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Mon, May 10

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

Fri, May 7

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)

Thu, May 6

nolden committed rMITK121d8b57de63: Update DCMQI to official v1.2.4 (authored by nolden).
Update DCMQI to official v1.2.4
Thu, May 6, 10:59 AM
nolden committed rMITK8a570d38b622: Update DCMQI to official v1.2.4 (authored by nolden).
Update DCMQI to official v1.2.4
Thu, May 6, 10:59 AM
nolden committed rMITK6bffce5572f5: Update DCMTK to 3.6.6 (authored by nolden).
Update DCMTK to 3.6.6
Thu, May 6, 10:58 AM
nolden committed rMITKeba7c6e68362: Update DCMTK to 3.6.6 (authored by nolden).
Update DCMTK to 3.6.6
Thu, May 6, 10:58 AM

Wed, May 5

nolden added a comment to T27437: Migrate MITK to use ITK 5.x .

Maybe something to keep an eye on: T28478 and https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/ThirdParty/DCMTK

Wed, May 5, 11:23 AM · MITK (v2021.10)
nolden created T28478: Update DCMTK version to 3.6.6.
Wed, May 5, 10:20 AM · MITK (v2021.10)
nolden added a comment to T28039: DICOM Seg loading error.

@kislinsk I think rMITK4f70ab9c4b4c47355f6cb725c48b8d3b3da81983 fixed it , but maybe you could just update to 1.2.4 instead of the hash. Or would this be something that could/should rather be done in a general "minor updates on all toolkits" task? Then this one could be closed resolved.

Wed, May 5, 10:11 AM · MITK (v2021.10)
nolden added a comment to T28039: DICOM Seg loading error.

Ok, sorry, forgot to mention: the original issue seems to be resolved, tested using the latest snapshot https://www.mitk.org/download/ci/snapshots/Windows/MITK-snapshots_2021-04-30-windows-x86_64.zip

Wed, May 5, 10:03 AM · MITK (v2021.10)
nolden added a comment to T28039: DICOM Seg loading error.

Given the dynamics of RACOON where this initially occured I would suggest to update dcmqi even to a more recent version. and if I understood correctly there were fixes to DCMTK as well related to DICOM SEG which originated from a MEVIS report, and could be adopted to choosing a patched DCMTK from the commontk organization on github.

Wed, May 5, 9:50 AM · MITK (v2021.10)

Thu, Apr 29

nolden triaged T28470: "Dataset" option for ZIP upload as Wishlist priority.
Thu, Apr 29, 3:15 PM · Kaapana (internal)

Wed, Apr 21

nolden created T28455: RT struct 3D visibility is not working correctly.
Wed, Apr 21, 11:30 AM · Request for Discussion, MITK (v2021.10)

Wed, Apr 14

nolden added a comment to T27437: Migrate MITK to use ITK 5.x .

@kislinsk thanks for taking over. The WIP stuff I put on github still could be useful, see comment above. let me know if I can help.

Wed, Apr 14, 9:57 AM · MITK (v2021.10)

Apr 1 2021

nolden created T28428: Re-enable code coverage testing in MITK CI.
Apr 1 2021, 2:04 PM · CI, MITK

Mar 25 2021

nolden added a comment to T28232: Shapemodels.

The topic came up in the Kaapana tech meeting again, because the current situation is causing problems there.

Mar 25 2021, 10:01 AM · Kaapana (internal), Request for Discussion, MITK

Mar 15 2021

nolden added a comment to T27968: CTP gets stuck on large import.

Not sure if this is related:

Mar 15 2021, 1:47 PM · Kaapana (internal)
nolden removed a project from T28374: Workbench crashes after DICOM retrieval : Missing Info.
Mar 15 2021, 9:52 AM · Next Milestone, DICOM, MITK
nolden closed T28374: Workbench crashes after DICOM retrieval as Resolved.

@gaoh thanks for pointing there, I will close this one as a duplicate

Mar 15 2021, 9:51 AM · Next Milestone, DICOM, MITK
nolden added a comment to T28207: MITK DicomBrowser q/r Retrieve part crash.

Another option for testing is to use dicomserver.co.uk , I think it is preconfigured in the Workbench. It's a public DICOM endpoint and the data there differs, but 5 min ago I was able to reproduce the crash with a retrieval from there. Just activate the checkbox in the MITK config table , query last month, select a few patients and retrieve. Worked for me to reproduce the crash.

