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Use this project to tag tasks and other stuff that should be discussed in the weekly MITK meeting.

Recent Activity

Today

kleina added a comment to T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label .

That is what I assumed... the labels created by multi-label plugin always contain only two values, if I am not mistaken: 0 and x with x e [1,2,3,...]. One could check for the label values and if there is only two different ones, use these two. This does not include the case when a label was created externally,e.g., by U-Net and contains several values in a single image.

Mon, Aug 2, 4:35 PM · Request for Discussion, MITK (v2021.10)
kalali added a project to T26172: 2D interpolation in MultiLabelSegmentation Editor only works for 1. label : Request for Discussion.
Mon, Aug 2, 4:21 PM · Request for Discussion, MITK (v2021.10)

Fri, Jul 30

s669m triaged T28653: website feedbacks - comments from Ralf as Normal priority.
Fri, Jul 30, 5:13 PM · Request for Discussion, Kaapana (internal)
kalali moved T27713: [Segmentation] Disable "New" button when no image is selected from MITK Meeting to Backlog on the Request for Discussion board.
Fri, Jul 30, 10:25 AM · MITK (v2021.10), Request for Discussion

Thu, Jul 29

s669m triaged T28648: To update helm install chart API response as Normal priority.
Thu, Jul 29, 2:55 PM · Request for Discussion, Kaapana (internal)

Wed, Jul 28

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.
Wed, Jul 28, 1:22 PM · Missing Info, MITK (v2021.10), Request for Discussion
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.
Wed, Jul 28, 1:22 PM · Missing Info, MITK (v2021.10), Request for Discussion
a178n closed T28523: Evaluate MITK segmentation survey, a subtask of T28499: Refactor/rewrite RegionGrowing3D tool, as Resolved.
Wed, Jul 28, 1:22 PM · Request for Discussion, MITK (v2021.10)
floca lowered the priority of T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value from Normal to Low.

Down prioritized it, because survey indicated currently low relevance.

Wed, Jul 28, 12:45 PM · Missing Info, MITK (v2021.10), Request for Discussion
s434n added a project to T28631: [PACS] Allow disabling of PACS tools: Request for Discussion.
Wed, Jul 28, 10:57 AM · Request for Discussion, MITK (v2021.10)

Tue, Jul 27

floca added a parent task for T28139: [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage: T28525: Design refactoring of LabelSetImage and associated classes.
Tue, Jul 27, 9:57 AM · Request for Discussion, MITK (v2021.10)
floca added a parent task for T28140: [MultiLabel Segmentation] Default parameter (unsigned int layer = 0) is unnecessary and causes problems: T28525: Design refactoring of LabelSetImage and associated classes.
Tue, Jul 27, 9:57 AM · Request for Discussion, MITK (v2021.10)

Wed, Jul 21

nolden updated subscribers of T28529: Replace Elasticsearch and Kibana with apache-licensed opensearch.

Thanks Hanno. I think @schererj is the original author, so maybe he can comment or we discuss it in the meeting.

Wed, Jul 21, 8:14 PM · Request for Discussion, Kaapana (internal)

Tue, Jul 20

kalali renamed T25804: [Selection concept] Set 'selected' property when using the new selection concept from Set 'selected' property when using the new selection concept to [Selection concept] Set 'selected' property when using the new selection concept.
Tue, Jul 20, 2:09 PM · MITK (v2021.10), Request for Discussion
kalali removed a parent task for T25804: [Selection concept] Set 'selected' property when using the new selection concept: T23751: Introduction of new selection concept.
Tue, Jul 20, 2:09 PM · MITK (v2021.10), Request for Discussion
kalali added a subtask for T25804: [Selection concept] Set 'selected' property when using the new selection concept: Restricted Maniphest Task.
Tue, Jul 20, 2:09 PM · MITK (v2021.10), Request for Discussion
kalali closed T28315: [Selection concept] Provide preference page option to show / hide helper nodes as Invalid.

I checked some of the most important plugin views and their storage inspectors / selection widgets and couldn't find something that needs to be tackled right now. I will close this task for now but we should keep an eye on the "helper nodes" appearing in some selection dialogs of specific plugin views.
And I agree that the the local plugin view should care for the right predicate.

Tue, Jul 20, 1:55 PM · Request for Discussion, MITK (v2021.10)

Mon, Jul 19

gaoh added a comment to T28529: Replace Elasticsearch and Kibana with apache-licensed opensearch.

So I tried it out. The problem are not the containeres (opensearch and opensearch-dashboard), but our plugin (workflow-trigger).
The plugin workflow-trigger has some package dependencies based on elastic/kibana. These dependencies have to be changed to the once of opensearch-dashboard.
So I tried to change it, but I get some yarn build issues.
So I am having different issues, probably it would be easier to restart the plugin form fresh. But for this, I would like to know, how the current plugin was created, to get an understanding, on how to create a similar one.
So the current issue is, that the package is searching for specific files, probably an opensearch-dashboard has to have a specific dir-order:

Mon, Jul 19, 11:37 AM · Request for Discussion, Kaapana (internal)

Fri, Jul 16

kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

Also, this solution still does not preserve the zoom but that's the next step.

