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MITK - DICOM Seg - not saved when started without terminal
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Description

  1. Download MITK for Linux & extract
  2. Open MitkWorkbench.sh with double click -> Run
  3. Load DICOM + Create new segmentation
  4. Save segmentation as DICOM SEG

-> File will NOT be saved
There is no warning,error or whatsoever

Version:
Current Release: 18.04.2

OS:
Ubuntu 16.04

Event Timeline

kislinsk triaged this task as High priority.Mar 3 2020, 4:12 PM

I reproduced it with the "Installer".

[63.469] Writing image: /home/hanno/mitk/seg.dcm
Input image size: [512, 512, 7]
CodeSequence Exception: missing value in code sequence
#63.470# ERROR: An error occurred during writing the DICOM Seg: JSON Exception: file could not be read.

But when using the current master, this problem does not occur.
@kislinsk could this be a problem, due to starting mitk via this script, therefore a linux "installer" problem? Otherwise, this is resolved in the current master...

I guess we have several of these subtle problems with our installers but to be sure we would need to check by building an installer from the current master and try it again.

Make sure that doxygen is installed (sudo apt install doxygen), set the MITK_BUILD_CONFIGURATION to WorkbenchRelease, build superbuild, then build package target in MITK build.

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?

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?

That is exactly what the packaging does. Pack everything together in a folder and make it executable independently from the workstation you built everything. Just make sure to set the MITK build configuration and install doxygen as written above. After you built everything, you can simply call "make package" in the MITK-build folder. This will create a tarball that you can extract just like the release.

gaoh claimed this task.

File is correctly saved in the current master.