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

Ariel Hernán Curiale curiale at gmail.com
Wed Aug 7 06:43:34 EDT 2013


Hi,

After rebuild the SimpleITK-0.6.1 the error is still there. The compilation of SimpleITK finish without any error.

I'm using:
ITK-4.4.0
Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn)
Python 2.7.5 from MacPort


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
|_________________________________

El 06/08/2013, a las 23:14, Matt McCormick escribió:

> Hi Ariel,
> 
> Your code works when I run it  with SimpleITK 0.6.1:
> 
> In [4]: im2
> Out[4]: <SimpleITK.Image; proxy of <Swig Object of type 'std::vector<
> itk::simple::Image >::value_type *' at 0x4fdf300> >
> 
> In [5]: print(im2)
> Image (0x44ea740)
>  RTTI typeinfo:   itk::Image<double, 2u>
>  Reference Count: 1
>  Modified Time: 1413
>  Debug: Off
>  Observers:
>    none
>  Source: (none)
>  Source output name: (none)
>  Release Data: Off
>  Data Released: False
>  Global Release Data: Off
>  PipelineMTime: 1250
>  UpdateMTime: 1412
>  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 (0x44ea910)
>      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
>      Reference Count: 1
>      Modified Time: 1409
>      Debug: Off
>      Observers:
>        none
>      Pointer: 0x506a530
>      Container manages memory: true
>      Size: 10000
>      Capacity: 10000
> 
> HTH,
> Matt
> 
> On Tue, Aug 6, 2013 at 8:26 PM, Ariel Hernán Curiale <curiale at gmail.com> wrote:
>> Hi Matt,
>> 
>> You are right, the vtk format is always 3D. If you have a 2D image  and save
>> it as vtk, then the writer automatically add the last dimension with a
>> spacing 1.
>> For example, this is the 2D image create with the python code:
>> 
>> ariel at Gohan:~/Uva/LPI/Proyectos/Python-ITK-VTK-QT/Ultrasonido/SpeckleTracking$
>> head -10 img.vtk
>> # vtk DataFile Version 3.0
>> VTK File Generated by Insight Segmentation and Registration Toolkit (ITK)
>> BINARY
>> DATASET STRUCTURED_POINTS
>> DIMENSIONS 100 100 1
>> SPACING 1.0000000000000000e+00 1.0000000000000000e+00 1.0000000000000000e+00
>> ORIGIN 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
>> POINT_DATA 10000
>> SCALARS scalars double 1
>> LOOKUP_TABLE default
>> .....
>> 
>> I don't know why the warning say that the spacing must be grater than 0
>> 
>> Ps: I can read this image using vtk.
>> 
>> Thanks for your quickly response.
>> 
>> 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
>> |_________________________________
>> 
>> El 06/08/2013, a las 17:52, Matt McCormick escribió:
>> 
>> 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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>> 
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