Page MenuHomePhabricator
Feed All Stories

Tue, Nov 22

floca committed rMITK7a869a55d24d: Fixed T29391 (authored by floca).
Fixed T29391
Tue, Nov 22, 11:57 AM
franza triaged T29412: List of MITK publications on web page is not up to date as High priority.
Tue, Nov 22, 11:56 AM · Request for Discussion, MITK
floca claimed T29391: [Segmentation] Prevent multi-label images to be saved as unsupported image formats.
Tue, Nov 22, 11:55 AM · MITK
kislinsk updated the task description for T29406: Make MITK compatible with Qt 6.
Tue, Nov 22, 9:44 AM · MITK
kislinsk updated the task description for T29406: Make MITK compatible with Qt 6.
Tue, Nov 22, 8:57 AM · MITK
kislinsk triaged T29406: Make MITK compatible with Qt 6 as Normal priority.
Tue, Nov 22, 8:56 AM · MITK

Mon, Nov 21

kalali added a comment to T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.

@kalali please indicate that it has breaking changes in your commit message and how to handle them/migrate. thanks.

Mon, Nov 21, 4:49 PM · Breaking Change, Noteworthy, MITK
kalali edited projects for T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations, added: Breaking Change; removed Request for Discussion.
Mon, Nov 21, 4:48 PM · Breaking Change, Noteworthy, MITK
kalali closed T29394: [mxn multi widget] Image cropper shows weird behavior as Resolved.
Mon, Nov 21, 4:33 PM · MITK
kalali committed rMITK84009201569b: Reset mapper for crosshair plane nodes (authored by kalali).
Reset mapper for crosshair plane nodes
Mon, Nov 21, 4:31 PM
kalali committed rMITK92a5bee04caa: Remove unnecessary layer information (authored by kalali).
Remove unnecessary layer information
Mon, Nov 21, 4:31 PM
kalali committed rMITK96b30f5acacf: Reset mapper everytime the data is changed (authored by kalali).
Reset mapper everytime the data is changed
Mon, Nov 21, 4:31 PM
kislinsk claimed T27701: Overhaul or remove PluginGenerator.
Mon, Nov 21, 2:02 AM · MITK, Next Milestone

Sun, Nov 20

Nils_Iseke added a comment to T27701: Overhaul or remove PluginGenerator.

Would be nice if a note is added to the documentation that the PluginGenerator is currently not active. :)

Sun, Nov 20, 9:09 AM · MITK, Next Milestone

Sat, Nov 19

floca added a project to T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations: Noteworthy.

@kalali please indicate that it has breaking changes in your commit message and how to handle them/migrate. thanks.

Sat, Nov 19, 8:11 PM · Breaking Change, Noteworthy, MITK

Fri, Nov 18

floca raised the priority of T29392: [Segmentation] Add dedicated writer to store multi-label images in nifti from Normal to High.
Fri, Nov 18, 8:04 PM · MITK (v2023.04), Next Milestone
floca added a comment to T29392: [Segmentation] Add dedicated writer to store multi-label images in nifti.

Expected output:

  • image for each label (file name: use specified name and add label value as suffix; will have no collision in the future as it is guaranteed with T29206 that label values will be unique throughout all groups)
  • json that contains the meta info
Fri, Nov 18, 8:03 PM · MITK (v2023.04), Next Milestone
kalali raised the priority of T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations from Low to Normal.
Fri, Nov 18, 12:32 PM · Breaking Change, Noteworthy, MITK
kalali added a parent task for T29386: [mxn multi widget] StdDisplay unnecessarily uses the crosshair manager: T29403: [mxn multi widget] Concept for crosshair data type.
Fri, Nov 18, 12:26 PM · MITK (v2023.04)
kalali added a subtask for T29403: [mxn multi widget] Concept for crosshair data type: T29386: [mxn multi widget] StdDisplay unnecessarily uses the crosshair manager.
Fri, Nov 18, 12:26 PM · MITK (v2023.04), Request for Discussion
kalali triaged T29403: [mxn multi widget] Concept for crosshair data type as Normal priority.
Fri, Nov 18, 12:26 PM · MITK (v2023.04), Request for Discussion
kalali added a parent task for T29335: [Segmentation] Show interactive warning for uninitialized render window geometry: T29402: [mxn multi widget] Concept for blocking individual render windows.
Fri, Nov 18, 11:32 AM · MITK (v2023.04)
kalali added a subtask for T29402: [mxn multi widget] Concept for blocking individual render windows: T29335: [Segmentation] Show interactive warning for uninitialized render window geometry.
Fri, Nov 18, 11:32 AM · MITK (v2023.04), Request for Discussion
kalali triaged T29402: [mxn multi widget] Concept for blocking individual render windows as Normal priority.
Fri, Nov 18, 11:32 AM · MITK (v2023.04), Request for Discussion
floca added a revision to T29391: [Segmentation] Prevent multi-label images to be saved as unsupported image formats: Unknown Object (Differential Revision).
Fri, Nov 18, 11:21 AM · MITK
floca added a revision to T29391: [Segmentation] Prevent multi-label images to be saved as unsupported image formats: Restricted Differential Revision.
Fri, Nov 18, 11:20 AM · MITK
floca added a comment to T29396: [Segmentation] Newly created labelset image has wrong image type.

