Page MenuHomePhabricator
Feed All Stories

Oct 8 2020

wiesenfa moved T27804: Message text from violin plot is cut off in the PDF report from In Progress to Done on the challengeR (v1.0) board.
Oct 8 2020, 10:58 AM · challengeR (v1.0)
wiesenfa committed rCHALLENGER885d495f0efe: violin text improve (authored by wiesenfa).
violin text improve
Oct 8 2020, 10:57 AM
kislinsk committed rMITKdec5293f1b9b: Revise documentation on MITK's top-level directories (authored by kislinsk).
Revise documentation on MITK's top-level directories
Oct 8 2020, 9:59 AM
kislinsk committed rMITK73b639869912: Fix review remarks (authored by kislinsk).
Fix review remarks
Oct 8 2020, 9:59 AM
kislinsk committed rMITK1197c0a39e29: Revise documentation on MITK's top-level directories (authored by kislinsk).
Revise documentation on MITK's top-level directories
Oct 8 2020, 9:59 AM
kislinsk closed T27818: [MITKDoc] Revise Top-level directories in documentation as Resolved by committing rMITKdec5293f1b9b: Revise documentation on MITK's top-level directories.
Oct 8 2020, 9:59 AM · MITK (v2021.02)
wiesenfa moved T27804: Message text from violin plot is cut off in the PDF report from Backlog to In Progress on the challengeR (v1.0) board.
Oct 8 2020, 7:47 AM · challengeR (v1.0)

Oct 7 2020

aguilera moved T27821: [shiny] Cookie notification disappears when pressing "Esc" from Backlog to Done on the webChallengeR board.
Oct 7 2020, 7:34 PM · webChallengeR
e148c moved T27832: Complete troublshooting from Backlog to In Progress on the challengeR board.
Oct 7 2020, 3:57 PM · challengeR (v1.0)
e148c created T27832: Complete troublshooting.
Oct 7 2020, 3:57 PM · challengeR (v1.0)
kompan triaged T27831: [MITKDoc]Add missing "the" in some view documentation page titles as Normal priority.
Oct 7 2020, 12:15 PM · MITK (v2021.02)

Oct 6 2020

zimmerer committed rMOOD8a0e9dd634f0: Add scripts to produce the challenge report (authored by zimmerer).
Add scripts to produce the challenge report
Oct 6 2020, 4:38 PM
e148c created T27829: [shiny] Disabling button "Next" when a text field is empty.
Oct 6 2020, 2:49 PM · webChallengeR
e148c created T27828: [shiny] Error message when wrong type in text field.
Oct 6 2020, 2:41 PM · webChallengeR
e148c created T27827: [shiny] Disabling button "Next" when checkbox "configure" is checked but nothing has been picked.
Oct 6 2020, 2:15 PM · webChallengeR
floca added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

@thomass OK. Thats enough info, thanks. No further testing for now. We do it in context of a release branch or/and explizit fixes.

Oct 6 2020, 12:45 PM · MITK (v2021.10), Missing Info, 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?

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 · MITK (v2021.10), Missing Info, Restricted Project
floca 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)

Oct 6 2020, 12:23 PM · MITK (v2021.10), Missing Info, Restricted Project
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
e148c created T27822: [shiny] Type of files can be changed in the file dialog.
Oct 6 2020, 11:36 AM · webChallengeR
e148c created T27821: [shiny] Cookie notification disappears when pressing "Esc".
Oct 6 2020, 11:34 AM · webChallengeR
kalali added a watcher for Next Milestone: kalali.
Oct 6 2020, 11:07 AM
kalali changed Deadline from Oct 9 2020, 12:00 AM to Oct 9 2020, 9:00 AM on T27100: [MITKDoc] Revise DataManager Plugin Documentation.
Oct 6 2020, 11:06 AM · Cleared, MITK (v2021.02)
kalali set Deadline to Oct 9 2020, 12:00 AM on T27100: [MITKDoc] Revise DataManager Plugin Documentation.
Oct 6 2020, 11:05 AM · Cleared, MITK (v2021.02)
onogur added a member for IMSY: r010a.
Oct 6 2020, 10:20 AM
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 · MITK (v2021.10), Missing Info, Restricted Project

