diff --git a/Components/Transforms/BSplineDeformableTransformWithDiffusion/elxBSplineTransformWithDiffusion.hxx b/Components/Transforms/BSplineDeformableTransformWithDiffusion/elxBSplineTransformWithDiffusion.hxx index ef717d463..b95423050 100644 --- a/Components/Transforms/BSplineDeformableTransformWithDiffusion/elxBSplineTransformWithDiffusion.hxx +++ b/Components/Transforms/BSplineDeformableTransformWithDiffusion/elxBSplineTransformWithDiffusion.hxx @@ -974,11 +974,11 @@ BSplineTransformWithDiffusion::ReadFromFile() } } - /** Task 4 - Remember the name of the TransformParametersFileName. + /** Task 4 - Remember the name of the TransformParameterFileName. * This will be needed when another transform will use this transform * as an initial transform (see the WriteToFile method) */ - this->SetTransformParametersFileName(this->GetConfiguration()->GetCommandLineArgument("-tp")); + this->SetTransformParameterFileName(this->GetConfiguration()->GetCommandLineArgument("-tp")); } // end ReadFromFile() diff --git a/Core/ComponentBaseClasses/elxTransformBase.h b/Core/ComponentBaseClasses/elxTransformBase.h index 3e6950ca9..a04a4d82c 100644 --- a/Core/ComponentBaseClasses/elxTransformBase.h +++ b/Core/ComponentBaseClasses/elxTransformBase.h @@ -223,9 +223,9 @@ class ITK_TEMPLATE_EXPORT TransformBase : public BaseComponentSE void SetInitialTransform(InitialTransformType * _arg); - /** Set the TransformParametersFileName. */ + /** Set the TransformParameterFileName. */ void - SetTransformParametersFileName(const std::string & filename); + SetTransformParameterFileName(const std::string & filename); /** Function to read transform-parameters from a file. */ virtual void @@ -394,8 +394,8 @@ class ITK_TEMPLATE_EXPORT TransformBase : public BaseComponentSE const InitialTransformType * GetInitialTransform() const; - /** Get the TransformParametersFileName. */ - itkGetStringMacro(TransformParametersFileName); + /** Get the TransformParameterFileName. */ + itkGetStringMacro(TransformParameterFileName); /** Function to transform coordinates from fixed to moving image. */ void @@ -423,7 +423,7 @@ class ITK_TEMPLATE_EXPORT TransformBase : public BaseComponentSE TransformPointsAllPoints() const; std::string - GetInitialTransformParametersFileName() const + GetInitialTransformParameterFileName() const { const InitialTransformType * const initialTransform = this->GetInitialTransform(); @@ -433,7 +433,7 @@ class ITK_TEMPLATE_EXPORT TransformBase : public BaseComponentSE } const auto t0 = dynamic_cast(initialTransform); - return t0->GetTransformParametersFileName(); + return t0->GetTransformParameterFileName(); } virtual ParameterMapType @@ -445,7 +445,7 @@ class ITK_TEMPLATE_EXPORT TransformBase : public BaseComponentSE {} /** Member variables. */ - std::string m_TransformParametersFileName; + std::string m_TransformParameterFileName; ParametersType m_TransformParameters; ParametersType m_FinalParameters; diff --git a/Core/ComponentBaseClasses/elxTransformBase.hxx b/Core/ComponentBaseClasses/elxTransformBase.hxx index 41d9d57e6..78e8fc430 100644 --- a/Core/ComponentBaseClasses/elxTransformBase.hxx +++ b/Core/ComponentBaseClasses/elxTransformBase.hxx @@ -436,12 +436,12 @@ TransformBase::ReadFromFile() */ this->GetAsITKBaseType()->SetUseComposition(howToCombineTransforms == "Compose"); - /** Task 4 - Remember the name of the TransformParametersFileName. + /** Task 4 - Remember the name of the TransformParameterFileName. * This will be needed when another transform will use this transform as an initial transform (see the WriteToFile * method), which is relevant for transformix, as well as for elastix (specifically * ElastixRegistrationMethod::GenerateData(), when InitialTransformParameterObject is specified). */ - this->SetTransformParametersFileName(configuration.GetCommandLineArgument("-tp")); + this->SetTransformParameterFileName(configuration.GetCommandLineArgument("-tp")); } // end