### Author:  [@basal](https://discourse.itk.org/u/basal)
#### Post date: [May 22, 2020, 7:46pm UTC](https://discourse.itk.org/t/defining-landmarks-file/3110/1 "2020-05-22T19:46:12Z")
Hi, I want to use the ThinPlateSpline code in ITK, I already have my landmarks but I do not know how I should define a readable file for landmarks for the code. I defined the landmarks in the txt file I have attached but the code is not working. Could any one help me? Thanks.
[myFile.txt](https://discourse.itk.org/uploads/short-url/c0j5OJkPFOXrBNWxBt5dVxxPzfz.txt) (1014 Bytes)
```auto
/ Command Line Arguments: Insight/Testing/Data/LandmarkWarping3Landmarks1.txt
// inputImage deformedImage deformationField
//
// Software Guide : BeginLatex
// This example deforms a 3D volume with the Thin plate spline.
// \index{ThinPlateSplineKernelTransform}
// Software Guide : EndLatex
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImage.h"
#include "itkResampleImageFilter.h"
// Software Guide : BeginCodeSnippet
#include "itkThinPlateSplineKernelTransform.h"
// Software Guide : EndCodeSnippet
#include "itkPointSet.h"
#include
int main( int argc, char * argv[] )
{
if( argc < 4 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " landmarksFile inputImage ";
std::cerr << "DeformedImage " << std::endl;
std::cerr << "deformationField" << std::endl;
return EXIT_FAILURE;
}
constexpr unsigned int ImageDimension = 3;
using PixelType = unsigned char;
using InputImageType = itk::Image< PixelType, ImageDimension >;
using ReaderType = itk::ImageFileReader< InputImageType >;
using DeformedImageWriterType = itk::ImageFileWriter< InputImageType >;
using FieldVectorType = itk::Vector< float, ImageDimension >;
using DisplacementFieldType = itk::Image< FieldVectorType, ImageDimension >;
using FieldWriterType = itk::ImageFileWriter< DisplacementFieldType >;
using CoordinateRepType = double;
using TransformType = itk::ThinPlateSplineKernelTransform< CoordinateRepType,
ImageDimension>;
using PointType = itk::Point< CoordinateRepType,
ImageDimension >;
using PointSetType = TransformType::PointSetType;
using PointIdType = PointSetType::PointIdentifier;
using ResamplerType = itk::ResampleImageFilter< InputImageType,
InputImageType >;
using InterpolatorType = itk::LinearInterpolateImageFunction<
InputImageType, double >;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( argv[2] );
try
{
reader->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
// Landmarks correspondances may be associated with the SplineKernelTransforms
// via Point Set containers. Let us define containers for the landmarks.
// Software Guide : EndLatex
// Define container for landmarks
// Software Guide : BeginCodeSnippet
PointSetType::Pointer sourceLandMarks = PointSetType::New();
PointSetType::Pointer targetLandMarks = PointSetType::New();
PointType p1; PointType p2;
PointSetType::PointsContainer::Pointer sourceLandMarkContainer =
sourceLandMarks->GetPoints();
PointSetType::PointsContainer::Pointer targetLandMarkContainer =
targetLandMarks->GetPoints();
// Software Guide : EndCodeSnippet
PointIdType id = itk::NumericTraits< PointIdType >::ZeroValue();
// Read in the list of landmarks
std::ifstream infile;
infile.open( argv[1] );
while (!infile.eof())
{
infile >> p1[0] >> p1[1] >> p1[2] >> p2[0] >> p2[1] >> p2[2];
// Software Guide : BeginCodeSnippet
sourceLandMarkContainer->InsertElement( id, p1 );
targetLandMarkContainer->InsertElement( id++, p2 );
// Software Guide : EndCodeSnippet
}
infile.close();
// Software Guide : BeginCodeSnippet
TransformType::Pointer tps = TransformType::New();
tps->SetSourceLandmarks(sourceLandMarks);
tps->SetTargetLandmarks(targetLandMarks);
tps->ComputeWMatrix();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
// The image is then resampled to produce an output image as defined by the
// transform. Here we use a LinearInterpolator.
