Page MenuHomePhabricator
Feed All Stories

Dec 7 2020

kislinsk triaged T28080: Microsoft Visual C++ Redistributable not included in packages anymore as Normal priority.
Dec 7 2020, 8:28 PM · Cleared, MITK (v2021.02)
kislinsk added a comment to T23249: Ensure openSSL availability for MITK installers using XNAT plugin or other REST services.

At least for XNAT this was recently resolved in T26449: XNAT connection failes due to missing OpenSSL connections.

Dec 7 2020, 8:17 PM · Restricted Project, CSI-HD, MITK
kislinsk closed T28060: CMake Policy CMP0091 does not work well with dependencies that are based on CMake version < 3.15 as Resolved.
Dec 7 2020, 8:15 PM · MITK
wiesenfa added a comment to T27925: Use cases of annotator option.

would defer to after release

Dec 7 2020, 3:58 PM · challengeR
wiesenfa added a comment to T27494: Check which files are still relevant.

please close if ok

Dec 7 2020, 3:58 PM · challengeR
wiesenfa committed rCHALLENGER77411271cd7a: fix podium (authored by wiesenfa).
fix podium
Dec 7 2020, 3:51 PM
wiesenfa committed rCHALLENGERd7c27e2a6dad: fix (authored by wiesenfa).
fix
Dec 7 2020, 3:51 PM
wiesenfa committed rCHALLENGER4a677bed212f: style (authored by wiesenfa).
style
Dec 7 2020, 3:51 PM
wiesenfa committed rCHALLENGER38ac623e8adc: add annotor (authored by wiesenfa).
add annotor
Dec 7 2020, 3:51 PM
wiesenfa added a comment to T27925: Use cases of annotator option.

added to documentation of as.challenge():
(arg annotator:) If multiple annotators annotated the test cases, a string specifying the name of the column that contains the annotator identifiers. Only applies to rang-then-aggregate. Use with caution: Currently not tested.

Dec 7 2020, 3:18 PM · challengeR
wiesenfa moved T27925: Use cases of annotator option from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 3:16 PM · challengeR
wiesenfa committed rCHALLENGER17905fc80c85: add man for annotator (authored by wiesenfa).
add man for annotator
Dec 7 2020, 3:16 PM
wiesenfa added a comment to T27971: Provide code for podium plot in vignette "Visualizations".

added

podium(ranking)

to vignette.
podium() does have a different syntax for layouting (it is not ggplot2 but base graphics) but vignette does not describe layouting for ggplot2 plots either

Dec 7 2020, 2:20 PM · challengeR (v1.0)
wiesenfa moved T27971: Provide code for podium plot in vignette "Visualizations" from Backlog to Done on the challengeR (v1.0) board.
Dec 7 2020, 2:18 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER6267c97aeb1b: T27971 podium in visualizations vignette (authored by wiesenfa).
T27971 podium in visualizations vignette
Dec 7 2020, 2:13 PM
wiesenfa committed rCHALLENGERf899ce83619a: add euclidean consensus man (authored by wiesenfa).
add euclidean consensus man
Dec 7 2020, 2:13 PM
wiesenfa committed rCHALLENGER269f169422a0: update man (authored by wiesenfa).
update man
Dec 7 2020, 2:13 PM
wiesenfa committed rCHALLENGERccd930a457fd: add details for euclidean consensus (authored by wiesenfa).
add details for euclidean consensus
Dec 7 2020, 2:13 PM
wiesenfa placed T27998: Interpretation of consensus ranking values needs further explanation up for grabs.
Dec 7 2020, 2:03 PM · challengeR (v1.0)
wiesenfa moved T27998: Interpretation of consensus ranking values needs further explanation from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 2:03 PM · challengeR (v1.0)
wiesenfa added a comment to T27998: Interpretation of consensus ranking values needs further explanation.

report() does not know what type of consensus ranking method had been used.
I added sentence
"Consensus ranking according to mean ranks across tasks if method="euclidean" where in case of ties (equal ranks for multiple algorithms) the average rank is used, i.e. ties.method="average"."
to help for consensus() and would suggest to also add this to the vignette/readme, but not to report. Could someone of you please take care of this?

