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floca committed rOBSHYPPOPY905460839b8c: Some smaller additions and proposals to the draft. (authored by floca).
Some smaller additions and proposals to the draft.
Wed, May 12, 8:36 PM
schererj added a comment to T28232: Shapemodels.

The problem is the MBI branch, which is afaik not public.
If there is a working Dockerfile, which can be publicly build, I'm happy to include it.
Additionally the models need to be put somewhere to be downloaded (also public in this case).
Hope this helps.

Wed, May 12, 4:53 PM · Kaapana (internal), Request for Discussion, MITK
schererj committed rKAAPANA7f408e671f74: reset api version (authored by schererj).
reset api version
Wed, May 12, 4:04 PM
schererj committed rKAAPANAce79ced300b8: debug. (authored by schererj).
debug.
Wed, May 12, 2:46 PM
schererj committed rKAAPANA430a24db0d15: new kube apis (authored by schererj).
new kube apis
Wed, May 12, 2:46 PM
schererj committed rKAAPANA907f5ccfd5e0: debug. (authored by schererj).
debug.
Wed, May 12, 2:46 PM
schererj committed rKAAPANAe500eb658d5e: kubernetes 1.20 adjustments (authored by schererj).
kubernetes 1.20 adjustments
Wed, May 12, 11:59 AM
schererj committed rKAAPANAd89c3145f697: adjustments (authored by schererj).
adjustments
Wed, May 12, 11:55 AM

Tue, May 11

schererj committed rKAAPANA6d89ed6cc955: adjusted ensemble to find fitting models (authored by schererj).
adjusted ensemble to find fitting models
Tue, May 11, 11:46 PM
schererj committed rKAAPANA366fc0191c27: small adjustments (authored by schererj).
small adjustments
Tue, May 11, 6:04 PM
kalali added a comment to T28204: Refactor LevelWindowManagerTest.

So I modified the "Assert"-functions to directly encapsule the CPPUNIT_ASSERT_MESSAGE calls in that function as you suggested. The error still occurs and now the problem is that I can't see where the error occurs because it happens inside the "Assert"-function (which is the same for each test). So that is not an option. Any other suggestions? I could split the test to test each node individually.

Tue, May 11, 2:08 PM · MITK (v2021.10)
kalali added a comment to T28204: Refactor LevelWindowManagerTest.

Ok so I found a bug for the test in line 320. This showed some complex behavior with the level window manager, which I don't want to address here.
However, the test in line 288 still randomly fails - when debugging in that line the test does not fail but fails in line 292.

Tue, May 11, 12:26 PM · MITK (v2021.10)
k656s committed rKAAPANA5a424608dafe: fixed daga installer removed old mitk stuff (authored by k656s).
fixed daga installer removed old mitk stuff
Tue, May 11, 11:49 AM
schererj committed rKAAPANA375acecc3b95: radiomics workflow gui-parameters (authored by schererj).
radiomics workflow gui-parameters
Tue, May 11, 11:29 AM
kalali added a comment to T28204: Refactor LevelWindowManagerTest.

Yes, I agree that this is not the most straight forward way to do it. There was a reasoning behind it to do it that way.
I will think about it - but currently it seems as if something is not correct with the tests, in a way that I am actually expecting wrong test results - so I need to rethink the expected results and change the true / false arguments accordingly.

Tue, May 11, 10:58 AM · MITK (v2021.10)
kislinsk added a comment to T28204: Refactor LevelWindowManagerTest.

Hm, I cannot answer this without looking into this in detail but a first step could be to improve the AssertImageForLevelWindowProperty function or maybe even encapsule the CPPUNIT_ASSERT_MESSAGE calls in that function instead the other way around since the error message one does receive currently doesn't tell much about what actually failed since it could be any or all of the three checks.

Tue, May 11, 10:51 AM · MITK (v2021.10)
k656s committed rKAAPANAc907038077cc: fixed port to 9443 fixed DKFZ 2018-2021 (authored by k656s).
fixed port to 9443 fixed DKFZ 2018-2021
Tue, May 11, 10:40 AM
k656s committed rKAAPANA951967c6c5ea: fixed radiomics container (authored by k656s).
fixed radiomics container
Tue, May 11, 10:40 AM
schererj committed rKAAPANAf701d572bbb8: ohif link fix (authored by schererj).
ohif link fix
Tue, May 11, 9:57 AM

Mon, May 10

schererj committed rKAAPANAededa34b272d: small adjustments (authored by schererj).
small adjustments
Mon, May 10, 5:35 PM
nolden added a comment to T28232: Shapemodels.

