tomwer/widgets/control/TimerOW.py +6 -5
- orangecontrib/tomwer/widgets/control/TomoObjSerieOW.py +5 -3
- orangecontrib/tomwer/widgets/control/VolumeSelector.py +8 -6
- orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py +10 -9
- orangecontrib/tomwer/widgets/control/icons/datadiscover.png +0 -0
- orangecontrib/tomwer/widgets/control/icons/datadiscover.svg +137 -0
- orangecontrib/tomwer/widgets/control/icons/nxtomomill.png +0 -0
- orangecontrib/tomwer/widgets/control/icons/nxtomomill.svg +5 -8
- orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py +13 -15
- orangecontrib/tomwer/widgets/debugtools/ObjectInspectorOW.py +3 -2
- orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py +10 -7
- orangecontrib/tomwer/widgets/edit/ImageKeyEditorOW.py +8 -5
- orangecontrib/tomwer/widgets/edit/ImageKeyUpgraderOW.py +5 -2
- orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py +6 -3
- orangecontrib/tomwer/widgets/edit/test/test_dark_flat_patch.py +8 -6
- orangecontrib/tomwer/widgets/edit/test/test_image_key_editor.py +3 -1
- orangecontrib/tomwer/widgets/edit/test/test_image_key_upgrader.py +3 -1
- orangecontrib/tomwer/widgets/edit/test/test_nxtomo_editor.py +3 -1
- orangecontrib/tomwer/widgets/other/PythonScriptOW.py +11 -11
- orangecontrib/tomwer/widgets/reconstruction/AxisOW.py +22 -27
- orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py +13 -11
- orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py +11 -9
- orangecontrib/tomwer/widgets/reconstruction/NabuOW.py +16 -14
- orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py +27 -32
- orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py +27 -34
- orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py +23 -25
- orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py +16 -18
- orangecontrib/tomwer/widgets/reconstruction/TofuOW.py +9 -7
- orangecontrib/tomwer/widgets/reconstruction/icons/nabu_2d.png +0 -0
- orangecontrib/tomwer/widgets/reconstruction/icons/nabu_2d.svg +8 -11
- orangecontrib/tomwer/widgets/visualization/DataViewerOW.py +8 -8
- orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py +6 -4
- orangecontrib/tomwer/widgets/visualization/LivesliceOW.py +4 -3
- orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py +4 -3
- orangecontrib/tomwer/widgets/visualization/RadioStackOW.py +6 -4
- orangecontrib/tomwer/widgets/visualization/SampleMovedOW.py +8 -6
- orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py +6 -3
- orangecontrib/tomwer/widgets/visualization/SliceStackOW.py +7 -5
- orangecontrib/tomwer/widgets/visualization/VolumeViewerOW.py +5 -4
- tomwer/__init__.py +1 -1
- tomwer/__main__.py +2 -1
- tomwer/app/axis.py +18 -14
- tomwer/app/canvas.py +7 -5
- tomwer/app/canvas_launcher/config.py +8 -6
- tomwer/app/canvas_launcher/environ.py +1 -2
- tomwer/app/canvas_launcher/mainwindow.py +23 -22
- tomwer/app/canvas_launcher/splash.py +1 -0
- tomwer/app/canvas_launcher/widgetsscheme.py +3 -3
- tomwer/app/darkref.py +7 -6
- tomwer/app/darkrefpatch.py +8 -6
- tomwer/app/diffframe.py +6 -4
- tomwer/app/imagekeyeditor.py +10 -10
- tomwer/app/imagekeyupgrader.py +8 -6
- tomwer/app/intensitynormalization.py +8 -8
- tomwer/app/lamino.py +5 -3
- tomwer/app/nabuapp.py +8 -6
- tomwer/app/nxtomoeditor.py +6 -5
- tomwer/app/radiostack.py +8 -6
- tomwer/app/rsync.py +3 -3
- tomwer/app/saaxis.py +22 -23
- tomwer/app/sadeltabeta.py +21 -21
- tomwer/app/samplemoved.py +8 -6
- tomwer/app/scanviewer.py +7 -6
- tomwer/app/sinogramviewer.py +8 -7
- tomwer/app/slicestack.py +8 -6
- tomwer/app/stopdatalistener.py +2 -1
- tomwer/core/futureobject.py +15 -6
- tomwer/core/log/logger.py +4 -3
- tomwer/core/log/processlog.py +0 -1
- tomwer/core/process/conditions/filters.py +3 -3
- tomwer/core/process/control/datadiscovery.py +7 -0
- tomwer/core/process/control/datalistener/datalistener.py +22 -21
- tomwer/core/process/control/datalistener/rpcserver.py +18 -28
- tomwer/core/process/control/datawatcher/datawatcher.py +15 -12
- tomwer/core/process/control/datawatcher/datawatcherobserver.py +11 -8
- tomwer/core/process/control/datawatcher/datawatcherprocess.py +7 -5
- tomwer/core/process/control/datawatcher/edfdwprocess.py +5 -15
- tomwer/core/process/control/datawatcher/hdf5dwprocess.py +3 -1
- tomwer/core/process/control/datawatcher/status.py +2 -0
- tomwer/core/process/control/nxtomomill.py +7 -6
- tomwer/core/process/control/scanlist.py +2 -1
- tomwer/core/process/control/scanselector.py +1 -0
- tomwer/core/process/control/scantransfer.py +12 -12
- tomwer/core/process/control/scanvalidator.py +7 -6
- tomwer/core/process/control/test/test_volume_link.py +5 -4
- tomwer/core/process/control/timer.py +4 -4
- tomwer/core/process/control/volumeselector.py +1 -0
- tomwer/core/process/control/volumesymlink.py +8 -9
- tomwer/core/process/edit/darkflatpatch.py +9 -12
- tomwer/core/process/edit/imagekeyeditor.py +11 -13
- tomwer/core/process/reconstruction/axis/axis.py +36 -38
- tomwer/core/process/reconstruction/axis/mode.py +2 -1
- tomwer/core/process/reconstruction/axis/params.py +23 -28
- tomwer/core/process/reconstruction/darkref/darkrefs.py +23 -27
- tomwer/core/process/reconstruction/darkref/darkrefscopy.py +14 -18
- tomwer/core/process/reconstruction/darkref/params.py +3 -1
- tomwer/core/process/reconstruction/lamino/tofu.py +11 -15
- tomwer/core/process/reconstruction/nabu/castvolume.py +15 -18
- tomwer/core/process/reconstruction/nabu/nabucommon.py +19 -20
- tomwer/core/process/reconstruction/nabu/nabuscores.py +16 -14
- tomwer/core/process/reconstruction/nabu/nabuslices.py +27 -22
- tomwer/core/process/reconstruction/nabu/nabuvolume.py +20 -22
- tomwer/core/process/reconstruction/nabu/utils.py +17 -15
- tomwer/core/process/reconstruction/normalization/__init__.py +1 -3
- tomwer/core/process/reconstruction/normalization/normalization.py +16 -21
- tomwer/core/process/reconstruction/normalization/params.py +2 -2
- tomwer/core/process/reconstruction/saaxis/__init__.py +1 -1
