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a178n (Ashis Ravindran)
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Nov 19 2020, 10:58 PM (53 w, 6 d)

Recent Activity

Yesterday

a178n added a comment to T28866: [Segmentation] Redundant label "recomputation" for Otsu/Watershed (& nnUNet) when any of the Preview-generated labels are selected to Confirm.

After being discussed in the MITK meeting, the decision is to include an option in the tools for users to select if the segmentation call should be made dynamically for every time step or not. This option can be provided either in the tool itself or in the Preferences. Thus, users can decide when the tool becomes IsTimePointChangeAwareOn()or IsTimePointChangeAwareOff().
This would further imply that the tool->GetMTime() won't change after a Preview is made and thus, a redundant call to ComputeMLPreview can be avoided.

Wed, Dec 1, 1:57 PM · MITK (v2022.04)

Thu, Nov 18

a178n added a comment to T28866: [Segmentation] Redundant label "recomputation" for Otsu/Watershed (& nnUNet) when any of the Preview-generated labels are selected to Confirm.

After some analysis, it is understood that there is a difference in the modified time of the tool and the segmentation. This is detected in the AutoMLSegmentationWithPreviewTool.DoUpdatePreview method if-case of this->GetMTime() > m_MLPreviewNode->GetData()->GetMTime().
This change in time happens because tool->IsTimePointChangeAwareOn() is called after the tool->UpdatePreview() call is made in the tool's GUI class, eg. QmitkOtsuTool3DGUI

Thu, Nov 18, 3:29 PM · MITK (v2022.04)
a178n created T28866: [Segmentation] Redundant label "recomputation" for Otsu/Watershed (& nnUNet) when any of the Preview-generated labels are selected to Confirm.
Thu, Nov 18, 3:17 PM · MITK (v2022.04)

Wed, Nov 3

a178n merged task T28830: [Segmentation Interpolation] Interpolation dropdown enabled even after segmentation node is toggled invisible into T28829: [Segmentation][Interpolation] Interpolation area is still enabled, when segmentation node is hidden..
Wed, Nov 3, 12:28 PM · MITK
a178n merged T28830: [Segmentation Interpolation] Interpolation dropdown enabled even after segmentation node is toggled invisible into T28829: [Segmentation][Interpolation] Interpolation area is still enabled, when segmentation node is hidden..
Wed, Nov 3, 12:28 PM · Checklist, MITK
a178n created T28830: [Segmentation Interpolation] Interpolation dropdown enabled even after segmentation node is toggled invisible.
Wed, Nov 3, 11:06 AM · MITK

Tue, Nov 2

a178n renamed T28822: [Segmentation Interpolation] Intepolation contour shown even after segmentation node is invisible from [Segmentation Interpolation] Intepolation areacontour shown to [Segmentation Interpolation] Intepolation contour shown even after segmentation node is invisible.
Tue, Nov 2, 7:42 PM · MITK
a178n created T28822: [Segmentation Interpolation] Intepolation contour shown even after segmentation node is invisible.
Tue, Nov 2, 7:38 PM · MITK
a178n renamed T28821: [Segmentation] Create (Smooth) Polygon Model hardly works for large images. from [Segmentation] Create Polygon Model hardly works for large images. to [Segmentation] Create (Smooth) Polygon Model hardly works for large images..
Tue, Nov 2, 6:13 PM · Checklist, MITK
a178n created T28821: [Segmentation] Create (Smooth) Polygon Model hardly works for large images..
Tue, Nov 2, 5:21 PM · Checklist, MITK
a178n created T28820: [Segmentation] Auto-Selection Mode Not responsive .
Tue, Nov 2, 5:10 PM · Checklist, MITK
a178n updated the task description for T28819: [View Navigator] View Names don't become bold when opened.
Tue, Nov 2, 3:50 PM · Checklist, MITK
a178n created T28819: [View Navigator] View Names don't become bold when opened.
Tue, Nov 2, 3:50 PM · Checklist, MITK
a178n created T28818: [View Navigator] Text Search Filter bug.
Tue, Nov 2, 3:39 PM · MITK
a178n created T28812: [View Navigator] Save Perspectives Not working.
Tue, Nov 2, 1:35 PM · MITK
a178n created T28811: [Volume Visualization] [UX] Missing labels for dropdowns.
Tue, Nov 2, 10:34 AM · Checklist, MITK
a178n added a project to T28810: Surface image Point Representation too small: Request for Discussion.
Tue, Nov 2, 8:16 AM · Request for Discussion, MITK
a178n added a comment to T28810: Surface image Point Representation too small.