Yes that's what I found out too. I wanted to test something by changing the threshold tool to accept a vector image and work with AccessVectorPixelTypeByItk_n and itk::VectorImage<TPixel, VImageDimension> VectorImageType; but let's discuss how we want to prioritize this.

Fri, Nov 18, 8:19 AM · MITK (v2023.04)
kalali added a comment to T29396: [Segmentation] Newly created labelset image has wrong image type.

Yes that's what I found out too. I wanted to test something by changing the threshold tool to accept a vector image and work with AccessVectorPixelTypeByItk_n and itk::VectorImage<TPixel, VImageDimension> VectorImageType; but let's discuss how we want to prioritize this.

Fri, Nov 18, 8:10 AM · MITK (v2023.04)

Thu, Nov 17

floca added a comment to T29396: [Segmentation] Newly created labelset image has wrong image type.

And we should add this case to our checklist in order to test seg not also with 3D and 3D+t, but also vector images.

Thu, Nov 17, 6:40 PM · MITK (v2023.04)
floca added a comment to T29396: [Segmentation] Newly created labelset image has wrong image type.

The problem is that Peter used a vector image. and now the mask is a vector image too, this is why the accessors do complain. I guess we have to fix the function that generates the plain segmentation image based on the image as template.

Thu, Nov 17, 6:39 PM · MITK (v2023.04)
kalali updated subscribers of T29396: [Segmentation] Newly created labelset image has wrong image type.

@floca The error seems to be inside AccessFixedTypeByItk_n, which produces a _accessByItkPixelTypeException (from inside Modules/Core/include/mitkImageAccessByItk.h

Thu, Nov 17, 6:07 PM · MITK (v2023.04)
kalali added a comment to T29396: [Segmentation] Newly created labelset image has wrong image type.

I looked into this and can verify the behavior.
I debugged and the crash happens inside ``
I tested other 3D tools, e.g. "Threshold" or "UL Threshold" (and even Otsu) and the following error message is shown:

Pixel type vector is not in (int)( unsigned int)( short)( unsigned short)( char)( unsigned char)(double)( float)
Thu, Nov 17, 6:01 PM · MITK (v2023.04)
kalali added a revision to T29394: [mxn multi widget] Image cropper shows weird behavior: Unknown Object (Differential Revision).
Thu, Nov 17, 5:08 PM · MITK
kalali added a comment to T29394: [mxn multi widget] Image cropper shows weird behavior.

When initializing the plane nodes inside CrosshairManager DataNode::SetMapper is called which results in the node's m_Mapper variable to hold a PlaneGeometryDataMapper2D at position 1 (mapper slot id is Standard2D = 1).
But if DataNode::GetMapper is called later with MapperSlotId = 1 the list m_Mappers is completely empty and a new mapper is created via the BoundingShapeObjectFactory.

Thu, Nov 17, 2:39 PM · MITK
r948e committed rMITKDIFFeecb00716e97: Polygonbutton not checkable anymore (authored by r948e).
Polygonbutton not checkable anymore
Thu, Nov 17, 2:11 PM
kalali added a comment to T29394: [mxn multi widget] Image cropper shows weird behavior.

Somehow it seems as if the BoundingShapeObjectFactory is the last factory to be checked for extra factories to create valid mappers and this one is then used (it overwrites previously existing mappers). I wonder why this does not happen for the StdMultiWidget.

