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Maniphest T27525

Problems while opening MITK scenes created with 2018.04 release with the current master
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Description

I just built an installer from the current Master and tried to load MITK scenes that my medical partners created. They should contain: a T1 image, a T2 image and various segmentations. While the 2018.04 release opens the file correctly, the current master just shows the T2 image.

An example scene is located here: E132-Projekte\temp_data\MITK_scene_bug

Was there any chages made to the dataloading?

Related Objects

Mentioned Here
T1: testbug1

Event Timeline

• kleina triaged this task as High priority.Jul 3 2020, 3:51 PM
• kleina lowered the priority of this task from High to Normal.
• kleina created this task.
floca added a project: Missing Info.Jul 3 2020, 5:40 PM
floca added a subscriber: floca.

Cannot reproduce the problem with the current develop. Just checked with all example projects. All worked fine T1 and T2 was visible?!?

• kleina added a comment.Jul 6 2020, 10:11 AM

What about the Segmentations? I was wrong, I tried with the current develop as well (sorry, was used to having the master branch on clone :-D).
I had Hanno also try it and the segmentations are missing for him as well.
I put an installer into the same folder, you can just start it from the bin folder to reproduce.

• kleina added a comment.Jul 6 2020, 10:17 AM

This is the error message, that was not there with the old installer:

82.43 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\wlaaaa_Be_f.nrrd via itk::ImageIOFactory...
82.43 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
82.44 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\wlaaaa_Be_f.nrrd:
bad allocation
82.44 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'wlaaaa_Be_f.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\wlaaaa_Be_f.nrrd:
bad allocation
82.44 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'wlaaaa_Be_f.nrrd'. Factory returned nullptr object.
82.47 core.mod.core.imgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\xlaaaa_T1.nrrd via itk::ImageIOFactory...
82.48 core.mod.core.imgIo: ioRegion: ImageIORegion (00B59B98)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
82.49 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\xlaaaa_T1.nrrd:
bad allocation
82.49 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'xlaaaa_T1.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\xlaaaa_T1.nrrd:
bad allocation
82.50 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'xlaaaa_T1.nrrd'. Factory returned nullptr object.
82.50 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\ylaaaa_Be_l.nrrd via itk::ImageIOFactory...
82.50 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
82.51 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\ylaaaa_Be_l.nrrd:
bad allocation
82.51 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'ylaaaa_Be_l.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\ylaaaa_Be_l.nrrd:
bad allocation
82.51 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'ylaaaa_Be_l.nrrd'. Factory returned nullptr object.
82.52 core.mod.core.imgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\zlaaaa_T2.nrrd via itk::ImageIOFactory...
82.54 core.mod.core.imgIo: ioRegion: ImageIORegion (00B59B98)
  Dimension: 3
  Index: 0 0 0
  Size: 771 1651 56
83.15 core.mod.core.imgIo: [239.824, 133.62, -1277.42]
83.16 core.mod.core.imgIo: [-211.934, -174.38, -310.036]
83.16 core.mod.core.imgIo: used time geometry: ProportionalTimeGeometry
83.16 core.mod.core.imgIo: number of image components: 1
83.19 core.mod.core.imgIo: ...finished!
83.23 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\amaaaa_S_f.nrrd via itk::ImageIOFactory...
83.23 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
83.23 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\amaaaa_S_f.nrrd:
bad allocation
83.24 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'amaaaa_S_f.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\amaaaa_S_f.nrrd:
bad allocation
83.24 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'amaaaa_S_f.nrrd'. Factory returned nullptr object.
83.24 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\bmaaaa_S_l.nrrd via itk::ImageIOFactory...
83.24 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
83.24 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\bmaaaa_S_l.nrrd:
bad allocation
83.24 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'bmaaaa_S_l.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\bmaaaa_S_l.nrrd:
bad allocation
83.25 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'bmaaaa_S_l.nrrd'. Factory returned nullptr object.
83.25 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\cmaaaa_Be_re.nrrd via itk::ImageIOFactory...
83.26 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
83.26 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\cmaaaa_Be_re.nrrd:
bad allocation
83.27 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'cmaaaa_Be_re.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\cmaaaa_Be_re.nrrd:
bad allocation
83.27 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'cmaaaa_Be_re.nrrd'. Factory returned nullptr object.
83.28 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\dmaaaa_S_m.nrrd via itk::ImageIOFactory...
83.28 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
83.29 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\dmaaaa_S_m.nrrd:
bad allocation
83.29 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'dmaaaa_S_m.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\dmaaaa_S_m.nrrd:
bad allocation
83.30 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'dmaaaa_S_m.nrrd'. Factory returned nullptr object.
83.31 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\emaaaa_S.nrrd via itk::ImageIOFactory...
83.31 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
83.32 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\emaaaa_S.nrrd:
bad allocation
83.33 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'emaaaa_S.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\emaaaa_S.nrrd:
bad allocation
83.33 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'emaaaa_S.nrrd'. Factory returned nullptr object.
83.34 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\fmaaaa_Be_m.nrrd via itk::ImageIOFactory...
83.35 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
83.35 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\fmaaaa_Be_m.nrrd:
bad allocation
83.36 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'fmaaaa_Be_m.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\fmaaaa_Be_m.nrrd:
bad allocation
83.37 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'fmaaaa_Be_m.nrrd'. Factory returned nullptr object.
83.38 core.mod.mltLbl.lblSetImgIo: loading C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\gmaaaa_Be_li.nrrd via itk::ImageIOFactory...
83.39 core.mod.mltLbl.lblSetImgIo: ioRegion: ImageIORegion (00B59A58)
  Dimension: 3
  Index: 0 0 0
  Size: 769 2661 60
83.39 core.mod.core.ioUtil ERROR: Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\gmaaaa_Be_li.nrrd:
bad allocation
83.40 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'gmaaaa_Be_li.nrrd'. Exception says: D:\dev_win\master\src\Modules\Core\src\IO\mitkIOUtil.cpp:559:
Exception occured when reading file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\gmaaaa_Be_li.nrrd:
bad allocation
83.41 core.mod.scnSer.scnReaderv1 ERROR: Error during attempt to read 'gmaaaa_Be_li.nrrd'. Factory returned nullptr object.
83.41 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
84.49 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
84.51 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
85.72 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
86.62 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
87.53 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
88.57 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
89.49 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
90.40 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
91.31 core.mod.scnSer.scnReaderv1 WARNING: BaseData properties stored in scene file, but BaseData could not be read
92.23 core.mod.scnSer.scnReader ERROR: There were errors while loading scene file C:/Users/kleina/AppData/Local/Temp/SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8/index.xml. Your data may be corrupted
92.23 core.mod.scnSer.scnIo ERROR: There were errors while loading scene file C:\Users\kleina\AppData\Local\Temp\SceneIOTempc45a968c-bf51-47f8-81d1-2b615ac016a8\index.xml. Your data may be corrupted
floca added a comment.Jul 6 2020, 12:02 PM
In T27525#205434, @kleina wrote:

