[Insight-users] Trouble reading and writing vector images
Gomez, Alberto
alberto.gomez at kcl.ac.uk
Wed Feb 24 04:49:23 EST 2010
I found this in the wiki:
http://www.itk.org/Wiki/ITK_File_Formats
So I think the best would be to store it in a mhd file (MetaImage). I
tried it and it worked fine. Thanks for pointing out that I should look
to the file format!
Alberto
Gomez Herrero, Alberto wrote:
> Hello,
>
> Thanks for your reply. I'll try to answer point by point:
>
> 1) What file format are you using for saving the vector image ?
>
> I am saving the images into gipl files. Actually I just do writer->SetFileName("myFile.gipl"); this is probably not the best for vector images... is there any particular format which is more suitable for this?
> 2) You email asks about itk::VectorImage, but the typedef
> that you show actually uses:
>
> pixeltype = itk::Vector
>
> are you actually using the itk::VectorImage in your code ?
>
> Indeed, I am not using the itk::VectorImage. I am using PixelType = itk::Vector, as adviced in the User Guide. I mentiones the itk::VectorImage because I thought that my problem might be solved if I used that class instead... but I am not using it at all.
>
> 3) That is great, the behaviour B) Is what I want.
>
> Thank you,
>
> Alberto
>
>
>
> Alberto Gomez
>
> Division of Imaging Sciences
> The Rayne Institute
> 4th Floor, Lambeth Wing
> St Thomas' Hospital
> London SE1 7EH
>
> email: alberto.gomez at kcl.ac.uk
> ________________________________________
> From: Luis Ibanez [luis.ibanez at kitware.com]
> Sent: 22 February 2010 23:32
> To: Gomez Herrero, Alberto
> Cc: Insight Users Mailing List
> Subject: Re: [Insight-users] Trouble reading and writing vector images
>
> Hi Alberto,
>
>
> 1) What file format are you using for saving the vector image ?
>
>
> 2) You email asks about itk::VectorImage, but the typedef
> that you show actually uses:
>
> pixeltype = itk::Vector
>
> are you actually using the itk::VectorImage in your code ?
>
> 3) The memory organization of
>
> itk::VectorImage< float, N > (A)
>
> will be different from the memory organization of
>
> itk::Image< itk::Vector< float, N > , N > (B)
>
> In the case of (A) you will have first all the values of the
> first vector component of all the pixels, followed by the
> values of all the second components of all the pixels,
> followed by the third component of all the pixels... etc.
>
> In the case of (B), you have first the N components of
> the first pixel, followed by the N components of the second
> pixel, followed by the N components of the third pixel...etc.
>
>
> Please clarify what code you are using, and what file format.
>
>
> Thanks
>
>
> Luis
>
>
>
> -----------------------------------
> On Mon, Feb 22, 2010 at 12:16 PM, Gomez, Alberto
> <alberto.gomez at kcl.ac.uk> wrote:
>
>> Hi all,
>>
>> I am having some unexpected results when reading and writing vector images.
>> The example would be the following. I have a vector image called
>> "fullVectors_resampled". I give a value to every pixel and then write it to
>> a file. Then I load it and the values have changed!!!
>>
>>
>> VectorImageType::IndexType index;
>> VectorImageType::PixelType vector;
>> vector[0] = 1;
>> vector[1] = 2;
>> vector[2]= 3;
>>
>> for (int i = 0;
>> i<fullVectors_resampled->GetLargestPossibleRegion().GetSize()[0]; i++ ){
>> index[0] = i;
>> for (int j = 0;
>> j<fullVectors_resampled->GetLargestPossibleRegion().GetSize()[1]; j++ ){
>> index[1]=j;
>> for (int k = 0;
>> k<fullVectors_resampled->GetLargestPossibleRegion().GetSize()[2]; k++ ){
>> index[2]=k;
>>
>> fullVectors_resampled->SetPixel(index, vector);
>>
>> }
>>
>> }
>> }
>>
>>
>> WriterVectorType::Pointer writer = WriterVectorType::New();
>> writer->SetFileName(filename);
>> writer->SetInput(fullVectors_resampled);
>> writer->Write();
>>
>>
>> ReaderVectorType::Pointer reader2 = ReaderVectorType::New();
>> reader2->SetFileName(filename);
>> reader2->Update();
>> VectorImageType::Pointer image1g2 = reader2->GetOutput();
>>
>>
>> for (int i = 0;
>> i<fullVectors_resampled->GetLargestPossibleRegion().GetSize()[0]; i++ ){
>> index[0] = i;
>> for (int j = 0;
>> j<fullVectors_resampled->GetLargestPossibleRegion().GetSize()[1]; j++ ){
>> index[1]=j;
>> for (int k = 0;
>> k<fullVectors_resampled->GetLargestPossibleRegion().GetSize()[2]; k++ ){
>> index[2]=k;
>>
>> std::cout <<
>> fullVectors_resampled->GetPixel(index) << " "
>> << image1g2->GetPixel(index) << std::endl;
>>
>> fullVectors_resampled->SetPixel(index, vector);
>>
>> }
>>
>> }
>> }
>>
>> As I am reading the image that I just wrote, I would expect that the vectors
>> are the same... but the output I get is:
>>
>> [1, 2, 3] [1, 1, 1]
>> [1, 2, 3] [2, 2, 2]
>> [1, 2, 3] [3, 3, 3]
>> [1, 2, 3] [1, 1, 1]
>> [1, 2, 3] [2, 2, 2]
>> [1, 2, 3] [3, 3, 3]
>> ...
>> ...
>> ...
>> ...
>> [1, 2, 3] [1, 1, 1]
>> [1, 2, 3] [2, 2, 2]
>> [1, 2, 3] [3, 3, 3]
>>
>> I think this has to do with how memory is organised in these images. I am
>> using the following definition for my VectorImageType:
>>
>> typedef itk::Vector<float, 3> VectorPixelType;
>> typedef itk::Image<VectorPixelType, 3> VectorImageType;
>>
>> And from the itkVectorImage documentation,
>>
>> "This class differs from Image
>> <http://www.itk.org/Doxygen316/html/classitk_1_1Image.html> in that it is
>> intended to represent multiple images. Each pixel represents /k/
>> measurements, each of datatype /TPixel/. The memory organization of the
>> resulting image is as follows: ... Pi0 Pi1 Pi2 Pi3 P(i+1)0 P(i+1)1 P(i+1)2
>> P(i+1)3 P(i+2)0 ... where Pi0 represents the 0th measurement of the pixel at
>> index i."
>>
>> Does this mean that my VectorImageType is organised Pi0 P(i+1)0 ... P(i)1
>> P(i+1)1...P(i)2 P(i+1)2... etc? Anyone has already experienced this? Is this
>> supposed to work this way?
>>
>>
>>
>>
>> --
>>
>> Alberto Gómez
>>
>> /Division of Imaging Sciences
>> The Rayne Institute
>> 4th Floor, Lambeth Wing
>> St Thomas' Hospital
>> London SE1 7EH /
>>
>> phone: +44 (0) 20 718 88364
>> email: alberto.gomez at kcl.ac.uk <mailto:alberto.gomez at kcl.ac.uk>
>>
>> _____________________________________
>> 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.html
>>
>> 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.html
>
> 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
>
--
Alberto Gómez
/Division of Imaging Sciences
The Rayne Institute
4th Floor, Lambeth Wing
St Thomas' Hospital
London SE1 7EH /
phone: +44 (0) 20 718 88364
email: alberto.gomez at kcl.ac.uk <mailto:alberto.gomez at kcl.ac.uk>
More information about the Insight-users
mailing list