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Fri, May 15

neher closed T27426: IVIM cmdapp should provide all fits as Resolved.
Fri, May 15, 2:17 PM · MITK Diffusion
neher committed rMITKDIFF14fb9c209ad8: Merge branch 'T27426-IvimFits' (authored by neher).
Merge branch 'T27426-IvimFits'
Fri, May 15, 2:16 PM
neher committed rMITKDIFF29b43221d388: All fits available (authored by neher).
All fits available
Fri, May 15, 2:16 PM
neher added a comment to T27426: IVIM cmdapp should provide all fits.

Pushed new branch T27426-IvimFits.

Fri, May 15, 2:16 PM · MITK Diffusion
neher triaged T27426: IVIM cmdapp should provide all fits as Normal priority.
Fri, May 15, 2:15 PM · MITK Diffusion
kleina committed rOBSHYPPOPY47e2639dcaee: uncommented customized pmap (authored by kleina).
uncommented customized pmap
Fri, May 15, 1:50 PM
kislinsk added a comment to T27413: MITK 2020 Workflow Q&A.

Uh, I noticed that it is possible to add aliases/workflows to Arcanist, that are sourced from the project repository. Could be a nice way of streamlining some things. I also noticed that there's already an arc feature feature/T12345-bla which boils down to a git checkout develop && git checkout -b feature/T12345-bla.

Fri, May 15, 1:27 PM · Restricted Project, CI, MITK (2020)
kislinsk added a revision to T27425: Add more configurations to .arcconfig: Unknown Object (Differential Revision).
Fri, May 15, 11:42 AM · MITK
kislinsk triaged T27425: Add more configurations to .arcconfig as Low priority.
Fri, May 15, 11:37 AM · MITK
gaoh closed T27181: MITK - DICOM Seg - not saved when started without terminal as Resolved.

File is correctly saved in the current master.

Fri, May 15, 11:27 AM · Cleared, MITK (2020)
kislinsk claimed T27413: MITK 2020 Workflow Q&A.
Fri, May 15, 11:01 AM · Restricted Project, CI, MITK (2020)
kislinsk added a comment to T27181: MITK - DICOM Seg - not saved when started without terminal.
In T27181#200032, @gaoh wrote:

then build package target in MITK build.

@kislinsk what do you mean with this? Is it just the "normal" process, aka cmake and make in MITK-build. Or do I have to configure something additionally?
I tried the normal way and got also the "normal structure": with a bin, lib, Modules etc folder. Whereas when I download the release 18.04, the libraries are directly packed into the bin folder?

Fri, May 15, 11:01 AM · Cleared, MITK (2020)
gaoh added a comment to T27181: MITK - DICOM Seg - not saved when started without terminal.

then build package target in MITK build.

@kislinsk what do you mean with this? Is it just the "normal" process, aka cmake and make in MITK-build. Or do I have to configure something additionally?
I tried the normal way and got also the "normal structure": with a bin, lib, Modules etc folder. Whereas when I download the release 18.04, the libraries are directly packed into the bin folder?

Fri, May 15, 10:00 AM · Cleared, MITK (2020)

Thu, May 14

eisenman committed rCHALLENGER48c2e17887e5: Test that reports for multi-task data set with bootstrapping are created (authored by eisenman).
Test that reports for multi-task data set with bootstrapping are created
Thu, May 14, 6:40 PM
eisenman committed rCHALLENGERe36073bb41d7: Test that reports for multi-task data set without bootstrapping are created (authored by eisenman).
Test that reports for multi-task data set without bootstrapping are created
Thu, May 14, 6:22 PM
eisenman committed rCHALLENGER9550cfc42ab9: Use default latex engine (authored by eisenman).
Use default latex engine
Thu, May 14, 6:22 PM
eisenman added a comment to T27412: Description of variability of achieved rankings across tasks is missing in short report.

The variable "boot_object" that was introduced to the develop branch by this fix is not available in this report. The short multi-task report is without bootstrapping.