Later on, I find that the option to change point size exists in Properties > material > pointSize. However, it seems unintuitive (?)

Tue, Nov 2, 8:14 AM · Request for Discussion, MITK

Nov 1 2021

a178n created T28810: Surface image Point Representation too small.
Nov 1 2021, 3:37 PM · Request for Discussion, MITK
a178n created T28809: [Properties] Surface Submenu auto collapse after 2D->Normals properties changed.
Nov 1 2021, 3:23 PM · MITK

Oct 31 2021

a178n created T28808: [Properties] Some Pointset 2D shape selection not shown in the image views.
Oct 31 2021, 7:43 AM · Checklist, Missing Info, MITK
a178n created T28807: [Properties] Changing any tree view element makes the tree view collapse.
Oct 31 2021, 7:13 AM · Request for Discussion, MITK

Oct 29 2021

a178n created T28803: [Properties] Fine-tune selection widget.
Oct 29 2021, 6:06 PM · Checklist, MITK

Oct 19 2021

a178n added a comment to T28755: [Segmentation] Labels can only be Confirmed once in Segmentation tools after Preview.

This issue was mentioned on 18.Oct.2021 by Fabian as his comment on the upcoming nnUNet tool.
This issue could be a duplicate. If so, please mark it as such.

Oct 19 2021, 2:23 PM · Request for Discussion, MITK
a178n created T28755: [Segmentation] Labels can only be Confirmed once in Segmentation tools after Preview.
Oct 19 2021, 2:21 PM · Request for Discussion, MITK

Oct 11 2021

a178n triaged T28724: nnUNet as a separate view in MITK as Normal priority.
Oct 11 2021, 9:42 AM · MITK, Request for Discussion

Sep 14 2021

a178n added a comment to T28691: AutoSegmentationWithPreviewTool tool manager won't support multi threading.
  1. Exception Handling: leading to Segmentation fault and Workbench crash
Sep 14 2021, 11:43 AM · MITK (v2022.04), Request for Discussion
a178n added a comment to T28691: AutoSegmentationWithPreviewTool tool manager won't support multi threading.

I did some debugging and found some more insights into the situation and workarounds.

Sep 14 2021, 11:30 AM · MITK (v2022.04), Request for Discussion

Sep 8 2021

a178n renamed T28691: AutoSegmentationWithPreviewTool tool manager won't support multi threading from AutoSegmentationWithPreviewTool tool manager calls won't support multi threading to AutoSegmentationWithPreviewTool tool manager won't support multi threading.
Sep 8 2021, 9:15 AM · MITK (v2022.04), Request for Discussion
a178n created T28691: AutoSegmentationWithPreviewTool tool manager won't support multi threading.
Sep 8 2021, 9:14 AM · MITK (v2022.04), Request for Discussion

Aug 24 2021

a178n added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

2- Tests using tmp_cropped.nii.gz

Aug 24 2021, 3:54 PM · MITK (v2022.04)
a178n added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

1- Tests using tmp.nii.gz
We tested multiple times the following workflow:

Aug 24 2021, 3:48 PM · MITK (v2022.04)
a178n added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

I did some testing (with Amir) on ubuntu 20.04 (32GB RAM). The issue could be replicated with a questionable increase in the utilization of RAM.
Fabian provided us a couple of files for testing, viz. tmp.nii.gz and tmp_cropped.nii.gz (same content, just removed some of the zeros around the ROI)

Aug 24 2021, 3:33 PM · MITK (v2022.04)

