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Feb 10 2021

kislinsk committed rMITK782e6a4d67e0: Improve build instructions (authored by kislinsk).
Improve build instructions
Feb 10 2021, 5:50 PM
kislinsk committed rMITK6370a9e9704e: Fix expected return type of watcher (authored by kislinsk).
Fix expected return type of watcher
Feb 10 2021, 5:50 PM
kislinsk committed rMITK4c3d4bcc9e54: Fix patching of DCMQI (authored by kislinsk).
Fix patching of DCMQI
Feb 10 2021, 5:50 PM
kislinsk committed rMITK0eea8feeb92c: Restore precision for geometry checks (authored by kislinsk).
Restore precision for geometry checks
Feb 10 2021, 5:50 PM
kislinsk committed rMITK77e63fe6e91a: Fix maximum number of characters in DCMQI's float serialization (authored by kislinsk).
Fix maximum number of characters in DCMQI's float serialization
Feb 10 2021, 5:50 PM
kislinsk committed rMITK45822d9bfb65: Fixed illegal reference to stack variable. (authored by floca).
Fixed illegal reference to stack variable.
Feb 10 2021, 5:50 PM
kislinsk committed rMITK62e5ec2d57f4: Use more strict epsilon on test data (authored by kislinsk).
Use more strict epsilon on test data
Feb 10 2021, 5:50 PM
kislinsk committed rMITKeadaa9900c20: Workarround fix for T27883 (authored by floca).
Workarround fix for T27883
Feb 10 2021, 5:50 PM
kislinsk committed rMITK6c89209c215f: Fixed review remarks (authored by floca).
Fixed review remarks
Feb 10 2021, 5:50 PM
kislinsk committed rMITKbc6fb90c633b: Clean up QmitkSlicesInterpolator::OnAccept3DInterpolationClicked() method (authored by kislinsk).
Clean up QmitkSlicesInterpolator::OnAccept3DInterpolationClicked() method
Feb 10 2021, 5:50 PM
kislinsk committed rMITK92794eb7895e: Make interpolated surfaces permanent (authored by kislinsk).
Make interpolated surfaces permanent
Feb 10 2021, 5:50 PM
kislinsk committed rMITK350fd80f4c19: Match number of time steps between segmentation and surface (authored by kislinsk).
Match number of time steps between segmentation and surface
Feb 10 2021, 5:49 PM
kislinsk committed rMITK85bb97375921: Include originating time step in interpolation data node. (authored by kislinsk).
Include originating time step in interpolation data node.
Feb 10 2021, 5:49 PM
kislinsk committed rMITKbc1da1092959: Match time bounds of interpolated surface with current segmentation time step (authored by kislinsk).
Match time bounds of interpolated surface with current segmentation time step
Feb 10 2021, 5:49 PM
kislinsk committed rMITK94f10fcc4792: Fix time geometry of interpolation feedback (authored by kislinsk).
Fix time geometry of interpolation feedback
Feb 10 2021, 5:49 PM
kislinsk committed rMITK84108aef89c0: Fix time geometry of contours surface (authored by kislinsk).
Fix time geometry of contours surface
Feb 10 2021, 5:49 PM
kislinsk committed rMITK71f9ffdc4ef9: Only show current time step in 2-d surface mapper (authored by kislinsk).
Only show current time step in 2-d surface mapper
Feb 10 2021, 5:49 PM
kislinsk committed rMITKfbcde9df00f2: Only show current time step in 3-d surface mapper (authored by kislinsk).
Only show current time step in 3-d surface mapper
Feb 10 2021, 5:49 PM
kislinsk committed rMITK3c263d7d6a5e: Release quickfix for T28275 (authored by floca).
Release quickfix for T28275
Feb 10 2021, 5:49 PM
kislinsk committed rMITK3b3045b97a87: Deactivated PickingTool for 4D images as a workarround fix for T28248 (authored by floca).
Deactivated PickingTool for 4D images as a workarround fix for T28248
Feb 10 2021, 5:49 PM
kislinsk committed rMITK996758edd9ba: Utilize properties to serialize time-related information for surfaces in MITK… (authored by kislinsk).
Utilize properties to serialize time-related information for surfaces in MITK…
Feb 10 2021, 5:49 PM
kislinsk committed rMITKef7786295fcd: Apply CTEST_BUILD_CONFIGURATION on Unix (authored by kislinsk).
Apply CTEST_BUILD_CONFIGURATION on Unix
Feb 10 2021, 5:49 PM
kislinsk committed rMITK039c4de01e27: Add methods for UTF-8 string conversion (authored by kislinsk).
Add methods for UTF-8 string conversion
Feb 10 2021, 5:49 PM
kislinsk committed rMITK0a46580499e7: Add test for UTF-8 string conversion (authored by kislinsk).
Add test for UTF-8 string conversion
Feb 10 2021, 5:49 PM
kislinsk committed rMITK1e80947ab662: Explicitly encode path, name, and MITK.IO.reader.inputlocation string… (authored by kislinsk).
Explicitly encode path, name, and MITK.IO.reader.inputlocation string…
Feb 10 2021, 5:49 PM
kislinsk committed rMITK15febaa0b465: Necessary warning suppressions for compiling MITK using Qt 5.15 (authored by nolden).
Necessary warning suppressions for compiling MITK using Qt 5.15
Feb 10 2021, 5:49 PM
kislinsk committed rMITK4f70ab9c4b4c: Switch back to official repository that includes the necessary fixes now (authored by kislinsk).
Switch back to official repository that includes the necessary fixes now
Feb 10 2021, 5:49 PM
kislinsk committed rMITK35b2dcdda02d: Remove all workarounds to handle render window menu visibility differently on… (authored by kislinsk).
Remove all workarounds to handle render window menu visibility differently on…
Feb 10 2021, 5:49 PM
kislinsk committed rMITKd9909f042f4a: Adapt to recent render window menu simplifications (authored by kislinsk).
Adapt to recent render window menu simplifications
Feb 10 2021, 5:49 PM
kislinsk committed rMITK2dfcbae6fee7: Remove volume rendering preference for multi-label segmentations (authored by kislinsk).
Remove volume rendering preference for multi-label segmentations
Feb 10 2021, 5:49 PM
kislinsk committed rMITK9b2f2d02ba44: Always react on changed preferences (authored by kislinsk).
Always react on changed preferences
Feb 10 2021, 5:49 PM
kislinsk committed rMITK8b3121fe3a76: Remove volume rendering preference for segmentations (authored by kislinsk).
Remove volume rendering preference for segmentations
Feb 10 2021, 5:49 PM
kislinsk committed rMITKb15e0ee6e757: Fix tooltip for auto-selection mode (authored by kislinsk).
Fix tooltip for auto-selection mode
Feb 10 2021, 5:49 PM
kislinsk committed rMITK885c1e2de487: Lower precision for rotation matrix check (authored by kislinsk).
Lower precision for rotation matrix check
Feb 10 2021, 5:49 PM
kislinsk committed rMITK9d72c939e513: 2021 Week 06 (Early February) (authored by kislinsk).
2021 Week 06 (Early February)
Feb 10 2021, 5:49 PM
kislinsk published a new version of 2021 Week 06 (Early February).
Feb 10 2021, 5:42 PM
kislinsk added a comment to T28000: MITK v2021.02.

