[Insight-users] write out all dicom header info

[Mathieu Malaterre]

Hi Clemens,

	Writing DICOM can become quickly complex. I believe for your question 
you need to re-read the ITK Software Guide, I have tried to describe 
most cases

Q: Why some data elements are not loaded ?
A: By default we do not load some binary elements that are considered 
too long. See for example: DicomImageReadPrintTags.cxx. To override this 
default behavior:

<quote>
// Software Guide : BeginLatex
//
// Here we override the gdcm default value of 0xfff with a value of 0xffff
// to allow the loading of long binary stream in the DICOM file.
// This is particularly useful when reading the private tag: 0029,1010
// from Siemens as it allows to completely specify the imaging parameters
//
// Software Guide : EndLatex
   dicomIO->SetMaxSizeLoadEntry(0xffff);
<quote>

Q: How can I write a DICOM image using a DICOM header read from a 
previous operation ?
A: You should have a look at DicomImageReadChangeHeaderWrite. In this 
example we read in a DICOM file, and change some info found in the 
header so that we rewrite the image with the header info changed.


   Writer1Type::Pointer writer1 = Writer1Type::New();

   writer1->SetInput( reader->GetOutput() );
   writer1->SetFileName( argv[2] );
   writer1->SetImageIO( gdcmImageIO );  // reuse the same GDCM IO


HTH
Mathieu


Eric Claus wrote:
> Hi Mathieu,
> I still have not been able to all the private tags written out.  I tried 
> making a custom dictionary of the private tags, although this still 
> misses a few tags (haven't been able to figure out why).  There was also 
> an earlier post to the list in which the header tags were printed out to 
> a text file 
> (http://public.kitware.com/pipermail/insight-users/2006-October/019862.html), 
> and I was thinking that I could apply a similar method for writing out 
> the header, but I couldn't figure it out.
> 
> I am curious about your comment though.  What would reusing the same 
> ImageIO look like?  I thought I was doing this already, although I have 
> to admit that I am pretty novice at programming in c, so I could be wrong.
> 
> Thanks,
> Eric
> 
> Mathieu Malaterre wrote:
>> Hi Eric,
>>
>>     Did you ever solve your issue ? I believe this is just a matter of 
>> reusing the same ImageIO used for reading for writing.
>>
>> HTH
>> -M
>>
>> Eric Claus wrote:
>>> Hi,
>>> I am trying to use ITK to read in 2 different DICOM images, combine 
>>> the images by taking the sqrt(image1^2 + image2^2) and then writing 
>>> out the image with the header from image1.  I have been successful in 
>>> reading and writing the images, but have been unable to figure out 
>>> how to write the entire header.  Is there any easy way to just copy 
>>> all the header info from one image to another?  The current program 
>>> appears to only write out the information that is part of the 
>>> MetaDictionary???  I pasted my code below if that is of any use to 
>>> anyone.
>>>
>>> Thanks in advance,
>>> Eric
>>>
>>>
>>> #include "itkImageFileReader.h"
>>> #include "itkImageFileWriter.h"
>>> #include "itkRescaleIntensityImageFilter.h"
>>> #include "itkGDCMImageIO.h"
>>> #include "itkImageRegionConstIterator.h"
>>> #include "itkImageRegionIterator.h"
>>>
>>> #include <list>
>>> #include <fstream>
>>>
>>> int main( int argc, char* argv[] )
>>> {
>>>
>>>  // Verify the number of parameters in the command line
>>>  // Should have nonzshim, zshim, outputname
>>>  if( argc < 3 )
>>>    {
>>>    std::cerr << "Usage: " << std::endl;
>>>    std::cerr << argv[0] << " nonzshimImage zshimImage outputImage\n";
>>>    return EXIT_FAILURE;
>>>    }
>>>
>>>  typedef signed short InputPixelType;
>>>  const unsigned int   InputDimension = 2;
>>>
>>>  typedef itk::Image< InputPixelType, InputDimension > InputImageType;
>>>
>>>
>>>  typedef itk::ImageFileReader< InputImageType > ReaderType;
>>>
>>>  ReaderType::Pointer reader = ReaderType::New();
>>>  reader->SetFileName( argv[1] );
>>>
>>>  ReaderType::Pointer reader2 = ReaderType::New();
>>>  reader2->SetFileName( argv[2] );
>>>  
>>>  try
>>>    {
>>>    reader->Update();
>>>    reader2->Update();
>>>    }
>>>  catch (itk::ExceptionObject & e)
>>>    {
>>>    std::cerr << "exception in file reader " << std::endl;
>>>    std::cerr << e << std::endl;
>>>    return EXIT_FAILURE;
>>>    }
>>>
>>>
>>> typedef itk::Image<InputPixelType, InputDimension> InputImageType;
>>> typedef itk::ImageRegionConstIterator< InputImageType > 
>>> ConstIteratorType;
>>> typedef itk::ImageRegionIterator< InputImageType > IteratorType;
>>>
>>>
>>> InputImageType::Pointer image = reader->GetOutput();   
>>> ConstIteratorType constIterator1( image, image->GetRequestedRegion() );
>>> IteratorType iterator1( image, image->GetRequestedRegion() );
>>>   InputImageType::Pointer image2 = reader2->GetOutput(); 
>>> ConstIteratorType constIterator2( image2, 
>>> image2->GetRequestedRegion() );
>>> IteratorType iterator2( image2, image2->GetRequestedRegion() );
>>>
>>>
>>>   ConstIteratorType in1( image, image->GetRequestedRegion() );
>>> ConstIteratorType in2( image2, image2->GetRequestedRegion() );
>>>
>>> IteratorType out( image2, image->GetRequestedRegion() );
>>>
>>> for ( in1.GoToBegin(), out.GoToBegin(), in2.GoToBegin(); 
>>> !in1.IsAtEnd(); ++in1, ++out, ++in2 )
>>> {
>>> out.Set( 0.5 + (1.33 * sqrt( (in1.Get()) * (in1.Get()) + (in2.Get()) 
>>> * (in2.Get()) )));
>>> }
>>>
>>> typedef itk::ImageFileWriter< InputImageType >  Writer1Type;
>>>
>>>  Writer1Type::Pointer writer1 = Writer1Type::New();
>>>
>>>  writer1->SetFileName( argv[3] );
>>>  writer1->SetInput( image2 );
>>>
>>>  try
>>>    {
>>>    writer1->Update();
>>>    }
>>>  catch (itk::ExceptionObject & e)
>>>    {
>>>    std::cerr << "exception in file writer " << std::endl;
>>>    std::cerr << e << std::endl;
>>>    return EXIT_FAILURE;
>>>    }
>>>
>>>    return EXIT_SUCCESS;
>>>
>>> }
>>>
>>>
>