ReadFromFile() @@ -452,15 +452,15 @@ TransformBase::ReadFromFile() template void -TransformBase::ReadInitialTransformFromFile(const std::string & transformParametersFileName) +TransformBase::ReadInitialTransformFromFile(const std::string & transformParameterFileName) { /** Create a new configuration, which will be initialized with * the transformParameterFileName. */ const auto configurationInitialTransform = Configuration::New(); - if (configurationInitialTransform->Initialize({ { "-tp", transformParametersFileName } }) != 0) + if (configurationInitialTransform->Initialize({ { "-tp", transformParameterFileName } }) != 0) { - itkGenericExceptionMacro("ERROR: Reading initial transform parameters failed: " << transformParametersFileName); + itkGenericExceptionMacro("ERROR: Reading initial transform parameters failed: " << transformParameterFileName); } this->ReadInitialTransformFromConfiguration(configurationInitialTransform); @@ -491,7 +491,7 @@ TransformBase::ReadInitialTransformFromConfiguration( /** Call the ReadFromFile method of the initialTransform. */ if (elx_initialTransform != nullptr) { - // elx_initialTransform->SetTransformParametersFileName(transformParametersFileName); + // elx_initialTransform->SetTransformParameterFileName(transformParameterFileName); elx_initialTransform->SetElastix(this->GetElastix()); elx_initialTransform->SetConfiguration(configurationInitialTransform); elx_initialTransform->ReadFromFile(); @@ -535,7 +535,7 @@ TransformBase::WriteToFile(std::ostream & transformationParameterInfo, if (firstSingleTransform != nullptr) { const std::string transformFileName = - std::string(m_TransformParametersFileName, 0, m_TransformParametersFileName.rfind('.')) + '.' + + std::string(m_TransformParameterFileName, 0, m_TransformParameterFileName.rfind('.')) + '.' + itkTransformOutputFileNameExtension; const itk::TransformBase::ConstPointer itkTransform = @@ -565,7 +565,7 @@ TransformBase::WriteToFile(std::ostream & transformationParameterInfo, else { TransformIO::Write(*compositeTransform, - std::string(m_TransformParametersFileName, 0, m_TransformParametersFileName.rfind('.')) + + std::string(m_TransformParameterFileName, 0, m_TransformParameterFileName.rfind('.')) + "-Composite." + itkTransformOutputFileNameExtension); } } @@ -614,7 +614,7 @@ TransformBase::CreateTransformParametersMap(const ParametersType & par /** Write the name of this transform. */ parameterMap = { { "Transform", { this->elxGetClassName() } }, { "NumberOfParameters", { Conversion::ToString(param.GetSize()) } }, - { "InitialTransformParameterFileName", { this->GetInitialTransformParametersFileName() } }, + { "InitialTransformParameterFileName", { this->GetInitialTransformParameterFileName() } }, { "HowToCombineTransforms", { combinationMethod } }, { "FixedImageDimension", { Conversion::ToString(FixedImageDimension) } }, { "MovingImageDimension", { Conversion::ToString(MovingImageDimension) } }, @@ -1318,22 +1318,22 @@ TransformBase::ComputeAndWriteSpatialJacobianMatrixImage() const /** - * ************** SetTransformParametersFileName **************** + * ************** SetTransformParameterFileName **************** */ template void -TransformBase::SetTransformParametersFileName(const std::string & filename) +TransformBase::SetTransformParameterFileName(const std::string & filename) { /** Copied from itkSetStringMacro. */ - if (filename == this->m_TransformParametersFileName) + if (filename == this->m_TransformParameterFileName) { return; } - this->m_TransformParametersFileName = filename; + this->m_TransformParameterFileName = filename; this->GetAsITKBaseType()->Modified(); -} // end SetTransformParametersFileName() +} // end SetTransformParameterFileName() /** diff --git a/Core/Kernel/elxElastixTemplate.hxx b/Core/Kernel/elxElastixTemplate.hxx index 17608168c..bffbe154b 100644 --- a/Core/Kernel/elxElastixTemplate.hxx +++ b/Core/Kernel/elxElastixTemplate.hxx @@ -779,7 +779,7 @@ ElastixTemplate::CreateTransformParameterFile(const s this->m_CurrentTransformParameterFileName = fileName; /** Set it in the Transform, for later use. */ - this->GetElxTransformBase()->SetTransformParametersFileName(fileName); + this->GetElxTransformBase()->SetTransformParameterFileName(fileName); /** Separate clearly in log-file. */ if (toLog) diff --git a/Core/Main/GTesting/itkTransformixFilterGTest.cxx b/Core/Main/GTesting/itkTransformixFilterGTest.cxx index 913b620c1..83665d48e 100644 --- a/Core/Main/GTesting/itkTransformixFilterGTest.cxx +++ b/Core/Main/GTesting/itkTransformixFilterGTest.cxx @@ -178,7 +178,7 @@ template auto CreateTransformixFilter(itk::Image & image, const itk::Transform & itkTransform, - const std::string & initialTransformParametersFileName = "NoInitialTransform", + const std::string & initialTransformParameterFileName = "NoInitialTransform", const std::string & howToCombineTransforms = "Compose") { const auto filter = CheckNew>>(); @@ -189,7 +189,7 @@ CreateTransformixFilter(itk::Image & { "Direction", CreateDefaultDirectionParameterValues() }, { "HowToCombineTransforms", { howToCombineTransforms } }, { "Index", ParameterValuesType(VImageDimension, "0") }, - { "InitialTransformParameterFileName", { initialTransformParametersFileName } }, + { "InitialTransformParameterFileName", { initialTransformParameterFileName } }, { "Origin", ParameterValuesType(VImageDimension, "0") }, { "ResampleInterpolator", { "FinalLinearInterpolator" } }, { "Size", ConvertToParameterValues(image.GetBufferedRegion().GetSize()) }, @@ -203,11 +203,11 @@ template itk::SmartPointer> RetrieveOutputFromTransformixFilter(itk::Image & image, const itk::Transform & itkTransform, - const std::string & initialTransformParametersFileName = "NoInitialTransform", + const std::string & initialTransformParameterFileName = "NoInitialTransform", const std::string & howToCombineTransforms = "Compose") { const auto transformixFilter = - CreateTransformixFilter(image, itkTransform, initialTransformParametersFileName, howToCombineTransforms); + CreateTransformixFilter(image, itkTransform, initialTransformParameterFileName, howToCombineTransforms); const auto output = transformixFilter->GetOutput(); EXPECT_NE(output, nullptr); return output; @@ -746,7 +746,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndDefaultTransform) const auto resampleImageFilter = CreateResampleImageFilter(*inputImage, translationTransform); const auto & expectedOutputImage = DerefRawPointer(resampleImageFilter->GetOutput()); - const std::string initialTransformParametersFileName = + const std::string initialTransformParameterFileName = GetDataDirectoryPath() + "/Translation(1,-2)/TransformParameters.txt"; for (const auto defaultTransform : { CreateTransform>(), @@ -756,7 +756,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndDefaultTransform) CreateTransform>() }) { const auto actualOutputImage = - RetrieveOutputFromTransformixFilter(*inputImage, *defaultTransform, initialTransformParametersFileName); + RetrieveOutputFromTransformixFilter(*inputImage, *defaultTransform, initialTransformParameterFileName); EXPECT_EQ(*actualOutputImage, expectedOutputImage); } @@ -789,7 +789,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndInverseTranslation) using ParametersValueType = double; - const std::string initialTransformParametersFileName = + const std::string initialTransformParameterFileName = GetDataDirectoryPath() + "/Translation(1,-2)/TransformParameters.txt"; const auto offset = itk::MakeVector(1.0, -2.0); @@ -799,7 +799,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndInverseTranslation) // makes the output image unequal to the input image. const