@norajitr thanks for the follow up. Could you attach the two (?) Dockerfiles here and post the network drive path? Maybe someone else from Kaapana (internal) could have a look then, too.

Mon, May 10, 5:20 PM · Kaapana (internal), Request for Discussion, MITK
floca added a comment to T28455: RT struct 3D visibility is not working correctly.

like to discuss this one.Why is there even two completely separate ways of loading the same dataset? Does this make sense?

I can not tell ad hoc which code would makes more sense. But I can tell directly that it makes no sense that the loading mechanisms execute different code to populate the properties. We had a simelar problem with doses once.

Mon, May 10, 5:11 PM · Request for Discussion, MITK (v2021.10)
schererj committed rKAAPANAba3cd1a89bb2: removed skipping for empty segmentations (authored by schererj).
removed skipping for empty segmentations
Mon, May 10, 4:42 PM
gaoh committed rKAAPANA31361f6822d1: Merge branch 'feature/T28185-logging-management' of https://phabricator.mitk. (authored by gaoh).
Merge branch 'feature/T28185-logging-management' of https://phabricator.mitk.
Mon, May 10, 4:30 PM
gaoh committed rKAAPANA9a0bad384f4e: add to extenstion manager (authored by gaoh).
add to extenstion manager
Mon, May 10, 4:30 PM
gaoh committed rKAAPANA772f36d51e12: first update, to sort and rearange the work in a reusable manner. (authored by gaoh).
first update, to sort and rearange the work in a reusable manner.
Mon, May 10, 4:30 PM
gaoh committed rKAAPANA45ec9666adb5: update to add helm charts (authored by gaoh).
update to add helm charts
Mon, May 10, 4:30 PM
gaoh committed rKAAPANA0c4bfef83e49: Add loggin managment from Elisabeth (authored by root <root@e230-pc07.ad.dkfz-heidelberg.de>).
Add loggin managment from Elisabeth
Mon, May 10, 4:30 PM
gaoh committed rKAAPANAafcba02ab2c9: update to add helm charts (authored by gaoh).
update to add helm charts
Mon, May 10, 4:30 PM
gaoh committed rKAAPANA6eca8b0d75e5: first update, to sort and rearange the work in a reusable manner. (authored by gaoh).
first update, to sort and rearange the work in a reusable manner.
Mon, May 10, 4:30 PM
gaoh committed rKAAPANA478699910290: Add loggin managment from Elisabeth (authored by root <root@e230-pc07.ad.dkfz-heidelberg.de>).
Add loggin managment from Elisabeth
Mon, May 10, 4:30 PM
kalali added a comment to T28204: Refactor LevelWindowManagerTest.

Since I modified and merged T28250 I wanted to continue here. I still get failed tests in line 288 and in line 320:

assertion failed
- Expression: AssertImageForLevelWindowProperty(false, true, false)
- "imageForLevelWindow" property not correctly set
assertion failed
- Expression: AssertImageForLevelWindowProperty(true, false, false)
- "imageForLevelWindow" property not correctly set
Mon, May 10, 4:21 PM · MITK (v2021.10)
gaoh committed rKAAPANA24b6eb99ed42: update to add helm charts (authored by gaoh).
update to add helm charts
Mon, May 10, 4:17 PM
kleina added a project to T28455: RT struct 3D visibility is not working correctly: Request for Discussion.
Mon, May 10, 3:12 PM · Request for Discussion, MITK (v2021.10)
kleina updated subscribers of T28455: RT struct 3D visibility is not working correctly.

I narrowed it down.

Mon, May 10, 3:11 PM · Request for Discussion, MITK (v2021.10)
schererj committed rKAAPANA85f83fb33620: algname change (authored by schererj).
algname change
Mon, May 10, 2:38 PM
schererj committed rKAAPANAaacdea031fa5: LocalSortGtOperator included (authored by schererj).
LocalSortGtOperator included
Mon, May 10, 1:30 PM
kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

If you load a RTStruct via DICOMBrwoser, the node has a special "visible" property for stdmulti.widget3 (the 3D view). You can enable/disbale it via the Properties plugin. #Workaround :-P

Mon, May 10, 11:51 AM · Request for Discussion, MITK (v2021.10)
kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

Ok, we tested it on several machines and it is as described above: After loading via DICOM Browser we can confirm the issue.

