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/*=========================================================================
Program: Advanced Normalization Tools
Copyright (c) ConsortiumOfANTS. All rights reserved.
See accompanying COPYING.txt or
https://github.com/stnava/ANTs/blob/master/ANTSCopyright.txt 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 "antsUtilities.h"
#include <algorithm>
#include "itkImageFileReader.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "vtkUnstructuredGrid.h"
#include "vtkUnstructuredGridWriter.h"
#include "vtkFloatArray.h"
#include "vtkPoints.h"
#include "vtkPointData.h"
namespace ants
{
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
ConvertVectorFieldToVTK(std::vector<std::string> args, std::ostream * out_stream = nullptr)
{
// put the arguments coming in as 'args' into standard (argc,argv) format;
// 'args' doesn't have the command name as first, argument, so add it manually;
// 'args' may have adjacent arguments concatenated into one argument,
// which the parser should handle
args.insert(args.begin(), "ConvertVectorFieldToVTK");
int argc = args.size();
char ** argv = new char *[args.size() + 1];
for (unsigned int i = 0; i < args.size(); ++i)
{
// allocate space for the string plus a null character
argv[i] = new char[args[i].length() + 1];
std::strncpy(argv[i], args[i].c_str(), args[i].length());
// place the null character in the end
argv[i][args[i].length()] = '\0';
}
argv[argc] = 0;
// class to automatically cleanup argv upon destruction
class Cleanup_argv
{
public:
Cleanup_argv(char ** argv_, int argc_plus_one_)
: argv(argv_)
, argc_plus_one(argc_plus_one_)
{}
~Cleanup_argv()
{
for (unsigned int i = 0; i < argc_plus_one; ++i)
{
delete[] argv[i];
}
delete[] argv;
}
private:
char ** argv;
unsigned int argc_plus_one;
};
Cleanup_argv cleanup_argv(argv, argc + 1);
// antscout->set_stream( out_stream );
if (argc < 3)
{
std::cout << "Usage: " << argv[0]
<< " inputDisplacementField outputVTKFile maskImage(optional) slice(optional) whichAxis(optional)"
<< std::endl;
return EXIT_FAILURE;
}
typedef float PixelType;
constexpr unsigned int ImageDimension = 3;
typedef itk::Image<PixelType, ImageDimension> ImageType;
typedef itk::Image<int, ImageDimension> MaskImageType;
typedef double RealType;
typedef itk::Vector<RealType, ImageDimension> VectorType;
typedef itk::Image<VectorType, ImageDimension> DisplacementFieldType;
typedef itk::ImageFileReader<DisplacementFieldType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
// reader->SetUseAvantsNamingConvention( true );
reader->Update();
MaskImageType::Pointer mask;
if (argc >= 4)
{
typedef itk::ImageFileReader<MaskImageType> MaskReaderType;
MaskReaderType::Pointer maskreader = MaskReaderType::New();
maskreader->SetFileName(argv[3]);
maskreader->Update();
mask = maskreader->GetOutput();
}
else
{
// ORIENTATION ALERT -- the original code here
// set the region, spacing, and origin without setting directions.
mask = AllocImage<MaskImageType>(reader->GetOutput(), 1);
}
int size[ImageDimension];
int totalsize = 1;
for (unsigned int i = 0; i < ImageDimension; i++)
{
size[i] = reader->GetOutput()->GetLargestPossibleRegion().GetSize()[i];
if (argc > 4 && std::stoi(argv[5]) == (int)i)
{
size[i] = 1;
}
totalsize *= size[i];
}
int totalPoints = totalsize;
vtkUnstructuredGrid * field = vtkUnstructuredGrid::New();
vtkPoints * points = vtkPoints::New();
points->Allocate(totalPoints);
vtkFloatArray * vectors = vtkFloatArray::New();
vectors->SetNumberOfComponents(3);
vectors->SetNumberOfTuples(totalPoints);
float x[3], v[3];
int offset = 0;
itk::ImageRegionIteratorWithIndex<MaskImageType> It(mask, mask->GetLargestPossibleRegion());
for (It.GoToBegin(); !It.IsAtEnd(); ++It)
{
DisplacementFieldType::IndexType idx = It.GetIndex();
if ((argc > 4 && idx[atoi(argv[5])] != std::stoi(argv[4])) || It.Get() == 0)
{
continue;
}
DisplacementFieldType::PointType point;
reader->GetOutput()->TransformIndexToPhysicalPoint(idx, point);
VectorType V = reader->GetOutput()->GetPixel(idx);
for (unsigned int i = 0; i < ImageDimension; i++)
{
x[i] = point[i];
v[i] = V[i];
}
// offset = idx[0] + idx[1]*(size[1]+1) + idx[2]*(size[1]+1)*(size[3]+1);
points->InsertPoint(offset, x);
vectors->InsertTuple(offset++, v);
}
field->SetPoints(points);
field->GetPointData()->SetVectors(vectors);
points->Delete();
vectors->Delete();
vtkUnstructuredGridWriter * writer = vtkUnstructuredGridWriter::New();
writer->SetInput(field);
// writer->SetFileTypeToBinary();
writer->SetFileName(argv[2]);
writer->Write();
return 0;
}
} // namespace ants
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