hm, strange. Ad hoc I cannot give a hint. Good you found a workarround. For further investigation, may be mitk::Image has special wrapping instruction, that interferes with your approach.
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Jul 30 2020
Jul 30 2020
• thomass added a revision to T27105: [MITKDoc] Revise Measurement Plugin Documentation: Unknown Object (Differential Revision).
floca edited projects for T27498: [Selection widgets] Define default for auto selection / listening mechanism, added: MITK (v2021.02), Restricted Project; removed MITK.
To finish this task, one should check/verify that all release relevant plugins follow the discussion result.
I'm setting up a clang 10 dart client right now. If that is submitting successfully I would close the task
• thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
I can reproduce the behavior for the US4DCyl but not for the heart 3D+t. But it looks exactly like the error for static segmentation and t=2 (that I showed during the telco).
floca committed rMITKc5e3da10dab6: T27692 Fixed mitk::IsSubGeometry for oblique geometries. (authored by floca).
T27692 Fixed mitk::IsSubGeometry for oblique geometries.
floca committed rMITKdac974bc335d: Fixed mitk::IsSubGeometry for oblique geometries. (authored by floca).
Fixed mitk::IsSubGeometry for oblique geometries.
Jul 29 2020
Jul 29 2020
Is this task resolved with the landing of {D360}?
kislinsk added a revision to T27612: Fix build errors with clang 10.x : Unknown Object (Differential Revision).
floca committed rMITKc72fa5e21c97: T25805 Cleaned up naming of DICOM related modules (authored by floca).
T25805 Cleaned up naming of DICOM related modules
floca committed rMITKec3a2c5a9588: Merge branch 'develop' into feature/T25805-merged (authored by floca).
Merge branch 'develop' into feature/T25805-merged
Fixed missed case sensitive naming change
Fixed review remarks
floca committed rMITK61b852be152c: Commit missed changes of one renamed directory (authored by floca).
Commit missed changes of one renamed directory
Cleaned up naming of DICOM related modules
floca closed T25805: Standardize/Rework DICOM module naming as Resolved by committing rMITKfb6195ff763a: Cleaned up naming of DICOM related modules.
floca committed rMITKe72944cdcf37: Renamed plugin org.mitk.gui.qt.dicom into org.mitk.gui.qt.dicombrowser (authored by floca).
Renamed plugin org.mitk.gui.qt.dicom into org.mitk.gui.qt.dicombrowser
Deleted branch bugfix/T27085-2DRegionGrowing.
kislinsk committed rMITK99e147b96882: Keep region grower thresholds within the pixel type extrema of the reference… (authored by kislinsk).
Keep region grower thresholds within the pixel type extrema of the reference…
kislinsk committed rMITKaf6ba9b47f82: Keep region grower thresholds within the pixel type extrema of the reference… (authored by kislinsk).
Keep region grower thresholds within the pixel type extrema of the reference…
Seems like I figured it out. What I had to do was to change SWIG_TypeQuery("_p_mitk__Image") to SWIG_TypeQuery("_p_itk__SmartPointerT_mitk__Image_t") and change the type of image to mitk::Image::Pointer *image. When passing Pic3D now and printing the number of dimensions, 3 is printed as one would expect. I will further investigate how to interact with other libraries like SimpleITK.
floca added a revision to T27001: Rename org.mitk.gui.qt.dicom to org.mitk.gui.qt.dicombrowser: Restricted Differential Revision.
floca committed rMITK65691bb2f0df: Fixed PerfusionMiniApp to also support 2 step linear model (authored by floca).
Fixed PerfusionMiniApp to also support 2 step linear model
floca committed rMITKb0e2beec1246: T27581 Fixed PerfusionMiniApp to also support 2 step linear model (authored by floca).
T27581 Fixed PerfusionMiniApp to also support 2 step linear model
I tried an approach like @floca suggested with the SWIG wrapping that is already available in MITK. Here is my code to transfer a MITK image from C++ to Python:
kalali added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
@thomass I checked Fast Marching 3D and re-opened T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images for the static mask cases.
Could you re-check the dynamic case? I tested it and with t = 0 I got a dynamic mask (4D) with a segmentation only on the first (0) timestep but with t != 0 I have the same problem as described in the mentioned task (green contour nowhere near the seed point).
kalali renamed T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images from Fast Marching 3D Tool only supported for first time step in 4D images to [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.
kalali added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
So Region Growing 3D seems to work and could probably be used for reference for other algorithms.
kalali renamed T27621: [Segmentation] 3D Threshold / UL Threshold does not use a timestep != 0 for static masks from [Segmentation] 3D Threshold does not use a timestep != 0 for static masks to [Segmentation] 3D Threshold / UL Threshold does not use a timestep != 0 for static masks.
kalali renamed T27622: [Segmentation] Make 3D Threshold / UL Threshold only for on a single timestep for a dynamic mask from [Segmentation] Make 3D Threshold only for on a single timestep for a dynamic mask to [Segmentation] Make 3D Threshold / UL Threshold only for on a single timestep for a dynamic mask.
