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Aug 2 2016

schwarzt added projects to T3099: Organize shape model distribution on CD: MITK, Bugzilla.
Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added a comment to T3049: Segmentation bundle: Lymph Node shapemodel segmentation spams an error message.

Thx Marco. Works for me with Rev. 20563 installer.
Will remove the Debug output, then close.

Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added projects to T3050: Shape model part: Abort button crashes: MITK, Bugzilla.
Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added a comment to T3049: Segmentation bundle: Lymph Node shapemodel segmentation spams an error message.

Removed debug output -> Resolved.

Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added a comment to T3050: Shape model part: Abort button crashes.

[SVN revision 20375]
FIX (#3050): Quickfix: Abort button now only stops segmentation; model remains in undefined state and is not removed. But does not crash app any more.

Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added a comment to T3049: Segmentation bundle: Lymph Node shapemodel segmentation spams an error message.

[SVN revision 20569]
FIX (#3049): Removed debug output; (Also made some error output more presentable).

Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added a comment to T3050: Shape model part: Abort button crashes.

[SVN revision 20377]
FIX (#3050): Controlled abort of segmentation. A binary image is still created. Abort can also be used to stop the segmentation when quality is sufficient.

Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added a comment to T3049: Segmentation bundle: Lymph Node shapemodel segmentation spams an error message.

As a quick fix, you can copy the file
/home/kast/public-html/Lymphnode_SM.zip
and extract it in your
/home/.mitk folder.

Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added a comment to T3049: Segmentation bundle: Lymph Node shapemodel segmentation spams an error message.

Cannot work in the moment with the installer.
The lymph node shape and appearance model are not distributed with MITK.
See T2979 for more information.

Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added a comment to T3049: Segmentation bundle: Lymph Node shapemodel segmentation spams an error message.

[SVN revision 20368]
FIX (#3049): Use binary version of appearance model

Aug 2 2016, 9:32 AM · Bugzilla, MITK
schwarzt added projects to T3021: App crashes when loading an image after closing ImageNavigator: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T3003: Severe memory leak in Segmentation: Shape Model part.

Seems to work now.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T3003: Severe memory leak in Segmentation: Shape Model part: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T3003: Severe memory leak in Segmentation: Shape Model part.

[SVN revision 20359]
FIX (#3003): Try to reset the ShapeModelGeometry3D when cleaning ShapeModelData

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T3003: Severe memory leak in Segmentation: Shape Model part.

[SVN revision 20322]
FIX (#3003): Clean up Shape Model Data after usage. Mostly fixes this problem.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T3003: Severe memory leak in Segmentation: Shape Model part.

[SVN revision 20317]
FIX (#3003): Make ClearData method public

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T3003: Severe memory leak in Segmentation: Shape Model part.

[SVN revision 20313]
FIX (#3003): Add ClearData method for ShapeModelData

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2990: 4D support for Segmentation bundle: Lymph node part;: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2988: 4D support for Segmentation bundle: Shape Model part.

Shape model should now be able to segment a single time step of a 4D image.
Time step has still to be set 'outside' of segmentation perspective, but segmentation is done on the correct time step, as is the creation and display of binary image.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2989: 4D support for Segmentation bundle: Contouring part; Please Test!.

Not necessary, seems to work as expected.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2989: 4D support for Segmentation bundle: Contouring part; Please Test!: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2988: 4D support for Segmentation bundle: Shape Model part.

[SVN revision 20213]
FIX (#2988): 4D image support for shape models in Segmentation module; also: Removed memory leak when creating binary image; adapted names for load to binary shape models

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2988: 4D support for Segmentation bundle: Shape Model part: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2987: Segmentation with shape model still crashes after finishing.

Forgot adding keyword 3M3

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2987: Segmentation with shape model still crashes after finishing.

[SVN revision 20360]
FIX (#2987): Also clear the model nodes

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2987: Segmentation with shape model still crashes after finishing.

Pressing the "Abort Segmentation" leads to the same (similar?) problem.
Considering this critical.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2987: Segmentation with shape model still crashes after finishing.

Missing step:

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2987: Segmentation with shape model still crashes after finishing: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2987: Segmentation with shape model still crashes after finishing.

Positively tested with current installer -> Works.
But, actual bug still not fixed.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2987: Segmentation with shape model still crashes after finishing.

[SVN revision 20361]
FIX (#2987): Do not clean filter on startup; set aborted to false again after abortion. Only clean filter once.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2987: Segmentation with shape model still crashes after finishing.

Bug still not fixed. But works for me now in Release mode.
Two ideas where it could come from:

  • ShapeModelData is not cleared correctly. A Problem, but most likely not cause of the bug.
  • Something with the tool event sending/receiving or methods triggered by them.

