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Feb 10 2021

kislinsk removed a subtask for T28000: MITK v2021.02: T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.
Feb 10 2021, 11:24 AM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk removed a parent task for T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS: T28000: MITK v2021.02.
Feb 10 2021, 11:24 AM · Auto-closed, MITK
kislinsk removed a project from T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS: MITK-ProjectTemplate.
Feb 10 2021, 11:24 AM · Auto-closed, MITK
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 · Auto-closed, MITK
kislinsk updated the task description for T28000: MITK v2021.02.
Feb 10 2021, 12:44 AM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk updated the task description for T28000: MITK v2021.02.
Feb 10 2021, 12:43 AM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28284: Render window menus not visible on macOS, a subtask of T28000: MITK v2021.02, as Resolved.
Feb 10 2021, 12:41 AM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28284: Render window menus not visible on macOS as Resolved.
Feb 10 2021, 12:41 AM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T28284: Render window menus not visible on macOS.

Deleted branch from rMITK MITK: bugfix/T28284-FixRenderWindowMenuVisibility.

Feb 10 2021, 12:40 AM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T28284: Render window menus not visible on macOS.

It was an alternative code path for handling render window menu visibility on macOS that is no longer needed, resp. now even broke the visibility handling. Now all supported platforms use the same code path and to make it work in the first place without any workarounds, a few adjustmens/simplifications were necessary. The visibility status is no longer coupled to the mouse move event, which was ill-formed from the beginning and resulted in trouble on different platforms like flickering on Linux. The visibility state is now way more effectively coupled to the enter and leave events of the render windows. There's also an immediate reaction now on resize events.

Feb 10 2021, 12:39 AM · Noteworthy, MITK (v2021.02)

Feb 9 2021

kislinsk added a project to T28284: Render window menus not visible on macOS: Noteworthy.
Feb 9 2021, 10:52 PM · Noteworthy, MITK (v2021.02)
kislinsk added a comment to T28284: Render window menus not visible on macOS.

Pushed new branch to rMITK MITK: bugfix/T28284-FixRenderWindowMenuVisibility.

Feb 9 2021, 10:51 PM · Noteworthy, MITK (v2021.02)
kislinsk updated the task description for T28000: MITK v2021.02.
Feb 9 2021, 7:47 PM · MITK-ProjectTemplate, MITK (v2021.02)
a178n added a comment to T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.

Closing an empty workbench or loaded workbench using X button on the title bar causes this.

Feb 9 2021, 7:00 PM · Auto-closed, MITK
floca created an object: Code Guarantees.
Feb 9 2021, 6:47 PM
floca added a comment to T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.

What views were opened or data loaded? Or was it an empty workbench?

Feb 9 2021, 5:48 PM · Auto-closed, MITK
a178n added a comment to T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.

Attaching full stacktrace herewith:

Feb 9 2021, 4:56 PM · Auto-closed, MITK
a178n updated the task description for T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.
Feb 9 2021, 4:55 PM · Auto-closed, MITK
a178n triaged T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS as Normal priority.
Feb 9 2021, 4:51 PM · Auto-closed, MITK
floca updated the task description for T28000: MITK v2021.02.
Feb 9 2021, 3:56 PM · MITK-ProjectTemplate, MITK (v2021.02)
kleina updated kleina.
Feb 9 2021, 1:52 PM
kislinsk updated the task description for T28000: MITK v2021.02.
Feb 9 2021, 1:33 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28127: Reopen segmentation in MITK as Resolved.

The fix was merged upstream and this task will be resolved with the merge of the current release branch this week.

Feb 9 2021, 1:30 PM · MITK (v2021.02), Restricted Project, Kaapana (internal)
kislinsk updated the task description for T28000: MITK v2021.02.
Feb 9 2021, 1:01 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Deleted branch from rMITK MITK: bugfix/T28285-Local8BitToUtf8.