- tomwer/core/process/reconstruction/saaxis/params.py +6 -7
- tomwer/core/process/reconstruction/saaxis/saaxis.py +44 -55
- tomwer/core/process/reconstruction/sadeltabeta/__init__.py +1 -1
- tomwer/core/process/reconstruction/sadeltabeta/params.py +9 -13
- tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +40 -46
- tomwer/core/process/reconstruction/scores/__init__.py +2 -2
- tomwer/core/process/reconstruction/scores/params.py +6 -9
- tomwer/core/process/reconstruction/scores/scores.py +10 -13
- tomwer/core/process/reconstruction/test/test_axis_params.py +4 -2
- tomwer/core/process/reconstruction/test/test_darkref.py +1 -2
- tomwer/core/process/reconstruction/test/test_darkref_copy.py +3 -1
- tomwer/core/process/reconstruction/test/test_paramsbase.py +1 -1
- tomwer/core/process/reconstruction/test/test_saaxis.py +11 -7
- tomwer/core/process/reconstruction/test/test_sadeltabeta.py +5 -4
- tomwer/core/process/reconstruction/test/test_utils.py +3 -2
- tomwer/core/process/script/python.py +6 -8
- tomwer/core/process/task.py +11 -12
- tomwer/core/process/test/test_axis.py +12 -9
- tomwer/core/process/test/test_conditions.py +8 -8
- tomwer/core/process/test/test_dark_and_flat.py +9 -8
- tomwer/core/process/test/test_data_listener.py +5 -3
- tomwer/core/process/test/test_data_transfer.py +14 -12
- tomwer/core/process/test/test_data_watcher.py +3 -1
- tomwer/core/process/test/test_lamino.py +3 -1
- tomwer/core/process/test/test_nabu.py +13 -12
- tomwer/core/process/test/test_normalization.py +7 -5
- tomwer/core/process/test/test_timer.py +2 -1
- tomwer/core/process/utils.py +9 -9
- tomwer/core/progress.py +3 -4
- tomwer/core/scan/blissscan.py +4 -2
- tomwer/core/scan/edfscan.py +26 -29
- tomwer/core/scan/futurescan.py +2 -1
- tomwer/core/scan/hdf5scan.py +21 -28
- tomwer/core/scan/scanbase.py +18 -18
- tomwer/core/scan/scanfactory.py +20 -21
- tomwer/core/scan/scantype.py +7 -0
- tomwer/core/scan/test/test_edf.py +2 -1
- tomwer/core/scan/test/test_future_scan.py +2 -1
- tomwer/core/scan/test/test_h5.py +5 -4
- tomwer/core/scan/test/test_process_registration.py +5 -3
- tomwer/core/scan/test/test_scan.py +11 -9
- tomwer/core/settings.py +1 -2
- tomwer/core/test/test_lamino.py +3 -2
- tomwer/core/test/test_scanutils.py +3 -2
- tomwer/core/test/test_utils.py +6 -4
- tomwer/core/utils/__init__.py +8 -6
- tomwer/core/utils/deprecation.py +2 -2
- tomwer/core/utils/image.py +4 -3
- tomwer/core/utils/locker.py +1 -1
- tomwer/core/utils/normalization.py +1 -0
- tomwer/core/utils/nxtomoutils.py +2 -1
- tomwer/core/utils/scanutils.py +9 -6
- tomwer/core/utils/slurm.py +2 -1
- tomwer/core/utils/time.py +2 -4
- tomwer/core/utils/volumeutils.py +2 -1
- tomwer/core/volume/__init__.py +1 -1
- tomwer/core/volume/edfvolume.py +4 -3
- tomwer/core/volume/hdf5volume.py +6 -8
- tomwer/core/volume/jp2kvolume.py +4 -3
- tomwer/core/volume/rawvolume.py +7 -7
- tomwer/core/volume/tiffvolume.py +8 -6
- tomwer/core/volume/volumebase.py +1 -0
- tomwer/core/volume/volumefactory.py +18 -18
- tomwer/gui/cluster/slurm.py +2 -0
- tomwer/gui/cluster/supervisor.py +4 -2
- tomwer/gui/cluster/test/test_cluster.py +5 -4
- tomwer/gui/cluster/test/test_supervisor.py +4 -2
- tomwer/gui/conditions/filter.py +7 -6
- tomwer/gui/control/actions.py +1 -0
- tomwer/gui/control/datadiscovery.py +168 -0
- tomwer/gui/control/datalist.py +29 -28
- tomwer/gui/control/datalistener.py +8 -4
- tomwer/gui/control/datareacheractions.py +2 -1
- tomwer/gui/control/datatransfert.py +3 -1
- tomwer/gui/control/datavalidator.py +11 -12
- tomwer/gui/control/datawatcher/configuration.py +12 -1
- tomwer/gui/control/datawatcher/controlwidget.py +116 -0
- tomwer/gui/control/datawatcher/datawatcher.py +63 -121
- tomwer/gui/control/datawatcher/datawatcherobserver.py +7 -9
- tomwer/gui/control/history.py +3 -1
- tomwer/gui/control/observations.py +7 -7
- tomwer/gui/control/scanselectorwidget.py +4 -2
- tomwer/gui/control/selectorwidgetbase.py +3 -1
- tomwer/gui/control/serie/seriecreator.py +11 -12
- tomwer/gui/control/singletomoobj.py +4 -4
- tomwer/gui/control/test/test_datadiscovery.py +27 -0
- tomwer/gui/control/test/test_datalist.py +7 -6
- tomwer/gui/control/test/test_datalistener.py +4 -4
- tomwer/gui/control/test/test_datavalidator.py +3 -1
- tomwer/gui/control/test/test_inputwidget.py +5 -4
- tomwer/gui/control/test/test_process_manager.py +3 -3
- tomwer/gui/control/test/test_scanselector.py +6 -4
- tomwer/gui/control/test/test_scanvalidator.py +6 -5
- tomwer/gui/control/test/test_single_tomo_obj.py +5 -3
- tomwer/gui/control/test/test_volume_dialog.py +7 -5
- tomwer/gui/control/test/test_volumeselector.py +8 -6
- tomwer/gui/control/volumeselectorwidget.py +2 -1
- tomwer/gui/debugtools/datasetgenerator.py +2 -1
- tomwer/gui/debugtools/objectinspector.py +6 -7
- tomwer/gui/edit/dkrfpatch.py +11 -10
- tomwer/gui/edit/imagekeyeditor.py +12 -12
- tomwer/gui/edit/nxtomoeditor.py +8 -7
- tomwer/gui/edit/test/test_dkrf_patch.py +10 -9
- tomwer/gui/edit/test/test_image_key_editor.py +8 -6
- tomwer/gui/edit/test/test_nx_editor.py +7 -5
- tomwer/gui/icons.py +3 -2
- tomwer/gui/illustrations.py +3 -2
- tomwer/gui/imagefromfile.py +3 -1
- tomwer/gui/qfolderdialog.py +14 -12
- tomwer/gui/reconstruction/axis/CompareImages.py +9 -8
- tomwer/gui/reconstruction/axis/__init__.py +1 -1
- tomwer/gui/reconstruction/axis/axis.py +9 -7
- tomwer/gui/reconstruction/axis/radioaxis.py +30 -32
- tomwer/gui/reconstruction/darkref/darkrefcopywidget.py +6 -5
- tomwer/gui/reconstruction/darkref/darkrefwidget.py +4 -2
- tomwer/gui/reconstruction/lamino/tofu/misc.py +3 -1
- tomwer/gui/reconstruction/lamino/tofu/projections.py +16 -8
- tomwer/gui/reconstruction/lamino/tofu/tofu.py +6 -3
- tomwer/gui/reconstruction/lamino/tofu/tofuexpert.py +5 -2
- tomwer/gui/reconstruction/lamino/tofu/tofuoutput.py +8 -5
- tomwer/gui/reconstruction/nabu/action.py +1 -0
- tomwer/gui/reconstruction/nabu/castvolume.py +6 -4
