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kalali (Amir Kalali)
Developer

Projects (6)

User Details

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

Recent Activity

Wed, Nov 25

kalali added a member for MITK: a178n.
Wed, Nov 25, 11:35 AM

Fri, Nov 20

kalali added a member for SIDT: a178n.
Fri, Nov 20, 11:43 AM
kalali lowered the priority of T24770: WeakPointer: Exception on OnDeleteEvent when closing MITK workbench from High to Normal.
Fri, Nov 20, 11:11 AM · MITK
kalali removed a project from T24770: WeakPointer: Exception on OnDeleteEvent when closing MITK workbench: Request for Discussion.
Fri, Nov 20, 11:11 AM · MITK

Thu, Nov 19

kalali triaged T27973: Setup non-development system for MITK installer tests as Normal priority.
Thu, Nov 19, 10:01 AM · Request for Discussion, Restricted Project, CI

Mon, Nov 16

kalali moved T26854: Unattended Qt installation from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Mon, Nov 16, 10:13 AM · CI, Restricted Project, MITK
kalali moved T26854: Unattended Qt installation from Backlog to Done on the CI board.
Mon, Nov 16, 10:13 AM · CI, Restricted Project, MITK
kalali added a comment to T26854: Unattended Qt installation.

This seems to be superfluous if {T27960} works for us.

Mon, Nov 16, 10:02 AM · CI, Restricted Project, MITK

Wed, Nov 11

kalali reopened T23274: RenderWindowPartActivated is not called in several plugins as "Open".

Generally this is still valid as it was only done in one plugin to show the idea behind it. We need to check if this is still a problem.

Wed, Nov 11, 12:02 PM · MICO (Demo_MICCAI_2017), MITK
kalali removed a project from T25057: Check IContextMenuActions and extension points: Auto-closed.
Wed, Nov 11, 12:00 PM · MITK
kalali reopened T25057: Check IContextMenuActions and extension points, a subtask of T25056: Refactor data manager context menu, as Open.
Wed, Nov 11, 11:59 AM · Noteworthy, MITK
kalali reopened T25057: Check IContextMenuActions and extension points as "Open".

This is still relevant and will be tackled after the release.

Wed, Nov 11, 11:59 AM · MITK

Oct 26 2020

kalali added a comment to T27906: Extend "Checkliste Segmentierung – Utilities".

I updated the document and added content to explicitly test

  • utilities / tools / operations on a 3D image
  • combination of 3D images with dynamic segmentation / surface
  • combination of 4D images with static segmentation / surface
  • combination of dynamic and static segmentation
Oct 26 2020, 2:14 PM · Cleared, MITK (2020)
kalali updated the task description for T27913: [Segmentation] Warnings in utilities view are inconsistent.
Oct 26 2020, 11:41 AM · MITK
kalali reopened T17656: ProgressBar for morphological operations as "Open".

I just stumbled upon this while testing the utilities with 4D data. Depending on the number of timesteps and the complexity of the operation the selected operation might take a while (you ca actually see the progress in the console output).
This should be discussed as I do not see any

whole new segmentation functionality this year

Oct 26 2020, 11:21 AM · Request for Discussion, MITK, Bugzilla
kalali triaged T27913: [Segmentation] Warnings in utilities view are inconsistent as Normal priority.
Oct 26 2020, 11:07 AM · MITK

Oct 23 2020

kalali moved T27907: Extend "Checkliste Documentation" from Backlog to Documentation on the MITK (2020) board.
Oct 23 2020, 12:22 PM · Cleared, MITK (2020)
kalali triaged T27907: Extend "Checkliste Documentation" as Normal priority.
Oct 23 2020, 12:22 PM · Cleared, MITK (2020)
kalali moved T27906: Extend "Checkliste Segmentierung – Utilities" from Backlog to Segmentation on the MITK (2020) board.
Oct 23 2020, 12:16 PM · Cleared, MITK (2020)
kalali triaged T27906: Extend "Checkliste Segmentierung – Utilities" as High priority.
Oct 23 2020, 12:16 PM · Cleared, MITK (2020)

Oct 15 2020

kalali added a comment to T27506: Extend checklists for segmentation view.

