[Insight-developers] Bug changing volume metadata by looking at it

Thu Aug 8 09:16:56 EDT 2013

Here is a test I wrote:

https://github.com/blowekamp/Slicer/commit/25cf25f5cc4d7c490fab5c21eb871418c32ab9e6

Here is the output which I think is confirming your suspicion:

335: test_VolumeOriginPrecision (LoadVolumeDisplaybleSceneModelClose.VolumesLoadSceneCloseTesting) ... Initial Origin: [547339, 218860, 20904.4]
335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367
335: vtkMRMLVolumeArchetypeStorageNode (0x7f8b3bc1fed0): ReadData: Cannot read file as a volume of type DiffusionTensorVolume[fullName = /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__]
335: 	Number of files listed in the node = 0.
335: 	File reader says it was able to read 0 files.
335: 	File reader used the archetype file name of /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__ []
335: 
335: 
335: 
335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 317
335: vtkMRMLVolumeArchetypeStorageNode (0x7f8b3bc160e0): ReadData: Failed to instantiate a file reader
335: 
335: 
335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367
335: vtkMRMLVolumeArchetypeStorageNode (0x7f8b3bbf9b90): ReadData: Cannot read file as a volume of type Volume[fullName = /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__]
335: 	Number of files listed in the node = 0.
335: 	File reader says it was able to read 0 files.
335: 	File reader used the archetype file name of /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__ []
335: 
335: 
335: 
335: Show module (name): "Volumes" 
335: setRange -1e+06 1e+06 
335: end setRange 
335: setRange -1e+06 1e+06 
335: end setRange 
335: setRange -1e+06 1e+06 
335: end setRange 
335: setRange -1e+06 1e+06 
335: end setRange 
335: setRange -1e+06 1e+06 
335: end setRange 
335: setRange -1e+06 1e+06 
335: end setRange 
335: setValues -32768 32767 
335: end setValues 
335: setValues -32768 32767 
335: end setValues 
335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367
335: vtkMRMLVolumeArchetypeStorageNode (0x7f8b3b38d580): ReadData: Cannot read file as a volume of type DiffusionTensorVolume[fullName = /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__]
335: 	Number of files listed in the node = 0.
335: 	File reader says it was able to read 0 files.
335: 	File reader used the archetype file name of /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__ []
335: 
335: 
335: 
335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 317
335: vtkMRMLVolumeArchetypeStorageNode (0x7f8b3b395ff0): ReadData: Failed to instantiate a file reader
335: 
335: 
335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367
335: vtkMRMLVolumeArchetypeStorageNode (0x7f8b3b393a40): ReadData: Cannot read file as a volume of type Volume[fullName = /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__]
335: 	Number of files listed in the node = 0.
335: 	File reader says it was able to read 0 files.
335: 	File reader used the archetype file name of /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__ []
335: 
335: 
335: 
335: Viewed Origin: (10000.0, 10000.0, 10000.0)
335: FAIL
335: 
335: ======================================================================
335: FAIL: test_VolumeOriginPrecision (LoadVolumeDisplaybleSceneModelClose.VolumesLoadSceneCloseTesting)
335: ----------------------------------------------------------------------
335: Traceback (most recent call last):
335:   File "/Users/blowekamp/src/Slicer/Modules/Loadable/Volumes/Testing/Python/LoadVolumeDisplaybleSceneModelClose.py", line 66, in test_VolumeOriginPrecision
335:     self.assertEqual(viewed_img.GetOrigin(), origin, "Origin changed after viewing")
335: AssertionError: Origin changed after viewing
335: 

On Aug 8, 2013, at 9:03 AM, Julien Finet <julien.finet at kitware.com> wrote:

> I'll look at it very soon. 
> My suspicion is that it is due to the current range of the spinboxes (probably currently set to 10000) ?.
> Thanks,
> Julien.
> 
> 
> On Thu, Aug 8, 2013 at 8:33 AM, Steve Pieper <pieper at ibility.net> wrote:
> Thanks for finding this Brad - I agree it should be fixed ASAP.  We may need to back out some of the precision/units GUI changes (or disable them again).
> 
> -Steve
> 
> 
> On Thu, Aug 8, 2013 at 8:16 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> We are experiencing a rather critical bug, that is changing our Origin, when viewing the "Volume Information" in the Volumes module. This is on yesterdays nightly. I don't know when it started to occur, as we are starting to look at some older dataset which were previously segmented.
> 
> This sounded similar to some issues mentioned during the TCON related to the double spin boxes or precision preferences.
> 
> Initially:
> 
> >>> lm1 = sitkUtils.PullFromSlicer("A Close")
> >>> print lm1
> 
> Image (0x13b2ca030)
>   RTTI typeinfo:   itk::Image<unsigned short, 3u>
>   Reference Count: 1
>   Modified Time: 3771
>   Debug: Off
>   Observers:
>     none
>   Source: (none)
>   Source output name: (none)
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 3597
>   UpdateMTime: 3770
>   RealTimeStamp: 0 seconds
>   LargestPossibleRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [2618, 1368, 325]
>   BufferedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [2618, 1368, 325]
>   RequestedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [2618, 1368, 325]
>   Spacing: [160, 160, 480]
>   Origin: [547339, 218860, 20904.4]
>   Direction:
> -1 0 0
> 0 -1 0
> 0 0 1
> 
> After viewing in Volumes module:
> >>> lm1 = sitkUtils.PullFromSlicer("A Close")
> >>> print lm1
> Image (0x13b222ad0)
>   RTTI typeinfo:   itk::Image<unsigned short, 3u>
>   Reference Count: 1
>   Modified Time: 4481
>   Debug: Off
>   Observers:
>     none
>   Source: (none)
>   Source output name: (none)
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 4307
>   UpdateMTime: 4480
>   RealTimeStamp: 0 seconds
>   LargestPossibleRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [2618, 1368, 325]
>   BufferedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [2618, 1368, 325]
>   RequestedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [2618, 1368, 325]
>   Spacing: [160, 160, 480]
>   Origin: [10000, 10000, 10000]
>   Direction:
> -1 0 0
> 0 -1 0
> 0 0 1
> 
> Note the change in the origin! We have also observed other odd behaviors such as ROI changing, location, but it's hard for me to figure how what has change with respect to where in those cases.
> 
> This data set is a little odd of us because the user specified the units in angstroms and not nano-meters, so everything is 10X bigger than normal.
> 
> I will continue to investigate and will write a test which uses synthetic data to reproduce the above, hopefully without needed so many pixels.
> 
> Thanks,
> Brad
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