[Insight-users] Using ExtraImageFilter via WrapITK

[David Chen]

I've written a python script that takes in a volume and tries to extract a Y slice using the ExtractImageFilter via WrapITK.  It keeps giving me a region error and I cannot figure out why.

Can anyone take a look at my script and its output and tell me what I'm doing wrong?

Here's the script:

> #!/usr/bin/env python
> 
> import itk
> from sys import argv
> 
> imageType = itk.Image[itk.UC, 3]
> readerType = itk.ImageFileReader[imageType]
> reader = readerType.New()
> reader.SetFileName( argv[1] )
> 
> size = itk.size(reader)
> print "\nInput image size: ", size
> 
> reader.UpdateOutputInformation()
> reader.UpdateLargestPossibleRegion()
> coronal = reader.GetOutput().GetLargestPossibleRegion()
> 
> ycut = size.GetElement(1)/2
> coronal.SetIndex(1, ycut)
> coronal.SetSize(1, 0);
> 
> extract = itk.ExtractImageFilter[itk.Image.UC3, itk.Image.UC2].New()
> extract.SetInput(reader.GetOutput())
> 
> 
> extract.SetDirectionCollapseToIdentity()
> extract.SetExtractionRegion(coronal)
> extract.UpdateOutputInformation()
> 
> print "\nExtract's input image: ", extract.GetOutput()
> print "\nThe ExtractImageFilter: ", extract
> print "\nExtract's region: ", extract.GetExtractionRegion()
> print "\nSize of the extract's output: ", itk.size(extract.GetOutput())
> 
> print "\nReader's region: ", reader.GetOutput().GetLargestPossibleRegion()
> 
> print "\n"
> 
> extract.Update()
> itk.write(extract.GetOutput(), "extract.png")


And here is its output:

> puget => ./itkextract.py ../Public/teapot.vtk
> Warning: Unknown parameter 'std::string' in template 'itk::MetaDataObject'
> 
> Input image size:  itkSize3 ([256, 256, 256])
> 
> Extract's input image:  Image (0x108d3f010)
>   RTTI typeinfo:   itk::Image<unsigned char, 2u>
>   Reference Count: 2
>   Modified Time: 203
>   Debug: Off
>   Observers: 
>     none
>   Source: (0x108db78c0) 
>   Source output index: 0
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 200
>   UpdateMTime: 0
>   RealTimeStamp: 0 seconds 
>   LargestPossibleRegion: 
>     Dimension: 2
>     Index: [0, 0]
>     Size: [256, 256]
>   BufferedRegion: 
>     Dimension: 2
>     Index: [0, 0]
>     Size: [0, 0]
>   RequestedRegion: 
>     Dimension: 2
>     Index: [0, 0]
>     Size: [0, 0]
>   Spacing: [1, 1.3095]
>   Origin: [0, 0]
>   Direction: 
> 1 0
> 0 1
> 
>   IndexToPointMatrix: 
>   1 0
> 0 1.3095
> 
>   PointToIndexMatrix: 
>   1 0
> 0 0.76365
> 
>   PixelContainer: 
>     ImportImageContainer (0x10cc2bbc0)
>       RTTI typeinfo:   itk::ImportImageContainer<unsigned long, unsigned char>
>       Reference Count: 1
>       Modified Time: 190
>       Debug: Off
>       Observers: 
>         none
>       Pointer: 0
>       Container manages memory: true
>       Size: 0
>       Capacity: 0
> 
> 
> The ExtractImageFilter:  ExtractImageFilter (0x108db78c0)
>   RTTI typeinfo:   itk::ExtractImageFilter<itk::Image<unsigned char, 3u>, itk::Image<unsigned char, 2u> >
>   Reference Count: 1
>   Modified Time: 200
>   Debug: Off
>   Observers: 
>     none
>   Number Of Required Inputs: 1
>   Number Of Required Outputs: 1
>   Number Of Threads: 24
>   ReleaseDataFlag: Off
>   ReleaseDataBeforeUpdateFlag: Off
>   Input 0: (0x108d1a090)
>   Output 0: (0x108d3f010)
>   AbortGenerateData: Off
>   Progress: 0
>   Multithreader: 
>     RTTI typeinfo:   itk::MultiThreader
>     Reference Count: 1
>     Modified Time: 188
>     Debug: Off
>     Observers: 
>       none
>     Thread Count: 24
>     Global Maximum Number Of Threads: 128
>     Global Default Number Of Threads: 24
>   ExtractionRegion: ImageRegion (0x108db79c0)
>   Dimension: 3
>   Index: [0, 128, 0]
>   Size: [256, 0, 256]
> 
>   OutputImageRegion: ImageRegion (0x108db79f8)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [256, 256]
> 
>   DirectionCollaspeStrategy: 1
> 
> 
> Extract's region:  itkImageRegion3([0, 128, 0], [256, 0, 256])
> 
> Size of the extract's output:  itkSize2 ([256, 256])
> 
> Reader's region:  itkImageRegion3([0, 128, 0], [256, 0, 256])
> 
> 
> Traceback (most recent call last):
>   File "./itkextract.py", line 39, in <module>
>     extract.Update()
> RuntimeError: /nfs/Users/dave/pkg/sitk-build/ITK/Modules/Core/Common/src/itkDataObject.cxx:387:

> Requested region is (at least partially) outside the largest possible region.


Thank you for any help.
Dave


David T. Chen, PhD                      [Lockheed Martin contractor]
mailto:dchen at mail.nih.gov               http://erie.nlm.nih.gov/~dave
phone:301.435.3264                      iphone:301.524.3174
Office of High Performance Computing and Communications
National Library of Medicine

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