Deleted branch from rMITK MITK: release/T28000-v2021.01.

Feb 10 2021, 4:21 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk added a comment to T28000: MITK v2021.02.

Pushed new branch to rMITK MITK: release/T28000-2021-Week-06.

Feb 10 2021, 4:19 PM · MITK-ProjectTemplate, MITK (v2021.02)
floca moved T28262: TimeGeometry inconsistent documentation and implementation of time bounds and checks from Backlog to MITK Meeting on the Request for Discussion board.
Feb 10 2021, 4:14 PM · Moved to git.dkfz.de, MITK (v2024.12)
kislinsk created an object: 2021 Week 06 (Early February).
Feb 10 2021, 3:45 PM
kislinsk updated subscribers of T24402: Improve clang-format support.

Adding @kalali to the subscribers as he also is interested in the definition of our clang format file.

Feb 10 2021, 3:33 PM · Auto-closed, MITK
kislinsk edited projects for T28294: [Documentation] std multiwidget does show a blank page on F1, added: MITK, Next Milestone; removed MITK (v2021.02).
Feb 10 2021, 3:15 PM · Restricted Project, MITK (v2022.04), Missing Info
thomass triaged T28294: [Documentation] std multiwidget does show a blank page on F1 as Normal priority.
Feb 10 2021, 2:58 PM · Restricted Project, MITK (v2022.04), Missing Info
kislinsk added a subtask for T28000: MITK v2021.02: T28283: Support building with Qt 5.15 .
Feb 10 2021, 2:55 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk added a parent task for T28283: Support building with Qt 5.15 : T28000: MITK v2021.02.
Feb 10 2021, 2:55 PM · MITK (v2021.02)
kislinsk closed T28283: Support building with Qt 5.15 as Resolved.

Is it really a minor change and we include it in the current release, but still we should not yet officially announce support of system Qt5.

Feb 10 2021, 2:55 PM · MITK (v2021.02)
floca closed T26080: [QmitkImageStatisticsTableModel] Multiple masks instead multiple timesteps as Resolved.
Feb 10 2021, 2:51 PM · MITK
a178n added a comment to T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS.

Update:
Problem is cannot be replicated anymore on my mac book (after a restart). Only Happens recurrently at certain times.

Feb 10 2021, 1:53 PM · Auto-closed, MITK
kislinsk added a revision to T28283: Support building with Qt 5.15 : Unknown Object (Differential Revision).
Feb 10 2021, 1:09 PM · MITK (v2021.02)
floca edited projects for T28293: [MITK Workbench] Closing Workbench results in "Problem report" in macOS, added: MITK; removed MITK (v2021.02).
Feb 10 2021, 12:34 PM · Auto-closed, MITK
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: Restricted 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 · Auto-closed, MITK
schererj added a project to T27968: CTP gets stuck on large import: Request for Discussion.
Feb 8 2021, 4:55 PM · Kaapana (internal)