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List:       insight-users
Subject:    [ITK-users] simpleitk Python ExtractImageFilter -- basic usage
From:       "Robert.Atwood () diamond ! ac ! uk" <Robert ! Atwood () diamond ! ac ! uk>
Date:       2018-05-24 15:53:42
Message-ID: 0ecfdf0cb1bb4eb08c75383a8f404f5a () diamond ! ac ! uk
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I'm sorry if I'm abit thick, but this doesn't work. 
I tried to read documents and old mailing list entries, but I don't find an answer, \
just in the past someone with a similar problem wound up using CropImageFilter \
instead. 


Can someone clarify why this doesn't work? I'd specifically LIKE to maintain the \
origin of the region as the origin of the original image. 


  1 import SimpleITK as sitk
  2
  3 
  4 rawimg = sitk.Image(50,60,70,sitk.sitkFloat32)
  5 newim=sitk.Extract(rawimg,(20,30,40),(0,0,0))



Traceback (most recent call last):
  File "./tryextract.py", line 12, in <module>
    newim=sitk.Extract(rawimg,(20,30,40),(0,0,0))
  File "/home/kny48981/.local/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", \
line 27140, in Extract  return _SimpleITK.Extract(*args, **kwargs)
RuntimeError: Exception thrown in SimpleITK Extract: \
/tmp/SimpleITK-build/ITK-prefix/include/ITK-4.13/itkExtractImageFilter.hxx:99: \
itk::ERROR: ExtractImageFilter(0x7f7eb17d8e80): Extraction Region not consistent with \
output image [kny48981@i12-ws011 pycircles]$ python ./tryextract.py  \
/dls/i12/data/2018/cm19662-3/tmp/bubble/onebub.tif -o /scratch/SSD/robert/onebub \
Traceback (most recent call last):  File "./tryextract.py", line 5, in <module>
    newim=sitk.Extract(rawimg,(20,30,40),(0,0,0))
  File "/home/kny48981/.local/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", \
line 27140, in Extract  return _SimpleITK.Extract(*args, **kwargs)
RuntimeError: Exception thrown in SimpleITK Extract: \
/tmp/SimpleITK-build/ITK-prefix/include/ITK-4.13/itkExtractImageFilter.hxx:99: \
itk::ERROR: ExtractImageFilter(0x7f8287a9e020): Extraction Region not consistent with \
output image


But the output image should be getting created (returned)  by the filter?So how can \
it not be consistent???   Or what's going on? 
Especially since it worked fine in a previous program with 2d data. 



I tried a bit harder and used the object interface, and compare 2d and 3d, and try to \
set the collapse strategy.. 

And it works in 2d but not in 3d, I really can't see why. 

  1 import SimpleITK as sitk
  2
  3 rawimg2d = sitk.Image(50,60,sitk.sitkFloat32)
  4 print rawimg2d.GetDimension()
  5 extractor2d=sitk.ExtractImageFilter()
  6 extractor2d.SetSize((20,30))
  7 extractor2d.SetIndex((5,6))
  8 extractor2d.SetDirectionCollapseToStrategy(extractor2d.DIRECTIONCOLLAPSETOIDENTITY)
  9 print "strategy, ",extractor2d.GetDirectionCollapseToStrategy()
 10 newimg2d=extractor2d.Execute(rawimg2d)
 11
 12 print "Finished 2d extractor"
 13
 14 rawimg3d = sitk.Image(50,60,70,sitk.sitkFloat32)
 15 print rawimg3d.GetDimension()
 16 extractor3d=sitk.ExtractImageFilter()
 17 extractor3d.SetSize((20,30,40))
 18 extractor3d.SetIndex((5,6,7))
 19 extractor3d.SetDirectionCollapseToStrategy(extractor3d.DIRECTIONCOLLAPSETOIDENTITY)
  20 print "strategy, ",extractor3d.GetDirectionCollapseToStrategy()
 21 newimg3d=extractor3d.Execute(rawimg3d)
 22 print "Finished 3d extractor"
 23


python ./tryextract.py  /

2
strategy,  1
Finished 2d extractor
3
strategy,  1
Traceback (most recent call last):
  File "./tryextract.py", line 21, in <module>
    newimg3d=extractor3d.Execute(rawimg3d)
  File "/home/kny48981/.local/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", \
line 27115, in Execute  return _SimpleITK.ExtractImageFilter_Execute(self, *args)
RuntimeError: Exception thrown in SimpleITK ExtractImageFilter_Execute: \
/tmp/SimpleITK-build/ITK-prefix/include/ITK-4.13/itkExtractImageFilter.hxx:99: \
itk::ERROR: ExtractImageFilter(0x7fbf77727bc0): Extraction Region not consistent with \
output image



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