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Nov 21 2019

kleina committed rOBSHYPPOPYbb1cfb13317d: CandidateDescriptor in extra file (actual code this time). (authored by kleina).
CandidateDescriptor in extra file (actual code this time).
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPYc61e3ab15d97: Code cleanup of MPIBlackboxFunction. (authored by kleina).
Code cleanup of MPIBlackboxFunction.
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPY3fd379043e07: Cleanup of HyppopySolver. loss_function uses loss_function_batch internally now. (authored by kleina).
Cleanup of HyppopySolver. loss_function uses loss_function_batch internally now.
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPYf09a89dc7736: Removed some TODOs and comments. (authored by kleina).
Removed some TODOs and comments.
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPY755be657e49d: Moved CandidateDescriptor to own file. (authored by kleina).
Moved CandidateDescriptor to own file.
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPY87002effbb4c: Cleanup of MPISolverWrapper. Removed some TODOs and comments. Worker now also… (authored by kleina).
Cleanup of MPISolverWrapper. Removed some TODOs and comments. Worker now also…
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPYa8ef7d01492f: Processed some comments. (authored by kleina).
Processed some comments.
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPYe722f3fd81d2: reimplemented call_batch in MPIBlackboxFunction. (authored by kleina).
reimplemented call_batch in MPIBlackboxFunction.
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPY7c48ce825346: Introduced CandidateDescriptor in Gridsearch_solver. Fixed typo in error… (authored by kleina).
Introduced CandidateDescriptor in Gridsearch_solver. Fixed typo in error…
Nov 21 2019, 1:50 PM
kleina committed rOBSHYPPOPYcaa03252837f: introduced CandidateDescriptor and changed loss_function_batch() according to… (authored by kleina).
introduced CandidateDescriptor and changed loss_function_batch() according to…
Nov 21 2019, 1:50 PM
kislinsk committed rMITKa24f3f773eed: Fix dependencies between Boost dylibs (authored by kislinsk).
Fix dependencies between Boost dylibs
Nov 21 2019, 1:50 PM
kislinsk added a comment to T26752: [macOS] Make Boost libraries use RPATH.

Pushed new branch T26752-Boost-RPATH-2.

Nov 21 2019, 1:50 PM · MITK
kislinsk triaged T26837: Create preference for anti-aliasing as Wishlist priority.
Nov 21 2019, 1:35 PM · Auto-closed, MITK
kislinsk closed T26815: New multi render window widget architecture breaks rendering mode handling as Resolved.
Nov 21 2019, 1:34 PM · Noteworthy, MITK
kislinsk committed rMITK7b0736a0dcd7: Merge branch 'T26815-Fixes' (authored by kislinsk).
Merge branch 'T26815-Fixes'
Nov 21 2019, 12:48 PM
kislinsk committed rMITK99152957745e: Remove unused parameter names (authored by kislinsk).
Remove unused parameter names
Nov 21 2019, 12:48 PM
kislinsk added a comment to T26815: New multi render window widget architecture breaks rendering mode handling.

Pushed new branch T26815-Fixes.

Nov 21 2019, 12:47 PM · Noteworthy, MITK
kislinsk committed rMITK7d3e2a1aafa3: Remove RenderingManager parameters and RenderingMode (authored by kislinsk).
Remove RenderingManager parameters and RenderingMode
Nov 21 2019, 12:28 PM
floca committed rMITKe935c1fc4f08: Merge branch 'T26717-static_masks_on_dynamic_images' Fixed T26717 (authored by floca).
Merge branch 'T26717-static_masks_on_dynamic_images' Fixed T26717
Nov 21 2019, 9:30 AM
kislinsk closed T26701: Build errors with Python 3.7 and latest gcc as Resolved.
Nov 21 2019, 9:22 AM · MITK

Nov 20 2019

thomass committed rMITKb5750690feff: Changes made to the datamanager plugin documentation, modified images and text (authored by thomass).
Changes made to the datamanager plugin documentation, modified images and text
Nov 20 2019, 3:19 PM
maleike updated the task description for T26835: Crash on change of Surface interpolation from Phong to Flat.
Nov 20 2019, 12:23 PM · Pull Request, MITK
maleike assigned T26835: Crash on change of Surface interpolation from Phong to Flat to kislinsk.
Nov 20 2019, 12:23 PM · Pull Request, MITK
maleike added a comment to T26835: Crash on change of Surface interpolation from Phong to Flat.