Dec 7 2020, 2:03 PM · challengeR (v1.0)
kalali added a comment to T28076: [Multilabel Segmentation] Corrector tool 2D does not respect multiple layers.

This task will be fixed with D447 (see https://phabricator.mitk.org/D447?vs=2005&id=2006#toc).

Dec 7 2020, 1:28 PM · MITK (v2021.02)
kalali triaged T28076: [Multilabel Segmentation] Corrector tool 2D does not respect multiple layers as Normal priority.
Dec 7 2020, 1:20 PM · MITK (v2021.02)
kalali closed T28051: [Multilabel Segmentation] Fill / Erase tool does not respect multiple layers as Resolved.

This task will be fixed with D447 (see D448#13472).

Dec 7 2020, 1:10 PM · MITK (v2021.02)
kalali closed T28051: [Multilabel Segmentation] Fill / Erase tool does not respect multiple layers, a subtask of T27807: [MultiLabel Segmentation] Inspection of module and plugin, as Resolved.
Dec 7 2020, 1:10 PM · MITK (v2024.12)
wiesenfa added a comment to T27775: only export functions to be used by user.

@eisenman do you want to do this with roxygen?

Dec 7 2020, 1:10 PM · challengeR
wiesenfa assigned T27494: Check which files are still relevant to eisenman.
Dec 7 2020, 1:09 PM · challengeR
wiesenfa assigned T28016: embed web app in package to eisenman.
Dec 7 2020, 1:09 PM · challengeR (v1.0)
wiesenfa claimed T27998: Interpretation of consensus ranking values needs further explanation.
Dec 7 2020, 1:08 PM · challengeR (v1.0)
wiesenfa moved T28016: embed web app in package from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 1:08 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER2ade85d374f7: fix tests (authored by wiesenfa).
fix tests
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGER3578ab9be39c: allow consensus named numeric vector or ordered character vector (authored by wiesenfa).
allow consensus named numeric vector or ordered character vector
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGER6fc162a3bcde: remove compare.rank (authored by wiesenfa).
remove compare.rank
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGER019ec7bb9392: remove winner.ranked (authored by wiesenfa).
remove winner.ranked
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGERb925ab764dba: fix (authored by wiesenfa).
fix
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGERdeb1db150dac: T27943 allow ordering numeric (authored by wiesenfa).
T27943 allow ordering numeric
Dec 7 2020, 1:07 PM
wiesenfa moved T27943: Plot function stability() raises error when used with default values from In Progress to Done on the challengeR (v1.0) board.
Dec 7 2020, 1:07 PM · challengeR (v1.0)
wiesenfa added a comment to T27494: Check which files are still relevant.

kept select.if(), winner(), extract.workfolow and compareRanks()
and removed everything not supported anymore.
as.warehouse (benchmarkUtils) is not exported, recommend to leave because this may come handy for specific situations

Dec 7 2020, 1:07 PM · challengeR
wiesenfa moved T27494: Check which files are still relevant from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 12:56 PM · challengeR
wiesenfa moved T27943: Plot function stability() raises error when used with default values from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 11:21 AM · challengeR (v1.0)
wiesenfa added a comment to T27494: Check which files are still relevant.

removed second()

Dec 7 2020, 11:19 AM · challengeR
kalali closed T27870: [Segmentation] Fast Marching 3D Tool can not clear preview segmentation masks as Resolved.
Dec 7 2020, 10:00 AM · MITK (v2021.02)
kalali committed rMITKb2d2a87ebd29: Clear preview segmentation in fast marching 3D (authored by kalali).
Clear preview segmentation in fast marching 3D
Dec 7 2020, 9:59 AM
kalali committed rMITK2e6b97654f2c: Update also if the seed points are empty (authored by kalali).
Update also if the seed points are empty
Dec 7 2020, 9:59 AM

Dec 6 2020

kislinsk added a comment to T26237: Improve performance for interactions in 2d widgets.

