<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Here is a test I wrote:<div><br></div><div><a href="https://github.com/blowekamp/Slicer/commit/25cf25f5cc4d7c490fab5c21eb871418c32ab9e6">https://github.com/blowekamp/Slicer/commit/25cf25f5cc4d7c490fab5c21eb871418c32ab9e6</a></div><div><br></div><div>Here is the output which I think is confirming your suspicion:</div><div><br></div><div><div>335: test_VolumeOriginPrecision (LoadVolumeDisplaybleSceneModelClose.VolumesLoadSceneCloseTesting) ... Initial Origin: [547339, 218860, 20904.4]</div><div>335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367</div><div>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__]</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>Number of files listed in the node = 0.</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>File reader says it was able to read 0 files.</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>File reader used the archetype file name of /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__ []</div><div>335: </div><div>335: </div><div>335: </div><div>335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 317</div><div>335: vtkMRMLVolumeArchetypeStorageNode (0x7f8b3bc160e0): ReadData: Failed to instantiate a file reader</div><div>335: </div><div>335: </div><div>335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367</div><div>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__]</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>Number of files listed in the node = 0.</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>File reader says it was able to read 0 files.</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>File reader used the archetype file name of /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__ []</div><div>335: </div><div>335: </div><div>335: </div><div>335: Show module (name): "Volumes" </div><div>335: setRange -1e+06 1e+06 </div><div>335: end setRange </div><div>335: setRange -1e+06 1e+06 </div><div>335: end setRange </div><div>335: setRange -1e+06 1e+06 </div><div>335: end setRange </div><div>335: setRange -1e+06 1e+06 </div><div>335: end setRange </div><div>335: setRange -1e+06 1e+06 </div><div>335: end setRange </div><div>335: setRange -1e+06 1e+06 </div><div>335: end setRange </div><div>335: setValues -32768 32767 </div><div>335: end setValues </div><div>335: setValues -32768 32767 </div><div>335: end setValues </div><div>335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367</div><div>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__]</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>Number of files listed in the node = 0.</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>File reader says it was able to read 0 files.</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>File reader used the archetype file name of /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__ []</div><div>335: </div><div>335: </div><div>335: </div><div>335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 317</div><div>335: vtkMRMLVolumeArchetypeStorageNode (0x7f8b3b395ff0): ReadData: Failed to instantiate a file reader</div><div>335: </div><div>335: </div><div>335: ERROR: In /Users/blowekamp/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367</div><div>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__]</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>Number of files listed in the node = 0.</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>File reader says it was able to read 0 files.</div><div>335: <span class="Apple-tab-span" style="white-space:pre"> </span>File reader used the archetype file name of /scratch/blowekamp/build/Slicer/Slicer-build/Modules/Loadable/Volumes/Testing/Python/_DUMMY_DOES_NOT_EXISTS__ []</div><div>335: </div><div>335: </div><div>335: </div><div>335: Viewed Origin: (10000.0, 10000.0, 10000.0)</div><div>335: FAIL</div><div>335: </div><div>335: ======================================================================</div><div>335: FAIL: test_VolumeOriginPrecision (LoadVolumeDisplaybleSceneModelClose.VolumesLoadSceneCloseTesting)</div><div>335: ----------------------------------------------------------------------</div><div>335: Traceback (most recent call last):</div><div>335: File "/Users/blowekamp/src/Slicer/Modules/Loadable/Volumes/Testing/Python/LoadVolumeDisplaybleSceneModelClose.py", line 66, in test_VolumeOriginPrecision</div><div>335: self.assertEqual(viewed_img.GetOrigin(), origin, "Origin changed after viewing")</div><div>335: AssertionError: Origin changed after viewing</div><div>335: </div></div><div><br></div><div><br><div><div>On Aug 8, 2013, at 9:03 AM, Julien Finet <<a href="mailto:julien.finet@kitware.com">julien.finet@kitware.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><div dir="ltr">I'll look at it very soon. <div>My suspicion is that it is due to the current range of the spinboxes (probably currently set to 10000) ?.<div>Thanks,</div><div>Julien.</div></div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Thu, Aug 8, 2013 at 8:33 AM, Steve Pieper <span dir="ltr"><<a href="mailto:pieper@ibility.net" target="_blank">pieper@ibility.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div>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).<br><br></div><div>-Steve<br></div></div><div class="gmail_extra">
<br><br><div class="gmail_quote"><div><div class="h5">On Thu, Aug 8, 2013 at 8:16 AM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hello,<br>
<br>
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.<br>
<br>
This sounded similar to some issues mentioned during the TCON related to the double spin boxes or precision preferences.<br>
<br>
Initially:<br>
<br>
>>> lm1 = sitkUtils.PullFromSlicer("A Close")<br>
>>> print lm1<br>
<br>
Image (0x13b2ca030)<br>
RTTI typeinfo: itk::Image<unsigned short, 3u><br>
Reference Count: 1<br>
Modified Time: 3771<br>
Debug: Off<br>
Observers:<br>
none<br>
Source: (none)<br>
Source output name: (none)<br>
Release Data: Off<br>
Data Released: False<br>
Global Release Data: Off<br>
PipelineMTime: 3597<br>
UpdateMTime: 3770<br>
RealTimeStamp: 0 seconds<br>
LargestPossibleRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [2618, 1368, 325]<br>
BufferedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [2618, 1368, 325]<br>
RequestedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [2618, 1368, 325]<br>
Spacing: [160, 160, 480]<br>
Origin: [547339, 218860, 20904.4]<br>
Direction:<br>
-1 0 0<br>
0 -1 0<br>
0 0 1<br>
<br>
After viewing in Volumes module:<br>
>>> lm1 = sitkUtils.PullFromSlicer("A Close")<br>
>>> print lm1<br>
Image (0x13b222ad0)<br>
RTTI typeinfo: itk::Image<unsigned short, 3u><br>
Reference Count: 1<br>
Modified Time: 4481<br>
Debug: Off<br>
Observers:<br>
none<br>
Source: (none)<br>
Source output name: (none)<br>
Release Data: Off<br>
Data Released: False<br>
Global Release Data: Off<br>
PipelineMTime: 4307<br>
UpdateMTime: 4480<br>
RealTimeStamp: 0 seconds<br>
LargestPossibleRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [2618, 1368, 325]<br>
BufferedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [2618, 1368, 325]<br>
RequestedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [2618, 1368, 325]<br>
Spacing: [160, 160, 480]<br>
Origin: [10000, 10000, 10000]<br>
Direction:<br>
-1 0 0<br>
0 -1 0<br>
0 0 1<br>
<br>
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.<br>
<br>
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.<br>
<br>
I will continue to investigate and will write a test which uses synthetic data to reproduce the above, hopefully without needed so many pixels.<br>
<br>
Thanks,<br>
Brad<br></div></div>
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