[Insight-users] Problems to read a vtk file using SimpleITK+Python
Bradley Lowekamp
blowekamp at mail.nih.gov
Wed Aug 7 11:35:36 EDT 2013
Please also include the list in your response.
What compiler was used to compile you macPort version of Python?
>>> import sys
>>> print(sys.version)
Brad
On Aug 7, 2013, at 10:51 AM, Ariel Hernán Curiale <curiale at gmail.com> wrote:
> Hi Brad,
>
> I could run the code using the version installed with easy_install but I prefer to use the version from the source code. I think that I have a problem with clang 4.2 + python. I'll try to find what is happen.
>
> Thanks a lot.
> __________________________________
> | 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 07/08/2013, a las 15:08, Bradley Lowekamp escribió:
>
>> 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
>>>>>
>>>>>
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>>>>>
>>>>> 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:
>>>>>
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>>>>>
>>>>>
>>>>>
>>>
>>> _____________________________________
>>> 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
>>>
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>>
>
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