I'm all in for that. We already discussed that we will focus again on this task T26754: Review checklists and its subtasks. This also includes

Automatic GUI testing

and

move as much tests as possible to Unit-Tests

Oct 15 2020, 9:56 AM · Restricted Project, Cleared, MITK (2020)

Oct 14 2020

kalali added a comment to T27506: Extend checklists for segmentation view.

The checklist don't say anything about multilabel segmentation. This should be addressed with a special focus on creating and combining multiple labels / layers.
I couldn't find any other checklist with a focus on the multilabel functionality.

Oct 14 2020, 3:42 PM · Restricted Project, Cleared, MITK (2020)
kalali added a comment to T27873: Extend "Checkliste Segmentierung – Manuelle Segmentierung mit Interpolation".

I updated the document and added content to explicitly tests

Oct 14 2020, 3:38 PM · Cleared, MITK (2020)
kalali triaged T27883: [Segmentation] Interpolation contour on static segmentation is only shown on timestep 0 as Normal priority.
Oct 14 2020, 2:55 PM · MITK (2020)
kalali renamed T27149: [Segmentation] Interpolation nodes / position nodes are not correctly hidden from Segmentation: interpolation nodes are not removed from data manager to [Segmentation] Interpolation nodes / position nodes are not correctly hidden.
Oct 14 2020, 2:27 PM · MITK (2020)
kalali added a comment to T27149: [Segmentation] Interpolation nodes / position nodes are not correctly hidden.

I can verify this behavior. Also, if you close the segmentation view while the position nodes are shown, they stay visible.
If you open the segmentation view again and select the 3-Dimensional interpolation, the position nods are still shown, although the checkbox is not checked.
Checking it and unchecking it will hide the position nodes again.

Oct 14 2020, 2:26 PM · MITK (2020)
kalali renamed T20110: [Multilabel Segmentation] Contour broken for 3D and 2D interpolation from Contour broken for 3D and 2D interpolation in multilabel segmentation plugin to [Multilabel Segmentation] Contour broken for 3D and 2D interpolation.
Oct 14 2020, 2:21 PM · Next Milestone, MITK
kalali claimed T27873: Extend "Checkliste Segmentierung – Manuelle Segmentierung mit Interpolation".
Oct 14 2020, 10:23 AM · Cleared, MITK (2020)

Oct 13 2020

kalali moved T27873: Extend "Checkliste Segmentierung – Manuelle Segmentierung mit Interpolation" from Backlog to Segmentation on the MITK (2020) board.
Oct 13 2020, 3:38 PM · Cleared, MITK (2020)
kalali triaged T27873: Extend "Checkliste Segmentierung – Manuelle Segmentierung mit Interpolation" as High priority.
Oct 13 2020, 3:36 PM · Cleared, MITK (2020)
kalali added a comment to T27850: Extend "Checkliste Segmentierung – 3D Segmentierung".

Similar to T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung" I updated the document and added content to explicitly tests different image types / segmentation types.
Additionally I tried to make both checklists more consistent.

Oct 13 2020, 3:34 PM · Cleared, MITK (2020)
kalali added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

So Region Growing 3D seems to work and could probably be used for reference for other algorithms.

Oct 13 2020, 2:42 PM · Missing Info, Restricted Project, MITK (2020)
kalali triaged T27872: [Segmentation] Region Growing 3D GUI does not provide a "Overwrite" checkbox as Normal priority.
Oct 13 2020, 2:41 PM · Restricted Project, Cleared, MITK (2020)
kalali created T27872: [Segmentation] Region Growing 3D GUI does not provide a "Overwrite" checkbox.
Oct 13 2020, 2:41 PM · Restricted Project, Cleared, MITK (2020)
kalali removed a subtask for T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation: T27870: [Segmentation] Fast Marching 3D Tool can not clear preview segmentation masks.
Oct 13 2020, 2:36 PM · Missing Info, Restricted Project, MITK (2020)
kalali removed a parent task for T27870: [Segmentation] Fast Marching 3D Tool can not clear preview segmentation masks: T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
Oct 13 2020, 2:36 PM · MITK (2020)
kalali renamed T27870: [Segmentation] Fast Marching 3D Tool can not clear preview segmentation masks from {Segmentation] Fast Marching 3D Tool can not clear preview segmentation masks to [Segmentation] Fast Marching 3D Tool can not clear preview segmentation masks.
Oct 13 2020, 1:01 PM · MITK (2020)
kalali moved T27870: [Segmentation] Fast Marching 3D Tool can not clear preview segmentation masks from Backlog to Segmentation on the MITK (2020) board.
Oct 13 2020, 12:22 PM · MITK (2020)
kalali triaged T27870: [Segmentation] Fast Marching 3D Tool can not clear preview segmentation masks as Normal priority.
Oct 13 2020, 12:22 PM · MITK (2020)
kalali added a comment to T26897: Build error: Could not find git for clone of qRestAPI.

