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/*=========================================================================
Program: ITK General
Module: $RCSfile: TensorDerivedImage.cxx,v $
Language: C++
Date: $Date: 2009/03/17 18:58:59 $
Version: $Revision: 1.2 $
Author: Jeffrey T. Duda (jtduda@seas.upenn.edu)
Institution: PICSL
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
=========================================================================*/
#include <stdio.h>
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
//#include "itkDiffusionTensor3D.h"
#include "itkVector.h"
//#include "itkTensorFractionalAnisotropyImageFilter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include <string>
#include "TensorFunctions.h"
#include "ReadWriteImage.h"
#include "itkRGBPixel.h"
int main( int argc, char *argv[] )
{
// Pixel and Image typedefs
typedef float PixelType;
typedef itk::Image<PixelType, 3> ScalarImageType;
typedef itk::ImageFileWriter<ScalarImageType> WriterType;
//typedef itk::Vector<PixelType, 6> TensorType;
typedef itk::SymmetricSecondRankTensor< float, 3 > TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::ImageFileReader<TensorImageType> ReaderType;
typedef itk::RGBPixel< float > ColorPixelType;
typedef itk::Image<ColorPixelType,3> ColorImageType;
typedef itk::ImageFileWriter<ColorImageType> ColorWriterType;
// Check for valid input paramters
if (argc < 3)
{
std::cout << "Usage: " << argv[0] << " tensorvolume outputvolume outputtype" << std::endl;
return 1;
}
// Input parameters
char * inputName = argv[1];
char * outputName = argv[2];
std::string outType = argv[3];
TensorImageType::Pointer dtimg;
ReadTensorImage<TensorImageType>(dtimg, inputName, false);
std::cout << "tensor_image: " << inputName << std::endl;
std::cout << "output_image: " << outputName << std::endl;
ScalarImageType::Pointer outImage;
ColorImageType::Pointer colorImage;
if (outType == "DEC") {
colorImage = ColorImageType::New();
colorImage->SetRegions(dtimg->GetLargestPossibleRegion() );
colorImage->SetSpacing(dtimg->GetSpacing());
colorImage->SetOrigin(dtimg->GetOrigin());
colorImage->SetDirection(dtimg->GetDirection());
colorImage->Allocate();
}
else {
outImage = ScalarImageType::New();
outImage->SetRegions(dtimg->GetLargestPossibleRegion() );
outImage->SetSpacing(dtimg->GetSpacing());
outImage->SetOrigin(dtimg->GetOrigin());
outImage->SetDirection(dtimg->GetDirection());
outImage->Allocate();
}
itk::ImageRegionIteratorWithIndex<TensorImageType> inputIt(dtimg,
dtimg->GetLargestPossibleRegion());
if ( (outType == "XX") || (outType == "xx") ) outType = "0";
if ( (outType == "XY") || (outType == "YX") || (outType == "xy") || (outType == "yx") ) outType = "1";
if ( (outType == "XZ") || (outType == "ZX") || (outType == "xz") || (outType == "zx") ) outType = "2";
if ( (outType == "YY") || (outType == "yy") ) outType = "3";
if ( (outType == "YZ") || (outType == "ZY") || (outType == "yz") || (outType == "zy") ) outType = "4";
if ( (outType == "ZZ") || (outType == "zz") ) outType = "5";
std::cout << "Calculating output..." << std::flush;
while (!inputIt.IsAtEnd())
{
if ((outType == "0") || (outType == "1") || (outType == "2") || (outType == "3") ||
(outType == "4") || (outType == "5"))
{
int idx = atoi(outType.c_str());
outImage->SetPixel(inputIt.GetIndex(),inputIt.Value()[idx]);
}
else if ((outType == "TR") || (outType == "MD"))
{
ScalarImageType::PixelType tr;
tr = inputIt.Value()[0] + inputIt.Value()[2] + inputIt.Value()[5];
if (tr < 0)
tr = 0;
if (tr != tr)
tr = 0;
if (outType == "TR") {
outImage->SetPixel(inputIt.GetIndex(),tr);
}
else {
outImage->SetPixel(inputIt.GetIndex(),tr/3.0);
}
}
else if (outType == "V")
{
//unsigned int invalids = 0;
bool success=true;
TensorType t = TensorLogAndExp<TensorType>(inputIt.Value(), true, success);
int current=1;
if (!success) current=0;
outImage->SetPixel(inputIt.GetIndex(),current);
//std::cout << "Found " << invalids << " invalid tensors" << std::endl;
}
else if (outType == "FA")
{
float fa = GetTensorFA<TensorType>(inputIt.Value());
outImage->SetPixel(inputIt.GetIndex(),fa);
}
else if (outType == "DEC") {
colorImage->SetPixel(inputIt.GetIndex(),
GetTensorRGB<TensorType>(inputIt.Value()));
++inputIt;
}
}
std::cout << "Done. " << std::endl;
if (outType == "DEC") {
std::cout << "output origin: " << colorImage->GetOrigin() << std::endl;
std::cout << "output size: " << colorImage->GetLargestPossibleRegion().GetSize() << std::endl;
std::cout << "output spacing: " << colorImage->GetSpacing() << std::endl;
std::cout << "output direction: " << colorImage->GetDirection() << std::endl;
}
else {
std::cout << "output origin: " << outImage->GetOrigin() << std::endl;
std::cout << "output size: " << outImage->GetLargestPossibleRegion().GetSize() << std::endl;
std::cout << "output spacing: " << outImage->GetSpacing() << std::endl;
std::cout << "output direction: " << outImage->GetDirection() << std::endl;
}
if (outType == "DEC") {
ColorWriterType::Pointer writer = ColorWriterType::New();
writer->SetInput( colorImage );
writer->SetFileName( outputName );
writer->Update();
}
else {
WriterType::Pointer writer = WriterType::New();
writer->SetInput( outImage );
writer->SetFileName( outputName );
writer->Update();
}
return 0;
}
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