- tomwer/gui/reconstruction/nabu/check.py +3 -2
- tomwer/gui/reconstruction/nabu/nabuconfig/base.py +5 -2
- tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py +6 -3
- tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py +4 -3
- tomwer/gui/reconstruction/nabu/nabuconfig/output.py +7 -5
- tomwer/gui/reconstruction/nabu/nabuconfig/phase.py +8 -6
- tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py +7 -7
- tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py +40 -33
- tomwer/gui/reconstruction/nabu/nabuflow.py +7 -4
- tomwer/gui/reconstruction/nabu/slices.py +14 -10
- tomwer/gui/reconstruction/nabu/slurm.py +1 -0
- tomwer/gui/reconstruction/nabu/volume.py +5 -3
- tomwer/gui/reconstruction/normalization/intensity.py +14 -13
- tomwer/gui/reconstruction/saaxis/corrangeselector.py +36 -35
- tomwer/gui/reconstruction/saaxis/dimensionwidget.py +5 -4
- tomwer/gui/reconstruction/saaxis/saaxis.py +17 -17
- tomwer/gui/reconstruction/saaxis/sliceselector.py +5 -5
- tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py +33 -36
- tomwer/gui/reconstruction/scores/scoreplot.py +19 -18
- tomwer/gui/reconstruction/test/test_axis.py +14 -13
- tomwer/gui/reconstruction/test/test_lamino.py +3 -2
- tomwer/gui/reconstruction/test/test_nabu.py +8 -6
- tomwer/gui/reconstruction/test/test_saaxis.py +17 -15
- tomwer/gui/reconstruction/test/test_sadeltabeta.py +15 -13
- tomwer/gui/samplemoved/__init__.py +8 -7
- tomwer/gui/samplemoved/selectiontable.py +4 -2
- tomwer/gui/stackplot.py +14 -13
- tomwer/gui/stacks.py +11 -9
- tomwer/gui/test/test_axis_gui.py +5 -4
- tomwer/gui/test/test_qfolder_dialog.py +2 -1
- tomwer/gui/utils/__init__.py +5 -5
- tomwer/gui/utils/buttons.py +1 -0
- tomwer/gui/utils/completer.py +1 -0
- tomwer/gui/utils/flow.py +4 -2
- tomwer/gui/utils/illustrations.py +1 -0
- tomwer/gui/utils/inputwidget.py +11 -17
- tomwer/gui/utils/lineselector/lineselector.py +6 -8
- tomwer/gui/utils/qt_utils.py +1 -0
- tomwer/gui/utils/scandescription.py +2 -0
- tomwer/gui/utils/splashscreen.py +1 -1
- tomwer/gui/utils/unitsystem.py +3 -1
- tomwer/gui/utils/vignettes.py +8 -8
- tomwer/gui/utils/waiterthread.py +2 -1
- tomwer/gui/visualization/dataviewer.py +20 -28
- tomwer/gui/visualization/diffviewer/diffviewer.py +17 -20
- tomwer/gui/visualization/diffviewer/shiftwidget.py +3 -1
- tomwer/gui/visualization/nxtomometadata.py +1 -0
- tomwer/gui/visualization/reconstructionparameters.py +13 -12
- tomwer/gui/visualization/scanoverview.py +5 -3
- tomwer/gui/visualization/sinogramviewer.py +3 -2
- tomwer/gui/visualization/test/test_dataviewer.py +3 -1
- tomwer/gui/visualization/test/test_diffviewer.py +8 -6
- tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py +5 -3
- tomwer/gui/visualization/test/test_reconstruction_parameters.py +5 -3
- tomwer/gui/visualization/test/test_sinogramviewer.py +10 -9
- tomwer/gui/visualization/test/test_stacks.py +8 -6
- tomwer/gui/visualization/test/test_volumeviewer.py +10 -8
- tomwer/gui/visualization/tomoobjoverview.py +7 -4
- tomwer/gui/visualization/volumeoverview.py +5 -3
- tomwer/gui/visualization/volumeviewer.py +15 -14
- tomwer/io/utils/__init__.py +3 -3
- tomwer/io/utils/h5pyutils.py +2 -1
- tomwer/io/utils/utils.py +17 -21
- tomwer/resources/__init__.py +1 -1
- tomwer/synctools/axis.py +3 -1
- tomwer/synctools/darkref.py +3 -2
- tomwer/synctools/datalistener.py +10 -6
- tomwer/synctools/datatransfert.py +2 -3
- tomwer/synctools/imageloaderthread.py +5 -3
- tomwer/synctools/rsyncmanager.py +3 -2
- tomwer/synctools/saaxis.py +3 -1
- tomwer/synctools/sadeltabeta.py +3 -1
- tomwer/synctools/stacks/control/datalistener.py +9 -12
- tomwer/synctools/stacks/edit/darkflatpatch.py +13 -12
- tomwer/synctools/stacks/edit/imagekeyeditor.py +12 -11
- tomwer/synctools/stacks/processingstack.py +3 -2
- tomwer/synctools/stacks/reconstruction/axis.py +12 -12
- tomwer/synctools/stacks/reconstruction/castvolume.py +8 -5
- tomwer/synctools/stacks/reconstruction/dkrefcopy.py +10 -9
- tomwer/synctools/stacks/reconstruction/lamino.py +9 -7
- tomwer/synctools/stacks/reconstruction/nabu.py +18 -17
- tomwer/synctools/stacks/reconstruction/normalization.py +12 -16
- tomwer/synctools/stacks/reconstruction/saaxis.py +13 -11
- tomwer/synctools/stacks/reconstruction/sadeltabeta.py +16 -14
- tomwer/synctools/test/test_darkRefs.py +4 -3
- tomwer/synctools/test/test_foldertransfer.py +14 -12
- tomwer/synctools/test/test_scanstages.py +8 -7
- tomwer/synctools/utils/scanstages.py +7 -5
- tomwer/tests/conftest.py +4 -4
- tomwer/tests/test_scripts.py +3 -2
- tomwer/tests/utils/__init__.py +5 -4
- tomwer/tests/utils/utilstest.py +5 -6
- tomwer/third_party/nabu/preproc/phase.py +7 -5
- tomwer/third_party/nabu/utils.py +3 -2
- tomwer/utils.py +12 -12
- tomwer/version.py +4 -4
- {tomwer-1.1.1.dist-info → tomwer-1.2.0a0.dist-info}/METADATA +2 -2
- {tomwer-1.1.1.dist-info → tomwer-1.2.0a0.dist-info}/RECORD +353 -345
- /tomwer-1.1.1-py3.8-nspkg.pth → /tomwer-1.2.0a0-py3.8-nspkg.pth +0 -0
- {tomwer-1.1.1.dist-info → tomwer-1.2.0a0.dist-info}/LICENSE +0 -0
- {tomwer-1.1.1.dist-info → tomwer-1.2.0a0.dist-info}/WHEEL +0 -0
- {tomwer-1.1.1.dist-info → tomwer-1.2.0a0.dist-info}/entry_points.txt +0 -0
- {tomwer-1.1.1.dist-info → tomwer-1.2.0a0.dist-info}/namespace_packages.txt +0 -0
- {tomwer-1.1.1.dist-info → tomwer-1.2.0a0.dist-info}/top_level.txt +0 -0
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from nabu.pipeline.config import get_default_nabu_config
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from nabu.pipeline.fullfield.nabu_config import (
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nabu_config as nabu_fullfield_default_config,
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)
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45
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-
from processview.core.manager import
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+