• thomass closed T27615: [Segmentation] Threshold and UL threshold show unwanted behavior on static and dynamic segmentations as Invalid.
duplicate of T27621
• thomass raised the priority of T27616: [Segmentation] Otsu creates static 3D segmentation regardless of segmentation choice from Normal to High.
kalali triaged T27621: [Segmentation] 3D Threshold / UL Threshold does not use a timestep != 0 for static masks as High priority.
Resolved with D369
Fix ImageCropper startup crash
Fix ImageCropper startup crash
kompan moved T27619: MR Perfusion: Use model fit result relation rules for predicate definition from Backlog to Perfusion on the MITK (v2021.02) board.
kompan triaged T27619: MR Perfusion: Use model fit result relation rules for predicate definition as Normal priority.
that was misleading since the statistics view is in the measurement toolkit view (actually it is quite confusing, maybe we can change that in general)
Merge branch 'T27618-UpdateReadme'
added ubuntu 20.04
Pushed new branch T27618-UpdateReadme.
kompan committed rMITK24158ffb55c1: Use mitkSingleNodeSelectionWidget instead of QmitkDataStorageComboBox. (authored by kompan).
Use mitkSingleNodeSelectionWidget instead of QmitkDataStorageComboBox.
kompan committed rMITKe8c6a0a2ad5a: Case sensitive spelling of QmitkSingelNodeSelectionWidget. (authored by kompan).
Case sensitive spelling of QmitkSingelNodeSelectionWidget.
Remove unrequired include file.
kompan committed rMITK8d63af91b336: Update GUI controls, when AIF mask and image selection has changed. (authored by kompan).
Update GUI controls, when AIF mask and image selection has changed.
Enable auto select for AIF mask.
kompan committed rMITK28cfe9a3e4fd: Replace AIF mask and image combo boxes with single node selection widgets. (authored by kompan).
Replace AIF mask and image combo boxes with single node selection widgets.
kompan committed rMITK1b6ec1748f4f: Rename OnSelectionChanged to OnNodeSelectionChanged. (authored by kompan).
Rename OnSelectionChanged to OnNodeSelectionChanged.
Change size policies.
kompan committed rMITKafa09efbeea1: Refactor AIF mask and AIF image selection using new selection concept. (authored by kompan).
Refactor AIF mask and AIF image selection using new selection concept.
Change mask selection to be optional.
kompan committed rMITK1e641f1b87ae: Activate auto select for time series selection. (authored by kompan).
Activate auto select for time series selection.
kompan committed rMITK73f49980871d: Merge branch 'feature/T27043-RefactorModelFitAndPharmacokineticsPluginToUseNewS… (authored by kompan).
Merge branch 'feature/T27043-RefactorModelFitAndPharmacokineticsPluginToUseNewS…
kompan committed rMITKeab41537a7bf: Narrow predicates for time series, mask and PDW image selection. (authored by kompan).
Narrow predicates for time series, mask and PDW image selection.
kompan committed rMITKcaf612b04010: Replace DataStorageComboBoxes with SingleNodeSelectionWidgets for timeseries… (authored by kompan).
Replace DataStorageComboBoxes with SingleNodeSelectionWidgets for timeseries…
• thomass added a revision to T27103: [MITKDoc] Revise Point Set Interaction Plugin Documentation: Restricted Differential Revision.
kompan committed rMITK234bec8db139: Use mitkSingleNodeSelectionWidget instead of QmitkDataStorageComboBox. (authored by kompan).
Use mitkSingleNodeSelectionWidget instead of QmitkDataStorageComboBox.
Introduced ModelFitResultRelationRule
Fixed review remarks
Fixed gcc compile errors
floca committed rMITK154cd9ee0f1c: Improved test coverage of SourceImageRelationRule and ModelFitResultRelationRule (authored by floca).
Improved test coverage of SourceImageRelationRule and ModelFitResultRelationRule
floca committed rMITKa1f71ea0ee6f: Fixed business logic in the ModelFitInspectorView (authored by floca).
Fixed business logic in the ModelFitInspectorView
floca committed rMITK58e8ee2b8bd9: Fixed T26142 by adding persistency for needed PropertyRule properties. (authored by floca).
Fixed T26142 by adding persistency for needed PropertyRule properties.
floca committed rMITK98394bbae559: Deprecated old modelfit UID scheme (now uses property rule) (authored by floca).
Deprecated old modelfit UID scheme (now uses property rule)
Added ModelFitResultRelationRule
floca closed T26142: Property persistence for property relation instance identifing (RII) properties, a subtask of T23754: DataStorage/Relationship clean up/refactoring, as Resolved.
Corrected ModelFit property description
Corrected include guard
Eventually related to changes in D360
• thomass triaged T27617: [ImageCropper] Workbench crashes when the plugin is opened as High priority.
• thomass moved T27608: [MITKDoc] Documentation Refurbish - Developer Manual from Backlog to Documentation on the MITK (v2021.02) board.
Jul 28 2020
Jul 28 2020
If you use Python 3.7/3.8, you need to install SWIG version 4.0.2. This solves the problem. Currently, SWIG version 3.0.2. is installed in the Superbuild.