[ITK] [ITK-users] Saving results .dcm files
Matias Montroull
matimontg at gmail.com
Wed Mar 16 20:10:18 EDT 2016
try this:
/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#include "itkGDCMImageIO.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"
#include "itkMetaDataObject.h"
#include <vector>
#include "itksys/SystemTools.hxx"
// Software Guide : BeginLatex
//
// This example illustrates how to read a 3D image from a non DICOM file
and write it as a series of DICOM slices.
// with some changed header information. Header
//
// Please note that modifying the content of a DICOM header is a very risky
// operation. The Header contains fundamental information about the patient
// and therefore its consistency must be protected from any data corruption.
// Before attempting to modify the DICOM headers of your files, you must
make
// sure that you have a very good reason for doing so, and that you can
ensure
// that this information change will not result in a lower quality of health
// care to be delivered to the patient.
//
// \index{DICOM!Writing Series}
//
// Software Guide : EndLatex
int main( int argc, char* argv[] )
{
if( argc < 3 )
{
std::cerr << "Usage: " << argv[0];
std::cerr << " InputImage OutputDicomDirectory" << std::endl;
return EXIT_FAILURE;
}
typedef signed short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( argv[1] );
try
{
reader->Update();
}
catch (itk::ExceptionObject &excp)
{
std::cerr << "Exception thrown while writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
typedef itk::GDCMImageIO ImageIOType;
typedef itk::NumericSeriesFileNames NamesGeneratorType;
ImageIOType::Pointer gdcmIO = ImageIOType::New();
const char * outputDirectory = argv[2];
itksys::SystemTools::MakeDirectory( outputDirectory );
typedef signed short OutputPixelType;
const unsigned int OutputDimension = 2;
typedef itk::Image< OutputPixelType, OutputDimension > Image2DType;
typedef itk::ImageSeriesWriter<
ImageType, Image2DType > SeriesWriterType;
NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
itk::MetaDataDictionary & dict = gdcmIO->GetMetaDataDictionary();
std::string tagkey, value;
tagkey = "0008|0060"; // Modality
value = "MR";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value );
tagkey = "0008|0008"; // Image Type
value = "DERIVED\\SECONDARY";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
tagkey = "0008|0064"; // Conversion Type
value = "DV";
itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
seriesWriter->SetInput( reader->GetOutput() );
seriesWriter->SetImageIO( gdcmIO );
ImageType::RegionType region =
reader->GetOutput()->GetLargestPossibleRegion();
ImageType::IndexType start = region.GetIndex();
ImageType::SizeType size = region.GetSize();
std::string format = outputDirectory;
format += "/imagen%03d.dcm";
namesGenerator->SetSeriesFormat( format.c_str() );
namesGenerator->SetStartIndex( start[2] );
namesGenerator->SetEndIndex( start[2] + size[2] - 1 );
namesGenerator->SetIncrementIndex( 1 );
seriesWriter->SetFileNames( namesGenerator->GetFileNames() );
try
{
seriesWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown while writing the series " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
El mié., 16 de mar. de 2016 a la(s) 16:27, Dženan Zukić <dzenanz at gmail.com>
escribió:
> Hi Abdelkhalek,
>
> the problem does not seem to be there. The attached example compiles
> fine for me.
>
> Regards,
> Dženan
>
> On Wed, Mar 16, 2016 at 8:33 AM, Abdelkhalek Bakkari
> <bakkari.abdelkhalek at hotmail.fr> wrote:
> > I tried to write the following code :
> >
> >
> > /////////////////// Begin Dicom Writer
> >
> > ReaderType::Pointer reader = ReaderType::New();
> > ImageIOType::Pointer gdcmIO = ImageIOType::New();
> > NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
> >
> > itksys::SystemTools::MakeDirectory( "slic" );
> > SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
> > seriesWriter->SetInput( reader->GetOutput() );
> > seriesWriter->SetImageIO( gdcmIO );
> > namesGenerator->SetOutputDirectory("slic");
> > seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames());
> > seriesWriter->SetMetaDataDictionaryArray(
> > reader->GetMetaDataDictionaryArray() );
> >
> > ////////////////// End Dicom Writer
> >
> > Some errors appear :
> >
> > c:\itk
> >
> 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxx(184):
> > error C2248: 'itk::Image<TPixel,VImageDimension>::~Image' : cannot access
> > protected member declared in class 'itk::Image<TPixel,VImageDimension>'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2> C:/ITK
> 4.8.1/Source/Modules/Core/Common/include\itkImage.h(279)
> > : see declaration of 'itk::Image<TPixel,VImageDimension>::~Image'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2>c:\itk