Thu, May 14, 6:14 PM · challengeR (v1.0)
eisenman committed rCHALLENGER62bebafef38d: Test that reports for single-task data set with bootstrapping are created (authored by eisenman).
Test that reports for single-task data set with bootstrapping are created
Thu, May 14, 5:38 PM
eisenman committed rCHALLENGER20f344722355: Test that report for single-task data set without bootstrapping is created (authored by eisenman).
Test that report for single-task data set without bootstrapping is created
Thu, May 14, 4:11 PM
floca added a comment to T27153: Fit CRMO2-model to mean value of ROI.

Wouldn't that be covered by the RoiBasedFitGenerator together with the CMRO2 Model?

Thu, May 14, 3:44 PM · Restricted Project
kislinsk closed T27418: Dashboard script file downloads do not work as Resolved.
Thu, May 14, 3:12 PM · CI, MITK
kislinsk committed rMITKf2f8663aacff: Disable raw file downloads from Phabricator (authored by kislinsk).
Disable raw file downloads from Phabricator
Thu, May 14, 3:11 PM
eisenman committed rCHALLENGER3a823f06d2f9: Find files when package is installed (authored by eisenman).
Find files when package is installed
Thu, May 14, 2:48 PM
wiesenfa added a comment to T27396: Represent single-task challenge as multi-task challenge with one task.

Something important I think is also, that all plot functions work outside of the report as intended (it is desirable that users can also create their own reports). This includes choosing the correct function and giving an error if a function does not work with single tasks, e.g.

Thu, May 14, 2:25 PM · challengeR (v1.0)
wiesenfa added a comment to T27396: Represent single-task challenge as multi-task challenge with one task.

Thanks.
In a single task situation, in practice a task will not have a name, so there should be no title and there should not be the need to set a task name I think....
I'll have a look at it, but please give me some time

Thu, May 14, 2:20 PM · challengeR (v1.0)
eisenman committed rCHALLENGER4c511e90e06e: List overview of contained plots (authored by eisenman).
List overview of contained plots
Thu, May 14, 2:01 PM
eisenman committed rCHALLENGER358c1201126c: Adapt example for single-task data set (authored by eisenman).
Adapt example for single-task data set
Thu, May 14, 1:27 PM
eisenman added a comment to T27396: Represent single-task challenge as multi-task challenge with one task.

Now I know what you were meaning with all your points ;)
I started to work on this during our hacking days on this branch. I managed to transform a single-task data set into multi-task data set including one task. I had to adapt some plot code. And for the reports many duplicate changes would have been necessary. So on the way, I decided to refactor the generation of the reports to lower the future maintenance effort: I extracted the report sections to separate files and include them depending on the variables isMultiTask and bootstrappingEnabled. So each text block and code snippet exists only once. And it's still possible to get four types of reports (single-task data set with and without bootstrapping, multi-task data set with and without bootstrapping). I compared the reports with the reference reports I generated from the master branch. They look the same apart from that the plots for single-task data sets are also labeled with the task name. The next step would be a general clean-up of the functionality that was used for single-task data sets.

Thu, May 14, 1:04 PM · challengeR (v1.0)
eisenman committed rCHALLENGER2dccd31860f1: Remove report functionality used for single-task data sets (authored by eisenman).
Remove report functionality used for single-task data sets
Thu, May 14, 12:41 PM
eisenman committed rCHALLENGER7e95abdd4b64: Remove unused report files (authored by eisenman).
Remove unused report files
Thu, May 14, 12:41 PM
eisenman committed rCHALLENGER86ba2005a955: Extract report sections to separate files and include them depending on… (authored by eisenman).
Extract report sections to separate files and include them depending on…
Thu, May 14, 12:01 PM
eisenman committed rCHALLENGER56d572ce781b: Move transformation to sanity check (authored by eisenman).
Move transformation to sanity check
Thu, May 14, 12:01 PM
aguilera moved T27412: Description of variability of achieved rankings across tasks is missing in short report from Backlog to Done on the challengeR (v1.0) board.
Thu, May 14, 11:55 AM · challengeR (v1.0)
wiesenfa added a comment to T27396: Represent single-task challenge as multi-task challenge with one task.