Before:

Dec 6 2020, 10:15 PM · MITK
kislinsk added a comment to T26237: Improve performance for interactions in 2d widgets.

Pushed new branch bugfix/T26237-ImprovePerformance.

Dec 6 2020, 9:02 PM · MITK
kislinsk claimed T26237: Improve performance for interactions in 2d widgets.

A profiling session revealed that a substantial amount of time during interaction with the 2d widgets is spent by the ITK object factory in the context of mitk::BaseGeometry when creating new instances of itk::BoundingBox, itk::VectorContainer, and itk::ScalableAffineTransform.

Dec 6 2020, 8:46 PM · MITK

Dec 4 2020

wiesenfa committed rCHALLENGER6144decf510d: delete funciton second() (unmaintained) (authored by wiesenfa).
delete funciton second() (unmaintained)
Dec 4 2020, 8:49 PM
wiesenfa placed T27971: Provide code for podium plot in vignette "Visualizations" up for grabs.
Dec 4 2020, 8:46 PM · challengeR (v1.0)
wiesenfa added a comment to T27971: Provide code for podium plot in vignette "Visualizations".

What is the problem?
in the extend of the vignette it would be simply

Dec 4 2020, 8:46 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER2e04538d9e1d: podium default topright legend (authored by wiesenfa).
podium default topright legend
Dec 4 2020, 8:44 PM
wiesenfa moved T27915: Podium plot shrinks for long algorithm names from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 8:40 PM · challengeR (v1.0)
wiesenfa added a comment to T27915: Podium plot shrinks for long algorithm names.

legend now always at bottom and dynamically adjusts to number of algorithms and algorithm name length.
Took me almost the day...

Dec 4 2020, 8:40 PM · challengeR (v1.0)
wiesenfa moved T27748: Decide on limit for algorithms in plot legends from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 8:39 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER26eb63cdef48: report podium plot dynamic legend bottom (authored by wiesenfa).
report podium plot dynamic legend bottom
Dec 4 2020, 8:38 PM
wiesenfa committed rCHALLENGER019b63757493: bottom legend in line plot if n.algorithms>20 (authored by wiesenfa).
bottom legend in line plot if n.algorithms>20
Dec 4 2020, 8:38 PM
wiesenfa committed rCHALLENGERdad94cd28be0: bottom legend in stacked frequency if n.tasks>20 (authored by wiesenfa).
bottom legend in stacked frequency if n.tasks>20
Dec 4 2020, 8:38 PM
kislinsk edited projects for T28060: CMake Policy CMP0091 does not work well with dependencies that are based on CMake version < 3.15, added: MITK; removed MITK (v2021.02).

It will be automatically listed in the changelog table regardless of the task status. :)

Dec 4 2020, 4:30 PM · MITK
floca added a comment to T28060: CMake Policy CMP0091 does not work well with dependencies that are based on CMake version < 3.15.

Thanks. No it works again.

Dec 4 2020, 3:33 PM · MITK
kislinsk moved T27992: Release of MITK CLIs from Backlog to MITK Meeting on the Request for Discussion board.
Dec 4 2020, 1:13 PM · MITK (v2021.02), Request for Discussion
kislinsk lowered the priority of T28060: CMake Policy CMP0091 does not work well with dependencies that are based on CMake version < 3.15 from High to Normal.
Dec 4 2020, 12:43 PM · MITK
kislinsk reopened T28060: CMake Policy CMP0091 does not work well with dependencies that are based on CMake version < 3.15 as "Open".

Maybe I should leave this task open until we came up with a minimum prototype...

Dec 4 2020, 12:43 PM · MITK
kislinsk closed T28060: CMake Policy CMP0091 does not work well with dependencies that are based on CMake version < 3.15 as Resolved.
Dec 4 2020, 12:42 PM · MITK
kislinsk added a comment to T26399: Workbench crash on simple tree model update.

Isn't (1) a requirement anyways? Let me just look it up in the Qt documentation...