> >
> 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxx(188):
> > error C2248: 'itk::Image<TPixel,VImageDimension>::Image' : cannot access
> > protected member declared in class 'itk::Image<TPixel,VImageDimension>'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2> C:/ITK
> 4.8.1/Source/Modules/Core/Common/include\itkImage.h(276)
> > : see declaration of 'itk::Image<TPixel,VImageDimension>::Image'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2>c:\itk
> >
> 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxx(188):
> > error C2248: 'itk::Image<TPixel,VImageDimension>::~Image' : cannot access
> > protected member declared in class 'itk::Image<TPixel,VImageDimension>'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2> C:/ITK
> 4.8.1/Source/Modules/Core/Common/include\itkImage.h(279)
> > : see declaration of 'itk::Image<TPixel,VImageDimension>::~Image'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2>c:\itk
> >
> 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxx(213):
> > error C2248: 'itk::Image<TPixel,VImageDimension>::~Image' : cannot access
> > protected member declared in class 'itk::Image<TPixel,VImageDimension>'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2> C:/ITK
> 4.8.1/Source/Modules/Core/Common/include\itkImage.h(294)
> > : compiler has generated 'itk::Image<TPixel,VImageDimension>::~Image'
> here
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2> c:\itk
> >
> 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxx(209) :
> > while compiling class template member function 'void
> >
> itk::ImportImageContainer<TElementIdentifier,TElement>::DeallocateManagedMemory(void)'
> > 2> with
> > 2> [
> > 2> TElementIdentifier=unsigned long,
> > 2> TElement=itk::Image<InputPixelType,2>
> > 2> ]
> > 2>c:\itk 4.8.1\source\modules\core\common\include\itkImage.hxx(151):
> error
> > C2248: 'itk::Image<TPixel,VImageDimension>::Image' : cannot access
> protected
> > member declared in class 'itk::Image<TPixel,VImageDimension>'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2> C:/ITK
> 4.8.1/Source/Modules/Core/Common/include\itkImage.h(276)
> > : see declaration of 'itk::Image<TPixel,VImageDimension>::Image'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2> c:\itk
> > 4.8.1\source\modules\core\common\include\itkImage.hxx(148) : while
> compiling
> > class template member function 'unsigned int
> > itk::Image<TPixel,VImageDimension>::GetNumberOfComponentsPerPixel(void)
> > const'
> > 2> with
> > 2> [
> > 2> TPixel=OutputImageType,
> > 2> VImageDimension=2
> > 2> ]
> > 2>c:\itk 4.8.1\source\modules\core\common\include\itkImage.hxx(151):
> error
> > C2248: 'itk::Image<TPixel,VImageDimension>::~Image' : cannot access
> > protected member declared in class 'itk::Image<TPixel,VImageDimension>'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> > 2> C:/ITK
> 4.8.1/Source/Modules/Core/Common/include\itkImage.h(279)
> > : see declaration of 'itk::Image<TPixel,VImageDimension>::~Image'
> > 2> with
> > 2> [
> > 2> TPixel=InputPixelType,
> > 2> VImageDimension=2
> > 2> ]
> >
> > Abdelkhalek Bakkari
> > Ph.D candidate in Computer Science
> > Institute of Applied Computer Science
> > Lodz University of Technology, Poland
> >
> >
> >
> >
> > ________________________________
> > From: kiran.j88 at gmail.com
> > Date: Wed, 16 Mar 2016 10:27:51 +0000
> > Subject: Re: [ITK-users] Saving results .dcm files
> > To: bakkari.abdelkhalek at hotmail.fr; insight-users at itk.org
> >
> >
> > Hi Abdelkhalek,
> >
> > Examples can be found in Chapter 1 of Book 2 of the ITK Software guide:
> > http://www.itk.org/ItkSoftwareGuide.pdf
> > See page 340 of the pdf.
> >
> > You can find the full source code for the examples on the ITK Doxygen
> pages,
> > e.g.:
> >
> http://www.itk.org/Doxygen/html/Examples_2IO_2DicomSeriesReadSeriesWrite_8cxx-example.html
> >
> > And there are more examples on the ITK wiki, e.g.:
> > http://itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
> >
> > Regards,
> > Kiran
> >
> >
> > On Wed, 16 Mar 2016 at 10:19 Abdelkhalek Bakkari
> > <bakkari.abdelkhalek at hotmail.fr> wrote:
> >
> >
> > Hi !
> >
> > I am looking for saving the results of ITK as .dcm files for a 3D image.
> > Any help ! Any suggestion ! please.
> >
> > Best regards,
> >
> > Abdelkhalek Bakkari
> > Ph.D candidate in Computer Science
> > Institute of Applied Computer Science
> > Lodz University of Technology, Poland
> >
> >
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> Visit other Kitware open-source projects at
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>
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--
Matias
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