Fix in https://github.com/MITK/MITK/pull/245, patches VTK

Nov 20 2019, 12:23 PM · Pull Request, MITK
maleike created T26835: Crash on change of Surface interpolation from Phong to Flat.
Nov 20 2019, 12:22 PM · Pull Request, MITK
floca committed rMITK4c70a3a1bb2e: Fixed the time geometry of the static masks (authored by floca).
Fixed the time geometry of the static masks
Nov 20 2019, 10:42 AM
kislinsk updated jenkins.
Nov 20 2019, 9:21 AM

Nov 19 2019

ramien committed rREGRCNN79767190c6fe: RA3D: backward written in CUDA, needs testing and finalization (authored by ramien).
RA3D: backward written in CUDA, needs testing and finalization
Nov 19 2019, 6:09 PM
kirchnth closed T19099: 2D Streaming in mitkWorkbench/BlueBerry (?) as Resolved.

This has been closed years ago - not sure why it has been reopened.

Nov 19 2019, 4:45 PM · Bugzilla, MITK
kislinsk added a revision to T26815: New multi render window widget architecture breaks rendering mode handling: Unknown Object (Differential Revision).
Nov 19 2019, 2:58 PM · Noteworthy, MITK
maleike added a comment to T26653: Github pull request 263 (Forward vtkInformation objects to MITK mappers - allow for VTK depth peeling).

@maleike

I re-enabled depth peeling support based on your pull request and also enabled depth peeling for volumes and FXAA. It works well for surfaces and volumes but totally breaks rendering of images/cross hair with opacity < 1. So this is not yet complete and I/we have to fix this before I am able to merge it.

Nov 19 2019, 2:16 PM · MITK, Noteworthy, Pull Request
floca committed rMITKb6cbc120c4b7: first draft for a fix (authored by floca).
first draft for a fix
Nov 19 2019, 12:27 PM
floca added a comment to T26167: ExtractSliceFilter handles 3D+t images inefficiently and inconsequently.

Pushed new branch T26167-ExtractSliceFilter_fix_generateoutputinformation.

Nov 19 2019, 12:26 PM · MITK
kislinsk updated jenkins.
Nov 19 2019, 9:29 AM

Nov 18 2019

floca committed rMITKe9dcc6542c5f: Added static mask feature to MultiLableSegmentation (authored by floca).
Added static mask feature to MultiLableSegmentation
Nov 18 2019, 8:52 PM
ramien committed rREGRCNN2fb7303bb227: RA3D: forward finished, needs testing, backward still pending (authored by ramien).
RA3D: forward finished, needs testing, backward still pending
Nov 18 2019, 7:20 PM
hettich committed rMITK4b22b922ed39: Merge branch 'T25664-catch-by-reference' (authored by hettich).
Merge branch 'T25664-catch-by-reference'
Nov 18 2019, 6:08 PM
hettich committed rMITK4ce7b084407e: fix some catch-by-value errors in MiniApps (authored by hettich).
fix some catch-by-value errors in MiniApps
Nov 18 2019, 6:08 PM

Nov 17 2019

floca committed rMITK22aff373263b: First draft to allow static masks for internal discussion. (authored by floca).
First draft to allow static masks for internal discussion.
Nov 17 2019, 10:17 PM

Nov 15 2019

ramien committed rREGRCNNdd5260634fe9: roi align 2d compiles as extension, 3D in progress (authored by ramien).
roi align 2d compiles as extension, 3D in progress
Nov 15 2019, 7:42 PM
ramien committed rREGRCNNa7c883c8efc9: nms-extension interface more inline w/ pytorch (authored by ramien).
nms-extension interface more inline w/ pytorch
Nov 15 2019, 7:42 PM
kalali raised a concern with rMITK99804079e0a8: Add container for Type, LineStyle and Color.
Nov 15 2019, 6:01 PM
kalali added inline comments to rMITKcdda996996fd: Add Function to update existing data.
Nov 15 2019, 5:57 PM
kalali raised a concern with rMITK61caf41dc62c: Add Function for returning index by string.
Nov 15 2019, 5:56 PM
kalali raised a concern with rMITK2ef6a51b13de: Add emplace.
Nov 15 2019, 5:38 PM
kalali raised a concern with rMITK7aa0559a1250: Add function to update existing data.
Nov 15 2019, 5:22 PM
kislinsk added a comment to T26815: New multi render window widget architecture breaks rendering mode handling.
  • Remove any mitk::RenderingManager and mitk::BaseRenderer::RenderingMode::Type parameters from function calls that generate corresponding compiler errors
  • Unify access to the rendering manager by always using the static method mitk::RenderingManager::GetInstance()
Nov 15 2019, 5:14 PM · Noteworthy, MITK
kislinsk committed rMITK5e0e87c36865: Handle RenderingManager like the singleton it is (authored by kislinsk).
Handle RenderingManager like the singleton it is
Nov 15 2019, 5:08 PM
kislinsk committed rMITKc348fdb4d8c8: Set default rendering mode to FXAA (authored by kislinsk).
Set default rendering mode to FXAA
Nov 15 2019, 5:08 PM
kislinsk committed rMITKa2a69caf2013: Merge remote-tracking branch 'origin/T26811-RenderingModePreference' into… (authored by kislinsk).
Merge remote-tracking branch 'origin/T26811-RenderingModePreference' into…
Nov 15 2019, 5:08 PM
kislinsk added a comment to T26815: New multi render window widget architecture breaks rendering mode handling.

Pushed new branch T26815-RemovePassingOfRenderingManagerAsParameter.

Nov 15 2019, 5:08 PM · Noteworthy, MITK
kalali raised a concern with rMITKea1cf2ffd166: Add new function for adding data.
Nov 15 2019, 5:06 PM
kalali added a comment to T26777: Refactoring QmitkChartExample.

I started reviewing the plugin.
Things I found will be directly mentioned in comments in your commits.

Nov 15 2019, 12:48 PM · Auto-closed, MITK
kalali raised a concern with rMITKf98609dac0c1: Modify functions for GUI.
Nov 15 2019, 12:43 PM
kalali raised a concern with rMITKcdda996996fd: Add Function to update existing data.
Nov 15 2019, 12:06 PM
kalali raised a concern with rMITK39cfb5c5df5e: Remove override.
Nov 15 2019, 12:04 PM
kalali added inline comments to rMITKcdda996996fd: Add Function to update existing data.
Nov 15 2019, 11:49 AM
kalali added inline comments to rMITK39cfb5c5df5e: Remove override.
Nov 15 2019, 11:40 AM
kalali added a comment to T26815: New multi render window widget architecture breaks rendering mode handling.

I see your point. I don't see a difference compared to the current situation neither.
I'm not specifically talking about performance issues here but rather envision a scenario where an StdMultiWidget (or any other AbstractMultiWidget) is used to display medical image for interaction purposes and another single render window, e.g. inside a DICOM preview plugin or similar, shows another medical image, e.g. and you don't want this to be reinitialized or zoomed or moved simultaneously with the interaction inside the StdMultiWidget.
This is just something to consider in the future and I also see the point in the caller vs callee issue. The new multi widget still struggles with all the RequestUpdateAll calls and similar so that it is not easy to use the new multi widget the correct way (see T26496).

Nov 15 2019, 9:51 AM · Noteworthy, MITK
kislinsk added a comment to T26815: New multi render window widget architecture breaks rendering mode handling.

Thanks for the comments. The rendering manager is already designed to be a singleton and only a singleton. There's flexibilty in terms of a rendering manager factory that is used to determine the actual implementation of a rendering manager (like the QmitkRenderingManager) but still a singleton one. So I think we would not loose anything with the new approach compared to the current situation. I even think that the rendering manager should stay a singleton in the future as it is kind of a bridge to VTK and at the end of the day to the single OpenGL context of the application despite all the possible renderers (sharing that context). Calling RequestUpdateAll() all over the place is a caller issue anyway in my opinion and not a callee issue. If this should ever be a relevant performance issue with multiple editors, we could check if we really need to update specific render windows based on their visibility, if we (or even VTK) are not already doing this.

Nov 15 2019, 12:14 AM · Noteworthy, MITK

Nov 14 2019

kalali added a comment to T26815: New multi render window widget architecture breaks rendering mode handling.

And you are right, the QmitkAbstracMultiWidget receives a rendering mode but each subclass (e.g. the QmitkStdMultiWidget) does not access and use it to create its QmitkRenderWindowWidget (however, here the rendering mode is passed to the QmitkRenderWindow).

Nov 14 2019, 6:38 PM · Noteworthy, MITK
kalali added a comment to T26795: scrolling in a 2d render window scrolls simultaneously in all three directions .

Should be fixed now. Different multi widgets use different action event handler.

Nov 14 2019, 6:12 PM · Noteworthy, MITK
kalali committed rMITK238c80ca2726: Remove general synchronization and use different action event handler (authored by kalali).
Remove general synchronization and use different action event handler
Nov 14 2019, 6:10 PM
kalali committed rMITK02fe2efd5495: Add different action event handler (authored by kalali).
Add different action event handler
Nov 14 2019, 6:10 PM
kalali added a comment to T26815: New multi render window widget architecture breaks rendering mode handling.

