CopyGeometry.cpp

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

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.

This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.

See LICENSE.txt or http://www.mitk.org for details.

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

#include <mitkImageCast.h>
#include <mitkImage.h>
#include <mitkIOUtil.h>
#include "mitkCommandLineParser.h"

using namespace mitk;
using namespace std;

int main(int argc, char* argv[])
{
    mitkCommandLineParser parser;

    parser.setTitle("Copy Geometry");
    parser.setCategory("Preprocessing Tools");
    parser.setDescription("Copies transformation matrix of one image to another");
    parser.setContributor("MBI");

    parser.setArgumentPrefix("--", "-");
    parser.addArgument("in", "i", mitkCommandLineParser::InputFile, "Input:", "input image", us::Any(), false);
    parser.addArgument("ref", "r", mitkCommandLineParser::InputFile, "Reference:", "reference image", us::Any(), false);
    parser.addArgument("alignCentroid", "a", mitkCommandLineParser::Bool, "align centroids", "align centroids", us::Any(), true);
    parser.addArgument("out", "o", mitkCommandLineParser::OutputFile, "Output:", "output image", us::Any(), false);

    map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
    if (parsedArgs.size()==0)
        return EXIT_FAILURE;

    // mandatory arguments
    string imageName = us::any_cast<string>(parsedArgs["in"]);
    string refImage = us::any_cast<string>(parsedArgs["ref"]);
    string outImage = us::any_cast<string>(parsedArgs["out"]);

    bool originOnly = false;

    // Show a help message
    if ( parsedArgs.count("alignCentroid") || parsedArgs.count("a"))
    {
      originOnly = true;
    }

      try
    {
      Image::Pointer source = mitk::IOUtil::LoadImage(refImage);
      Image::Pointer target = mitk::IOUtil::LoadImage(imageName);
      if (originOnly)
      {
        // Calculate correction to align centroids
        double c[3];
        c[0] = source->GetGeometry()->GetOrigin()[0]
               + source->GetGeometry()->GetExtent(0)/2.0
               - target->GetGeometry()->GetOrigin()[0]
               - target->GetGeometry()->GetExtent(0)/2.0;

        c[1] = source->GetGeometry()->GetOrigin()[1]
               + source->GetGeometry()->GetExtent(1)/2.0
               - target->GetGeometry()->GetOrigin()[1]
               - target->GetGeometry()->GetExtent(1)/2.0;


        c[2] = source->GetGeometry()->GetOrigin()[2]
               + source->GetGeometry()->GetExtent(2)/2.0
               - target->GetGeometry()->GetOrigin()[2]
               - target->GetGeometry()->GetExtent(2)/2.0;

        double newOrigin[3];
        newOrigin[0] = target->GetGeometry()->GetOrigin()[0] +c[0];
        newOrigin[1] = target->GetGeometry()->GetOrigin()[1] +c[1];
        newOrigin[2] = target->GetGeometry()->GetOrigin()[2] +c[2];

        target->GetGeometry()->SetOrigin(newOrigin);
      }
      else
      {
        mitk::BaseGeometry* s_geom = source->GetGeometry();
        mitk::BaseGeometry* t_geom = target->GetGeometry();

        t_geom->SetIndexToWorldTransform(s_geom->GetIndexToWorldTransform());
        target->SetGeometry(t_geom);
      }
        mitk::IOUtil::SaveImage(target, outImage);
    }
    catch (itk::ExceptionObject e)
    {
        std::cout << e;
        return EXIT_FAILURE;
    }
    catch (std::exception e)
    {
        std::cout << e.what();
        return EXIT_FAILURE;
    }
    catch (...)
    {
        std::cout << "ERROR!?!";
        return EXIT_FAILURE;
    }
    return EXIT_SUCCESS;
}