[Insight-users] Problems to read a vtk file using SimpleITK+Python
Ariel Hernán Curiale
curiale at gmail.com
Tue Aug 6 16:26:52 EDT 2013
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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