from processview.core.manager import DatasetState, ProcessManager
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from processview.core.superviseprocess import SuperviseProcess
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+
from tomoscan.esrf.scan.utils import get_data
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from tomoscan.io import HDF5File
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+
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+
import tomwer.version
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from tomwer.core.process.reconstruction.nabu.nabucommon import (
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-
ResultSlurmRun,
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ResultsLocalRun,
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+
ResultSlurmRun,
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+
ResultsRun,
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ResultsWithStd,
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)
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from tomwer.core.scan.scanfactory import ScanFactory
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from .params import SADeltaBetaParams
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-
from tomwer.core.scan.scanbase import TomwerScanBase
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-
from tomwer.core.utils import logconfig
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-
from tomwer.core.process.task import Task
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from tomwer.core.scan.hdf5scan import HDF5TomoScan
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from tomoscan.io import HDF5File
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from tomoscan.esrf.scan.utils import get_data
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-
import tomwer.version
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from tomwer.core.process.reconstruction.nabu.nabuslices import (
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+
SingleSliceRunner,
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run_single_slice_reconstruction,
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)
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from tomwer.core.process.reconstruction.
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+
from tomwer.core.process.reconstruction.scores import (
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ComputedScore,
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ScoreMethod,
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apply_roi,
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compute_score,
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get_disk_mask_radius,
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)
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from tomwer.core.process.task import Task
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from tomwer.core.progress import Progress
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from
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from tomwer.core.
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from tomwer.core.
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from tomwer.core.
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from tomwer.core.process.reconstruction.scores import get_disk_mask_radius, apply_roi
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from tomwer.core.process.reconstruction.nabu.nabuslices import SingleSliceRunner
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-
from tomwer.core.volume.volumefactory import VolumeFactory
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+
from tomwer.core.scan.hdf5scan import HDF5TomoScan
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+
from tomwer.core.scan.scanbase import TomwerScanBase
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from tomwer.core.scan.scanfactory import ScanFactory
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from tomwer.core.utils import logconfig
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from tomwer.core.utils.scanutils import data_identifier_to_scan
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from tomwer.core.volume.volumefactory import VolumeFactory
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+
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from ..nabu import utils as nabu_utils
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from .params import SADeltaBetaParams
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_logger = logging.getLogger(__name__)
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@@ -113,22 +119,20 @@ def one_slice_several_db(
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dry_run = configuration.dry_run
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cluster_config = configuration.cluster_config
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_logger.info(
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-
"launch reconstruction of slice {} and delta / beta: {}"
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slice_index, delta_beta_s
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-
)
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f"launch reconstruction of slice {slice_index} and delta / beta: {delta_beta_s}"
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)
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if isinstance(slice_index, str):
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if not slice_index == "middle":
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raise ValueError("slice index {} not recognized"
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+
raise ValueError(f"slice index {slice_index} not recognized")
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elif not len(slice_index) == 1:
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raise ValueError("only manage one slice")
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else:
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slice_index = list(slice_index.values())[0]
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advancement = Progress("sa-delta-beta - slice {} of {}"
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+
advancement = Progress(f"sa-delta-beta - slice {slice_index} of {scan}")
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config = configuration.nabu_params.copy()
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_logger.info("start reconstruction of {}"
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+
_logger.info(f"start reconstruction of {scan}")
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# if scan contains some center of position copy it to nabu
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if scan.axis_params is not None and scan.axis_params.relative_cor_value is not None:
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if "reconstruction" in config:
|
@@ -136,7 +140,7 @@ def one_slice_several_db(
|
|
136
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cor_nabu_ref = scan.axis_params.relative_cor_value + scan.dim_1 / 2.0
|
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config["reconstruction"]["rotation_axis_position"] = str(cor_nabu_ref)
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|
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_logger.info("set nabu reconstruction parameters to {}"
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+
_logger.info(f"set nabu reconstruction parameters to {scan}")
|
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scan.nabu_recons_params = config
|
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|
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db_reconstructions = {}
|
@@ -285,8 +289,7 @@ def one_slice_several_db(
|
|
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data = get_data(slice_url)
|
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except Exception as e:
|
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_logger.error(
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"Fail to compute a score for {}. Reason is {}"
|
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"".format(volume_identifier, str(e))
|
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|
+
f"Fail to compute a score for {volume_identifier}. Reason is {e}"
|
290
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)
|
291
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datasets_[db] = (slice_url, None)
|
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else:
|
@@ -297,14 +300,12 @@ def one_slice_several_db(
|
|
297
300
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data = data.reshape(data.shape[0], data.shape[1])
|
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else:
|
299
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raise ValueError(
|
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"Data is expected to be 2D. Not {
|
303
|
+
f"Data is expected to be 2D. Not {data.ndim}D"
|
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)
|
302
305
|
elif data.ndim == 2:
|
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pass
|
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else:
|
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-
raise ValueError(
|
306
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"Data is expected to be 2D. Not {}".format(data.ndim)
|
307
|
-
)
|
308
|
+
raise ValueError(f"Data is expected to be 2D. Not {data.ndim}D")
|
308
309
|
|
309
310
|
datasets_[db] = (slice_url, data)
|
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return datasets_
|
@@ -411,9 +412,7 @@ class SADeltaBetaProcess(
|
|
411
412
|
elif isinstance(scan, dict):
|
412
413
|
scan = ScanFactory.create_scan_object_frm_dict(scan)
|
413
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|
else:
|
414
|
-
raise ValueError(
|
415
|
-
"input type of {}: {} is not managed" "".format(scan, type(scan))
|
416
|
-
)
|
415
|
+
raise ValueError(f"input type of {scan}: {type(scan)} is not managed")
|
417
416
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# insure scan contains some parameter regarding sa delta / beta
|
418
417
|
if scan.sa_delta_beta_params is None:
|
419
418
|
scan.sa_delta_beta_params = SADeltaBetaParams()
|
@@ -458,18 +457,13 @@ class SADeltaBetaProcess(
|
|
458
457
|
slice_index = self.get_configuration().get("slice_index", None)
|
459
458
|
|
460
459
|
if db_res is None:
|
461
|
-
info =
|
462
|
-
"fail to compute delta/beta scores of slice {} for scan {}."
|
463
|
-
"".format(slice_index, scan)
|
464
|
-
)
|
460
|
+
info = f"fail to compute delta/beta scores of slice {slice_index} for scan {scan}."
|
465
461
|
_logger.processFailed(info, extra=extra)
|
466
462
|
ProcessManager().notify_dataset_state(
|
467
463
|
dataset=scan, process=self, state=DatasetState.FAILED, details=info
|
468
464
|
)
|
469
465
|
else:
|
470
|
-
info = "delta/beta scores of slice {} for scan {} computed."
|
471
|
-
slice_index, scan
|
472
|
-
)
|
466
|
+
info = f"delta/beta scores of slice {slice_index} for scan {scan} computed."
|
473
467
|
_logger.processSucceed(info, extra=extra)
|
474
468
|
ProcessManager().notify_dataset_state(
|
475
469
|
dataset=scan,
|
@@ -496,7 +490,7 @@ class SADeltaBetaProcess(
|
|
496
490
|
if not isinstance(score_rois, dict):
|
497
491
|
raise TypeError("score_rois is expected to be a dict")
|
498
492
|
process_file = scan.process_file
|
499
|
-
process_name = "tomwer_process_"
|
493
|
+
process_name = f"tomwer_process_{process_index}"
|
500
494
|
|
501
495
|
if scan.saaxis_params.scores in (None, {}):
|
502
496
|
return
|
@@ -1,6 +1,6 @@
|
|
1
|
-
from .scores import ScoreMethod # noqa F401
|
2
1
|
from .params import SABaseParams # noqa F401
|
3
|
-
from .scores import compute_score # noqa F401