I wonder how this is related to our findings from December last year.

Oct 13 2020, 10:51 AM · Noteworthy, MITK

Oct 12 2020

kalali moved T27850: Extend "Checkliste Segmentierung – 3D Segmentierung" from Backlog to Segmentation on the MITK (2020) board.
Oct 12 2020, 10:51 AM · Cleared, MITK (2020)
kalali triaged T27850: Extend "Checkliste Segmentierung – 3D Segmentierung" as High priority.
Oct 12 2020, 10:47 AM · Cleared, MITK (2020)
kalali added a comment to T27847: [MITKDoc] Chart Example view documentation.

Should we put this on "Next Milestone" since the chart example will probably not be included in any installer?

Oct 12 2020, 10:43 AM · MITK, Next Milestone
kalali moved T27847: [MITKDoc] Chart Example view documentation from Backlog to Documentation on the MITK (2020) board.
Oct 12 2020, 10:41 AM · MITK, Next Milestone

Oct 9 2020

kalali closed T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation, a subtask of T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation, as Resolved.
Oct 9 2020, 2:36 PM · Missing Info, Restricted Project, MITK (2020)
kalali closed T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation as Resolved.
Oct 9 2020, 2:36 PM · MITK (2020)
kalali added a comment to T27721: [Segmentation] 2D Fast Marching crashes with 4D image and static segmentation.

I landed the changes of D423. For the next steps, consider T27507#211912.

Oct 9 2020, 2:36 PM · MITK (2020)
kalali committed rMITKece31f3c79b9: 2D Fast Marching segmentation crashes with 4D image and static segmentation (authored by kalali).
2D Fast Marching segmentation crashes with 4D image and static segmentation
Oct 9 2020, 2:35 PM
kalali committed rMITKa3e155361a43: Transform current time step from reference image to working image (authored by kalali).
Transform current time step from reference image to working image
Oct 9 2020, 2:35 PM
kalali closed T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation, a subtask of T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation, as Resolved.
Oct 9 2020, 2:33 PM · Missing Info, Restricted Project, MITK (2020)
kalali closed T27800: [Segmentation] Live Wire crashes with 4D image and static segmentation as Resolved.

I landed the changes of D424. For the next steps, consider T27507#211912.

Oct 9 2020, 2:33 PM · MITK (2020)
kalali committed rMITK98f05ef6825b: Live Wire segmentation crashes with 4D image and static segmentation (authored by kalali).
Live Wire segmentation crashes with 4D image and static segmentation
Oct 9 2020, 2:32 PM
kalali committed rMITKe9da1a8162ac: Transform current time step from reference image to working image (authored by kalali).
Transform current time step from reference image to working image
Oct 9 2020, 2:31 PM
kalali added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

We had a discussion about refactoring the segmentation tools (similar to {D380}). The idea is to outsource redundant code into base classes (e.g. time-management, slice extraction, input data checks etc.) to have a single point of truth for the starting point of the different segmentation-tool-algorithms. This would make the tools less error prone and can simplify testing (even allow automatic testing for the input management steps) (see T27800#211467).

Oct 9 2020, 12:18 PM · Missing Info, Restricted Project, MITK (2020)
kalali added a comment to T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung".

