[ITK-users] [ITK] simpleitk Python ExtractImageFilter -- basic usage
Robert.Atwood at diamond.ac.uk
Robert.Atwood at diamond.ac.uk
Fri May 25 05:13:52 EDT 2018
Done!
> -----Original Message-----
> From: Lowekamp, Bradley (NIH/NLM/LHC) [C]
> [mailto:blowekamp at mail.nih.gov]
> Sent: 24 May 2018 18:54
> To: Atwood, Robert (DLSLtd,RAL,SCI); insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] simpleitk Python ExtractImageFilter -- basic
> usage
>
> Can you please post you question to discourse?
>
> https://discourse.itk.org
>
> On 5/24/18, 12:12 PM, "Robert.Atwood at diamond.ac.uk"
> <Robert.Atwood at diamond.ac.uk> wrote:
>
> 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 at 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.DIRECTIONCOLLAPS
> ETOIDENTITY)
> 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.DIRECTIONCOLLAPS
> ETOIDENTITY)
> 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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