|
4
2
|
from .scores import ComputedScore # noqa F401
|
3
|
+
from .scores import ScoreMethod # noqa F401
|
5
4
|
from .scores import apply_roi # noqa F401
|
5
|
+
from .scores import compute_score # noqa F401
|
6
6
|
from .scores import get_disk_mask_radius # noqa F401
|
@@ -28,10 +28,11 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "04/05/2021"
|
29
29
|
|
30
30
|
|
31
|
-
from tomwer.core.cluster.cluster import SlurmClusterConfiguration
|
32
|
-
from tomwer.core.process.reconstruction.scores import ScoreMethod
|
33
31
|
from typing import Optional, Union
|
34
32
|
|
33
|
+
from tomwer.core.cluster.cluster import SlurmClusterConfiguration
|
34
|
+
from tomwer.core.process.reconstruction.scores.scores import ScoreMethod
|
35
|
+
|
35
36
|
|
36
37
|
class SABaseParams:
|
37
38
|
"""Parameters for the semi-automatic axis calculation"""
|
@@ -79,8 +80,7 @@ class SABaseParams:
|
|
79
80
|
raise ValueError("the only valid indexes values is 'middle'")
|
80
81
|
elif not isinstance(indexes, (type(None), dict)):
|
81
82
|
raise TypeError(
|
82
|
-
"index should be an instance of int or None and "
|
83
|
-
"not {}".format(type(indexes))
|
83
|
+
f"index should be an instance of int or None and not {type(indexes)}"
|
84
84
|
)
|
85
85
|
self._slice_indexes = indexes
|
86
86
|
|
@@ -91,9 +91,7 @@ class SABaseParams:
|
|
91
91
|
@nabu_params.setter
|
92
92
|
def nabu_params(self, params: dict):
|
93
93
|
if not isinstance(params, dict):
|
94
|
-
raise TypeError(
|
95
|
-
"params should be a dictionary and not {}" "".format(type(params))
|
96
|
-
)
|
94
|
+
raise TypeError(f"params should be a dictionary and not {type(params)}")
|
97
95
|
self._nabu_params = params
|
98
96
|
|
99
97
|
@property
|
@@ -144,8 +142,7 @@ class SABaseParams:
|
|
144
142
|
raise TypeError("format should be a str")
|
145
143
|
if format_ not in self._VALID_FILE_FORMAT:
|
146
144
|
raise ValueError(
|
147
|
-
"requested format ({}) is invalid. valid ones "
|
148
|
-
"are {}".format(format_, self._VALID_FILE_FORMAT)
|
145
|
+
f"requested format ({format_}) is invalid. valid ones are {self._VALID_FILE_FORMAT}"
|
149
146
|
)
|
150
147
|
self._file_format = format_
|
151
148
|
|
@@ -28,12 +28,13 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "18/02/2021"
|
29
29
|
|
30
30
|
|
31
|
-
from silx.utils.enum import Enum as _Enum
|
32
|
-
import numpy
|
33
|
-
import sys
|
34
31
|
import logging
|
32
|
+
import sys
|
35
33
|
from typing import Union
|
36
34
|
|
35
|
+
import numpy
|
36
|
+
from silx.utils.enum import Enum as _Enum
|
37
|
+
|
37
38
|
_logger = logging.getLogger(__name__)
|
38
39
|
|
39
40
|
|
@@ -76,7 +77,7 @@ class ComputedScore:
|
|
76
77
|
elif method is ScoreMethod.TOMO_CONSISTENCY:
|
77
78
|
return self.tomo_consistency
|
78
79
|
else:
|
79
|
-
raise ValueError("{} is an unrecognized method"
|
80
|
+
raise ValueError(f"{method} is an unrecognized method")
|
80
81
|
|
81
82
|
|
82
83
|
def compute_tomo_consistency(
|
@@ -160,11 +161,11 @@ def compute_score(
|
|
160
161
|
elif data.shape[2] == 1:
|
161
162
|
data = data.reshape(data.shape[0], data.shape[1])
|
162
163
|
else:
|
163
|
-
raise ValueError("Data is expected to be 2D. Not {
|
164
|
+
raise ValueError(f"Data is expected to be 2D. Not {data.ndim}D")
|
164
165
|
elif data.ndim == 2:
|
165
166
|
pass
|
166
167
|
else:
|
167
|
-
raise ValueError("Data is expected to be 2D. Not {
|
168
|
+
raise ValueError(f"Data is expected to be 2D. Not {data.ndim}D")
|
168
169
|
if method is ScoreMethod.TOMO_CONSISTENCY:
|
169
170
|
try:
|
170
171
|
return compute_tomo_consistency(
|
@@ -177,9 +178,7 @@ def compute_score(
|
|
177
178
|
except ImportError:
|
178
179
|
return None
|
179
180
|
except Exception as e:
|
180
|
-
_logger.warning(
|
181
|
-
"Fail to compute 'tomo consistency' score. " "Reason is {}".format(e)
|
182
|
-
)
|
181
|
+
_logger.warning(f"Fail to compute 'tomo consistency' score. Reason is {e}")
|
183
182
|
return None
|
184
183
|
else:
|
185
184
|
fct = _METHOD_TO_FCT.get(method, None)
|
@@ -187,7 +186,7 @@ def compute_score(
|
|
187
186
|
if fct is not None:
|
188
187
|
return fct(data)
|
189
188
|
else:
|
190
|
-
raise ValueError("{} is not handled"
|
189
|
+
raise ValueError(f"{method} is not handled")
|
191
190
|
|
192
191
|
|
193
192
|
def get_disk_mask_radius(datasets_) -> int:
|
@@ -214,7 +213,5 @@ def apply_roi(data, radius, url) -> numpy.array:
|
|
214
213
|
try:
|
215
214
|
return data[min_y:max_y, min_x:max_x]
|
216
215
|
except Exception:
|
217
|
-
_logger.error(
|
218
|
-
"Fail to apply roi for {}. Take the entire dataset".format(url.path())
|
219
|
-
)
|
216
|
+
_logger.error(f"Fail to apply roi for {url.path()}. Take the entire dataset")
|
220
217
|
return data
|
@@ -1,11 +1,13 @@
|
|
1
1
|
import os
|
2
|
+
|
3
|
+
import numpy
|
2
4
|
import pytest
|
5
|
+
|
3
6
|
from tomwer.core.process.reconstruction.axis.params import (
|
4
|
-
AxisResource,
|
5
7
|
AxisCalculationInput,
|
8
|
+
AxisResource,
|
6
9
|
)
|
7
10
|
from tomwer.core.utils.scanutils import MockHDF5
|
8
|
-
import numpy
|
9
11
|
|
10
12
|
|
11
13
|
def test_axis_resource(tmp_path):
|
@@ -28,11 +28,10 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "24/11/2021"
|
29
29
|
|
30
30
|
|
31
|
-
from tomwer.core.utils.scanutils import MockEDF
|
32
|
-
from tomwer.core.utils.scanutils import MockHDF5
|
33
31
|
from tomwer.core.process.reconstruction.darkref.darkrefs import (
|
34
32
|
requires_reduced_dark_and_flat,
|
35
33
|
)
|
34
|
+
from tomwer.core.utils.scanutils import MockEDF, MockHDF5
|
36
35
|
|
37
36
|
|
38
37
|
def test_quick_run_necessary_edf(tmpdir):
|
@@ -1,7 +1,9 @@
|
|
1
1
|
import os
|
2
|
+
|
2
3
|
import numpy
|
3
4
|
import pytest
|
4
5
|
from silx.io.dictdump import dicttoh5
|
6
|
+
|
5
7
|
from tomwer.core.process.reconstruction.darkref.darkrefscopy import DarkRefsCopy
|
6
8
|
from tomwer.core.utils.scanutils import MockHDF5
|
7
9
|
|