Jul 28 2021

a178n closed T28523: Evaluate MITK segmentation survey, a subtask of T28320: [Segmentation] Region growing does not work if seed point is already inside a segmentation, as Resolved.
Jul 28 2021, 1:22 PM · MITK (v2022.04), Missing Info, Request for Discussion
a178n closed T28523: Evaluate MITK segmentation survey, a subtask of T28244: [Segmentation] Fast Marching Tool not really responsive for large images, as Resolved.
Jul 28 2021, 1:22 PM · MITK (v2022.04)
a178n closed T28523: Evaluate MITK segmentation survey, a subtask of T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value, as Resolved.
Jul 28 2021, 1:22 PM · MITK (v2022.04), Missing Info, Request for Discussion
a178n closed T28523: Evaluate MITK segmentation survey, a subtask of T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep, as Resolved.
Jul 28 2021, 1:22 PM · MITK (v2022.04)
a178n closed T28523: Evaluate MITK segmentation survey, a subtask of T28145: SetRegionTool does not work as expected (flood fill like) with concentric structures., as Resolved.
Jul 28 2021, 1:22 PM · MITK (v2022.04)
a178n closed T28523: Evaluate MITK segmentation survey, a subtask of T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms, as Resolved.
Jul 28 2021, 1:22 PM · MITK (v2022.04)
a178n closed T28523: Evaluate MITK segmentation survey as Resolved.
Jul 28 2021, 1:22 PM · MITK (v2021.10)
a178n closed T28523: Evaluate MITK segmentation survey, a subtask of T28499: Refactor/rewrite RegionGrowing3D tool, as Resolved.
Jul 28 2021, 1:22 PM · MITK (v2022.04), Request for Discussion
a178n added a comment to T28523: Evaluate MITK segmentation survey.

Currently, we received 4 responses in total.
Segmentation survey responses now kept as a docx file at hub.dkfz.de in
E230 Group 5 > MITK Planning > Development > MITK Segmentation Survey 2021

Jul 28 2021, 1:22 PM · MITK (v2021.10)

Jun 17 2021

a178n added a comment to T28523: Evaluate MITK segmentation survey.

Hi,
Currently, we have only 3 responses (including Fabian's).
Here is the data:

Jun 17 2021, 2:18 PM · MITK (v2021.10)

Jun 7 2021

a178n closed T28354: Update MITK documentation on CMAKE build for plugins as Resolved.
Jun 7 2021, 12:14 PM · Next Milestone, MITK (v2021.10)
a178n committed rMITK3ba83dab9cb8: Update Cmake FAQ in plugins (authored by a178n).
Update Cmake FAQ in plugins
Jun 7 2021, 12:08 PM
a178n committed rMITK8d52be146e96: update (authored by a178n).
update
Jun 7 2021, 12:08 PM
a178n committed rMITK792f2d494aa8: D489 review fixes (authored by a178n).
D489 review fixes
Jun 7 2021, 12:08 PM
a178n committed rMITK39f0e7f533f7: D489 revision update (authored by a178n).
D489 revision update
Jun 7 2021, 12:08 PM
a178n committed rMITK7f30b5b45cee: Update Cmake FAQ in plugins (authored by a178n).
Update Cmake FAQ in plugins
Jun 7 2021, 12:07 PM

Apr 22 2021

a178n added a comment to T28354: Update MITK documentation on CMAKE build for plugins.

Changes are pushed into the new branch T28353-cmake_faq branch.

Apr 22 2021, 7:25 AM · Next Milestone, MITK (v2021.10)
a178n added a comment to T28354: Update MITK documentation on CMAKE build for plugins.

Pushed new branch to rMITK MITK: feature/T28354-cmake_faq.

Apr 22 2021, 7:17 AM · Next Milestone, MITK (v2021.10)

Apr 14 2021

a178n edited projects for T28354: Update MITK documentation on CMAKE build for plugins, added: MITK (v2021.10), Next Milestone; removed Missing Info, Restricted Project.
Apr 14 2021, 11:45 AM · Next Milestone, MITK (v2021.10)

Mar 15 2021

a178n added a comment to T28354: Update MITK documentation on CMAKE build for plugins.
  1. I want to use a plugin, how do I activate it?
Mar 15 2021, 4:55 PM · Next Milestone, MITK (v2021.10)

Mar 10 2021

a178n triaged T28354: Update MITK documentation on CMAKE build for plugins as Low priority.
Mar 10 2021, 8:19 AM · Next Milestone, MITK (v2021.10)

Feb 10 2021

a178n added a comment to T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.

Update:
Problem is cannot be replicated anymore on my mac book (after a restart). Only Happens recurrently at certain times.

Feb 10 2021, 1:53 PM · MITK

Feb 9 2021

a178n added a comment to T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.

Closing an empty workbench or loaded workbench using X button on the title bar causes this.

Feb 9 2021, 7:00 PM · MITK
a178n added a comment to T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.