One point I want to mention here, before I dive deeper into the problem is that we cannot use multiple rendering manager, if we rely on each class accessing the singleton rendering manager. So far this was probably never a problem but we should consider this in the future.
Having a single rendering manager means having all existing render windows available in that rendering manager and thus always updating them all e.g. on request update all.
We are not able to distinguish e.g. between the render windows of the std multi widget and another render window (e.g. a small preview render window inside a plugin view).

Nov 14 2019, 6:03 PM · Noteworthy, MITK
kislinsk updated the task description for T26815: New multi render window widget architecture breaks rendering mode handling.
Nov 14 2019, 5:01 PM · Noteworthy, MITK
kislinsk triaged T26815: New multi render window widget architecture breaks rendering mode handling as Normal priority.
Nov 14 2019, 4:58 PM · Noteworthy, MITK
kislinsk created T26815: New multi render window widget architecture breaks rendering mode handling.
Nov 14 2019, 4:58 PM · Noteworthy, MITK
kislinsk closed T26811: Default preferences do not work as expected as Resolved.
Nov 14 2019, 4:25 PM · MITK
petersej triaged T26814: PytorchExperiment resuming doesn't work as expected as High priority.
Nov 14 2019, 3:51 PM · trixi
kislinsk committed rMITK848604959b86: Merge branch 'T26811-RenderingModePreference' into releases/2018-04 (authored by kislinsk).
Merge branch 'T26811-RenderingModePreference' into releases/2018-04
Nov 14 2019, 3:31 PM
kislinsk committed rMITK20ecc5df4581: Sync rendering mode preference with actual rendering mode (authored by kislinsk).
Sync rendering mode preference with actual rendering mode
Nov 14 2019, 3:30 PM
kislinsk added a comment to T26811: Default preferences do not work as expected.

Pushed new branch T26811-RenderingModePreference.

Nov 14 2019, 3:30 PM · MITK
kislinsk claimed T26811: Default preferences do not work as expected.
Nov 14 2019, 3:25 PM · MITK
ramien committed rREGRCNN6a8852e5b68a: tested nms, cuda & own numpy fine, slight inconsistency in torch.ops.nms on cpu (authored by ramien).
tested nms, cuda & own numpy fine, slight inconsistency in torch.ops.nms on cpu
Nov 14 2019, 1:23 PM

Nov 13 2019

ramien committed rREGRCNNfed8fcd0fa93: nms cuda extension finished, now has 3D capability (authored by ramien).
nms cuda extension finished, now has 3D capability
Nov 13 2019, 5:40 PM
kalali added a comment to T26795: scrolling in a 2d render window scrolls simultaneously in all three directions .

This fixes the problem but another problem arises, which is due to the use of the DisplayActionEventFunctions and the implementation inside QmitkAbstractMultiWidget:
A widget can either have a synchronized or a de-synchronized interaction. However, in the case of the StdMultiWidget all interactions are de-synchronized, except for the SetCrosshair-action. So in the StdMultiWidget-case we have to handle the action events differently.

Nov 13 2019, 3:27 PM · Noteworthy, MITK
kislinsk triaged T26811: Default preferences do not work as expected as Normal priority.
Nov 13 2019, 3:03 PM · MITK
kalali committed rMITK061bb2663fb7: Set desynchronized interaction as default (authored by kalali).
Set desynchronized interaction as default
Nov 13 2019, 2:58 PM
kalali added a comment to T26795: scrolling in a 2d render window scrolls simultaneously in all three directions .

Pushed new branch T26795-Disable-simultaneous-scrolling.

Nov 13 2019, 2:58 PM · Noteworthy, MITK
kislinsk committed rMDba22141a1dba: Update reference screenshots for dual depth peeling (authored by kislinsk).
Update reference screenshots for dual depth peeling
Nov 13 2019, 2:24 PM
kislinsk committed rMITKc6a443f12af4: Merge branch 'T26653-MasterIntegrationFixes' (authored by kislinsk).
Merge branch 'T26653-MasterIntegrationFixes'
Nov 13 2019, 2:08 PM
kislinsk committed rMITK41b49b3ca47c: Replace RenderingMode::Standard by FastApproximateAntiAliasing (authored by kislinsk).
Replace RenderingMode::Standard by FastApproximateAntiAliasing
Nov 13 2019, 2:07 PM
kislinsk added a comment to T26653: Github pull request 263 (Forward vtkInformation objects to MITK mappers - allow for VTK depth peeling).

