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IDProjectCategoryView StatusDate SubmittedLast Update
0009766ITKpublic2009-10-22 13:542011-01-13 17:00
ReporterKevin H. Hobbs 
Assigned ToBradley Lowekamp 
PrioritynormalSeveritymajorReproducibilitysometimes
StatusclosedResolutionfixed 
PlatformOSOS Version
Product Version 
Target VersionFixed in Version 
Summary0009766: Extract after UpdateOutputInformation produces junk
DescriptionI would like to extract an image region from a MetaImage (.mhd) file without ever loading the entire image into memory.

In order to do this I set up a reader and call reader->UpdateOutputInformation();

Then I GetLargestPossibleRegion() from the reader's output and compute the sub-region I would like to extract.

I give this sub-region to an ExtractImageFilter and write the output to a file.

The resulting image looks like the wrong region was read and reshaped into my extracted region.

I mentioned this along with code and a picture on the ITK-users list here :
http://www.itk.org/pipermail/insight-users/2009-October/033310.html [^]

The image I used is:
http://crab-lab.zool.ohiou.edu/kevin/input.mhd [^]
http://crab-lab.zool.ohiou.edu/kevin/input.raw [^]

I have seen this issue on two computers( murron and gargon ) both running the nightly dashboard build of ITK. Both use 64-bit linux. murron uses Fedora 11, gargon uses Fedora 10.

This issue does not occur if I call Update instead of UpdateOutputInformation on the reader.

This issue does not occur if I convert the input image to VTK or Analyse format.
TagsNo tags attached.
Resolution Date
Sprint
Sprint Status
Attached Filescxx file icon ExtractBug.cxx [^] (1,584 bytes) 2009-10-22 13:54
png file icon slices.png [^] (20,390 bytes) 2009-10-22 13:56


patch file icon bug9766.patch [^] (4,855 bytes) 2009-11-02 15:10 [Show Content]

 Relationships

  Notes
(0018196)
Kevin H. Hobbs (developer)
2009-10-22 14:03

The left side of slices.png shows a slice of the image produced with Update called on the reader before the piece was extracted.

The right side shows the same slice of the image produced with UpdateOutputInformation called on the reader.
(0018287)
Bradley Lowekamp (developer)
2009-10-29 16:32

I have been able to reproduce the problem with my own code.
(0018321)
Bradley Lowekamp (developer)
2009-11-02 15:52

Submitted experimental build with attached patch.
http://www.cdash.org/CDash/buildSummary.php?buildid=462277 [^]

Committed new test:

http://public.kitware.com/cgi-bin/viewcvs.cgi/Testing/Code/IO/CMakeLists.txt.diff?cvsroot=Insight&r1=1.235&r2=1.236 [^]
http://public.kitware.com/cgi-bin/viewcvs.cgi/Testing/Code/IO/itkIOTests.cxx.diff?cvsroot=Insight&r1=1.83&r2=1.84 [^]
http://public.kitware.com/cgi-bin/viewcvs.cgi/Testing/Code/IO/itkImageFileReaderStreamingTest2.cxx?cvsroot=Insight&rev=1.1&view=markup [^]

Which can be manually run with:
itkIOTests itkImageFileReaderStreamingTest2 Insight/Testing/Data/Input/HeadMRVolume.mha

Once the patch is committed this test will be added to cmake's test.
(0018342)
Bradley Lowekamp (developer)
2009-11-04 11:14

Julien committed the patch:
http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/MetaIO/metaImage.cxx.diff?cvsroot=Insight&r1=1.119&r2=1.120 [^]
(0018377)
Bradley Lowekamp (developer)
2009-11-09 15:40

The test appears to be passing with the metaIO patch.

 Issue History
Date Modified Username Field Change
2009-10-22 13:54 Kevin H. Hobbs New Issue
2009-10-22 13:54 Kevin H. Hobbs File Added: ExtractBug.cxx
2009-10-22 13:56 Kevin H. Hobbs File Added: slices.png
2009-10-22 14:03 Kevin H. Hobbs Note Added: 0018196
2009-10-26 14:18 Luis Ibanez Status new => assigned
2009-10-26 14:18 Luis Ibanez Assigned To => Luis Ibanez
2009-10-28 14:14 Bradley Lowekamp Assigned To Luis Ibanez => Bradley Lowekamp
2009-10-29 16:32 Bradley Lowekamp Note Added: 0018287
2009-10-29 16:32 Bradley Lowekamp Status assigned => confirmed
2009-11-02 15:10 Bradley Lowekamp File Added: bug9766.patch
2009-11-02 15:52 Bradley Lowekamp Note Added: 0018321
2009-11-03 19:16 Julien Jomier Status confirmed => assigned
2009-11-03 19:16 Julien Jomier Assigned To Bradley Lowekamp => Julien Jomier
2009-11-03 20:32 Julien Jomier Assigned To Julien Jomier => Bradley Lowekamp
2009-11-04 11:14 Bradley Lowekamp Note Added: 0018342
2009-11-09 15:40 Bradley Lowekamp Note Added: 0018377
2009-11-09 15:40 Bradley Lowekamp Status assigned => resolved
2009-11-09 15:40 Bradley Lowekamp Resolution open => fixed
2010-10-21 12:31 Gabe Hart Status resolved => closed
2011-01-13 17:00 Source_changeset_attached => VTK master a2bd8391
2011-01-13 17:00 Source_changeset_attached => VTK master 020ef709


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