Fri, Jul 16, 1:00 PM · Cleared, MITK (v2021.10)

Thu, Jul 15

kalali added a revision to T28490: Segmentation plugin: "new" segmentation should not run reinit!: Restricted Differential Revision.
Thu, Jul 15, 10:38 PM · Cleared, MITK (v2021.10)
kalali updated subscribers of T28490: Segmentation plugin: "new" segmentation should not run reinit!.

We discussed this and two important points were made:

  • The difference between RenderWindowManager::InitializeViews(RenderingManager::GetInstance(), image->GetTimeGeometry()); and RenderWindowManager::InitializeViewsByBoundingObjects(RenderingManager::GetInstance(), dataStorage); is reasonable and important - even for a single data node (e.g. brain.nrrd, where the image itself is somehow rotated / tilted).
  • We definitely want to reset the geometry automatically such that the current view geometry of the renderer matches with the segmentation geometry. That way the user can immediately start drawing. We don't want the user to have to care for the correct geometry aligning manually.
Thu, Jul 15, 10:35 PM · Cleared, MITK (v2021.10)
s434n added a subtask for T26485: [Segmentation] PACS mode is active while segmentation is drawn: T28631: [PACS] Allow disabling of PACS tools.
Thu, Jul 15, 5:07 PM · MITK (v2021.10), Request for Discussion
nolden added a project to T28618: Login procedure in install_platform.sh can be confusing for private registry mode: Request for Discussion.
Thu, Jul 15, 10:05 AM · Kaapana (internal)

Wed, Jul 14

kislinsk lowered the priority of T28262: TimeGeometry inconsistent documentation and implementation of time bounds and checks from Unbreak Now! to High.
Wed, Jul 14, 11:09 AM · MITK (v2021.10), Request for Discussion

Mon, Jul 12

kalali moved T28490: Segmentation plugin: "new" segmentation should not run reinit! from Backlog to MITK Meeting on the Request for Discussion board.

We need to look deeper into the segmentation plugin to find out if it is possible to create and draw a segmentation without a correctly initialized reference image.

Mon, Jul 12, 6:13 PM · Cleared, MITK (v2021.10)

Wed, Jul 7

kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

So I dug a little bit deeper using brain.nrrd as test data:

Wed, Jul 7, 5:39 PM · Cleared, MITK (v2021.10)
kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

So my conclusion from this: [...] It seems as there is a difference between the initialization that is performed when loading the image and the initialization that is performed when calling InitializeViews or using the reinit-action from the context menu.

Wed, Jul 7, 12:05 PM · Cleared, MITK (v2021.10)
floca moved T26485: [Segmentation] PACS mode is active while segmentation is drawn from Segmentation to Cycle on the MITK (v2021.10) board.
Wed, Jul 7, 10:24 AM · MITK (v2021.10), Request for Discussion

Tue, Jul 6

kalali added a comment to T28490: Segmentation plugin: "new" segmentation should not run reinit!.

I see no difference between calling InitializeViews with the new Enum value NO_UPDATE and not calling InitializeViews at all, solely using mitk::RenderingManager::GetInstance()->RequestUpdateAll() to correctly set the rendering geometry without changing the view after a new segmentation nodes has been created.
However, both variants do not allow segmenting on the new segmentation node as the warning message shows, stating that a reinit should be performed on the segmentation image. The warning message appears in the scenario where I changed the camera view before creating a new segmentation:

NO_UPDATE_02.png (1×2 px, 229 KB)

Tue, Jul 6, 4:49 PM · Cleared, MITK (v2021.10)
kleina placed T27713: [Segmentation] Disable "New" button when no image is selected up for grabs.
Tue, Jul 6, 1:13 PM · MITK (v2021.10), Request for Discussion
kleina moved T27713: [Segmentation] Disable "New" button when no image is selected from Cycle to Segmentation on the MITK (v2021.10) board.
Tue, Jul 6, 1:13 PM · MITK (v2021.10), Request for Discussion
kleina added a comment to T27713: [Segmentation] Disable "New" button when no image is selected.

I looked into this (to be honest, I did not read Amirs last comment): I totally agree. I fixed the issue, which was not to complicated, but there is a lot of spaghetti code involved. I agree with Amirs suggestion to not fix it this way.

Tue, Jul 6, 1:12 PM · MITK (v2021.10), Request for Discussion
kleina closed T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change as Resolved.

I tested it again with feedback from @kalali and @s434n. The behavior that the tool has is ok for now. I adapted the checklist accordingly. We found some minor issues, that we propose to fix on the near future:

Tue, Jul 6, 12:58 PM · Request for Discussion, MITK (v2021.10)
kalali added a comment to T26485: [Segmentation] PACS mode is active while segmentation is drawn.

To add to this: Point 2 sounds reasonable and that's what happens when the MITK mode is activated: The Segmentation Tool deactivates the left mouse click of the MITK mode.
However, this is not implemented for the PACS mode and would require additional complex logic.