Thu, Nov 17, 12:23 PM · MITK
kalali closed T29383: [mxn multi widget] Crosshair does not show a gap as Resolved.
Thu, Nov 17, 9:55 AM · MITK
kalali committed rMITK11d249cdf16a: Show crosshair gap (authored by kalali).
Show crosshair gap
Thu, Nov 17, 9:53 AM
kalali committed rMITKae1adc478989: Reuse the existing plane geometry data (authored by kalali).
Reuse the existing plane geometry data
Thu, Nov 17, 9:53 AM
neher triaged T29396: [Segmentation] Newly created labelset image has wrong image type as Normal priority.
Thu, Nov 17, 9:42 AM · MITK (v2023.04)
kalali claimed T29394: [mxn multi widget] Image cropper shows weird behavior.
Thu, Nov 17, 9:37 AM · MITK
kalali added a comment to T29394: [mxn multi widget] Image cropper shows weird behavior.

It seems as if there is something wrong with - check "mitk::CoreObjectFactory::CreateMapper but I have to go a little bit deeper. Maybe this is also related to {D755} because the crosshair planes do not get a specific mapper set.

Thu, Nov 17, 9:37 AM · MITK

Wed, Nov 16

r948e created T29395: Fix Polygon Bug.
Wed, Nov 16, 4:36 PM · MITK Diffusion
kalali triaged T29394: [mxn multi widget] Image cropper shows weird behavior as Normal priority.
Wed, Nov 16, 4:26 PM · MITK
kalali updated the task description for T29240: [mxn multi widget] Allow different time navigation controller for each individual render window.
Wed, Nov 16, 3:51 PM · MITK (v2023.04)
kalali edited parent tasks for T29240: [mxn multi widget] Allow different time navigation controller for each individual render window, added: T29393: [mxn multi widget] Concept for individual render window synchronization; removed: T28578: [mxn multi widget] Optimization of the mxn multi widget.
Wed, Nov 16, 3:49 PM · MITK (v2023.04)
kalali added a subtask for T29393: [mxn multi widget] Concept for individual render window synchronization: T29240: [mxn multi widget] Allow different time navigation controller for each individual render window.
Wed, Nov 16, 3:49 PM · MITK
kalali removed a subtask for T28578: [mxn multi widget] Optimization of the mxn multi widget: T29240: [mxn multi widget] Allow different time navigation controller for each individual render window.
Wed, Nov 16, 3:49 PM · MITK
kalali added a comment to T29393: [mxn multi widget] Concept for individual render window synchronization.

I added T24704: [Multi widget] Rules for updating the render windows as a somewhat related task.

Wed, Nov 16, 3:47 PM · MITK
kalali removed a subtask for T28578: [mxn multi widget] Optimization of the mxn multi widget: T24704: [Multi widget] Rules for updating the render windows.
Wed, Nov 16, 3:46 PM · MITK
kalali added a subtask for T29393: [mxn multi widget] Concept for individual render window synchronization: T24704: [Multi widget] Rules for updating the render windows.
Wed, Nov 16, 3:46 PM · MITK
kalali edited parent tasks for T24704: [Multi widget] Rules for updating the render windows, added: T29393: [mxn multi widget] Concept for individual render window synchronization; removed: T28578: [mxn multi widget] Optimization of the mxn multi widget.
Wed, Nov 16, 3:46 PM · Request for Discussion, MITK
kalali triaged T29393: [mxn multi widget] Concept for individual render window synchronization as Normal priority.
Wed, Nov 16, 3:46 PM · MITK
kalali closed T25604: New concept for switching between different render windows, a subtask of T25603: Combine render window manager with custom multi widget, as Invalid.
Wed, Nov 16, 3:03 PM · Restricted Project, MITK
kalali closed T25604: New concept for switching between different render windows as Invalid.

This task is invalid since we moved the functionality of the render window manager to render window specific drop-down menus. More discussion about the concept will happen in T29297: [mxn multi widget] Optimize data accessibility inside render windows.

Wed, Nov 16, 3:03 PM · Auto-closed, Request for Discussion, Restricted Project, MITK
kalali closed T25601: Modernize render window manager as Resolved.
Wed, Nov 16, 2:59 PM · Restricted Project, MITK
kalali added a comment to T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.

