[ITK-users] [ITK] simpleitk Python ExtractImageFilter -- basic usage

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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Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom