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Dec 17 2020

eisenman created T28123: Add notes for Linux users to readme.
Dec 17 2020, 6:46 PM · challengeR (v1.0)
eisenman moved T28097: test errors in aggregateThenRank and rankThenAggregate from In Progress to Done on the challengeR (v1.0) board.
Dec 17 2020, 6:38 PM · challengeR (v1.0)
eisenman committed rCHALLENGER1239f2bdc6aa: Merge branch 'feature/T28097-IrrelevantRowOrder' into develop (authored by eisenman).
Merge branch 'feature/T28097-IrrelevantRowOrder' into develop
Dec 17 2020, 6:37 PM
eisenman committed rCHALLENGER19b804226ac7: Remove irrelevant tests that assume a specific row order (authored by eisenman).
Remove irrelevant tests that assume a specific row order
Dec 17 2020, 6:36 PM
eisenman claimed T28097: test errors in aggregateThenRank and rankThenAggregate.
Dec 17 2020, 6:05 PM · challengeR (v1.0)
eisenman moved T28097: test errors in aggregateThenRank and rankThenAggregate from Backlog to In Progress on the challengeR (v1.0) board.
Dec 17 2020, 6:03 PM · challengeR (v1.0)
eisenman moved T28119: Unit tests are failing on Ubuntu due to mismatching messages from In Progress to Done on the challengeR (v1.0) board.
Dec 17 2020, 6:03 PM · challengeR (v1.0)
eisenman committed rCHALLENGER016b847dbb7a: Merge branch 'feature/T28119-MismatchingStringsWithQuotationMarks' into develop (authored by eisenman).
Merge branch 'feature/T28119-MismatchingStringsWithQuotationMarks' into develop
Dec 17 2020, 6:02 PM
eisenman committed rCHALLENGER4374432aa096: Check only for beginning of error message to avoid escaped quotation marks (authored by eisenman).
Check only for beginning of error message to avoid escaped quotation marks
Dec 17 2020, 6:01 PM
wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

platform is output with Sys.info(); linux and Mac systems are equal and windows may differ

Dec 17 2020, 5:55 PM · challengeR (v1.0)
wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

good idea!
otherwise you could use a platform dependent expect_equal but I think your idea is sufficient

Dec 17 2020, 5:53 PM · challengeR (v1.0)
eisenman created T28122: Fix layout of logos at the end of the readme file.
Dec 17 2020, 5:47 PM · challengeR (v1.0)
eisenman moved T27998: Interpretation of consensus ranking values needs further explanation from In Progress to Done on the challengeR (v1.0) board.
Dec 17 2020, 5:44 PM · challengeR (v1.0)
eisenman committed rCHALLENGER3f9e443d1f47: Merge branch 'feature/T27998-ConsensusRankingExplanation' into develop (authored by eisenman).
Merge branch 'feature/T27998-ConsensusRankingExplanation' into develop
Dec 17 2020, 5:43 PM
eisenman committed rCHALLENGER598a4d4ccc2d: Add explanation of consensus ranks (authored by eisenman).
Add explanation of consensus ranks
Dec 17 2020, 5:42 PM
eisenman added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

After investing several hour trying different encodings, e.g. using raw strings, I still don't find a way to make this work. I also don't see a way of changing the source message, because it's originating from another package.

Dec 17 2020, 5:20 PM · challengeR (v1.0)
eisenman added a comment to T28121: Remove parallel bootstrapping from quick-start scripts.

We should definitely keep it in the README.

Dec 17 2020, 5:16 PM · challengeR (v1.0)
wiesenfa added a comment to T28121: Remove parallel bootstrapping from quick-start scripts.

would mention it there at least though because bootstrapping may be time consuming

Dec 17 2020, 5:14 PM · challengeR (v1.0)
wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

don't think its necessary. there is anyway ordering applied to it in later stages.
otherwise ranking step (rank.aggregated.list()) could always do the ordering directly (then the test would check whether ordering is working). As mentioned before I avoided such change before the release because of (very unlikely) risk of breaking something in the first level hierarchy

Dec 17 2020, 5:13 PM · challengeR (v1.0)
eisenman created T28121: Remove parallel bootstrapping from quick-start scripts.
Dec 17 2020, 5:02 PM · challengeR (v1.0)
eisenman added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

Is the order of the rows relevant in any processing step? If not, the tests can be removed. Currently, I don't see a way making it work for both systems I have available for testing (Win10, R 3.6.3 and Ubuntu 18.04, R 4.0.3).

Dec 17 2020, 4:59 PM · challengeR (v1.0)
wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

I do see those as well on Mac

Dec 17 2020, 4:46 PM · challengeR (v1.0)
wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

R 4.0.2.
testthat previously 2.3.2, now 3.0.1.
the issue is however not connected to test_that I see that in the first 2 tests in aggregate-then-rank the ordering in the data set is not used but sorted

Dec 17 2020, 4:45 PM · challengeR (v1.0)
eisenman added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

The platform might not be the (only) reason.
@wiesenfa: Which version of R and testthat are you using?

Dec 17 2020, 1:50 PM · challengeR (v1.0)
eisenman updated the task description for T28119: Unit tests are failing on Ubuntu due to mismatching messages.
Dec 17 2020, 1:45 PM · challengeR (v1.0)
eisenman updated the task description for T28119: Unit tests are failing on Ubuntu due to mismatching messages.
Dec 17 2020, 1:22 PM · challengeR (v1.0)
eisenman triaged T28120: Write release notes for challengeR v1.0 as High priority.
Dec 17 2020, 1:03 PM · challengeR (v1.0)
eisenman moved T28119: Unit tests are failing on Ubuntu due to mismatching messages from Backlog to In Progress on the challengeR (v1.0) board.
Dec 17 2020, 1:02 PM · challengeR (v1.0)
eisenman triaged T28119: Unit tests are failing on Ubuntu due to mismatching messages as High priority.
Dec 17 2020, 1:01 PM · challengeR (v1.0)
floca added a subtask for T28118: Refactoring of SegTool2D: T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.
Dec 17 2020, 11:50 AM · MITK (v2021.02)
floca added a parent task for T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation: T28118: Refactoring of SegTool2D.
Dec 17 2020, 11:50 AM · MITK (v2021.10), Missing Info, Restricted Project
floca added a parent task for T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps: T28118: Refactoring of SegTool2D.
Dec 17 2020, 11:50 AM · Missing Info, MITK (v2021.02)
floca added a subtask for T28118: Refactoring of SegTool2D: T26975: 2D Fast Marching for 4D data intermediate state displays segmentation in other timesteps.
Dec 17 2020, 11:50 AM · MITK (v2021.02)
floca triaged T28118: Refactoring of SegTool2D as High priority.
Dec 17 2020, 11:49 AM · MITK (v2021.02)
eisenman created T28117: Keep track of licenses of dependencies.
Dec 17 2020, 12:26 AM · challengeR
eisenman placed T27494: Check which files are still relevant up for grabs.
Dec 17 2020, 12:17 AM · challengeR
eisenman edited projects for T27494: Check which files are still relevant, added: challengeR; removed challengeR (v1.0).

Ok, we can keep them in this release.

Dec 17 2020, 12:16 AM · challengeR
eisenman edited projects for T27925: Use cases of annotator option, added: challengeR; removed challengeR (v1.0).
Dec 17 2020, 12:13 AM · challengeR
eisenman edited projects for T27775: only export functions to be used by user, added: challengeR; removed challengeR (v1.0).

Discussed with @wiesenfa that this issue is not critical for release v1.0.

Dec 17 2020, 12:13 AM · challengeR
eisenman moved T27291: update license file from In Progress to Done on the challengeR (v1.0) board.
Dec 17 2020, 12:09 AM · challengeR (v1.0)
eisenman committed rCHALLENGER381233357a63: Merge branch 'feature/T27291-AdaptLicense' into develop (authored by eisenman).
Merge branch 'feature/T27291-AdaptLicense' into develop
Dec 17 2020, 12:06 AM
eisenman committed rCHALLENGER53cc163e1907: Remove CSV file (authored by eisenman).
Remove CSV file
Dec 17 2020, 12:03 AM

Dec 16 2020

eisenman committed rCHALLENGERa8d863aa9084: Change license to GPLv2 or later to be compatible with licenses of dependencies (authored by eisenman).
Change license to GPLv2 or later to be compatible with licenses of dependencies
Dec 16 2020, 11:59 PM
eisenman added a comment to T27291: update license file.

Recap: The initially chosen license (GPLv3) is not compatible with GPLv2 only licenses of dependencies (e.g. ggplot2, relations)

Dec 16 2020, 11:44 PM · challengeR (v1.0)
eisenman moved T27291: update license file from Backlog to In Progress on the challengeR (v1.0) board.
Dec 16 2020, 9:25 AM · challengeR (v1.0)
thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

as name property, the name of the RT node is provided correctly.
I created a working example with Pic3D for comparison.
Looking at both caaaaa.xml files, the only difference I notice is that the corrupted one is encoded with UTF-8 but otherwise it looks similar (as far as I see).

Dec 16 2020, 9:12 AM · Request for Discussion, MITK
floca added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

Which node is it? you can look up the name if you look into caaaaa.xml

Dec 16 2020, 8:45 AM · Request for Discussion, MITK
thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

<?xml version="1.0" encoding="UTF-8"?>
<Version Writer="C:\Development\MITK-dev\src\Modules\SceneSerialization\src\mitkSceneIO.cpp" Revision="$Revision: 17055 $" FileVersion="1"/>

Dec 16 2020, 8:40 AM · Request for Discussion, MITK
thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

sorry just saw the message. I put it in the shared folder.

Dec 16 2020, 8:07 AM · Request for Discussion, MITK

Dec 15 2020

floca added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

could you provied (e.g. via nextcloud) such an invalid scene file?

Dec 15 2020, 4:20 PM · Request for Discussion, MITK
thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

As Ralf pointed out, it is actually not related to the GenericProperty as such but it seems that the scene does not even contain any nrrd files after saving and that is why it breaks

Dec 15 2020, 3:50 PM · Request for Discussion, MITK
floca committed rRTTBf16003785168: Fixed T27214 also for RTTB as it will have the same problems. (authored by floca).
Fixed T27214 also for RTTB as it will have the same problems.
Dec 15 2020, 9:32 AM
floca committed rMPa47d55585495: Fixed T27214 (authored by floca).
Fixed T27214
Dec 15 2020, 9:21 AM

Dec 14 2020

wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

seems to not fail on windows machines. but does on my Mac (and thus might also on linux). minor issue, defer to post 1.0.0

Dec 14 2020, 6:47 PM · challengeR (v1.0)
eisenman claimed T27998: Interpretation of consensus ranking values needs further explanation.
Dec 14 2020, 3:14 PM · challengeR (v1.0)
floca added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

Do you have still problems with crashes? If yes, this is almost certainly not due to the GenericProperty thing, as they have no relevance for dose visualization and scenes without dose do not crash but also cannot load the GenericProperty.

Dec 14 2020, 2:53 PM · Request for Discussion, MITK
thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

GenericProperty associated to key 'MITK.IO.reader.DICOM.PixelSpacingInterpretation'
GenericProperty associated to key 'MITK.IO.reader.DICOM.ReaderImplementationLevel'
GenericProperty associated to key 'dicomseriesreader.PixelSpacingInterpretation'
GenericProperty associated to key 'dicomseriesreader.ReaderImplementationLevel' still need to be changed