We will add the two suggested changes as a hotfix / release patch because

  • we should definitely avoid workbench crashes
  • also old legacy segmentations / scene files will provoke the crash
Wed, Nov 16, 2:28 PM · MITK
s434n removed a parent task for T29297: [mxn multi widget] Optimize data accessibility inside render windows: T28578: [mxn multi widget] Optimization of the mxn multi widget.
Wed, Nov 16, 1:21 PM · MITK (v2023.04)
s434n removed a subtask for T28578: [mxn multi widget] Optimization of the mxn multi widget: T29297: [mxn multi widget] Optimize data accessibility inside render windows.
Wed, Nov 16, 1:21 PM · MITK
s434n added a parent task for T29392: [Segmentation] Add dedicated writer to store multi-label images in nifti: T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.
Wed, Nov 16, 11:43 AM · MITK (v2023.04), Next Milestone
s434n added a subtask for T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash: T29392: [Segmentation] Add dedicated writer to store multi-label images in nifti.
Wed, Nov 16, 11:43 AM · MITK
s434n triaged T29392: [Segmentation] Add dedicated writer to store multi-label images in nifti as Normal priority.
Wed, Nov 16, 11:43 AM · MITK (v2023.04), Next Milestone
s434n updated subscribers of T29391: [Segmentation] Prevent multi-label images to be saved as unsupported image formats.
Wed, Nov 16, 11:38 AM · MITK
s434n added a parent task for T29391: [Segmentation] Prevent multi-label images to be saved as unsupported image formats: T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.
Wed, Nov 16, 11:38 AM · MITK
s434n added a subtask for T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash: T29391: [Segmentation] Prevent multi-label images to be saved as unsupported image formats.
Wed, Nov 16, 11:38 AM · MITK
s434n triaged T29391: [Segmentation] Prevent multi-label images to be saved as unsupported image formats as Unbreak Now! priority.
Wed, Nov 16, 11:37 AM · MITK
floca removed a project from T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash: Request for Discussion.
Wed, Nov 16, 11:35 AM · MITK
floca moved T29389: Python utility module from Backlog to MITK Meeting on the Request for Discussion board.
Wed, Nov 16, 11:00 AM · Next Milestone, Request for Discussion, MITK
floca moved T29381: Move Multilabel classes to Core module from Backlog to MITK Meeting on the Request for Discussion board.
Wed, Nov 16, 10:59 AM · MITK, Request for Discussion
floca moved T29390: How to ease the handling of external generated segmentations from Backlog to MITK Meeting on the Request for Discussion board.
Wed, Nov 16, 10:59 AM · MITK (v2023.04), Request for Discussion
kalali added a comment to T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.

The seg predicate of the view is wrong. Should not be able to select the nifti at all.

Also seg in nifti form have to be converted into label image currently via context menu "convert to segmentation".

Wed, Nov 16, 9:26 AM · MITK
kalali renamed T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash from [Segmentation] Loading a nifty segmentation (nii) leads to a crash to [Segmentation] Loading a nifti segmentation (nii) leads to a crash.
Wed, Nov 16, 9:24 AM · MITK
kalali added a revision to T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash: Unknown Object (Differential Revision).
Wed, Nov 16, 9:21 AM · MITK
kalali moved T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash from Backlog to MITK Meeting on the Request for Discussion board.
Wed, Nov 16, 8:40 AM · MITK
kalali moved T26959: [Segmentation] Newly created LabelSet segmentation is not displayed as "outline binary" from MITK Meeting to Backlog on the Request for Discussion board.
Wed, Nov 16, 8:39 AM · MITK (v2023.04), Checklist, Request for Discussion

Tue, Nov 15

floca added a comment to T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.

Is this reason for a patch release?

Tue, Nov 15, 8:27 PM · MITK
floca updated the task description for T29390: How to ease the handling of external generated segmentations.
Tue, Nov 15, 8:26 PM · MITK (v2023.04), Request for Discussion
floca created T29390: How to ease the handling of external generated segmentations.
Tue, Nov 15, 8:12 PM · MITK (v2023.04), Request for Discussion
floca added a comment to T29389: Python utility module.

That would also help to avoid problems like T29388

Tue, Nov 15, 8:01 PM · Next Milestone, Request for Discussion, MITK
floca created T29389: Python utility module.
Tue, Nov 15, 8:00 PM · Next Milestone, Request for Discussion, MITK
floca added a comment to T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.