@@ -91,8 +93,8 @@ def test_save_reduced_frames_to_be_copied(tmp_path):
|
|
91
93
|
test save_flats_to_be_copied and save_darks_to_be_copied functions
|
92
94
|
"""
|
93
95
|
# create raw data
|
94
|
-
from tomoscan.scanbase import ReducedFramesInfos
|
95
96
|
from silx.io.url import DataUrl
|
97
|
+
from tomoscan.scanbase import ReducedFramesInfos
|
96
98
|
|
97
99
|
raw_data = tmp_path / "raw_data"
|
98
100
|
raw_data.mkdir()
|
@@ -1,5 +1,5 @@
|
|
1
|
-
from tomwer.core.process.reconstruction.paramsbase import _ReconsParam, _get_db_fromstr
|
2
1
|
from tomwer.core.process.reconstruction.darkref.params import DKRFRP
|
2
|
+
from tomwer.core.process.reconstruction.paramsbase import _get_db_fromstr, _ReconsParam
|
3
3
|
|
4
4
|
|
5
5
|
def test_paramsbase():
|
@@ -28,17 +28,21 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "27/02/2021"
|
29
29
|
|
30
30
|
|
31
|
-
import unittest
|
32
|
-
from tomwer.core.process.reconstruction.scores.scores import compute_score_contrast_std
|
33
|
-
from tomwer.core.process.reconstruction.scores.scores import _METHOD_TO_FCT
|
34
|
-
from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisProcess
|
35
|
-
from tomwer.core.process.reconstruction.saaxis.params import SAAxisParams
|
36
|
-
from tomwer.core.utils.scanutils import MockHDF5
|
37
31
|
import os
|
38
|
-
import tempfile
|
39
32
|
import shutil
|
33
|
+
import tempfile
|
34
|
+
import unittest
|
35
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+
|
40
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|
import numpy
|
41
37
|
|
38
|
+
from tomwer.core.process.reconstruction.saaxis.params import SAAxisParams
|
39
|
+
from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisProcess
|
40
|
+
from tomwer.core.process.reconstruction.scores.scores import (
|
41
|
+
_METHOD_TO_FCT,
|
42
|
+
compute_score_contrast_std,
|
43
|
+
)
|
44
|
+
from tomwer.core.utils.scanutils import MockHDF5
|
45
|
+
|
42
46
|
|
43
47
|
class TestScoreFunctions(unittest.TestCase):
|
44
48
|
"""Test all the score functions"""
|
@@ -28,15 +28,16 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "27/02/2021"
|
29
29
|
|
30
30
|
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31
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+
import os
|
32
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+
import shutil
|
33
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+
import tempfile
|
31
34
|
import unittest
|
35
|
+
|
32
36
|
from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
|
33
|
-
SADeltaBetaProcess,
|
34
37
|
SADeltaBetaParams,
|
38
|
+
SADeltaBetaProcess,
|
35
39
|
)
|
36
40
|
from tomwer.core.utils.scanutils import MockHDF5
|
37
|
-
import os
|
38
|
-
import tempfile
|
39
|
-
import shutil
|
40
41
|
|
41
42
|
|
42
43
|
class TestSADeltaBetaProcess(unittest.TestCase):
|
@@ -28,16 +28,16 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "03/08/2020"
|
29
29
|
|
30
30
|
|
31
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+
import code
|
32
|
+
import logging
|
33
|
+
|
34
|
+
import tomwer.version
|
31
35
|
from tomwer.core.process.task import Task
|
36
|
+
from tomwer.core.scan.edfscan import EDFTomoScan
|
32
37
|
from tomwer.core.scan.scanbase import TomwerScanBase
|
33
38
|
from tomwer.core.scan.scanfactory import ScanFactory
|
34
|
-
from tomwer.core.scan.edfscan import EDFTomoScan
|
35
39
|
from tomwer.core.utils.scanutils import data_identifier_to_scan
|
36
40
|
from tomwer.core.utils.volumeutils import volume_identifier_to_volume
|
37
|
-
import tomwer.version
|
38
|
-
import logging
|
39
|
-
import code
|
40
|
-
|
41
41
|
|
42
42
|
_logger = logging.getLogger(__name__)
|
43
43
|
|
@@ -53,9 +53,7 @@ class PythonScript(
|
|
53
53
|
elif isinstance(scan, (TomwerScanBase, type(None))):
|
54
54
|
scan = scan
|
55
55
|
else:
|
56
|
-
raise ValueError(
|
57
|
-
"input type of {}: {} is not managed" "".format(scan, type(scan))
|
58
|
-
)
|
56
|
+
raise ValueError(f"input type of {scan}: {type(scan)} is not managed")
|
59
57
|
# load volume
|
60
58
|
volume = volume_identifier_to_volume(self.inputs.volume)
|
61
59
|
|
tomwer/core/process/task.py
CHANGED
@@ -34,22 +34,21 @@ __license__ = "MIT"
|
|
34
34
|
__date__ = "27/07/2021"
|
35
35
|
|
36
36
|
|
37
|
-
import h5py
|
38
|
-
import numpy
|
39
|
-
from datetime import datetime
|
40
|
-
from typing import Union
|
41
|
-
from silx.io.dictdump import dicttoh5
|
42
|
-
from collections import namedtuple
|
43
|
-
from silx.io.dictdump import h5todict
|
44
|
-
from tomoscan.io import HDF5File
|
45
|
-
import typing
|
46
37
|
import logging
|
47
|
-
from silx.io.utils import h5py_read_dataset
|
48
38
|
import multiprocessing
|
39
|
+
import typing
|
40
|
+
from collections import namedtuple
|
41
|
+
from datetime import datetime
|
42
|
+
from typing import Union
|
43
|
+
|
44
|
+
import h5py
|
45
|
+
import numpy
|
49
46
|
import silx
|
50
|
-
from ewokscore.taskwithprogress import TaskWithProgress as _EwoksTaskWithProgress
|
51
47
|
from ewokscore.task import Task as _EwoksTask
|
52
|
-
|
48
|
+
from ewokscore.taskwithprogress import TaskWithProgress as _EwoksTaskWithProgress
|
49
|
+
from silx.io.dictdump import dicttoh5, h5todict
|
50
|
+
from silx.io.utils import h5py_read_dataset
|
51
|
+
from tomoscan.io import HDF5File
|
53
52
|
|
54
53
|
mult_manager = multiprocessing.Manager()
|
55
54
|
|
@@ -28,21 +28,24 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "05/04/2019"
|
29
29
|
|
30
30
|
|
31
|
+
import os
|
31
32
|
import shutil
|
32
33
|
import tempfile
|
33
34
|
import unittest
|
34
|
-
|
35
|
-
import os
|
35
|
+
|
36
36
|
import h5py
|
37
|
-
|
38
|
-
from
|
39
|
-
|
40
|
-
from tomwer.core.scan.scanbase import TomwerScanBase
|
41
|
-
from tomwer.core.process.reconstruction.axis.params import AxisRP
|
37
|
+
import numpy
|
38
|
+
from silx.io.utils import h5py_read_dataset
|
39
|
+
|
42
40
|
from tomwer.core.process.reconstruction.axis.mode import AxisMode
|
43
|
-
from tomwer.core.