Feb 9 2021, 12:53 PM · Checklist, MITK (v2022.10)
kislinsk removed a parent task for T28285: DICOM with 'ä' in filename not readable on Windows: T28000: MITK v2021.02.
Feb 9 2021, 12:51 PM · Checklist, MITK (v2022.10)
kislinsk removed a subtask for T28000: MITK v2021.02: T28285: DICOM with 'ä' in filename not readable on Windows.
Feb 9 2021, 12:51 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk lowered the priority of T28285: DICOM with 'ä' in filename not readable on Windows from Unbreak Now! to Normal.
Feb 9 2021, 12:51 PM · Checklist, MITK (v2022.10)
kislinsk placed T28285: DICOM with 'ä' in filename not readable on Windows up for grabs.

Dear future assignee of this task,

Feb 9 2021, 12:49 PM · Checklist, MITK (v2022.10)
kislinsk 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 ;)

The test looks reasonable and passes also on Linux.

One improvement could be to output the string (and maybe the hex version) in the WARNING output if the conversion fails.

And did you look into boost? There is also some conversion stuff

Feb 9 2021, 12:39 PM · Checklist, MITK (v2022.10)
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 · Checklist, MITK (v2022.10)
kislinsk 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

After checking this box, MITK loads the data without code changes, but DataNode name is just a single slash "/" ... ;)

Feb 9 2021, 11:51 AM · Checklist, MITK (v2022.10)
kislinsk added a revision to T28285: DICOM with 'ä' in filename not readable on Windows: Unknown Object (Differential Revision).
Feb 9 2021, 11:43 AM · Checklist, MITK (v2022.10)
floca committed rRTTB81858ad9609d: Changed the referencing of dependencies to target (authored by floca).
Changed the referencing of dependencies to target
Feb 9 2021, 11:36 AM
kislinsk added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Pushed new branch to rMITK MITK: bugfix/T28285-Local8BitToUtf8.

Feb 9 2021, 11:35 AM · Checklist, MITK (v2022.10)
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 · Checklist, MITK (v2022.10)
kleina added a member for MIC: j038k.
Feb 9 2021, 11:16 AM
kleina added a member for Deep Learning: j038k.
Feb 9 2021, 11:15 AM
kislinsk committed rMDef499f5897d7: Add image file with German Umlaut in filename (authored by kislinsk).
Add image file with German Umlaut in filename
Feb 9 2021, 10:55 AM
floca added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Hi you both, thanks for the digging.
I also tend too follow @nolden propsal 1) declaring it a kown issue and 2) returning a meaningfull error message, of invalid characters are used.

Feb 9 2021, 10:44 AM · Checklist, MITK (v2022.10)
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 · Checklist, MITK (v2022.10)
kislinsk claimed T28285: DICOM with 'ä' in filename not readable on Windows.
Feb 9 2021, 2:10 AM · Checklist, MITK (v2022.10)
kislinsk added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Uh, maybe I made it more dramatic than it is. We can also do the complete opposite and stay with toLocal8Bit(). That means, that we only need conversion when writing the path and name into the properties. I wrote a Local8BitToUtf8() function and it works in a first test. We can also use it to pass an UTF-8 string to the GDCM reader. Didn't check for all code locations where to do it but its late already and tomorrow is another day. :-)

Feb 9 2021, 2:09 AM · Checklist, MITK (v2022.10)

Feb 8 2021

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

I also looked into this and one of the problems/differences to "back in the days" is that Qt nowadays assumes by default that C-strings in the constructor of QString are UTF-8 encoded. So, for example, Marco, if you change toLocal8Bit() in QmitkIOUtil to toUtf8(), you get working strings in the GUI (can be easily tested with a MessageBox::information()), but invalid strings for most of the readers, as they assume the local codepage. So we can have one or the other, but not both at the moment. The thing is that QmitkIOUtil works with QString, but mitk::IOUtil uses std::string in the structure that holds the file path (LoadInfo). This is then later used to be stuffed into StringProperty for the name property or the path property. Qt of course assumes these strings to be UTF-8 and hence we see the ?'s in the GUI.

