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thomass (Sarina Thomas)
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Projects (10)

User Details

User Since
Aug 1 2016, 12:10 PM (225 w, 5 d)

Recent Activity

Wed, Nov 25

thomass closed T27696: Dicom loading does not work for some 4D data with the latest installer as Resolved.
Wed, Nov 25, 8:25 AM · DICOM, Missing Info, MITK

Tue, Nov 24

thomass added a project to T28008: [Mapper] Levelwindow overwrites vtkLookUpTable Range with levelwindow range : Request for Discussion.

apparently a vtkLoopUpTable is set automatically so the property as such cannot be used to handle custom vtkLookUpTables

Tue, Nov 24, 4:07 PM · Request for Discussion, MITK
thomass triaged T28008: [Mapper] Levelwindow overwrites vtkLookUpTable Range with levelwindow range as Normal priority.
Tue, Nov 24, 2:25 PM · Request for Discussion, MITK

Oct 22 2020

thomass added a comment to T27904: Feature request: Colorbars to interpret data in MITK.

In T26382 the recent developments are summarized.

Oct 22 2020, 3:04 PM · MITK
thomass triaged T27904: Feature request: Colorbars to interpret data in MITK as Normal priority.
Oct 22 2020, 12:59 PM · MITK

Oct 6 2020

thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

@thomass Thanks.
Now I might be nasty. Have you also checked everything wenn loading to 4D images with different time geometry? E.G. So that the selected time step in the navigator must not correspond to the same time step of the image you segment on?

With two 4D images 3D+t-Heart and US4Dcyl it crashes indeed when

  • using the Add tool on the static 3D+t Heart on timestep 0
  • changing the timestep and then use the Add tool again

I couldn't reproduce the crash when combining 4D_TEE_Data_MV and US4Dcyl (yet)

Could you please check (if not done already), if this scenario also crashes if you do it with a static segmentation?
This info is important for the decission, if we have to fix it directly or just partialy deactivate the dynamic option for this cycle. (Curently static segs on 4D images are more relevant then dynamic segs).

Oct 6 2020, 12:34 PM · Missing Info, Restricted Project, MITK (2020)
thomass closed T27825: Example MITK-Video on Measurements View as Resolved.
Oct 6 2020, 12:07 PM · Restricted Project
thomass triaged T27825: Example MITK-Video on Measurements View as Normal priority.
Oct 6 2020, 12:07 PM · Restricted Project
thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

@thomass Thanks.
Now I might be nasty. Have you also checked everything wenn loading to 4D images with different time geometry? E.G. So that the selected time step in the navigator must not correspond to the same time step of the image you segment on?

Oct 6 2020, 8:30 AM · Missing Info, Restricted Project, MITK (2020)

Oct 5 2020

thomass added a project to T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels: Request for Discussion.
Oct 5 2020, 1:06 PM · Cleared, MITK (2020)
thomass moved T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels from Backlog to Segmentation on the MITK (2020) board.
Oct 5 2020, 1:06 PM · Cleared, MITK (2020)
thomass updated the task description for T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels.
Oct 5 2020, 1:00 PM · Cleared, MITK (2020)
thomass updated the task description for T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels.
Oct 5 2020, 1:00 PM · Cleared, MITK (2020)
thomass triaged T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels as High priority.
Oct 5 2020, 1:00 PM · Cleared, MITK (2020)
thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

Static Segmentation:
-ADD: A segmentation is drawn on timestep 0, if I change the timestep, the segmentation remains and I can add a new segmentation on timestep !=0, both segmentations are visible since I only have one timestep --> As axpected
-SUBSTRACT: The drawn segmentation can be removed independent from the timestep 0 and timestep !=0 --> As expected
-CORRECTION: The drawn segmentation is removed independent from the timestep 0 and timestep !=0 --> As expected
-PAINT: Painted segmentation occurs on timestep 0. When changing the timestep, the painted segmentation is added to the static segmentation --> As expected
-WIPE: Segmentation is wiped on timestep 0 and wiped on timestep !=0 --> As expected
-RegionGrowing2D: Region Growing is applied on timestep 0 (fits to the image). When changing the timestep, the region growing result fits to the timestep. No crash. Quite slow updates. --> As expected
-FILL: Different timesteps can be filled. When changing the timestep, the segmentation remains --> As expected
-ERASE: Different timesteps can be erased. --> As expected
-LiveWire: T27800
-2D FastMarching: T27721

Oct 5 2020, 9:36 AM · Missing Info, Restricted Project, MITK (2020)
thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

It really suprises me that FastMarching2D crashes now since I explictly played with timesteps in T26975. But maybe I truly overlooked something, then I am sorry.