Oct 5 2020

kislinsk added a revision to T27818: [MITKDoc] Revise Top-level directories in documentation: Unknown Object (Differential Revision).
Oct 5 2020, 2:41 PM · MITK (v2021.02)
kislinsk claimed T27818: [MITKDoc] Revise Top-level directories in documentation.
Oct 5 2020, 2:38 PM · MITK (v2021.02)
kislinsk triaged T27818: [MITKDoc] Revise Top-level directories in documentation as Normal priority.
Oct 5 2020, 2:07 PM · MITK (v2021.02)
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 (v2021.02)
thomass moved T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels from Backlog to Segmentation on the MITK (v2021.02) board.
Oct 5 2020, 1:06 PM · Cleared, MITK (v2021.02)
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 (v2021.02)
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 (v2021.02)
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 (v2021.02)
kompan updated the task description for T27815: Modelfit Generic Data Fitting missing start parameters.
Oct 5 2020, 12:24 PM · MITK (v2024.06)
kompan triaged T27815: Modelfit Generic Data Fitting missing start parameters as Normal priority.
Oct 5 2020, 12:12 PM · MITK (v2024.06)
kompan removed a project from T27745: [MITKDoc] Revise Model Fit Generic View Documentation: Cleared.
Oct 5 2020, 12:03 PM · MITK (v2022.04)
kalali added a subtask for T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation: T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.
Oct 5 2020, 11:10 AM · MITK (v2021.10), Missing Info, Restricted Project
kalali added a parent task for T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps: T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
Oct 5 2020, 11:10 AM · Missing Info, MITK (v2021.02)
kalali 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, 11:08 AM · MITK (v2021.10), Missing Info, Restricted Project
floca 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 5 2020, 10:54 AM · MITK (v2021.10), Missing Info, Restricted Project
kompan triaged T27814: Refactor ModelFit Generic Data Fitting view to use new selection concept as Normal priority.
Oct 5 2020, 10:48 AM · MITK (v2024.06), Cleared
kompan triaged T27813: Curve Description Parameters View progress bar 99% as Normal priority.
Oct 5 2020, 10:36 AM · MITK (v2023.12)
kalali moved T27665: PlanarFigure tests show error with DICOMTagsOfInterestAddHelper from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Oct 5 2020, 10:32 AM · Auto-closed, Restricted Project, MITK
kalali added a project to T27665: PlanarFigure tests show error with DICOMTagsOfInterestAddHelper: Restricted Project.
Oct 5 2020, 10:31 AM · Auto-closed, Restricted Project, MITK
wiesenfa claimed T27778: turn off networks.
Oct 5 2020, 10:16 AM · challengeR (v1.0)
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 · MITK (v2021.10), Missing Info, Restricted Project
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 · MITK (v2021.10), Missing Info, Restricted Project

Oct 4 2020

kalali added a parent task for T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation: T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
Oct 4 2020, 2:50 PM · MITK (v2021.02)
kalali added a subtask for T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation: T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.
Oct 4 2020, 2:50 PM · MITK (v2021.10), Missing Info, Restricted Project
kalali added a parent task for T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation: T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
Oct 4 2020, 2:50 PM · MITK (v2021.02)
kalali added a subtask for T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation: T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation.
Oct 4 2020, 2:50 PM · MITK (v2021.10), Missing Info, Restricted Project
floca reopened T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation as "Open".

It seems (see @kalali latest findings T27721 T27800) that there are more problems in the 2D tools then thought.

Oct 4 2020, 2:40 PM · MITK (v2021.10), Missing Info, Restricted Project
floca added a comment to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.
  1. There is a basic flaw in the design which should be discussed instead of just fixing the symptoms with the suggested fix

You are right. I have looked into the Tool2D code base. And I think the only proper solution is to make an complete overhaul and refactoring like I did for the AutoTools (3D). Meaning to check all implicit or explicite usages of time(points) and also clean up and generalize code, as also several 2D tools do a lot of same stuff but just a little bit different, may be due to different developers. But thats not good for maintenance an so on...

Oct 4 2020, 2:31 PM · MITK (v2021.02)
floca added a comment to T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation.
  1. There is a basic flaw in the design which should be discussed instead of just fixing the symptoms with the suggested fix

You are right. I have looked into the Tool2D code base. And I think the only proper solution is to make an complete overhaul and refactoring like I did for the AutoTools (3D). Meaning to check all implicit or explicite usages of time(points) and also clean up and generalize code, as also several 2D tools do a lot of same stuff but just a little bit different, may be due to different developers. But thats not good for maintenance an so on...