Feb 8 2021, 11:52 PM · Checklist, MITK (v2022.10)
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 · Checklist, MITK (v2022.10)
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 · Checklist, MITK (v2022.10)
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 · Checklist, MITK (v2022.10)
floca added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

This is a problem that becomes visible in gdcm and it is not the first time that we encouter it.
Currently the gdcm reader fails to open the file. I assume it is correlated with gdcm changes of how to handle filenames under windows in gdcm (gdcmReader.cxx 836ff)

void Reader::SetFileName(const char *uft8path)

Here some conversion between utf8 and utf16 was introduced and this string:

"C:/Users/floca/Downloads/sämple.IMA"

is changed to:

L"C:/Users/floca/Downloads/s�mple.IMA"

and for the later string the loading fails.

Feb 8 2021, 6:04 PM · Checklist, MITK (v2022.10)
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
schererj added a project to T27968: CTP gets stuck on large import: Request for Discussion.
Feb 8 2021, 4:55 PM · Kaapana (internal)
schererj moved T27968: CTP gets stuck on large import from Backlog to Discussion on the Kaapana (internal) board.
Feb 8 2021, 4:54 PM · Kaapana (internal)
schererj moved T28232: Shapemodels from Backlog to Discussion on the Kaapana (internal) board.
Feb 8 2021, 4:37 PM · Auto-closed, Kaapana (internal), Request for Discussion, 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 · Checklist, MITK (v2022.10)
kislinsk added a comment to T28285: DICOM with 'ä' in filename not readable on Windows.

Additional info: This is not a DICOM reader problem in the first place, as the filename string encoding seems to be unexpected (see screenshot above). Other readers work but the node still appears with a dummy symbol in the data node name.

Feb 8 2021, 2:32 PM · Checklist, MITK (v2022.10)
kislinsk triaged T28285: DICOM with 'ä' in filename not readable on Windows as Unbreak Now! priority.
Feb 8 2021, 2:30 PM · Checklist, MITK (v2022.10)
kislinsk added a subtask for T28000: MITK v2021.02: T28285: DICOM with 'ä' in filename not readable on Windows.
Feb 8 2021, 2:30 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk added a parent task for T28285: DICOM with 'ä' in filename not readable on Windows: T28000: MITK v2021.02.
Feb 8 2021, 2:30 PM · Checklist, MITK (v2022.10)
kislinsk updated the task description for T28285: DICOM with 'ä' in filename not readable on Windows.
Feb 8 2021, 2:30 PM · Checklist, MITK (v2022.10)
kislinsk renamed T28285: DICOM with 'ä' in filename not readable on Windows from DICOM not readable to DICOM with 'ä' in filename not readable on Windows.
Feb 8 2021, 2:28 PM · Checklist, MITK (v2022.10)
neher created T28285: DICOM with 'ä' in filename not readable on Windows.
Feb 8 2021, 2:06 PM · Checklist, MITK (v2022.10)
j038k updated j038k.
Feb 8 2021, 12:53 PM
kislinsk triaged T28284: Render window menus not visible on macOS as Unbreak Now! priority.
Feb 8 2021, 7:43 AM · Noteworthy, MITK (v2021.02)

Feb 7 2021

floca updated the task description for T28000: MITK v2021.02.
Feb 7 2021, 3:20 PM · MITK-ProjectTemplate, MITK (v2021.02)
floca added a comment to T28248: [Segmentation] Picking 3D Tool creates a 3D segmentation out of a 4D image.

Deactivated for 4D images as a work arround fix for the release. Will be removed if this tool is properly refactored.

Feb 7 2021, 3:14 PM · MITK (v2021.10)

Feb 5 2021

floca 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.

I can understand the reasoning. But adding this feature last minute would basically mean to move the release again and also to test again. And we should realy try to get into the time based pattern.

Feb 5 2021, 6:02 PM · MITK (v2021.02)
floca 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, 5:51 PM · MITK (v2021.02)
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
floca added a comment to T28282: Workbench does not start when building with Qt 5.15 on Linux.

If this is caused in UseRegEx() then its preconditions are not meet anymore. Meaning that for whatever reasons the RegEx strings are not valid any more when using Qt 5.15. I would also guess that something in the intialization behavior changes and therfore some string constants are not initialized when used.
Which activator causes this?

