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Transform VTK files in accordance with their format and floating point precision #1253

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merged 2 commits into from
Oct 23, 2024
Merged

Transform VTK files in accordance with their format and floating point precision #1253

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90c64c5
ENH: Transform binary VTK input file to binary output file
N-Dekker Oct 15, 2024
15bcdc3
ENH: Transform float VTK input file to float output file
N-Dekker Oct 16, 2024
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124 changes: 78 additions & 46 deletions Core/ComponentBaseClasses/elxTransformBase.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -916,63 +916,95 @@ template <typename TElastix>
void
TransformBase<TElastix>::TransformPointsSomePointsVTK(const std::string & filename) const
{
/** Typedef's. \todo test DummyIPPPixelType=bool. */
using DummyIPPPixelType = float;
using MeshTraitsType =
itk::DefaultStaticMeshTraits<DummyIPPPixelType, FixedImageDimension, FixedImageDimension, CoordRepType>;
using MeshType = itk::Mesh<DummyIPPPixelType, FixedImageDimension, MeshTraitsType>;

/** Read the input points. */
const auto meshReader = itk::MeshFileReader<MeshType>::New();
meshReader->SetFileName(filename);
log::info(std::ostringstream{} << " Reading input point file: " << filename);
try
{
meshReader->Update();
}
catch (const itk::ExceptionObject & err)
{
log::error(std::ostringstream{} << " Error while opening input point file.\n" << err);
}

const auto & inputMesh = *(meshReader->GetOutput());

/** Some user-feedback. */
log::info(" Input points are specified in world coordinates.");
const unsigned long nrofpoints = inputMesh.GetNumberOfPoints();
log::info(std::ostringstream{} << " Number of specified input points: " << nrofpoints);

/** Apply the transform. */
log::info(" The input points are transformed.");
const itk::CommonEnums::IOComponent pointComponentType = [&filename] {
const itk::SmartPointer<itk::MeshIOBase> meshIO =
itk::MeshIOFactory::CreateMeshIO(filename.c_str(), itk::IOFileModeEnum::ReadMode);
meshIO->SetFileName(filename);
meshIO->ReadMeshInformation();
return meshIO->GetPointComponentType();
}();

// Reads a mesh from a VTK file, transforms the mesh, and writes the transformed mesh.
const auto ReadAndTransformAndWriteMesh = [&filename, this](auto coordinate) {
// The `coordinate` parameter just specifies the requested coordinate type.
(void)coordinate;

using DummyIPPPixelType = unsigned char;
using MeshType = itk::Mesh<
DummyIPPPixelType,
FixedImageDimension,
itk::DefaultStaticMeshTraits<DummyIPPPixelType, FixedImageDimension, FixedImageDimension, decltype(coordinate)>>;

/** Read the input points. */
const auto meshReader = itk::MeshFileReader<MeshType>::New();
meshReader->SetFileName(filename);
log::info(std::ostringstream{} << " Reading input point file: " << filename);
try
{
meshReader->Update();
}
catch (const itk::ExceptionObject & err)
{
log::error(std::ostringstream{} << " Error while opening input point file.\n" << err);
}

typename MeshType::ConstPointer outputMesh;
const auto & inputMesh = *(meshReader->GetOutput());

try
{
outputMesh = Self::TransformMesh(inputMesh);
}
catch (const itk::ExceptionObject & err)
{
log::error(std::ostringstream{} << " Error while transforming points.\n" << err);
}
/** Some user-feedback. */
log::info(" Input points are specified in world coordinates.");
const unsigned long nrofpoints = inputMesh.GetNumberOfPoints();
log::info(std::ostringstream{} << " Number of specified input points: " << nrofpoints);

const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());
/** Apply the transform. */
log::info(" The input points are transformed.");

if (const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
!outputDirectoryPath.empty())
{
/** Create filename and file stream. */
const std::string outputPointsFileName = configuration.GetCommandLineArgument("-out") + "outputpoints.vtk";
log::info(std::ostringstream{} << " The transformed points are saved in: " << outputPointsFileName);
typename MeshType::ConstPointer outputMesh;

try
{
itk::WriteMesh(outputMesh, outputPointsFileName);
outputMesh = Self::TransformMesh(inputMesh);
}
catch (const itk::ExceptionObject & err)
{
log::error(std::ostringstream{} << " Error while saving points.\n" << err);
log::error(std::ostringstream{} << " Error while transforming points.\n" << err);
}

const Configuration & configuration = itk::Deref(Superclass::GetConfiguration());

if (const std::string outputDirectoryPath = configuration.GetCommandLineArgument("-out");
!outputDirectoryPath.empty())
{
/** Create filename and file stream. */
const std::string outputPointsFileName = configuration.GetCommandLineArgument("-out") + "outputpoints.vtk";
log::info(std::ostringstream{} << " The transformed points are saved in: " << outputPointsFileName);

try
{
const auto writer = itk::MeshFileWriter<MeshType>::New();
writer->SetInput(outputMesh);
writer->SetFileName(outputPointsFileName);

if (itk::Deref(meshReader->GetModifiableMeshIO()).GetFileType() == itk::IOFileEnum::Binary)
{
writer->SetFileTypeAsBINARY();
}

writer->Update();
}
catch (const itk::ExceptionObject & err)
{
log::error(std::ostringstream{} << " Error while saving points.\n" << err);
}
}
};

if (pointComponentType == itk::CommonEnums::IOComponent::FLOAT)
{
ReadAndTransformAndWriteMesh(float());
}
else
{
ReadAndTransformAndWriteMesh(double());
}

} // end TransformPointsSomePointsVTK()
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44 changes: 44 additions & 0 deletions Testing/PythonTests/transformix_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -541,6 +541,50 @@ def test_zero_translation_of_vtk_2d_points(self) -> None:
output_mesh = reader.GetOutput()
self.assert_equal_mesh(output_mesh, input_mesh)

def test_zero_translation_of_vtk_2d_points_binary(self) -> None:
"""Tests zero-translation of VTK points in 2D"""

source_directory_path = pathlib.Path(__file__).resolve().parent
output_directory_path = self.create_test_function_output_directory()

parameter_directory_path = source_directory_path / "TransformParameters"

input_mesh = itk.Mesh[itk.D, 2].New()
for i in range(4):
input_mesh.SetPoint(
i, (self.random_finite_float32(), self.random_finite_float32())
)

writer = itk.MeshFileWriter[itk.Mesh[itk.D, 2]].New()
writer.SetInput(input_mesh)
writer.SetFileTypeAsBINARY()
writer.SetFileName(str(output_directory_path / "inputpoints.vtk"))
writer.Write()

subprocess.run(
[
str(self.transformix_exe_file_path),
"-def",
str(output_directory_path / "inputpoints.vtk"),
"-tp",
str(parameter_directory_path / "Translation(0,0).txt"),
"-out",
str(output_directory_path),
],
capture_output=True,
check=True,
)

# Note that itk.meshread does not work, as the following produces a 3D mesh, instead of a 2D
# mesh.
#
# output_mesh = itk.meshread(str(output_directory_path / "outputpoints.vtk"))
reader = itk.MeshFileReader[itk.Mesh[itk.D, 2]].New()
reader.SetFileName(str(output_directory_path / "outputpoints.vtk"))
reader.Update()
output_mesh = reader.GetOutput()
self.assert_equal_mesh(output_mesh, input_mesh)

def test_translation_deformation_field(self) -> None:
"""Tests zero-translation of VTK points in 2D"""

Expand Down
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