Dec 4 2020, 12:37 PM · MITK, Request for Discussion
kislinsk added a comment to T28062: Fix IsotropicWavelets (ITK) dependency.

Deleted branch bugfix/T28062-FixIsotropicWaveletsDep.

Dec 4 2020, 12:31 PM · MITK (v2021.02)
kislinsk closed T28062: Fix IsotropicWavelets (ITK) dependency as Resolved.

The actual issue seems to be network troubles so maybe a server is down or something similar. Should resolve itself either now/today or the next days. Anyway, as we now made the dependency explicit, this task was not a complete waste of time. :-)

Dec 4 2020, 12:30 PM · MITK (v2021.02)
kislinsk committed rMITK24edc5c4c833: Make IsotropicWavelets dependency explicit (authored by kislinsk).
Make IsotropicWavelets dependency explicit
Dec 4 2020, 12:27 PM
kislinsk committed rMITK15ae7b34fd0f: Merge branch 'bugfix/T28062-FixIsotropicWaveletsDep' into develop (authored by kislinsk).
Merge branch 'bugfix/T28062-FixIsotropicWaveletsDep' into develop
Dec 4 2020, 12:27 PM
kislinsk added a comment to T28062: Fix IsotropicWavelets (ITK) dependency.

Pushed new branch bugfix/T28062-FixIsotropicWaveletsDep.

Dec 4 2020, 12:26 PM · MITK (v2021.02)
wiesenfa added a comment to T27748: Decide on limit for algorithms in plot legends.

max number of tasks / algorithms now 20 in stacked frequency and line plots, respectively for legend appear on right, otherwise put on bottom of plot. could also be put to lower number

Dec 4 2020, 12:00 PM · challengeR (v1.0)
wiesenfa added a comment to T27748: Decide on limit for algorithms in plot legends.

only podium plots and line plots actually require algorithms in legend, otherwise algorithm is identifiable from x-axis or facet label. Now, these redundant legends are removed.
besides that stacked frequency plots have colored tasks and respective legend

Dec 4 2020, 11:52 AM · challengeR (v1.0)
kalali moved T26399: Workbench crash on simple tree model update from Backlog to MITK Meeting on the Request for Discussion board.
Dec 4 2020, 11:50 AM · MITK, Request for Discussion
wiesenfa committed rCHALLENGER126a4af6fa0c: remove legend if algorithm identifiable in x-axis (authored by wiesenfa).
remove legend if algorithm identifiable in x-axis
Dec 4 2020, 11:41 AM
wiesenfa committed rCHALLENGER4b396c8ddc14: introduce n.tasks in Rmd (authored by wiesenfa).
introduce n.tasks in Rmd
Dec 4 2020, 11:41 AM
wiesenfa committed rCHALLENGER527c8578ee15: introduce n.tasks and n.algorithms in Rmd files (authored by wiesenfa).
introduce n.tasks and n.algorithms in Rmd files
Dec 4 2020, 11:41 AM
wiesenfa committed rCHALLENGERced7c6c06339: improve reporting of used aggregation method (authored by wiesenfa).
improve reporting of used aggregation method
Dec 4 2020, 11:41 AM
wiesenfa committed rCHALLENGER11b645ebaac1: hide output of task names in report 4.2.1 (authored by wiesenfa).
hide output of task names in report 4.2.1
Dec 4 2020, 11:41 AM
kislinsk added a comment to T28062: Fix IsotropicWavelets (ITK) dependency.

I added an explicit private target dependency to IsotropicWavelets in BasicImageProcessing as it is the only module where it is used.

Dec 4 2020, 11:15 AM · MITK (v2021.02)
kislinsk renamed T28062: Fix IsotropicWavelets (ITK) dependency from Remove unused ITKIsotropicWavelets dependency to Fix IsotropicWavelets (ITK) dependency.
Dec 4 2020, 11:14 AM · MITK (v2021.02)
kislinsk reopened T28062: Fix IsotropicWavelets (ITK) dependency as "Open".

