[ITK] [ITK-users] 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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Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
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
The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
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