Problem does not occur anymore when commenting out both:
m_ToolManager->NewNodesGenerated.Send(); (ln 249)
m_ToolManager->ActivateTool( -1 ); (ln 251)
in ShapeModelTool.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2979: Organize shape models distribution.

Does no longer block #3049, as the models are distributed with the installer.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2979: Organize shape models distribution.

Verified, works for me with installer Rev. 20568.
Does no longer block #2698, then, as models are theoretically always available. Will open a new bug for CD distribution.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2979: Organize shape models distribution.

Special case is the Lymph node shape model: 2 Files, together 72 kB.
These are in the moment not supported to be loaded from the internet.
Could these be somehow included in the installer? E.g. as Qt resource?

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2973: Enable slice interactor while shape model placement.

[SVN revision 20596]
FIX (#2973): Signal was not emitted any more when tool was zero.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2973: Enable slice interactor while shape model placement.

[SVN revision 20312]
FIX (#2973): Quickfix: Only emit button clicked signal when not a shape model tool.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2973: Enable slice interactor while shape model placement: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2973: Enable slice interactor while shape model placement.

Reopened.
Sometimes slice interactor is not restored after lymph node segmentation finished.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2961: Segmentation of 3D+t images not working.

Known issue: See T2987

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2961: Segmentation of 3D+t images not working.

It is still possible to press continue after crash.
-> Works for me.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2946: Crash after creating segmentation: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2930: Shape Model disappeares when selecting it in data manager.

Would it be possible to not show the model at all in data manager, then?
At least for 3M, the user should anyways not be able to do something with the model except for using it for segmentation.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2928: Initialize shape model matrix by image: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2929: Use binary shape models always.

[SVN revision 20247]
FIX (#2929): Use binary appearance model

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2928: Initialize shape model matrix by image.

[SVN revision 20235]
FIX (#2928): Don't use matrix for LV wall models because of shear strain

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2928: Initialize shape model matrix by image.

Have tried some matrix initialization from the image.
Still initializes shape model upside down for images with non-CT geometry.
As debugging is not possible due to non-stop exceptionsin the "segmentation" module, I am not able and willing to continue working on this bug.
I will not remodel support for non-uniform geometries again.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2929: Use binary shape models always.

Changed for all models;
Hannes, added a zip with lymph node models to your directory.
Would it be possible to load them via internet, too?

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2928: Initialize shape model matrix by image.

[SVN revision 20184]
FIX (#2928): Fix liver default init (actually it never worked before...)

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2929: Use binary shape models always.

Got all except liver model. Will convert it.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2929: Use binary shape models always.

[SVN revision 20248]
FIX (#2929): Use binary shape model

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2928: Initialize shape model matrix by image.

Okay, fixed.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2928: Initialize shape model matrix by image.

For the LV wall models, the geometry matrix is a matrix product of rotation and shear strain. Because the models were trained on the sheared data, they do not need to be sheared again explicitely.
But, sole rotation can't be extracted or estimated from the matrix.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2928: Initialize shape model matrix by image.

[SVN revision 20092]
FIX (#2928): Initialize shape model by image matrix

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2929: Use binary shape models always: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2929: Use binary shape models always.

Changed title; password protection should not be necessary.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2928: Initialize shape model matrix by image.

[SVN revision 20174]
FIX (#2928): Only do default transform and matrix init if no automatic method is available

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2930: Shape Model disappeares when selecting it in data manager: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2927: Make 2D Geometries coordinate systems consistent with 3D.

[SVN revision 21076]
FIX (#2927): Make 2D index coordinates corner based.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2927: Make 2D Geometries coordinate systems consistent with 3D: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2927: Make 2D Geometries coordinate systems consistent with 3D.

AbstractTransformGeometry already tests this more or less -> All tests added -> Closed.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2927: Make 2D Geometries coordinate systems consistent with 3D.

Trying to fix this today.
-> Requesting core mod again.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2927: Make 2D Geometries coordinate systems consistent with 3D.

[SVN revision 21199]
ADD (#2927): Simple test for coordinate system consistency

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2927: Make 2D Geometries coordinate systems consistent with 3D.

Added change request. Requesting core mod.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2907: RenderWindows show wrong plane after loading a 2D image.

I talked about this with Daniel S. yesterday. Don't think it is a coordinate system problem.
Rendering problems without initialization are quite obvious, from where should the renderer, SliceNavigationController etc. now the image geometries?

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2907: RenderWindows show wrong plane after loading a 2D image.

Problem does not occur any more.
Most likely because images are now reinited after loading.
Note: This does not actually solve the initial problem, which is still unknown.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2883: Check for NaN's in mitk::Geometry3D still necessary? Speed considerations..