The seg predicate of the view is wrong. Should not be able to select the nifti at all.

Tue, Nov 15, 7:55 PM · MITK
kalali added a comment to T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.

I added a first fix to avoid crashes. More changes are required:
Inside QmitkSegmentationView::UpdateGUI() the two functions m_Controls->layersWidget->UpdateGUI() and m_Controls->labelsWidget->UpdateGUI() are called. They both require the working image to be a LabelSetImage, otherwise the GUI elements will stay deactivated. Also, since no layer is available the toolselectionboxes stay deactivated.

Tue, Nov 15, 6:31 PM · MITK
kalali added a revision to T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash: Unknown Object (Differential Revision).
Tue, Nov 15, 6:27 PM · MITK
kalali added a project to T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash: Request for Discussion.
Tue, Nov 15, 5:53 PM · MITK
kalali updated subscribers of T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash.
Tue, Nov 15, 5:53 PM · MITK
kalali triaged T29388: [Segmentation] Loading a nifti segmentation (nii) leads to a crash as Unbreak Now! priority.
Tue, Nov 15, 5:52 PM · MITK

Mon, Nov 14

neher closed T29323: Fix windows dcl as Resolved.
Mon, Nov 14, 11:05 AM · MITK Diffusion

Fri, Nov 11

kalali added a revision to T29385: [mxn multi widget] Pixel value view does not change on crosshair selection: Restricted Differential Revision.
Fri, Nov 11, 6:58 PM · MITK (v2023.04)
kalali triaged T29386: [mxn multi widget] StdDisplay unnecessarily uses the crosshair manager as Normal priority.
Fri, Nov 11, 5:23 PM · MITK (v2023.04)
d587s added a member for MIC: m052r.
Fri, Nov 11, 11:40 AM
kalali updated the task description for T29385: [mxn multi widget] Pixel value view does not change on crosshair selection.
Fri, Nov 11, 11:06 AM · MITK (v2023.04)

Thu, Nov 10

kalali renamed T29385: [mxn multi widget] Pixel value view does not change on crosshair selection from [mxn to [mxn multi widget] Pixel value view does not change on crosshair selection.
Thu, Nov 10, 6:10 PM · MITK (v2023.04)
kalali created T29385: [mxn multi widget] Pixel value view does not change on crosshair selection.
Thu, Nov 10, 6:09 PM · MITK (v2023.04)
kalali added a revision to T29383: [mxn multi widget] Crosshair does not show a gap: Restricted Differential Revision.
Thu, Nov 10, 6:09 PM · MITK

Wed, Nov 9

kalali triaged T29383: [mxn multi widget] Crosshair does not show a gap as Normal priority.
Wed, Nov 9, 7:57 PM · MITK
kalali closed T19284: Display Update with crosshair interaction (Scrolling/..) is inefficient as Resolved.

I looked into this and although I understand the problem, the issue does not really exist, as far as I can see:

  • changing the slice via scrolling will call SliceNavigationController::SelectSliceByPoint
  • calling SliceNavigationController::SelectSliceByPoint will call SliceNavigationController::SendCreatedWorldGeometryUpdate
  • calling SliceNavigationController::SendCreatedWorldGeometryUpdate will InvokeEvent(GeometryUpdateEvent(m_CreatedWorldGeometry, m_Slice->GetPos()))
  • invoking the event will lead to a call to BaseRenderer::UpdateGeometry

-> until here I agree with the task description

Wed, Nov 9, 6:48 PM · MITK (v2022.10), Bugzilla

Nov 9 2022

neher committed rMITKDIFFd1afc9dc572a: Update build configurations to use opencv (authored by neher).
Update build configurations to use opencv
Nov 9 2022, 2:26 PM
neher committed rMITKDIFF66d50f918b54: Merge branch 'T29356-Infibtion' into T29356-InfibtionToMaster (authored by neher).
Merge branch 'T29356-Infibtion' into T29356-InfibtionToMaster
Nov 9 2022, 1:11 PM
neher placed T26413: Nifti2 support up for grabs.
Nov 9 2022, 11:38 AM · Missing Info, MITK
neher added a comment to T26413: Nifti2 support.

Unfortunately not solved. Same error.

Nov 9 2022, 11:37 AM · Missing Info, MITK