I think this should be well thought through before putting into action

Thu, May 14, 11:42 AM · challengeR (v1.0)
kompan updated the task description for T27153: Fit CRMO2-model to mean value of ROI.
Thu, May 14, 11:35 AM · Restricted Project
reinkea added a comment to T27407: Warnings are shown in multi-task challenge report for violin plot.

Yes, this results in Na, but they shouldn't be treated like before; you're right. @wiesenfa: What do you propose for the plots? Should we just remove the warnings?

Thu, May 14, 11:03 AM · challengeR (v1.0)
wiesenfa created T27420: report text.
Thu, May 14, 10:58 AM · challengeR (v1.0)
wiesenfa added a comment to T27407: Warnings are shown in multi-task challenge report for violin plot.

it's not because of missing test cases. It is because in certain situation no Kendall can be computed. Don't use treat.na for this.

Thu, May 14, 10:53 AM · challengeR (v1.0)
reinkea added a comment to T27407: Warnings are shown in multi-task challenge report for violin plot.

This is due to the fact that missing values cannot be plotted:

Thu, May 14, 10:49 AM · challengeR (v1.0)
neher closed T27417: Fix readers as Resolved.
Thu, May 14, 9:40 AM · MITK Diffusion
reinkea moved T27412: Description of variability of achieved rankings across tasks is missing in short report from Done to v1.0 on the challengeR board.
Thu, May 14, 9:38 AM · challengeR (v1.0)
neher lowered the priority of T26056: [MITK Diffusion] Integrated MIC Bet update in MITK Diffusion from High to Normal.
Thu, May 14, 9:24 AM · MITK Diffusion
neher lowered the priority of T26879: Account for voxel size in TRK header matrix from Normal to Low.
Thu, May 14, 9:24 AM · MITK Diffusion
neher raised the priority of T26879: Account for voxel size in TRK header matrix from Low to Normal.
Thu, May 14, 9:24 AM · MITK Diffusion
neher lowered the priority of T26879: Account for voxel size in TRK header matrix from Normal to Low.
Thu, May 14, 9:24 AM · MITK Diffusion
neher lowered the priority of T27070: Planar figure to image fails from High to Normal.
Thu, May 14, 9:24 AM · MITK Diffusion
neher triaged T27419: Fix dartclient documentation build as High priority.
Thu, May 14, 9:24 AM · MITK Diffusion
neher raised the priority of T27417: Fix readers from High to Unbreak Now!.
Thu, May 14, 9:23 AM · MITK Diffusion
aguilera moved T27325: Plot titles in rankingHeatmap missing in multi task report from In Progress to Done on the challengeR (v1.0) board.
Thu, May 14, 9:23 AM · challengeR (v1.0)
aguilera moved T27404: Fix the 2.1 section title format of the report from In Progress to Done on the challengeR (v1.0) board.
Thu, May 14, 9:22 AM · challengeR (v1.0)
aguilera moved T27408: Description of cluster analysis contains unnecessary symbol from In Progress to Done on the challengeR (v1.0) board.
Thu, May 14, 9:22 AM · challengeR (v1.0)
aguilera moved T27410: Correct description of variability of achieved rankings across tasks from In Progress to Done on the challengeR (v1.0) board.
Thu, May 14, 9:22 AM · challengeR (v1.0)
kislinsk added a comment to T27418: Dashboard script file downloads do not work.

Pushed new branch bugfix/T27418-DashboardScriptDownloadWorkaround.

Thu, May 14, 9:16 AM · CI, MITK
kislinsk merged T24757: Raw file downloads in CTest scripts don't work anymore with Phabricator URLs into T27418: Dashboard script file downloads do not work.
Thu, May 14, 9:13 AM · CI, MITK
kislinsk merged task T24757: Raw file downloads in CTest scripts don't work anymore with Phabricator URLs into T27418: Dashboard script file downloads do not work.
Thu, May 14, 9:13 AM · Restricted Project, MITK
kislinsk triaged T27418: Dashboard script file downloads do not work as Unbreak Now! priority.
Thu, May 14, 9:06 AM · CI, MITK
reinkea moved T27412: Description of variability of achieved rankings across tasks is missing in short report from v1.0 to Done on the challengeR board.
Thu, May 14, 8:47 AM · challengeR (v1.0)
reinkea committed rCHALLENGERf1524ebcaced: Add the description of blob plots for the short report on multiple tasks as it… (authored by reinkea).
Add the description of blob plots for the short report on multiple tasks as it…
Thu, May 14, 8:44 AM
reinkea claimed T27412: Description of variability of achieved rankings across tasks is missing in short report.
Thu, May 14, 8:27 AM · challengeR (v1.0)
neher committed rMITKDIFF0653d492a577: Merge branch 'T27417-FixReaders' (authored by neher).
Merge branch 'T27417-FixReaders'
Thu, May 14, 8:25 AM
neher committed rMITKDIFFe11dd618dc39: Read --> DoRead (authored by neher).
Read --> DoRead
Thu, May 14, 8:24 AM
neher added a comment to T27417: Fix readers.

