In T27507#211505, @floca wrote:@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?
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Oct 6 2020
Oct 6 2020
• thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
Oct 5 2020
Oct 5 2020
kislinsk added a revision to T27818: [MITKDoc] Revise Top-level directories in documentation: Unknown Object (Differential Revision).
kislinsk triaged T27818: [MITKDoc] Revise Top-level directories in documentation as Normal priority.
• thomass updated the task description for T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels.
• thomass updated the task description for T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels.
• thomass triaged T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels as High priority.
kompan updated the task description for T27815: Modelfit Generic Data Fitting missing start parameters.
kompan removed a project from T27745: [MITKDoc] Revise Model Fit Generic View Documentation: Cleared.
kalali added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
In T27507#211481, @thomass wrote: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.
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?
kompan triaged T27814: Refactor ModelFit Generic Data Fitting view to use new selection concept as Normal priority.
kalali moved T27665: PlanarFigure tests show error with DICOMTagsOfInterestAddHelper from Restricted Project Column to Restricted Project Column on the Restricted Project board.
kalali added a project to T27665: PlanarFigure tests show error with DICOMTagsOfInterestAddHelper: Restricted Project.
• 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
• 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 4 2020
Oct 4 2020
floca reopened T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation as "Open".
floca added a comment to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.
In T27800#211261, @kalali wrote:
- 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...
floca added a comment to T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation.
In T27800#211261, @kalali wrote:
- 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 2 2020
Oct 2 2020
redundant
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.
T27791 - Optimized RT mime types
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…
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….
kalali closed T24775: Refactor plugins to use the new node selection widgets, a subtask of T23751: Introduction of new selection concept, as Resolved.
I removed T27060: [Segmentation] Rework InterpolationWidget to not depend on data manager view directly as subtask and now this can be closed!
kalali awarded T24775: Refactor plugins to use the new node selection widgets a 100 token.
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.
kalali updated the task description for T24775: Refactor plugins to use the new node selection widgets.
kalali triaged T27810: [Multilabel Segmentation] Inconsistencies and unclear functionality in operations of Utilities view as Normal priority.
kalali triaged T27809: [Segmentation Utilities] "Labels" tabs in operations of Utilities view is empty as Normal priority.
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.
• aguilera moved T27779: [shiny] Clarifications on page "Configure ranking" from In Progress to Done on the webChallengeR board.
Oct 1 2020
Oct 1 2020
kalali updated the task description for T27807: [MultiLabel Segmentation] Inspection of module and plugin.
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: Unknown Object (Maniphest Task).
kalali triaged T27807: [MultiLabel Segmentation] Inspection of module and plugin as Normal priority.
kalali added a comment to T27712: Preference "Show as volume rendering" does not display segmentation volume in 4-window view.
Same / related: T19522: Segmentation not displayed in 3d-render window
kalali renamed T26397: Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK from Multilabel Segmentation fil ecannot be converted to multilabel segmentation in MITK to Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK.
kalali added a comment to T27712: Preference "Show as volume rendering" does not display segmentation volume in 4-window view.
I can verify this behavior. It worked before with my 2018.04 installer.
stacked frequency plots are quite neglected. They are not mentioned in the paper. Are they interesting or should they be removed entirely?
what about
keep S3, compareRanks and extract.workflow
but do not export (i.e. remove from namespace) compareRanks and extract.workflow. they can then only be accessed e.g. by challengeR:::compareRanks(). These might be of practical use.
?
Sep 30 2020
Sep 30 2020
• aguilera moved T27780: [shiny] Links should open in new tabs from Backlog to Done on the webChallengeR board.
eisenman committed rCHALLENGER60750f087cfe: Merge branch 'feature/T27450-ConsistentUseOfSmallBetter' into develop (authored by eisenman).
Merge branch 'feature/T27450-ConsistentUseOfSmallBetter' into develop
eisenman committed rCHALLENGERe5a5908287d2: Consistently use smallBetter to specify that small metric values indicate… (authored by eisenman).
Consistently use smallBetter to specify that small metric values indicate…
Clean up