Mar 15 2021, 9:50 AM · MITK (v2021.10)

Mar 12 2021

nolden triaged T28374: Workbench crashes after DICOM retrieval as High priority.
Mar 12 2021, 3:45 PM · Next Milestone, DICOM, MITK

Feb 19 2021

nolden triaged T28323: Workbench aborts if passed an invalid command line option as Low priority.
Feb 19 2021, 5:50 PM · MITK
nolden added a comment to T28282: Workbench does not start when building with Qt 5.15 on Linux.

Interesting catch. There is no call to regex_match in our code. If I understand it correctly the stack object is just created to check if an exception happens during construction, but maybe this is just another variant of the issue described for the library. A possible workaround could be to explicitly create and destroy the regex objects in our code, with explicit exception catching and re-throwing.

Feb 19 2021, 5:13 PM · MITK
nolden added a comment to T28232: Shapemodels.

@norajitr maybe a bit more background on the ticket for you:

Feb 19 2021, 10:39 AM · Kaapana (internal), Request for Discussion, MITK

Feb 18 2021

nolden added a comment to T28302: MITK CI jobs for Kaapana.

I would like to have files versioned / with different names. If it's necessary to have a download link that doesn't change I can help with a script to create a "latest" link, had that for MITK nightlies back in the days

Feb 18 2021, 11:45 AM · CI, MITK

Feb 12 2021

nolden added a comment to T28302: MITK CI jobs for Kaapana.

Following this, are there some requirements that need to be specified here T28280?

Feb 12 2021, 12:02 PM · CI, MITK

Feb 10 2021

nolden added a comment to T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.

I tried running the Workbench on Linux both with valgrind as well as AdressSanitizer. Unfortunately there is a lot of noise from memory leaks and stuff, but I did not spot anything obvious which could be the cause.

Feb 10 2021, 10:47 AM · MITK

Feb 9 2021

nolden added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

I did not dive into Windows APIs, so I just hope you know what you are doing ;)

Feb 9 2021, 12:27 PM · Next Milestone, MITK
nolden added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

I did some Googling, it seems that starting with 2019 release, Windows 10 has a UTF8 mode. It's a bit difficult to enable: "old" control panel -> region -> Administrative settings -> Change System locale -> Enable UTF8

Feb 9 2021, 11:34 AM · Next Milestone, MITK
nolden added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

That's a thorough dive in the topic ... Yes, toUtf8(), and nicely prints the correct Umlaut in the message box, telling you the file doesn't exist ;) I only had a quick glance around, and since a lot of stuff goes though ITK, and ITK decided to stay with local 8bit as far as I understand, I also think this would be the way to go. But I could really live with declaring this a "Known issue". Maybe something on the application user level would be nice, like

if toUtf8 != toLocal8Bit then show error
Feb 9 2021, 10:02 AM · Next Milestone, MITK

Feb 8 2021

nolden added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Ok, the GDCM unicode windows fix was introduced in the 3.0 series: https://github.com/malaterre/GDCM/commit/d4dfa144b941c6cc4da87f9795f7f5aba2bb7481

Feb 8 2021, 7:28 PM · Next Milestone, MITK
nolden added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Ok, I did look around a bit more. To summarize, I guess going for the "local 8bit representation" seems to be the most feasible way, since ITK also assumes this and I think we have a lot of ITK file handling code.

Feb 8 2021, 7:17 PM · Next Milestone, MITK
nolden added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Ok, I debugged to SetFileName @floca mentioned, it gets called from GDCMImageIO::InternalReadImageInformation in ITK

Feb 8 2021, 6:59 PM · Next Milestone, MITK
nolden added a comment to T24402: Improve clang-format support.

Mostly as a reminder I tried on top of the branch above:

Feb 8 2021, 5:46 PM · MITK
nolden added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Oh no, I can remember similar issues with German Ubuntu and "Arbeitsfläche" ... Basically, CI clients should probably always have a path compontent like /bäh / included to catch new issues like this one, and build system stuff, which is also a candidate.

Feb 8 2021, 3:00 PM · Next Milestone, MITK

Feb 5 2021

nolden added a comment to T28283: Support building with Qt 5.15 .

I don't know why this was not linked automatically: https://phabricator.mitk.org/D469

Feb 5 2021, 3:50 PM · MITK (v2021.02)
nolden added a comment to T28283: Support building with Qt 5.15 .

I was hoping a bit to include it in the release, if the release would e.g. be used for kaapana containers for a longer time this could be helpful at some point. But of course it's not strictly necessary.

Feb 5 2021, 3:49 PM · MITK (v2021.02)
nolden added a comment to T28282: Workbench does not start when building with Qt 5.15 on Linux.

