[Insight-users] Re: extraction of a portion of an images?

[Luis Ibanez]

This is a multi-part message in MIME format.
--------------080800040004070204050706
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 8bit


Hi Zein,

An Example on image Extraction was just added last night to

     Insight/Examples/ExtractImageFilter

It is here attached too.

This example takes parameters from the command line.
Reads an image, extract a portion from the image and
writes the extracted piece into another file.

The command should look like:

"ExtractImageRegion  input.mha output.mha  12 20 25   100 200 100"

This will extracts a region starting at pixel (12,20,25) and
with size (100,200,100).

Please let us know if you encounter any problem using
this filter.

Thanks

Luis

================================================


Zein Salah wrote:
> Hi Luis,
> 
>  
> 
> I want to extract a portion of a volume image (a cubic region). I have 
> looked at the testing example of extractimagefilter in 
> insight/testing/...... The example is too complicated. The docmumentation in
> 
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1ExtractImageFilter.html
> is also somehow not helpfull. 
> 
> Can you please provide with simplest code to do the job??
> 
> Many thanks in advanced...
> 
> Zein

> 
> ->8<------------->8<------------->8<------------->8<------------->8<------------->8<-
> Zein I. Salah
> Universität Tübingen, WSI-GRIS
> Sand 14
> 72076 Tübingen
> Email: salah@gris.uni-tuebingen.de <mailto:salah@gris.uni-tuebingen.de>  
> / zeinsalah@hotmail.com <mailto:zeinsalah@hotmail.com>
> Tel.: (07071) 29 75465 (GRIS) , (07071) 96 44 39 (privat)
> 
==============================================

--------------080800040004070204050706
Content-Type: text/plain;
 name="ExtractImageRegion.cxx"
Content-Transfer-Encoding: 7bit
Content-Disposition: inline;
 filename="ExtractImageRegion.cxx"

/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: ExtractImageRegion.cxx,v $
  Language:  C++
  Date:      $Date: 2002/08/23 00:56:53 $
  Version:   $Revision: 1.1 $

  Copyright (c) 2002 Insight 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.

=========================================================================*/
#include <iostream>

#include <itkImage.h>
#include <itkImageFileWriter.h>
#include <itkImageFileReader.h>
#include <itkMetaImageIO.h>
#include <itkExtractImageFilter.h>

int main(int argc, char **argv)
  {

  if( argc < 9 )
    { 
    std::cerr << "Usage: ExtractImageRegion inputImageFile outputImageFile ";
    std::cerr << "xStart yStart zStart  xSize ySize zSize " << std::endl;
    return 1;
    }

  // Declare the image
  typedef itk::Image<unsigned short, 3> ImageType;


  // Declare a Reader
  typedef itk::ImageFileReader< ImageType > VolumeReaderType;
  VolumeReaderType::Pointer reader = VolumeReaderType::New();

  // Set the filename
  reader->SetFileName( argv[1] );

  // Declare the Extract filter
  typedef itk::ExtractImageFilter< ImageType, ImageType > ExtractFilterType;
  ExtractFilterType::Pointer extractor = ExtractFilterType::New();

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

  ImageType::SizeType  size;
  ImageType::IndexType index;

  index[0] = atoi( argv[3] );
  index[1] = atoi( argv[4] );
  index[2] = atoi( argv[5] );

  size[0] = atoi( argv[6] );
  size[1] = atoi( argv[7] );
  size[2] = atoi( argv[8] );

  ImageType::RegionType region;
  region.SetIndex( index );
  region.SetSize( size );

  extractor->SetExtractionRegion( region );

  // Declare a Writer
  typedef itk::ImageFileWriter< ImageType > VolumeWriterType;
  VolumeWriterType::Pointer writer = VolumeWriterType::New();

  // Add the MetaImage format to the writer
  writer->SetImageIO( itk::MetaImageIO::New() );

  // Set the filename
  writer->SetFileName( argv[2] );

  // Set the image to write
  writer->SetInput( extractor->GetOutput() );

  // Write the image 
  writer->Update();

  }

--------------080800040004070204050706--