// Software Guide : EndLatex
// Set the resampler params
InputImageType::ConstPointer inputImage = reader->GetOutput();
ResamplerType::Pointer resampler = ResamplerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
resampler->SetInterpolator( interpolator );
InputImageType::SpacingType spacing = inputImage->GetSpacing();
InputImageType::PointType origin = inputImage->GetOrigin();
InputImageType::DirectionType direction = inputImage->GetDirection();
InputImageType::RegionType region = inputImage->GetBufferedRegion();
InputImageType::SizeType size = region.GetSize();
// Software Guide : BeginCodeSnippet
resampler->SetOutputSpacing( spacing );
resampler->SetOutputDirection( direction );
resampler->SetOutputOrigin( origin );
resampler->SetSize( size );
resampler->SetTransform( tps );
// Software Guide : EndCodeSnippet
resampler->SetOutputStartIndex( region.GetIndex() );
resampler->SetInput( reader->GetOutput() );
//Set and write deformed image
DeformedImageWriterType::Pointer deformedImageWriter =
DeformedImageWriterType::New();
deformedImageWriter->SetInput( resampler->GetOutput() );
deformedImageWriter->SetFileName( argv[3] );
try
{
deformedImageWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
// The deformation field is computed as the difference between the input and
// the deformed image by using an iterator.
// Software Guide : EndLatex
// Compute the deformation field
DisplacementFieldType::Pointer field = DisplacementFieldType::New();
field->SetRegions( region );
field->SetOrigin( origin );
field->SetSpacing( spacing );
field->Allocate();
using FieldIterator = itk::ImageRegionIterator< DisplacementFieldType >;
FieldIterator fi( field, region );
fi.GoToBegin();
TransformType::InputPointType point1;
TransformType::OutputPointType point2;
DisplacementFieldType::IndexType index;
FieldVectorType displacement;
while( ! fi.IsAtEnd() )
{
index = fi.GetIndex();
field->TransformIndexToPhysicalPoint( index, point1 );
point2 = tps->TransformPoint( point1 );
for ( unsigned int i = 0;i < ImageDimension;i++)
{
displacement[i] = point2[i] - point1[i];
}
fi.Set( displacement );
++fi;
}
//Write computed deformation field
FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
fieldWriter->SetFileName( argv[4] );
fieldWriter->SetInput( field );
try
{
fieldWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
```
---
### Author:  [@dchen](https://discourse.itk.org/u/dchen)
#### Post date: [May 23, 2020, 12:36am UTC](https://discourse.itk.org/t/defining-landmarks-file/3110/2 "2020-05-23T00:36:32Z")
Looking at the code, I think you want to remove all the brackets and commas and only separate the numbers with spaces.
---
### Author:  [@basal](https://discourse.itk.org/u/basal)
#### Post date: [May 23, 2020, 12:48am UTC](https://discourse.itk.org/t/defining-landmarks-file/3110/3 "2020-05-23T00:48:38Z")
Thank you very much. It works.
---
### Author:  [@dchen](https://discourse.itk.org/u/dchen)
#### Post date: [May 23, 2020, 12:53am UTC](https://discourse.itk.org/t/defining-landmarks-file/3110/4 "2020-05-23T00:53:07Z")
I’m glad you got it to work. C++ is not the best language for text processing, so it can be hard to comprehend.
---
### Author:  [@basal](https://discourse.itk.org/u/basal)
#### Post date: [May 24, 2020, 4:15am UTC](https://discourse.itk.org/t/defining-landmarks-file/3110/5 "2020-05-24T04:15:38Z")
Regarding TPS algorithm, when I ran the code, the output image is black. I expected to see similar image to the input but it seems the algorithm is not working. Does anyone could help me with that ? I have attached landmark file and input image.
[Huma01-LungProjectionSample-6.nrrd](https://discourse.itk.org/uploads/short-url/DrWyhtqXI74unNMJtCeIc9EbGw.nrrd) (2.2 MB)
[Landmarks61.txt](https://discourse.itk.org/uploads/short-url/7XEfAQrBuYtAutssy4nb6fjH3ko.txt) (888 Bytes)