Feb 5 2021, 2:51 PM · MITK
floca edited projects for T28283: Support building with Qt 5.15 , added: MITK, Next Milestone; removed MITK (v2021.02).
Feb 5 2021, 2:42 PM · MITK (v2021.02)
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 · Auto-closed, Request for Discussion, MITK
nolden created T28281: Review C++ warnings configuration.
Feb 5 2021, 1:59 PM · Auto-closed, Request for Discussion, MITK
kalali placed T28265: [Checklist] Overhaul ViewNavigator checklists to be in line with the latest changes to the checklists up for grabs.
Feb 5 2021, 11:40 AM · MITK (v2022.04)
kalali placed T26485: [Segmentation] PACS mode is active while segmentation is drawn up for grabs.
Feb 5 2021, 11:39 AM · MITK (v2021.10)
kalali placed T25056: Refactor data manager context menu up for grabs.
Feb 5 2021, 11:14 AM · MITK (v2024.06), Noteworthy
kalali placed T25643: Context menu adds its default actions multiple times up for grabs.
Feb 5 2021, 11:14 AM · MITK (v2022.10)
nolden created T28279: [Interaction] Improve image cropper cross hair interaction.
Feb 5 2021, 10:51 AM · Auto-closed, 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 4 2021

kislinsk updated the task description for T28000: MITK v2021.02.
Feb 4 2021, 11:43 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28271: Segmentation interpolation does not work in dynamic images with t != 0 as Resolved.
Feb 4 2021, 11:40 PM · MITK (v2021.02)
kislinsk closed T28271: Segmentation interpolation does not work in dynamic images with t != 0, a subtask of T28000: MITK v2021.02, as Resolved.
Feb 4 2021, 11:40 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk added a comment to T28271: Segmentation interpolation does not work in dynamic images with t != 0.

Deleted branch from rMITK MITK: bugfix/T28271-3DInterpolation.

Feb 4 2021, 11:33 PM · MITK (v2021.02)
floca updated the task description for T28000: MITK v2021.02.
Feb 4 2021, 10:36 PM · MITK-ProjectTemplate, MITK (v2021.02)
floca removed a subtask for T28000: MITK v2021.02: T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep.
Feb 4 2021, 10:34 PM · MITK-ProjectTemplate, MITK (v2021.02)
floca removed a parent task for T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep: T28000: MITK v2021.02.
Feb 4 2021, 10:34 PM · MITK (v2024.06)
floca renamed T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep from [Segmentation] 4D Segmentation returns error message when point is not on the correct timestep to [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep.
Feb 4 2021, 10:34 PM · MITK (v2024.06)
floca edited projects for T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep, added: MITK, Next Milestone; removed MITK (v2021.02).

The tool is a mess. Overhaul for this is not realistic. I deactivate the tool for dynamic images as a quick fix. I will reactivate it after rework.

Feb 4 2021, 10:33 PM · MITK (v2024.06)
kislinsk added a comment to T28271: Segmentation interpolation does not work in dynamic images with t != 0.

Diving into it, it turned out to be not that hard to fix as it was just the combination of two "bugs/missing features" that appeared to be so chaotic without knowing the interference of both issues.

Feb 4 2021, 9:43 PM · MITK (v2021.02)
floca claimed T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep.
Feb 4 2021, 8:01 PM · MITK (v2024.06)
floca added a comment to T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep.

Oh fudge.... I totally have overlooked the tool. 😱

Feb 4 2021, 8:00 PM · MITK (v2024.06)
kislinsk added a comment to T28271: Segmentation interpolation does not work in dynamic images with t != 0.

Pushed new branch to rMITK MITK: bugfix/T28271-3DInterpolation.

Feb 4 2021, 5:46 PM · MITK (v2021.02)
thomass added a comment to T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep.

Probably it would just help to replace the MITK Error by a warning? This is also done when there is no point set at all.

Feb 4 2021, 2:50 PM · MITK (v2024.06)
thomass added a parent task for T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep: T28000: MITK v2021.02.
Feb 4 2021, 2:48 PM · MITK (v2024.06)