Oct 5 2020, 9:01 AM · Missing Info, Restricted Project, MITK (2020)

Sep 25 2020

thomass moved T27789: [Segmentation] Disentangle Clipping Plane plugin from segmentation from Backlog to Segmentation on the MITK (2020) board.
Sep 25 2020, 11:42 AM · MITK (2020)
thomass triaged T27789: [Segmentation] Disentangle Clipping Plane plugin from segmentation as Normal priority.
Sep 25 2020, 11:41 AM · MITK (2020)
thomass removed a project from T27184: Clipping plane deformation tool doesn't show updates in 3d window: Request for Discussion.

Request discussion result:

Sep 25 2020, 11:37 AM · Missing Info, Restricted Project, MITK (2020)
thomass committed rMITK1223fbcd0327: T27772 rename fit inspector views in manual overview (authored by thomass).
T27772 rename fit inspector views in manual overview
Sep 25 2020, 11:22 AM
thomass closed T27772: Clean up ModelFitInspector in TOC of doxygen documentation as Resolved by committing rMITK1223fbcd0327: T27772 rename fit inspector views in manual overview.
Sep 25 2020, 11:22 AM · Cleared, MITK (2020)
thomass added a revision to T27772: Clean up ModelFitInspector in TOC of doxygen documentation: Unknown Object (Differential Revision).
Sep 25 2020, 11:20 AM · Cleared, MITK (2020)
thomass added a project to T27184: Clipping plane deformation tool doesn't show updates in 3d window: Request for Discussion.
Sep 25 2020, 11:17 AM · Missing Info, Restricted Project, MITK (2020)

Sep 18 2020

thomass added a comment to T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung".

I think the things you changed are all reasonable, the things I would add (I can not do it atm because I don't have access to the document)

Sep 18 2020, 2:39 PM · Restricted Project, Cleared, MITK (2020)

Sep 16 2020

thomass added a comment to T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung".

I agree :)

Sep 16 2020, 1:35 PM · Restricted Project, Cleared, MITK (2020)
thomass added a comment to T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung".

just started to have a look.

Sep 16 2020, 12:06 PM · Restricted Project, Cleared, MITK (2020)

Sep 4 2020

thomass committed rMITK0ec8c07ca152: T27691 changed subpages in Phenotyping doc to refs to fix linkingproblems (authored by thomass).
T27691 changed subpages in Phenotyping doc to refs to fix linkingproblems
Sep 4 2020, 8:58 PM
thomass closed T27691: [MITKDoc] Documentation links reference "The Phenotyping" subpages as Resolved by committing rMITK0ec8c07ca152: T27691 changed subpages in Phenotyping doc to refs to fix linkingproblems.
Sep 4 2020, 8:58 PM · MITK (2020)

Sep 3 2020

kalali awarded T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation a Cup of Joe token.
Sep 3 2020, 10:21 PM · Missing Info, Restricted Project, MITK (2020)
thomass updated the task description for T27703: [Segmentation] Watershed segmentation crashes on images when high threshold is chosen.
Sep 3 2020, 5:05 PM · MITK
thomass triaged T27703: [Segmentation] Watershed segmentation crashes on images when high threshold is chosen as Normal priority.
Sep 3 2020, 5:03 PM · MITK
thomass updated subscribers of T27184: Clipping plane deformation tool doesn't show updates in 3d window.

@kislinsk @kalali I have in mind that you recently had a look at the ClippingPlane. Since the clipping plane does not show the expected behavior, does it make sense to rewrite the documentation for it? I have in mind you even considered to declare it deprecated.

Sep 3 2020, 3:47 PM · Missing Info, Restricted Project, MITK (2020)
thomass updated subscribers of T27093: [MITKDoc] Revise Segmentation Plugin.