Valgrind shows some reading beyond memory boundaries, around mitkCoreActivator.cpp:129 and 218. Since it is the last line of all the AddPropertyPersistence calls there and all the creating of temp objects in there, I was wondering if it could be some reference to deleted temp objects issues. Just an idea.

Feb 5 2021, 3:31 PM · MITK
nolden added a comment to T28282: Workbench does not start when building with Qt 5.15 on Linux.

It's the CoreActivator if I read this correcty:

Feb 5 2021, 2:59 PM · MITK
nolden created T28283: Support building with Qt 5.15 .
Feb 5 2021, 2:14 PM · MITK (v2021.02)
nolden added a comment to T28282: Workbench does not start when building with Qt 5.15 on Linux.

And I just tested: as expected the unit tests do pass, I think it has to be a side effect of dlopen'ing the activator

Feb 5 2021, 2:13 PM · MITK
nolden updated subscribers of T28282: Workbench does not start when building with Qt 5.15 on Linux.

@floca the comment I mention was written by you, line 112, any spontaneous idea?

Feb 5 2021, 2:11 PM · MITK
nolden created T28282: Workbench does not start when building with Qt 5.15 on Linux.
Feb 5 2021, 2:05 PM · MITK
nolden added a comment to T28281: Review C++ warnings configuration.

In addition, suppressing deprecation warnings is in most cases no solution that lasts forever

Feb 5 2021, 2:00 PM · Request for Discussion, MITK
nolden created T28281: Review C++ warnings configuration.
Feb 5 2021, 1:59 PM · Request for Discussion, MITK
nolden created T28279: Improve image cropper cross hair interaction .
Feb 5 2021, 10:51 AM · MITK
nolden triaged T28278: Image cropper doesn't work with PACS like mouse interaction as Low priority.
Feb 5 2021, 10:46 AM · Next Milestone, MITK
nolden triaged T28277: Empty Preferences page "Input Devices" as Low priority.
Feb 5 2021, 10:38 AM · MITK

Feb 1 2021

nolden added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

Who should I assign as reviewer for this?

Feb 1 2021, 5:31 PM · MITK

Jan 27 2021

nolden renamed T28206: Renaming segmentation or planar figure based ROI nodes breaks histogram from Renaming segmentation or planar figure based ROI nodes break histogram to Renaming segmentation or planar figure based ROI nodes breaks histogram.
Jan 27 2021, 10:50 AM · MITK, Next Milestone
nolden triaged T28206: Renaming segmentation or planar figure based ROI nodes breaks histogram as Unbreak Now! priority.
Jan 27 2021, 10:50 AM · MITK, Next Milestone
nolden added a comment to T27578: 2021.1 Linux installer does not work on Fedora.

Additional comment: the missing library doesn't prevent the Workbench from starting, but some/all DICOM functionality is missing which can be confusing

Jan 27 2021, 9:22 AM · MITK (v2021.10)
nolden raised the priority of T27578: 2021.1 Linux installer does not work on Fedora from High to Unbreak Now!.
Jan 27 2021, 9:18 AM · MITK (v2021.10)
nolden added a comment to T27578: 2021.1 Linux installer does not work on Fedora.

Ok, I just re-checked: Ubuntu 20.04 still has librwrap installed , so installer works. For Fedora there is no workaround , so either

Jan 27 2021, 9:18 AM · MITK (v2021.10)
nolden renamed T27578: 2021.1 Linux installer does not work on Fedora from Make sure libwrap isn't linked anymore to 2021.1 Linux installer does not work on Fedora.
Jan 27 2021, 9:18 AM · MITK (v2021.10)
nolden added a parent task for T27578: 2021.1 Linux installer does not work on Fedora: T28000: MITK v2021.02.
Jan 27 2021, 9:00 AM · MITK (v2021.10)
nolden added a subtask for T28000: MITK v2021.02: T27578: 2021.1 Linux installer does not work on Fedora.
Jan 27 2021, 9:00 AM · MITK-ProjectTemplate, MITK (v2021.02)

Jan 25 2021

nolden committed rMITKe02f5dfbc3b2: Summary: Applied some C++ style fixes (authored by nolden).
Summary: Applied some C++ style fixes
Jan 25 2021, 4:14 PM
nolden committed rMITK9fea04d2ed70: Applied some automated const FixIts to range-based loops (authored by nolden).
Applied some automated const FixIts to range-based loops
Jan 25 2021, 4:14 PM
nolden committed rMITK265001cf6a94: Added assignment operator to mitk::Vector (authored by nolden).
Added assignment operator to mitk::Vector
Jan 25 2021, 4:14 PM

Jan 21 2021

nolden renamed T28159: Officially support MITK using system Qt from Oficially support MITK using system Qt to Officially support MITK using system Qt.
Jan 21 2021, 9:41 AM · CI, Kaapana (internal), Request for Discussion, MITK
nolden added a comment to T28159: Officially support MITK using system Qt.