Pushed new branch T27417-FixReaders.

Thu, May 14, 8:24 AM · MITK Diffusion
neher triaged T27417: Fix readers as High priority.
Thu, May 14, 8:23 AM · MITK Diffusion
kompan closed T27373: ModelFit: Generate absolute curve data as Resolved.
Thu, May 14, 8:12 AM · Restricted Project, MITK

Wed, May 13

floca triaged T27416: DICOM Seg IO skips empty slices when storing DICOM seg as Normal priority.
Wed, May 13, 10:34 PM · Cleared, HiGHmed, DICOM, MITK (2020)
floca edited projects for T26949: DICOM SEG - 3D segmentations with only one slice cannot be reloaded as DICOM SEG , added: MITK (2020), Missing Info, DICOM; removed MITK.

The reason is still unkown. But if you store the segs without skipping the empty slices, then mitk is able to load also segs with one slice.

Wed, May 13, 10:24 PM · MITK, DICOM, Missing Info
kislinsk closed T27415: Change Arcanist default merge base to origin/develop as Resolved.
Wed, May 13, 9:34 PM · MITK
kislinsk committed rMITK8b671b20b5eb: Change Arcanist merge base to origin/develop (authored by kislinsk).
Change Arcanist merge base to origin/develop
Wed, May 13, 9:30 PM
kislinsk added a comment to T27415: Change Arcanist default merge base to origin/develop.

Pushed new branch feature/T27415-ChangeArcMergeBase.