Oct 4 2020, 2:30 PM · MITK (v2021.02)

Oct 2 2020

wiesenfa closed T27811: turn off networks in report as Invalid.

redundant

Oct 2 2020, 9:45 PM · challengeR (v1.0)
aguilera added a member for webChallengeR: eisenman.
Oct 2 2020, 3:34 PM
aguilera added members for webChallengeR: reinkea, e148c.
Oct 2 2020, 3:34 PM
reinkea added a member for challengeR: e148c.
Oct 2 2020, 3:33 PM
kalali added a comment to T27060: [Segmentation] Rework InterpolationWidget to not depend on data manager view directly.

Is this a feature that is widely used? Typically the position nodes are not visible, only if they are explicitly shown by changing the data manager's preferences.
But I like the idea of being able to jump to different slices of a segmentation, regardless of the interpolation. I see this as a possibility to check the different parts of a segmentation easily and quickly being able to switch between different "parts" of a segmentation.

Oct 2 2020, 1:59 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca committed rMITKe064ac2779a9: T27791 - Optimized RT mime types (authored by floca).
T27791 - Optimized RT mime types
Oct 2 2020, 1:34 PM
floca committed rMITKa2a5729a227a: Optimized check order of Dose mime type to minimize the usage of readers for… (authored by floca).
Optimized check order of Dose mime type to minimize the usage of readers for…
Oct 2 2020, 1:34 PM
floca closed T27791: Optimize RT Mime Types as Resolved by committing rMITKa2a5729a227a: Optimized check order of Dose mime type to minimize the usage of readers for….
Oct 2 2020, 1:34 PM · MITK
wiesenfa created T27811: turn off networks in report.
Oct 2 2020, 1:05 PM · challengeR (v1.0)
kalali closed T24775: Refactor plugins to use the new node selection widgets, a subtask of T23751: Introduction of new selection concept, as Resolved.
Oct 2 2020, 12:58 PM · Noteworthy, MITK
kalali closed T24775: Refactor plugins to use the new node selection widgets as Resolved.

I removed T27060: [Segmentation] Rework InterpolationWidget to not depend on data manager view directly as subtask and now this can be closed!

Oct 2 2020, 12:58 PM · MITK, Restricted Project, Cleared
wiesenfa moved T27286: interactive plots from v1.0 to Backlog on the challengeR board.
Oct 2 2020, 12:58 PM · challengeR
kalali awarded T24775: Refactor plugins to use the new node selection widgets a 100 token.
Oct 2 2020, 12:57 PM · MITK, Restricted Project, Cleared
wiesenfa claimed T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name.
Oct 2 2020, 12:57 PM · challengeR (v1.0)
kalali renamed T27060: [Segmentation] Rework InterpolationWidget to not depend on data manager view directly from Rework InterpolationWidget in SegmentationView to not depend on data manager view directly to [Segmentation] Rework InterpolationWidget to not depend on data manager view directly.
Oct 2 2020, 12:56 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali removed a subtask for T27034: Refactor Segmentation plugin to use new selection concept: T27060: [Segmentation] Rework InterpolationWidget to not depend on data manager view directly.
Oct 2 2020, 12:56 PM · MITK
kalali removed a parent task for T27060: [Segmentation] Rework InterpolationWidget to not depend on data manager view directly: T27034: Refactor Segmentation plugin to use new selection concept.
Oct 2 2020, 12:56 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali updated the task description for T24775: Refactor plugins to use the new node selection widgets.
Oct 2 2020, 12:54 PM · MITK, Restricted Project, Cleared
kalali triaged T27810: [Multilabel Segmentation] Inconsistencies and unclear functionality in operations of Utilities view as Normal priority.
Oct 2 2020, 12:34 PM · MITK (v2022.10), Cleared, Restricted Project
kalali triaged T27809: [Segmentation Utilities] "Labels" tabs in operations of Utilities view is empty as Normal priority.
Oct 2 2020, 11:57 AM · MITK (v2023.12), Request for Discussion
wiesenfa claimed T27793: Plot titles are missing in some line plots.
Oct 2 2020, 11:19 AM · challengeR (v1.0)
wiesenfa claimed T27802: Revise signature of function testThenRank.
Oct 2 2020, 11:18 AM · challengeR (v1.0)
wiesenfa claimed T27804: Message text from violin plot is cut off in the PDF report.
Oct 2 2020, 11:18 AM · challengeR (v1.0)
kislinsk added a comment to T27806: Meaning of 2D images in MITK.