@kislinsk anyone from the MITK CI team who could take over?

Jan 21 2021, 9:38 AM · CI, Kaapana (internal), Request for Discussion, MITK

Jan 19 2021

nolden added a comment to T28039: DICOM Seg loading error.

Changes have landed . @neher could you test again using a nightly build?

Jan 19 2021, 3:25 PM · MITK (v2021.10)
nolden committed rMITK15ecdf8d92aa: Update DCMQI to v1.2.3 (authored by nolden).
Update DCMQI to v1.2.3
Jan 19 2021, 2:54 PM
nolden committed rMITKad45666d2a3f: Update DCMQI to v1.2.3 (authored by nolden).
Update DCMQI to v1.2.3
Jan 19 2021, 2:54 PM
nolden claimed T28039: DICOM Seg loading error.
Jan 19 2021, 10:44 AM · MITK (v2021.10)
nolden added a comment to T28039: DICOM Seg loading error.

Just submitted a Differential

Jan 19 2021, 10:23 AM · MITK (v2021.10)
nolden triaged T28174: Fix minor C++ style issues as Normal priority.
Jan 19 2021, 10:05 AM · MITK

Jan 15 2021

nolden added a comment to T28159: Officially support MITK using system Qt.

Thank. New command-line interface looks nice, but the challenge is where to put the credentials, especially if you want to put the script open source like in the Kaapana dockerfiles.

Jan 15 2021, 12:14 PM · CI, Kaapana (internal), Request for Discussion, MITK

Jan 14 2021

nolden added a project to T28159: Officially support MITK using system Qt: CI.
Jan 14 2021, 3:51 PM · CI, Kaapana (internal), Request for Discussion, MITK
nolden updated the task description for T28159: Officially support MITK using system Qt.
Jan 14 2021, 3:50 PM · CI, Kaapana (internal), Request for Discussion, MITK
nolden created T28159: Officially support MITK using system Qt.
Jan 14 2021, 3:46 PM · CI, Kaapana (internal), Request for Discussion, MITK

Dec 2 2020

nolden added a comment to T28039: DICOM Seg loading error.

I contacted dcmqi upstream, thanks @fedorov for the quick reply.

Dec 2 2020, 4:16 PM · MITK (v2021.10)
nolden updated subscribers of T28039: DICOM Seg loading error.

@kast @weihs do you assume it's the same problem you have with your data? Could you share your DICOM seg?

Dec 2 2020, 1:19 PM · MITK (v2021.10)
nolden added a comment to T28049: DataUpload fails with Firefox.

PS: Chrome upload works but data doesn't show up in meta

Dec 2 2020, 1:07 PM · Kaapana (internal)
nolden created T28049: DataUpload fails with Firefox.
Dec 2 2020, 1:00 PM · Kaapana (internal)

Nov 30 2020

nolden added a comment to T28039: DICOM Seg loading error.

I tested with the latest develop:

WARNING: SliceThickness is present and is 1. using it!
ERROR: JSON parameter file could not be parsed!
You can validate the JSON file here: http://qiicr.org/dcmqi/#/validators
Exception details (probably not very useful): LargestUInt out of Int range
#11.518# ERROR: An error occurred while reading the DICOM Seg file: JSON Exception: file could not be read.
#11.520# ERROR: Unknown read error occurred reading /home/nolden/Downloads/Lungs_seg_Left lung_1.dcm
Nov 30 2020, 2:07 PM · MITK (v2021.10)

Nov 27 2020

nolden committed rMITK6eaeaca7975f: Fix uninitialized reference warning/error (authored by nolden).
Fix uninitialized reference warning/error
Nov 27 2020, 9:21 AM
nolden committed rMITK857976ed83c8: Fix uninitialized reference warning/error (authored by nolden).
Fix uninitialized reference warning/error
Nov 27 2020, 9:20 AM

Nov 26 2020

nolden added a comment to T28006: MatchPointRegistration module compilation fails with Clang 11.

https://phabricator.mitk.org/D443

Nov 26 2020, 4:20 PM · MITK
nolden added a comment to T28006: MatchPointRegistration module compilation fails with Clang 11.