Attaching full stacktrace herewith:

Feb 9 2021, 4:56 PM · MITK
a178n updated the task description for T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.
Feb 9 2021, 4:55 PM · MITK
a178n triaged T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS as Normal priority.
Feb 9 2021, 4:51 PM · MITK

Jan 31 2021

a178n added a comment to T28258: [Segmentation] Core dumped at multiple instances while Closing Project.

Hi Ralf, Stefan & others involved,
I am sorry for attracting unnecessary concerns on a bug which never really existed.

Jan 31 2021, 11:17 PM · Missing Info, MITK (v2021.02)
a178n added a comment to T28258: [Segmentation] Core dumped at multiple instances while Closing Project.

I have finally found the fix! This bug is due to my GPU driver.
My laptop has an AMD Radeon dedicated GPU and MITK uses it by default for rendering its "Standard Display".
I checked the crash log using Event Viewer and found that atio6axx.dll was the culprit here. This is an AMD driver related DLL file.
I switched the default GPU for Mitk workbench to the onboard integrated graphics and that's it!
Problem solved. I am attaching the working screen recording herewith :-)

Jan 31 2021, 11:14 PM · Missing Info, MITK (v2021.02)
a178n added a comment to T28258: [Segmentation] Core dumped at multiple instances while Closing Project.

I even extracted the same scene to reproduce your issues as close as possible but it just works for me. Can you please close the workbench, delete the DKFZ folder in %APPDATA%/../Local, and then try again? What locale do you use on your system? Maybe that's the difference.

Jan 31 2021, 11:01 PM · Missing Info, MITK (v2021.02)
a178n added a comment to T28258: [Segmentation] Core dumped at multiple instances while Closing Project.

Hi Ralf,
Sure. I can reproduce the crash with both conditions viz. data from MITK-Data folder and with segmentation view closed. Here is the screen recording.

Jan 31 2021, 7:08 PM · Missing Info, MITK (v2021.02)
a178n added a comment to T28258: [Segmentation] Core dumped at multiple instances while Closing Project.

Nothing special that I can see. The moment it crashes, the terminal window also closes quickly. I am attaching a screen recording with the terminal screen. From this run (as in the attached video), I feel, maybe the issue/bug has nothing to do with Segmentation. I only noticed it in the context of testing 'Segmentation'.

Jan 31 2021, 5:48 PM · Missing Info, MITK (v2021.02)
a178n added a comment to T28258: [Segmentation] Core dumped at multiple instances while Closing Project.

FYI- Since I am in windows now, I can't really see if "Core dumped" is the real error message. I merely use it synonymously with the word "Crashed".

Jan 31 2021, 3:08 PM · Missing Info, MITK (v2021.02)
a178n added a comment to T28258: [Segmentation] Core dumped at multiple instances while Closing Project.

Thanks for reporting. Several questions:

  1. did you stumble upon it by accident/random testing or was it while you went through the check lists (so is this covered by the checklist, so that we can find such errors also in other releases?)
  2. Were all crashes with the Win installer?
  3. Which segmentation view did you use? classic or multi label?
  4. Wich views are open in the workbench when you experienced the crashes?

I was not able to reproduce the problems on my machine. 🤔 Can any one else verify that problem on their system?

Jan 31 2021, 3:03 PM · Missing Info, MITK (v2021.02)
a178n triaged T28258: [Segmentation] Core dumped at multiple instances while Closing Project as Normal priority.
Jan 31 2021, 11:01 AM · Missing Info, MITK (v2021.02)
a178n triaged T28257: [Segmentation] Core dumped when switching from LiveWire Tool to other tools as Normal priority.
Jan 31 2021, 10:14 AM · MITK (v2021.02)

Jan 30 2021

a178n triaged T28255: [Multilabel 2D segmentation] Core dumped when switching from LiveWireTool to other tools. as Normal priority.
Jan 30 2021, 6:47 PM · MITK (v2021.02)
a178n triaged T28254: [Multilabel 2D segmentation] Correction Tool as Normal priority.
Jan 30 2021, 6:23 PM · MITK (v2021.02)

Jan 29 2021

a178n added a comment to T28242: Live Wire Segmentation bug.

Cool, one less to thing to worry about. :)

Jan 29 2021, 7:03 PM · MITK-ProjectTemplate, MITK (v2021.02)
a178n triaged T28242: Live Wire Segmentation bug as Normal priority.
Jan 29 2021, 5:25 PM · MITK-ProjectTemplate, MITK (v2021.02)