Dec 14 2020, 2:39 PM · Request for Discussion, MITK
thomass updated the task description for T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.
Dec 14 2020, 2:28 PM · Request for Discussion, MITK (v2021.10)
thomass triaged T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change as Low priority.
Dec 14 2020, 2:26 PM · Request for Discussion, MITK (v2021.10)
kalali added a parent task for T28076: [Multilabel Segmentation] Corrector tool 2D does not respect multiple layers: T27807: [MultiLabel Segmentation] Inspection of module and plugin.
Dec 14 2020, 2:20 PM · MITK (v2021.02)
kalali added a subtask for T27807: [MultiLabel Segmentation] Inspection of module and plugin: T28076: [Multilabel Segmentation] Corrector tool 2D does not respect multiple layers.
Dec 14 2020, 2:20 PM · Moved to git.dkfz.de, MITK (v2024.12)
eisenman closed T28016: embed web app in package as Invalid.

The idea of the web app is to lower the entry level for users that are not familiar with and/or don't want to install R (as this is already a hurdle for some of them).

Dec 14 2020, 2:15 PM · challengeR (v1.0)
kalali closed T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels as Resolved.
Dec 14 2020, 2:15 PM · Cleared, MITK (v2021.02)
kalali closed T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels, a subtask of T27807: [MultiLabel Segmentation] Inspection of module and plugin, as Resolved.
Dec 14 2020, 2:15 PM · Moved to git.dkfz.de, MITK (v2024.12)
kalali committed rMITK106261292196: Fix T28076 by using the new function for retrieving the active pixel value (authored by kalali).
Fix T28076 by using the new function for retrieving the active pixel value
Dec 14 2020, 2:14 PM
kalali committed rMITK754b4e125e92: Use active layer and label for live wire (authored by kalali).
Use active layer and label for live wire
Dec 14 2020, 2:14 PM
kalali closed T28076: [Multilabel Segmentation] Corrector tool 2D does not respect multiple layers as Resolved by committing rMITK106261292196: Fix T28076 by using the new function for retrieving the active pixel value.
Dec 14 2020, 2:14 PM · MITK (v2021.02)
kalali committed rMITK7d013e1fd185: Provide single function for retrieving the active pixel value (authored by kalali).
Provide single function for retrieving the active pixel value
Dec 14 2020, 2:14 PM
kalali committed rMITK0fe048a6581e: Make sure the code of different tools is consistent (authored by kalali).
Make sure the code of different tools is consistent
Dec 14 2020, 2:14 PM
kalali committed rMITK8c26ebc9309f: Check for labelsetimage and use the correct pixel value (authored by kalali).
Check for labelsetimage and use the correct pixel value
Dec 14 2020, 2:14 PM
kalali renamed T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung" from Extend "Checkliste MultiLabel Segmentierung – Manuelle Segmentierung / 2D Segmentierung" to Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung".
Dec 14 2020, 2:11 PM · MITK (v2022.04)
wiesenfa moved T28112: colors in box plots multitask not consistent from In Progress to Done on the challengeR (v1.0) board.
Dec 14 2020, 2:09 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER018edb100eae: T28112: respect algo colors in boxplots (authored by wiesenfa).
T28112: respect algo colors in boxplots
Dec 14 2020, 2:08 PM
wiesenfa moved T28112: colors in box plots multitask not consistent from Backlog to In Progress on the challengeR (v1.0) board.
Dec 14 2020, 2:07 PM · challengeR (v1.0)
wiesenfa created T28112: colors in box plots multitask not consistent.
Dec 14 2020, 1:33 PM · challengeR (v1.0)
kalali moved T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung" from Backlog to Test/Checklists on the MITK (v2021.02) board.
Dec 14 2020, 1:24 PM · MITK (v2022.04)
kalali moved T28110: Extend checklists for multilabel segmentation view from Backlog to Test/Checklists on the MITK (v2021.02) board.
Dec 14 2020, 1:23 PM · MITK (v2022.04)
floca closed T22412: Workbench crashes when using 2D Region Growin on DWI Image (.nii) on Ubuntu 16.04 as Wontfix.

Closed. @neher or who ever might stumple upon the prolem again, is welcome to open it again and provide data. :)

Dec 14 2020, 1:07 PM · Missing Info, Request for Discussion, MITK (v2021.02)
kalali triaged T28111: Extend "Checkliste MultiLabel Segmentierung – 2D Segmentierung" as High priority.
Dec 14 2020, 12:52 PM · MITK (v2022.04)
thomass added a comment to T25152: Cannot compare TemporoSpatialStringProperty.

Since solution 1 worked well for me and seems to be more generic, I would vote for 1.

Dec 14 2020, 12:46 PM · Auto-closed, MITK
kalali triaged T28110: Extend checklists for multilabel segmentation view as High priority.
Dec 14 2020, 12:37 PM · MITK (v2022.04)
kalali updated the task description for T27506: Extend checklists for segmentation view.
Dec 14 2020, 12:31 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27906: Extend "Checkliste Segmentierung – Utilities".
Dec 14 2020, 12:31 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27873: Extend "Checkliste Segmentierung – Interpolation".
Dec 14 2020, 12:31 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27737: Extend "Checkliste Segmentierung – Optionen".
Dec 14 2020, 12:30 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung".
Dec 14 2020, 12:30 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27850: Extend "Checkliste Segmentierung – 3D Segmentierung".
Dec 14 2020, 12:30 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27737: Extend "Checkliste Segmentierung – Optionen".
Dec 14 2020, 12:30 PM · MITK (v2022.04), Cleared
kalali updated the task description for T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung".
Dec 14 2020, 12:29 PM · MITK (v2022.04), Cleared
kalali moved T28108: [Release Checklists] Prepare release checklists from Backlog to Test/Checklists on the MITK (v2021.02) board.
Dec 14 2020, 12:27 PM · MITK
kalali updated the task description for T28108: [Release Checklists] Prepare release checklists.
Dec 14 2020, 12:24 PM · MITK
kalali added a comment to T22412: Workbench crashes when using 2D Region Growin on DWI Image (.nii) on Ubuntu 16.04.

Also crashes with normal 4D images. In Multilabel segmentation 2D region crowing, too.

Dec 14 2020, 12:22 PM · Missing Info, Request for Discussion, MITK (v2021.02)
neher triaged T28109: Check correct association of Segs with origin DICOM as High priority.
Dec 14 2020, 12:21 PM · Kaapana (internal)
floca added a comment to T22412: Workbench crashes when using 2D Region Growin on DWI Image (.nii) on Ubuntu 16.04.

@neher or @jaegerp can someone provide test data? Otherwise I would close this task for now, because I cannot check or reproduce the problem without data.

Dec 14 2020, 12:15 PM · Missing Info, Request for Discussion, MITK (v2021.02)
floca added a comment to T27817: [Multilabel] Live Wire tool always assigns first label when being used with multiple labels.

Can D447 landed and this issue closed? If nothing speaks against it, it would be good, before I turning the rest of the seg tools upside down. Thanks.

Dec 14 2020, 12:11 PM · Cleared, MITK (v2021.02)
kalali added a parent task for T27506: Extend checklists for segmentation view: T28108: [Release Checklists] Prepare release checklists.
Dec 14 2020, 11:52 AM · MITK (v2022.04), Cleared
kalali added a subtask for T28108: [Release Checklists] Prepare release checklists: T27506: Extend checklists for segmentation view.
Dec 14 2020, 11:52 AM · MITK
kalali triaged T28108: [Release Checklists] Prepare release checklists as Normal priority.
Dec 14 2020, 11:52 AM · MITK
kalali moved T27506: Extend checklists for segmentation view from Segmentation to Test/Checklists on the MITK (v2021.02) board.
Dec 14 2020, 11:05 AM · MITK (v2022.04), Cleared
kalali moved T27716: Extend "Checkliste Segmentierung – Manuelle Segmentierung / 2D Segmentierung" from Segmentation to Test/Checklists on the MITK (v2021.02) board.
Dec 14 2020, 11:05 AM · MITK (v2022.04), Cleared