Mon, May 10, 11:32 AM · Request for Discussion, MITK (v2021.10)
kalali moved T28204: Refactor LevelWindowManagerTest from Backlog to Cycle on the MITK (v2021.10) board.
Mon, May 10, 11:00 AM · MITK (v2021.10)
kalali edited projects for T28204: Refactor LevelWindowManagerTest, added: MITK (v2021.10); removed MITK.
Mon, May 10, 11:00 AM · MITK (v2021.10)
kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

@s434n and I tried this on Windows and Linux. It looks like, if you load the data via "classical drag'n'drop", it works as expected. If we use the DICOM browser to load the exact same dataset, we can reproduce @nolden's issue.

Mon, May 10, 10:43 AM · Request for Discussion, MITK (v2021.10)
kalali closed T28250: [LevelWindowManager] Different behavior in AutoTopMost case and fallback case as Resolved.
Mon, May 10, 10:36 AM · Breaking Change, MITK (v2021.10)
kalali committed rMITKbe464bfe51da: T28250 Level window manager update function not consistent (authored by kalali).
T28250 Level window manager update function not consistent
Mon, May 10, 10:35 AM
kalali committed rMITKebf8757b2828: Make protected members private; remove comments (authored by kalali).
Make protected members private; remove comments
Mon, May 10, 10:35 AM
kalali committed rMITK9751f1d41d9c: Use return early to simplify the code structure (authored by kalali).
Use return early to simplify the code structure
Mon, May 10, 10:35 AM
kalali committed rMITK1d0306cddd48: Rename vector of data nodes (authored by kalali).
Rename vector of data nodes
Mon, May 10, 10:35 AM
kalali committed rMITK1ea1daa42d05: Use "auto" to simplify the code (authored by kalali).
Use "auto" to simplify the code
Mon, May 10, 10:35 AM
kalali committed rMITKc1756ccd4526: Remove "levelwindow"-property check (authored by kalali).
Remove "levelwindow"-property check
Mon, May 10, 10:35 AM
kalali committed rMITK135694ca36ca: Rename function and invert logic (authored by kalali).
Rename function and invert logic
Mon, May 10, 10:35 AM
kalali committed rMITKbcbe13e0349f: Clean class and function (authored by kalali).
Clean class and function
Mon, May 10, 10:35 AM
kalali committed rMITKe69fa735b71b: Refactor function names and parameters (authored by kalali).
Refactor function names and parameters
Mon, May 10, 10:35 AM
kalali committed rMITK27cfe7f01ba4: Clean comments and remove unnecessary comments (authored by kalali).
Clean comments and remove unnecessary comments
Mon, May 10, 10:35 AM
kleina added a comment to T28332: Support cascaded MPI processing.

Sure, here it is:
https://phabricator.mitk.org/rOBSHYPPOPYa340b927d14acdef69cea4e64b92524270066920

Mon, May 10, 9:32 AM · Hyppopy

Sun, May 9

schererj committed rKAAPANAcc835e4b59b9: label collect fix and logging cleanup (authored by schererj).
label collect fix and logging cleanup
Sun, May 9, 5:46 PM
schererj committed rKAAPANA68b87de28f68: test sat (authored by schererj).
test sat
Sun, May 9, 1:22 AM

Sat, May 8

norajitr added a comment to T28232: Shapemodels.

After talking with Marco, I have looked for the whereabouts of dockerfiles (liver-mri and multiorgan-seg), working commits for MITK (a0dedffb74d) and for MBI-builds (56ad5bf7064) and trained models. @schererj: I sent you this information via email in October 2020, and shared the trained models on the network drives. Can you confirm? What information do you need to keep the shape models operational?

Sat, May 8, 4:18 PM · Kaapana (internal), Request for Discussion, MITK
schererj committed rKAAPANAd919ebe5ad83: progress (authored by schererj).
progress
Sat, May 8, 11:18 AM
schererj committed rKAAPANAafd1a3a476b1: included delete series fix (authored by schererj).
included delete series fix
Sat, May 8, 10:26 AM
schererj committed rKAAPANA0e9067785680: new workflow layout (authored by schererj).
new workflow layout
Sat, May 8, 10:26 AM

Fri, May 7

floca added a comment to T28332: Support cascaded MPI processing.

I updated the draft in the branch directly (same file).

  • I did not change the send/recv to scatter/gather. In my opinion send/recv makes more sense, but we can discuss this.
  • In my opinion, we maybe don't need the "cleaning up" up the mpi_processes here, because it might be taken care of by our current implementation.