I looked again at the tests we have inside the checklist and I think it is still very long and many steps are redundant - because only the clicked tool-button changes and the underlying segmentation algorithm produces different results.
I think it is clearer and even better for testing a specific tool / algorithm, if we somehow separate the tests for different tools.
Also,

If necessary, I might need a helping hand because static/dynamic*single/double*2DTools/3DTools = many test cases

Oct 9 2020, 11:00 AM · Restricted Project, Cleared, MITK (2020)
kalali added a parent task for T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Oct 9 2020, 10:02 AM · Cleared, MITK (2020)
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels.
Oct 9 2020, 10:02 AM · Next Milestone, MITK
kalali updated the task description for T27737: Extend "Checkliste Segmentierung – Optionen".
Oct 9 2020, 9:16 AM · Restricted Project, Cleared, MITK (2020)
kalali closed T27100: [MITKDoc] Revise DataManager Plugin Documentation as Resolved.
Oct 9 2020, 8:42 AM · Cleared, MITK (2020)

Oct 8 2020

kalali closed T27096: [MITKDoc] Revise MultiLabel Segmentation Utilities Plugin Documentation as Resolved.

Open problems will be tackled in subtasks of T27807: [MultiLabel Segmentation] Inspection of module and plugin, e.g. T27809 and T27810.

Oct 8 2020, 3:47 PM · MITK (2020)
kalali committed rMITK9988ae5bac9b: Rename multilabel segmentation documentation file and reference utilities page (authored by kalali).
Rename multilabel segmentation documentation file and reference utilities page
Oct 8 2020, 3:46 PM
kalali committed rMITK028a2733ca29: Revise MultiLabel Segmentation Utilities Plugin Documentation (authored by kalali).
Revise MultiLabel Segmentation Utilities Plugin Documentation
Oct 8 2020, 3:46 PM
kalali committed rMITK7e2a8474f87b: Fix spelling mistake and change order of operations (authored by kalali).
Fix spelling mistake and change order of operations
Oct 8 2020, 3:46 PM
kalali committed rMITK0e6dc95f8904: Modify section names, add documentation of "Convert to Multilabel" operation (authored by kalali).
Modify section names, add documentation of "Convert to Multilabel" operation
Oct 8 2020, 3:45 PM
kalali committed rMITKade3a7af5722: Update documentation images (authored by kalali).
Update documentation images
Oct 8 2020, 3:45 PM
kalali committed rMITK753a7c885905: Update documentation (authored by kalali).
Update documentation
Oct 8 2020, 3:45 PM
kalali committed rMITK9dc46e260b85: Add missing image (authored by kalali).
Add missing image
Oct 8 2020, 3:45 PM
kalali committed rMITKac64132d5453: Add documentation images (authored by kalali).
Add documentation images
Oct 8 2020, 3:45 PM
kalali committed rMITK8668a49caa13: Draft first revision (authored by kalali).
Draft first revision
Oct 8 2020, 3:45 PM

Oct 6 2020

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 (2020)
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 (2020)

Oct 5 2020

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 · Missing Info, Restricted Project, MITK (2020)
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 (2020)
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 · Missing Info, Restricted Project, MITK (2020)
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 · Restricted Project, MITK
kalali added a project to T27665: PlanarFigure tests show error with DICOMTagsOfInterestAddHelper: Restricted Project.
Oct 5 2020, 10:31 AM · Restricted Project, MITK

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 (2020)
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 · Missing Info, Restricted Project, MITK (2020)
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 (2020)
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 · Missing Info, Restricted Project, MITK (2020)

Oct 2 2020

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 · MITK
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
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
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 · MITK
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 · MITK
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 · Restricted Project, Next Milestone, MITK
kalali triaged T27809: [Multilabel Segmentation] "Labels" tabs in operations of Utilities view is empty as Normal priority.
Oct 2 2020, 11:57 AM · MITK
kalali updated the task description for T27806: Meaning of 2D images in MITK.
Oct 2 2020, 8:51 AM · 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 · Restricted Project, MITK, Cleared
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: Multilable segmentation does not work with US DICOM images.
Oct 1 2020, 2:55 PM · Next Milestone, MITK
kalali added a parent task for T27571: Multilable segmentation does not work with US DICOM images: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Oct 1 2020, 2:55 PM · Missing Info, MITK (2020), 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 · Next Milestone, MITK
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 (2020)