[Insight-users] Error even after fixing ITK bug /CombiningImageSeriesReader and RawImageIO

[Andreas Keil]

Dear Xabi,

you are absolutely right. Now it works perfectly and as mentioned in my
previous reply, I was wrong when balming bugs in ITK.

However, a comment in ImageSeriesReader's SetImageIO would be nice, giving
a hint that one has to specify the format of a single file. I reported
this as a request to the ITK bug tracking system.

Kind regards,
Andreas.


-----Original Message-----
From: insight-users-bounces+andreas.keil=cs.tum.edu at itk.org
[mailto:insight-users-bounces+andreas.keil=cs.tum.edu at itk.org] On Behalf
Of Xabier Artaechevarria Artieda
Sent: Monday, March 12, 2007 09:50
To: insight-users at itk.org
Subject: RE: [Insight-users] Error even after fixing ITK bug
/CombiningImageSeriesReader and RawImageIO

Hi Andreas,

in fact, I think the problem is another. You are reading 2D raw  
images, then you should not set the third dimension in the "io" object  
(dimension, spacing...). I think you should set the parameters of the  
raw reader as if you were reading just one 2D slice.

Hope that helps,
Xabi


-- 
Xabier Artaechevarria
Cancer Imaging Laboratory
Centre for Applied Medical Research
www.cima.es



Andreas Keil <andreas.keil at cs.tum.edu> ha escrito:

> Hi Xabi,
>
> thank you for your hint. Your are probably right that specifying
> 	io->SetFileDimensionality(2);
> is correct. Unfortunately, this does not help. I still get the same
error
> of only reading one file.
>
> Andreas
>
>
> -----Original Message-----
> From: insight-users-bounces+andreas.keil=cs.tum.edu at itk.org
> [mailto:insight-users-bounces+andreas.keil=cs.tum.edu at itk.org] On Behalf
> Of Xabier Artaechevarria Artieda
> Sent: Friday, March 09, 2007 17:17
> To: insight-users at itk.org
> Subject: Re: [Insight-users] Error even after fixing ITK bug /
> CombiningImageSeriesReader and RawImageIO
>
> Hi Andreas,
> I think the following line could solve the problem:
>
> io->SetFileDimensionality(Dimension);
>
> Good luck,
> Xabi
>
> --
> Xabier Artaechevarria
> Cancer Imaging Laboratory
> Centre for Applied Medical Research
> www.cima.es
>
>
>
> Andreas Keil <andreas.keil at cs.tum.edu> ha escrito:
>
>> Hello,
>>
>> I'd like to read image data from a series of raw files containing a 2D
>> slice each, e.g. a 620x480x191 voxel volume in the files "data.001" to
>> "data.191". Therefore, I set up an ImageSeriesReader and a RawImageIO
in
>> the following way:
>>
>>
>
-------------------------------------------------------------------------
>> #include "itkImage.h"
>> #include "itkImageSeriesReader.h"
>> #include "itkRawImageIO.h"
>> #include "itkNumericSeriesFileNames.h"
>>
>> typedef float PixelType;
>> const int Dimension = 3;
>> typedef itk::Image<PixelType, Dimension> ImageType;
>> ImageType::Pointer itkImg = ImageType::New();
>>
>> typedef itk::ImageSeriesReader<ImageType> ReaderType;
>> ReaderType::Pointer reader = ReaderType::New();
>>
>> typedef itk::RawImageIO<PixelType, Dimension> ImageIOType;
>> ImageIOType::Pointer io = ImageIOType::New();
>>
>> io->SetDimensions(0, 620);
>> io->SetDimensions(1, 480);
>> io->SetDimensions(2, 191);
>> io->SetSpacing(0, 1.0);
>> io->SetSpacing(1, 1.0);
>> io->SetSpacing(2, 1.0);
>> io->SetOrigin(0, 0.0);
>> io->SetOrigin(1, 0.0);
>> io->SetOrigin(2, 0.0);
>> io->SetHeaderSize(0);
>> io->SetByteOrderToLittleEndian();
>> io->SetFileTypeToBinary();
>> io->SetFileDimensionality(Dimension);
>> io->SetPixelType(itk::ImageIOBase::SCALAR);
>> io->SetNumberOfComponents(1);
>>
>> typedef itk::NumericSeriesFileNames NameGeneratorType;
>> NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>> nameGenerator->SetSeriesFormat("data.%03d");
>> nameGenerator->SetStartIndex(1);
>> nameGenerator->SetEndIndex(191);
>>
>> reader->SetImageIO(io);
>> reader->SetFileNames(nameGenerator->GetFileNames());
>>
>> // read image into ITK image
>> reader->Update();
>> itkImg = reader->GetOutput();
>>
>
-------------------------------------------------------------------------
>>
>> However, even after fixing a bug (which I'll report asap) in
>> itkImageSeriesReader.txx where the two lines
>>
>>     dimSize[m_NumberOfDimensionsInImage] = m_FileNames.size();
>>     spacing[m_NumberOfDimensionsInImage] = interSliceSpacing;
>>
>> had to be fixed by adding -1 in the index, I still can't read an image
>> series with RawImageIO. I get an ITK exception telling me that only one
>> 1190400 bytes could be read (which is the size of one slice) instead of
>> 227366400 bytes (which is the whole volume's size). It seems to me that
>> the RawImageIO object wants to read all data from the first file, which
>> is, of course, impossible. How can I tell the
> ImageSeriesReader/RawImageIO
>> that I want to read the input from all 191 files?
>>
>> Thank you,
>> Andreas.