Pushed new branch T26653-MasterIntegrationFixes.

Nov 13 2019, 2:07 PM · MITK, Noteworthy, Pull Request
kalali triaged T26810: QmitkOverlayManagerView crashes when the view is closed and the focus is changed to another view as High priority.
Nov 13 2019, 1:54 PM · Auto-closed, Restricted Project, MITK
kislinsk closed T26653: Github pull request 263 (Forward vtkInformation objects to MITK mappers - allow for VTK depth peeling) as Resolved.
Nov 13 2019, 1:12 PM · MITK, Noteworthy, Pull Request
kislinsk committed rMITK1a024cf7b34a: Merge remote-tracking branch 'origin/releases/2018-04' (authored by kislinsk).
Merge remote-tracking branch 'origin/releases/2018-04'
Nov 13 2019, 1:02 PM
kislinsk committed rMITKa140adda1005: Merge branch 'T26653-ReenableDepthPeeling' into releases/2018-04 (authored by kislinsk).
Merge branch 'T26653-ReenableDepthPeeling' into releases/2018-04
Nov 13 2019, 12:45 PM
kislinsk added a comment to T26653: Github pull request 263 (Forward vtkInformation objects to MITK mappers - allow for VTK depth peeling).

All remaining issues solved by @maleike. I reintroduced the rendering mode preference but instead of switching between "Standard" (default, basically equivalent to "nothing") and "Depth Peeling" it now allows to switch between "No anti-aliasing" and "Fast Approximate Anti-Aliasing (FXAA)" (default). Depth peeling is always enabled as it only kicks in if there are translucent objects in the scene and in the worst case it is preferable to have not the fasted rendering instead of having a broken rendering. The future will show if we there is really a need to additionally add quality options regarding depth peeling.

Nov 13 2019, 12:43 PM · MITK, Noteworthy, Pull Request
kislinsk committed rMITKa9d670f8470c: Merge remote-tracking branch 'maleike/allow-vtk-depth-peeling' into T26653… (authored by kislinsk).
Merge remote-tracking branch 'maleike/allow-vtk-depth-peeling' into T26653…
Nov 13 2019, 12:37 PM
maleike committed rMITK5487c2164c30: Patch VTK to propagate property keys down VTK assemblies and prop assemblies (authored by maleike).
Patch VTK to propagate property keys down VTK assemblies and prop assemblies
Nov 13 2019, 12:37 PM
kislinsk awarded T26653: Github pull request 263 (Forward vtkInformation objects to MITK mappers - allow for VTK depth peeling) a Party Time token.
Nov 13 2019, 12:34 PM · MITK, Noteworthy, Pull Request
kalali added a comment to T26795: scrolling in a 2d render window scrolls simultaneously in all three directions .

I remember having seen this error but I thought I fixed it. Currently, I cannot reproduce it, using the latest master 8a6a7a85.
Could you give a precise description of the steps to take in order to reproduce this bug?

Nov 13 2019, 11:57 AM · Noteworthy, MITK

Nov 12 2019

ramien committed rREGRCNNd5aca31b6e2a: retina_net docstring fix (authored by ramien).
retina_net docstring fix
Nov 12 2019, 8:37 PM
ramien committed rREGRCNNa715cd44054a: 2D torch nms as cpp extension compiled from source + analysis file for… (authored by ramien).
2D torch nms as cpp extension compiled from source + analysis file for…
Nov 12 2019, 8:37 PM
kirchnth triaged T26808: mitkPhotoacousticVolumeTest fails on Ubuntu (only) as Normal priority.
Nov 12 2019, 5:48 PM · MITK, Photoacoustics
kirchnth closed T26798: mitkPAFilterServiceTest fails as Resolved.
Nov 12 2019, 5:45 PM · MITK, Photoacoustics
jaegerp added a member for Medical Detection Toolkit: m113r.
Nov 12 2019, 2:42 PM

Nov 11 2019

kirchnth committed rMITK8a6a7a858b95: Merge branch 'T26759-radiusfixforrealz' (authored by kirchnth).
Merge branch 'T26759-radiusfixforrealz'
Nov 11 2019, 7:02 PM
kirchnth committed rMITK5e48a9541d24: Merge branch 'master' of https://phabricator.mitk.org/source/mitk (authored by kirchnth).
Merge branch 'master' of https://phabricator.mitk.org/source/mitk
Nov 11 2019, 7:02 PM