Pointed out by @kislinsk in T27095 but as stated before, it belongs to this documentation task not the multi-label one ;)

Sep 3 2020, 10:41 AM · MITK (2020)

Sep 2 2020

thomass added a revision to T27095: [MITKDoc] Revise MultiLabel Segmentation Plugin Documentation: Unknown Object (Differential Revision).
Sep 2 2020, 1:10 PM · MITK (2020)
thomass updated the task description for T27698: [Segmentation] Segmentation toolbox is never enabled in multi-label segmentation view.
Sep 2 2020, 10:24 AM · MITK (2020)
thomass triaged T27698: [Segmentation] Segmentation toolbox is never enabled in multi-label segmentation view as High priority.
Sep 2 2020, 10:24 AM · MITK (2020)
thomass added a comment to T27697: Documentation feedback received from testers .

should work now

Sep 2 2020, 10:22 AM · MITK
thomass updated the task description for T27697: Documentation feedback received from testers .
Sep 2 2020, 10:21 AM · MITK
thomass added a comment to T27696: Dicom loading does not work for some 4D data with the latest installer.

I just received an E-Mail that the problem could be related to the data source (some server or network drive) so maybe no MITK issue after all :)

Sep 2 2020, 10:04 AM · DICOM, Missing Info, MITK
thomass added a comment to T27697: Documentation feedback received from testers .

I would suggest that at least the plugin feedback in the GoogleDocs and the toplevel-> main page /MITKUserManual should be corrected before the Release. The rest should be corrected soon after.

Sep 2 2020, 8:36 AM · MITK
thomass updated subscribers of T27697: Documentation feedback received from testers .
Sep 2 2020, 8:34 AM · MITK
thomass updated the task description for T27697: Documentation feedback received from testers .
Sep 2 2020, 8:33 AM · MITK
thomass triaged T27697: Documentation feedback received from testers as Normal priority.
Sep 2 2020, 8:33 AM · MITK
thomass added a comment to T26934: Multiple logos in screenshot when using screenshot maker plugin.

@kislinsk: should we further investigate this or have a known issue section in the documentation?

Sep 2 2020, 8:12 AM · MITK
thomass triaged T27696: Dicom loading does not work for some 4D data with the latest installer as Normal priority.
Sep 2 2020, 7:47 AM · DICOM, Missing Info, MITK

Sep 1 2020

thomass added a comment to T27669: Dicom import issue with MITK binaries (package) and Ubuntu.

The log information in the console which Jonas reported doesn't turn up. So the console doesn't show any new information after the reader is selected.
I will ask about the HDD / IO.

Sep 1 2020, 6:12 PM · Missing Info, DICOM, MITK
thomass added a comment to T27669: Dicom import issue with MITK binaries (package) and Ubuntu.

I am not sure if that is related but today one of my cooperation partners reported that she couldn't open an 4D image in MITK (Latest develop installer).
On my laptop it just works fine. On her laptop, however, she doesn't even get to the logging point. It doesn't show anything, it just stops (She closed the workbench after 10 Minutes).
I asked her whether it was an ancient laptop, but no ;)

Sep 1 2020, 5:56 PM · Missing Info, DICOM, MITK
thomass added a revision to T27691: [MITKDoc] Documentation links reference "The Phenotyping" subpages: Unknown Object (Differential Revision).
Sep 1 2020, 4:29 PM · MITK (2020)
thomass claimed T27691: [MITKDoc] Documentation links reference "The Phenotyping" subpages.
Sep 1 2020, 4:21 PM · MITK (2020)
thomass committed rMITK288df1f125b1: T27106 Rework Volumevisualization Documentation (authored by thomass).
T27106 Rework Volumevisualization Documentation
Sep 1 2020, 4:06 PM
thomass closed T27106: [MITKDoc] Revise Volume Visualization Plugin Documentation as Resolved by committing rMITK288df1f125b1: T27106 Rework Volumevisualization Documentation.
Sep 1 2020, 4:05 PM · Cleared, MITK (2020)
thomass committed rMITK572613b0ccca: T27672 Enable Measurement selection with autoselection (authored by thomass).
T27672 Enable Measurement selection with autoselection
Sep 1 2020, 12:50 PM
thomass closed T27672: [Measurement] Planar figures are disabled when the image is already loaded as Resolved by committing rMITK572613b0ccca: T27672 Enable Measurement selection with autoselection.
Sep 1 2020, 12:50 PM · MITK (2020)

Aug 31 2020

thomass added a comment to T27094: [MITKDoc] Revise Segmentation Utilities Plugin Documentation.
  1. To my knowledge it should generate a mask out of a Surface and in MITKData there should be some...I will have a look
  2. That is rather a bug, because in Phenotyping there is a reference that shouldn't be there, maybe we can remove that.
Aug 31 2020, 2:16 PM · Cleared, MITK (2020)
thomass triaged T27689: RTDose image can not be serialized and workbench crashes upon loading as High priority.
Aug 31 2020, 11:19 AM · Request for Discussion, MITK

