[Insight-users] 3D level set segmentation: How to use the ImageSeriesWriter

[Luis Ibanez]

Hi John,


Please take a look at the examples:


      Insigtht/Examples/IO
           ImageSeriesReadWrite.cxx
           ImageSeriesReadWrite2.cxx

and if you continue experiencing any problems
please post your source code to the mailing list.

Reading a series and writing a series should be
a very straight forward task.


    Thanks


        Luis


-------------------
John Dailey wrote:
> I am having problems with extending geodesic active contours to 3d as
> well.  I am fairly certain that my problems are related to how I try
> to write the image out at the end of the pipeline.
> 
> I sent the following message to the list a few days ago, but I haven't
> gotten any responses (actually no message I have sent to the list in
> the last month has gotten any responses, I am starting to wonder if
> there is something wrong with how I am sending to the list.  Are you
> folks getting my emails?)
> 
> Thanks,
> John
> 
> <begin quoted message>
> I am having some problems using the itkImageSeriesWriter.  I am quite
> certain that I must be setting things up wrong, or not understanding
> what it is supposed to be used for, or something.
> 
> In debugging my 3d segmentation code, I realized that I can't even get
> the image series writer to work (and that might be why my segmentation
> isn't working).
> 
> I wrote a little code that runs the ImageSeriesReader, casts the pixel
> type and then runs the ImageSeriesWriter (going to a different file
> name).  The code doesn't do anything (it should result in a copy of my
> image series, right?), and I am hoping someone can help me figure out
> why.  One thing I noticed that I think might be relevant is that when
> I just call update on the reader, or the caster instead of the writer,
> the runtime of the code is much longer.  Like it is reading the images
> and casting them in the case where update is called on the caster
> rather than the writer, where when it is called on the writer, the
> code just returns...
> 
> Any ideas?
> 
> Thanks for helping me out, I am still trying to figure out how ITK works...
> 
> -John
> 
> 
> 
> 
> 
> Here is the program I wrote:
> 
> #include "itkImage.h"
> #include "itkRescaleIntensityImageFilter.h"
> #include <iostream>
> #include <string>
> 
> #include "itkImageSeriesWriter.h"
> #include "itkImageSeriesReader.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkPNGImageIO.h"
> 
> 
> int main( int argc, char *argv[] )
> {
>  if( argc < 4 )
>    {
>    std::cerr << "Missing Parameters " << std::endl;
>    std::cerr << "Usage: " << argv[0];
>    std::cerr << " inputImage  outputImage #ofSlices"  << std::endl;
>    return 1;
>    }
> 
>  typedef   float           InternalPixelType;
>  const     unsigned int    Dimension = 3;
>  typedef itk::Image< InternalPixelType, Dimension >  InternalImageType;
> 
>  typedef unsigned char OutputPixelType;
>  typedef itk::Image< OutputPixelType, Dimension-1 > OutputImageType;
>  typedef itk::Image< OutputPixelType, Dimension > OutputSeriesType;
> 
> 
> 
>  // We instantiate reader and writer types in the following lines.
>  //
>        typedef itk::NumericSeriesFileNames    NameGeneratorType;
> 
>        NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>        const std::string infilebase = argv[1];
>        const unsigned int first = 0;
>        const unsigned int last  = atoi( argv[3] );
> 
>        std::string seriesFormat = infilebase+"%03d.png";
>        nameGenerator->SetSeriesFormat(seriesFormat.c_str());
>        nameGenerator->SetStartIndex(first);
>        nameGenerator->SetEndIndex(last);
>        nameGenerator->SetIncrementIndex(1);
>        std::cout <<"seriesFormat:"<<seriesFormat.c_str()<<std::endl;
> 
>        NameGeneratorType::Pointer outGenerator = NameGeneratorType::New();
>        const std::string outfilebase = argv[2];
> 
>        std::string outFormat = outfilebase+"%03d.png";
>        outGenerator->SetSeriesFormat(outFormat.c_str());
>        outGenerator->SetStartIndex(first);
>        outGenerator->SetEndIndex(last);
>        outGenerator->SetIncrementIndex(1);
> 
>  typedef  itk::ImageSeriesReader< InternalImageType > ReaderType;
>  typedef  itk::ImageSeriesWriter< OutputImageType, OutputSeriesType
> 
>>WriterType;
> 
> 
>  ReaderType::Pointer reader = ReaderType::New();
>  WriterType::Pointer writer = WriterType::New();
> 
>        reader->SetImageIO(itk::PNGImageIO::New());
>        reader->SetFileNames(nameGenerator->GetFileNames());
> 
>        writer->SetImageIO(itk::PNGImageIO::New());
>        writer->SetFileNames(outGenerator->GetFileNames());
> 
>  typedef itk::RescaleIntensityImageFilter<
>                               InternalImageType,
>                               OutputImageType >   CastFilterType;
> 
>  CastFilterType::Pointer casterA = CastFilterType::New();
>  casterA->SetInput(reader->GetOutput() );
>  writer->SetInput( casterA->GetOutput() );
> 
> 
>  try
>    {
>    //casterA->Update();
>    writer->UpdateLargestPossibleRegion();
>    }
>  catch( itk::ExceptionObject & excep )
>    {
>    std::cerr << "Exception caught !" << std::endl;
>    std::cerr << excep << std::endl;
>    }
> 
> 
>  return 0;
> }
> <end quoted message>
> 
> 
> 
> 
> On Fri, Jul 18, 2008 at 7:48 AM, Luca Antiga <luca.antiga at gmail.com> wrote:
> 
>>Dear Gokhan,
>> geodesic active contours have been widely used even in large datasets
>>(surely larger than the ones you're mentioning), provided you have enough
>>memory available.
>>One of two things may be happening:
>>1. you're not running out of memory and your operative system starts
>>swapping on the virtual memory
>>2. there's a problem with the way you extended the code to 3D.
>>The first point is easy to check (just look at a memory monitor or listen to
>>the sounds emitted by your hard drive). For the second, you'll have to post
>>a code snippet for us to take a look.
>>Regards
>>
>>Luca
>>
>>
>>
>>On Jul 18, 2008, at 4:35 PM, Gokhan Mustafa Uzunbas wrote:
>>
>>
>>>Dear ITK users I am tring to do a level set based segmentation using
>>>GeodesicActiveContourImageFilter.cxx sample in ITK. 2D works fine but when I
>>>try on 3D data I observed that fast marching filter can not initialize a
>>>simple sphere although I gave seed points and radius. It gets in a while
>>>loop in FastMarchingImageFilter to compute a signed distance function and
>>>can not get out.
>>>I do not know how much more I should wait but it seems it is not usable
>>>when image dimensions are 500 x 500 x 25.
>>>Are there anyone who could succeed to run those segmentation filters in
>>>3D?
>>>If anyone could help or point me, please? Thank you in advance.
>>>
>>>Gokhan
>>>_______________________________________________
>>>Insight-users mailing list
>>>Insight-users at itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
>>
>>_______________________________________________
>>Insight-users mailing list
>>Insight-users at itk.org
>>http://www.itk.org/mailman/listinfo/insight-users
>>
> 
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