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

Wed Aug 7 09:08:28 EDT 2013

Hello,

If you try to download the build distribution for your system python, it the error there?

/usr/bin/easy_install SimpleITK

Also did you run the tests for you compilation of SimpleITK? any failures?

Brad

On Aug 7, 2013, at 6:43 AM, Ariel Hernán Curiale <curiale at gmail.com> wrote:

> 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
>>> 
>>> |_________________________________
>>> 
>>> 
>>> 
>>> _____________________________________
>>> 
>>> Powered by www.kitware.com
>>> 
>>> 
>>> Visit other Kitware open-source projects at
>>> 
>>> http://www.kitware.com/opensource/opensource.html
>>> 
>>> 
>>> Kitware offers ITK Training Courses, for more information visit:
>>> 
>>> http://www.kitware.com/products/protraining.php
>>> 
>>> 
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> 
>>> http://www.itk.org/Wiki/ITK_FAQ
>>> 
>>> 
>>> Follow this link to subscribe/unsubscribe:
>>> 
>>> http://www.itk.org/mailman/listinfo/insight-users
>>> 
>>> 
>>> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20130807/1f363080/attachment.htm>