Wed, May 13, 9:29 PM · MITK
kislinsk triaged T27415: Change Arcanist default merge base to origin/develop as Unbreak Now! priority.
Wed, May 13, 9:17 PM · MITK
aguilera committed rCHALLENGER4736036e7c76: Merge branch 'feature/T27325-PlotTitlesInRankingHeatmapMissingInMultiTaskReport… (authored by aguilera).
Merge branch 'feature/T27325-PlotTitlesInRankingHeatmapMissingInMultiTaskReport…
Wed, May 13, 6:40 PM
aguilera moved T27410: Correct description of variability of achieved rankings across tasks from Backlog to In Progress on the challengeR (v1.0) board.
Wed, May 13, 6:35 PM · challengeR (v1.0)
aguilera committed rCHALLENGER4dc158e8d9c7: add title for multi-task report (authored by aguilera).
add title for multi-task report
Wed, May 13, 6:34 PM
aguilera committed rCHALLENGER3232fdd1dbaa: Merge branch 'feature/T27408-DescriptionOfClusterAnalysisContainsUnnecessarySym… (authored by aguilera).
Merge branch 'feature/T27408-DescriptionOfClusterAnalysisContainsUnnecessarySym…
Wed, May 13, 6:26 PM
aguilera committed rCHALLENGERbb1fa3178b8e: Merge branch 'feature/T27410-CorrectDescriptionOfVariabilityOfAchievedRankingsA… (authored by aguilera).
Merge branch 'feature/T27410-CorrectDescriptionOfVariabilityOfAchievedRankingsA…
Wed, May 13, 6:23 PM
aguilera committed rCHALLENGERebc385e0828e: Merge branch 'feature/T27404-FixThe2.1SectionTitleFormatOfTheReport' into… (authored by aguilera).
Merge branch 'feature/T27404-FixThe2.1SectionTitleFormatOfTheReport' into…
Wed, May 13, 6:10 PM
aguilera committed rCHALLENGER0fc570a5bc8f: description of section 3.1.1 corrected (authored by aguilera).
description of section 3.1.1 corrected
Wed, May 13, 4:19 PM
aguilera claimed T27410: Correct description of variability of achieved rankings across tasks.
Wed, May 13, 4:19 PM · challengeR (v1.0)
aguilera committed rCHALLENGER183d022ad12d: symbol removed from multi-task template reports (authored by aguilera).
symbol removed from multi-task template reports
Wed, May 13, 4:05 PM
aguilera moved T27408: Description of cluster analysis contains unnecessary symbol from Backlog to In Progress on the challengeR (v1.0) board.
Wed, May 13, 4:02 PM · challengeR (v1.0)
aguilera claimed T27408: Description of cluster analysis contains unnecessary symbol.
Wed, May 13, 3:51 PM · challengeR (v1.0)
aguilera claimed T27404: Fix the 2.1 section title format of the report.
Wed, May 13, 3:45 PM · challengeR (v1.0)
floca moved T27357: Check/Update DICOMTags of interest from Backlog to DICOM SEG on the MITK (2020) board.
Wed, May 13, 2:33 PM · Cleared, HiGHmed, MITK (2020)
floca triaged T27414: Adapt CMake version macro to generate version description with "no official release" as Normal priority.
Wed, May 13, 2:32 PM · MITK (2020), CI
floca updated the task description for T27413: MITK 2020 Workflow Q&A.
Wed, May 13, 2:28 PM · Restricted Project, CI, MITK (2020)
floca triaged T27413: MITK 2020 Workflow Q&A as High priority.
Wed, May 13, 2:26 PM · Restricted Project, CI, MITK (2020)
aguilera committed rCHALLENGERa54e3c203d50: add title for multi-task plot (authored by aguilera).
add title for multi-task plot
Wed, May 13, 1:59 PM
aguilera committed rCHALLENGERedcac207610b: add title for multi-task plots (authored by aguilera).
add title for multi-task plots
Wed, May 13, 1:31 PM
eisenman triaged T27412: Description of variability of achieved rankings across tasks is missing in short report as High priority.
Wed, May 13, 1:30 PM · challengeR (v1.0)
aguilera committed rCHALLENGER3977ba02ff24: Revert "add title for multi-task" (authored by aguilera).
Revert "add title for multi-task"
Wed, May 13, 1:24 PM
aguilera added a reverting change for rCHALLENGERb89f8dcbfb70: add title for multi-task: rCHALLENGER3977ba02ff24: Revert "add title for multi-task".
Wed, May 13, 1:24 PM
eisenman added a comment to T27326: autolayout networks in multi task report ugly.

Ok, I saw it now what is generated for the data set that comes with the package:

Wed, May 13, 1:17 PM · challengeR (v1.0)
aguilera moved T27404: Fix the 2.1 section title format of the report from Backlog to In Progress on the challengeR (v1.0) board.
Wed, May 13, 1:16 PM · challengeR (v1.0)
aguilera committed rCHALLENGERa73c2faf31d1: fix line break (authored by aguilera).
fix line break
Wed, May 13, 1:16 PM
eisenman triaged T27411: Improve labels in cluster dendrogram as High priority.
Wed, May 13, 1:14 PM · challengeR (v1.0)
eisenman triaged T27410: Correct description of variability of achieved rankings across tasks as High priority.
Wed, May 13, 1:02 PM · challengeR (v1.0)
floca updated the task description for T27409: Specifiy and implement cleaning policies for MITK tasks.
Wed, May 13, 12:19 PM · Cleared, Restricted Project, MITK (2020)
floca triaged T27409: Specifiy and implement cleaning policies for MITK tasks as Normal priority.
Wed, May 13, 12:18 PM · Cleared, Restricted Project, MITK (2020)
aguilera updated the task description for T27404: Fix the 2.1 section title format of the report.
Wed, May 13, 11:18 AM · challengeR (v1.0)
aguilera committed rCHALLENGERb89f8dcbfb70: add title for multi-task (authored by aguilera).
add title for multi-task
Wed, May 13, 11:08 AM