Let me know when you had time to look at it and if there are any questions. I'd like to discuss it a bit.

Could you point me to the commit? I cannot find it ?!?

Fri, May 7, 9:41 PM · Hyppopy
schererj committed rKAAPANA79bb014e6337: progress (authored by schererj).
progress
Fri, May 7, 9:14 PM
floca added a comment to T28320: [Segmentation] Region growing does not work if seed point is already inside a segmentation.

Hm, due to the facts that (1) the feature is missing since 2016 and no one ever complaint, (2) it is not documented in the help and (3) I am not sure why one would like to behave differently when clicking in an area that is segmented, I would just skip the code path. Yes.
But I would go further then. You don't need the whole inside check any more. I would completly remove everythin below line 332 and directly call OnMousePressedOutside(nullptr, interactionEvent); then.

Fri, May 7, 9:14 PM · MITK (v2021.10), Request for Discussion
p212r committed rKAAPANA38cea5c4f37a: Add multi series per study deletion optimization (authored by p212r).
Add multi series per study deletion optimization
Fri, May 7, 5:46 PM
p212r committed rKAAPANA220d086eef6e: Merge branch 'feature/delete-from-platform-dag' into develop (authored by p212r).
Merge branch 'feature/delete-from-platform-dag' into develop
Fri, May 7, 5:46 PM
p212r committed rKAAPANA358b87462eb5: Use DICOMwebClient for upload (authored by p212r).
Use DICOMwebClient for upload
Fri, May 7, 5:46 PM
p212r committed rKAAPANA1c0f11ec1b3a: Move dcm web delete functionality in HelperDcmWeb (authored by p212r).
Move dcm web delete functionality in HelperDcmWeb
Fri, May 7, 5:46 PM
p212r committed rKAAPANA965cd564653e: Add inital version of dcm-query DAG (authored by p212r).
Add inital version of dcm-query DAG
Fri, May 7, 5:40 PM
p212r committed rKAAPANA6f564434663b: Merge branch 'feature/T28352-dicom-query-retrieve' into develop (authored by p212r).
Merge branch 'feature/T28352-dicom-query-retrieve' into develop
Fri, May 7, 5:40 PM
p212r committed rKAAPANA8f3c0d1f7f42: Add inital version of dcm-query processing container (authored by p212r).
Add inital version of dcm-query processing container
Fri, May 7, 5:40 PM
eisenman created T28484: [external] Improve documentation on significance ranking.
Fri, May 7, 4:45 PM · challengeR
s434n added a comment to T28481: [Checklist] [Test data] Define publicly available user test data.

I've started a draft for a message to send around, found here if you want to have a look or add something: https://hub.dkfz.de/s/HzpkipeWRkq3K8K

Fri, May 7, 3:11 PM · MITK (v2021.10)
kalali updated subscribers of T28320: [Segmentation] Region growing does not work if seed point is already inside a segmentation.

I quickly modified the code to see if this works potentially. For this I set m_PaintingPixelValue to 1 for both cases and used the OnMousePressedOutside-function also for a mouse pressed inside:

m_PaintingPixelValue = inside ? 1 : 1;
Fri, May 7, 2:38 PM · MITK (v2021.10), Request for Discussion
kalali added a comment to T28320: [Segmentation] Region growing does not work if seed point is already inside a segmentation.

I started looking into this and what I found inside mitk::RegionGrowingTool::OnMousePressed:

if (inside)
      {
        MITK_DEBUG << "Clicked inside segmentation";
        // For now, we're doing nothing when the user clicks inside the segmentation. Behaviour can be implemented via
        // OnMousePressedInside()
        // When you do, be sure to remove the m_PaintingPixelValue check in OnMouseMoved() and OnMouseReleased()
        return;
      }
      else
      {
        MITK_DEBUG << "Clicked outside of segmentation";
        OnMousePressedOutside(nullptr, interactionEvent);
      }

Looking at the file history it doesn't look like that was implemented in MITK at anytime.
So we can actually discuss if we want to allow such a functionality and if, what the obstacles are.

