[Insight-users] Problems to read a vtk file using SimpleITK+Python
Ariel Hernán Curiale
curiale at gmail.com
Wed Aug 7 13:49:26 EDT 2013
Brad,
I found that I can run the code (using SimpleITK from source or the version installed with easy_install) from a ipython console, but if I use the Spyder Enviroment I can run the code only the first time when I start a fresh ipython console (inside the spyder).
I did a simple test. First I ran the code using SimpleITK (testWriteVTKFile.py) and I could read the vtk image, then I ran another code using scipy and matplotlib (EstudioPesos.py) and finally I tried to run again the testWriterVTKFile.py again but I couldn't read the image again. This is the output inside the spyder:
Python 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))] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Imported NumPy 1.7.1, SciPy 0.12.0, Matplotlib 1.2.1
Type "scientific" for more details.
>>> runfile(r'/Users/ariel/Uva/LPI/Proyectos/Python-ITK-VTK-QT/testWriteVTKFile.py', wdir=r'/Users/ariel/Uva/LPI/Proyectos/Python-ITK-VTK-QT')
Image (0x7ff50a26c3a0)
RTTI typeinfo: itk::Image<double, 2u>
Reference Count: 1
Modified Time: 462
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 (0x7ff50a26c580)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 460
Debug: Off
Observers:
none
Pointer: 0x7ff50a9eb000
Container manages memory: true
Size: 10000
Capacity: 10000
--------------
Here I could read the image
----------------------------------
>>> runfile(r'/Users/ariel/Uva/LPI/Proyectos/Python-ITK-VTK-QT/Ultrasonido/SpeckleTracking/EstudioPesos.py', wdir=r'/Users/ariel/Uva/LPI/Proyectos/Python-ITK-VTK-QT/Ultrasonido/SpeckleTracking')
runfile(r'/Users/ariel/Uva/LPI/Proyectos/Python-ITK-VTK-QT/testWriteVTKFile.py', wdir=r'/Users/ariel/Uva/LPI/Proyectos/Python-ITK-VTK-QT')
>>> Image (0x7ff50c601500)
RTTI typeinfo: itk::Image<double, 2u>
Reference Count: 1
Modified Time: 1565
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 (0x7ff50a655820)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 1563
Debug: Off
Observers:
none
Pointer: 0x7ff50b99aa00
Container manages memory: true
Size: 10000
Capacity: 10000
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/spyderlib/widgets/externalshell/sitecustomize.py", line 538, in runfile
execfile(filename, namespace)
File "/Users/ariel/Uva/LPI/Proyectos/Python-ITK-VTK-QT/testWriteVTKFile.py", line 29, in <module>
im = sitk.ReadImage("img.vtk")
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 4393, in ReadImage
return _SimpleITK.ReadImage(*args)
RuntimeError: Exception thrown in SimpleITK ReadImage: /Users/ariel/Applications/InsightToolkit-4.4.0/Modules/Core/Common/include/itkImageBase.hxx:189:
itk::ERROR: Image(0x7ff50c00e150): A spacing of 0 is not allowed: Spacing is [8, 0]
Thank again for your time.
__________________________________
| 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 18:24, Ariel Hernán Curiale escribió:
> 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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