Argh... it is actually used in BasicImageProcessing without being specified as dependency. :-( I will investigate if it is just a header that is included or if we need to revert and try to fix the retrival issue of the remote module.

Dec 4 2020, 10:15 AM · MITK (v2021.02)
kislinsk closed T28062: Fix IsotropicWavelets (ITK) dependency as Resolved.
Dec 4 2020, 9:59 AM · MITK (v2021.02)
kislinsk added a comment to T28062: Fix IsotropicWavelets (ITK) dependency.

Deleted branch bugfix/T28062-RemoveITKIsotropicWaveletsDependency.

Dec 4 2020, 9:58 AM · MITK (v2021.02)
kislinsk committed rMITK23b915bd3a92: Remove unused IsotropicWavelets module (authored by kislinsk).
Remove unused IsotropicWavelets module
Dec 4 2020, 9:58 AM
kislinsk committed rMITKa723c00cf64d: Merge branch 'bugfix/T28062-RemoveITKIsotropicWaveletsDependency' into develop (authored by kislinsk).
Merge branch 'bugfix/T28062-RemoveITKIsotropicWaveletsDependency' into develop
Dec 4 2020, 9:58 AM
kislinsk added a comment to T28062: Fix IsotropicWavelets (ITK) dependency.

Pushed new branch bugfix/T28062-RemoveITKIsotropicWaveletsDependency.

Dec 4 2020, 9:57 AM · MITK (v2021.02)
kislinsk updated the task description for T28062: Fix IsotropicWavelets (ITK) dependency.
Dec 4 2020, 9:55 AM · MITK (v2021.02)
kislinsk triaged T28062: Fix IsotropicWavelets (ITK) dependency as Normal priority.
Dec 4 2020, 9:55 AM · MITK (v2021.02)
wiesenfa moved T27915: Podium plot shrinks for long algorithm names from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:55 AM · challengeR (v1.0)
wiesenfa moved T27748: Decide on limit for algorithms in plot legends from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:55 AM · challengeR (v1.0)
wiesenfa moved T27707: na.treat obligatory for report from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 9:36 AM · challengeR (v1.0)
wiesenfa moved T27707: na.treat obligatory for report from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:36 AM · challengeR (v1.0)
wiesenfa committed rCHALLENGER6ee0e3a4dbd1: messages if na.treat not specified and NA present (authored by wiesenfa).
messages if na.treat not specified and NA present
Dec 4 2020, 9:35 AM
kislinsk added a project to T28061: Use official ITK release tarball instead of snapshot: Noteworthy.
Dec 4 2020, 9:24 AM · Noteworthy, MITK (v2021.02)
kislinsk closed T28061: Use official ITK release tarball instead of snapshot as Resolved.
Dec 4 2020, 9:22 AM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T28061: Use official ITK release tarball instead of snapshot.

Deleted branch bugfix/T28061-UseOfficialITKTarball.

Dec 4 2020, 9:22 AM · Noteworthy, MITK (v2021.02)
kislinsk committed rMITK23d75d193a19: Use official ITK release tarball (authored by kislinsk).
Use official ITK release tarball
Dec 4 2020, 9:21 AM
kislinsk committed rMITK6cbf68ecc068: Merge branch 'bugfix/T28061-UseOfficialITKTarball' into develop (authored by kislinsk).
Merge branch 'bugfix/T28061-UseOfficialITKTarball' into develop
Dec 4 2020, 9:21 AM
kislinsk added a comment to T28061: Use official ITK release tarball instead of snapshot.

Pushed new branch bugfix/T28061-UseOfficialITKTarball.

Dec 4 2020, 9:20 AM · Noteworthy, MITK (v2021.02)
kislinsk triaged T28061: Use official ITK release tarball instead of snapshot as Normal priority.
Dec 4 2020, 9:19 AM · Noteworthy, MITK (v2021.02)

Dec 3 2020

wiesenfa claimed T27748: Decide on limit for algorithms in plot legends.
Dec 3 2020, 10:22 PM · challengeR (v1.0)