[Insight-users] RGBImageSeriesReadWrite

[Luis Ibanez]

Hi Michelle,

The most likely suspect are the indices of images that you
are asking to read. It may be that you are going one image
past the end, or that your generated filenames don't quite
match what you think you are passing.

An easy way to confirm is to print out the internal list of
filesnames in the series before you attempt to read it.



You can do this with code such as:


    typedef std::list< std::string >   NamesType;

    NamesType & list = namesGenerator->GetFileNames();

    for(int i=0; i<list.size(); i++)
      {
      std::cout << "file " << i << " = " << list[i] << std::endl;
      }


from the results of that print out, you should revisit
your setup for the lines:


 >   nameGenerator->SetStartIndex( first );
 >   nameGenerator->SetEndIndex( last );
 >   nameGenerator->SetIncrementIndex( 1 );
 >   nameGenerator->SetSeriesFormat( "vwe%04d.png" );




Regards,


     Luis



---------------------------
Michelle Anne Borkin wrote:

> I'm a new user to ITK and am trying to get a series of .png images read.
> The sample program "RGBImageReadWrite" worked fine on an individual image.
> I then tried to use the sample program "RGBImageSeriesReadWrite" to read
> the whole series, but it keeps crashing (see error message below).  I even
> converted my file names to match the ones in this sample program.  Has
> anyone encountered this (or similar problems) with this program?  Any
> suggestions?
> 
> Thanks,
> Michelle
> 
> _______________________
> 
> Window's Error messages:
> 
> "Debug Error!
> 
> Program: ...K\RGBImageSeriesReadWrite\Debug\RGBImageSeriesReadWrite.exe
> 
> This application has requested the Runtime to terminate it in an unusual
> way.  Please
> 
> contact the application's support team for more information.
> 
> (Press Retry to debug the application)
> 
> [After hitting Retry:]
> 
> RGBImageSeriesReadWrite.exe has encountered a problem and needs to
> close."
> 
> 
> _______________________
> The code is below:
> 
> /*=========================================================================
> 
>   Program:   Insight Segmentation & Registration Toolkit
>   Module:    $RCSfile: RGBImageSeriesReadWrite.cxx,v $
>   Language:  C++
>   Date:      $Date: 2004/12/22 21:10:15 $
>   Version:   $Revision: 1.4 $
> 
>   Copyright (c) Insight Software Consortium. All rights reserved.
>   See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for
> details.
> 
>      This software is distributed WITHOUT ANY WARRANTY; without even
>      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
>      PURPOSE.  See the above copyright notices for more information.
> 
> =========================================================================*/
> 
> //  Software Guide : BeginLatex
> //
> //  RGB images are commonly used for representing data acquired from
> //  cryogenic sections, optical microscopy and endoscopy. This example
> //  illustrates how to read and write RGB color images to and from a file.
> //  This requires the following headers as shown.
> //
> //  \index{itk::RGBPixel!Image}
> //  \index{RGB!writing Image}
> //  \index{RGB!reading Image}
> //
> //  Software Guide : EndLatex
> 
> // Software Guide : BeginCodeSnippet
> #include "itkRGBPixel.h"
> #include "itkImage.h"
> #include "itkImageSeriesReader.h"
> #include "itkImageFileWriter.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkPNGImageIO.h"
> // Software Guide : EndCodeSnippet
> 
> 
> int main( int argc, char ** argv )
> {
>   // Verify the number of parameters in the command line
>   if( argc < 4 )
>     {
>     std::cerr << "Usage: " << std::endl;
>     std::cerr << argv[0] << "first last  outputRGBImageFile " <<
> std::endl;
>     return -1;
>     }
> 
> 
>   // Software Guide : BeginLatex
>   //
>   // The \doxygen{RGBPixel} class is templated over the type used to
>   // represent each one of the red, green and Blue components. A typical
>   // instantiation of the RGB image class might be as follows.
>   //
>   //  \index{itk::RGBPixel!Instantiation}
>   //
>   // Software Guide : EndLatex
> 
>   // Software Guide : BeginCodeSnippet
>   typedef itk::RGBPixel< unsigned char >        PixelType;
>   const unsigned int Dimension = 3;
> 
>   typedef itk::Image< PixelType, Dimension >    ImageType;
>   // Software Guide : EndCodeSnippet
> 
> 
>   // Software Guide : BeginLatex
>   //
>   // The image type is used as a template parameter to instantiate
>   // the reader and writer.
>   //
>   // \index{itk::ImageSeriesReader!RGB Image}
>   // \index{itk::ImageFileWriter!RGB Image}
>   //
>   // Software Guide : EndLatex
> 
>   // Software Guide : BeginCodeSnippet
>   typedef itk::ImageSeriesReader< ImageType >  ReaderType;
>   typedef itk::ImageFileWriter<   ImageType >  WriterType;
> 
>   ReaderType::Pointer reader = ReaderType::New();
>   WriterType::Pointer writer = WriterType::New();
>   // Software Guide : EndCodeSnippet
> 
> 
>   const unsigned int first = atoi( argv[1] );
>   const unsigned int last  = atoi( argv[2] );
> 
>   const char * outputFilename = argv[3];
> 
>   // Software Guide : BeginCodeSnippet
>   typedef itk::NumericSeriesFileNames    NameGeneratorType;
> 
>   NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
> 
>   nameGenerator->SetStartIndex( first );
>   nameGenerator->SetEndIndex( last );
>   nameGenerator->SetIncrementIndex( 1 );
> 
>   nameGenerator->SetSeriesFormat( "vwe%04d.png" );
>   // Software Guide : EndCodeSnippet
> 
> 
> 
>   //  Software Guide : BeginLatex
>   //
>   //  The ImageIO object that actually performs the read process
>   //  is now connected to the ImageSeriesReader.
>   //
>   //  Software Guide : EndLatex
> 
>   // Software Guide : BeginCodeSnippet
>   reader->SetImageIO( itk::PNGImageIO::New() );
>   // Software Guide : EndCodeSnippet
> 
> 
> 
> 
>   //  Software Guide : BeginLatex
>   //
>   //  The filenames of the input and output files must be provided to the
>   //  reader and writer respectively.
>   //
>   //  Software Guide : EndLatex
> 
>   // Software Guide : BeginCodeSnippet
>   reader->SetFileNames( nameGenerator->GetFileNames()  );
> 
>   writer->SetFileName( outputFilename );
>   // Software Guide : EndCodeSnippet
> 
>   try
>     {
>     reader->Update();
>     }
>   catch( itk::ExceptionObject & excp )
>     {
>     std::cerr << "Error reading the series " << std::endl;
>     std::cerr << excp << std::endl;
>     }
> 
>   ImageType::Pointer image = reader->GetOutput();
>   writer->SetInput( image );
> 
> 
>   //  Software Guide : BeginLatex
>   //
>   //  Finally, execution of the pipeline can be triggered by invoking the
>   //  Update() method in the writer.
>   //
>   //  Software Guide : EndLatex
> 
>   // Software Guide : BeginCodeSnippet
>   writer->Update();
>   // Software Guide : EndCodeSnippet
> 
>   //  Software Guide : BeginLatex
>   //
>   //  You may have noticed that apart from the declaraton of the
>   //  \code{PixelType} there is nothing in this code that is specific for
> RGB
>   //  images. All the actions required to support color images are
> implemented
>   //  internally in the \doxygen{ImageIO} objects.
>   //
>   //  Software Guide : EndLatex
> 
> 
>   return 0;
> }
> 
> 
> 
> 
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