Tue, Jul 6, 11:12 AM · MITK (v2021.10), Request for Discussion
s434n claimed T26485: [Segmentation] PACS mode is active while segmentation is drawn.
Tue, Jul 6, 10:32 AM · MITK (v2021.10), Request for Discussion

Mon, Jul 5

s434n added a comment to T26485: [Segmentation] PACS mode is active while segmentation is drawn.

André, Amir and I discussed the problem a bit and found multiple problems and ideas. The general question is: what is the intended behavior? Some options are:

  1. only one interaction can be active at any time. This would mean activating a segmentation tool would deactivate any PACS functionality and vice versa. Not really what we want, since it prohibits using regular MITK interaction behavior (e.g. zooming with the right mouse button) while segmenting
  2. only one left-mouse-button interaction is active at any time. Activating a segmentation tool would automatically disable left-mouse-button usage for display purposes
  3. multiple interactors can operate on the same events, i.e. PACS + segmentation at the same time is intended behavior, if the user wishes to do so. To make this useful, it should be possible to deactivate PACS interaction, either by allowing to click a button again to deselect it or by providing an additional button that does nothing on left clicks.
Mon, Jul 5, 5:18 PM · MITK (v2021.10), Request for Discussion
s434n added a comment to T26485: [Segmentation] PACS mode is active while segmentation is drawn.

The problem really seems to be the disabling / resetting of interactors that was mentioned in an earlier comment, even with the fix that corrects the resetting when the tool is deactivated again. Correct usage would be:

  1. moving around the gui, using PACS
  2. selecting a segmentation tool (which deactivates other interactors)
  3. only using the segmentation tool, without changing the view
  4. deactivating the segmentation tool (and thus reenabling previous interactors)
  5. -> everything works as intended

When a PACS tool is selected after step 2, this messes up the active interaction and after the segmentation tool is deactivated it resets to what was previously selected, before the tool was activated.

Mon, Jul 5, 1:19 PM · MITK (v2021.10), Request for Discussion

Jul 1 2021

nolden added a comment to T28529: Replace Elasticsearch and Kibana with apache-licensed opensearch.

So this task as an _evaluation_ task has a high priority in my opinion. If it turns out to be a bigger thing to replace please stop and we should discuss again

Jul 1 2021, 1:47 PM · Request for Discussion, Kaapana (internal)
nolden added a comment to T28529: Replace Elasticsearch and Kibana with apache-licensed opensearch.

If this is not a big deal, i.e. if it really works after switching to the replacement there would be a big benefit. So it would be great if someone could at least try it and report some results, like how much work it would be. After that we could decide how to prioritize, but from my understanding it would make our Kaapana license task much easier

Jul 1 2021, 1:46 PM · Request for Discussion, Kaapana (internal)
s669m moved T28599: Nested-V pods accessibility of GPU which is running on Kaapana Powered Server from Discussion to Resolved on the Kaapana (internal) board.
Jul 1 2021, 10:27 AM · Request for Discussion, Kaapana (internal)
s669m added a comment to T28600: Kaapana containerd version is 1.2.5 which is 2 years old: Need to update that.

When I install Kaapana using installation script the containerd version is 1.2.5 which is 2 years old.

Jul 1 2021, 10:24 AM · Request for Discussion, Kaapana (internal)
k656s moved T28600: Kaapana containerd version is 1.2.5 which is 2 years old: Need to update that from Discussion to Community-Day Tasks on the Kaapana (internal) board.
Jul 1 2021, 10:20 AM · Request for Discussion, Kaapana (internal)
k656s moved T28529: Replace Elasticsearch and Kibana with apache-licensed opensearch from Discussion to Community-Day Tasks on the Kaapana (internal) board.
Jul 1 2021, 10:09 AM · Request for Discussion, Kaapana (internal)
k656s added a comment to T28529: Replace Elasticsearch and Kibana with apache-licensed opensearch.

@nolden which priority does this have? In a long run, we probably replace the elasticsearch kibana stack with another technology

Jul 1 2021, 10:08 AM · Request for Discussion, Kaapana (internal)
s669m triaged T28600: Kaapana containerd version is 1.2.5 which is 2 years old: Need to update that as Normal priority.
Jul 1 2021, 9:44 AM · Request for Discussion, Kaapana (internal)
s669m triaged T28599: Nested-V pods accessibility of GPU which is running on Kaapana Powered Server as Normal priority.
Jul 1 2021, 9:15 AM · Request for Discussion, Kaapana (internal)

Jun 30 2021

kalali moved T28490: Segmentation plugin: "new" segmentation should not run reinit! from Segmentation to Cycle on the MITK (v2021.10) board.
Jun 30 2021, 9:41 AM · Cleared, MITK (v2021.10)

Jun 28 2021

kleina added a comment to T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.

Additionally, I would not auto-confirm as a default. As a user I would first finish the outline and then correct it if needed. I would be really frustrated, if that is then not possible anymore.

Jun 28 2021, 4:57 PM · Request for Discussion, MITK (v2021.10)
kleina claimed T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.
Jun 28 2021, 4:47 PM · Request for Discussion, MITK (v2021.10)
kleina added a project to T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change: Request for Discussion.
Jun 28 2021, 4:43 PM · Request for Discussion, MITK (v2021.10)