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TransformReadWrite.cxx
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TransformReadWrite.cxx
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/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginLatex
//
// \index{itk::TransformReader}
// \index{itk::TransformWriter}
//
// This example shows how to read and write a transform
// using the \doxygen{TransformFileReader} and
// \doxygen{TransformFileWriter}.
// Let's first include the two appropriate header files.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkTransformFileReader.h"
#include "itkTransformFileWriter.h"
// Software Guide : EndCodeSnippet
#include "itkAffineTransform.h"
#include "itkBSplineTransform.h"
#include "itkCompositeTransform.h"
#include "itkTransformFactory.h"
int
main(int argc, char * argv[])
{
if (argc < 2)
{
std::cerr << "Usage: " << argv[0] << " transformFile" << std::endl;
return EXIT_FAILURE;
}
const char * transformFileName = argv[1];
using ScalarType = double;
constexpr unsigned int Dimension = 3;
using CompositeTransformType =
itk::CompositeTransform<ScalarType, Dimension>;
auto composite = CompositeTransformType::New();
using AffineTransformType = itk::AffineTransform<ScalarType, Dimension>;
auto affine = AffineTransformType::New();
AffineTransformType::InputPointType cor;
cor.Fill(12);
affine->SetCenter(cor);
composite->AddTransform(affine);
constexpr unsigned int SplineOrder = 5;
using BSplineTransformType =
itk::BSplineTransform<ScalarType, Dimension, SplineOrder>;
using BSplineTransformFType =
itk::BSplineTransform<float, Dimension, SplineOrder>;
// By default only BSpline transforms of order 3 are registered.
// Manually register this order 5 bspline for both float and double
// scalar types, so that we can read the correct order transform.
itk::TransformFactory<BSplineTransformType>::RegisterTransform();
itk::TransformFactory<BSplineTransformFType>::RegisterTransform();
auto bspline = BSplineTransformType::New();
BSplineTransformType::OriginType origin;
origin.Fill(100);
BSplineTransformType::PhysicalDimensionsType dimensions;
dimensions.Fill(1.5 * 9.0);
bspline->SetTransformDomainOrigin(origin);
bspline->SetTransformDomainPhysicalDimensions(dimensions);
BSplineTransformType::ParametersType parameters(
bspline->GetNumberOfParameters());
bspline->SetParameters(parameters);
bspline->SetIdentity();
composite->AddTransform(bspline);
// Software Guide : BeginLatex
//
// The transform reader and writer is templated. The conversion is precision
// done if necessary when writing or reading the file. We create a writer
// using smart pointers.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using TransformWriterType = itk::TransformFileWriterTemplate<ScalarType>;
auto writer = TransformWriterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We add a CompositeTransform with the
// SetInput() function. This function takes any \doxygen{Transform}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
writer->SetInput(composite);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Then we set the filename using the SetFileName() function.
// Then we call the Update()function to write the transform(s)
// onto the disk.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
writer->SetFileName(transformFileName);
// Software Guide : EndCodeSnippet
try
{
// Software Guide : BeginCodeSnippet
writer->Update();
// Software Guide : EndCodeSnippet
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Error while saving the transforms" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// In order to read a transform file, we instantiate a TransformFileReader.
// Like the writer, the reader is templated.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ReadScalarType = float;
using TransformReaderType =
itk::TransformFileReaderTemplate<ReadScalarType>;
auto reader = TransformReaderType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We then set the name of the file we want to read, and call the
// Update() function.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
reader->SetFileName(transformFileName);
// Software Guide : EndCodeSnippet
try
{
// Software Guide : BeginCodeSnippet
reader->Update();
// Software Guide : EndCodeSnippet
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Error while reading the transform file" << std::endl;
std::cerr << excp << std::endl;
std::cerr << "[FAILED]" << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// The transform reader is templated and it returns a list
// of \doxygen{Transform}'s. Even thought the reader instantiate the
// appropriate transform class when reading the file, it is up to the user
// to do the appropriate cast. To get the output list of transform we use
// the GetTransformList() function.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
const TransformReaderType::TransformListType * transforms =
reader->GetTransformList();
std::cout << "Number of transforms = " << transforms->size() << std::endl;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We then use an STL iterator to go through the list of transforms. We show
// here how to do the proper casting of the resulting transform.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ReadCompositeTransformType =
itk::CompositeTransform<ReadScalarType, Dimension>;
auto it = transforms->begin();
if (!strcmp((*it)->GetNameOfClass(), "CompositeTransform"))
{
ReadCompositeTransformType::Pointer compositeRead =
static_cast<ReadCompositeTransformType *>((*it).GetPointer());
compositeRead->Print(std::cout);
}
// Software Guide : EndCodeSnippet
return EXIT_SUCCESS;
}