|
41
|
+
from tomwer.core.process.reconstruction.axis.params import AxisRP
|
44
42
|
from tomwer.core.process.task import Task
|
45
|
-
from
|
43
|
+
from tomwer.core.scan.edfscan import EDFTomoScan
|
44
|
+
from tomwer.core.scan.scanbase import TomwerScanBase
|
45
|
+
from tomwer.core.utils.scanutils import MockEDF, MockHDF5
|
46
|
+
from tomwer.tests.utils import UtilsTest
|
47
|
+
|
48
|
+
from ..reconstruction.axis.axis import AxisProcess
|
46
49
|
|
47
50
|
|
48
51
|
class TestAxisIO(unittest.TestCase):
|
@@ -28,16 +28,16 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "19/07/2018"
|
29
29
|
|
30
30
|
|
31
|
-
import unittest
|
32
31
|
import shutil
|
33
32
|
import tempfile
|
33
|
+
import unittest
|
34
34
|
|
35
|
-
from tomwer.core.utils.scanutils import MockEDF
|
36
|
-
from tomwer.core.scan.scanbase import TomwerScanBase
|
37
35
|
from tomwer.core.process.conditions.filters import (
|
38
|
-
RegularExpressionFilter,
|
39
36
|
FileNameFilter,
|
37
|
+
RegularExpressionFilter,
|
40
38
|
)
|
39
|
+
from tomwer.core.scan.scanbase import TomwerScanBase
|
40
|
+
from tomwer.core.utils.scanutils import MockEDF
|
41
41
|
|
42
42
|
|
43
43
|
class TestConditionalFilter(unittest.TestCase):
|
@@ -46,10 +46,10 @@ class TestConditionalFilter(unittest.TestCase):
|
|
46
46
|
"""
|
47
47
|
|
48
48
|
def testPattern1(self):
|
49
|
-
|
50
|
-
self.assertTrue(
|
51
|
-
self.assertTrue(
|
52
|
-
self.assertTrue(
|
49
|
+
filter_ = RegularExpressionFilter("name10")
|
50
|
+
self.assertTrue(filter_.isFiltered("toto") is True)
|
51
|
+
self.assertTrue(filter_.isFiltered("name10") is False)
|
52
|
+
self.assertTrue(filter_.isFiltered("name100") is False)
|
53
53
|
|
54
54
|
def testInputOutput(self):
|
55
55
|
pass
|
@@ -32,18 +32,19 @@ import os
|
|
32
32
|
import shutil
|
33
33
|
import tempfile
|
34
34
|
import unittest
|
35
|
+
|
35
36
|
import numpy
|
36
|
-
from
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
37
|
+
from tomoscan.esrf.scan.utils import get_data
|
38
|
+
|
39
|
+
from tomwer.core.process.reconstruction.darkref.params import DKRFRP
|
40
|
+
from tomwer.core.process.reconstruction.darkref.params import ReduceMethod as cMethod
|
41
|
+
from tomwer.core.scan.hdf5scan import HDF5TomoScan
|
41
42
|
from tomwer.core.scan.scanbase import TomwerScanBase
|
43
|
+
from tomwer.core.utils.scanutils import MockEDF, MockHDF5
|
44
|
+
from tomwer.tests.utils import UtilsTest
|
45
|
+
|
42
46
|
from ..reconstruction.darkref.darkrefs import DarkRefs
|
43
47
|
from ..reconstruction.darkref.darkrefscopy import DarkRefsCopy
|
44
|
-
from tomwer.tests.utils import UtilsTest
|
45
|
-
from tomwer.core.scan.hdf5scan import HDF5TomoScan
|
46
|
-
from tomoscan.esrf.scan.utils import get_data
|
47
48
|
|
48
49
|
|
49
50
|
class TestDarkRefIO(unittest.TestCase):
|
@@ -28,11 +28,13 @@ __license__ = "MIT"
|
|
28
28
|
__date__ = "09/06/2020"
|
29
29
|
|
30
30
|
|
31
|
-
import unittest
|
32
|
-
import tempfile
|
33
|
-
import shutil
|
34
31
|
import os
|
32
|
+
import shutil
|
33
|
+
import tempfile
|
34
|
+
import unittest
|
35
|
+
|
35
36
|
import h5py
|
37
|
+
|
36
38
|
from tomwer.core.process.control.datalistener.rpcserver import _BaseDataListenerThread
|
37
39
|
|
38
40
|
|
@@ -30,25 +30,27 @@ __date__ = "05/04/2019"
|
|
30
30
|
|
31
31
|
import gc
|
32
32
|
import os
|
33
|
-
import
|
33
|
+
import shutil
|
34
|
+
import tempfile
|
34
35
|
import time
|
36
|
+
import unittest
|
37
|
+
|
38
|
+
import h5py
|
35
39
|
import numpy
|
36
40
|
import pytest
|
37
|
-
import
|
38
|
-
import
|
39
|
-
import
|
41
|
+
from nxtomomill.converter import from_h5_to_nx
|
42
|
+
from nxtomomill.io.config.hdf5config import TomoHDF5Config
|
43
|
+
from tomoscan.esrf.scan.hdf5scan import ImageKey
|
40
44
|
from tomoscan.io import HDF5File
|
45
|
+
from tomoscan.validator import is_valid_for_reconstruction
|
46
|
+
|
47
|
+
from tomwer.core.process.control.datalistener import DataListener
|
48
|
+
from tomwer.core.process.control.scantransfer import ScanTransfer
|
41
49
|
from tomwer.core.scan.hdf5scan import HDF5TomoScan
|
42
|
-
from tomwer.core.utils.scanutils import MockEDF
|
43
50
|
from tomwer.core.scan.scanbase import TomwerScanBase
|
44
|
-
from tomwer.core.
|
45
|
-
from tomwer.tests.utils import UtilsTest
|
51
|
+
from tomwer.core.utils.scanutils import MockEDF
|
46
52
|
from tomwer.synctools.rsyncmanager import RSyncManager
|
47
|
-
from tomwer.
|
48
|
-
from nxtomomill.converter import from_h5_to_nx
|
49
|
-
from nxtomomill.io.config.hdf5config import TomoHDF5Config
|
50
|
-
from tomoscan.validator import is_valid_for_reconstruction
|
51
|
-
from tomoscan.esrf.scan.hdf5scan import ImageKey
|
53
|
+
from tomwer.tests.utils import UtilsTest
|
52
54
|
|
53
55
|
|
54
56
|
class TestDataTransferIO(unittest.TestCase):
|
@@ -30,10 +30,12 @@ __date__ = "05/04/2019"
|
|
30
30
|
|
31
31
|
import os
|
32
32
|
import time
|
33
|
+
|
33
34
|
import pytest
|
35
|
+
|
36
|
+
from tomwer.core.process.control.datawatcher import DataWatcher
|
34
37
|
from tomwer.core.process.control.datawatcher.status import DET_END_XML, PARSE_INFO_FILE
|
35
38
|
from tomwer.core.utils.scanutils import MockEDF
|
36
|
-
from tomwer.core.process.control.datawatcher import DataWatcher
|
37
39
|
from tomwer.core.utils.threads import LoopThread
|
38
40
|
|
39
41
|
|