Many years ago it was decided that we handle 2d images as 3d images with a single slice. While not correct as the pixel spacing in z-direction is completely made up, it reduced some code and edge cases and was found to be an okay-ish simplification. On the other hand it rarely leads to issues that were found to be worth having them as the reduced code and edge cases gave way more benefits in comparison. One reason for this discussion in the first place was the segmentation btw as additional 2d cases regularily broke even more code than all the 4d cases. So eventually it was said, that it will be kind of guaranteed that loaded images will be presented at least as 3d images. It is still possible to generate 2d images in code and that's why there still should be checks if an image has less than 3 dimensions.

Oct 2 2020, 10:30 AM · Auto-closed, Request for Discussion, Restricted Project, MITK
aguilera moved T27779: [shiny] Clarifications on page "Configure ranking" from In Progress to Done on the webChallengeR board.
Oct 2 2020, 10:06 AM · webChallengeR
kalali updated the task description for T27806: Meaning of 2D images in MITK.
Oct 2 2020, 8:51 AM · Auto-closed, Request for Discussion, Restricted Project, MITK
floca triaged T27806: Meaning of 2D images in MITK as Normal priority.
Oct 2 2020, 8:37 AM · Auto-closed, Request for Discussion, Restricted Project, MITK

Oct 1 2020

kalali merged T22330: 3D and 2D interpolation does not work in the multilabelsegmentation plugin into T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View.
Oct 1 2020, 3:02 PM · MITK (v2023.04), Restricted Project
kalali merged task T22330: 3D and 2D interpolation does not work in the multilabelsegmentation plugin into T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View.
Oct 1 2020, 3:02 PM · MITK
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T27571: Multilabel segmentation does not work with US DICOM images.
Oct 1 2020, 2:55 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali added a parent task for T27571: Multilabel segmentation does not work with US DICOM images: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Oct 1 2020, 2:55 PM · MITK (v2021.10), Missing Info, Restricted Project
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T23981: Multilabel color map should disable interpolation.
Oct 1 2020, 2:54 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali added a parent task for T23981: Multilabel color map should disable interpolation: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Oct 1 2020, 2:54 PM · Restricted Project, MITK
kalali merged task T20109: Update documentation for the multilabel segmentation plugin into T27095: [MITKDoc] Revise MultiLabel Segmentation Plugin Documentation.
Oct 1 2020, 2:53 PM · MITK
kalali merged T20109: Update documentation for the multilabel segmentation plugin into T27095: [MITKDoc] Revise MultiLabel Segmentation Plugin Documentation.
Oct 1 2020, 2:53 PM · MITK (v2021.02)
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View.
Oct 1 2020, 2:51 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali added a parent task for T27319: [Segmentation] Correctly implement interpolation features for Multilabel Segmentation View: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Oct 1 2020, 2:51 PM · MITK (v2023.04), Restricted Project
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T25445: MultiLabel segmentation mapper is very slow.
Oct 1 2020, 2:51 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali added a parent task for T25445: MultiLabel segmentation mapper is very slow: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Oct 1 2020, 2:51 PM · Moved to git.dkfz.de, MITK (v2024.12), Request for Discussion
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T26397: Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK.
Oct 1 2020, 2:50 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali added a parent task for T26397: Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Oct 1 2020, 2:50 PM · MITK
kalali added a parent task for T20110: [Multilabel Segmentation] Contour broken for 3D and 2D interpolation: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Oct 1 2020, 2:50 PM · Next Milestone, MITK
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T20110: [Multilabel Segmentation] Contour broken for 3D and 2D interpolation.
Oct 1 2020, 2:50 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T27637: [Segmentation] Multilabel label name dialog on label creation is a UX problem.
Oct 1 2020, 2:49 PM · Moved to git.dkfz.de, MITK (v2024.12)