What about the Segmentations? I was wrong, I tried with the current develop as well (sorry, was used to having the master branch on clone :-D).
I had Hanno also try it and the segmentations are missing for him as well.
I put an installer into the same folder, you can just start it from the bin folder to reproduce.

Yes, I can see the segmentations. Also, none of the error messages are showing up on my log screen.

Please check, with the installer (send you the powerfolder link via mail).

• kleina added a comment.Jul 6 2020, 12:54 PM

With the installer you send me it worked :-(
I fetched and pulled develop this morning. What else should I try to narrow it down?

floca added a comment.Jul 6 2020, 4:45 PM

Which configuration did you used to build it? Was it a clean build?

• kleina added a comment.Jul 6 2020, 5:15 PM

It was a clean build with MITK_BUILD_CONFIGURATION = WorkbenchRelease. I also enabled XNAT and only build "release". But I think that's all.

floca added a comment.Jul 24 2020, 5:43 PM

@kleina do you still have the problem?

• kleina added a comment.Jul 28 2020, 10:23 AM

I do. I can build the current develop and let you know, if something changed for me.

kislinsk closed this task as Wontfix.Mar 10 2021, 9:02 AM
kislinsk added a project: Auto-closed.
kislinsk added a subscriber: kislinsk.

Hi there! 🙂

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