[Insight-users] Problems to read a vtk file using SimpleITK+Python
Ariel Hernán Curiale
curiale at gmail.com
Wed Aug 7 12:24:27 EDT 2013
I'm sorry I forgot include the list.
The compiler used to compile python was:
>> print(sys.version)
2.7.5 (default, Aug 1 2013, 00:59:40)
[GCC 4.2.1 Compatible Apple Clang 4.1 ((tags/Apple/clang-421.11.66))]
These are the compiler that I have in the system:
1)
/usr/bin/clang++ -> clang
/usr/bin/cc -> clang
Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn)
Target: x86_64-apple-darwin11.4.2
Thread model: posix
2)
/usr/bin/g++ -> ../llvm-gcc-4.2/bin/llvm-g++-4.2
/usr/bin/gcc -> llvm-gcc-4.2
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
3)
/usr/bin/i686-apple-darwin11-llvm-g++-4.2 -> ../llvm-gcc-4.2/bin/i686-apple-darwin11-llvm-g++-4.2
/usr/bin/i686-apple-darwin11-llvm-gcc-4.2 -> ../llvm-gcc-4.2/bin/i686-apple-darwin11-llvm-gcc-4.2
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
I set the the variable CC to /usr/bin/cc and then I download and installed the python by mac port.
__________________________________
| 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 17:35, Bradley Lowekamp escribió:
> 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
>>>>>>
>>>>>>
>>>>>> 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
>>>
>>
>
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