Not really 3M3 relevant.
Most likely not so great effect on execution speed.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2885: Strange function in mitk::Geometry3D().

[SVN revision 20007]
FIX (#2401): Adapt convenience method for WorldToIndex with Itk Index to
corrected MITK coordinate system, and therefore rounding.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2884: BackTransform in Geometry3D still uses the unstable ITK Matirx inversion.

Fixed by using ->GetInverse.
Relocated Multiplication with inverse matrix to seperate method
MultiplyWithWorldToIndex.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2885: Strange function in mitk::Geometry3D().

It seems that in this function the 0.5 pixel offset is calculated a second time (but wrong for negative values(?) ).

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2884: BackTransform in Geometry3D still uses the unstable ITK Matirx inversion.

Req. core mod.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2883: Check for NaN's in mitk::Geometry3D still necessary? Speed considerations..

Thomas or Daniel,
can you try to run a long lasting registration with and without these lines:

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2885: Strange function in mitk::Geometry3D().

Req. core mod

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2885: Strange function in mitk::Geometry3D(): MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2884: BackTransform in Geometry3D still uses the unstable ITK Matirx inversion.

[SVN revision 20058]
FIX (#2884): Use stable matrix inversion; relocated multiplication to separate function.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2885: Strange function in mitk::Geometry3D().

Fixed by above commit

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2884: BackTransform in Geometry3D still uses the unstable ITK Matirx inversion: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2885: Strange function in mitk::Geometry3D().

Looking at mitk::Geometry3D, there are still some remnants from before voxel center change, as well as not adapted mehtods (not noticed because they are not used). This class has to be cleaned up for the new coordinate system.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2885: Strange function in mitk::Geometry3D().

Not the pixel offset is changed, but rounded.
Anyhow, the rounding is not compatible with the changed coordinate systems anymore.
Must use floor().

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2883: Check for NaN's in mitk::Geometry3D still necessary? Speed considerations..

Patch for possible removal of NaN check in inner loop

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2883: Check for NaN's in mitk::Geometry3D still necessary? Speed considerations.: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2883: Check for NaN's in mitk::Geometry3D still necessary? Speed considerations..

Added patch. Daniel, please have a look at it.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to F368: NoNaNCheckGeometry3D.patch.

Patch for possible removal of NaN check in inner loop

Aug 2 2016, 9:31 AM
schwarzt added projects to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

[SVN revision 19959]
FIX (#2874): Add SetPoints() method to mitkPointLocator which takes itk PointSets

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2877: Comment out misleading options MITK_ITK_SOURCE_DIR for CMake GUI.

[SVN revision 19964]
FIX (#2877): Removed options MITK_ITK_SOURCE_DIR and MITK_VTK_SOURCE_DIR in CMake GUI

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

Closed.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added projects to T2877: Comment out misleading options MITK_ITK_SOURCE_DIR for CMake GUI: MITK, Bugzilla.
Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

Closing anyway to keep bug list more managable.
Test T2442 is still open.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

Due to ITK templatings, PointSet has to be further defined...

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

[SVN revision 19987]
FIX (#2874): Further define itk::PointSet template. Also use check if rebuild needed for Mitk and Itk point sets.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

Not 3M3 relevant.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

Okay, not closed because tests are missing. (#2442).
But fixed.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

Fixed -> Closed.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2877: Comment out misleading options MITK_ITK_SOURCE_DIR for CMake GUI.

Fixed.

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2874: Add SetPoints() method to mitkPointLocator which takes itk PointSets.

Will also add checks if MITK or ITK pointsets have changed for speed considerations. (As already done for Vtk pointsets.)

Aug 2 2016, 9:31 AM · Bugzilla, MITK
schwarzt added a comment to T2849: TotalVariationFilter used in BasicImageProcessing is internal.

Just found it:
Warning: org.mitk.gui.qt.basicimageprocessing is missing requirements and won't be built. Missing: MitkSB;MitkDiffusionImagingMBI

Aug 2 2016, 9:30 AM · Bugzilla, MITK
schwarzt added a comment to T2849: TotalVariationFilter used in BasicImageProcessing is internal.

I will check it.

Aug 2 2016, 9:30 AM · Bugzilla, MITK
schwarzt added a comment to T2849: TotalVariationFilter used in BasicImageProcessing is internal.

Seems to work.
Let's check tomorrows dart client, then close.

Aug 2 2016, 9:30 AM · Bugzilla, MITK
schwarzt added projects to T2849: TotalVariationFilter used in BasicImageProcessing is internal: MITK, Bugzilla.
Aug 2 2016, 9:30 AM · Bugzilla, MITK
schwarzt added projects to T2848: Auto select newly created child nodes: MITK, Bugzilla.
Aug 2 2016, 9:30 AM · Bugzilla, MITK