elx::DefaultConstruct> identityTransform; - EXPECT_NE(*(RetrieveOutputFromTransformixFilter(*inputImage, identityTransform, initialTransformParametersFileName)), + EXPECT_NE(*(RetrieveOutputFromTransformixFilter(*inputImage, identityTransform, initialTransformParameterFileName)), *inputImage); // The inverse of the transform from the TransformParameters.txt file. @@ -810,7 +810,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndInverseTranslation) }(); EXPECT_EQ(*(RetrieveOutputFromTransformixFilter( - *inputImage, *inverseTranslationTransform, initialTransformParametersFileName)), + *inputImage, *inverseTranslationTransform, initialTransformParameterFileName)), *inputImage); for (const auto matrixOffsetTransform : @@ -820,7 +820,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndInverseTranslation) { matrixOffsetTransform->SetOffset(inverseOffset); EXPECT_EQ( - *(RetrieveOutputFromTransformixFilter(*inputImage, *matrixOffsetTransform, initialTransformParametersFileName)), + *(RetrieveOutputFromTransformixFilter(*inputImage, *matrixOffsetTransform, initialTransformParameterFileName)), *inputImage); } @@ -836,7 +836,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndInverseTranslation) }(); const auto inverseBSplineOutputImage = RetrieveOutputFromTransformixFilter( - *inputImage, *inverseBSplineTransform, initialTransformParametersFileName, "Add"); + *inputImage, *inverseBSplineTransform, initialTransformParameterFileName, "Add"); ExpectAlmostEqualPixelValues(*inverseBSplineOutputImage, *inputImage, 1e-15); } @@ -852,7 +852,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndScale) using ParametersValueType = double; - const std::string initialTransformParametersFileName = + const std::string initialTransformParameterFileName = GetDataDirectoryPath() + "/Translation(1,-2)/TransformParameters.txt"; elx::DefaultConstruct> scaleTransform; @@ -862,7 +862,7 @@ GTEST_TEST(itkTransformixFilter, CombineTranslationAndScale) translationTransform.SetOffset(itk::MakeVector(1.0, -2.0)); const auto transformixOutput = - RetrieveOutputFromTransformixFilter(*inputImage, scaleTransform, initialTransformParametersFileName); + RetrieveOutputFromTransformixFilter(*inputImage, scaleTransform, initialTransformParameterFileName); elx::DefaultConstruct> translationAndScaleTransform; translationAndScaleTransform.AddTransform(&translationTransform); diff --git a/Core/Main/itkElastixRegistrationMethod.hxx b/Core/Main/itkElastixRegistrationMethod.hxx index 6b6290517..890e58cb7 100644 --- a/Core/Main/itkElastixRegistrationMethod.hxx +++ b/Core/Main/itkElastixRegistrationMethod.hxx @@ -196,7 +196,7 @@ ElastixRegistrationMethod::GenerateData() // Pass the last initial transform parameter file name to the argument map, in order to have it stored by // elx::TransformBase::ReadFromFile(), so that it can be retrieved later by - // elx::TransformBase::GetInitialTransformParametersFileName(). Use "-tp", instead of "-t0", to avoid actual file + // elx::TransformBase::GetInitialTransformParameterFileName(). Use "-tp", instead of "-t0", to avoid actual file // reading of the initial transforms, as they are already in memory. argumentMap["-tp"] = initialTransformParameterFileName; } diff --git a/Testing/itkTransformixFilterTest.cxx b/Testing/itkTransformixFilterTest.cxx index 324baa9f6..aa81f221a 100644 --- a/Testing/itkTransformixFilterTest.cxx +++ b/Testing/itkTransformixFilterTest.cxx @@ -38,7 +38,7 @@ main(int argc, char * argv[]) return 1; } const char * movingImageFile = argv[1]; - const char * transformParametersFile = argv[2]; + const char * transformParameterFile = argv[2]; const char * transformedImageFile = argv[3]; /** Other typedef. */ @@ -47,7 +47,7 @@ main(int argc, char * argv[]) auto movingImage = itk::ReadImage(movingImageFile); auto parameterObject = elastix::ParameterObject::New(); - parameterObject->ReadParameterFile(transformParametersFile); + parameterObject->ReadParameterFile(transformParameterFile); parameterObject->Print(std::cout); using TransformixType = itk::TransformixFilter;