[Insight-users] Re: getting pixel values from 3d image

[Luis Ibanez]

Hi Sharad,


The ChangeInformationFilter will not have any effect
in your image if you don't connect the filter to the
pipeline.



You MUST replace the line


     writer->SetInput( reader->GetOutput() );




with the two following lines

     imgspacing->SetInput( reader->GetOutput() );
     writer->SetInput( imagspacing->GetOutput() );



Regards,


   Luis



---------------------------------------
sharad at hermes.eng.fsu.edu wrote:

> Hi Luis 
> 
> i followed what you said about the spacing the program doesnt give any
> error but i am not sure if the setoutput spacing did any difference to my 
> final image can you look at my code and tell me if anything is wrong.
> thanks 
> 
> regards
> sharad
> 
> #############
> 
> 
> #include "itkNumericSeriesFileNames.h"
> #include "itkImageSeriesReader.h"
> #include "itkImageFileWriter.h"
> #include "itkImage.h"
> #include <vector>
> #include <string>
> #include <stdio.h>
> #include <itkChangeInformationImageFilter.h>
> 
> int main(int argc, char * argv[])
> {
> std::cout << argv[1] << std::endl;
>   typedef itk::Image<unsigned char,3> Image3DType;
> 
>   // Verify the number of parameters in the command line
>   if( argc < 4 )
>     {
>     std::cerr << "Usage: " << std::endl;
>     std::cerr << argv[0] << "StartIndex  EndIndex inputImageFileBaseName
> outputImageFile" << std::endl;
>     std::cerr << " Example:  StartIndex = 1 , EndIndex =
> 100,inputImageFileBaseName = myI00%d.png" << std::endl;
>     std::cerr << " will read myI001.png, ..., myI100.png.  100 png files" 
> << std::endl;
>     std::cerr << " if outputImageFile = my.mha then it will output a file 
> my.mha which is in meta format" << std::endl;
>     std::cerr << " if outputImageFile = my.gipl then it will output a
> file my.gipl which is in gipl format" << std::endl;
>     std::cerr << " ./readPngWrite3DGiplNew 0 1 myImages00%d.png outp.mha
> "  << std::endl;
>     std::cerr << " will read in myImages000.png and myImages001.png,
> output outp.mha in meta format " << std::endl;
>     return -1;
>     }
> 
>   const int  StartIndex  = (int) atof(argv[1]);
>   const int  EndIndex    = (int) atof(argv[2]);
>   const char * inImFileBase = argv[3];
>   const char * ouImFileName = argv[4];
>   
> //  
> 
> 
>   //std::cout << argv[4] << std::endl;
> 
>   //
>   // Here we generate filenames like
>   // myImage000.png, myImage001.png  .... to myImage200.png
>   // The most important thing is that the seriess must be
>   // same size!!!!!!!!!!!!!!
>   //
> 
> 
>   itk::NumericSeriesFileNames::Pointer fileIter =
>                       itk::NumericSeriesFileNames::New();
> 
>   fileIter->SetStartIndex( StartIndex );
>   fileIter->SetEndIndex( EndIndex );
>   fileIter->SetIncrementIndex( 1 );
>   //const char * inputFileNameBase = ( const char * ) strcat( (char *)
> //inImFileBase, (char *) "00%d.png");
>   //std::cout << inputFileNameBase  << std::endl;
>   //std::cout << argv[3] << std::endl;
>    //std::cout << argv[4] << std::endl;
>   //fileIter->SetSeriesFormat("myImages00%d.png");
> 
>    
>   fileIter->SetSeriesFormat(inImFileBase);
> 
>   itk::ImageSeriesReader<Image3DType>::Pointer reader =
> itk::ImageSeriesReader<Image3DType>::New();
>   reader->SetFileNames( fileIter->GetFileNames() );
> 
>   
>   reader->Update();
>   
> 
> 
> double spacing[3]; /*new */
> 	  
> spacing[0] = 0.1; // spacing in mm along X
> spacing[1] = 0.1; // spacing in mm along Y
> spacing[2] = 0.50; // spacing in mm along Z
> 
> itk::ChangeInformationImageFilter<Image3DType>::Pointer imgspacing =
> itk::ChangeInformationImageFilter<Image3DType>::New();
>   
> imgspacing->SetOutputSpacing( spacing );
> 
> 
> 
> 
> 
>   //
>   //  Here we save the image in GIPL format
>   //  or any other forms which itk understand!
>   //  The user only need to give the correct
>   //  file extention !
>   //
>   itk::ImageFileWriter< Image3DType >::Pointer writer =
>                    itk::ImageFileWriter< Image3DType >::New();
> 
>   writer->SetInput(   reader->GetOutput()  );
>    //writer->SetFileName("myImage.mha");
>    //return 0;
> 
>   writer->SetFileName(ouImFileName);
>   
>   try
> 
>   {
>     writer->Update();
>     }
>   catch( itk::ExceptionObject & err )
>     {
>     std::cout << "ExceptionObject caught !" << std::endl;
>     std::cout << err << std::endl;
>     return -1;
>     }
> 
>   
>   return 0;
> }
> 
> 
>