Aug 28 2020

thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

Region growing task can be found here T27684

Aug 28 2020, 12:05 PM · Missing Info, Restricted Project, MITK (2020)
thomass added a revision to T27672: [Measurement] Planar figures are disabled when the image is already loaded: Unknown Object (Differential Revision).
Aug 28 2020, 11:55 AM · MITK (2020)
thomass added a revision to T27106: [MITKDoc] Revise Volume Visualization Plugin Documentation: Unknown Object (Differential Revision).
Aug 28 2020, 11:29 AM · Cleared, MITK (2020)

Aug 27 2020

thomass claimed T27095: [MITKDoc] Revise MultiLabel Segmentation Plugin Documentation.
Aug 27 2020, 11:23 AM · MITK (2020)
thomass claimed T27099: [MITKDoc] Revise Clipping Plane Plugin Documentation.
Aug 27 2020, 11:20 AM · Cleared, MITK (2020)
thomass triaged T27684: [Segmentation] Improve Region Growing 2D algorithm and interaction as High priority.
Aug 27 2020, 8:28 AM · MITK (2020)

Aug 21 2020

thomass added a comment to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.

Crash fixed by D380 :)

Aug 21 2020, 2:17 PM · MITK (2020), Bugzilla

Aug 14 2020

thomass committed rMITK92d4566b0ea0: T27105 correct renaming of measurement documentation image (authored by thomass).
T27105 correct renaming of measurement documentation image
Aug 14 2020, 3:46 PM
thomass added a comment to T27672: [Measurement] Planar figures are disabled when the image is already loaded.

Proposed a fix in D388, maybe there is a more elegant way but it works now

Aug 14 2020, 2:04 PM · MITK (2020)
thomass updated subscribers of T27672: [Measurement] Planar figures are disabled when the image is already loaded.

@kalali this looks like a bug introduced by the selection concept?

Aug 14 2020, 1:16 PM · MITK (2020)
thomass triaged T27672: [Measurement] Planar figures are disabled when the image is already loaded as High priority.
Aug 14 2020, 1:16 PM · MITK (2020)

Aug 13 2020

thomass committed rMITKdfa0c14e9cfe: rework documentation, replace images and add autoselect (authored by thomass).
rework documentation, replace images and add autoselect
Aug 13 2020, 2:23 PM
thomass closed T27105: [MITKDoc] Revise Measurement Plugin Documentation as Resolved by committing rMITKdfa0c14e9cfe: rework documentation, replace images and add autoselect.
Aug 13 2020, 2:23 PM · Cleared, MITK (2020)

Aug 10 2020

thomass committed rMITK18ddd2ed4fc8: rewrote some sections and enabled auto select (authored by thomass).
rewrote some sections and enabled auto select
Aug 10 2020, 10:06 AM
thomass closed T27098: [MITKDoc] Revise Image Cropper Plugin Documentation as Resolved by committing rMITK18ddd2ed4fc8: rewrote some sections and enabled auto select.
Aug 10 2020, 10:06 AM · Cleared, MITK (2020)

Aug 7 2020

thomass added a comment to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.

Oh I didn’t look into the Differential yet, only tried it with the current develop. The crash I observed in with FastMarching3D

Aug 7 2020, 8:49 PM · MITK (2020), Bugzilla
thomass added a comment to T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.

So I have a fix for the contour problem but what is missing is that the pointset is still drawn on timestep 0 instead of the current timestep and I have to figure out why.

Aug 7 2020, 2:46 PM · Missing Info, MITK (2020)
thomass committed rMITK36d69b77aeaf: rewrote some sections and added new image (authored by thomass).
rewrote some sections and added new image
Aug 7 2020, 2:31 PM
thomass closed T27107: [MITKDoc] Revise Screenshot Maker Plugin Documentation as Resolved by committing rMITK36d69b77aeaf: rewrote some sections and added new image.
Aug 7 2020, 2:31 PM · Cleared, MITK (2020)
thomass added a comment to T18436: [Segmentation] Fast Marching 3D Tool only supported for first time step in 4D images.

I also experience a crash in the tool:

Aug 7 2020, 1:12 PM · MITK (2020), Bugzilla
thomass updated subscribers of T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
Aug 7 2020, 8:46 AM · Missing Info, Restricted Project, MITK (2020)
thomass added a comment to T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.

File is FastMarchingTool.cpp

Aug 7 2020, 8:42 AM · Missing Info, MITK (2020)
thomass added a comment to T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.