I can confirm this fixes the issue, I can merge it tomorrow

Nov 26 2020, 4:18 PM · MITK

Nov 24 2020

nolden created T28006: MatchPointRegistration module compilation fails with Clang 11.
Nov 24 2020, 9:25 AM · MITK

Nov 23 2020

nolden committed rMITKff0027eee2cb: Patch VTK to fix Freetype build error on GCC 10 (authored by nolden).
Patch VTK to fix Freetype build error on GCC 10
Nov 23 2020, 5:39 PM
nolden committed rMITK3ee32df042fb: Patch VTK to fix Freetype build error on GCC 10 (authored by nolden).
Patch VTK to fix Freetype build error on GCC 10
Nov 23 2020, 5:38 PM
nolden triaged T27995: Upgrade CDash to 3.0 as Wishlist priority.
Nov 23 2020, 2:04 PM · CI, MITK
nolden added a comment to T27959: MITK with VTK 9 fails on Fedora CI clients.

I can confirm this patches fixes the problem. @kislinsk : hotfix oder feature branch?

Nov 23 2020, 1:49 PM · MITK
nolden added a comment to T27959: MITK with VTK 9 fails on Fedora CI clients.
diff --git a/Rendering/FreeType/vtkFreeTypeTools.cxx b/Rendering/FreeType/vtkFreeTypeTools.cxx
index c54289dc60..03b899c4da 100644
--- a/Rendering/FreeType/vtkFreeTypeTools.cxx
+++ b/Rendering/FreeType/vtkFreeTypeTools.cxx
@@ -378,8 +378,7 @@ FTC_CMapCache* vtkFreeTypeTools::GetCMapCache()
 }
Nov 23 2020, 1:34 PM · MITK

Nov 17 2020

nolden created T27968: CTP gets stuck on large import.
Nov 17 2020, 3:50 PM · Kaapana (internal)

Oct 20 2020

nolden added a comment to T27902: Handle slashes in installer names.

Ups ;) Replace with - or _?

Oct 20 2020, 2:10 PM · MITK (v2021.02)

Oct 19 2020

nolden added a comment to T27894: Linux nightly installer doesn't start on Fedora.

I was just about to add a note that there is the general question how to handle python in installers. I guess for just having the basic runtime available it would be ok to just load libpython3.so or libpython3.8.so and let the system take the right one from the right path. But on Windows I guess most people don't install Python in system locations. Anyway I think this could be fixed even with the current packaging if we need it for 2020, but I'm just reporting, no pressure from my side ;)

Oct 19 2020, 1:25 PM · MITK (v2021.02)
nolden edited projects for T27894: Linux nightly installer doesn't start on Fedora, added: MITK (v2021.02); removed MITK.
Oct 19 2020, 1:08 PM · MITK (v2021.02)
nolden created T27894: Linux nightly installer doesn't start on Fedora.
Oct 19 2020, 1:07 PM · MITK (v2021.02)

Oct 15 2020

nolden added a comment to T27887: Make package fails when using system Qt packages on Ubuntu 20.04.

Pushed new branch hotfix/T27887-fix-packaging-with-system-qt.

Oct 15 2020, 4:14 PM · MITK
nolden triaged T27887: Make package fails when using system Qt packages on Ubuntu 20.04 as Unbreak Now! priority.
Oct 15 2020, 3:58 PM · MITK

Oct 9 2020

nolden added a comment to T27383: Update external toolkits.

OpenCV 3.4.11 (https://opencv.org/releases/)

Oct 9 2020, 11:55 AM · Noteworthy, MITK (v2021.02)
nolden added a comment to T27383: Update external toolkits.

Trivial should be:

Oct 9 2020, 11:54 AM · Noteworthy, MITK (v2021.02)
nolden added a comment to T27669: Dicom import issue with MITK binaries (package) and Ubuntu.

PS: as an explanation, one theory is that the install-zip-package still references libraries from the build machine which causes the different behaviour

Oct 9 2020, 11:34 AM · Missing Info, DICOM, MITK
nolden added a comment to T27669: Dicom import issue with MITK binaries (package) and Ubuntu.

@nolden I tried the "make package" and it went through without any issues.
Should I upload the result here? Or is it just about the information that there are no error?
Could you please explain what you mean with "target machine"?

Oct 9 2020, 11:33 AM · Missing Info, DICOM, MITK

Sep 25 2020

nolden added a comment to T27669: Dicom import issue with MITK binaries (package) and Ubuntu.

@schererj we looked at the debug output, thanks. Unfortunately it seems to be complicated ... I would ask you to try another thing:

Sep 25 2020, 12:09 PM · Missing Info, DICOM, MITK