Fri, May 7, 2:29 PM · MITK (v2021.10), Request for Discussion
schererj committed rKAAPANA742aa9b26fdc: added ensemble combination method (authored by schererj).
added ensemble combination method
Fri, May 7, 1:02 PM
nolden closed T28039: DICOM Seg loading error as Resolved.
Fri, May 7, 9:30 AM · MITK (v2021.10)
nolden closed T28478: Update DCMTK version to 3.6.6 as Resolved.
Fri, May 7, 9:30 AM · MITK (v2021.10)
schererj committed rKAAPANA890dc330a624: working ensemble evaluation with new workflow (authored by schererj).
working ensemble evaluation with new workflow
Fri, May 7, 8:52 AM
schererj committed rKAAPANAbadf1da11fb8: dice evaluation container (authored by schererj).
dice evaluation container
Fri, May 7, 8:52 AM

Thu, May 6

eisenman closed T28482: challangeR Patch v1.0.2 as Resolved.
Thu, May 6, 7:16 PM · challengeR
eisenman moved T28482: challangeR Patch v1.0.2 from In Progress to Done on the challengeR board.
Thu, May 6, 7:15 PM · challengeR
eisenman closed T28465: Wrong numer of algorithms shown in report summary as Resolved.
Thu, May 6, 7:15 PM · challengeR
eisenman closed T28453: [external] Error when all metric values are the same as Resolved.
Thu, May 6, 7:15 PM · challengeR
eisenman committed rCHALLENGER962cff05d226: Merge branch 'release/T28482-v1.0.2' (authored by eisenman).
Merge branch 'release/T28482-v1.0.2'
Thu, May 6, 7:08 PM
eisenman committed rCHALLENGER503cd659b1a1: Merge tag 'v1.0.2' into develop (authored by eisenman).
Merge tag 'v1.0.2' into develop
Thu, May 6, 7:08 PM
eisenman committed rCHALLENGER54e3fd8d7184: Bump version number (authored by eisenman).
Bump version number
Thu, May 6, 7:05 PM
eisenman committed rCHALLENGER9863d7e12065: Add release notes (authored by eisenman).
Add release notes
Thu, May 6, 7:05 PM
eisenman moved T28482: challangeR Patch v1.0.2 from Backlog to In Progress on the challengeR board.
Thu, May 6, 6:42 PM · challengeR
eisenman renamed T28453: [external] Error when all metric values are the same from bug when all metric values are the same to [external] Error when all metric values are the same.
Thu, May 6, 6:41 PM · challengeR
eisenman triaged T28482: challangeR Patch v1.0.2 as High priority.
Thu, May 6, 6:40 PM · challengeR
kalali added a project to T28250: [LevelWindowManager] Different behavior in AutoTopMost case and fallback case: Breaking Change.
IMPORTANT: ClearPropObserverLists has been renamed to ClearPropertyObserverMaps; CreatePropObserverLists has been renamed to CreatePropertyObserverMaps; IgnoreNode has been renamed to HasLevelWindowRenderingMode
Thu, May 6, 3:51 PM · Breaking Change, MITK (v2021.10)
kalali updated the task description for T26754: Review checklists.
Thu, May 6, 2:16 PM · MITK (v2021.10), Restricted Project
kalali closed T26989: [Checklist] GUI test data originates from different sources, a subtask of T26754: Review checklists, as Resolved.
Thu, May 6, 2:12 PM · MITK (v2021.10), Restricted Project
kalali closed T26989: [Checklist] GUI test data originates from different sources as Resolved.

Obviously it was not clear what we are expecting here so I will close this task and refer to two new tasks for the specific topics mentioned here:

Thu, May 6, 2:12 PM · MITK (v2021.10), Restricted Project
kalali added a subtask for T26754: Review checklists: T28481: [Checklist] [Test data] Define publicly available user test data.
Thu, May 6, 2:11 PM · MITK (v2021.10), Restricted Project
kalali added a parent task for T28481: [Checklist] [Test data] Define publicly available user test data: T26754: Review checklists.
Thu, May 6, 2:11 PM · MITK (v2021.10)
kalali moved T28481: [Checklist] [Test data] Define publicly available user test data from Backlog to Cycle on the MITK (v2021.10) board.
Thu, May 6, 2:11 PM · MITK (v2021.10)
kalali triaged T28481: [Checklist] [Test data] Define publicly available user test data as Normal priority.
Thu, May 6, 2:11 PM · MITK (v2021.10)
kalali added a subtask for T26754: Review checklists: T28480: [Checklist] [Test data] Define publicly available location to store user test data.
Thu, May 6, 2:10 PM · MITK (v2021.10), Restricted Project
kalali added a parent task for T28480: [Checklist] [Test data] Define publicly available location to store user test data: T26754: Review checklists.
Thu, May 6, 2:10 PM · MITK (v2021.10)