I can partly confirm it.

Aug 7 2020, 8:07 AM · Missing Info, MITK (2020)

Aug 6 2020

thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

2D Segmentation tools:

Aug 6 2020, 3:45 PM · Missing Info, Restricted Project, MITK (2020)

Aug 4 2020

thomass triaged T27646: [Data manager] Option to change color of segmentation disappeared in data manager as Normal priority.
Aug 4 2020, 2:31 PM · Request for Discussion, MITK

Aug 3 2020

thomass added a comment to T27641: [Segmentation] Watershed does always generate a 3D static seg. Even if dynamic segmentation was generated..

Test image: 3D+t Heart

Aug 3 2020, 9:49 AM · Cleared, MITK (2020)
thomass closed T27642: [Segmentation] Watershed segmentation always creates a second segmentation which is 3D even if the image is 4D and dynamic as Invalid.

duplicate to T27641

Aug 3 2020, 9:49 AM · MITK (2020)
thomass triaged T27642: [Segmentation] Watershed segmentation always creates a second segmentation which is 3D even if the image is 4D and dynamic as High priority.
Aug 3 2020, 9:47 AM · MITK (2020)
thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

You totally right and the reason why I oversaw this is when I double checked:

Aug 3 2020, 9:43 AM · Missing Info, Restricted Project, MITK (2020)

Aug 2 2020

thomass closed T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation as Resolved.

All issues have been adressed in respective subtasks.

Aug 2 2020, 5:26 PM · Missing Info, Restricted Project, MITK (2020)
thomass closed T26840: Mission Homepage Reorganization as Resolved.
Aug 2 2020, 4:05 PM · MITK

Jul 31 2020

thomass added a revision to T27107: [MITKDoc] Revise Screenshot Maker Plugin Documentation: Unknown Object (Differential Revision).
Jul 31 2020, 5:21 PM · Cleared, MITK (2020)
thomass committed rMITK582aadc6da8d: Update text and pngs of the point set interaction documentation (authored by thomass).
Update text and pngs of the point set interaction documentation
Jul 31 2020, 11:30 AM
thomass closed T27103: [MITKDoc] Revise Point Set Interaction Plugin Documentation as Resolved by committing rMITK582aadc6da8d: Update text and pngs of the point set interaction documentation.
Jul 31 2020, 11:30 AM · Cleared, MITK (2020)

Jul 30 2020

thomass added a revision to T27098: [MITKDoc] Revise Image Cropper Plugin Documentation: Restricted Differential Revision.
Jul 30 2020, 2:59 PM · Cleared, MITK (2020)
thomass claimed T27107: [MITKDoc] Revise Screenshot Maker Plugin Documentation.
Jul 30 2020, 1:06 PM · Cleared, MITK (2020)
thomass added a revision to T27105: [MITKDoc] Revise Measurement Plugin Documentation: Unknown Object (Differential Revision).
Jul 30 2020, 10:52 AM · Cleared, MITK (2020)
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).

Jul 30 2020, 9:34 AM · Missing Info, Restricted Project, MITK (2020)

Jul 29 2020

thomass closed T27615: [Segmentation] Threshold and UL threshold show unwanted behavior on static and dynamic segmentations as Invalid.

duplicate of T27621

Jul 29 2020, 1:03 PM · MITK (2020)
thomass raised the priority of T27616: [Segmentation] Otsu creates static 3D segmentation regardless of segmentation choice from Normal to High.
Jul 29 2020, 1:02 PM · Breaking Change, MITK (2020)
thomass closed T27617: [ImageCropper] Workbench crashes when the plugin is opened as Resolved.

Resolved with D369

Jul 29 2020, 11:55 AM · MITK (2020)
thomass added a comment to T27097: [MITKDoc] Revise Statistics Plugin Documentation.

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)

Jul 29 2020, 10:58 AM · Cleared, MITK (2020)
thomass added a revision to T27103: [MITKDoc] Revise Point Set Interaction Plugin Documentation: Restricted Differential Revision.
Jul 29 2020, 10:37 AM · Cleared, MITK (2020)
thomass added a comment to T27617: [ImageCropper] Workbench crashes when the plugin is opened.

Eventually related to changes in D360

Jul 29 2020, 10:02 AM · MITK (2020)
thomass triaged T27617: [ImageCropper] Workbench crashes when the plugin is opened as High priority.
Jul 29 2020, 9:00 AM · MITK (2020)