[Insight-users] Problems to read a vtk file using SimpleITK+Python

[Matt McCormick]

Hi Ariel,

The VTK file format [1] is always 3D, so a non-zero spacing will need
to be specified if using this format.

HTH,
Matt

[1] www.vtk.org/VTK/img/file-formats.pdf


On Tue, Aug 6, 2013 at 3:00 PM, Ariel Hernán Curiale <curiale at gmail.com> wrote:
> Hi,
> I create a simple example to show you the problem that I'm getting when I'm
> trying to read a vtk file. I'm using the last release of SimpleITK
> (SimpleITK-0.6.1) and python.
> In this example, I create, write and read a simple image.
>
> Here is the code:
> -------------------------
> import SimpleITK as sitk
> import scipy as sc
>
> dim = (100, 100)
> origin = (0, 0)
> spacing = (0.834496, 0.8223519)
> img = sc.zeros(dim)
>
> img[20:40, 20:40] = 1
>
> img_sitk = sitk.GetImageFromArray(img)
> img_sitk.SetOrigin(origin)
> img_sitk.SetSpacing(spacing)
>
> print img_sitk
> sitk.Show(img_sitk)
> sitk.WriteImage(img_sitk,"img.vtk")
>
> im = sitk.ReadImage("img.vtk")
>
> reader = sitk.ImageFileReader()
> reader.SetFileName("img.vtk")
> im2 = reader.Execute()
> --------
>
>
> The img_sitk seems to be created properly:
> ----
> Image (0x7f9a95ff8550)
>   RTTI typeinfo:   itk::Image<double, 2u>
>   Reference Count: 1
>   Modified Time: 3295
>   Debug: Off
>   Observers:
>     none
>   Source: (none)
>   Source output name: (none)
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 0
>   UpdateMTime: 0
>   RealTimeStamp: 0 seconds
>   LargestPossibleRegion:
>     Dimension: 2
>     Index: [0, 0]
>     Size: [100, 100]
>   BufferedRegion:
>     Dimension: 2
>     Index: [0, 0]
>     Size: [100, 100]
>   RequestedRegion:
>     Dimension: 2
>     Index: [0, 0]
>     Size: [100, 100]
>   Spacing: [0.834496, 0.822352]
>   Origin: [0, 0]
>   Direction:
> 1 0
> 0 1
>
>   IndexToPointMatrix:
> 0.834496 0
> 0 0.822352
>
>   PointToIndexMatrix:
> 1.19833 0
> 0 1.21602
>
>   Inverse Direction:
> 1 0
> 0 1
>
>   PixelContainer:
>     ImportImageContainer (0x7f9a960309b0)
>       RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
>       Reference Count: 1
>       Modified Time: 2866
>       Debug: Off
>       Observers:
>         none
>       Pointer: 0x7f9a95352200
>       Container manages memory: true
>       Size: 10000
>       Capacity: 10000
>
>
>
> But when I try to read the image using sitk.ReadImage or
> sitk.ImageFileReader I'm getting this error:
> ----
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/SimpleITK-0.6.1_g1387a-py2.7-macosx-10.7-x86_64.egg/SimpleITK.py",
> line 4371, in Execute
>     return _SimpleITK.ImageFileReader_Execute(self)
> RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute:
> /Users/ariel/Applications/InsightToolkit-4.4.0/Modules/Core/Common/include/itkImageBase.hxx:189:
> itk::ERROR: Image(0x7f9a95d9d640): A spacing of 0 is not allowed: Spacing is
> [1, 0]
> ----
>
>
>
> It seems to be a bug but, I don't know if I'm doing something wrong.
>
>
> Cheers,
> __________________________________
> | Ariel Hernán Curiale Ph.D Student
> | ETSI Telecomunicación
> | Universidad de Valladolid
> | Campus Miguel Delibes
> | 47011 Valladolid, Spain
> | Phone: 983-423000 ext. 5590
> | Web: www.curiale.com.ar
> |_________________________________
>
>
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